Documenti di Didattica
Documenti di Professioni
Documenti di Cultura
Foreword
ii
iii
Dean, Sastry Pantula, for working with the department to secure time release (for KA) to work
on this project. Special thanks are due to our colleagues in the Biochemistry and Biophysics department for their friendship, collegiality and encouragement. The department, the College of Science and OSU could not have made our task any
easier or more pleasant.
Kevin Ahern
Indira Rajagopal
Taralyn Tan
Finally, we would like to thank the many hundreds of students, past and present, who have inspired us to write this book. This is for you. It is
a special pleasure for KA and IR to have one of
you return as a co-author to help create a textbook that is truly free for all. We hope you find
the book helpful in your own education.
The book is best used (currently) on iBooks (available for Macs and iPads), which allows readers to
click on figures to enlarge them, watch video lectures relevant to each topic, listen to the selected
songs, and link out to the internet to find more
information simply by clicking on any term.
Other formats, such as PDF and Kindle, allow access to all of the hyperlinks, but not all of the multimedia. If someone is interested in converting
this book into a native Android format that can
use all of the multimedia in the iPad version,
wed love to speak with you. If you are using the
PDF version, you can download the Metabolic
Melody songs at http:www.davincipress.com
We hope you find these features useful and that
they help you learn biochemistry.
We would love to hear from you. Please take a
few minutes after youve had a chance to use the
book to tell us how the book has worked for you
(email to ahernk1@gmail.com)
iv
Copyright / Disclaimer
Disclaimer
Every eort was made to ensure that information contained in this publication was as accurate as possible at the time
of publication (August 26, 2016). However, Kevin Ahern, Indira Rajagopal, and Taralyn Tan make no claims that the
information contained anywhere in this publication is, in fact correct, so users assume responsibility for all ways in
which they use the information herein. This publication is therefore provided as is and all responsibility for use of
information herein resides solely on the user. Further, Kevin Ahern, Indira Rajagopal, and Taralyn Tan make no claims
about medical validity and oer no medical advice regarding anything stated in this books nor to hyperlinks to any
other content provided here. Kevin Ahern, Indira Rajagopal, and Taralyn Tan oer no advice of any sort. Anyone
seeking medical or other advice needs to consult medical or other relevant professionals for such advice.
Licensing and credits for Images shown in the appendix at the end of the book.
1
In the Beginning
YouTube Lectures
by Kevin
HERE & HERE
incredibly
harsh con-
ditions -
from a
few de-
grees
that he
above ab-
named cells.
solute
Subsequent
zero to
examination
300F,
of other liv-
the vac-
ing things
revealed
that they,
too, were,
without ex-
ception,
made up of
cells. To-
varied envi-
day, we
ronments, all
living things
share some
common char-
acteristics.
ticeable of
these is that
from hum-
mingbirds to
humpback
whales, from
fungi to frogs,
Cells
All cells, no matter what kind, have a plasma
membrane that serves as a boundary for the
cell, separating it from its surroundings. They
produce.
Prokaryotic and
eukaryotic cells
Organisms may be divided into
two major groups, the prokaryotes and the eukaryotes. The cells of the former
lack a nucleus and other organelles, while those of the
latter are characterized by numerous internal, membranebounded compartments, including a nucleus.
Figure 1.6 - Interplay between autotrophs and
heterotrophs
Cells may be aerobic (i.e., use oxygen) or anaerobic (able to live without oxygen). Some
anaerobic cells are obligate anaerobes, that is,
they require an environment free of oxygen.
Table 1.1
10
nucleus in not being enclosed by a nuclear envelope (Figure 1.7). The proteins associated
Bacteria
exterior surfaces,
bacteria have
otic histones, while those in bacteria are different from both eukaryotic and archaeal DNA
packaging proteins.
tion, bacterial cells may have flagella that enable them to move through their surround-
ings.
Interestingly, bacteria can communicate, not
only with members of their own species, but
also with other bacterial species, using chemical signals, in a process called quorum sens11
Archaea
The first archaeans to be stud-
ied were all found in harsh environments such as salt flats and
Figure 1.9 Archaeal membrane, top, showing unusual ether linkages and isoprene
chains and bacterial membrane, below.
Wikipedia
saccharides.
Amoeba. Multicellular
eukaryotes include plants,
Eukaryotes
Organelles
thropods.
specialized functions.
ganelles.
metabolism and targeted protein synthesis and folding), the Golgi apparatus (protein modification and secretion), peroxisomes (oxidation of very long chain fatty
acids), chloroplasts
(plants - photosynthesis), plastids (synthesis and
storage of compounds in
plants), lysosomes (animals - hydrolytic enzymes),
endosomes (contain endocytosed material), and
vacuoles.
The presence of multiple
compartments within the
cell permits reactions requiring specific conditions
to be carried out in isolation from the rest of the
mation of disulfide
bonds in proteins is
possible in the conditions within the endoplasmic reticulum,
but would not readily
occur in the different
environment of the cytosol. The presence of
membrane-bounded
compartments also allows reactants to be
more concentrated because of the smaller volume of the organelle.
Eukaryotic DNA in a
cell is divided into sev-
YouTube Lectures
by Kevin
HERE & HERE
15
synthesis. This
dynamic, with
is not as odd as it
both microfila-
seems, because
these organ-
crotubules dis-
assembling and
rearranging them-
karyotes that
selves on an ongo-
ing basis, as
dosymbionts
needed. Inter-
within ancient
mediate fila-
eukaryotic cells
came integrated
rebuilt, at spe-
The cytoskeleton
cell.
17
Tissues
Cells in multicellular organisms are organized
Connective tissue
membranes, the
their bodies - epithelium, connective tissue, nerve tissue, and muscle tissue. The
first of these, epithelial tissues line the cavities and surfaces of blood vessels and organs
in the body (Figure 1.16). Epithelial cells are
categorized by their shapes: squamous, columnar, and cuboidal. These can be organized in a
single cell layer or in layers of two or more
cells deep (referred to as stratified or layered).
Glands are all comprised of epithelial cells.
meninges (cover
of brain) and the spinal cord are composed of
connective tissue. Apart from the blood and
lymph, connective tissues contain three main
components. They are 1) cells; 2) ground substance; and 3) fibers. Blood and lymph contain components 1 and 2, but not 3. Cell types
found in connective tissue include adipocytes, fibroblasts, mast cells, macrophages, and leucocytes.
18
Nerve tissue
The nervous system of humans contains two main components. The
brain and spinal cord comprise the
central nervous system (CNS) and
nerves branching from these make up
the peripheral nervous system. The peripheral nervous system is responsible
for regulating bodily functions and actions. In the central nervous system
(CNS), the tissue types are referred to
as grey matter or white matter. In the
peripheral nervous system (PNS), tis-
Muscle tissue
Muscle tissue is formed during embryonic development by a process
known as myogenesis. Mammals have three types of muscle tissue - 1) skeletal/striated
YouTube Lectures
by Kevin
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19
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
20
Biochemistry, Biochemistry
To the tune of Oh Christmas Tree
Metabolic Melodies Website HERE
Biochemistry Biochemistry
I wish that I were wiser
I feel Im in way oer my head
I need a new advisor
Biochemistry Biochemistry
Im truly in a panic
Your mechanisms murder me
I should have learned organic
Biochemistry Biochemistry
Reactions make me shiver
Theyre in my heart and in my lungs
Theyre even in my liver
Biochemistry, Biochemistry
Complementary bases
Match the bonds of H and hold the strands
Together till theyre pulled apart
Around the nucleus
Hydrogen bonding fuels (ahhhhhhhhh)
22
Biochem is Beautiful
To the tune of Everything is Beautiful
Metabolic Melodies Website HERE
Students study molecules with
All of the structures they possess
Proteins, fats and DNAs
There must be a million ways
To evaluate our knowledge for the test
Biochem is beautiful
Our professor says
From the sugar in our cells
To actions of HDLs
There is no enzyme
That can lower Delta G
They just work all the time
On transition energy
Biochem is beautiful
Saying it with zest
Would be so much easier
If I could just ace the test
Biochem is beautiful
Saying it with zest
Would be so much easier
If I could just ace the test
fade
Certain chemistry
chemistry that often involves enormous macromolecules, and that happens in the aqueous
-Michael Adams.
To understand biochemistry, one must pos-
try. You will encounter these functional groups as you study the biosynthetic and breakdown pathways that build and recycle the
24
25
tivity.
For example, in a molecule of water, with hydrogen covalently bonded to oxygen, the electrons are pulled toward the oxygen, which is
more electronegative. Because of this, there is
a slightly greater negative charge near the oxygen atom of water, compared to the hydrogen
(which, correspondingly has a slightly higher
positive charge). This unequal charge distribution sets up a dipole, with one side being somewhat negative and the other somewhat positive. Because of this, the molecule is de-
scribed as polar.
Hydrogen bonds between water molecules
Table 1.2
Electronegativity
Electronegativity is a measure of the affinity a nucleus has
for outer shell electrons (Table
1.2). High electronegativity corresponds to high affinity. Elec-
26
can dissolve in water. They are called hydrophilic. Molecules possessing both characteristics are called amphiphilic.
Weak interactions
Hydrogen bonds are one kind of electrostatic
(i.e., based on charge) interaction between dipoles. Other forms of electrostatic interactions that are important in biochemistry include weak interactions between a polar
molecule and a transient dipole, or between
two temporary dipoles. These temporary dipoles result from the movement of electrons
in a molecule. As electrons move around, the
Figure 1.20 Hydrogen bonds (dotted
lines) between water molecules
Wikipedia
drogen bonds or other dipole-dipole interactions are weak, because of their large numbers, they can result in quite strong interactions between molecules.
Oxidation/reduction
Oxidation involves loss of electrons and reduction results in gain of electrons. For
27
Ionization
Ionization of biomolecules, by contrast
to determine whether a reaction will be spontaneous, by taking into consideration two fac-
Stereochemistry
entropy (S).
28
G = H = TS
G values.
ergy G is given by
Gtotal = G1 + G2 = Z + Y
G = H - TS
Gtotal = G1 + G2
Catalysis
changed by the reaction. Because catalysts remain unchanged at the end of a reaction, a sin-
anced equation. Large values of Keq correspond to favorable reactions (more C and D
tions in cells are called enzymes, while ribozymes are RNA molecules that act as cata-
G = -RTlnKeq
lysts.
29
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
30
Bridge
Bridge
Three point one four one five nine two six five
No end to Pis digits its absurd
Endlessly reminding me that Ive
BEEN SO OUT-num-bered
Elemental Learning
To the tune of "Sentimental Journey"
Metabolic Melodies Website HERE
Gonna do
Some elemental learning
Studying for my degree
Elevate
My supplemental earnings
With atomic chemistry
Learning bout
The subatomic units
In an atoms nucleus
Balance charge
With all of the electrons
Or an ion youll possess
Neutrons
Theyre the chargeless bits in
Atoms
Protons sometimes wish they had em
Gotta have an a-dequate supply
In nuclei
If you dont
Therell be a price for payin
For the instability
Water everywhere
YouTube Lectures
by Kevin
HERE & HERE
having a partial positive charge (typically designated as +) and the oxygen has a partial
negative charge (written as -). Thus, water is
33
a polar molecule because charges are distributed around it unevenly, not symmetrically.
Water as a solvent
Water (Figure 1.23) is described as a
solvent because of its ability to solvate
(dissolve) many, but not all, molecules.
Molecules that are ionic or polar dissolve
readily in water, but non-polar substances
dissolve poorly in water, if at all. Oil, for
example, which is non-polar, separates from
Solubility
The solubility of materials in water is based in
free energy changes, as measured by G. Re-
Table 1.3
34
dissolves.
Water organization
G = H - TS,
where T is the temperature in Kelvin. For a
process to be favorable, the G for it must be
less than zero.
35
Since mixing a non-polar substance with water doesnt generally have any significant heat
component, the G is positive. This means,
then, that dissolving a non-polar compound
in water is not favorable and does not occur to
any significant extent. Further, when the
non-polar material associates with itself and
not water, then the water molecules are free
Figure 1.26 - A phospholipid - an
amphiphilic substance
The difference is
tions.
Amphiphilic
substances
Next, we consider
mixing of an
amphiphilic
substance, such as a
drogen bonds. In
Wikipedia
sodium ions
attached to the fatty
acids in soap readily
come off in aqueous
36
37
portion of the protein (water excluded). Interaction of the non-polar amino acids turns
out to be a driving force for the folding of
proteins as they are being made in an aqueous solution.
Hydrogen bonds
The importance of hydrogen bonds in biochemistry (Figure 1.30) is hard to overstate. Linus Pauling himself said,
. . . . I believe that as the methods of structural chemistry are further applied to
physiological problems it will be found that
the significance of the hydrogen bond for
physiology is greater than that of any other
single structural feature.
38
molecule, it means
also that the
charges are
Partial charges
39
Table 1.4
Each hydrogen bond is relatively weak (compared to a covalent bond, for example - Table
antibody-antigen.
40
Table 1.5
41
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by Kevin
HERE & HERE
the food.
thus reducing hydroxide concentration. Similarly, if I dump excess hydroxide (as NaOH, for exam-
Acids vs bases
pH =
-Log[H+]
42
H+
and
A-
A-
can release
can
equation.
pH = pKa + log
([Ac-]/[HAc])
Table 1.6
Weak acids
Weak acids and bases differ from
their strong counterparts. When
you put one mole of acetic acid
(HAc) into pure water, only a tiny
percentage of the HAc molecules
dissociate into H+ and Ac-. Clearly,
43
UPS
Weak acids are critical for life because their
affinity for protons causes them to behave
like a UPS. Were not referring to the UPS
that is the United Parcel Service, but instead, to the encased battery backup systems
for computers called Uninterruptible Power
Supplies that kick on to keep a computer running during a power failure. The battery in a
laptop computer is a UPS, for example.
(by adding a strong base like NaOH) to the solution causes the H+
ions to react with
OH- ions to make
water. Consequently, the concentration of H+ ions
would go down and
the pH would go
up.
However, in contrast to the situation with a solution
of pure water, there
is a backup source
of H+ available in
the form of H2CO3.
Here is where the
44
sociation constant
and is a measure of
the strength of an
a weak acid is a
sociates as
HA H+ + A-,
changes in pH by re-
Ka = [H+][A-]/[HA]
Henderson-Hasselbalch
It is useful to be able to predict the response
of the H2CO3 system to changes in
H+
concen-
Constant pKa
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by Kevin
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[H2CO3])
This simple equation defines the relationship
between the pH of a solution and the ratio of
HCO3- and
buffer. It resists
pH = pKa + log
45
the behavior.
Buffered vs non-buffered
Buffering region
By contrast, the acetate buffers pH after adding the same amount of HCl is 4.74. Thus, the
pure water.
Buffer capacity
It is important to note that buffers have ca-
[A-] = [HA]
This is consistent with the Henderson Hasselbalch equation and the titration curve.
When [A-] = [HA], pH = 6.37 + Log(1). Since
Log(1) = 0, pH = 6.37 = pKa for carbonic acid.
Thus for any buffer, the buffer will have maximum strength and display flattening of its titration curve when [A-] = [HA] and when pH
46
concentration.
47
References
1.http://www.lpi.usra.edu/lunar/missions/apollo/
apollo_12/experiments/surveyor/
16371641. doi:10.1351/PAC-REC-10-01-02
ton).
Prediction
How does one predict the charge for an amino
acid at a given pH? A good rule of thumb for
YouTube Lectures
by Kevin
HERE & HERE
48
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Henderson Hasselbalch
To the tune of "My Country 'Tis of Thee
Metabolic Melodies Website HERE
Henderson Hasselbalch
You put my brain in shock
Oh woe is me
The pKas can make
Me lie in bed awake
They give me really bad headaches
Oh hear my plea
Ode to Bicarbonate
To the tune of "Song Sung Blue"
Metabolic Melodies Website HERE
H-2-O
Ionizes slowly
You should know
Its behavior wholly
C-O-2
Made in oxidation
Inside you
Decarboxylation
Thus its so
Thanks to bicarb buffer
In blood flow
You dont have to suffer
Protons stow
In the bicarb buffer
Never grow
2
Structure & Function
Introduction
structure.
- Linus Pauling
52
late to function.
Biological molecules
As noted earlier, water is the most abundant
Building blocks
53
ing cells.
ids and the four bases, are, with minor reservations, the same throughout Nature."
- Francis Crick
YouTube Lectures
by Kevin
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same 20 amino acids. Linked together in long chains called polypeptides, amino acids are the building blocks for
54
55
Non-Polar
Carboxyl
Amine
Aromatic
Hydroxyl
Other
Alanine
Aspartic Acid
Arginine
Phenylalanine
Serine
Asparagine
Glycine
Glutamic Acid
Histidine
Tryptophan
Threonine
Cysteine
Lysine
Tyrosine
Tyrosine
Glutamine
Isoleucine
Leucine
Selenocysteine
Methionine
Pyrrolysine
Proline
Valine
mans.
tigue.
R-group chemistry
56
57
link HERE.
coded solely by the AUG codon. It is the initiator amino acid in protein synthesis, being the first one incorporated into protein
chains. In
prokaryotic cells,
the first methionine in a
protein is
formylated.
Wikipedia
link HERE.
Proline
(Pro/P) is
the only
amino acid
58
over 12, making it positively charged at cellular pH. It is coded for by six codons - CGU,
link HERE.
link HERE.
encoded by AAA and AAG. It has an Rgroup that can readily ionize with a charge
droxylysine is used to flag proteins for export from the cell. Lysine is often added to
animal feed because it is a limiting amino acid
60
in signaling processes. In
dopaminergic cells of
the brain, tyrosine hydroxylase converts tyrosine to l-dopa, an immediate precursor of dopamine. Dopamine, in turn,
is a precursor of norepinephrine and epinephrine. Tyrosine is also a precursor of thyroid hormones and melanin.
Wikipedia link HERE.
Hydroxyl amino
acids
Serine (Ser/S) is one of
61
62
biosynthetic
pathway for
link HERE.
YouTube Lectures
by Kevin
HERE & HERE
HERE.
CAG and is readily made by amidation of glutamate. Glutamine is the most abundant
Ionizing groups
HERE.
pact on the activity of a protein. Most proteins have relatively narrow ranges of optimal
64
R-groups; or 4) other
functional groups (such
as sulfates or phosphates) added to amino
acids posttranslationally - see
below.
Carnitine
Not all amino acids in
a cell are found in proteins. The most common examples include
ornithine (arginine metabolism), citrulline
(urea cycle), and carnitine (Figure 2.12).
Figure 2.10 - Titration curve for aspartic acid
Image by Penelope Irving
activity that typically correspond to the environments in which they are found (Figure
2.11). It is worth noting that formation of peptide bonds between amino acids removes
ionizable hydrogens
65
66
Post-translational
modifications
After a protein is synthesized, amino acid side
chains within it can be
chemically modified, giving rise to more diversity
of structure and function
(Figure 2.14). Common
alterations include phosphorylation of hydroxyl groups of serine,
threonine, or tyrosine.
Lysine, proline, and histidine can have hydroxyls added to amines in
their R-groups. Other
modifications to amino acids in proteins include ad-
67
Building polypeptides
Although amino acids serve
other functions in cells, their
YouTube Lectures
by Kevin
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chain made up of just a few amino acids linked together is called an oligopeptide (oligo=few) while a typi-
68
69
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Youre Cysteine
To the tune of Youre Sixteen
Metabolic Melodies Website HERE
Bridge
That sulfhydryl in your chain
Can oxidize, but I dont complain
It gives support to all peptides
So proteins need to have disulfides
Bridge
A U-G-U or U-G-C
In secret code at the cell's decree
Youre in my skin and in my bone
And even in my glutathione
Protein diversity
acids, with each protein having a characteristic and unique amino acid sequence.
YouTube Lectures
by Kevin
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73
Levels of structure
The significance of the
unique sequence, or order,
of amino acids, known as
the proteins primary
structure, is that it dictates the 3-D conformation
the folded protein will
have. This conformation,
in turn, will determine the
function of the protein.
We shall examine protein
structure at four distinct
levels (Figure 2.17) - 1)
how sequence of the amino
acids in a protein (primary structure) gives
identity and characteristics
to a protein (Figure
2.18); 2) how local interactions between one part of
the polypeptide backbone
Figure 2.17 - Four Levels of Protein Structure
74
Subtle changes
75
Protein synthesis
Synthesis of proteins occurs in the ribosomes and proceeds by joining the carboxyl terminus of the first amino acid
to the amino terminus of the next one
(Figure 2.19). The end of the protein that
has the free -amino group is referred to as
the amino terminus or N-terminus.
The other end is called the carboxyl terminus or C-terminus , since it contains
Figure 2.19 Linking of amino acids through
peptide bond formation
76
Primary structure
Primary structure is the ultimate determinant of the overall conformation of a protein.
The primary structure of any protein arrived
at its current state as a result of mutation and
selection over evolutionary time. Primary
structure of proteins is mandated by the sequence of DNA coding for it in the genome.
Regions of DNA specifying proteins are
known as coding regions (or genes).
The base sequences of these regions directly
specify the sequence of amino acids in proteins, with a one-to-one correspondence between the codons (groups of three consecutive bases) in the DNA and the amino acids in
the encoded protein. The sequence of codons
in DNA, copied into messenger RNA, specifies
Figure 2.21 - From RNA to amino acids the genetic code
Wikipedia
a sequence of amino acids in a protein. (Figure 2.21). The order in which the amino acids are joined together in protein synthesis
boxyl terminus.
is being made.
interaction of a particular amino acid Rgroup may be different than if the helix had
77
can create (in some cases) opportunities for interactions that wouldnt have
been possible without the bend or prevent (in
other cases) similar interaction possibilities.
Secondary structure
As protein synthesis progresses, interactions between amino acids close to each other
begin to occur, giving rise to local patterns
called secondary structure. These secondary structures include the well known helix and -strands. Both were predicted
by Linus Pauling, Robert Corey, and Herman Branson in 1951. Each structure has
unique features.
-helix
The -helix has a coiled structure, with 3.6
amino acids per turn of the helix (5 helical
turns = 18 amino acids). Helices are predominantly right handed - only in rare cases,
such as in sequences with many glycines can
left handed - helices form. In the -helix, hydrogen bonds form between C=O groups
and N-H groups in the polypeptide backbone
that are four amino acids distant. These hydrogen bonds are the primary forces stabilizing the -helix.
We use the terms rise, repeat, and pitch to
describe the parameters of any helix. The re-
78
strand/sheet
A helix is, of course, a three-dimensional object. A flattened form of helix in two dimen79
Turns
scription for a -
sometimes referred to
in a curtain. -strands
can be organized to
other arrangements.
spectively.
secondary struc-
Figure 2.26 -
strand
80
peptide bonds
-turns - separation by four peptide bonds
-turns - separation by five bonds
Of these, the -turns are the most common
form and the -turns are theoretical,
YouTube Lectures
by Kevin
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310 helices
In addition to the -helix, -strands, and
various turns, other regular, repeating
structures are seen in proteins, but occur
much less commonly. The 310 helix is the
81
-helices
A -helix may be
thought of as a
special type of helix. Some
sources describe
it as an -helix
with an extra
amino acid
stuck in the middle of it (Figure
2.32). -helices
82
Figure 2.33 - Planes (light blue) defined by the double-bonded character of the
peptide bond
Image by Aleia Kim
gion.
Figures 2.33 and 2.34 that the amino to carboxyl direction is right to left.
Ramachandran plots
In 1963, G.N. Ramachandran, C. Ra-
83
Secondary structure
prediction
Figure 2.34 - , , and rotational angles in a peptide
Image by Aleia Kim
bond. Double bonds cannot, of course, rotate, but the bonds on either side of it have
84
Hydrophobicity
YouTube Lectures
by Kevin
HERE & HERE
in each of these
structures. Using
clues to structure
these tendencies,
and, sometimes,
cellular location.
to 80% accuracy,
A prime example
predict regions of
is the hydropho-
secondary
bicity (water-
structure in a
avoiding tenden-
protein based
cies) of some R-
solely on amino
acid sequence.
aqueous environ-
such R-groups
rence in primary
sequence of three
be on the outside
consecutive
surface of a
amino acids
folded protein.
However, this
dencies higher
available HERE.
mains are are buried in the hydrophobic environment in the middle of the lipid bilayer.
85
Random coils
Some sections of a protein assume no regular,
discernible structure and are sometimes said
to lack secondary structure, though they
may have hydrogen bonds. Such segments
are described as being in random coils and
may have fluidity to their structure that results in them having multiple stable forms.
Random coils are identifiable with spectroscopic methods, such as circular dichroism
Table 2.4 - Hydropathy Scores
Wikipedia
86
Tertiary structure
Proteins are distinguished from each other
by the sequence of amino acids comprising
them. The sequence of amino acids of a protein determines protein shape, since the
chemical properties of each amino acid are
forces that give rise to intermolecular interactions to begin to create secondary struc-
(HERE).
Supersecondary structure
Another element of protein structure is harder
87
Protein stabilizing
forces
lize proteins.
Globular proteins
Hydrogen bonds
88
YouTube Lectures
by Kevin
HERE & HERE
Individual hy-
drogen bonds
regular repeating
are much
structures, such
weaker than a
as helices or
covalent bond,
pleats, in pro-
but collectively,
teins (secon-
dary struc-
strong forces.
ture).
Consider liquid
water, which con-
Ionic
interactions
tains enormous
numbers of hy-
Ionic interac-
drogen bonds
(Figure 2.41).
These forces
help water to re-
main liquid at
room temperature. Other molecules lacking
hydrogen bonds of equal or greater molecular
weight than water, such as methane or carbon dioxide, are gases at the same tempera-
Wikipedia
lizing protein
structure that
arise from ioni-
zation of R-groups in the amino acids comprising a protein. These include the carboxyl
amino acids (HERE), the amine amino acids
89
by Kevin Ahern
excluded water has a higher entropy than water interacting with the hydrophobic side
are found in protein interiors - so they can exclude water and increase entropy.
Disulfide bonds
Disulfide bonds, which are made when two
sulfhydryl side-chains of cysteine are
brought into close proximity, covalently join
together different protein regions and can
give great strength to the overall structure
(Figures 2.42 & 2.43).
Hydrophobic forces
Hydrophobic forces stabilize
protein structure as a result of interactions that favor the exclusion of
water. Non-polar amino acids
(commonly found in the interior of
90
ing proteins as well. Hydroxylation of lysine and proline in strands of collagen can
result in cross-linking of these groups and the
resulting covalent bonds help to strengthen
and stabilize the collagen.
Folding models
Two popular models of protein folding are currently under investigation. In the first (diffusion collision model), a nucleation event begins the process, followed by secondary
structure formation. Collisions between the
Figure 2.43 - Cystine Two cysteines joined
by a disulfide bond
These joined residues of cysteine are sometimes referred to as cystine. Disulfide bonds
tein structure.
to 1000 seconds) and can occur during synthesis - the amino terminus of a protein
the case.
Folding process
Post-translational modifications
91
Getting stuck
As the folding process proceeds towards an energy minimum (bottom of the funnel in
Figure 2.44), a protein can
get stuck in any of the local
minima and not reach the final folded state. Though the
folded state is, in general,
more organized and therefore
has reduced entropy than the
unfolded state, there are two
forces that overcome the entropy decrease and drive the
process forward.
The first is the magnitude of
the decrease in energy as
shown in the graph. Since
Figure 2.44 Folding funnel energy model of folding
Wikipedia
G = H -TS,
92
Structure prediction
angles. If each of these had only three conformations, that would result in 3198 differ-
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points of stabilization based on geometry and any regular secondary structure (e.g.,
-helix) varies very little from one to another. Folded structures, though, have an
enormous number of possible structures as
shown by Levinthals Paradox.
Spectroscopy
Because of our inability to accurately predict
tertiary structure based on amino acid sequence, proteins structures are actually determined using techniques of spectroscopy. In
these approaches, proteins are subjected to
varied forms of electromagnetic radiation and
the ways they interact with the radiation allows researchers to determine atomic
Levinthals paradox
In the late 1960s, Cyrus Levinthal outlined the magnitude of the complexity
of the protein folding problem. He
pointed out that for a protein with
93
Prions
Prions are infectious protein particles that
cause transmissible spongiform encephalopathies (TSEs), the best known of
which is Mad Cow disease. Other manifesta-
Insoluble deposits
Misfolded proteins will
commonly form aggregates
called amyloids that are
harmful to tissues containing
them because they change from
94
Function
PrPc. Stanley Prusiner, who discovered prions and coined the term, received the Nobel
Misfolded
95
Amyloids
play a role.
Amyloid
Amyloid refers to collections of
small proteins (36-43 amino acids)
that appear to play a role in Alzheimers disease. (Tau protein is
the other factor.) They are, in fact,
the main components of amyloid
plaques found in the brains of patients suffering from the disease and
arise from proteolytic cleavage of a
larger amyloid precursor glycoprotein called Amyloid Precursor
96
precursor protein.
Huntingtin
Molecular chaperones
Trinucleotide repeat
97
In heat shock
Figure 2.50 - Action of Hsp70 (blue) to
facilitate proper folding of a protein
(orange)
Image by Aleia Kim
folding or aggregation.
Chaperonins
GroEL/GroES may not be able to undo aggregated proteins, but by facilitating proper folding, it provides competition for misfolding as
a process and can reduce or eliminate problems arising from improper folding. GroEL
is a double-ring 14mer with a hydrophobic
region that can facilitate folding of sub-
substrate protein.
Protein breakdown
Another protein complex that has an important function in the lifetime dynamics of proteins is the proteasome (Figure 2.52). Proteasomes, which are found in all eukaryotes
and archaeans, as well as some bacteria,
function to break
down unneeded or
damaged proteins by
proteolytic degradation. Proteasomes
help to regulate the
concentration of some
proteins and degrade
ones that are misfolded.
tides yields individual amino acids, thus facilitating their recycling in cells. Proteins are
targeted for degradation in eukaryotic proteasomes by attachment to multiple copies of a
small protein called ubiquitin (8.5 kDa - 76
amino acids). The enzyme catalyzing the reaction is known as ubiquitin ligase. The resulting polyubiquitin chain is bound by the
proteasome and degradation begins. Ubiquitin was named due to it ubiquitously being
found in eukaryotic cells.
Ubiquitin
Ubiquitin (Figure 2.53) is a small (8.5
kDa) multi-functional protein found in eukaryotic cells. It is commonly added to target proteins by action of ubiquitin ligase enzymes
(E3 in Figure 2.54). One (ubiquitination)
100
lular location and changed protein-protein interactions. The latter may alter affect inflam-
scribed elsewhere in the book, the 3-D structure of proteins is important for their func-
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form.
Intrinsically disordered proteins
and disordered regions within
proteins have, in fact, been
known for many years, but were
regarded as an anomaly. It is
only recently, with the realization that IDPs and IDP regions
are widespread among eukaryotic proteins, that it has been
recognized that the observed disorder is a "feature, not a bug".
Comparison of IDPs shows that
they share sequence characteristics that appear to favor their dis-
102
post-translational modifica-
in cells.
Metamorphic proteins.
103
by the laws of physics and chemistry, metamorphic proteins are a relatively new discovery. It was known, of course, that prion proteins were capable of folding into alternative
structures, but metamorphic proteins appear to be able to toggle back and
forth between two stable struc-
Interestingly, renaturation
ample is the signaling molecule, lymphotactin. Lymphotactin has two biological functions that are
from forming.
Irreversible denaturation
Chaperonins role
In other cases, the folding process of some proteins in the cell relied upon action of chaper-
References
1.
https://en.wikipedia.org/wiki/Van_der_W
aals_force
Quaternary structure
A fourth level of protein structure is that of
quaternary structure. It refers to structures that arise as a result of interactions between multiple polypeptides. The units can
be identical multiple copies or can be different
polypeptide chains. Adult hemoglobin is a
good example of a protein with quaternary
structure, being composed of two identical
105
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
My Old Enzymes
To the tune of "Auld Lang Syne"
Metabolic Melodies Website HERE
Hemoglobin
Wikipedia
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by Kevin
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109
posed primarily of primary and second structure, with little folding of the chains. Thus,
they have very little tertiary structure and
are fibrous in nature. Proteins exhibiting
these traits are commonly insoluble in water
and are referred to as fibrous proteins (also
called scleroproteins). The examples described in this category are found exclusively
in animals where they serve roles in flesh,
connective tissues and hardened external
structures, such as hair. They also contain
the three common fibrous protein structures
-helices (keratins), -strands/sheets (fibroin & elastin) and triple helices (collagen). The fibrous proteins have some commonality of amino acid sequence. Each possesses an abundance of repeating sequences
of amino acids with small, non-reactive side
groups. Many contain short repeats of sequences, often with glycine.
Keratins
The keratins are a family of related animal proteins that take numerous forms. -keratins
are structural components of the outer layer
of human skin and are integral to hair, nails,
claws, feathers, beaks, scales, and hooves.
Keratins provide strength to tissues, such as
We wouldnt be too popular
If keratins were globular
Our nails and hair would be as knots
Their structures folded up like clots
No strength theyd have and oh by gosh
Theyd rearrange with every wash
110
Elastin
Fibroin
An insoluble fibrous
prised of anti-
is made by linking
parallel -strands
tropoelastin pro-
teins together
gether to form -
structure of fibroin is
a short repeating se-
linked by desmos111
Collagen
Collagen is the most abun-
occupying up to a third of
collagen form. Processing of the pre-procollagen in the endoplasmic reticulum results in glycosylation, removal of the pre
112
Lamins
Hydroxylation reactions
Hydroxylation of proline and lysine side
chains occurs post-translationally in a reaction catalyzed by prolyl-4-hydroxylase and
lysyl-hydroxylase (lysyl oxidase), respectively. The reaction requires vitamin C.
Since hydroxylation of these residues is essential for formation of
stable triple helices at body tem-
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perature, vitamin C deficiency results in weak, unstable collagen and, consequently, weakened connective tissues. It is
the cause of the disease known as scurvy. Hydrolyzed collagen is used to make gelatin,
which is important in the food industry. collagens. Wikipedia link HERE
113
Leucine zipper
A common feature of many eukaryotic DNA
binding proteins, leucine zippers are characterized by a repeating set of leucine residues
in a protein that interact like a zipper to faFigure 2.63 - Leucine zipper
bound to DNA
Wikipedia
vor dimerization. Another part of the domain has amino acids (commonly arginine
and lysine) that allow it to interact with the
jun.
Zinc fingers
114
Helix-turn-helix domain
Helix-turn-helix is a common domain
found in DNA binding proteins, consisting
115
116
teins.
Basement membrane
Intermediate Filaments
cytoskeleton in many
comprised of over 70
basement membrane
different proteins.
(average diameter = 10
Basement membranes provide an interface of interaction between cells and the environment around
them, thus facilitating signaling processes.
They play roles in differentiation during embryogenesis and also in maintenance of func-
the microfilaments
(7 nm) and the microtubules (25 nm).
The intermediate filament components include fibrous proteins, such as the keratins
and the lamins, which are nuclear, as well as
cytoplasmic forms. Intermediate filaments
Actin
length.
found in most types of eukaryotic cells, comprising as much as 20% of the weight of muscle cells. Similar proteins have been identi-
Six types
There are six different types of intermediate
filaments. Type I and II are acidic or basic
117
Vimentin
Tubulin
A third type of filament
found in cells is that of
the microbutules.
Comprised of a polymer
of two units of a globular
protein called tubulin,
microtubules provide
rails for motor proteins to move organelles and other cargo
from one part of a cell to
another. Microtubules
and tubulin are discussed in more detail
HERE.
118
of cholesterol.
Mucin
Mucins are a group of proteins found in ani-
Syndecans
mucins.
In addition to lubrication, mucins also
help to control mineralization, such as
bone formation in vertebrate organisms
and calcification in echinoderms. They
also play roles in the immune system
by helping to bind pathogens. Mucins
are commonly secreted onto mucosal surfaces (nostrils, eyes, mouth, ears, stomach, genitals, anus) or into fluids, such as
saliva. Because of their extensive mucosylation, mucins hold a considerable
amount of water (giving them the slimy
feel) and are resistant to proteolysis.
Vinculin
Vinculin (Figure 2.72) is a membrane
cytoskeletal protein found in the focal
119
ligands, such as growth factors, fibronectin, collagens (I, III, and IV) and
antithrombin-1. Syndecans typically have 3-5
heparan sulfate and chondroitin sulfate
chains attached to them.
Heparan sulfate can be cleaved at the site of a
wound and stimulate action of fibroblast
growth factor in the healing process. The role
of syndecans in cell-cell adhesion is shown
in mutant cells lacking syndecan I that do not
adhere well to each other. Syndecan 4 is also
known to adhere to integrin. Syndecans can
also inhibit the spread of tumors by the ability
of the syndecan 1 ectodomain to suppress
growth of tumor cells without affecting normal epithelial cells.
Defensin
Defensins (Figure 2.73) are a group of
small cationic proteins (rich in cysteine residues) that serve as host defense peptides in
120
cells.
Focal adhesions
In the cell, focal adhesions are structures
Ankyrin
Focal adhesions
121
Integrins
In multicellular organisms,
cells need connections, both to
Spectrin
Spectrin (Figures
2.75 & 2.76) is a protein
of the cellular cytoskeleton that plays an important role in maintaining
its structure and the integrity of the plasma
membrane. In animals,
spectrin gives red blood
cells their shape. Spectrin is located inside the
122
123
Selectins
Figure 2.78 - Extracellular ectodomain of a
cadherin
Integrins also help to modulate signal transduction through tyrosine kinase receptors in the cell membrane by regulating
their signals.
Cadherins
Cadherins (Figure 2.78) constitute a type-1
class of transmembrane proteins playing
important roles in cell adhesion. They require
calcium ions to function, forming adherens
junctions that hold tissues together (See Fig-
sal lamina and affect cell differentiation, migration, and adhesion. They are secreted into
the extracellular matrix where they are incorporated and are essential for tissue maintenance and survival. When laminins are defective, muscles may not form properly and give
rise to muscular dystrophy.
Laminins are associated with fibronectin,
entactin, and perlecan proteins in type IV collagen networks and bind to integrin receptors in the plasma membrane. As a consequence, laminins contribute to cellular attachment, differentiation, shape, and movement.
The proteins are trimeric in structure, having
one -chain, a -chain, and a -chain. Fifteen
combinations of different chains are known.
Vitronectin
Vitronectin is a glycoprotein (75kDa)
found in blood serum (platelets), the extracellular matrix, and in bone. It promotes
Figure 2.79 - Selectin bound to a sugar
Wikipedia
involved in the inflammatory processes of asthma, psoriasis, multiple scleroris, and rheumatoid arthritis.
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Laminins
Laminins are extracellular matrix glycoproteins that a major components of the ba-
125
Catenins
ting is concerned.
inhibition).
When catenin
genes are mutated, cadherin
cell adhesions
can disappear
and tumorigenesis may result.
Catenins have
been found to be
associated with
colorectal and numerous other
forms of cancer.
Glycophorins
All of the membrane proteins
126
tein myoglobin.
Cooperativity and
allosterism - quaternary
structure
Quaternary structure, of course describes the interactions of individual
subunits of a multi-subunit protein
(Figure 2.81). The result of these
interactions can give rise to important biological phenomena, such as
cooperative binding of substrates to a protein and allosteric
effects on the action of an enzyme.
Allosteric effects can occur by a series of mechanisms, but a common
feature is that binding of an effector
to an enzyme subunit causes (or
locks) the enzyme in either a T-
127
Cooperativity
Cooperativity is defined as
CO2 transport
Cooperativity is only one of many
fascinating structural aspects of hemoglobin
that help the body to receive oxygen where it
is needed and pick it up
where it is abundant.
tached to a histidine
Hemoglobin also
of the product of
cellular respiration
(carbon dioxide)
Since each
producing it to the
hemoglobin subunit
lungs where it is
induced to change
Wikipedia
binding of oxygen to
hemoglobin, binding of
other molecules to
128
129
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by Kevin
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130
Bohr effect
The Bohr Effect was first described
over 100 years ago by Christian Bohr,
father of the famous physicist, Niels
Bohr. Shown graphically (Figures
2.86, 2.87, and 2.88), the observed effect is that hemoglobins affinity for
oxygen decreases as the pH decreases
and as the concentration of carbon dioxide increases. Binding of the proInteractive 2.2 - Hemoglobin in the presence
(top) and absence (bottom) of oxygen
Figure 2.85 - Sequential model of binding. The sequential model is one way to
explain hemoglobins cooperativity. Squares represent no oxygen bound. Circles
represent subunits bound with oxygen and rounded subunits correspond to units
whose affinity for oxygen increases by interacting with a subunit that has bound
oxygen.
Image by Aleia Kim
131
2,3-BPG
Another molecule favoring the release of oxygen
by hemoglobin is 2,3bisphosphoglycerate
(also called 2,3-BPG or
just BPG - Figure 2.89).
Like protons and carbon
dioxide, 2,3-BPG is produced by actively respirFigure 2.86 - The Bohr effect with respect to pH changes
Image by Aleia Kim
to facilitate structural
changes in them. Most
commonly, the amino
acid affected by protons
is histidine #146 of the
strands. When this
happens, the ionized
histidine can form an
ionic bond with the side
chain of aspartic acid
#94, which has the effect
of stabilizing the T-state
(reduced oxygen binding
state) and releasing oxygen. Other histidines
and the amine of the
132
Smokers
Notably, the blood of smokers is higher in the
concentration of 2,3-BPG than non-smokers,
133
Fetal hemoglobin
Adult hemoglobin releases
Figure 2.90 - Binding of oxygen (left) and carbon monoxide
(right) by a heme group of hemoglobin
Carbon dioxide
Carbon dioxide binds to form a carbamate
when binding the -amine of each globin
chain. The process of forming this structure
releases a proton, which helps to further enhance the Bohr effect. Physiologically, the
binding of CO2 and H+ has significance because actively respiring tissues (such as contracting muscles) require oxygen and release
protons and carbon dioxide. The higher the
concentration of protons and carbon dioxide, the more oxygen is released to feed the
tissues that need it most.
About 40% of the released protons and
about 20% of the carbon dioxide are carried
134
BPG. This
is in con-
trast to fe-
tal hemo-
globin,
which has a
slightly dif-
ferent con-
figuration
(22) than
adult hemoglobin
(22). Fe-
tal hemoglo-
bin has a
greater af-
finity
gen
than
maternal he-
135
rounded to forming the shape of a sickle (Figure 2.94). Rounded red blood cells readily
make it through tiny capillaries, but sickleshaped cells do not.
Worse, they block the flow of other blood
cells. Tissues where these blockages occur are
already low in oxygen, so stopping the flow of
blood through them causes them to go quickly
anaerobic, causing pain and, in some cases,
death of tissue. In severe circumstances,
Polymerization
Under conditions of low oxygen, these hydrophobic patches will associate with each other
to make long polymers of hemoglobin molecules. The result is that the red blood cells
containing them will change shape from being
136
death may
clude trans-
result. The
fusion,
disease is
pain man-
referred to
agement,
as an ane-
and avoid-
mia be-
ance of
cause the
heavy exer-
sickling of
tion. The
the red
drug hy-
blood cells
droxyu-
targets
rea has
them for
been
removal by
the blood
monitor-
linked to
reduction
in number
activating expression of the fetal hemoglobin gene, which typically is not synthesized to
Heterozygote advantage
weeks of age.
Oxygen binding
vival.
dant ATP is essential for muscular contraction and animals move around a lot - to catch
prey, to exercise, to escape danger, etc., hav-
tant.
This is particularly a concern deep inside tissues where diffusion of oxygen alone (as occurs in insects) does not deliver sufficient
quantities necessary for long term survival.
High affinity
surviving without it. Two other important oxygen binding proteins besides
hemoglobin are myoglobin and hemocyanin.
Myoglobin
Myoglobin is the primary oxygen-storage
ter suited for oxygen storage than delivery. The protein exists as a single subunit of
globin (in contrast to hemoglobin, which contains four subunits) and is related to the
138
when needed and holding onto it under all other conditions. Myoglobin
holds the distinction of being the
first protein for which the 3D structure was determined by X-ray crystallography by John Kendrew in
1958, an achievement for which he
later won the Nobel Prize.
Hemocyanin
Hemocyanin is the protein transporting oxygen in the bodies of molluscs and arthropods. It is a coppercontaining protein found not
139
Superstructures comprised of dimer or hexamer complexes are arranged in chains or clusters and have molecular weights of over 1500
kDa.
140
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
141
Oh isn't it great?
What proteins can do
Especially ones that bind to O2
Hemoglobin's moving around
142
Heme
To the tune of Jean
Metabolic Melodies Website HERE
1) microfilaments (composed of
an actin polymer) and 2) microtubules (composed of a polymer of
tubulin.
convert it into mechanical force. These operate at the cellular and organismal level and
Actin
145
ing and maintenance of cell junctions. In conjunction with other proteins, actin has numerous interactions
with the cell membrane. The - and
-forms of actin are components of
the cytoskeleton and facilitate motility inside of cells. -actin is important
in muscle tissues, where it is used by
myosin in the mechanical process of
contraction (See HERE).
Monomeric and polymeric forms of
actin play roles in cellular activities relating to motion. Two parallel F-actin
strands can pair with each other and
create a double helical structure with
2.17 subunits per turn of the helix.
Helical F-actin in muscles contains tropomyosin, which covers the actin binding sites for myosin in resting muscles
to prevent contraction. Other proteins bound to actin muscle filaments
146
Polymerization
Polymerization of actin begins with a nucleat-
147
Two proteins play roles in modulating polymer growth. Thymosin functions on the end
of actin filaments to control growth. Profilin works on G-actin monomers exchanging
ADP for ATP, promoting addition of monomers to a growing chain.
crotubules only grow in one direction. tubulin is found on the plus end of the tubule
(growth end = plus end) and -tubulin is exposed on the other end (non-growth end = minus end). Dimers of -tubulin/-tubulin are
incorporated into growing microtubules in
this orientation. If a dimer is bound to GDP
F-actin filaments are held together by relatively weak bonds compared to the covalent
bonds of the monomers of nucleic acids,
thus allowing for easier disassembly when
desired.
Actins amino acid sequence is optimized,
having diverged only a relatively small
amount (20%) between algae and humans.
Mutations in the actin gene result in muscular diseases and/or deafness.
Tubulin
Tubulin proteins are the monomeric building blocks of eukaryotic microtubules (Figure 2.104 & 2.105). Bacterial (TubZ) and
archaeon (FtsZ) equivalents are known. The
-tubulin and -tubulin proteins polymerize
to make microtubule structures in the cytoplasm of cells. Microtubules are major components of the cytoskeleton of eukaryotic
cells, providing structural support, transport
within the cell, and functions necessary for
segregation of DNAs during cell division.
148
in microtubule organizing
centers (MTOCs), an exam-
fall apart,
whereas those
bound to GTP stably assemble into
microtubules.
Microtubules
Microtubules,
along with microfilaments and intermediate filaments (see
HERE) consti-
149
on microtubule tracks
(Figure 2.108 & Movie
Motor proteins
From the transport of materials within a cell
to the process of cytokinesis where one cell
splits into two in mitosis, a cell has needs for
motion at the molecular level. Secretory vesicles and organelles must be transported.
Chromosomes must be separated in mitosis and meiosis.
The proteins dynein and kinesin (Figure
2.106) are necessary for intracellular movement. These motor proteins facilitate the
movement of materials inside of cells along
microtubule rails. These motor proteins
150
Dyneins are placed into two groups - cytoplasmic and axonemal (also called ciliary or
flagellar dyneins - Figure 2.109). Dyneins
are more complex in structure than kinesins
with many small polypeptide units. Notably,
plants do not have dynein motor proteins, but
do contain kinesins.
Myosin
An important group of motor proteins in
the cell is the myosins. Like kinesins and
Movie 2.4 The motor protein kinesin
walking down a microtubule
Wikipedia
ment of dyneins, which are said to do retrograde transport toward the cell center. Both
proteins provide movement functions necessary for the processes of mitosis and meiosis. These include spindle formation, chromosome separation, and shuttling of organelles, such as the mitochondria, Golgi apparatuses, and vesicles.
Kinesins are comprised of two heavy chains
and two light chains. The head motor domains of heavy chains (in the feet) use energy
of ATP hydrolysis to do mechanical work for
the movement along the microtubules. There
are at least fourteen distinct kinesin families
and probably many related ones in addition.
151
Structure
Myosins have six subunits, two heavy chains
and four light chains. Myosin proteins have
domains frequently described as a head
and a tail (Figure 2.111). Some also describe an intermediate hinge region as a
neck. The head portion of myosin is the
part that binds to actin. It uses energy
from ATP hydrolysis to move along
the actin filaments. In muscles, myosin
proteins form aggregated structures referred to as thick filaments. Movements
are directional.
152
Structural considerations of
muscular contraction
Before we discuss the steps in the process of
muscular contraction, it is important to describe anatomical aspects of muscles and nomenclature.
There are three types of muscle tissue - skeletal (striated), smooth, and (in vertebrates) cardiac. We shall
I-band. Within the sarcomere is an entire Aband with its central H-zone. Within the Hzone are located tails of myosin fibers, with
the head pointed
concern our-
outwards from
selves mostly
there projecting
muscle tissue.
Muscles may be
side of the A-
activated by the
central nervous
lighter moving
case of smooth
ter.
twitch or fast
twitch.
Sarcomeres
Sarcomeres are described as the basic units
comprising striated muscles and are comprised of thick (myosin) and thin (actin) filaments and a protein called titin. The filaments slide past each other in muscular con-
Wikipedia
pied with thick myosin filaments. The Aband contains intact thick filaments overlaying thin filaments except in the central H
zone, which contains only thick filaments. In
the center of the H-zone is a line, known as
the M-line. It contains connecting elements
of the cellular cytoskeleton.
153
Sarcoplasmic
reticulum
The sarcoplasmic re-
ticulum (Figure
2.114) is a name for the
of the sarcomere.
Sarcolemma
the outside of it. The glyocalyx contains polysaccharides and connects with the base-
Movement direction
154
movement.
Muscular contraction
the terminal.
156
apse and then binds to nicotinic acetylcholine receptors on the neuromuscular junction, activating them.
E. Activation of the receptor stimulates
opening gates of sodium and potassium
channels, allowing sodium to move into
the cell and potassium to exit. The polarity
of the membrane of the muscle cell (called
a sarcolemma - Figure 2.111) changes
rapidly (called the end plate potential).
F. Change in the end plate potential results
in opening of voltage sensitive ion channels
specific for sodium or potassium only to
157
causes tropomyosin to move slightly, allowing access to myosin binding sites on the
microfilament (also called thin filament)
that it was covering (Figure 2.116).
J. Myosin (bound to ATP) cleaves the ATP
to ADP and Pi, which it holds onto in its
head region and then attaches itself to the
exposed binding sites on the thin filaments
causing inorganic phosphate to be released
from the myosin followed by ADP (Figure
2.117).
K. Release of ADP and Pi is tightly coupled to
open, creating an action potential (voltage change) that spreads throughout the
cell in all directions.
G. The spreading action potential depolarizes the inner muscle fiber and opens calcium channels on the sarcoplasmic reticulum (Figure 2.115).
H. Calcium released from the sarcoplasmic
reticulum binds to troponin on the actin
filaments (Figure 2.115).
I. Troponin alters the structure of the tropomyosin to which is it bound. This
158
159
to troponin.
Relaxation of the muscle tension
occurs as the action potential in
the muscle cell dissipates. This happens because all of the following
things happen 1) the nerve signal
stops; 2) the neurotransmitter
is degraded by the enzyme acetylcholinesterase; and 3) the calcium concentration declines because it is taken up by the sarcoplasmic reticulum.
It should be noted that the sarcoplasmic reticulum is always taking
Figure 2.122 - Sarcomere Anatomy
Wikipedia
160
toskeletons functions.
covering myosin binding sites on actin, myosin loses its attachment to actin and the thin
filaments slide back to their original posi-
The interactions of tropomyosin with the cytoskeleton are considerably more complicated
Tropomyosin
40 tropomyosins.
Troponin
The troponins involved in muscular contraction are actually a complex of three proteins
known as troponin I, troponin C, and tro-
161
Titin
Titin (also known as connectin) is
the molecular equivalent of a
spring that provides striated muscle cells with elasticity. It is the
third most abundant protein in
muscle cells. The protein is enormous, with 244 folded individual
protein domains spread across 363
Figure 2.125 - Troponin complex of muscle. Blue =
troponin C, magenta = troponin T , green =
troponin I
ing).
ments to help regulate the process of muscular contraction. Troponin I prevents bind-
Unstructured sequences
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Actinin
the M and Z lines in the sarcomere (Figure 2.123). Tension created in titin serves to
limit the range of motion of the sar-
162
Muscles, of course, enable the motion of animals and the energy required for muscle contraction is ATP. To have stores of energy
readily available, muscles have, in addition to
ATP, creatine phosphate for energy and
glycogen for quick release of glucose to
make more energy. The synthesis of creatine
phosphate is a prime example of the effects of
concentration on the synthesis of high energy
molecules. For example, creatine phosphate has an energy of hydrolysis of -43.1
kJ/mol whereas ATP has an energy of hydrolysis of -30.5 kJ/mol. Creatine phosphate,
Figure 2.126 - Phosphorylation of
creatine (phosphocreatine) - making
of a creatine phosphate battery
Image by Aleia Kim
each muscle.
163
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Information molecules
cules perform.
were combined by James Watson and Francis Crick to form a model of DNA that we are
166
made up of a pair of
DNA strands, has at
its core, bases joined
by hydrogen bonds
to form base pairs adenine always
paired with
thymine, and guanine invariably
paired with cytosine. Two hydrogen
bonds are formed between adenine and
thymine, but three
hydrogen bonds hold
together guanine and
cytosine (Figure
2.127).
The complementary
structure immediately suggested to
Watson and Crick
how DNA might be
167
Building blocks
coded protein.
Structure
168
deoxyribose)
to a nucleoside monophosphate
169
discussed later.
Deoxyribonucleotides
170
Hydrogen bonds
Hydrogen bonds between the base pairs
hold a nucleic acid duplex together, with
two hydrogen bonds per A-T pair (or per A-U
171
cussed below.
Wikipedia
Superhelicity
Short stretches of linear DNA duplexes exist
in the B-form and have 10.5 base pairs per
turn. Double helices of DNA in the cell can
vary in the number of base pairs per turn they
Z-DNA
The A-form and the B-form stand
in contrast to another form of
DNA, known as the Z-form. ZDNA, as it is known, has the same
base-pairing rules as the B and A
forms, but instead has the helices
twisted in the opposite direction,
making a left-handed helix (Figure 2.133). The Z-form has a
sort of zig-zag shape, giving rise to
the name Z-DNA.
Figure 2.133 - From left to right, the A-, B-, and Zforms of DNA
172
cles to replication.
Wikipedia
Such adjustments
can occur in three
173
Parameters
To understand topologies, we introduce
the concepts of writhe and linking
number. First, imagine either opening
a closed circle of DNA and either removing one twist or adding one twist and then
re-forming the circle. Since the strands
have no free ends, they cannot relieve the
induced tension by re-adding or removing
the twists at their ends, respectively. Instead, the tension is relieved by superhelices that form with crossing of the double
strands over each other (figure 8 structures in Figure 2.136). Though it is not
apparent to visualize, each crossing of the
double strands in this way allows twists to
the DNA.
Topological isomers
As noted, so-called relaxed
DNA has 10.5 base pairs per turn.
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174
RNA
The structure of RNA (Figure 2.137) is
175
Secondary structure
RNA world
176
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Base pairing
Base pairing in RNA is slightly differ-
zymes. It is for this reason scientists think that RNA was the first
genetic material, because it could
to a limited extent, also base pair with guanine, giving rise to many more possibilities
Stability
177
Catalysis
DNA packaging
DNA is easily the largest
macromolecule in a cell.
The single chromosome
in small bacterial cells, for
179
These proteins are known as Nucleoid Associated Proteins and include ones named
Bacteria
Eukaryotes
The method eukaryotes use for compacting DNA in the nucleus is considerably
different, and with
good reason - eukaryotic DNAs are typically much larger than
prokaryotic DNAs, but
called a nucleoid (Figure 2.142). It contains about 60% DNA with much of the remainder comprised of RNAs and transcription factors. Bacteria do not have histone
180
Octamer
The core of 8 proteins is called an octamer.
The stretch of DNA wrapped around the octamer totals about 147 base pairs and makes 1
2/3 turns around it. This complex is referred
to as a core particle (Figure 2.144). A
linker region of about 50-80 base pairs separate core particles. The term nucleosome
then refers to a a core particle plus a linker region (Figure 2.143). Histone H1 sits near the
junction of the incoming DNA and the histone
core. It is often referred to as the linker hisFigure 2.143 - Structure of a nucleosome
Wikipedia
181
concern for the processes of DNA replication and (particularly) gene expression
where specific regions of DNA must be transcribed. Altering chromatin structure is therefore an essential function for transcriptional activation in eukaryotes. One stratFigure 2.145 - Amino acid sequence (1letter code) of histone H3 of S.
cerevisiae. Arginines (R) and lysines (K)
shown in red.
egy involves adding acetyl groups to the positively charged lysine side chains to loosen
their grip on the negatively charged DNA,
thus allowing greater access of proteins
involved in activating transcrip-
Histones
Histone proteins are similar in
structure and are rich in basic
amino acids, such as lysine and
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182
a compound that one wants to test the mutagenicity of is added. To the other vial, noth-
Ames test
the plate with the cells from the vial with the
gene will be
made and the
organism will
be able to grow
without histidine.
A culture of the
bacterium lacking the functional gene is
grown with the
supply of histidine it requires.
It is split into
two vials. To
one of the vials,
183
other hand, if there was no significant difference in the number of colonies on each plate,
then that would suggest it is not mutagenic.
The test is not perfect - it identifies about 90%
of known mutagens - but its simplicity and inexpensive design make it an excellent choice
for an initial screen of a compound.
184
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Links to their Web pages are below
185
Histones
To the tune of "Meet the Flintstones"
Metabolic Melodies Website HERE
186
B-DNA
To the tune of Y-M-C-A
Metabolic Melodies Website HERE
Phosphates
Are in nucleotides
I say phosphates
Cover bases inside
I say phosphates
Span the 5 and 3 primes
Theres no need - to - be - real - mixed - up
Proteins
Full of amino As
I say proteins
Come from mRNAs
I say proteins
Require tRNAs
There is more you - need - to trans-late
Bases
Carry info you see
I say bases
Are all complementry
I say bases
Like A,T,G and C
They have got - to - be all - paired - up
Codons
Like our friend U-A-C
I say codons
Come in clusters of three
I say codons
Have one base wobble ee
Now you can - go - forth - and - tran-slate
Major Groovy
To the tune of Feelin Groovy
Metabolic Melodies Website HERE
Introduction
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Carbohydrates are literally hydrates of carbon. This designation derives from the generalized
formula of simple monosaccharides,
189
Monosaccharides
The most common monosaccharides include
appropriate.
190
hexose. The list that follows gives the common sugars and their descriptors.
Ribose = aldo-pentose
Glucose = aldo-hexose
Galactose = aldo-hexose
Mannose = aldo-hexose
Fructose = keto-hexose
Diastereomers
Sugars may have multiple asymmetric carbons and thus differ from each other in the
configuration of hydroxyl groups on asymmetric carbons. Two sugars having the same
chemical form (aldoses, for example) and the
191
ror
im-
glucose.
tion in another sugar, the two sugars are mirror images of each other (Figure 2.151). Mir-
192
Boat/chair conformations
193
Modified monosaccharides
Many modifications can occur on
sugar residues (Figure 2.156).
Common ones include oxidation,
reduction, phosphorylation, and
substitution of an amine or an acetylamine for a hydroxyl. The ones that
affect the anomeric hydroxyl group
make glycosides (Figure 2.157),
whereas modifications that dont affect the anomeric hydroxyl,
(glucose-6-phosphate, for example), do not.
Figure 2.156 - Modified sugars. Locations of
glycosidic carbon indicated with red asterisks.
All are glycosides except N-acetylglucosamine
forms resemble boat structures, which others resemble chairs or envelopes (Figure
2.155). The stablest (and thus most abundant) of these forms have all of the hydoxyls
in the equatorial positions, resulting in less
steric hindrance.
Oxidation/reduction
The last considerations for simple
sugars relative to their structure are
their chemical reactivity and modifi-
194
Figure 2.158 - A positive Benedicts test starting at left and moving right
Wikipedia
The aldehyde group of aldoses is very susceptible to oxidation, whereas ketoses are less
so, but can easily be oxidized if, like fructose,
disaccharides, such as lactose and maltose are reducing sugars since they have at
least one anomeric carbon free, allowing
that part of the sugar to linearize and yield
195
of glycosaminoglycans, proteoglycans,
droitin sulfate, hyaluronic acid, and keratan sulfate. Glucuronic acid is also a precursor of ascorbic acid (Vitamin C) in organisms that synthesize this compound.
Glucuronic
acid
Sugar alcohols
One oxida-
tion product
of glucose is
glucuronic
bon molecule
where the
CH2OH on car-
cose), galactitol
dized to a car-
(galactose), arabi-
boxylic acid
tol (arabinose),
bose). Most of
these compounds
have a sweetness of
UDP-glucuronyltransferase enzymes to
considerably fewer
196
tion. Last, they are poorly absorbed by intestines, and so have a low glycemic index.
Artificial sweeteners
Artificial sweeteners are compounds that
stimulate taste receptors for sweetness, but
are metabolized for energy inefficiently at
best. Such compounds frequently are many
times sweeter than table sugar (sucrose) on
4
1
197
Disaccharides
Disaccharides (Figure 2.163) are made
up of two monosaccharides. The most
common ones include
sucrose (glucose and
fructose), lactose (galactose and glucose),
and maltose (glucose
galactopyranosyl-(14)-D-glucose, or more
bond.
Oligosaccharides
198
also can pose significant problems when organs are transplanted from
one individual
into another,
with rejection of
donated organs,
in some cases.
Organelle
targeting
The oligosaccharides that
are attached to
proteins may
also determine
joint movement.
Glycosylation
Sugars are commonly attached to proteins in
a process called glycosylation. Typically the
attachment is to a hydroxyl or other functional group. The majority of proteins synthesized in the endoplasmic reticulum are glycosylated. Five classes of glycosylated products (called glycans if multiple carbohydrates are attached via glycosidic bonds)
are known. They include:
199
teins.
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the sugars of the glycan are glycosidic (involve anomeric carbon) and usually occur between
carbons one and four. The consensus
Steps
is assembled as follows:
N-linked glycosylation
acetylglucosamine donate N-
and it is the most common type of such alteration. The process 1) occurs in the endoplasmic reticulum, 2) involves building a part
of the glycosyl chain on a molecule called dolichol pyrophosphate before transfer to the
200
protein.
Last alterations
201
O-Linked protein
glycosylation
O-linked glycosylation is
one of five types of glycosylation that occurs to proteins
in all kingdoms of biology. The
process is initiated primarily in
the Golgi apparatus of
eukaryotic cells, though a few
such linkages start in the endoplasmic reticulum. The
modification occurs on the oxyFigure 2.167 - Major N-glycan types - green =
mannose, blue = N-acetylglucosamine, red = glucose
Wikipedia
plex glycans.
autoimmune diseases.
202
cretions.
Other sugars
teins.
Phospho-linked glycosylation
are known.
Glypiation
glycosylphosphatidylinositol (GPI) as a
for glycosylation.
The linkage occurs at the carboxyl terminus of the protein through one or more phos-
C-linked glycosylation
Figure 2.169 - Common modified sugars in glycosylated proteins - from left - two
sialic acids (N-acetylneuraminic acid and 2-keto-3-deoxynonic acid), -L-fucose,
N-acetylglucosamine, and N-acetylgalactosamine
203
Glycoproteins
Glycoproteins are
a very diverse collection of saccharidecontaining proteins
with many functions. Attachment
of the saccharide to
the protein is
known as glycosylation. Secreted extracellular proteins
and membrane proteins with exposed
extracellular regions
are often glycosylated. Saccha-
rides attached to
these may be short
(oligosaccharides) or very large (polysaccharides). Glycoproteins play important
roles in the immune system in antibodies
and as components of the major histocompatibility complex (MHC). They are important for interactions between sperms and
eggs, in connective tissues and are abundant
in egg whites and blood plasma. Two glycoproteins (gp41 and gp120) are part of the
HIV viral coat and are important in the infection process. Some hormones, such as
erythropoietin, human chorionic gonadotropin, follicle-stimulating hormone
Glycation
Glycation is a chemical process (nonenzymatic) that occurs when a protein or
lipid covalently binds to a sugar, such as glucose or fructose. Glycation differs from glycosylation in that the latter process is controlled by enzymes and results in specific attachment of specific sugars to biomolecules.
Glycation, by contrast, is driven by two properties of monosaccharides 1) their chemistry
and 2) their concentration. Glycations may be
endogenous (occurring in an organism) or exogenous (occurring external to an organism).
teins.
204
eat.
Cooking
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Monomeric Unit
Glycogen
Glucose
Cellulose
Glucose
Amylose
Glucose
Callose
Glucose
Chitin
N-acetylglucosamine
Xylan
Xylose
Mannan
Mannose
Chrysolaminarin
Glucose
Nutritional
polysaccharides
This group of polysaccharides is used exclusively for
storage of sugar residues.
They are easily easily broken
down by the organism making
them, allowing for rapid release
Polysaccharides
Long polymers of sugar residues are called
Amylose
plants needs.
Structural polysaccharides
207
Chitin
Chitin (Figure 2.176) is another
structural polysaccharide, being comprised of N-acetylglucosamine units
joined by -1,4 linkages. It is a primary
component of the cell walls of fungi
Figure 2.174 - Cellulose with -1,4 links
between glucose sugars
Pectins
Another group of structural polysaccharides is
the pectins (Figure 2.178). These com-
sugars).
Monomer sugars of polysaccharides besides glucose
include xylose, mannose, galacFigure 2.175
Xylose
208
Lectins
Lectins are not carbohydrates, but proteins that specifically bind to carbohydrate
molecules found in animals and plants (where
they are known as phytohemagglutinins) and
are each highly specific for certain sugars.
They function in cellular and molecular recognition, as well as cell adhesion. One lectin recognizes hydrolytic enzymes containing
Figure 2.177 - Chitin in the wing of a sap
beetle
Wikipedia
immune disorders.
tion of choles-
terol from
food. Pectins
hydrates in the
Figure 2.178 - A
powdered form of
pectin
sorption.
209
as neuraminidase clus-
haled or ingested.
against microorganisms.
modulate inflamma-
organs.
Biofuels
est in using fuels made by biological processes is growing. Biofuels are made
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Agarose is a polysac-
tabolism. In bio-
charide polymer of
fuel production
anhydro-L-
galactopyranose
containing cellu-
lose is digested a)
enzymatically (by
peating structure
shown in Figure
2.182. Addition of
agaropec-
tin cre-
ates the
material
known
as agar.
yield methane.
Both substances
Agar/agarose
A polysaccharide product that has numerous uses in laboratories is agar/agarose.
make
Figure 2.183 - Agar plates for
culturing bacteria
gel-like
structures
Glycosaminoglycans
Another variation on the polyFigure 2.181 Biofuel-powered bus
211
found in connective tissue (linked to collagen) and they also act as lubricants for joints
(hyaluronic acid in synovial fluid), as
anti-clotting agents (heparin) and as components of mucus where they help to protect
against infection.
Chondroitin sulfate
Chondroitin sulfate (Figure 2.185) is a
glycosaminoglycan found in cartilage with a
a modified N-acetylgalactosamine. At
acetylglucosamine or N-
212
erty is uncertain. It is
to resist compression.
Chondroitin sulfate is
is a protection against
eign materials.
pound is a component of
the extracellular ma-
Heparin
Heparin (Figures 2.186 & 2.187) is a
modified polysaccharide whose biological
function is unclear, but whose ability to
prevent clotting of blood is used for
medical purposes. Heparin does not dissolve blood clots. Rather, it acts to prevent conversion of fibrinogen to fibrin
(see HERE).
Whether or not heparin is actually used
213
Hyaluronic acid
Hyaluronic acid (also known as
hyaluronan or hyaluronate) is a gly-
Synovial Fluid
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an increase in concentration.
migration whereas directed cell migration occurs via the interaction between hyaluronic
Function in skin
Proteoglycans
Glycosaminoglycans are commonly found
attached to proteins and these are referred
to as proteoglycans. Linkage between
the protein and the glycosaminoglycan is
its degradation.
For some cancers the plasma level of hyaluronic acid correlates with malignancy. Hyaluronic acid levels have been used as a marker
for prostate and breast cancer and to follow
disease progression. The compound can to
used to induce healing after cataract surgery.
Hyaluronic acid is also abundant in the granulation tissue matrix that replaces a fibrin clot
during the healing of wounds. In wound healing, it is thought that large polymers of hyaluronic acid appear early and they physically
make room for white blood cells to mediate an
immune response.
Breakdown
Breakdown of hyaluronic acid is catalyzed by
enzymes known as hyaluronidases. Hu215
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216
217
Hyaluronic Acid
To the tune of Rudolph the Red-Nosed Reindeer
Hyaluronic Acid
Acting almost magically
Placed just beneath the kneecap
Lubricating the debris
218
Structural Lullaby
To the tune of "Brahms' Lullaby"
Metabolic Melodies Website HERE
In your sleep
You can keep
Learning more about sugars
Fischer schemes
Haworth rings
D & L and everything
Hydroxides
Cant collide
Favring chair over boat form
Spatial guides
Coincide
With the way structures form
219
Lipids
Lipids are a diverse group of molecules
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Fatty acids
The most ubiquitous lipids in cells are the
fatty acids. Found in fats, glycerophospholipids, sphingolipids and serving as as
220
221
222
togenic diet.
Numbering
written as cis-6.
223
Fats/oils
Fats and oils are the primary energy storage
forms of animals and are also known as triacylglycerols and triglycerides, since they consist of a glycerol molecule linked via ester
bonds to three fatty acids (Figure 2.196).
Fats and oils have the same basic structure.
We give the name fat to those compounds that
are solid at room temperature and the name
oil to those that are liquid at room temperature. Note that biological oils are not the
same as petroleum oils.
Increasing the number of unsaturated fatty
acids (and the amount of unsaturation in a
given fatty acid) in a fat decreases the melting temperature of it. Organisms like fish,
which live in cool environments, have fats
with more unsaturation and this is why fish
oil contains polyunsaturated fatty acids.
Adipocytes
Fats are stored in the body in specialized cells
known as adipocytes. Enzymes known as lipases release fatty acids from fats by hydrolysis reactions (Figure 2.197). Triacylglycercol lipase (pancreatic - Figure
2.198) is able to cleave the first two fatty ac-
224
as ethanolamine,
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Phosphatidylethanolamines
Since all glycerolipids can have a variety of
fatty acids at positions 1 and 2 on the glycerol,
they all are families of compounds. The phosphatidylethanolamines are found in all living cells and are one of the most common
phosphatides, making up about 25% of them.
Figure 2.198 - Pancreatic
lipase
Fats can be synthesized by replacing the phosphate on phosphatidic acid with a fatty
acid.
Glycerophospholipids
Glycerophospholipids (phosphoglycerides) are important components of the
lipid bilayer of cellular membranes. Phosphoglycerides are structurally related to fats,
as both are derived from phosphatidic acid
(Figure 2.199). Phosphatidic acid is a simple glycerophospholipid that is usually converted into phosphatidyl compounds. These
are made by esterifying various groups, such
225
Phosphatidylcholines
Phosphatidylcholines (Figure
2.201) are another group of important
membrane components. They tend to
be found more commonly on the outer
leaflet of the plasma membrane.
Nutritionally, the compounds are readily obtained from eggs and soybeans.
Phosphatidylcholines are moved across
membranes by PhosphatidylchoFigure 2.200 - Four common components of
phosphatides
Wikipedia
precursors of phosphatidylcholines.
Cardiolipins
Phosphatidylserines
phosphatidylserines appear on
226
tron transport
chain to maintain
its structure. The
ATP synthase enzyme (Complex V)
of the oxidative
phosphorylation
system also binds
four molecules of
by a diphosphoglycerol (Figure 2.202). It is
an important membrane lipid, constituting
about 20% of the inner mitochondrial
membrane and is found in organisms from
bacteria to humans. In both plants and animals, it is found almost totally in the inner
mitochondrial membrane.
The molecules appear to be required for both
Complex IV and Complex III of the elec-
cardiolipin. It has
been proposed that cardiolipin functions as a
proton trap in the process of proton pumping
by Complex IV.
Cardiolipin also plays a role in apoptosis. As
shown in Figure 2.203, oxidation of cardiolipin by a cardiolipin-specific oxygenase
causes cardiolipin to move from the inner mitochondrial membrane to the outer one, helping to form a permeable pore and facilitating
227
Inositol
Though technically not a lipid itself, inositol
is found in many lipids. Inositol is a derivative of cyclohexane containing six hydroxyl groups - one on each carbon (Figure
2.205. It has nine different stereoisomers
Figure 2.204 - Diacylglycerol
that of sucrose).
Diacylglycerol
considered a vita-
(phosphatidylinositol-4,5-bisphosphate) are
min. Phosphory-
ing cascade.
naling processes.
228
Hydroxyls on carbons 3,4, and 5 of the inositol ring are targets for phosphory-
Phosphoinositides
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Compounds based on phosphatidylinositol (PI) are often called phosphoinositides. These compounds have important
Phosphatidylinositol-4,5bisphosphate
Phosphatidylinositol-4,5-bisphosphate
Figure 2.207 - Structure of PIP 2
229
Plasmalogens
specific kinases.
nels.
At the phosphate tail, the most commonly at-
Phosphatidylinositol (3,4,5)trisphosphate
Phosphatidylinositol
(3,4,5)-trisphosphate
(PIP3) is an important
molecule for the activation
of signaling proteins, such
as AKT, which activates
anabolic signaling pathways related to growth and
survival. PIP3 can be
dephosphorylated by phosphatase PTEN to yield
PIP2 and can be synthesized from PIP2 by kinase
action of Class I PI 3-
230
Lecithin
Lecithin is a generic term for a combination
of lipid substances that includes phosphoric
acid, glycerol, glycolipids, triglycerides,
and phospholipids. Lecithin is a wetting
agent helpful with emulsification and encapsulation and is even used as an anti-sludge additive in motor lubricants. Lecithin is used in
candy bars to keep cocoa and cocoa butter
from separating. Though considered safe as a
food ingredient, lecithin can be converted by
gut bacteria to trimethylamine-N-oxide
which may contribute to cholesterol deposition and atherosclerosis.
Sphingolipids
Fatty acids are also components of a broad
class of molecules called sphingolipids.
Sphingolipids are structurally similar to glycerophospholipids, though they are synthesized completely independently of them starting with palmitic acid and the amino acid
serine. Sphingolipids are named for the
amino alcohol known as sphingosine (Fig-
231
2.212). Addition of a
complex oligosaccharide creates a ganglioside.
Complex sphingolipids
may play roles in cellular
recognition and signalFigure 2.211 Schematic structure of a sphingolipid
in plasma membrane
232
Prostaglandins
A collection of molecules acting like hormones, prostaFigure 2.213 - Arachidonic acid drawn as straight (top)
and bent (bottom)
Eicosanoids
Fatty acids made from omega-6 and
233
Interesting prostaglandins
234
Leukotrienes
Another group of eicosanoid compounds
are the leukotrienes (Figure 2.219). Like
prostaglandins, leukotrienes are made from
arachidonic acid. The enzyme catalyzing
their formation is a dioxygenase known as
arachidonate 5-lipoxygenase. Leukotrienes are involved in regulating immune responses. They are found in leukocytes and
other immunocompetent cells, such as neutrophils, monocytes, mast cells, eosino-
phils, and basophils. Leukotrienes are associated with production of histamines and
Thromboxanes
Prostacyclin
Prostacyclin (also known as
235
Cholesterol
work on it. Evidence for cholesterols importance comes from the study of brain tissue
where it comprises 10-15% of the dry mass.
Membrane flexibility
In animal cells, cholesterol provides for membrane flexibility that allows for cellular
movement that is in contrast to plant and bacterial cells with fixed structures. Cholesterol
is made in many cells of the body, with the
liver making the greatest amount. The anabolic pathway leading to synthesis of cholesterol is known as the isoprenoid pathway
and branches of it lead to other molecules including other fat-soluble vitamins.
236
Reducing
cholesterol
levels
Strategies for reducing cholesterol in the
body focus primarily
Packaging
Cholesterols (and other lipids) hydro-
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237
Membrane
function
of cholesterol exits
the body in the fe-
In membranes, cho-
lesterol is important as
to penicillin are
transmission of signals
hibit cholesterol
recycling. One of
these is ezetimibe,
shown in Figure
2.224.
group of lipoprotein
238
brane.
Vitamin A
Sources
Light sensitivity
bound to the
239
When exposed to light of a particular wavelength, the tail of the retinal molecule will
Vitamin D
The active form of vitamin D plays important roles in the intestinal absorption of calcium and phosphate and thus in healthy
Figure 2.229 - Cholecalciferol - Vitamin D 3
Vitamin D4 - 22-Dihydroergocalciferol
mone.
Vitamin D5 - Sitocalciferol
Forms of vitamin D
tem.
Mechanism of action
Calcitriol moves in the body bound to a vitamin D binding protein, which delivers it to
target organs. Calcitriol inside of cells acts by
binding a vitamin D receptor (VDR), which
results in most of the vitamins physiological
effects. After binding calcitriol, the VDR migrates to the nucleus where it acts as a transcription factor to control levels of expression of calcium transport proteins (for example) in the intestine. Most tissues respond to
VDR bound to calcitriol and the result is moderation of calcium and phosphate levels in
cells.
Deficiency/excess
Deficiency of vitamin D is a cause of the disease known as rickets, which is characterized
241
Vitamin E
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(Figure 2.234).
Vitamin E also can affect enzyme
activity. The compound can inhibit
Action
Vitamin E scavenges oxygen
242
Vitamin K
Like the other fat-soluble vitamins, Vitamin K comes in multiple forms (Figure 2.235) and
is stored in fat tissue in the body.
There are two primary forms of
the vitamin - K1 and K2 and the
Figure 2.234 - Lipid peroxidation reactions
Deficiency/excess
Deficiency of vitamin E
can lead to poor conduction
of nerve signals and other
issues arising from nerve
problems. Low levels of the
vitamin may be a factor in
low birth weights and premature deliveries. Deficiency, however, is rare,
and not usually associated
with diet.
Excess Vitamin E reduces
vitamin K levels, thus reducing the ability to clot
blood. Hypervitaminosis of
243
Action
tle occur.
Sources
244
Glucocorticoids
Steroids
Mineralocorticoids
Mineralocorticoids are steroid hor-
245
Androgens
Androgens are steroid hormones that act
by binding androgen receptors to stimulate
development and maintenance of male char-
Progestagens
Progestagens (also called gestagens) are
steroid hormones that work to activate the
progesterone receptor upon binding to it.
Synthetic progestagens are referred to as progestins. The most common progestagen is
progesterone (also called P4 - Figure
2.240) and it has functions in maintaining
pregnancy. Progesterone is produced primarily in the diestrus phase of the estrous cycle by
acteristics in vertebrates. Androgens are precursors of estrogens (see below). The primary androgen is testosterone (Figure
2.241). Other important androgens include
dihydrotestosterone (stimulates differentiation of penis, scrotum, and prostate in embryo) and androstenedione (common precursor of male and female hormones).
Estrogens
The estrogen steroid hormones are a class of
compounds with important roles in menstrual
and estrous cycles. They are the most important female sex hormones. Estrogens act by
246
chemotherapeutic
treatment when
estrogenresponsive tu-
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Cannabinoids
Cannabinoids are a group of chemicals that
Figure 2.241 - Testosterone - An
androgen
nabinoids (man-made).
Endocannabinoids are
Cannabinoid receptors
major estrogen.
Estrogens are made from the androgen
hormones testosterone and androstenedione in a reaction catalyzed by
the enzyme known as aromatase. Inhibition of this enzyme with aromatase inhibitors, such as exemestane, is a strategy for stopping estrogen production. This may be part of a
247
Lipoxins
Lipoxins (Figure 2.245) are eicosanoid
Figure 2.244 - Anandamide - An
endocannabinoid
Anandamide
Anandamide (N-arachidonoylethanolamine
thesis of 15R-hydroxyeicosatetraenoic
248
and bone marrow in a pathway that is conserved across a wide range of biology.
Porphobilinogen
Porphobilinogen (Figure 2.248) is a pyrrole
molecule involved in porphyrin metabolism.
It is produced from aminolevulinate by action
of the enzyme known as ALA dehydratase.
Porphobilinogen is acted upon by the enzyme
porphobilinogen deaminase. Deficiency of
the latter enzyme (and others in porphyrin metabolism) can result in a condition known as
Figure 2.246 - Structure of heme B
`
dominal pain and numerous psychiatric issues. Both Vincent van Gogh and King
Heme
Heme groups are a collection of protein/
enzyme cofactors containing a large heterocyclic aromatic ring known as a porphyrin
ring with a ferrous (Fe++) ion in the middle.
An example porphyrin ring with an iron
(found in Heme B of hemoglobin), is shown
in Figure 2.246. When contained in a protein, these are known collectively as hemoproteins (Figure 2.247).
Heme, of course, is a primary component of
hemoglobin, but it is also found in other proteins, such as myoglobin, cytochromes,
and the enzymes catalase and succinate dehydrogenase. Hemoproteins function in
oxygen transport, catalysis, and electron
transport. Heme is synthesized in the liver
249
target protein.
Sugars can be removed/added after the transfer to the protein. Levels of dolichol in the
Dolichols
Dolichol is a name for a group
of non-polar molecules made
by combining isoprene units
together. Phosphorylated
forms of dolichols play central
roles in the N-glycosylation
of proteins. This process,
which occurs in the endoplasmic reticulum of eukary-
250
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name of ter-
Synthesis
Terpenes, like steroids, are synthesized starting with simple building blocks known as isoFigure 2.250 - Pine tree resin - A
source of terpenes
Wikipedia
prenes. There are two of them - dimethylallyl pyrophosphate and the related isopentenyl pyrophosphate and (Figures 2.252
Terpenes
Terpenes are members of a class of non-
thesis.
in terpenes.
251
Examples
Figure 2.252 - Dimethylallyl pyrophosphate
Caffeine
(many units).
252
253
ApoA-I
Lipoprotein
Complex(es)
Function
HDL
ApoA-II
HDL
Inhibit LCAT
ApoA-IV
Chylomicrons /
HDL
Activate LCAT
AboB-48
Chylomicrons
Cholesterol Transport
AboB-100
VLDL / LDL
ApoC-I
VLDL / LDL
Unknown
ApoC-II
All
Activate Lipoprotein
Lipase
ApoC-III
All
ApoD
HDL
Unknown
ApoE
VLDL /
Chylomicrons /
HDL
Clearance of
Chylomicrons Remnants
and VLDLs
Gene editing
ApoB-48 and ApoB-100 are interesting in being coded by the same gene,
but a unique mRNA sequence editing
event occurs that converts one into the
other. ApoB-100 is made in the liver,
but ApoB-48 is made in the small intestine. The small intestine contains
an enzyme that deaminates the cyti-
Apolipoproteins
Each lipoprotein complex contain a characteristic set of apolipoproteins, as shown in
Figure 2.256. ApoC-II and ApoC-III are
notable for their presence in all the lipoprotein complexes and the roles they play in ac-
254
and monoacyl glycerol are absorbed by intestinal cells (enterocytes) and reassembled back
Movement
Exogenous
pathway
Dietary fat entering the
body from the intestinal
system must be transported, as appropriate, to
places needing it or storing it. This is the function of the exogenous
255
This is accomplished by
receptors in the liver
that recognize and bind
to the ApoE of the chylomicrons. The bound
complexes are then internalized by endocytosis,
degraded in the lysosomes, and the cholesterol is disbursed in
liver cells.
Endogenous
pathway
The liver plays a central
role in managing the
bodys needs for lipids.
mic reticulum.
Exocytosis
256
Figure 2.260 - Movement of lipids in the body - Green = exogenous pathway; Blue =
endogenous pathway; Purple = reverse transport pathway
Image by Aleia Kim
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257
258
LDL receptors
on their liver cells.
when it is mature, it returns its load of cholesterol back to the liver or, alternatively, to LDL
erly functioning
cholesterol.
ishes.
259
though, are correlated with formation of atherosclerotic plaques (Figure 2.263 &
2.264) and incidence of atherosclerosis, leading
to the description
of them as bad
cholesterol. This
is because when
LDL levels are
very high, plaque
formation begins.
It is thought that
reactive oxygen
species (higher in
the blood of smokers) causes partial
oxidation of fatty
acid groups in the
LDLs. When levels are high, they
tend to accumu-
the epithelial cells on the inside of the arteries. Macrophages of the immune system take
up the damaged LDLs (including the cholesterol).
Good cholesterol
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HDLs are able to remove cholesterol from foam cells. This occurs as a result of contact between
the ApoA-I protein of the HDL and
261
to contract the disease and those homozygous for it are 15 times as likely to do so. It is
not known why this gene or allele is linked to
the disease. The three alleles differ only
slightly in amino acid sequence, but the
changes do cause notable structural differences. The E4 allele is associated with increased calcium ion levels and apoptosis after injury. Alzheimers disease is associated
with accumulation of aggregates of the amyloid peptide. ApoE does enhance the proteolytic breakdown of it and the E4 isoform is
not as efficient in these reactions as the other
isoforms.
262
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
263
264
Prostaglandins!
To the tune of "Oklahoma!"
Metabolic Melodies Website HERE
Prossss-taglandins
The ei-co-sa-noids creating pain
Are the ones to blame - when you get inflamed
And ouch(!) - they hurt inside your brain
Prossss-taglandins
Every throb and ache gets magnified
If you hope to win, cyclo-oxygen's
Generation's got to be denied
The Vioxx has all been recalled
So go get yourself Tylenol-ed
And if you aaaaaaaaaaaaache
Blame PGH synthaaaaaaaaase!
We must complain that
You make the aches prostaglandins
Prostaglandin - D2, F1, G2, E2
Prostaglandin, it's you
265
3
Membranes
267
Lipid bilayers
terol, proteins, glycolipids, glycerophospholipids, and sphingolipids. The last two of these
will, when mixed vigorously with
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ing; and 6) store energy in electrochemical gradients for ATP production (oxidative phos-
268
tion of cellular
membranes.
Plasma membranes differ from
cell walls both in
the materials comprising them and in
their flexibility.
Cell walls will be
covered near the
end of this chapter
(HERE).
Facilitated
diffusion
In other cases, no
external energy is
required and they
move by diffusion
through specific cellular channels.
This is referred to
as facilitated diffusion. Before we
discuss movement
of materials across
membranes, it is
appropriate we discuss the composi-
269
Hydrophilic heads
The composition of the hydrophilic heads varies considerably. In glycerophospholip-
270
Sphingolipids
In sphingolipids (Figure 3.4), the hydrophilic head can contain a phosphate
linked to ethanolamine or choline
and this describes the structure of sphingomyelin, an important component of
neural membranes. Most sphingolipids
lack the phosphate and have instead a hydrophilic head of a single sugar (cerebrosides) or a complex oligosaccharide (gangliosides).
Water exclusion
In each case, the glycerophospholipid
or sphingolipid has one end that is po-
271
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Composition bias
The plasma membrane has distinct biases of composition relative
to its inside and the outside (Figure 3.7). First, glycosylation (of
lipids and proteins) has the
sugar groups located almost exclusively on the outside of the cell,
away from the cytoplasm (Figure
Figure 3.7 - Differential distribution of membrane
lipids by inner and outer leaflet
Image by Pehr Jacobson
272
Organelle membranes
Bias of lipid composition also exists with
respect to organelle membranes. The unusual diphosphodiglycerolipid known as
cardiolipin, for example, is almost only
found in mitochondrial membranes (see
HERE) and like phosphatidylserine, its
movement is an important step in apoptosis. In signaling, phosphatidylinositols play important roles providing second messengers upon being cleaved
(see HERE).
Lateral diffusion
Movement of lipids within each leaflet of
Figure 3.9 - Distribution of lipids in
organelle membranes
Transverse diffusion
273
sphingolipids from outer leaflet to inner leaflet (cytoplasmic side) of cell. Floppases
move membrane lipids in the opposite direction. Scramblases move in either direction.
274
Membrane fluidity
Cholesterols function in the lipid bilayer
is complex (Figure 3.13). It influences
membrane fluidity. Figure 3.14 shows
the phase transition for a membrane as it is
heated, moving from a more frozen character to that of a more fluid one as the temperature rises. The mid-point of this transition, referred to as the Tm, is influenced by
the fatty acid composition of the lipid bilayer
compounds. Longer and more saturated
fatty acids will favor higher Tm values,
whereas unsaturation and short fatty acids
will favor lower Tm values. It is for this reason
that fish, which live in cool environments,
Figure 3.12 - Structure of a
flippase
Wikipedia
275
Figure 3.15 - A lipid raft - 1 = Non-raft membrane / 2 = Lipid raft / 3 = Lipid raft
associated transmembrane protein / 4 = Non-raft membrane protein / 5 =
Glycosylation modifications (on glycoproteins and glycolipids) / 6 = GPIanchored protein / 7 = Cholesterol / 8 = Glycolipid
Features
range of fluidity.
Lipid rafts
Cholesterol is also abundantly found in
membrane structures called lipid
rafts. Depicted in Figure 3.15,
lipid rafts are organized structures within the membrane typi-
ing areas of the bilayer. The higher concentration of cholesterol in the rafts may be due to
its greater ability to associate with
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to ligands in signaling. After receptor activation takes place at a lipid raft, the signaling
276
Barrier
Transport of materials
across membranes is essential for a cell to exist. The
lipid bilayer is an effective
barrier to the entry of most
molecules and without a
means of allowing food molecules to enter a cell, it would
die. The primary molecules
that move freely across the
lipid bilayer are small, uncharged ones, such as H2O,
CO2, CO, and O2, so larger
molecules, like glucose,
that the cell needs for energy, would be effectively exFigure 3.16 - A sphingolipid (left) associating with
cholesterol (right)
cluded if there were not proteins to facilitate its movement across the membrane.
globulin E signaling, insulin receptor signaling and others. For more on signaling, see
Membrane proteins
HERE.
Proteins in a lipid bilayer can vary in quantity enormously, depending on the mem-
277
Transmembrane
proteins
Transmembrane proteins are integral membrane proteins that completely span from one side of
a biological membrane to
the other and are firmly embedded in the membrane
(Figure 3.18). Transmem-
278
transport of molecules
into or out of the cell.
Example of integrated/
transmembrane proteins
include those involved in
transport (e.g., Na+/K+
ATPase), ion channels
(e.g., potassium channel
of nerve cells) and signal
transduction across the
lipid bilayer (e.g., GProtein Coupled Receptors).
Peripheral membrane
Finer classification
A more detailed classification scheme further
categorizes the integral and anchored proteins
into six different types (Figure 3.20). Type
I and Type II have only one portion of the
protein pass through the membrane. They
differ in the orientation of the amine and carboxyl end with respect to inside/outside.
Type I transmembrane proteins have the
amino terminus on the outside and carboxy
terminus on the inside, whereas Type II pro-
279
Osmotic pressure
sure.
Blood types
Equalizing
concentrations
The liquid on the right
does not completely
move to the left,
though, as might be expected if the only force
involved is equalizing
281
sure of a dilute solution mathematically behaves like the ideal gas law
Posmotic = nRT/V
where n is the number of moles, R is the gas
MolarityParticles = MolaritySucrose.
However, for salts, like KOH, which forms
two ions in solution (K+ and OH-),
MolarityParticles = 2* MolarityKOH.
Significant consideration
V is the volume.
with molarity, so
Posmotic = MR*T
where M is the molarity of the dissolved molecules, R* is the gas constant expressed in (L
Posmotic term, so
= MR*T
Remember when
calculating the
molarity to include the molarity of each particle. For example, when one
dissolves sucrose in solution, it does not
split into smaller
particles, so
282
Figure 3.24 - The plant cell wall protects the plasma membrane from rupture in
hypotonic conditions
membrane.
Hypotonic, hypertonic,
isotonic
We consider three situations
(Figure 3.23). First, if the con-
centration of solutes is greater inside the cell than outside, water will tend to
283
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Membranes: Transport
Wikipedia
Terminology
A protein involved in moving only one molecule across a membrane is called a uniport
cules in the same direction across the membrane are called symports (also called syn286
ionophores.
287
For example, the blood concentration of glucose is sufficiently high that red blood cells
can use facilitated diffusion as a means of
Facilitated diffusion
As noted, the driving force for facilitated diffusion is concentration,
meaning that in facilitated diffusion,
materials will only move from a
288
Ion channels
Ion channels are poreforming membrane proteins
in the membranes of all cells
that regulate movement of
289
Control mechanisms
senger.
Sound waves cause mechanical
deformation of hair cells in the
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by light causes them to close, triggering a series of events that result in a signal being sent the
brain about the perception of light.
290
HERE).
Hydration shell
Voltage gated channels are essential for
portant to understand
cussed in more
depth HERE.
Ion movement
through
channels
channels to select
large is intuitive -
matic reaction.
is too small.
Comparable to enzymes
Potassium channels that are selective for
this is rooted in
tion energy is
mostly prohibitive
tion.
For potassium
molecules to oc-
lipid bilayer
cisely positioned
carbonyl groups
is why ion
help to stabilize
channel/transport
the ion as it
cally unfavorable (requires net input of energy) but the same process for a potassium
Energy factor
Gramicidin
Gramicidins (Movie 3.1) are antibiotic
polypeptides synthesized by the soil bacterium known as Bacillus brevis. These small
pentadecapeptides (15 amino acids) are synthesized by the bacterium to kill other bacteria.
When released by the Bacillus brevis, the
gramicidins insert themselves in the membranes of Gram positive bacteria and allow the movement of sodium ions into the target cells, ultimately killing them. Gramicidins
can also cause hemolysis in humans so they
Movie 3.1 - Gramicidin A
used topically.
Ion balance
The movement of ions across a lipid
bilayer is tightly regulated, and with
good reason. Maintaining a proper
balance of ions inside and outside of
cells is important for maintaining osmotic balance. It is also important
inside and outside of organelles
like the mitochondria and chloroplasts for energy generation. If the
ionic balance of a cell is sufficiently
disturbed by an uncontrolled ionophore, a cell may die.
293
Transporter proteins
Aquaporins
moved.
Porins
Porins are proteins containing a -barrel
structure that crosses the cell membrane/
Binding of the proper molecule causes a conformational change in the shape of the protein
(an eversion) which results in a flipping of the
open side of the protein to the other side of
the lipid bilayer. In this way, the molecule is
moved. Like ion channels, transporter proteins facilitate movement of materials in ei-
294
ther direction, driven only by the concentration difference between one side and the
other.
far are driven solely by a concentration gradient - moving from higher concen-
glucose transporter
uses a sodium gradient as a force for actively
transporting glucose into a cell. Thus, it is
port uses ATP energy.
Active transport
Na+/K+ ATPase
An important integral membrane transport protein is the Na+/K+ ATPase
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295
(in nerve cells) for creating the sodium and potassium gradients necessary for signal transmission. Failure of the system to function results in swelling of the cell due to movement
of water into the cell through osmotic pressure. The transporter expends about one
having a phosphorylated aspartate intermediate and is present across the biological kingdoms - bacteria, archaeans, and eukaryotes.
296
ATPase types
Nerve transmission
Now that you have seen how the
Na+/K+ ATPase functions, it is appropriate to discuss how nerve cells
Figure 3.39 - Schematic structure of V-ATPases
Wikipedia
The V-type and F-type ATPases are very similar in structure. The V-type (Figure 3.39)
uses ATP to pump protons into vacuoles
and lysosomes, whereas F-types use proton
gradients of the mitochondria and chloroplasts to make ATP.
A-ATPases (A1AO-ATPases) are found
in function.
the neuron releases neurotransmitters that exit the nerve cell and travel
across the junction to a recipient cell
where a response is generated. That response may be creating another nerve
signal, if the adjacent cell is a nerve cell
or it may be a muscular contraction
if the recipient is a muscle cell (Figure
3.41).
stimulate muscle
contraction.
Signals travel
through neurons,
ultimately arriving
at junctions with
other nerve cells or
target cells such as
muscle cells. Note
that neurons do
not make physical
contact with each
other or with muscle cells. The tiny
space between two
neurons or between
a neuron and a muscle cell is called the
synaptic cleft. At
the synaptic cleft,
Figure 3.41 - (1) The action potential reaches the axon terminal;
(2) voltage-dependent calcium gates open - calcium enters the
axon terminal; (3) neurotransmitter vesicles fuse with the
presynaptic membrane and release acetylcholine (ACh); (4) ACh
binds to postsynaptic receptors on the sarcolemma; (5) ion
channels open in response and allow sodium ions to flow into
the muscle cell; (6) The flow of sodium ions into the muscle cell
generates an action potential which travels to the myofibril and
results in muscle contraction.
Wikipedia
299
Signal source
Creation of a nerve signal begins
with a stimulus to the nerve
cell. In the case of muscle contraction, the motor cortex of
propriate motor neurons, stimulating them to generate a nerve impulse. How is such an impulse
generated?
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Resting potential
In the unstimulated state, all cells, including
nerve cells, have a small voltage difference
(called the resting potential) across the
plasma membrane, arising from unequal
pumping of ions across the membrane.
The Na+/K+ ATPase, for example, pumps sodium ions out of the cell and potassium ions
into cells. Since three sodium ions get
pumped out for every two potassium ions
pumped in, a charge and chemical gradient is
created. It is the charge gradient that gives
rise to the resting potential.
Initiation of signal
The signal generated by a motor neuron begins with opening of sodium channels in
the membrane of the nerve cell body causing a rapid influx of sodium ions into the
nerve cell. This step, called depolarization
(Figure 3.42), triggers an electrochemical
300
301
Moving signal
This chemical and electrical
change that creates the ac-
302
303
The pump
works in conjunction with
the Na+/K+
Na+/glucose
transporter
rate pump is known as secondary active transport. For intestinal mucosa, the pump transports glucose out of the gut and
304
Calcium pumps
contraction and play important roles as signaling molecules within cells. In addition,
when calcium concentrations rise too high,
DNA in chromosomes can precipitate. Calcium concentration in cells is therefore managed carefully. It is kept very low in the cytoplasm as a result of action of pumps, both in
the plasma membrane, which pump calcium outwards from the cytoplasm and in organelles, such as the endoplasmic reticulum (sarcoplasmic reticulum of muscle
cells), which pump calcium out of the cytoplasm and into these organelles.
Opening of calcium channels, then, increases
calcium concentration quickly in the cytoplasm resulting in a quick response, whether
the intention is signaling or contraction of a
Na+/Ca++ transporter
One calcium pump of interest uses the sodium
gradient as an energy source. It is the
sodium/calcium pump. This electrogenic
antiport system uses sodiums movement
into the cell as a driving force to move calcium
out of the cell, although its direction can reverse in some circumstances. The pump is a
high capacity system to move a lot of calcium
quickly, moving up to 5000 calcium ions per
second and is found in many tissues with
many functions.
305
Digitalis
for contraction of heart muscle. Calcium efflux from the cells is the normal operation of
the pump, however, during the upstroke of
the cycle, there is a large movement of sodium
ions into the heart cell. When this occurs, the
pump reverses and pumps Na+ out and Ca++
in briefly. Since calcium helps stimulate contraction of cardiac muscle, this can help make
the heart beat stronger and is the focus of the
use of digitalis to treat congestive heart fail-
ABC transporters
ABC transporters are another class of
transmembrane proteins that use ATP energy to transport things against concentration
gradients (Figures 3.47 & 3.48). This protein superfamily includes hundreds of proteins (48 in humans alone) and spans all extant phyla from prokaryotes to humans.
These proteins function not only in mem-
ure.
lation.
Transport
306
Disease
ABC transporters
307
compounds.
Cystic fibrosis
a PDZ domain.
Cystic fibrosis (CF) is a an autosomal recessive genetic disorder arising from muta-
Lactose permease
epithelial tissue
membranes exerts
mechanism is classi-
fied as a secondary
active transport
wardly directed H+
electrochemical
gradient as an en-
Function
tose is transported
production of sweat,
GLUTs
308
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Glut 4
GLUT 4 is regulated by insulin and is found
primarily in adipose and striated muscle tis-
309
sugar to favor movement of various GLUT proteins (including GLUT 4) from intracellular
vesicles to the cell membrane, thus stimulating uptake of the glucose. GLUT 4 is also
found in the hippocampus where, if trafficking is disrupted, the result can be depressive
behavior and cognitive dysfunction.
For all of the GLUT proteins, a key to keeping
the glucose in the cell is phosphorylation of
it by the glycolysis enzyme, hexokinase, in
the cytoplasm. Phosphorylated molecules
cannot enter GLUTs and dont have an easy
means of exiting the cell.
310
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
311
Distance Ed
To the tune of Mister Ed
Metabolic Melodies Website HERE
Bridge
A classroomclass meets every week the same time every day
But DistanceEd is most unique - its flexible schedules okay
312
I know he said it
That's why I dread it
'cause I skipped Friday's
Extra credit
'twil pro'bly haunt me
That lowly ze-ro
Grade in BB three five oh
It could be steric
Or esoteric
That carbons get so
Anomeric
I'm too hysteric
Better let it go
This song's for BB three five oh
313
this section.
Endocytosis
Besides transporter proteins
314
Receptor mediated
endocytosis
The process of receptor mediated
endocytosis is a relatively specific
means of bringing molecules into
cells because it requires the incoming
material to be somehow associated
with a specific cell surface receptor.
In the example of Figure 3.53, the
receptor is the cellular LDL receptor.
Clathrin-coated invaginations, as
315
Non-clathrin
endocytosis
Caveolins
Caveolins have affinity for cholesterol and
associate with it in the membrane of cells,
causing the formation of membrane invaginations of about 50 nm. The caveolin proteins
can oligomerize and this is important for
316
Macropinocytosis
A phenomenon known as cell drinking,
macropinocytosis literally involves a cell
taking a gulp of the extracellular fluid. It
does this, as shown in Figure 3.56, by a simple invagination of ruffled surface features of
the plasma membrane. A pocket results,
which pinches off internally to create a vesicle containing extracellular fluid and dissolved molecules. Within the cytosol, this internalized vesicle will fuse with endosomes
and lysosomes. The process is non-specific
Figure 3.56 - Macropinocytosis
317
Endosomes
Internalized material from endocytosis that
doesnt involve phagocytosis passes through
an internalized structure called an endosome. Endosomes are membrane bounded
structures inside of eukaryotic cells that
play a role in endocytosis (Figure 3.59).
They have a sorting function for material internalized into the cell, providing for retrieval of
Figure 3.58 - Phagocytosis by a
neutrophil (yellow) of an Anthrax
bacillus (orange)
Wikipedia
Phagocytosis
Phagocytosis is a process whereby relatively
large particles (0.75m in diameter) are intenalized. Cells of the immune system, such
as neutrophils, macrophages, and others,
use phagocytosis to internalize cell debris,
apoptotic cells, and microorganisms.
The process operates through specific receptors on the surface of the cell and phagocytosing cell engulfs its target by growing
around it. The internalized structure is
known as a phagosome, which quickly
merges with a lysosome to create a phagolysosome (Figure 3.58), which subjects the
engulfed particle to toxic conditions to kill it,
318
Membrane fusion
Fusion is a membrane
process where two distinct lipid bilayers
sis occur.
Exocytosis
The process of exocytosis is
When the fusion proceeds through both leaflets of both bilayers, an aqueous bridge results
and the contents of the two structures mix.
Common processes involving membrane
fusion (Figure 3.60) include fertili-
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3.61). Artificial membranes such as liposomes can also fuse with cellular mem319
whereas t-
SNARES can be
erned by fusion, as
many bilayer-coated
branes of targeted
compartments.
SNARE proteins
with increases of
Mediation of fusion of
intracellular cal-
vesicles in exocytosis
cium. Fusion of
synaptic vesi-
teins known as
cles in neuro-
SNAREs (Soluble
transmission re-
sults in activation
of voltage-
large superfamily of
dependent cal-
cium channels in
yeast to mammals.
Influx of calcium
fusion coincides
Wikipedia
vesicle fusion.
In the endocrine
system, binding of
hormones to G
protein coupled
receptors activate the IP3/DAG
system to in-
helps to stimulate
320
well, yielding
opening of the
contents of the
vesicle chamber to its target
(usually outside
the cell).
Shuttles
Another way to
transport items
across a membrane for which
there is no specific transport
system available
is the use of shut-
tles. Shuttles
are important
when there is no
Wikipedia
In the process of membrane fusion (Figure 3.62), the v-SNAREs of a secretory vesicle (upper left) interact with the t-SNAREs of
a target membrane (bottom). The v- and tSNAREs zipper themselves together to bring
the membrane vesicle and the target membrane closer together.
Zippering also causes flattening and lateral
tension of the curved membrane surfaces, favoring hemifusion of the outer layers of each
membrane. Continued tension results in subsequent fusion of the inner membranes as
Glycerol
phosphate shuttle
The first of these methods is the least efficient,
but it is rapid. It found
commonly in muscles
which have needs for
rapid energy and brain
tissue. This shuttle is
referred to as the glycerol phosphate shuttle and is shown in Figure 3.63. It operates
in the intermembrane space between
the inner and outer mitochondrial memFigure 3.63 - Glycerol phosphate shuttle system in the
intermembrane space of a mitochondrion
Image by Pehr Jacobson
322
Malate-aspartate shuttle
323
in the process.
Acetyl-CoA shuttle
for -ketoglutarate.
Inside the mitochondrion, malate
is reoxidized to oxaloacetate and
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cumulate.
324
Figure 3.65 - Structure of connexons joining two cells. Bundles of six copies of
connexin proteins in the plasma membrane of each cell comprise the connexon
structures
Cell junctions
1. Gap junctions
2. Adherens junctions, (Anchoring Junctions, desmosomes and hemidesmosomes)
3. Tight junctions
protein complexes
on the cytoplasmic
side of the cell membranes of epithelial and endothelial tissues that link
cells to each other
or to the extracellular matrix.
They correspond to
the fascia adherens
found in nonepithelial/nonFigure 3.66 - Two means of intercellular communication in plant
cells - apoplastic pathway (through cell wall) and symplastic
pathway (through the plasodesma)
endothelial cells.
Gap junctions
Gap junctions are specialized structures
made up of two sets of structures called connexons (one from each cell - see Figure
3.65) directly link the cytoplasms of the
connected cells. Gap junctions are regulated to control the flow of molecules, ions,
and electrical impulses between cells. In
plants, similar structures known as plasmodesmata traverse the cell wall (Figure
3.66) and perform similar functions.
Adherens junctions
Adherens junctions (Figure 3.67) are
326
Tight junctions
Tight junctions (Figure 3.68) are a network of protein strands
that seal cells together
and restrict the flow of
ions in the spaces between them. The effect
of their structure is to
restrict the movement
Figure 3.68 - Tight junctions
327
Liposomes
The spontaneous ability of
Figure 3.69 - A glypiated protein linked to
a membrane-embedded inositol-based
molecule. The protein portion is above
the red phosphate ion
Image by Pehr Jacobson
GPI anchors
Membrane proteins attached to glycosylphosphatidylinositol (also known as a
GPI anchor) are referred to as being glypiated. The proteins, which play important
roles in many biochemical processes, are attached to the GPI anchor at their carboxyl terminus.
phosphoglycerolipid and
sphingolipid
compounds to
form lipid bilayers is exploited in the formation of artificial membranous
structures called
liposomes (Figure 3.69). Liposomes are useful
for delivering
their contents
into cells via
328
ganization of
amino acids
can be recognized
by computer analy-
the cytoplasm.
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Hydropathy index
bilayer, as labeled.
Figure 3.71 Hydropathy index for
amino acids. More
positive values
indicate higher
hydrophobicity.
Wikipedia
Cell walls
Cells walls are found in many
cells, including plants, fungi,
and bacteria, but are not found
329
a plasma membrane,
and then the cytoplasm. Gram nega-
periplasmic space,
330
331
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
332
BB Wonderland
To the tune of Winter Wonderland
Metabolic Melodies Website HERE
333
Thank
there's a
God
video
334
4
"A clever man commits no
minor blunders."
Goethe
Catalysis
sis occurs.
the mind, boosting reaction rates by 1024 over 1 trillion trillion times faster than an un-
335
catalyst. Chemical catalysts, such as platinum, can speed reactions, but enzymes
Equilibrium
336
but it does not relate to absolute concentrations. What happens when a biochemical reaction is at equilibrium is that the concentrations of reactants and products do not change
over time. This does not mean that the reactions have stopped. Remember that reactions
are reversible, so there is a forward reaction
G = ln{[Products]/[Reactants],
since the G is zero. Because G itself is
zero at equilibrium, then [Products] = [Reactants]. This is the only circumstance where
[Products] = [Reactants] at equilibrium.
Concentration matters
So, contrary to the perceptions of many stu-
Similarly,
dents, the concentrations of products and reactants are not equal at equilibrium, unless
[B]T0 = [B]T+5
337
Dynamic reactions
The reactions occurring in cells, though, are
and
[A]T0 = [B]T0
338
Figure 4.3 - Energy changes during the course of an uncatalyzed reaction (solid
green line) and a catalyzed reaction (dotted green line).
Image by Aleia Kim
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Module
Activation energy
HERE
In Figure 4.3, the activation energy for a catalyzed reaction is overlaid. As you can see, the reac-
339
Exceptions
energy is lowered.
Reversibility
The extent to
physiology.
which reactions
minor exceptions
ward is a function
to the reversibility
of reactions,
energy difference
appearance of a
substrate or
tion. Consider
the first reaction
below which is
the percentage of
molecules that will be present as products at
equilibrium. It is worth noting that since an
enzyme lowers the activation energy for a re-
action that it can speed the reversal of a reaction just as it speeds a reaction in the forward
direction. At equilibrium, of course, no
In the forward direction, carbonic acid is produced from water and carbon dioxide.
340
reaction is pulled in the direction of the molecule being lost and reversal cannot occur unless the missing molecule is replaced. In the
second reaction occurring on the right, carbonic acid (H2CO3) is removed by ionization. This too would limit the reaction going
in metabolic pathways.
incredible efficiency as a
catalyst.
Changes
cations, or structural
General
mechanisms of action
Substrate binding
they bind.
(molecule involved in the reaction being catalyzed), but also place it in a position to be electronically induced to react, either within itself
Induced fit
These changes in shape are explained, in part,
Active site
Reactions in an enzyme are catalyzed at a specific location
within it known as the active
site. Substrates bind at the active site and are oriented to
provide access for the relevant
portion of the molecule to the
electronic environment of the
enzyme where catalysis occurs.
Enzyme flexibility
As mentioned earlier, a difference between an enzyme and a
342
state, which
dergo signifi-
Types of Reactions
is a lower activ-
cant structural
laxed) state,
which has
greater activ-
ity.
Induced Fit
The Koshland
flexible and change shape on binding substrate. Changes in shape help to 1) aid binding
of additional substrates in reactions involving more than one substrate and/or 2) facilitate formation of an electronic environment in
the enzyme that favors catalysis. This model is
in contrast to the Fischer Lock and Key Model
of catalysis which considers enzymes as hav-
ter binding of
substrate. In
this case, the
two substrates
are brought
into very close
proximity by
the induced fit
Induced Fit
model of catalysis postulates that enzymes are
alteration af-
Reaction types
Enzymatic reactions can be of several types,
as shown in Figure 4.7.
Enzymes that catalyze reactions involving
more than one substrate, such as
A+BC+D
Ordered binding
The Koshland model is consistent with
multi-substrate binding enzymes that exhibit
can act in two different ways. In one mechanism, called sequential reactions, at some
point in the reaction, both substrates will be
bound to the enzyme. There are, in turn, two
343
NADH + Pyruvate
Lactate + NAD+
Random binding
A second mechanism of binding/catalysis is
exhibited by creatine kinase which catalyzes
the following reaction:
Creatine + ATP
344
substrates. Examples of this type of enzyme include the class of enzymes known
as transaminases. A general form of the
reactions catalyzed by these enzymes is
shown in Figure 4.8.
In reversible transaminase reactions, an
oxygen and an amine are swapping between the molecules. It can be represented
Enzyme kinetics
To understand how an enzyme enhances the rate of a reaction, we
Figure 4.12 - EP complex - the reaction is
complete.
E + S ES -> E + P
where E is enzyme, S is substrate, and P is product. In this
scheme, ES is the EnzymeSubstrate complex, which is simply
the enzyme bound to its substrate.
We could define the ES state a bit
further with
E + S ES -> ES* -> EP -> E + P
where ES* is the activated state
and EP is the enzyme-product com-
Equilibrium
At equilibrium, the ratio of product to reactant does not change.
That is a property of equilibrium.
Since the system is closed, the concentration of product over time will not
change. The velocity will thus be zero
under these conditions and we will
have learned nothing about the reaction if we wait too long to study it.
Velocity
Figure 4.15 - Concentration of product (P), substrate (S), enzyme (E), and enzyme-substrate
complex (ES) versus time for an enzymatic reaction
347
it to bind to
the enzyme in
a timely fashion (when substrate concentration is low).
This would
not give an accurate measure of velocity,
since the enzyme would be
inactive a
good deal of
the time. Because of this,
we assume
Figure 4.17 - Steady state versus non-steady state conditions
saturation of
the enzyme
with substrate
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established and under these condiModule
tions, there is very little if any of
HERE
Steady state
The other two assumptions are re-
pared to enzyme
state
Consequently, at low concentrations of substrate, the rate of increase of [P] is almost lin-
the kinetic properties of an enzyme are conducted. To perform an analysis, one would do
zyme, and then a different amount of substrate in each tube, ranging from tiny
Experimental considerations
concentration.
Non-linear increase
As the substrate concentration increases, however, the velocity of the reaction in tubes with
higher substrate concentration ceases to in-
349
Vmax
Two terms in the equation above
require explanation. The first is
Vmax. It refers to the maximum velocity of an enzymatic reaction.
Maximum velocity for a reaction
occurs when an enzyme is saturated with substrate. Saturation
Figure 4.19 - Linear relationship between [P] and
[S] at low [S]
released. Saturation ensures that another substrate is always instantly available. The unit of
Vmax is concentration of product per time =
[P]/time.
On a plot of initial velocity versus substrate
Saturation
velocity.
350
Affinities of enzymes
for substrates vary considerably, so knowing
Km helps us to understand how well an enzyme is suited to the
substrate being used.
Measurement of Km depends on the measurement of Vmax.
Common mistake
A common mistake students make in describing Vmax is saying that
Km
The second term is Km (also
known as Ks). Referred to as the
Michaelis constant, Km is the sub-
is a substrate concentration
and is the amount of substrate it
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Module
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Kcat
351
second. Note
sometimes
interact
a calculated
differently upon
value, it cannot
binding of a
be read from a V
substrate or an
vs [S] graph as
external
molecule. See
ATCase
(HERE) for an
Amazing Kcat
values
example.
A Kcat value of
of product per
Perfect
enzymes
Now, if we think
1000 molecules
about what an
ideal enzyme
might be, it
352
Speed
Speed is a dangerous thing. The faster a reaction proceeds in catalysis by an en-
maximal Kcat / Km values are all approximately the same. Such enzymes are referred to as being
perfect because they have
Diffusion limitation
Why should there be a maximum possible
value of Kcat / Km? The answer is that
movement of substrate to the enzyme becomes the limiting factor for perfect enzymes. Movement of substrate by diffusion
in water has a fixed rate at any temperature
and that limitation ultimately determines
the maximum speed an enzyme can catalyze
at. In a macroscopic world analogy, factories cant make products faster than suppliers can deliver materials. It is safe to say for
a perfect enzyme that the only speed limit it
353
Dissociation constant
In studying proteins and ligands, it is imporFigure 4.24 - Triose phosphate
isomerase-catalyzed reaction
occurs as
4.24.
L + P <=> LP
The enzyme appears to have evolved this ability because at lower velocities, there is break-
LP <=> L + P
354
association constant.
Ka = 1/Kd
such as
Double reciprocal
JxKy <=> xJ + yK
both the velocity and the substrate concentration. The inverted values are then plotted
Lineweaver-Burk plots
The study of enzyme kinetics is typically the most math intensive component
of biochemistry and one of the most
daunting aspects of the subject for many
students. Although attempts are made
to simplify the mathematical considerations, sometimes they only serve to confuse or frustrate students. Such is the
355
Molecularity of
reactions
The term molecularity refers to the number of molecules that
must come together
in order for a reaction to take place.
Reactions of the sort
of A -> B (where A
is the reactant and
B is the product)
are unimolecular,
356
concentration of both
A and B and its rate
will be related to the
product of the concentration of A and of B.
Coenzymes
Organic molecules
that assist enzymes
and facilitate catalysis are co-factors
called coenzymes.
The term co-factor is
a broad category usually subdivided into
inorganic ions and co-
357
called a
stopped flow
instrument.
It loads an
enzyme solution and a
substrate
into separate
syringes
whose output is
pointed into
Figure 4.30 - Stopped flow instrument for studying pre-steady state
kinetics
Wikipedia
Earlier events
Events occurring prior to the conditions of
steady state are referred to as pre-steady
state. Depending on the enzyme, in as short
as a few milliseconds, steady state conditions
can be present meaning that if one hopes to
study formation of reaction intermediates in
pre-steady state, tools for this analysis must
work very rapidly. One instrument commonly
used for studying pre-steady state kinetics is
a mixing
chamber.
The solutions are rap-
idly mixed and measurements of product concentration begin. With a stopped flow instrument, dead times (time between mixing and
detection) can be achieved of as small as 0.3
msec.
Ribozymes
Proteins do not have a monopoly on acting
as biological catalysts. Some RNA molecules
are also capable of speeding reactions. The
most famous of these molecules was discovered by Tom Cech in the early 1980s Studying
excision of an intron in Tetrahymena, Cech
was puzzled at his inability to find any proteins catalyzing the process. Ultimately, the
catalysis was recognized as coming from the
intron itself. It was a self-splicing RNA and
since then, many other examples of catalytic
358
28S rRNA of the eukaryotic ribosome catalyze the formation of peptide bonds.
Not unusual
Ribozymes, however, are not rarities of na-
They have been shown to be capable via selection to evolve self-replication. Indeed, ribozymes actually answer a chicken/egg
dilemma - which came first, enzymes
that do the work of the cell or nucleic acids that carry the information required to
produce the enzymes. As both carriers of
genetic information and catalysts, ribozymes are likely both the chicken and the
egg in the origin of life.
359
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
360
Enzymes!
To the tune of Downtown
Metabolic Melodies Website HERE
Reactions alone
Could starve your cells to the bone
Thank God we all produce
Enzymes
Units arrange
To make the chemicals change
Because you always use
Enzymes!
361
Inhibition
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mendously important in maintaining homeostasis, permitting cells to respond in controlled ways to changes in both
internal and external conditions.
362
Competitive inhibition
As a result, methotrexate competes with folate for binding to the enzyme. The more
Inhibitor binding
When the drug methotrexate is present, some of the DHFR enzyme binds
to it, instead of to folate, and during
the time methotrexate is bound, the enzyme is inactive and unable to bind folate. Thus, the enzyme is inhibited. Notably, the binding site on DHFR for
363
amount of the
methotrexate inhibitor
is added to each tube. At
low concentrations of substrate, the methotrexate
competes for the enzyme
effectively, but at high concentrations of substrate,
the inhibitor will have a
much reduced effect, since
the substrate outcompetes
it, due to its higher concen-
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Module
HERE
No effect on Vmax
concentrations, it does.
Increased Km
competitive inhibition.
substrate. It only appears to do so. This is because of the way that competitive inhibi-
Non-competitive inhibition
could be reduced and eventually overwhelmed with increasing amounts of substrate. This was because increasing substrate made increasing percentages of the
enzyme active. With noncompetitive inhibition, increasing the amount of substrate has no effect on the percentage of enzyme that is active. Indeed, in noncompetitive inhibition,
the percentage of enzyme in-
366
Uncompetitive inhibition
A third type of enzymatic inhibition is that of uncompetitive
inhibition, which has the odd
property of a reduced Vmax as
Figure 4.39 - Lineweaver Burk plots of uninhibited
reactions (green) and non-competitively inhibited
reactions (purple).
Image by Aleia Kim
Reducing the amount of enzyme present reduces Vmax. In competitive inhibition, this
doesnt occur detectably, because at high substrate concentrations, there is essentially
binds only to the enzyme-substrate (ES) complex (Figure 4.40). The inhibitor-bound
complex forms mostly under concentrations
367
By Le Chateliers Principle, a
shift occurs to form additional ES complex, resulting
in less free enzyme and more
enzyme in the forms ES and
ESI (ES with inhibitor). Decreases in free enzyme correspond to an enzyme with
greater affinity for its substrate. Thus, paradoxically,
uncompetitive inhibition
both decreases Vmax and inFigure 4.41 - V 0 vs [S] plot for uncompetitive inhibition
(blue) and uninhibited reactions (red)
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Suicide inhibition
In contrast to the first three types of inhibition, which involve reversible binding of
the inhibitor to the enzyme, suicide inhibition is irreversible, because the inhibitor
becomes covalently bound to the enzyme
during the inhibition. Suicide inhibition
rather closely resembles competitive inhibition because the inhibitor generally
resembles the substrate and binds to the
active site of the enzyme. The primary
difference is that the suicide inhibitor is
chemically reactive in the active site and
makes a bond with it that precludes its removal. Such a mechanism is that employed by penicillin (Figure 4.43),
which covalently links to the bacterial enzyme, DD transpeptidase and stops it
from functioning. Since the normal function of the enzyme is to make a bond necessary for the peptidoglycan complex of
the bacterial cell wall, the cell wall cannot properly form and bacteria cannot
reproduce.
Control of enzymes
It is appropriate to talk at this point about
mechanisms cells use to control enzymes.
There are four general methods that are employed. They include 1) allosterism; 2) covalent modification; 3) access to substrate;
369
Allosterism
The term allosterism refers to the fact that
the activity of certain enzymes can be affected
by the binding of small molecules. Molecules
causing allosteric effects come in two classifications. Ones that are substrates for the enzymes they affect are called homotropic effectors and those that are not substrates are
called heterotropic effectors.
The homotropic effectors usually are activators of the enzymes they bind to and the re-
sults of their action can be seen in the conversion of the hyperbolic curve typical of a V0
vs. [S] plot for an enzyme (Figure 4.18) , be-
Allosteric inhibition
Allosterically, regulation of these enzymes
The V0 vs. [S] plot of allosteric enzyme reactions resembles the oxygen binding curve of
hemoglobin (see Figure 2.83). Even
though hemoglobin is not an enzyme and is
thus not catalyzing a reaction, the similarity of
the plots is not coincidental. In both cases,
the binding of an external molecule is being
measured directly, in the hemoglobin plot,
and indirectly by the V0 vs. [S] plot, since substrate binding is a factor in enzyme reaction
velocity.
the T-state (T=tight), it has a reduced affinity for substrate and it is through this
means that the reaction is slowed.
Allosteric activation
On the other hand, when an enzyme is activated by effector binding, it converts to the Rstate (R=relaxed) and binds substrate much
more readily. When no effector is present, the
enzyme may be in a mixture of T- and Rstates.
370
Feedback inhibition
Pathway control
Notably, though, cholesterol is the endproduct of the pathway that HMG-CoA reductase catalyzes a reaction in. When enzymes
ATCase
the enzyme Aspartate Transcarbamoylase (ATCase). This enzyme, which catalyzes a step in
the synthesis of py-
rimidine nucleo-
tides, has 12
cient control of an
entire pathway. By
inhibiting an early
catalytic subunits
enzyme in a path-
regulatory subunits.
The catalytic
drolysis required
duced, assuming
there are not alternate supply methods.
to either ATP or
CTP. If they bind to
ATP, the enzyme
371
Figure 4.46 - Plots of V 0 vs. [S] for ATCase. Left - Allosteric effect of aspartate.
Right - Allosteric effects of ATP (activator) and CTP (inhibitor)
Image by Pehr Jacobson
R-state
The R-state of ATCase allows the substrate to
lytic action of the enzyme by favoring the Rstate. Thus, aspartate, which is a sub-
fectors of ATCase.
By contrast, if the enzyme binds to CTP on
one of its regulatory subunits, the subunits
Allosteric models
372
MWC model
states change.
vice versa) independently of the binding of effectors. Flipping between T-states and R-
Sequential model
373
Morpheein model
A large number of enzymes, including prominent ones like citrate synthase, acetyl-CoA car-
Cascades
morpheein model.
374
scheme the first enzyme activated proteolytically cleaves the second zymogen, causing it to be activated,
which in turn activates a third
and this may proceed through several levels of enzymatic action (Figure
4.50).
The advantage of cascades is that they allow a
large amount of zymogens to become activated fairly quickly, since there is an amplification of the signal at each level of catalysis.
Zymogens are also abundant in blood. Blood
clotting involves polymerization of a protein
known as fi-
Phosphorylation/
dephosphorylation
Another common mechanism for control of
enzyme activity by covalent modification is
phosphorylation. The phosphorylation of
enzymes (on the side chains of serine, threonine or tyrosine residues) is carried out by
protein kinases. Enzymes activated by phos-
brin. Since
random formation of fibrin is
extremely hazardous because
it can block the
flow of blood,
potentially causing heart
attack/stroke,
the body synthesizes fibrin as a
zymogen (fibrinogen) and
its activation
results from a
cascade of activations of pro-
375
Reduction/oxidation
vated, as a result.
376
These include sedoheptulose 1,7bisphosphatase, ribulose-5-phosphate kinase, fructose 1,6-bisphosphatase, and glyceraldehyde 3-phosphate dehydrogenase. Thus,
in the light, electrons flow, causing NADPH to
accumulate and ferredoxin to push electrons
in the direction of these enzymes above, activating them and favoring the Calvin cycle. In
the dark, the concentration of reduced
NADPH, reduced ferredoxin, and reduced thioredoxin fall, resulting in loss of electrons by
the Calvin cycle enzymes (oxidations that reform disulfide bonds) and the Calvin cycle
inactivates.
377
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Catalyze
To the tune of Close to You
Metabolic Melodies Website HERE
My enzymes
Truly are inclined
To convert
Things they bind
Turn the key
Covalently
Cat-a-lyze
How do cells
Regulate these roles?
Allo-ster
-ic controls
Two forms, you see
States R and T
Mod-u-late
Competing inhibition keeps
The substrates from the active site
They raise Km, but leave Vmax and shirk
While the non-competers bind elsewhere
And lift the plot made on Lineweaver-Burk
Other ways
Enzymes can be blocked
When things bind
Then get locked
Stuck not free
Tied to the key
Su-i-cide
379
Catalysis: Mechanism
Introduction
Chymotrypsin
380
Figure 4.52 - Substrate binding sites (S1 pockets) of three serine proteases
Image by Aleia Kim
site called a catalytic triad (Figure 4.53). It consists of aspartic acid, histidine, and serine.
The serine is activated in the reaction mechanism to form a nucleophile in these enzymes and gives
the class their name. With the exception of the recognition that occurs at the substrate binding
site, the mechanism shown here
Specificity
As a protease, chymotrypsin acts fairly specifically, cutting not all peptide bonds, but only
those that are adjacent to relatively nonpolar amino acids in the protein. One of the
amino acids it cuts adjacent to is phenylalanine. The enzymes action occurs in
two phases a fast phase that occurs first and
Substrate binding
The process starts with the binding of the substrate in the S1 pocket (Figure 4.54). The S1
pocket in chymotrypsin has a hydrophobic hole in which the substrate is bound. Preferred substrates will include amino acid side
381
chains that are bulky and hydrophobic, like phenylalanine. If an ionized side
chain, like that of glutamic
acid binds in the S1 pocket, it
will quickly exit, much like water would avoid an oily interior.
Shape change on
binding
When the proper substrate
binds in the S1 pocket, its presence induces an ever so slight
change in the shape of the enzyme. This subtle shape change on the binding of the proper substrate starts the steps of
the catalysis. Since the catalytic process
only starts when the proper substrate binds,
this is the reason that the enzyme shows speci-
382
383
long. They are grouped in two broad categories - 1) those that are chymotrypsin-like
and 2) those that are subtilisin-like. Though
subtilisin-type and chymotrypsin-like enzymes use the same mechanism of action, including the catalytic triad, the enzymes are
otherwise not related to each other by sequence and appear to have evolved independently. They are, thus, an example of convergent evolution - a process where evolution
(Figure 4.59) that performs a nucleophilic attack on the phenylalanineserine bond (Figure 4.60), releasing it
and replacing the proton on serine. The
second peptide is released in the process
and the reaction is complete with the enzyme back in its original state (Figure
4.61).
Serine proteases
The list of serine proteases is quite
384
sin K.
Caspases
sponse.
Cysteine proteases
Cysteine proteases (also known
as thiol proteases) catalyze the
There are 12 known human caspases. The enzymes are synthesized as pro-caspase zymogens with a prodomain and two other
385
groups of caspases.
Metalloproteases
tion).
teases use zinc as their metal, but a few use cobalt, coordinated to the protein by three
386
used - histidine, aspartate, glutamate, arginine, and lysine. The water is the target of
action of the metal which, upon binding of the
proper substrate, abstracts a proton to create
a nucleophilic hydroxyl group that attacks
the peptide bond, cleaving it (Figure
4.63). Since the nucleophile here is not attached covalently to the enzyme, neither of
the cleaved peptides ends up attached to the
enzyme during the catalytic process. Examples of metalloproteases include carboxypeptidases, aminopeptidases, insulinases and thermolysin.
Aspartyl proteases
As the name suggests, aspartyl proteases use
aspartic acid in their catalytic mechanism
(Figures 4.63 & 4.65). Like the metalloproteases, aspartyl proteases activate a water to
387
Examples
Threonine proteases
comes attached to
ornithine, in-
to act as a nu-
stead of water.
cleophile. The
ated, however,
Protease
inhibitors
not by a cata-
Molecules which
rather as a result
of threonines
own -amine
as protease in-
group abstracting
hibitors. These
nucleophile is cre-
a proton.
Because of this,
the nucleophilic threonine in a threonine protease must be at the n-terminus of the enzyme. Nucleophilic attack of the peptide
bond in the target protease results in breakage of the bond to release one peptide and the
other is covalently attached to serine, like the
serine proteases. Also, as with the serine
come in a variety
of forms and have
biological and me-
388
process.
require for catalysis. Zinc-containing metalloproteases, for example, are very sensitive to
Anti-viral Agents
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therapies as well.
389
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Links to their Web pages are below
I Lost a Lung
To the tune of I Left My Heart in San Francisco
Metabolic Melodies Website HERE
391
start all
again
392
Protein Wonderland
To the tune of Winter Wonderland
Metabolic Melodies Website HERE
Mechan-i-sm . . determines
How an en . . zyme is workin
Here are the ways
That each elastase
Breaks a peptide bond so easily
393
Alkoxides
Break peptides
Nucleophiles give bonds the fits
394
Blood clotting
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Cellular response
Injury to the epithelial lining of
a blood vessel begins the process
of coagulation almost instantly. The
395
Molecular response
Amplification
396
gen to fibrin.
Nomenclature
A note about nomenclature - the zymogen
factors in the molecular response are generally labeled with Roman numerals. A lowercase, subscripted a is used to designate an activated form.
The tissue factor pathway functions to create a thrombin burst, a process in which
thrombin is activated very quickly. This is the
initiation phase. It is fairly straightforward because it has one focus - activation of throm-
Figure 4.69 - Intrinsic and extrinsic pathways of blood coagulation. The aim is
making a fibrin clot (lower right)
Wikipedia
397
Initiation phase
The initiation phase of the molecular response begins when Fac-
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Amplification phase
398
Transglutaminase
399
Hemophilia
Hemophilia is a hereditary genetic disor-
Wikipedia
afflicted individuals. The disease is Xlinked and thus occurs much more com-
400
von Willebrands
disease
A related disease to hemophilia that is also
genetically linked is von
Willebrands Disease.
The von Willebrand
factor plays a role in
both the cellular and
the molecular responses in blood clotting. First, the factor is
a large multimeric glycoprotein present in
blood plasma and also
Figure 4.75 - Blood cells enmeshed in a fibrin clot
Hemophilia B spread
through the royal families
great-grandsons suffered
Ib glycoprotein. Second, it
response, playing a protective role for it. In the absence of the von Wille-
401
ders.
Blood thinners
clotting.
Vitamin K action
desired clotting.
The first, and more common of these is aspirin. Aspirin is an inhibitor of the production
of prostaglandins. Prostaglandins are molecules with 20 carbons derived from arachi-
prothrombin and other blood clotting proteins. Vitamin K serves as an enzyme cofactor
that helps to catalyze addition of an extra carboxyl group onto the side chain of glutamic acid residues of several clotting enzymes (see
HERE). This modifica-
402
near the site of the wound in the cellular response to clotting helps to stimulate activation of proteins in the serine protease cascade of the molecular response.
Vitamin K comes in several forms. It is best
described chemically as a group of 2-methyl1,4-naphthoquinone derivatives. There are
five different forms recognized as vitamin Ks
Figure 4.78 - Warfarin
Hemorrhaging danger
It is very critical that the proper amount of
warfarin be given to patients. Too much can
result in hemorrhaging. Patients must have
403
their clotting times checked regularly to ensure that they are taking the right dose of
anti-coagulant medication. Diet and the metabolism of Vitamin K in the body can affect
liver as the zymogen known as plasminogen. Several different enzymes can activate
it.
Plasmin
Clots, once made in the body, do not remain
there forever. Instead, a tightly regulated en-
404
Tissue plasmino-
Fibronectin
gen activator
Fibronectin is a
as a co-factor, is
glycoprotein
clude urokinase
cellular matrix
plasminogen ac-
tivator (using
urokinase plasmi-
ceptor as a co-
tracellular pro-
factor), kallikrein
(plasma serine pro-
teins, including
collagen, fibrin,
and heparan sul-
Plasmin inhibition
Plasmins activity can also be inhibited. Plasminogen activator inhibitor, for example,
can inactivate tPA and urokinase. After
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Angiostatin is a sub-domain of
plasmin produced by auto-proteolytic cleavage. It blocks the growth of new blood vessels
and is being investigated for its anti-cancer
properties.
is localized to the site of the wound, assisting in formation of the blood clot to stop bleeding. In the initial stages of wound healing,
plasma fibronectin interacts with fibrin in
clot formation. It also protects tissue sur-
405
Embryogenesis
Fibronectin is essential for embryogenesis.
Deleting the gene in mice causes lethality before birth. This is likely due to its role in migration and guiding the attachment of cells as
the embryo develops. Fibronectin also has a
406
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
The vitamin Ks
Help to . . . . bind to cee-ays
Adding C-O-. . . . O-H to amend things
Um-m-um-um-um-um
408
5
Energy
409
Energy: Basics
Introduction
Oxidative energy
410
processes. Catabolic processes are often oxidative in nature and energy releasing.
selves, they would not occur, as they are reversing oxidation and decreasing entropy
(making many small things into a larger one).
To overcome this energy barrier, cells must ex-
411
Energy coupling
The synthesis of the
many molecules needed
by cells needs the input
of energy to occur. Cells
overcome this energy obstacle by using ATP to
drive the reaction (Figure 5.6). The energy
needed to drive reactions is harvested in
very controlled condi-
412
modynamics with respect to increasing disorder of a system. Cells are very organized or
ordered structures, leading some to mistakenly conclude that life somehow violates the
413
where, you could not do this. However, with the input of energy, you
compounds. In each of
Biological energy
There are, of course, other reasons that organ-
414
is available (reducing
the enthalpy, H), the
free energy can also be reduced.
Cells must work within the laws of thermody-
so, we begin to see the role of energy in determining the directions chemical reactions take.
G = H TS,
G = H TS
415
For a reaction
aA bB
tants},
G = G + RTln([B]b/[A]a)
G = G + RTln({Products}/{Reactants})
cC bB + dD
G = G + RTln{([B]b[D]d)/([A]a[C]c)}
Importance of G
If one starts out at standard conditions, where everything except protons is at 1M, the RTln({Products}/
{Reactants}) term is zero, so the
G term equals the G, and the
G determines the direction the
reaction will take (only under those
conditions). This is why people say
that a negative G indicates an energetically favorable reaction,
whereas a positive G corresponds to an unfavorable one.
416
{Reactants} decreases, the value of the natural log term becomes less positive (more nega-
G = H TS
proteins.
change equation,
417
top.
Potential energy
Such gradients function like batteries and contain potential energy. When the potential energy is harvested by cells, they can create
G = RTln[C2/C1]
To move it in the direction of C1 (to the outside of the cell) the expression would be
418
G = RTln[C1/C2]
cell than outside.
Since C2 is smaller than C1 (i.e., there are
fewer glucose molecules inside the cell) then
the G is negative and diffusion would be
Using C2 to indicate the concentration of materials inside the cell and C1 for the concentration outside the cell (as before),
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then the free energy for movement of an ion from top to bottom is given by the following equation
outside) the G would be positive, so movement in the direction of C2 would not be favored and instead the glucose would tend to
move towards C1 , that is, out of the cell.
G = RTln[C2/C1] + ZF
Note here that this equation must take into
consideration both the concentration differ-
419
Reduction potential
In discussing chemical potential, we must also
consider reduction potential. Reduction
potential measures the tendency of a chemical
to be reduced by electrons. It is also desig-
Relative measures
Absolute reduction potentials are difficult to
measure, so reduction potentials are typically
defined relative to a reference electrode. In
420
Direction and
voltage measured
The direction and magniFigure 5.11 - Reference electrode for measuring reduction
potentials.
Image by Pehr Jacobson
negative.
421
Movement of electrons
voltages. Just as the standard Gibbs free energy change is the Gibbs free energy change
under standard conditions, so, too, is the standard reduction potential E the reduction po-
Adjustment
Because of this adjustment, a slightly different
standard reduction potential is defined and
7 as G.
will vary with the concentration of each chemical species in the cell. The relationship between the reduction potential E and the standard reduction potential E is given by the following equation (also called the Nernst
equation)
G = -nFE
422
contributor to the total synthesis of triphosphates by cells. An example substrate phosphorylation comes from glycolysis.
Phosphoenolpyruvate (PEP) + ADP
Pyruvate + ATP
This reaction has a very negative G (-31.4
kJ/mol), indicating that the PEP contains
more energy than ATP, thus tending to energetically favor ATPs synthesis. Other triphos-
phates can be made by substrate level phosphorylation, as well. For example, GTP can
be synthesized by the following citric acid cy-
kJ/mol) than the first reaction which produces ADP (G = -30.5 kJ/mol).
Since triphosphates are the currency that
meet immediate needs of the cell, it is important to understand how triphosphates are
made. There are three phosphorylation
mechanisms 1) substrate level; 2) oxidative; and 3) photophosphorylation. We
consider them here individually.
cle reaction.
Succinyl-CoA + GDP + Pi
423
Reaction coupling
Last, an unusual way of synthesizing ATP by
favorable reaction. There are numerous parallels in the real world. Movement of automobiles is energetically unfavorable, but cou-
ATP source
Orotate + PRPP
OMP + PPi
since
G = G + RTln {[OMP][PPi]
[Orotate][PRPP]}
PPi + H2O
Pi + Pi
reactions are additional tools for cells to overcome energy barriers, just like coupling energetically favorable processes to energetically
unfavorable ones.
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425
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
426
Oh Delta G
To the tune of Danny Boy
Metabolic Melodies Website HERE
427
Woe is me
My substrates are losing entropy
Causing gains in Gibbs free energy
Oh I can't lose no en - tro- py
Re-a-lly
I could use a source of enthalpy
To combat the rise in Delta G
Oh I believe in enthalpy
I crave en-er-gy
Don't you see?
It's getting worse
My re-actions all
Soon will stall
And then rever-r-r-se
ATP
It's the metabolic currency
Guess I'll spend a bit judiciously
To help reduce the Delta G
Help reduce the Delta G
428
lation. In this way, the oxidation of sugars and fatty acids is coupled to the synthesis
429
Electron transport
Further, the proposal
states that the gradient is
created when NADH and
FADH2 transfer their electrons to an electron
transport system (ETS)
located in the inner mitochondrial membrane.
Movement of electrons
through a series of of electron carriers is coupled to
the pumping of protons
out of the mitochonFigure 5.14 - Overview of electron transport (bottom left
and top right) and oxidative phosphorylation (top left yellow box) in the mitochondrion
Chemiosmotic model
Dr. Peter Mitchell introduced a radical proposal in 1961 to explain the mechanism by
which mitochondria make ATP. It is known
as the chemiosmotic hypothesis and has
been shown over the years to be correct.
Mitchell proposed that synthesis of ATP in
mitochondria depends on an electrochemical gradient, across the mitochondrial inner membrane, that arises ulti-
ATP synthase
In oxidative phosphorylation, ATP synthesis
is accomplished as a result of protons reentering the mitochondrial matrix via the
transmembrane ATP synthase complex,
which combines ADP with inorganic phos-
430
Considerations
The process has three primary considerations.
Tight coupling
to exist between
electron transport and the synthesis of ATP
(called oxidative
phosphorylation). Chemicals
which permeabilize the inner mitochondrial membrane to protons
cause uncoupling,
that is, they allow
the protons to leak
back into the mitochondrial matrix,
rather than
thesis of ATP.
seen in Figure 5.16 and Figure 5.17, electrons move from one complex to the next, not
Power plants
431
Figure 5.16 - Flow of electrons from NADH into the electron transport system.
Entry is through complex I
Image by Aleia Kim
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Module
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Figure 5.17 - Flow of electrons from FADH 2 into the electron transport chain.
Entry is through complex II.
Image by Aleia Kim
432
Traffic cop
Both Complex I and II pass
electrons to the inner membranes coenzyme Q (CoQ
- Figures 5.18 & 5.19). In
each case, coenzyme Q accepts electrons in pairs and
passes them off to Complex
III (CoQH2-cytochrome c reductase) singly. Coenzyme
Q thus acts as a traffic cop,
regulating the flow of electrons through the ETS.
Docking station
Figure 5.18 - Complex I embedded in the inner
mitochondrial membrane. The mitochondrial matrix at
at the top
Wikipedia
carrier cause it to be reduced, whereas the carrier giving up the electrons is oxidized.
Complex III is a docking station or interchange for the incoming electron carrier (coenzyme Q) and the outgoing car-
433
Potential energy
As discussed earlier, electrochemical gradients have potential energy. Students may
think of the process as charging the battery.
Just like a charged battery, the potential arising from the proton differential across the
membrane can be used to do things. In the
mitochondrion, what the proton gradient does
is facilitate the production of ATP from ADP
and Pi. This process is known as oxidative
Figure 5.19 - Complex II embedded in
inner mitochondrial membrane.
Matrix is up.
Wikipedia
phosphorylation, because the phosphorylation of ADP to ATP is dependent on the oxidative reactions occurring in the mitochondria.
the ETS.
Proton pumping
Complex I
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and deposit them in the intermembrane space (between the inner and outer
membranes of the mitochondrion). The effect of this redistribution is to increase the
434
CoQ binding site. Other inhibitors include ADP-ribose (binds to the NADH
site) and piericidin A (rotenone analog).
The process of electron transfer through
complex I is reversible and when this occurs, superoxide (a reactive oxygen
species) may be readily generated.
Complex II
Complex II (also called succinate dehydrogenase or succinate-coenzyme Q reductase ) is a membrane bound enzyme
of the citric acid cycle that plays a role
in the electron transport process,
Figure 5.20 - Movement of electrons through
complex I from NADH to coenzyme Q. The
mitochondrial matrix is at the bottom
Image by Aleia Kim
435
Coenzyme Q
Coenzyme Q (Figure 5.23) is a 1,4 benzoquinone whose name is often given as
Coenzyme Q10, CoQ, or Q10. The 10 in
the name refers to the number of isoprenyl units it contains that anchor it to
the mitochondrial inner membrane. CoQ is a vitamin-like lipid substance found in most eukaryotic cells
as a component of the electron transport system. The requirement for CoQ
increases with increasing energy needs of
cells, so the highest concentrations of
CoQ in the body are found in tissues that
are the most metabolically active - heart,
Wikipedia
Three forms
CoQ is useful because of its ability to
436
or no extra electrons (fully oxidized - ubiquinone). This ability allows CoQ to provide
transition between the first part of the electron transport system that moves electrons in pairs and the last part of the system
that moves electrons one at a time.
Complex III
Complex III (also known as coenzyme Q: cytochrome c oxidoreductase or the cytochrome bc1 complex - Figure 5.24) is the
third electron accepting complex of the electron transport system. It is a transmembrane protein with multiple subunits present in the mitochondria of all aerobic
eukaryotic organisms and and the cell mem-
437
to re-make QH2. The other pair is donated singly to two different cytochrome c molecules.
Step one
The Q-cycle happens in a two step process.
First, a ubiquinol (CoQH2) and a ubiquinone (CoQ) dock at Complex III. Ubiquinol
transfers two electrons to Complex III. One
electron goes to a docked cytochrome c, reducing it and it exits (replaced by an oxidized cytochrome c). The other goes to the docked
uniquinone to create the semi-reduced semiubiquinone (CoQ.-) and leaving behind a ubiquinone, which exits. This is the end of step 1.
Step two
The gap left behind by the ubiquinone (Q)
that departed is replaced by another ubiquinol (QH2). It too donates two electrons to
Figure 5.25 - The Q-cycle. Matrix is
down.
Image by Aleia Kim
Q-cycle
In the Q-cycle, electrons are
passed from ubiquinol (QH2) to
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Cytochrome c
Cytochrome c (Figure 5.26) is a small
(12,000 Daltons), highly conserved protein,
438
Wikipedia
loosely associated with the inner mitochondrial membrane where it functions in electron transport. It contains
a heme group which is used to carry a single electron from Complex III to Complex IV. Cytochrome c also plays an important role in apoptosis in higher organisms. Damage to the mitochondrion
that results in release of cytochrome c can
stimulate assembly of the apoptosome
and activation of the caspase cascade
that leads to programmed cell death.
Complex IV
Complex IV, also known as cytochrome c
oxidase is a 14 subunit integral membrane protein at the end of the electron transport chain (Figure 5.27). It
is responsible for accepting one electron
439
Oxidative phosphorylation
ous predictions.
Respirasome
There has been speculation for many years
that a super-
complex of
tron trans-
electron car-
port stops
riers in the
or if the in-
inner
ner mito-
mem-
chondrial
brane of
mem-
the mito-
branes im-
chondrion
permeabil-
may exist in
ity to pro-
tons is com-
dividual car-
promised,
riers making
oxidative
physical con-
phosphoryla-
tact with
each other.
This would
make for
more effi-
cient transfer reactions, minimize the production of reactive oxygen species and be similar to metabolons of metabolic pathway enzymes,
ATP synthase
440
This is usually not a desirable circumstance and there are some controls to reduce its occurrence.
will be higher inside of the mitochondrion and ADP concentration be higher outside the mito-
Interactive Learning
Module
HERE
oxidative phosphorylation
and has effects on respiratory
control (see HERE).
Another important consideration is
that when ATP is made in oxida-
441
nanomachine that
phosphate must
also be imported
a gradient of pro-
tons flowing
This is accom-
through it from
plished by action
the intermem-
of the phosphate
brane space
translocase,
which is a sym-
to depict in a sin-
phosphate into
the mitochondrial
the synthase
a proton.
There is evidence
that the two translocases and ATP
illustrate the
multi-subunit nature of this membrane protein,
442
subunits.
Rotation of unit
443
Figure 5.31 - Loose (L), Tight (T), and Open (O) structures of the F 1 head of ATP
synthase. Change of structure occurs by rotation of -protein (purple) in center as a
result of proton movement. Individual and units do not rotate
Image by Aleia Kim
Respiratory control
port.
ADP dependence
be tightly coupled.
Interdependence
444
At rest
Exercise
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Module
HERE
carrier, NADPH.
Links to exercise
oxidative processes.
Rest
Exercise
FAD, respectively.
Oxidized carriers, such as
NAD+
needed by catabolic pathways, like glycolysis, the citric acid cycle, and fatty acid oxidation. Anabolic pathways, such as fatty
acid/fat synthesis and gluconeogenesis
rely on reduced electron carriers, such as
446
Rest
When exercise stops, NADH and FADH2 levels rise (because electron transport is slowing) causing catabolic pathways to slow/
stop. If one does not have the proper amount
The first group for discussion are the inhibitors. In tightly coupled mitochondria, inhibiting either electron transport or oxidative phosphorylation has the effect of inhibiting the other one as well.
447
in-
Rotenone
Rotenone, which is a plant product, is used
as a natural insecticide that is permitted for
organic farming. When mitochondria are
treated with this, electron transport will
stop at Complex I and so, too, will the pumping of protons out of the matrix. When this ocFigure 5.34 - Oligomycin A An inhibitor of ATP synthase
2,4-DNP
Respiratory
control can be
completely de-
stroyed by using a
thal.
brane to pro-
of ATP synthase.
made.
1.
1.
O2 use high
2.
2.
3.
3.
4.
4.
Catabolism high
5.
versa
rapidly
449
generated.
Dangerous drug
els.
Thermogenin
One of the byproducts of uncou-
is dissipated as heat.
loss aid.
Alternative oxidase
450
Energy efficiency
Figure 5.36 - Alternative oxidase (AOX) of fungi, plants, and protozoa bypasses
part of electron transport by taking electrons from CoQ and passing them to
oxygen.
451
Endogenous pro-
anything but
duction of ROS is
directed towards
intracellular sig-
naling (H2O2
and defense.
have controls in
example, have
extent to which
NADPH oxi-
Wikipedia
dase (Figure
5.38) embedded
in the exterior
in fact, yield
heat, they are used as sources of heat in some
NADPH + 2O2
NADP+ + 2O2 + H+
452
453
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be phagocytosed.
A common endogenous source of superoxide is the electron transport chain. Superoxide can be produced when movement of
electrons into and out of the chain dont
match well. Under these circum-
Aging
Wikipedia
cause damage leading to mutation. If it reacts with the aconitase enzyme, ferrous iron
454
Health
The importance of catalase for health is uncer-
hand, mice engineered to produce higher levels of catalase, in at least one study, lived
Catalase
The enzyme,
which employs
four heme groups
in its catalysis,
works extremely
rapidly, converting
up to 40,000,000
455
Superoxide dismutase
Another important enzyme for protection
against reactive oxygen species is superoxide
dismutase (SOD), which is found, like catalase, in virtually all organisms living in an oxy-
1. O2- + Enzyme-Cu++
O2 + Enzyme-Cu+
2. O2- + Enzyme-Cu+ + 2H+
shown in red):
The enzyme thus works by a ping-pong
H2O2 + Enzyme-Cu++
ent forms.
456
Mixed function
oxidases
Other enzymes catalyzing reactions involving oxygen include the mixed function
oxidases. These enzymes
use molecular oxygen for two
different purposes in one reaction. The mixed function
part of the name is used to indicate reactions in which two
different substrates are being
Figure 5.44 - Peroxynitrites effects on cells lead to
necrosis or apoptosis
oxidized simultaneously.
Wikipedia
457
RH + O2 + NADPH + H+
reducing power
cohol.
458
plastocyanin reductase
tains cytochromes b6
containing cytochromes
CYP2E1.
iron is reduced.
Cytochromes
Cytochromes are
heme-containing pro-
Iron-Sulfur
Proteins
Iron-sulfur proteins
movement of electrons.
wide variety of biological systems and processes. They include roles in photosynthesis
in chloroplasts. Ferredoxins are classified
structurally by the iron-sulfur clustered centers they contain. Fe2S2 clusters (Figure
5.50) are found in chloroplast membranes
and can donate electrons to glutamate synthase, nitrate reductase, and sulfite reductase
and serve as electron carriers between reductase flavoproteins and bacterial dioxyge-
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Ferredoxin
Ferredoxins are iron-sulfur containing
proteins performing electron transfer in a
Ferritin
Ferritin is an intracellular iron-storage protein found in almost all living organisms, from
bacteria to higher plants and animals. It is a
globular protein complex with 24 subunits
460
age.
consequently are
in neurological and/
Monoamine
oxidases
Monoamine oxidases are enzymes that catalyze the oxidative deamination of monoamines, such as serotonin, epinephrine, and dopamine. Removal of the amine with oxygen results in
the production of an aldehyde and ammonia. The enzymes are found inside and outside of the central nervous system.
There are two types of monoamine oxidase enzymes - MAO-A and MAO-B. MAO-A is particularly important for oxidizing monoamines
consumed in the diet. Both MAO-A and
MAO-B play important roles in inactivating
monoaminergic neurotransmitters. Both
enzymes act on dopamine, tyramine (Fig-
461
Oxidative damage
DNA damage theory of aging
afford opportuni-
duce 8-oxo-
guanine (Fig-
dized nucleobase
commonly pro-
cumulation of
duced lesion in
pecially to the
DNA would be
action of reactive
oxygen species
462
Antioxidants
There is a growing interest in the subject of
antioxidants because of health concerns
DNAs.
463
as vitamins C, A, and
The glutamate is
E, glutathione, and
cysteine by a peptide
oxide dismutase,
group carboxyl of
oxidases.
amine of cysteine.
The bond between cys-
Health effects
Oxidation by ROS is
normal peptide
carboxyl of cysteine
Glutathione
The major endogenous antioxidant found
in cells spanning most living systems, glutathione is a tripeptide protecting cells
against damage caused by reactive oxygen species and heavy metals (Figures
5.55 & 5.56). The three amino acids in
glutathione (glutamate, cysteine, and
glycine) are joined in an unusual fashion.
464
Disulfide-joined glutathiones can be separated by reduction of their bonds with glutathione reductase, using electrons from
NADPH for the reduction.
Resveratrol
Categorized as a stilbenoid, resveratrol (Fig-
Non-ribosomal synthesis
Glutathione is not made by ribosomes.
Rather, two enzymes catalyze its synthesis.
The enzyme -glutamylcysteine synthetase catalyzes the joining of the gluta-
from ATP.
465
Summary
In summary, energy is needed for cells to perform the functions that they must carry out in
order to stay alive. At its most basic level, this
means fighting a continual battle with entropy, but it is not the only need for energy
that cells have.
References
1. Winge, D.R., Mol Cell Biol. 2012 Jul;
32(14): 26472652. doi:
10.1128/MCB.00573-12
466
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Im a Little Mitochondrion
To the tune of Im a Lumberjack
Metabolic Melodies Website HERE
N-A-D
To the tune of Penny Lane
Metabolic Melodies Website HERE
Energy: Photophosphorylation
Photophosphorylation
thetic bacteria.
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by Kevin
HERE & HERE
470
mitochondrion
movement of protons during
ATP synthesis out of the thylakoid space in photosynthesis
versus into the mitochondrial
matrix in oxidative phosphorylation
nature of the terminal electron
acceptor NADP+ in photosynthesis versus O2 in oxidative phosphorylation.
Electron transport:
chloroplasts vs
mitochondria
chloroplasts during photosynthesis is opposite that of electron transport in mitochondria. In photosynthesis, water is the source of
Differences
Some of the differences include :
the source of the electrons
H2O for photosynthesis versus NADH/FADH2 for oxidative phosphorylation
direction of proton pumping
into the thylakoid space
of the chloroplasts versus
outside the matrix of the
471
ing to potential.
Steps
Solar power
through this scheme in plants requires energy from photons in two places to lift the
energy of the electrons sufficiently.
Last, it should be noted that photosynthesis
actually has two phases, referred to as the
light cycle (described above) and the dark
cycle, which is a set of chemical reactions
that captures CO2 from the atmosphere and
fixes it, ultimately into glucose. The dark
cycle is also referred to as the Calvin Cycle
and is discussed HERE.
Photosynthesis
Photosynthesis is an energy capture process
found in plants and other organisms to harvest light energy and convert it into chemical energy. This photochemical energy is
stored ultimately in carbohydrates which
472
Chloroplasts
Chloroplasts are found in almost all aboveground plant cells, but are primarily concentrated in leaves. The interior of a leaf, below
the epidermis is made up of photosynthesis
tissue called mesophyll, which can contain up
to 800,000 chloroplasts per square millimeter.
The chloroplasts membrane has a phospholipid inner membrane, a phospholipid
outer membrane, and a region between them
called the intermembrane space (Figure
Wikipedia
5.61). Within the inner chloroplast membrane is the stroma, in which the chloroplast
DNA and the enzymes of the Calvin cycle are
located. Also within the stroma are stacked,
flattened disks known as thylakoids which
are defined by their thylakoid membranes.
The space within the thylakoid membranes
are termed the thylakoid spaces or thylakoid
lumen. The protein complexes containing the
light-absorbing pigments, known as photosystems, are located on the thylakoid membrane.
Besides chlorophylls, carotenes and xanthophylls are also present, allowing for absorption of light energy over a wider range.
The same pigments are used by green algae
and land plants.
Brown algae and diatoms add fucoxanthin
(a xanthophyll) and red algae add phycoerythrin to the mix. In plants and algae, the pig-
473
ure 5.63).
The thylakoid membrane does its magic using four major protein complexes.
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474
Manganese
centers
An intermediate Oxygen Evolving Complex (OEC) contains
four manganese centers
that provide the immediate replacement electron that PSII requires.
After four electrons
have been donated by
the OEC to PS II, the
OEC extracts four electrons from two water
Interactive Learning
Module
Light harvesting
HERE
molecules, liberating
475
which holds it until the next excitation process begins with absorption of another photon
of light at 700 nm by PS I.
Absorption of light at PS I
476
photons of light.
chemical forms.
Cyclic photophosphorylation
477
Photosynthetic energy
The output of the photophosphorylation
part of photosynthesis (O2, NADPH, and
ATP), of course, is not the end of the process
of photosynthesis. For the growing plant, the
NADPH and ATP are used to capture carbon
dioxide from the atmosphere and convert it
(ultimately) into glucose and other important carbon compounds. This, as noted previously, occurs in the Calvin Cycle (see
478
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Photosynthesis is Divine
To the tune of Scarborough Fair
Metabolic Melodies Website HERE
Photosynthesis is divine
Fixing carbon using sunshine
It's thanks to plants that we've got a prayer
They pull CO2 from the air
Reaping energy from the sun
It's efficient second to none
You grab the photons almost at will
Protoporphyrin chlorophyll
Light reactions of System II
Split up water, making O2
Electrons pass through schemes labeled 'Z'
Pumping protons gradiently
ATP's made due to a shift
Of the protons spinning quite swift
480
6
Metabolism
(anabolism).
481
482
Metabolism: Sugars
Glycolysis
YouTube Lectures
by Kevin
HERE & HERE
483
484
485
Reaction 1
Glucose gets a phosphate from ATP to
make glucose-6-phosphate (G6P) in a
reaction catalyzed by the enzyme hexokinase, a transferase enzyme.
Figure 6.4 - Reaction #1 - Phosphorylation of
glucose - catalyzed by hexokinase
Cycle and the Pentose Phosphate Pathway (PPP) contain intermediates in common
with glycolysis, so in that sense, almost any
Other pathways
and galactose.
Intermediates of glycolysis and gluconeogenesis that are common to other pathways include glucose-6-phosphate (PPP, glycogen metabolism), Fructose-6-phosphate
(Calvin Cycle, PPP), Glyceraldehyde-3phosphate (Calvin Cycle, PPP), dihydroxyacetone phosphate (PPP, glycerol
metabolism, Calvin Cycle), 3phosphoglycerate (Calvin Cycle, PPP),
phosphoenolpyruvate (C4 plant metabolism, Calvin Cycle), and pyruvate (fermentation, acetyl-CoA genesis, amino acid metabolism). It is worth noting that glycerol from
the breakdown of fat can readily be metabolized to dihydroxyacetone phosphate
(DHAP) and thus enter the glycolysis path-
486
Reaction 2
Next, G6P is converted to
fructose-6-phosphate (F6P), in
a reaction catalyzed by the enzyme
phosphoglucoisomerase.
Figure 6.5 - The centrality of glucose-6-phosphate
in metabolism
G6P F6P
has a much higher Km (lower affinity) for glucose. This is important, because the liver is a
487
only slight
A variant enzyme
changes in
concentration
of reactants.
pyrophosphate
rather than ATP as
Reaction 3
F6P + ATP
F1,6BP +
ADP + H+
The second
input of en-
from hydrolysis of
the pyrophosphate,
that reaction is reversible.
Reaction 4
F1,6BP D-GLYAL3P + DHAP
getically favorable.
PFK-1 is the most important regulatory
enzyme in the pathway and this reaction is the ratelimiting step. It is
also one of three essentially irreversible
reactions in glycoly-
sis.
488
and bacteria).
Reaction 5
DHAP D-GLYAL3P
In the next step, DHAP is converted to DGLYAL3P in a reaction catalyzed by the en-
there is less chance of the intermediate escaping and causing damage in the cell.
Reaction 6
D-GLYAL3P + NAD+ + Pi
D-1,3BPG + NADH + H+
489
Reaction 7
D-1,3BPG + ADP
3PG + ATP
The two phosphates in
Figure 6.10 - Reaction #6 - Oxidation of GLYAL3P, catalyzed
by glyceraldehyde-3-phosphate dehydrogenase
490
Reaction 8
3-PG 2-PG
Conversion of the 3-PG
intermediate to 2-PG
(2Figure 6.12 - Reaction #8 - Conversion of 3-PG to 2-PG
phosphoglycerate)
occurs by an important
mechanism. An inter-
Though there are a few substrate level phosphorylations in cells (including another one at
(catalyzed by
phosphoglycer-
ate mutase - a
mutase enzyme)
is 2,3-BPG. This
intermediate,
which is stable, is
frequency by the
enzyme instead
of being con-
491
tion.
Wikipedia
Reaction 10
verted to 2-PG.
Reaction 9
2-PG PEP + H2O
jor source.
2-PG is converted
by enolase (a lyase) to phosphoenolpyruvate (PEP)
by removal of water,
creating a very high
energy intermediate.
The reaction is readily reversible, but
with PEP, the cell
492
HERE).
mation of cataracts.
493
glyceraldehyde.
Mannose metabolism
Phosphorylation of glyceraldehyde by tri-
494
Glycerol metabolism
Glycerol is an important molecule for the
synthesis of fats, glycerophospholipids,
and other membrane lipids. Most commonly it is made into glycerol-3phosphate (Figure 6.22) and the
495
Pyruvate metabolism
As noted, pyruvate produced in glycolysis
can be oxidized to acetyl-CoA, which is itself
oxidized in the citric acid cycle to carbon
dioxide. That is not the only metabolic fate
of pyruvate, though (Figure 6.23).
Pyruvate is a starting point for gluconeogenesis, being converted to oxaloacetate in
the mitochondrion in the first step. Pyruvate in animals can also be reduced to lactate
by adding electrons from NADH (Figure
6.24). This reaction produces NAD+ and is
critical for generating the latter molecule to
keep the glyceraldehyde-3-phosphate dehydrogenase reaction of glycolysis (reaction
#6) going under conditions when there is no
Figure 6.22 - Reactions in glycerol
metabolism
Image by Penelope Irving
oxygen.
This is because oxygen is necessary for the
as well.
496
nitrogen from an
amine donor, such as
glutamic acid. Pyruvate can also be converted into oxaloacetate by carboxylation
low).
mentation).
497
aloacetate), and pyruvate decarboxylase (a part of pyruvate dehydrogenase that makes acetaldehyde in bacteria and yeast).
Catalytic action and regulation of
the pyruvate dehydrogenase
complex is discussed in the section on the citric acid cycle
(HERE).
Gluconeogenesis
The anabolic counterpart to glycolysis is gluconeogenesis
(Figure 6.26), which occurs
mostly in the cells of the liver and
498
Bypassing pyruvate
kinase
Two of the enzymes (pyruvate carboxylase and
PEP carboxykinase PEPCK) catalyze reactions that bypass pyruvate kinase. F1,6BPase
bypasses PFK-1 and
G6Pase bypasses hexokinase. Notably, pyruvate
carboxylase and G6Pase
are found in the mitochondria and endoplasmic reticulum, respectively, whereas the other
two are found in the cytoplasm along with all of
Biotin
An important coenzyme used by pyruvate carboxylase is biotin (Figure 6.27). Biotin is commonly
used by carboxylases to carry CO2
to incorporate into the substrate.
499
tabolism.
Reciprocal regulation
All of the enzymes of glycolysis and nine of
the eleven enzymes of gluconeogenesis are
all in the cytoplasm, necessitating a coordinated means of controlling them.
Cells generally need to minimize
the extent to which paired anabolic and catabolic pathways
are occurring simultaneously,
Glycolysis Only
Gluconeogenesis Only
above).
500
ent pathways.
Reciprocal allosteric
effects
For example, in glycolysis,
the enzyme known as phos-
Reciprocal covalent
effects
In glycogen metabolism, the
phofructokinase (PFK-1)
is allosterically activated by
501
making them more active, whereas phosphorylation of glycogen synthase makes it less active. Conversely,
dephosphorylation has the reverse effects
on these enzymes - phosphorylase kinase and
glycogen phosphorylase become
less active and glycogen synthase becomes more active.
Interactive Learning
Module
HERE
F1,6BP)
Pyruvate kinase
It might also seem odd that
sis pathway.
503
lase reaction.
Reactions pulled
made.
As noted above, the aldolase reaction is energetically unfavorable (high positive G),
504
F2,6BP regulation
Regulation of PFK-1 by F2,6BP is sim-
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by Kevin
HERE & HERE
PFK-1 regulation
gluconeogenesis intermediate
2 - Figure 6.31).
Cori cycle
505
cle cells, so they dump it into the blood. Lactate travels in the blood to the liver, which
Figure 6.33 - Overlap between the Cori cycle and the glucose alanine cycle
506
delivered.
sion.
of quick energy. Because of this, the polysaccharides stored in plants are somewhat less
complicated than those of animals. Plants
store glucose for energy in the form of amylose (Figure 6.34 and see HERE) and amylopectin and for structural integrity in the
form of cellulose (see HERE). These structures differ in that cellulose contains glucose
units solely joined by -1,4 bonds, whereas
amylose has only -1,4 bonds and amylopectin has -1,4 and -1,6 bonds.
Polysaccharide
metabolism
Sugars are metabolized rapidly in the body and that is one
of the primary reasons they are
used. Managing levels of glucose in the body is very important - too much leads to compli-
507
Figure 6.35 - Glycogen Structure - -1,4 links with -1,6 branches every 7-10
residues
Glycogen
Just as in gluconeogenesis, the cell has a separate mechanism for glycogen synthesis that is
distinct from glycogen breakdown. As noted
previously, this allows the cell to separately
control the reactions, avoiding futile cycles,
and enabling a process to occur efficiently
(synthesis of glycogen) that would not occur if
508
Glycogen breakdown
Breakdown of glycogen involves 1) release of glucose-1-phosphate (G1P),
2) rearranging the remaining glycogen
(as necessary) to permit continued
breakdown, and 3) conversion of G1P to
G6P for further metabolism. G6P can
be 1) used in glycolysis, 2) converted to
glucose by gluconeogenesis, or 3) oxidized in the pentose phosphate pathway.
Glycogen phosphorylase (sometimes
simply called phosphorylase) catalyzes
breakdown of glycogen into glucose-1Phosphate (G1P - Figure 6.36). The reaction that produces G1P from glycogen
is a phosphorolysis, not a hydrolysis
reaction. The distinction is that hydrolysis reactions use water to cleave bigger
molecules into smaller ones, but phosphorolysis reactions use phosphate instead for
the same purpose. Note that the phosphate is
Interactive Learning
Module
Glycogen debranching
enzyme
HERE
Glycogen phosphorylase will only act on nonreducing ends of a glycogen chain that are at
509
be converted to Glucose-6-Phosphate
hexokinase or glucokinase.
Regulation of glycogen metabolism is manG1P can be converted to G6P by action of an
GPa/GPb
allosteric
regulation
Glycogen phosphorylase exists
in two different
covalent forms
one form with
phosphate
(called GPa here)
and one form
lacking phosphate (GPb here).
GPb is converted
to GPa by phos-
phorylation by
an enzyme known as phosphorylase ki-
active) state (Figure 6.39). It is for this reason that people tend to think of GPa
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by Kevin
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AMP. Unless a cell is low in energy, AMP concentration is low. Thus GPb is not converted
511
than GPb. It is important, therefore, to understand the controls on the enzymes that interconvert GPa and GPb. This is accomplished by
the enzyme phosphorylase kinase, which
transfers phosphates from 2 ATPs to GPb to
form GPa.
Phosphorylase kinase itself has two covalent
forms phosphorylated (active) and dephosphorylated (inactive). It is phosphorylated by
the enzyme Protein Kinase A (PKA - ). Another way to activate the enzyme is allosterically with calcium (Figure 6.41). Phosphory-
512
513
role. It can remove phosphates from phosphorylase kinase (inactivating it) and form GPa,
converting it to the less
likely to be active GPb.
Regulation of phosphoprotein phosphatase
activity occurs at several
levels. Two of these are
shown in Figures 6.42
& 6.43.
In Figure 6.42, phosphoprotein phosphatase
is shown being inactivated by phosphorylaFigure 6.42 - Inactivation of phosphoprotein phosphatase by
protein kinase A via phosphorylation of PI-1 (Inhibitor) and
the G M binding protein
Image by Pehr Jacobson
tion of an inhibitor
(called PI-1 - see below).
This happens as a result
of cascading actions
from binding of epineph-
their own activity. Interfering with their ability to convert GTP to GDP can have dire conse-
Interactive Learning
Module
HERE
PI-1
The inhibitor PI-1 can block activity of phosphpoprotein phos-
Another regulatory
mechanism
Another way to regulate phosphoprotein phosphatase in the
liver involves GPa directly (Figure
6.43). In liver cells, phosphoprotein
phosphatase is bound to a protein
called GL. GL can also bind to GPa.
As shown in the figure, if the three
proteins are complexed together (top
of figure), then PP1 (phosphoprotein
phosphatase) is inactive. When glucose is present (such as when the
liver has made too much glucose),
then the free glucose binds to the GPa
and causes GPa to be released from
the GL.
This has the effect of activating phosphoprotein phosphatase, which begins dephosphorylating enzymes. As
shown in the figure, two such enzymes are GPa (making GPb) and glycogen synthase b, making glycogen synthase a. These dephosphorylations have opposite effects
Figure 6.43 - Regulation of phosphoprotein
phosphatase (PP-1) activity by GPa
tive.
Glycogen synthesis
binds to a cell.
515
Steps
Let us first consider the steps in glycogen synthesis. 1) Glycogen synthesis from glucose involves phosphorylation to form G6P, and
isomerization to form G1P (using phospho-
516
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by Kevin
HERE & HERE
Primer requirements
Figure 6.46 - Reciprocal regulation by the phosphorylation cascade - glycogen breakdown activated / glycogen
synthesis inhibited
Image by Penelope Irving
517
Effect of phosphorylation
In glycogen synthesis, protein kinase A phosphorylates the active form of glycogen synthase (GSa), and converts it into the usually
inactive b form (called GSb).
Note the conventions for glycogen synthase
and glycogen phosphorylase. For both enzymes, the more active forms are called the 'a'
forms (GPa and GSa) and the less active forms
are called the 'b' forms (GPb and GSb). The ma-
jor difference, however, is that GPa has a phosphate, but GSa does not and GPb has no phos-
Interactive Learning
Module
HERE
Big picture
In the big picture, binding of epinephrine or
glucagon to appropriate cell receptors stimu-
518
Cellulose synthesis
UDP-glucose + Cellulosen
sible ones - GDP-glucose and UDPglucose, depending on which cellulose synthase is involved. In plants, cellulose provides
support to cell walls.
UDP + Cellulosen+1
The GDP-glucose reaction is the same except
with substitution of GDP-glucose for UDP-
519
Oxidation #1
Sucrose + UDP
G6P + NADP+
UDP-glucose + Fructose
The enzyme is named for the reverse reaction.
6-Phosphoglucono--lactone + NADPH
The enzyme catalyzing the reaction is G6P de-
tide synthesis.
YouTube Lectures
by Kevin
HERE & HERE
and glyceraldehyde-3-phosphate
parasite.
The multiple entry points and multiple outputs gives the cell tremendous flexibility to
meet its needs by allowing it to use a variety
of materials to make any of these products.
Hydrolysis
Reaction #2 is a hydrolysis and it is catalyzed
by 6-phosphogluconolactonase. The reac-
520
Ru-5-P
Ribose-5-phosphate (R-5-P)
6-Phosphoglucono--lactone + H2O
Epimerization
Reaction 4b (catalyzed by Ru-5-P epime-
6-phosphogluconate (6-PG) + H+
Decarboxylation
sequent reactions.
Ru-5-P
by 6-phosphogluconate dehydrogenase.
Xylulose-5-phosphate (Xu-5-P)
6-PG + NADP+
Transketolase reactions
The other reactions dont really have an order
to them and whether they occur or not depends on cellular needs. The first enzyme,
transketolase, is flexible in terms of its
substrate/product combinations and is used
not only in PPP, but also in the Calvin cycle
of plants. It catalyzes the next two reactions
Xu-5-P + R-5-P
Isomerization
Reaction 4a: The enzyme catalyzing
where.
521
making R-5-P) or tryptophan (by making E4-P) even if the oxidative reactions of PPP are
inhibited.
GLYAL-3-P + F6P
Glycolysis intermediates
In the reversible reactions of the pentose phos-
GLYAL-3-P + S-7-P
E-4-P + F6P
TPP co-factor
Transketolase uses thiamine pyrophosphate (TPP) to catalyze reactions. TPPs thia-
522
zole rings nitrogen and sulfur atoms on either side of a carbon, allow it to donate a proton and act as an acid, thus forming a carbanion, which gets stabilized by the adjacent tetravalent nitrogen (Figures 6.50 & 6.51)).
The stabilized carbanion plays important
roles in the reaction mechanism of enzymes,
such as transketolase that use TPP as a co-
factor. Commonly, the carbanion acts as a nucleophile that attacks the carbonyl carbon of
the substrate. Such is the case with
transketolase. Attack by the carbanion
breaks the carbonyl bond on the substrate and
covalently links it to the ionized carbon of
TPP, thus allowing it to carry the carbonyl
group to the other substrate for attachment.
In this way, two carbons are moved from Xu5-P to E-4-P to make F6P (from E-4-P) and
GLYAL-3-P (from Xu-5-P). Similarly, S-7-P
and GLYAL-3-P are made from R-5-P and
Xu-5-P, respectively.
Thiamines
Thiamines are a class of compounds involved
Glyceraldehydes a product
Sedoheptulose is too
Each with a trailing phosphate
But we are not quite through
Thiamine pyrophosphate
(TPP) is an enzyme cofactor
found in all living systems derived from thiamine by action
zyme in the pentose phosphate pathway, also uses it as a coenzyme. Besides these reactions, TPP is also required for oxidative decarboxylation of
524
Figure 6.52 - The Calvin cycle - The resynthesis phase has multiple steps and is
described below.
Image by Aleia Kim
tivated acetaldehyde.
Thiamine deficiency
525
zyme known as thiaminase, foods with compounds that counter thiamine action (tea, coffee), and chronic diseases, including diabetes,
gastrointestinal diseases, persistent vomiting.
People with severe alcoholism often are defi-
cient in thiamine.
Calvin cycle
glucose.
Carbon dioxide
photosynthetic organ-
Light-Independent Cycle,
cell/chloroplast simply is
Assimilation
gle glucose.
Instead, six molecules of
Ru1,5BP (30 carbons) gain
1) assimilation of CO2
2) reduction reactions
526
Cyclic pathway
phosphoglycerate.
Figure 6.54 - Resynthesis phase of the Calvin cycle - All paths lead to regenerating
Ru1,5BP, which is the aim of the resynthesis phase. Glycolysis/gluconeogenesis
intermediates shown in blue. Enzyme numbers explained in text.
527
Resynthesis phase
The resynthesis phase (Figure 6.54) requires multiple steps, but only utilizes two enzymes unique to plants - sedoheptulose-1,7
bisphosphatase and phosphoribulokinase. RUBISCO is the third (and only other)
enzyme of the pathway that is unique to
plants.
2 - G3PDH
3 - Triosephosphate Isomerase
4 - Aldolase
5 - Fructose 1,6 bisphosphatase
6 - Transketolase
7 - Phosphopentose Epimerase
8 - Phosphoribulokinase
9 - Sedoheptulose 1,7 bisphosphatase
10 - Phosphopentose Isomerase
Reactions
The resynthesis phase begins with conversion
of the 3-PG molecules into GLYAL3P (there
are actually 10 GLYAL3P molecules involved
1 - Phosphoglycerate kinase
bisphosphate
(S1,7BP). The phosphate at position #1 is
528
cleaved by sedoheptulose-1,7
bisphosphatase to yield S-7-P.
Transketolase (another PPP enzyme) catalyzes transfer to two car-
yield Ru1,5BP.
Photorespiration
In the Calvin cycle of photosynthesis, the
enzyme ribulose-1,5-bisphosphate carboxylase (RUBISCO) catalyzes the addition
of carbon dioxide to ribulose-1,5bisphosphate (Ru1,5BP) to create two molecules of 3-phosphoglycerate. Molecular
oxygen (O2), however, competes with CO2 for
this enzyme, so about 25% of the time, the
molecule that gets added is not CO2, but
rather O2 (Figure 6.55). When this happens,
the following reaction occurs
Ru1,5BP + O2
529
point of oxygenation
of Ru1,5BP is the
same as the carboxylation of Ru1,5BP reactions, but there are
significant energy
costs associated with
it, making the process less efficient.
C4 plants
The Calvin cycle is
the means by which
plants assimilate carbon dioxide from the
atmosphere, ultimately into glucose.
Plants use two general strategies for doing so. The first is
employed by plants
called C3 plants
(most plants) and it
simply involves the
pathway described
above. They are
called C3 plants because the first stable
intermediate after absorbing carbon dioxide contains three
530
loss of water.
Capture by PEP
In C4 plants, carbon dioxide is captured in
Peptidoglycan synthesis
glucosamine-1phosphate
531
9. A pentapeptide chain of glycines (pentaglycine) is linked to lysine of the pentapeptide chain to create a Dolichol-PP-Nacetylmuramic acid-N-acetylglucosaminedecapeptide. The pentaglycine serves as cross
links in the overall structure.
10. Dolichol-PP is removed to yield NFigure 6.59 - Penicillin
acetylmuramic acid-N-acetylglucosaminedecapeptide
532
pentapeptide of another.
The enzyme catalyzing the addition of the N-acetylmuramic
YouTube Lectures
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is because syn-
drate enzymes.
thesis of a pep-
Activity of en-
tidoglycan
zymes in the
complex is in-
single bacte-
creased. Most
rium requires
of the basic
millions of cy-
metabolic
cles of reac-
pathways are
tions above.
thought to use
Even slowing
metabolons.
They include
glycolysis,
major effect on
bacterial
cycle, nucleo-
growth. On
tide metabo-
lism, glyco-
transpeptidase.
Metabolons
Hypoxia
GLUT 1
GLUT 3
Aldolase
cells to 1) import more glucose and 2) metabolize it more rapidly when it arrives. This
is to be expected because anaerobic sugar
metabolism is only about 1/15th as efficient as
Enolase
GLYAL3P dehydrogenase
Hexokinase
PFK-1
Phosphoglycerate kinase
Pyruvate Kinase
Covalent modification
HIFs are regulated partly by an interesting covalent modification. When oxygen concen-
conditions exist.
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
535
Gluconeogenesis
To the tune of Supercalifragelisticexpialidocious
Metabolic Melodies Website HERE
When cells have lots of ATP and NADH too
They strive to store this energy as sugar yes they do
Inside of mitochondria they start with pyruvate
(slow) Carboxylating it to make oxaloacetate
Oh gluconeogenesis is so exhilarating
Memorizing it can really be exasperating
Liver cells require it so theres no need for debating
Gluconeogenesis is so exhilarating
536
3-B-P-G
2-B-P-G
Lose a water
PEP gets a high energy state
Just to make py-ru-vate
At a high rate
Add a phosphate
With PFK
F1,6BP is made up this way
So we can run and play
Aldolase breaks it and then it releases
DHAP and a few G-3-Pieces
These both turn in to 1,3 BPG
Adding electrons onto NAD
537
In My Liver
To the tune of And I Love Her
Metabolic Melodies Website HERE
If I am missing meals
On busy days
Thats whenmy body steals
Glucose away
From my liver
It startswith glucagon
When Im weakkneed
The hormoneacts to spawn
New energy
In my liver
Bridge
The signaling
Acts rapidly
c-A-M-Ps
Fire upkinase
Phosphorylasethen gets
Re-activated
So glycogenbegets
Glucosephosphated
In my liver
Instrumental
538
When Im exercisin
It is not surprisin
That insulin is absentee
But when it flows
Then my glycogen grows
And nobody knows like me
Epinephrines crazy
Absent when Im lazy
Made when I am scared you see
Then when it flows, all my glycogen goes
And G1P grows in me
My hormones they are treating my fine
539
Acetyl-CoA
The molecule feeding the citric acid cycle is
acetyl-CoA and it can be obtained from pyruvate (from glycolysis), from
YouTube Lectures
by Kevin
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540
cycle.
Anabolically, acetyl-CoA is also very important for providing building blocks for synthesis of fatty acids, ketone bodies, amino
acids and cholesterol. Other citric acid cy-
Figure 6.63 - Amino acid metabolism and the citric acid cycle. Amino acids
boxed in yellow are made from the indicated intermediate. Amino acids in blue
are made into the intermediate in catabolism.
Image by Aleia Kim
541
Pyruvate decarboxylation
The pyruvate dehydrogenase enzyme is a
complex of multiple copies of three subunits
that catalyze the decarboxylation of pyruvate to form acetyl-CoA. The reaction
mechanism requires use of five coenzymes.
Pyruvate dehydrogenase is an enormous complex in mammals with a size five times greater
than ribosomes.
Subunits
The three subunits are designated by E1, E2,
and E3. E2 is also referred to as dihydroli-
542
E3.
tions of pyruvate
poamide.
dehydrogenase
can be broken
Reductive
acetylation
Reductive acetyla-
of the subunits.
(Step B) as the 2-
carbon hy-
quentially occur-
droxyethyl unit
is transferred to
lipoamide on
carboxylation
E2. (Lipoamide is
of pyruvate; 2)
oxidation of the
decarboxylated
product; and 3)
Catalysis
The catalytic process begins after binding of
the pyruvate substrate with activation of the
thiamine pyrophosphate coenzyme
through formation of an ylide intermediate.
The nucleophilic carbanion of the ylide at-
543
Oxidation step
Transfer of the hydroxyethyl
(Step E) and completing the overall cycle. Then enzyme can then
begin another catalytic round by
binding to a pyruvate.
it).
The acetyl group is then
transferred from lipoamide to coenzyme A
in E2 (Step C in Figure
6.65), forming acetylCoA, which is released
and leaving reduced sulfhydryls on the lipoamide. In order for
the enzyme to return to its
original state, the disulfide bond on lipoamide
must be re-formed. This
occurs with transfer of electrons from reduced lipoamide to an FAD covalently bound to E3 (Step
D). This reduces FAD to
FADH2.
Formation of NADH
In the last step in the proc-
544
Product inhibition
Thus, the products of the pyruvate
dehydrogenase reaction inhibit
subunit.
Covalent modification
545
546
Acetyl-CoA + Oxaloacetate
Citrate + CoA-SH
Insulin also also activates pyruvate kinase
and the glycolysis pathway to use internal-
nitase.
adrenergic receptor has no effect on pyruvate kinase, though the insulin cascade
Citrate
Isocitrate
Isocitrate is a branch point in plants and bacteria for the glyoxylate cycle (see HERE).
Oxidative decarboxylation of isocitrate by
Acetyl-CoA for
the pathway can
come from a variety of sources.
The reaction joining it to OAA is
catalyzed by citrate synthase
and the G is
fairly negative.
This, in turn,
helps to pull
the malate dehydrogenase
reaction preceding it in the cycle.
547
nase.
Isocitrate + NAD+
-ketoglutarate +
NAD+
+ CoA-SH
drogenase and employs the same five coenzymes NAD+, FAD, CoA-SH, thiamine
pyrophosphate, and lipoamide.
Regeneration of oxaloacetate
The remainder of the citric acid cycle involves
conversion of the four carbon succinyl-CoA
into oxaloacetate. Succinyl-CoA is a branch
point for the synthesis of heme (see HERE).
Succinyl-CoA is converted to succinate in a reaction catalyzed by succinyl-CoA synthetase (named for the reverse reaction) and
a GTP is produced, as well the only substrate level phosphorylation in the cycle.
Succinyl-CoA + GDP + Pi
able. Succinate is also produced by metabolism of odd-chain fatty acids (see HERE).
Wikipedia
548
Succinate Oxidation
nase.
Fumarate + H2O
Succinate + FAD
L-Malate
Fumarate + FADH2
action and participates in the electron transport system, funneling electrons from the FADH2 it
gains in the reaction to coen-
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Rare oxidation
Conversion of malate to oxaloacetate by malate dehydrogenase is a rare biological oxidation that has a
G with a positive value
(29.7 kJ/mol).
L-Malate + NAD+
Oxaloacetate + NADH
The reaction is pulled by
the energetically favorable
Figure 6.72 - Succinate dehydrogenase reaction
Image by Aleia Kim
conversion of oxaloacetate
to citrate in the citrate
549
genesis.
Regulated enzymes
Regulation of the
citric acid cycle
Allosteric regulation
of the citric acid cycle is pretty straightforward. The molecules
involved are all
substrates/products
of the pathway or molecules involved in energy transfer.
Substrates/products
that regulate or affect
the pathway include
acetyl-CoA and
succinyl-CoA .
Inhibitors and
activators
High energy molecular
550
Cataplerotic molecules
activated by AMP).
Anaplerotic/
cataplerotic
pathway
Aconitase is picky
Binds substrates specially
Creating isocitrate
Which has no symmetry
to absorb metabolic byproducts gives great flexibility to cells. When citric acid cycle intermediates are taken from the
pathway to make other
molecules, the term used
Kevin Ahern
Anaplerotic molecules
Anaplerotic molecules replenishing citric acid
Glyoxylate cycle
A pathway related to the citric acid
cycle found only in plants and bacteria is the glyoxylate cycle (Figures
6.74 & 6.75). The glyoxylate cycle,
which bypasses the decarboxylation reactions while using most of the
non-decarboxylation reactions of the
citric acid cycle, does not operate in
animals, because they lack two enzymes necessary for it isocitrate
552
553
is particularly important for plant seed germination (Figure 6.76), since the seedling is
not exposed to sunlight. With the glyoxylate
cycle, seeds can make glucose from stored
lipids.
Because animals do not run the glyoxylate cycle, they cannot produce glucose from acetylCoA in net amounts, but plants and bacteria
can. As a result, plants and bacteria can turn
acetyl-CoA from fat into glucose, while aniFigure 6.76 - A gingko seed embryo
Wikipedia
mals cant. Bypassing the oxidative decarboxylations (and substrate level phos-
aloacetate.
cycle.
contrast with the citric acid cycle is apparent. After one turn of the citric acid cycle, a
Carbohydrate needs
oxidation.
turn of the glyoxylate cycle results in two oxone. The extra oxaloacetate of the glyoxylate
554
energy for cells, whereas the glyoxylate cycles main function is anabolic - to allow production of glucose from fatty acids in
plants and bacteria. The two pathways are
physically separated from each other (glyoxylate cycle in glyoxysomes / citric acid cycle
in mitochondria), but nonetheless a coordinated regulation of them is important.
The enzyme that appears to provide controls
for the cycle is isocitrate dehydrogenase.
In plants and bacteria, the enzyme can be inactivated by phosphorylation by a kinase
found only in those cells. Inactivation causes
isocitrate to accumulate in the mitochondrion
and when this happens, it gets shunted to the
glyoxysomes, favoring the glyoxylate cycle.
Acetyl-CoA metabolism
Acetyl-CoA is one of the most connected
metabolites in biochemistry, appearing in
fatty acid oxidation/synthesis, pyruvate
oxidation, the citric acid cycle, amino acid
anabolism/catabolism, ketone body metabolism, steroid/bile acid synthesis, and (by extension from fatty acid metabolism) prostaglandin synthesis . Most of these pathways
555
Overlapping pathways
HMG-CoA
formation
Both pathways also include addition of two
more carbons to
acetoacetyl-CoA from
a third acetyl-CoA to
form hydroxy-methylglutaryl-CoA, or HMGCoA, as it is more commonly known. It is at
this point that the two
Figure 6.80 - Diverging biosynthetic pathways for ketone
bodies (left) and cholesterol biosynthesis (right)
Image by Penelope Irving
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557
ergy source.
Acidosis
Ketosis
When a body is producing
ketone bodies for its energy, this state in the body is
known as ketosis. Formation of ketone bodies in the
liver is critical. Normally
glucose is the bodys primary energy source. It
comes from the diet, from
the breakdown of storage carbohydrates, such as glycogen, or from glucose synthesis (gluconeogenesis).
Since the primary stores of
glycogen are in muscles
and liver and since gluconeogenesis occurs only in liver,
559
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
A further oxidation
Gives one trans fumarate
Which gains a water on the
Next step to make malate
562
sis of fat, let us first discuss the movement of dietary fat and oil (triglyc-
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563
Breakdown of fat
Breakdown of fat in adipocytes requires
catalytic action of three enzymes. The first
564
triacylglycerol lipase.
It removes the first fatty
acid from the fat. Diacylglyceride lipase removes the second one
and monoacylglyceride lipase removes
the third. As noted, only
the first one is regulated
and it appears to be the
rate limiting reaction
when active.
Epinephrine
activation
As shown in Figure
6.84, activation of hormone sensitive triacylglycerol lipase
(HSTL) is accomplished
by epinephrine stimulation process and that it
overlaps with the same
activation that stimulates
glycogen breakdown
and gluconeogenesis.
This coordination is very
Figure 6.84 - Breakdown of fat in adipocytes
pathways stimulated by
the epinephrine signal-
565
brane receptor.
Perilipin
Fat synthesis
566
567
Transport
Steps
568
ing one.
Enzymes of -oxidation
Two of the enzymes of -oxidation are notable. The first is acyl-CoA dehydrogenase,
been associated with sudden infant death syndrome. Reactions two and three in oxidation are catalyzed by enoyl-CoA hy-
569
yields an NADH.
intermediate is formed.
Thiolase
repeated in the citric acid cycle reaction catalyzed by malate dehydrogenase yielding
oxaloacetate.
570
Differences
First, since there is no electron
transport system in peroxisomes,
the reduced electron carriers produced in oxidation there must have
their own recycling process. Peroxisomes accomplish this by transferring electrons and protons from
Metabolism of this intermediate is odd. Sequentially, the following steps occur (Figure
6.90) 1) carboxylation to make Dmethylmalonyl-CoA; 2) isomerization to Lmethylmalonyl-CoA; 3) rearrangement to
Peroxisomal oxidation
Extra enzymes
four, cis-3-enoyl-CoA
isomerase will convert the bond
to a trans bond between carbons
two and three and -oxidation can
proceed as normal.
572
2,4 dienoyl-CoA
reductase
damage.
-oxidation
tion in signaling.
goes hydroxylation and oxidation on carbon number two (in contrast to carbon three
of -oxidation), followed by decarboxylation and production of an unbranched intermediate that can be further oxidized by the oxidation pathway. Though -oxidation is a
relatively minor metabolic pathway, the inability to perform the reactions of the path-
nate.
acetyl-CoA.
its).
A second level of
control of fatty acid
availability is by
regulation of carnitine acyl transferase (Figure
6.87 - see HERE).
This enzyme controls the swapping
of CoA on an acylCoA molecule for
carnitine, a necessary step for the
fatty acid to be imported into the mitochondrion for
oxidation.
574
Figure 6.95 - Fatty acid synthesis is the reverse of fatty acid oxidation chemically
575
reduce the ketone; 4) a dehydrase (DH) to catalyze removal of water; 5) a reductase (ER) to reduce the
trans double bond and 6) a
thioesterase (TE) to cleave
the finished palmitoylCoA into palmitic acid
and CoA-SH.
In the middle of the complex is a site for binding the
ACP portion of the growing
fatty acid chain to hold it as
the other part of the fatty
acid is rotated into positions
around the enzyme complex
for each catalysis. In bacteria, these six activities are
found on separate enzymes
and are not part of a complex.
Cytoplasmic
reactions
and malonyl-CoA have their CoA portions replaced by a carrier protein known as ACP
(acyl-carrier protein) to form acetyl-ACP
(catalyzed by acetyl-CoA : ACP transacylase - MAT in Figure 6.97) and malonylACP (catalyzed by malonyl-CoA : ACP
transacylase - MAT in Figure 6.97). Joining of a fatty acyl-ACP (in this case, acetylACP) with malonyl-ACP splits out the car-
577
Dehydration
Next, water is removed from carbons 2 and 3 of the hydroxyl in-
dehydrase - DH on Figure
lyzed by 2,3-trans-enoyl-ACP
6.97. This yields a trans
doubled-bonded molecule. Last,
the double bond is hydrogenated
to yield a saturated intermediate
by 2,3-trans-enoyl-ACP re-
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578
A.
579
Unusual
oxidation
reaction
Removal of elecFigure 6.99 - Elaidic acid - A rare trans fatty acid in biology
sequently, these two must be provided in the diet and are referred
to as essential fatty acids.
Almost all desaturases make cis, not trans
double bonds. There are a few minor exceptions to this, in cattle, for example (Figure
6.99). The trans fatty acids found in trans
fat of prepared food are produced not by biological processes, but rather by the process of
580
Prostaglandin synthesis
(Figure 6.100).
581
(PLD) cleaves the R group from the phosphate part of the molecule.
Since the fatty acid on position #2
(where PLA2 cuts) is most commonly
unsaturated, PLA2 is an important
phosopholipase for hydrolyzing the unsaturated fatty acid known as arachidonic acid from glycerophospholipids. Release of arachidonic acid from
membranes is necessary for synthesis of
prostaglandins.
Inhibition of the release of arachidonic acid from membranes is the
Figure 6.101 - Cleavage sites for four
phospholipiases on a glycerophospholipid phospholipases A 1 (PLA1), A 2 (PLA2), C (PLC),
and D (PLD)
Lipocortin
with it.
Phospholipase A2
glycerophospholipids produces
fatty acids and either glycerol3-phosphate or other substances. Figure 6.101 shows
Second strategy
582
Non-steroidal
drugs
Molecules inhibiting cyclooxygenases are
Targeting inhibitors
Some NSAID inhibitors, such as aspirin, bind
to all types of COX enzymes. Newer COX inhibitors target the COX-2 enzyme specifically
because it was believed to be a better target
for relief of joint pain than COX-1 enzymes
which are synthesized by most cells. COX-2
enzymes are found more specifically in joints
so the thinking was that specific inhibition of
them would not affect the COX-1 enzymes
583
Imbalance
Other compounds known to inhibit COX enzymes include some flavonoids, some components of fish oil, hyperforin, and vitamin
D.
Connections to other
pathways
There are several connections between fats and fatty acid metabolism and other metabolic pathways. Diacylglycerol (DAG - Fig-
585
cle.
Obesity is an increasing problem in the western world. It is, in fact, the leading prevent-
Resistin
Adipokines
Adipokines are adipose
tissue-synthesized cytokines. The class of molecules
includes leptin (first discovered adipokine) and hundreds
of other such compounds.
These include adiponectin
(regulates glucose levels and
fatty acid oxidation), apelin
(control of blood pressure, angiogenesis promotion, vasodilator release, increased water
intake), chemerin (stimula-
586
the body.
Leptin
infancy.
Physiology
Leptin levels
Leptin levels in the body are highest between
midnight and early morning, presumably to
suppress appetite. Though it is produced by
fat cells, levels of leptin in humans do not
strictly reflect levels of fat. For example,
early in fasting, leptin levels fall before fat levels fall. Sleep deprivation can reduce leptin
levels, as can increasing levels of testosterone and physical exercise.
587
Behavioral effects
Ghrelin
Ghrelin is a peptide hormone made by
cells in the gastrointestinal tract when the
tanoic acid to a serine at position 3. Circulating levels of ghrelin increase before eating and
decrease afterwards. There appears to be a
588
increase.
ing behavior and there is a negative correlation between levels of ghrelin and weight.
Neuropeptide Y
Stress effects
In mice and monkeys, repeated stress and
high fat, high sugar diets stimulate neuro-
589
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
590
591
592
Sugars are the building blocks of carbohydrates, amino acids are the building
blocks of proteins and nucleotides are
the building blocks of the nucleic acids
- DNA and RNA. Another crucial building block is acetyl-CoA, which is used to
build many lipid substances, including
fatty acids, cholesterol, fat soluble vitamins, steroid hormones, prostaglandins, endocannabinoids, and the
bile acids. Indeed, acetyl-CoA goes
into more different classes of molecule
593
594
Isoprenoids
nones in the electron transport chain, isoprenoids are ubiquitous in cells. Iso-
prenoids are a large, diverse and ancient group of molecules that are
found in all three domains of life.
As noted earlier, they are compo-
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6.112.
595
First, they reduce the production of mevalonate, which restricts the amount of substrate available to make cholesterol. Second,
and perhaps more importantly, they increase
production of LDL receptors in the liver,
which favors uptake and destruction of LDLs,
thus lowering serum cholesterol levels.
tion, joining together two acetyl-CoA molecules to make acetoacetyl-CoA. In the sec-
ond reaction catalyzed by HMG-CoA synthase, a third acetyl-CoA is joined to form the
six carbon compound known as hydroxy-
Regulation
Biologically, the HMG-CoA reductase en-
- HMG-CoA reductase.
Statins
Medically, HMG-CoA reductase is the target of a class of drugs known as statins (Figure 6.113 & Movie 6.1), which are used to
reduce cholesterol levels in people. These
competitive inhibitors, which compete
with HMG-CoA for binding have two effects.
levels of glucose in the blood activate the enzyme. Phosphorylation by AMPactivated protein kinase inhibits its activity. Interestingly, the same enzyme phosphorylates and inactivates acetyl-CoA carboxylase - the only regulatory enzyme controlling
fatty acid synthesis. Transcription of
the gene encoding HMG-CoA reductase
596
phosphate (DMAPP).
Isoprenes
597
Squalene
Two farnesyl-pyrophosphates join to create
the 30-carbon compound known as
squalene. Squalene, in a complicated rearrangement involving reduction and molecular oxygen forms a cyclic intermediate known
as lanosterol (Figure 6.116) that resembles
cholesterol. Conversion of lanosterol to cholesterol is a lengthy process involving 19 steps
that occur in the endoplasmic reticulum.
The cholesterol biosynthesis pathway from
lanosterol is a long one and requires significant amounts of reductive and ATP energy.
As noted earlier (see HERE), cholesterol has
598
599
hibitors are prescribed to prevent the formation of estrogens and slow tumor growth.
Two commonly used inhibitors include
exemestane (a suicide inhibitor - Figure 6.121) and anastrozole (a competitive inhibitor).
600
geranylgeranyl pyrophosphate.
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601
Vitamin A Synthesis
Vitamin A is important for many cellular functions related to growth, differentiation and organogenesis during embryonic development, tissue maintenance,
and vision, to name a few.
There are three main active forms of the
vitamin, retinal, retinol and retinoic
acid, each with its own set of functions.
Retinal, complexed with the protein, opsin, is found in the rod cells of the retina
Figure 6.123 - Four bile acids
during digestion. Converting the very nonpolar cholesterol to a bile acid involves oxidation of the terminal carbon on the side
chain off the rings. Other alterations to increase the polarity of these compounds include hydroxylation of the rings and linkage
to other polar compounds.
Common bile acids include cholic acid, chenodeoxycholic acid, glycocholic acid, taurocholic acid, and deoxycholic acid (Figure
6.123). Another important consideration
about bile acids is that their synthesis reduces
the amount of cholesterol available and pro-
602
-carotene is found
in carrots and other
orange vegetables,
and is converted in
the body to vitamin
A. Catalytic action by
-Carotene 15,15
monooxygenase
cleaves -carotene to
form retinal (the aldehyde form used in vision).
The enzyme retinol
dehydrogenase
catalyzes reduction
of retinal to retinol
(storage form). Oxidation of retinal creates another important retinoid known
as retinoic acid.
This form of vitamin
A cannot be reduced
back to retinal and
thus cannot be used
for vision or storage.
Instead, retinoic acid
has roles in embryonic development.
Retinoic acid acts
through binding to
the Retinoic Acid
Receptor (RAR).
603
yields N-acylsphinganine,
which is a ceramide (Figure 6.126). A ceramide
can be converted into a
cerebroside by addition
of a glucose from UDPglucose (Figure 6.127).
If a few other simple sugars
are added to the cerebroside, a globoside is created.
If, instead of adding sugar,
Figure 6.125 - Synthesis of dihydrosphingosine from
serine and palmitoyl-CoA
RAR binds to DNA and affects transcription of several important sets of genes important for differentiation. These include the
Hox genes, which control anterior/posterior
patterning in early embryonic development.
Sphingolipid synthesis
Synthesis of sphingolipids, which are found
primarily in brain and nerve tissue, begins
a phosphocholine is
added from phosphatidylcholine, then sphingomye-
Sphingolipid breakdown
In the overall metabolism of sphingolipids, the greatest problems arise with their catabolism. Figure 6.128 illustrates the nu-
with palmitoyl-CoA
and serine that combine to make an 18carbon amine called
3-keto-sphinganine
(Figure 6.125). Reduction of that by
NADPH yields dihydrosphingosine and addition of a fatty acid
from an acyl-CoA
604
605
Figure 6.128 - Enzymes involved in sphingolipid breakdown and the diseases associated with their absence in parentheses. NANA = N-acetyl-neuraminic Acid / Glc =
glucose / Gal = galactose / GalNAc = N-acetyl-galactosamine
Wikipedia
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606
Glycerophospholipid metabolism
phatidate cytidylyltransferase.
CDP-diacylglycerol + PPi
CDP-diacylglycerol + Serine
plays an important role in glycerophospholipid synthesis, serving as part of an activated intermediate for synthesis of phos-
Phosphatidylserine + CMP
ergy input.
607
Phosphocholine + CTP
Phosphatidylserine and phosphatidyle-
CDP-choline + PPi
Then the CDP donates the phosphocholine
to a diacylglycerol to made phosphatidyl-
Phosphatidylethanolamine + Serine
CDP-choline + Diacylglycerol
Phosphatidylserine + Ethanolamine
Similarly, phosphatidylserine and phos-
Phosphatidylcholine + CMP
Synthesis of other important glycerophos-
Phosphatidylserine + Choline
Phosphatidylserine
Phosphatidylcholine + Serine
Phosphatidylglycerol can be made from
glycerol-3-phosphate and CDP-diacylglycerol
CDP-diacylglycerol + Glycerol-3-phosphate
Phosphatidylethanolamine + CO2
Phosphatidylethanolamine can serve as a
precursor in an alternative pathway for making phosphatidylcholine (SAM = SAdenosyl Methioinine / SAH = SAdenosyl Homocysteine)
Phosphatidylglycerol + CMP
Cardiolipin, which is essentially a diphosphatidyl compound can be made by joining
CDP-diacylglyerol with phosphatidylglycerol
Phosphatidylethanolamine + 3 SAM
CDP-diacylglycerol + Phosphatidylglycerol
Phosphatidylcholine + 3 SAH
Cardiolipin
608
Glycine + Succinyl-CoA
-aminolevulinic acid
Joining of two -aminolevulinic acid molecules together with splitting out of two molecules of water yields porphobilinogen.
2 -aminolevulinic acid
Porphobilinogen + 2H2O
Figure 6.130 - Heme C
CDP-diacylglycerol + Inositol
Phosphatidylinositol + CMP
4 Porphobilinogen
Hydroxymethylbilane
Next, a series of reactions involving 1) loss of
Heme synthesis
The porphyrin ring found in the hemes of
animals, fungi, and protozoa (Figure 6.130)
is synthesized starting from very simple compounds (Figure 6.131). The process is a bit
complicated, occurring between the cyto-
water; 2) loss of four molecules of carbon dioxide; 3) loss of two more carbon dioxides, loss
of six protons and electrons and (finally) 4) addition of Fe++ with loss of two protons yields
heme. Individual heme molecules may be
further processed.
609
Porphyria
Defects in enzymes of the pathway can also
lead to porphyrias, diseases in which one
or more of the intermediates in the heme
synthesis pathway accumulate due to deficiency of the enzyme necessary to convert
the accumulating material into the next
molecule in the pathway. The accumulation
of purplish intermediates gave the diseases
the name porphyria from the Greek word
for purple.
610
Breakdown of heme
Catabolism of heme (Figure
6.133) begins in macrophages
within the spleen . Targets for
degradation are hemes within
damaged red blood cells, which
get removed from the blood supply due to their appearance. It is
because of this system, for example, that sickle cell anemia is
classified as an anemia (decrease
in red blood cells or hemoglobin
in the blood). After cells have
sickled, they lose their shape and
are more likely to be removed
from the blood by this process,
leaving the patient weakened
from low blood cell counts.
The first biochemical step in catabolism is conversion of heme to biliverdin. This reaction is catalyzed by heme
oxygenase and requires electrons from
NADPH. In the process, Fe++ is re-
manifestations of the disease, cutaneous porphyrias cause skin problems on exposure to light. This
need, for patients with certain
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rubin by biliverdin reductase and is secreted from the liver into bile. Bacteria in the
611
612
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
To Make a Cholesterol
To the tune of When Johnny Comes Marching Home
Metabolic Melodies Website HERE
614
615
Transamination
anabolic pathways.
616
-ketoacid + Glutamate
to distinguish them.
ure 6.134.
Glutamate and glutamine play central
roles in transamination, each containing
one more amine group than ketoglutarate and glutamate, respectively.
Transamination reactions, as noted earlier, occur by a ping-pong mechanism and involve
swaps of amines and oxygens in Schiff base
reactions. Two amino acids, glutamine
and asparagine are the products of gaining
an amine in their respective R-groups in reactions involving ammonium ion.
Synthesis varies
It is also important to recognize that organisms differ considerably in the amino acids
that they can synthesize. Humans, for example, cannot make 9 of the 20 amino acids
needed to make proteins, and the number of
these that can be synthesized in needed
amounts varies between adults and children.
Amino acids that cannot be made by an organism must be in the diet and are called essential amino acids. Non-essential amino
acids are those an organism can make in sufficient quantities (Figure 6.135). Though
amino acids do not have a common pathway
617
-ketoglutarate family
This family of amino acids arises from ketoglutarate of the citric acid cycle. It includes the amino acids glutamic acid, glutamine, proline, and arginine. It is also
called the glutamate family, since all the
amino acids in it derive from glutamate.
Glutamate
make glutamate.
618
Glutamine
Synthesis of glutamine proceeds
from glutamate via catalysis of
the enzyme glutamine synthetase, one of the most important regulatory enzymes in all of
amino acid metabolism (Figure
6.136).
Regulation of the enzyme is complex, with many allosteric effectors. It can also be controlled by
covalent modification by adenylylation of a tyrosine residue in
the enzyme (Figure 6.137). In
the figure, PA and PD are regulatory proteins facilitating conversion of the enzyme.
619
ure 6.138).
pyrroline-5-carboxylate reductase.
1-pyrroline-5-carboxylate + NAD(P)H + H+
Proline
Synthesis of proline starts with several reactions acting on glutamate. They are shown
L-proline + NAD(P)+
1. ATP + L-glutamate
Arginine
Arginine is a molecule synthe-
(Glutamate-5-kinase)
H+
(Glutamate-5-semialdehyde dehydrogenase)
620
The last means of making arginine is by reversing the methylation of asymmetric dimethylarginine (ADMA - Figure 6.140). ADMA is
lowing manner
Arginine + Water
Ornithine + Urea
Arginine can also be made starting with gluta-
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mate. This 5 step pathway leading to ornithing is illustrated at the top of the next page
(enzymes in blue). Ornithine, as noted above
can readily be converted to arginine.
621
1. Glutamate + Acetyl-CoA
(Acetylglutamate synthetase)
N-acetylglutamate + CoA-SH
2. N-acetylglutamate + ATP
(N-acetylglutamate kinase)
N-acetyl--glutamyl phosphate
3. N-acetyl--glutamyl phosphate + NAD(P)H
(N-acetylglutamate dehydrogenase)
N-acetylaglutamate--semialdehyde + NAD(P)+
4. N-acetylaglutamate--semialdehyde + Glutamate
nase.
Transamination by phosphoser-
(Transaminase)
N-acetylornithine + -ketoglutarate
5. N-acetylornithine + H2O
(N-acetylornithinase)
Ornithine + Acetate
Serine family
Serine is a non-essential amino acid synthesized from several sources. One starting
point is the glycolysis intermediate,
1. 3-phosphohydroxypyruvate + Glutamate
2. O-phosphoserine + H2O
3-phosphohydroxypyruvate + NADH + H+
O-phosphoserine + -ketoglutarate
Serine + Pi
622
cleotide synthesis.
ines, and is the precursor for glycine, cysteine, and tryptophan in bacteria, as well as
for sphingolipids and folate. Serine in the
active site of serine proteases is essential
for catalysis. A serine in the active site of
acetylcholinesterases is the target of nerve
gases and insecticides.
Cysteine
Cysteine can be synthesized from several
sources. One source is the metabolism of the
other sulfur-containing amino acid, methionine. This begins with formation of SAdenosyl-Methionine (SAM), catalyzed by
methionine adenosyltransferase.
Glycine
Methionine + ATP
SAM + Pi + PPi
SAM is a methyl donor for methyl transfer
reactions and that is the next step in the
pathway - donation of a methyl group (cata-
lyzed by transmethylase)
623
SAM + Acceptor
Another route to making cysteine is a twostep process that begins with serine, catalyzed first by serine-O-acetyltransferase
SAH + CH3-Acceptor
Serine + Acetyl-CoA
CoA-SH + O-acetyl-L-serine
SAH
and then by cysteine synthase
Homocysteine + Adenosine
O-acetyl-L-serine + H2S
L-cysteine + Acetate
On the path to making cysteine, homocysteine reacts as follows (catalyzed by cystathionine -synthase).
Homocysteine + Serine
Cystathionine
2 Cysteine + 2 NAD+
teine
Cystathionine + H2O
L-cysteine + Sulfite
624
Asparagine
Asparagine, too, is an amino acid produced
in a simple transamination reaction. In
this case, the precursor is aspartate and the
amine donor is glutamine (catalyzed by asparagine synthetase)
Image by Aleia Kim
Aspartate family
Metabolism of aspartic acid is similar to
that of glutamate. Aspartic acid can arise
from transamination of a citric acid
cycle intermediate (oxaloacetate).
Aspartate can also be gener-
Methionine
Metabolism of methionine over-
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Asparagine + H2O
Aspartate + NH4+
Further, aspartate can be produced by reversal of a reaction in the urea cycle (see
1 - Aspartokinase
HERE)
2 - Aspartate-semialdehyde dehydrogenase
3 - Homoserine dehydrogenase
4 - Homoserine O-transsuccinylase
5 - Cystathionine--synthase
6 - Cystathionine--lyase
7 - Methionine synthase
625
626
Threonine
Though threonine is chemically similar to serine, the metabolic pathway leading to
threonine does not overlap with that of ser-
Dimethylglycine + Methionine
In this reaction, a methyl group is transferred
to homocysteine from glycine betaine to
make the methionine. Glycine betaine is a
trimethylated amine of glycine found in
plants. It is a byproduct of choline metabolism.
Bacteria, mitochondria, and chloroplasts use
a modified form of methionine, N-formylmethionine (Figure 6.142), as the first
amino acid incorporated into their proteins. Formylation of methionine occurs
tRNA formyltransferase
Lysine
7 - Succinyl-diaminopimelate desucciny-
lase
8 - Diaminopimelate epimerase
9 - Diaminopimelate decarboxylase
ure 6.144):
1 - Aspartokinase
2 - Aspartate-semialdehyde dehydroge-
nase
3 - 4-hydroxy-tetrahydrodipicolinate
synthase
4 - 4-hydroxy-tetrahydrodipicolinate re-
ductase
5 - 2,3,4,5-tetrahydropyridine-2,6-
dicarboxylate N-succinyltransferase
6 - Succinyl-diaminopimelate transaminase
628
629
in its synthesis.
Erythrose-4-phosphate and
phosphenolpyruvate (PEP) also
6.146 to 6.148.
and erythrose-4-phosphate
(Figure 6.145). All three aromatic amino acids are also important sources of hormones, neuro-
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ment melanin.
Tryptophan synthesis
630
Regulation
Regulation of tryptophan synthesis in bacteria
occurs partly via a process called attenuation
that operates through the
trp operon. In this
mechanism, low levels of
tryptophan slow ribosomal movement (and
translation) through the
operon. This is particularly important because
bacteria can have transcription and translation occurring simultaneFigure 6.147 - The route to tryptophan - making chorismic
acid from shikimic acid
Wikipedia
631
acids. It is used sometimes to help in treatment of sleep disorders. Some reports have
indicated that children with autism have abnormal melatonin pathways with low levels of
the hormone.
Blue light
Melatonin
Melatonin is a compound made from tryptophan that is found in a wide spectrum of
biological systems, including plants, animals,
fungi, and bacteria. In animals, it acts as a
hormone for circadian rhythm synchronization, signaling the onset of darkness each day.
It has effects on the timing of sleep, seasonal
632
Serotonin
Serotonin, or 5hydroxytryptamine, is a
monoamine neurotransmitter derived
from tryptophan. Blood
platelets store serotonin
and release it when they
bind to a clot, causing
vasoconstriction. Serotonin plays a role in
cognitive functions and
enhances memory and
learning. Serotonin is
Figure 6.149 - Tryptophan is a precursor of serotonin,
melatonin, and niacin
widely thought to be a
contributor to feelings
of happiness and well-
633
Niacin
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NADPH. The last pairs of molecules are essential as electron acceptors/carriers for most
to the disease known as pellagra, while insufficient amounts of niacin in the diet are linked
Auxins
634
or roots, depending on the relative concentrations of auxins and cytokinins supplied in the
medium.
635
Phenylalanine
Chorismate
PKU
Phenylalanine is linked to the genetic disease
Prephenate
ylpyruvate.
Prephenate
newborns are routinely tested for PKU. Phenylalanine is a component of the artificial sweet-
phenylalanine.
Phenylpyruvate + Glutamate
Phenylalanine + -ketoglutarate
Alternatively, phenylalanine can obtain its
amine group in a transamination reaction
from alanine.
Phenylpyruvate + Alanine
Figure 6.154 - Aspartame - a
methyl ester of the aspartic acidphenylalanine dipeptide
Phenylalanine + Pyruvate
636
Hydroxylation of phenylalanine by aromatic amino acid hydroxylase (phenylalanine hydroxylase) yields tyrosine.
Tyrosine
Because tyrosine is made from phenylalanine and the latter is an essential
amino acid in humans, it is not clear
whether to classify tyrosine as essential or
non-essential. Some define it as a conditionally essential amino acid. Others simply categorize it as non-essential.
As noted above, tyrosine can arise as a result
of hydroxylation of phenylalanine. In addition, plants can synthesize tyrosine by oxidation of prephenate followed by transamination of the resulting 4hydroxyphenylpyruvate (Figure 6.155).
The hydroxyl group on tyrosine is a target
for phosphorylation by protein kinase enzymes involved in signal transduction path-
637
response.
In photosystem II of chloroplasts, tyro-
Figure 6.158 - Synthesis of thyroid hormones from tyrosine and movement in the
body
Wikipedia
Tyrosine metabolites
stream.
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639
Chemical messenger
Figure 6.159 - A portion of pheomelanin - Arrows
show directions of polymer extension
cholesterol levels.
cosa in the digestive system and in the immune system, it reduces lymphocyte activity.
Dopamine
made by removing a carboxyl group from LDOPA. Dopamine is synthesized in the brain
Epinephrine
-adrenergic receptors.
Effects
system.
Medical considerations
Norepinephrine may be injected to over-
Norepinephrine
Glutamate + Pyruvate
Pyruvate family
The family of amino acids derived from pyruvate has four members, each with a simple
Alanine + -ketoglutarate
aliphatic side chain no longer than four carbons. The simplest of these is alanine.
tially toxic amines. This pathway may be particularly important in the brain.
Alanine
Alanine is the amino acid that is most easily
isoleucine.
Glucose-alanine cycle
The glucose-alanine cycle is
Leucine
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an important nitrogen cycle related to the Cori cycle that occurs between muscle and liver cells in the body (see
sis. It is the only amino acid to stimulate muscle protein synthesis, and as a dietary supple642
3-hydroxy-3-methyl-2-oxobutanoate + NADP(P)H
,-dihydroxyisovalerate + NAD(P)+
Loss of water, catalyzed by dihydroxyacid
dehydratase produces -ketoisovalerate.
,-dihydroxyisovalerate
-ketoisovalerate + H2O
This molecule is a branch point for synthesis
of leucine and valine. Addition of an acetyl
group from acetyl-CoA yields isopropylmalate (catalyzed by isopropylmalate synthase).
-acetolactate
3-hydroxy-3-methyl-2-oxobutanoate
-isopropylmalate + CoA-SH
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isopropylmalate.
-isopropylmalate
molecule at the point in the metabolic pathway where synthesis of valine branches from
that of leucine. In fact, -ketoisovalerate is
-isopropylmalate.
Oxidation by isopropylmalate dehydrogenase and
NAD+,
gives -
ketoisocaproate.
-isopropylmalate +
NAD+
-ketoisocaproate + NADH
-ketoisovalerate + Glutamate
Valine + -ketoglutarate
Isoleucine
Transamination of it (catalyzed by leucine
column).
-ketoisocaproate + Glutamate
Leucine + -ketoglutarate
Valine
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-aceto--hydroxybutyrate + Pyruvate
-keto--methylvalerate + Glutamate
,-dihydroxy--methylvalerate + CO2
Isoleucine + -ketoglutarate
,-dihydroxy--methylvalerate
-keto--methylvalerate + 2
ransamination (using glutamate and valine
isoleucine transaminase) yields isoleucine.
as substrates.
Isoleucine has a second asymmetric center
within it, but only one isomeric form of the
four possible ones from the two centers is
found biologically.
645
Regulation of synthesis
balances shifts in favor of production of isoleucine and since isoleucine competes with
valine and leucine for hydroxyethyl-TPP,
synthesis of these two amino acids goes down.
When isoleucine concentration increases,
threonine deaminase is inhibited, shifting
the balance back to production of valine and
leucine.
preventing transcription from terminating prematurely and allowing leucine metabolic enzymes to be made. Thus, leucine levels in
the cell control the synthesis of enzymes necessary to make it.
Histidine family
Synthesis of histidine literally occurs in a
class by itself - there are no other amino acids
Attenuation
Enzyme names
1 = Ribose-phosphate diphosphokinase
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2= ATPphosphoribosyltransferase
3 = Phosphoribosyl-ATP pyrophospohydrolase
4 = Phosphoribosyl-AMP cyclohydrolase
5 = ProFAR-I (N[(5phosphoribosyl)formimino]-5aminoimidazole-4-carboxamide ribonucleotide isomerase)
6 = Imidazole glycerol-phosphate syn-
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Ribose-5-Phosphate + ATP
(1)
PRPP + AMP
PRPP + ATP
(2)
PRATP
Image by Aleia Kim
thase (IGPS)
7 = midazole glycerol-phosphate dehydratase
PRATP
(3)
PRAMP + PPi
8 = Histidinol-phosphate aminotransferase
9 = Histidinol-phosphate phosphatase
10 = Histidinol dehydrogenase
PRAMP
(4)
ProFAR
Abbreviations used
1 - PRPP = Phosphoribosyl Pyrophosphate
2. PRATP = Phosphoribosyl ATP
3. PRAMP = Phosphoribosyl AMP
4. ProFAR = (N-[(5-
ProFAR
(5)
PRFAR
phosphoribosyl)formimino]-5-aminoimidazol
e-4-carboxamide) ribonucleotide
5. PRFAR = (N-[(5phosphoribulosyl)formimino]-5-aminoimidaz
ole-4-carboxamide) ribonucleotide
6. IGP = Imidazole glycerol-phosphate
7. AICAR = 5-phosphoribosyl-4carboximide-5-aminoimidazole
8. IAP = Imidazole acetol-phosphate
9. -KG = -ketoglutarate
PRFAR + Glutamine
(6)
IGP + Glutamate + AICAR
IGP
7
IAP
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IAP + Glutamate
(8)
Histidinol-phosphate + -KG
Histidinol-phosphate
(9)
Histidinol + Pi
Histidinol + 2 NAD+
(10)
Histidine + 2 NADH + 2 H+
Selenocysteine
A cysteine analog commonly referred to as
the 21st amino acid, selenocysteine (Figure 6.163) is an unusual amino acid occasionally found in proteins. Although it is
rare, selenocysteine has been found in proteins in bacteria, archaea and eukaryotes.
In contrast to amino acids such as phosphos-
648
to a selenocysteine.
tion.
nocysteine, such as Semethylselenocysteine, are found in Astragalus, Allium, and Brassica species.
Stop codon
The specifics of the process of translation
will be described elsewhere in the book, but
to get selenocysteine into a protein, the
tRNA carrying selenocysteine pairs with a
stop codon (UGA) in the mRNA in the ribosome. Thus, instead of stopping translation, selenocysteine can incorporated into a
growing protein and translation continues
instead of stopping.
649
tein.
Urea cycle
rated instead.
Pyrrolysine
Like selenocysteine, pyrrolysine is a
rare, unusual, genetically encoded amino
acid found in some cells. Proteins containing it are enzymes involved in methane metabolism and so far have been
found only methanogenic archaeans
and one species of bacterium. The
amino acid is found in the active site
of the enzymes containing it. It is sometimes referred to as the 22nd amino acid.
Synthesis of the amino acid biologically
begins with two lysines. One is converted to (3R)-3-Methyl-D-ornithine,
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thetase I.
fish is one reason that an aquarium periodically requires cleaning and replacement of water.
line.
ducing a molecule of urea. Of the five reactions, three occur in the cytoplasm and two
take place in the mitochondrion. (The reaction making carbamoyl phosphate, catalyzed by carbamoyl phosphate synthetase is not shown in the figure.)
Citrulline + Pi
The citrulline is transported out to the cytoplasm by the ornithine-citrulline anti-
Ornithine synthesis
nate synthase.
proline.
651
652
ger of ammonia.
arginine.
Argininosuccinate
Arginine + Fumarate
the cycle.
Arginine + H2O
Ornithine + Urea
Urea is less toxic than ammonia and is released in the urine. Some organisms make
uric acid for the same reason.
Acetyl-CoA + L-glutamate
It is worth noting that aspartic acid, ammonia, and bicarbonate enter the cycle and fumarate and urea are produced by it. Points
to take away include 1) ammonia is converted to urea using bicarbonate and the
amine from aspartate; 2) aspartate is converted to fumarate which releases more energy than if aspartate were converted to oxaloacetate, since conversion of fumarate to
malate to oxaloacetate in the citric acid cycle generates an NADH, but direct conversion of aspartate to oxaloacetate does not; and
3) glutamate and aspartate are acting as
shuttles to funnel ammonia into the cycle.
CoA-SH + N-acetyl-L-glutamate
At the substrate level, all of the other enzymes
of the urea cycle are controlled by the concentrations of substrates they act upon.
Only at high concentrations are the enzymes
fully utilized.
Complete deficiency of any urea cycle enzyme is fatal at birth, but mutations resulting
in reduced expression of enzymes can have
mixed effects. Since the enzymes are usually
not limiting for these reactions, increasing
substrate can often overcome reduced enzyme
653
Energy generation
Ammonia accumulation
However, if the deficiencies are sufficient, ammonium can accumulate and this can be
quite problematic, especially in the brain,
where mental deficiencies or lethargy can result. Reduction of ammonium concentration
relies on the glutamate dehydrogenase reaction (named for the reverse reaction).
Glutamate +
NADP+
to 2 ATP, the cycle uses 4 ATP. Thus, the cycle either breaks even in the worst case or generates 2 ATPs in the best case.
Glutamine + ADP + Pi
The result of these reactions is that ketoglutarate and glutamate concentrations will be reduced and the concentration of
glutamine will increase. For the brain, this
is a yin/yang situation. Removal of ammonia
is good, but reduction of -ketoglutarate
654
cetate and fumarate. Enzymes involved include 1) tyrosine transaminase; 2) phydroxylphenylpyruvate dioxygenase; 3) homogentisate
dioxygenase; 4) maleylacetoacetate cis-trans-isomerase;
and 5) 4-fumaryl acetoacetate hydrolase.
Breakdown of leucine is a
multi-step process ultimately
yielding the ketone body acetoacetate and acetyl-CoA.
Branched chain amino acids
Figure 6.167 - Results of amino acid catabolism
Tyrosine catabolism
Breakdown of tyrosine (Figure 6.169) is a five step
process that yields acetoa-
655
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656
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Links to their Web pages are below
Urea!
Urea!
Youve just made some urea!
The body handles many things
Requiring its attention
Like balancing aminos for
Uremia prevention
Urea!
Urea!
They call the stuff urea!
Urea!
Urea!
Go out and take a pee, yeah!
Urea!
Urea!
Have yourself a pee, yeah!
658
659
Metabolism: Nucleotides
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660
tion rates.
Pathways of nucleotide metabolism are organized in two major groups and one minor
one. These include, respectively, metabolism
of 1) purines; 2) pyrimidines; and 3) deoxyribonucleotides. Each group can be further subdivided into pathways that make nucleotides from simple precursors (de novo
Ribose-5-phosphate + ATP
0
PRPP + AMP
pathways) and others that use pieces of nucleotides to reassemble full ones (salvage
pathways). Notably, de novo synthesis pathways for all of the nucleotides begin with synthesis of ribonucleotides. Deoxyribonucleotides are made from the ribonucleotides.
661
662
37C), so it has been proposed that it is shuttled directly from PRPP amidotransferase to
GAR synthetase for the next reaction.
ribosylglycinamide formyltransferase,
fGAM + ATP
5
GAR + ADP + Pi
tetrahydrofolate (N10-formyl-THF or
fTHF) by phosphoribosylglycinamide
formyltransferase (GART).
GAR + fTHF
3
fGAR + THF
Next, the double bonded oxygen in the ring is
replaced with an amine in a reaction catalyzed
AIR + HCO36
CAIR + 2H+
Aspartic acid is then added to donate its
amine group and fumarate will be lost in the
reaction that follows this one. The enzyme involved here is phosphoribosyl-
by phosphoribosylformylglycinamidine
synthase (PFAS) that uses glutamine and
produces glutamate. The reaction requires
energy from ATP (top of next column).
663
aminoimidazole-succinocarboxamide syn-
thase (PAICS)
code.
SAICAR
8
AICAR + Fumarate
Reaction #9 involves another formylation reaction, catalyzed by phosphoribosylaminoimidazolecarboxamide formyltransferase (ATICE1).
AICAR + fTHF
9
FAICAR + THF
be in short supply.
FAICAR
10
IMP + H2O
664
carboxamide ribotide
IMP = inosine monophosphate
Adenylosuccinate + GDP + Pi
Regulation
It is worth repeating that synthesis of GMP
Adenylosuccinate
AMP + Fumarate
branch.
5-PRA = 5-phosphoribosylamine
fGAR = Phosphoribosyl-N-
formylglycineamide
THF = Tetrahydrofolate
fTHF = N10-formyl-Tetrahydrofolate
fGAM = 5'Phosphoribosylformylglycinamidine
AIR = 5-Aminoimidazole ribotide
CAIR = 5'-Phosphoribosyl-4-carboxy-5aminoimidazole
SAICAR = Phosphoribosylaminoimidazolesuccinocarboxamide
AICAR = 5-Aminoimidazole-4-carboxamide
ribonucleotide
FAICAR = 5-Formamidoimidazole-4-
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Partial activity
High levels of GMP
and low levels of AMP
would result in PRPP
amidotransferase
being slightly active,
due to the fact GMP
will fill one allosteric
site, but low AMP levels will mean second allosteric site will likely
be unfilled. This lowered (but not completely inhibited) activity of PRPP amidotransferase will allow for limited production of 5PRA and the rest of the
pathway intermediates,
so it will remain active.
Figure 6.174 - The path from IMP (top) to AMP and GMP
Image by Aleia Kim
AMP +H2O
IMP + NH4+
low.
cess or scarcity of any nucleotide of any nucleotide can result in an increased tendency to
Proper balance
mutation.
els can be maintained in a fairly narrow concentration range. Properly balancing nucleotide levels
in cells is critical. It is likely for
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GTP requires action of kinase enzymes. Each monophosphate nucleotide form has its own specific nucleoside monophos-
made.
Other mechanisms
vant reaction.
AMP + ATP
NADPH + GMP
2 ADP
The adenylate kinase reaction is reversible
and is used to generate ATP when the cells
GMP + ATP
GDP + ADP
or guanine to GMP.
Hypoxanthine + PRPP
In going from the diphosphate form to the triphosphate form, the picture is simple - one en-
IMP + PPi
zyme catalyzes the reaction for all diphosphates (ribose and deoxyribose forms). It
is known as nucleoside diphosphate kinase or
(more commonly) NDK or NDPK and it cata-
Guanine + PRPP
GMP + PPi
(d)XTP + (d)YDP
(d)XDP + (d)YTP
where X and Y refer to any base.
phosphoribosyltransferase
668
Adenine + PRPP
AMP + PPi
Medical perspective
Adenine salvage
The enzyme known as adenine phosphori-
Balance
adenine bases.
669
ATCase is a classic enzyme exhibiting allosteric regulation and feedback inhibition, having both homotropic and heterotropic effectors (Figure 6.179 and see
HERE). With 12 subunits (6 regulatory and 6
states - a low activity T-state and a high activity R-state. Binding of the aspartate substrate to the active site shifts the equilibrium in favor of the R-state.
670
671
mitochondrion from the cytoplasm. In reaction 4, dihydroorotate is oxidized to orotate. The enzyme catalyzing the reaction is dihy-
droorotate dehydrogenase.
Dihydroorotate + NAD+
4
Regulation
As was seen with the first enzyme of the pathway, high concentration of purine nucleotides stimulates synthesis of pyrimidines
and high concentration of pyrimidines turns
off the pathway that synthesizes them.
Dihydroorotase catalyzes reaction 3 and is
found in the cytoplasm, as is ATCase.
Orotate + NADH + H+
Reaction #5, catalyzed by orotate phosphoribosyl transferase, involves connection of
orotate to ribose to yield a nucleotide orotidine-5-monophosphate (OMP).
Orotate + PRPP
5
Carbamoyl Aspartate
3
Dihydroorotate + H2O
OMP + PPi
Last, OMP is converted to uridine-5monophosphate (UMP) by action of a fasci-
672
lase.
OMP
tion takes place in 18 milliseconds, a speed increase of about 1017. Remarkably, the enzyme
UMP + CO2
an example for the incredible ability of an enzyme to speed a reaction. The decarboxylation
shown in Figure 6.180. In mammals, the activities of OMP decarboxylase and orotate
phosphoribosyl transferase are contained on the same protein.
A monophosphate kinase (UMP/CMP
kinase) catalyzes conversion of UMP to
UDP.
The same enzyme will also phosphorylate
CMP to CDP and dCMP to dCDP. Like
UMP + ATP
Figure 6.181 - OMP decarboxylase bound to
an OMP analog at the active site
Wikipedia
UDP + ADP
673
UDP + XTP
UTP + XDP
CTP Synthase
UTP is the substrate for synthesis of CTP via
catalysis by CTP synthase.
the reaction of adenylate kinase, the reaction above, when run in the reverse direction,
can be a source of ATP when the cell is low on
energy.
The next step, catalyzed by NDPK, uses energy of any triphosphate nucleotide (XTP) to
produce UTP from UDP.
674
CTP.
CTP is the only nucleotide synthesized de novo directly as a triphosphate, since it arises directly
from UTP. Since deoxyribonu-
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Enzymes of note
675
nucleosides/nucleotides in either
direction if they should get out of balance.
Two other reactions in the figure are
worth mentioning. Both UTP and
CTP are converted in the breakdown
process to UMP and CMP, respectively. Both of these reactions are important for deoxyribonucleotide metabolism. In each case, the monophosphate derivatives are phosphorylated,
creating diphosphate derivatives (UDP
and CDP) that are substrates for RNR
Figure 6.185 - Catabolism and salvage of nucleotides from DNA and RNA
Wikipedia
action 3), apyrase (reaction 4), NDP phosphatase (reaction 5), UMP/CMP kinase
1 = CTP Synthase
2 = NTP Phosphatase
3 = NDPK
4 = Apyrase
5 = NDP Phosphatase
6 = UMP/CMP Kinase
7 = Pyrimidine-specific 5 Nucleotidase
9 = Cytidine Deaminase
10 = Uridine Nucleosidase
counter for the UTP to CTP reaction catalyzed by CTP synthetase. Countered reactions allow cells to balance concentrations of
11 = Uridine Phosphorylase
12 = Uracil Phosphoribosyltransferase
676
NDPK
Deoxyribonucleotide metabolism
677
zyme.
mechanism. Class
containing a large
subunit (known as
in eukaryotes, eu-
or R1) and a
bacteria, bacte-
small subunit
riophages, and
(known as or
R2). The R1
subunit contains
regulatory binding
electron (convert-
to generate a free
radical on a tyro-
R2 subunit houses
a tyrosine residue
in aerobic conditions.
Class II RNRs use 5-deoxyadenosyl cobalamin (vitamin B12) to generate a radical and
work under aerobic or anaerobic conditions. They are found in eubacteria, archaebacteria, and bacteriophages. Class
III RNRs generate a glycine radical using Sadenosyl methionine (SAM) and an ironsulfur center. They work under anaerobic
678
of a suflhydryl in RNR.
679
Regulation
In addition to RNRs unusual
reaction mechanism, the enzyme also has a complex system
of regulation, with two sets of
allosteric binding sites, both
found in the R1 subunit. Because a single enzyme, RNR, is
responsible for the synthesis of
all four deoxyribonucleotides, it is necessary to have
mune system.
Allosteric effectors
enzyme.
In addition to regulation by
deoxyribonucleotides and
hibited by hydroxyurea.
dTTP synthesis
phosphorylated by NDPK
active site.
Students sometimes confuse
the active site of RNR with
tides.
682
ure 6.192.
683
5-fluorouracil
Yet another important inhibitor of thymidine
synthesis is used to treat cancer. This compound, 5-fluorouracil (Fig-
Nucleotides
The multi-component structure of nucleotides, though (base, sugar, phos-
a suicide inhibitor of
thymidylate synthase.
Salvage synthesis
684
Nucleotide catabolism
Besides salvage and being
built into nucleic acids, nucleotides can also be broken
down into simpler component molecules. Some of
these molecules, such as uric
acid, can have significant impact on organisms (see
HERE).
Purine catabolism
Breakdown of purine nucleotides starts with nucleoside
monophosphates, which can
be produced by breakdown of
an RNA, for example, by a nuclease (Figure 6.196).
Metabolism of AMP and
GMP converge at xanthine.
First, AMP is dephosphorylated by nucleotidase to
create adenosine, which is
then deaminated by adenosine deaminase to yield
inosine. Alternatively,
AMP can be deaminated by
AMP deaminase to yield
IMP.
IMP is also an intermediate
in the synthesis pathway for
Figure 6.196 - Catabolism of purines - part I
Image by Pehr Jacobson
purine anabolism.
Dephosphorylation of
685
xanthine oxidase.
Hypoxanthine + H2O + O2
Xanthine oxidase enters the picture a second time in the next reaction catalyzing a second reaction by a similar mechanism to the
Xanthine + H2O2
Uric acid can be excreted into the urine (in humans) or broken down into allantoin by the
uricase enzyme. Since humans lack the en-
Xanthine + H2O + O2
Uric acid
Uric acid is problematic in some higher organisms (including humans) because it is not
very soluble in water. Consequently it precipitates out of solution, forming crystals (Figure
6.198). Those crystals can accumulate in
joints and (frequently) in the big toe. Such a
condition is known as gout.
Wikipedia
acid.
Pyrimidine catabolism
Catabolism of uridine and thymidine nucleotides is shown above (Figure 6.200).
Catabolism of cytidine nucleotides pro-
687
-alanine is a rate-limiting precursor of carnosine, a dipeptide of histidine and alanine (Figure 6.201). Carnosine
functions as an antioxidant that
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Hydrolysis of both these intermediates yields ammonium ion and carbon dioxide (which are made into urea) plus 3aminoisobutyrate for the thymine path-
688
Sugars
Last, but not least, the sugars ribose and deoxyribose can be recycled (ribose) or catabolized (ribose and deoxyribose). In the case of
ribose, it can be reattached to bases by phos-
phorylase enzymes, such as uridine phosphorylase, or converted into PRPP for the
same purpose, to create nucleosides.
Ribose-5-phosphate is an intermediate in
the pentose phosphate pathway, allowing
it to be converted into other sugars or broken down in glycolysis.
Deoxyribose-5-phosphate can be broken
into two pieces by deoxyribose-5-phosphate
aldolase. The products of this reaction are
glyceraldehyde-3-phosphate and acetaldehyde. The former can be oxidized in glycolysis and the latter can be converted into
acetyl-CoA for further metabolism.
689
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Deoxynucleotides
(to the tune of "Ticket to Ride")
Metabolic Melodies Website HERE
Deoxynucleoti - ides
Thats what the enzyme provi-i-ides
Deoxynucleotides
Are on the way
Oh deoxynucleotides
Deoxynucleoti-i-ides
Deoxynucleotides
Give B-forms
That oxygens gone
That oxygens gone
That oxygens gone
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7
Information
Processing
Man cannot discover new oceans unless he has the courage to lose sight
of the shore.
-Andre Gide
693
The nature of this information, how it is copied and passed on, how it is read and interpreted, and how it gives rise to the cellular ac-
694
Introduction
Genomes
We use the word genome to describe all of
the genetic material of the cell. That
formation passed on from one generation to the next? Key experiments, done between the 1920s
and the 1950s, established con-
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vincingly that this genetic information was carried by DNA. In 1953, with the
elucidation of the structure of DNA, it was pos-
695
like mitochondria
and chloroplasts
positories, so that it is
chondrial or chloro-
bioinformatics have
scientists began to determine the complete sequence of the genomes of many organisms, in the hope of better understanding how the
696
Genes
697
eration.
Matters of size
A common-sense assumption about genomes would be that if
genes specify proteins,
then the more proteins
an organism made, the
more genes it would
need to have, and thus,
the larger its genome
would be. Comparison
of various genomes
shows, surprisingly, that
there is not necessarily a
Introns
698
Other non-coding
sequences
What other kinds of non-coding se-
YouTube Lectures
by Kevin
HERE & HERE
Transposable sequences
ate.
699
we understand more about genomes, it is becoming evident that the so-called junk DNA
is anything but.
700
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Transposon
To the tune of Delta Dawn
Metabolic Melodies Website HERE
Trans-po-son
All that movin' hither yon
Youre insertin' yourself in the chromosomes
I guessits why they say
Yourethe jumpin' DNA
Movinand affectin' proteomes
Transposon
All thebattle lines are gone
Over mechanismsBarbara did surmise
It's good the truth came out
There willnever be a doubt
She truly did deserve the Nobel prize
Transposon
All thebattle lines are gone
Over mechanismsBarbara did surmise
It's good the truth came out
There willnever be a doubt
She truly did deserve the Nobel prize
Lyrics by Kevin Ahern
No Recording Yet For This Song
Copying instructions
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by Kevin
HERE & HERE
703
Building materials
What are the ingredients necessary for building a new DNA
molecule? As noted above, the
original, or parental DNA molecule serves as the template.
New DNA molecules are assembled across from each template
by joining together free DNA
nucleotides as directed by the
base pairing rules, with As
across from Ts and Gs across
from Cs.
704
cleotides.
Challenges
705
bacteria, yeast, and other systems. These investigations have revealed that DNA replication is carried out by the action of a large number of proteins that act together as a complex protein machine. Numerous proteins involved in replication have been identified and
characterized, including multiple different
DNA polymerases in both prokaryotes
and eukaryotes. Although the specific proteins involved are different in bacteria and
eukaryotes, it is useful to understand the basic
considerations that are relevant in all cells. A
generalized account of the steps in DNA replication is presented below, focused on the challenges mentioned above.
The sheer number of nucleotides to be copied is enormous: e.g., in human cells, on the
order of several billions.
Figure 7.11 - Replication of
DNA
Wikipedia
placed with DNA nucleotides and the resulting DNA fragments must be joined.
The copying of all the parental DNA must
be accurate, so that mutations are not introduced into the newly made DNA..
Addressing challenges
With this in mind, we can begin to examine
how cells deal with each of these challenges.
Our understanding of the process of DNA
706
707
(Figure 7.15).
Unwinding
Once a small
region of the
DNA is
opened up at
each origin
of replication, the
DNA helix
Figure 7.16 - Multiple replication bubble on a eukaryotic chromosome
Image by Martha Baker
helicase.
YouTube Lectures
by Kevin
HERE & HERE
708
Figure 7.17 - View of a eukaryotic DNA replication fork with helicase shown in
blue
Wikipedia
stranded template.
Topoisomerases
The reason this is problematic is that it is not
possible to rotate the entire length of a chromosome, with its millions of base-pairs, as
the DNA at the replication fork is unwound.
How, then, is this problem solved? Enzymes
called topoisomerases can relieve the topological stress caused by local unwinding of
709
Single-strand DNA
binding protein
Once the two strands of
the parental DNA molecule are separated, they
must be prevented from
going back together to
form double-stranded
DNA. To ensure that unwound regions of the parental DNA remain singlestranded and available for
copying, the separated
strands of the parental
DNA are bound by many
molecules of a protein
called single-strand
DNA binding protein
Figure 7.18 - Proteins at a prokaryotic DNA replication fork
Image by Martha Baker
710
lymerase can add the first new DNA nucleotide (Figure 7.12).
Sliding clamp
Once a primer provides a free 3'OH for extension, other proteins get into the act. These
proteins are involved in loading the DNA polymerase onto the primed template and keeping it associated with the DNA. The first of
Figure 7.19 - Top view of the sliding
clamp (outside) surrounding DNA
strand (inside)
these is the clamp loader. As its name suggests, the clamp loader helps to load a protein
complex called the sliding clamp onto the
DNA at the replication fork (Figure 7.19 and
711
ribonucleotide,
complementary to the template, is added onto
the 3' end of the previous nucleotide, starting
with the 3'OH on the end of the RNA primer.
The importance of the 3OH group lies in the
nature of the reaction that builds a chain of nucleotides.
staying associated with the template for a long time before dissociating is known as the processivity of the enzyme. In the pres-
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by Kevin
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incoming deoxy-
712
Leading strand
We know that DNA polymerases can only build
a new DNA strand in the 5'
to 3' direction. We also
Figure 7.22 - Bidirectional DNA replication with template
strand (a), leading strand (b), Okazaki fragments (c),
replication fork (d), RNA primer (e), and DNA extended
RNA primers (f)
Wikipedia
leading strand can be synthesized continuously in the 5' to 3' direction because it is being made in the same direction that the replication fork is opening up.
Lagging strand
The synthesis of the other new strand, called
the lagging strand, also proceeds in the 5 to
3 direction. But because the template strands
are running in opposite directions, the lagging
strand is being extended in the direction opposite to the opening of the replication fork
(Figure 7.22). As the replication fork opens
up, the region behind the original start point
for the lagging strand will need to be copied.
This means another RNA primer must be
laid down and extended. This process repeats
713
Primer removal
We have seen that each newly synthesized
piece of DNA starts out with an RNA primer,
ever, the end of one Okazaki fragment is adjacent to the RNA primer at the beginning of
the next Okazaki fragment. DNA polymerase
I has an exonuclease activity acting in the 5
to 3 direction that removes the RNA nucleotides ahead of it, while the polymerase activity
replaces the RNA nucleotides with dNTPs.
Once all the RNA nucleotides have been re-
714
still remains.
Ensuring accuracy in the copying of so much
information
Accuracy
How accurate is the copying of information
by DNA polymerase? As you are aware,
changes in DNA sequence (mutations)
can change the amino acid sequence of
the encoded proteins and that this is often, though not always, deleterious to the
functioning of the organism. When billions
of bases in DNA are copied during replication, how do cells ensure that the newly synthesized DNA is a faithful copy of the original information?
DNA polymerases, as we have noted earlier work fast (averaging 50 bases a second
in human cells and up to 200 times faster
in E. coli). Yet, both human and bacterial
cells seem to replicate their DNA quite accurately. This is because replicative DNA polymerases have a proofreading function
that enables the polymerase to detect when
the wrong base has been inserted across
from a template strand, back up and remove the mistakenly inserted base, before
continuing with synthesis (Figure 7.24).
Figure 7.24 - Error corrected by DNA
polymerases
Multiple activities
This is possible because most DNA po-
715
tivity.
Eukaryotic polymerases
ity inserts the correct base and proceeds with extending the strand.
In other words, the DNA po-
DNA polymerases
As noted earlier, both prokaryotic and eukaryotic cells have
multiple DNA polymerases. In
E.coli, for example, DNA po-
716
The enzyme alternates between its polymerizing activity and its proofreading activity.
717
Termination of replication
718
Telomeres
What effect does the loss of sequence from the
ends of the chromosomes have on cells? We
know that the ends of chromosomes are characterized by structures called telomeres (Figure 7.28). Telomeres are made up of many
copies of short repeated sequences (in humans, the repeat is TTAGGG) and special proteins that specifically bind to these sequences.
720
YouTube Lectures
by Kevin
HERE & HERE
Telomerase
feat.
721
RNA template
mere sequence.
Wikipedia
722
Figure 7.32 - Growing telomeres with telomerase and DNA polymerase. First,
the 3 end of the template is extended by telomerase, then DNA polymerase
completes synthesis of the lagging strand
Wikipedia
723
tone cores to make nucleosomes. The nucleosome structure must be disrupted to make
DNA available for replication and restored after replica-
monitors the
tion is com-
accuracy of
pleted (Fig-
DNA replica-
ure 7.33).
Ahead of the
lomerase
replication
keeps chromo-
fork, chroma-
somes that
tin structure is
will be passed
disassembled
on to off-
by ATP-
spring from
dependent
shortening.
chromatin re-
Between
modeling com-
them, these
two activities
ensure that
the genetic in-
new nucleosomes must be reassembled behind the replication fork. Since replication
724
725
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Complementary Bases
To the tune of California Dreamin
Metabolic Melodies Website HERE
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by Kevin
HERE & HERE
DNA damage
All DNA suffers damage over
time, from exposure to ultraviolet
and other radiation, as well as
from various chemicals in the environment (Figures 7.34 & 7.35). Even chemical
reactions naturally occurring within cells can
give rise to compounds that can damage DNA.
As you already know, even minor changes in
729
Distinguishing
strands
Importantly, the
mismatch repair
system must have a
means to distinguish the newly
730
an exonuclease that help unwind and remove the region containing the mismatch.
731
732
YouTube Lectures
by Kevin
HERE & HERE
larly.)
733
Types of damage
to DNA.
change the physical structure of the DNA helix, but they can cause problems because ura-
cytosine.
Removing damage
strands.
734
Suicide enzyme
O6-methylguanine in DNA can also be removed by direct reversal, with the help of the
enzyme O6-methylguanine methyltransferase. This is a very unusual enzyme that
removes the methyl group from the guanine
and transfers it onto a cysteine residue in the
enzyme. The addition of the methyl group
to the cysteine renders the enzyme nonfunctional.
As you know, most enzymes are catalysts
that remain unchanged over the course of the
reaction, permitting a single enzyme molecule
to repeatedly catalyze a reaction. Because the
O6-methylguanine methyltransferase
does not fit this description, it is sometimes
not regarded as a true enzyme. It has also
been called a suicide enzyme, because the enzyme dies as a result of its own activity.
Excision repair
Excision repair is another common strategy.
Figure 7.41- Direct repair of thymine
dimers by photolyase
Pehr Jacobsen
Excision repair is a general term for the cutting out and re-synthesizing of the damaged
region of a DNA. There are several different
735
736
tein.
Strand nicking
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by Kevin
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737
Uracil-DNA glycosylase
Repair of double-strand
breaks
While all the repair mechanisms discussed so far fixed damage on one
strand of DNA using the other, undamaged strand as a template,
these mechanisms cannot repair damage to both strands. What happens if
both strands are damaged? Ionizing
radiation, exposure to certain chemicals, or reactive oxygen species generated in the cell can lead to doublestrand breaks (DSBs) in DNA.
Figure 7.44 - Base excision repair by uracil-DNA
glycosylase. The yellow uracil base has been
flipped out of the DNA helix for excision
738
739
740
chromatid.
Nuclease action
741
mode, ignoring the template and incorporating random nucleotides into the new strand.
suffer extensive damage to their DNA as a result of UV exposure, they turn on the coordinated expression of a large number of genes
that are necessary for DNA repair. These include the uvr genes needed for nucleotide
excision repair and recA, which is involved
in homologous recombination. In addition to these mechanisms, which can carry out
error-free repair, the SOS response can also
induce the expression of translesion polymerases encoded by the dinA, dinB and
umuCD genes.
How are all these genes induced in a coordi742
prevents transcription of the downstream genes. Expression of the genes requires the removal of LexA from its binding
for accurate DNA repair as well as errorprone translesion synthesis. The various
743
744
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Mismatch Site
To the tune of Silent Night
Metabolic Melodies Website HERE
Information flow
747
tion in DNA.
748
tion!). Yet, we
But, apart
from copying
one, rather
ball of a trillion
than both
strands of
DNA, how is
ferent kinds of
transcrip-
tion differ-
lication of
DNA? DNA
replication
have identical
DNA turn out so
different?
The answer lies in gene expression, which
is the process by which the information in
DNA is used. Although all the cells in a baby
have the same DNA, each different cell type
uses a different subset of the genes in that
DNA to direct the synthesis of a distinctive
set of RNAs and proteins. The first step in
gene expression is transcription, which we
will examine next (Figure 7.52).
Transcription
Transcription is the process of copying information from DNA sequences into RNA se-
Wikipedia
serves to
copy all the
genetic material of the
quences. This process is also known as DNAdependent RNA synthesis. When a sequence
of DNA is transcribed, only one of the two
DNA strands is copied into RNA. We will con-
RNA synthesis
Like DNA polymerases,
RNA polymerases synthesize new strands only
in the 5' to 3' direction,
but because they are making RNA, they use ribonuFigure 7.54 - The four ribonucleotides for making RNA
750
phodiester bond.
One important difference between DNA polymerases and RNA polymerases is that
the latter do not require a primer to start
making RNA. Once RNA polymerases are in
the right place to start copying DNA, they just
begin making RNA by joining together RNA
nucleotides complementary to the DNA template.
Starting points
This, of course, brings us to an obvious question- how do RNA polymerases "know" where
to start copying on the DNA?
Unlike the situation in replication, where
every nucleotide of the parental DNA must
eventually be copied, transcription, as we
have already noted, only copies selected portions of the DNA into RNA at any given time.
Consider the challenge here: in a human cell,
Promoters
It turns out that patterns in the DNA sequence indicate where RNA polymerase
should start and end transcription. These
sequences are recognized by the RNA polymerase or by proteins that help RNA polymerase determine where it should bind the
DNA to start transcription. A DNA sequence
at which the RNA polymerase binds to start
transcription is called a promoter. The DNA
sequence that indicates the endpoint of transcription, where the RNA polymerase should
stop adding nucleotides and dissociate from
the template is known as a terminator sequence. The promoter and terminator,
thus, bracket the region of the DNA that is to
be transcribed.
751
moters.
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by Kevin
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pressed.
A -10 sequence: this is a 6 bp region cenWhat is special about a promoter sequence?
752
-10 Sequence
T
77%
A
76%
T
60%
A
61%
56%
82%
-35 Sequence
T
69%
T
70%
61%
56%
54%
54%
It is important to understand that each nucleotide in a consensus sequence is simply the one
that appeared at that position in the majority
of promoters examined, and does not mean
that the entire consensus sequence is found in
all promoters. In fact, few promoters have -10
and -35 sequences that exactly match the con-
753
Loose association
Holoenzyme binding
able to bind specifically to promoter sequences. The initial binding of the holoen754
and dissociate from the template. Some terminator sequences, known as intrinsic termi-
Elongation
core polymerase can move along the template, unwinding the DNA ahead of it to main-
Termination
As mentioned earlier, a sequence of nucleotides called the terminator is the signal to
Intrinsic terminators
In intrinsic terminators, this sequence in
the RNA has self-complementary regions that
can base-pair with each other to form a hairpin structure that contains a GC-rich run in
the stem of the hairpin. This hairpin is fol-
755
RNA polymerase.
Rho-dependent termination
dependent termination requires the formation of a hairpin structure in the RNA that
causes pausing of the RNA polymerase.
Meanwhile, rho binds to a region of the transcript called the rho utilization site (rut) and
moves along the RNA till it reaches the
paused RNA polymerase. It then acts on the
RNA-DNA hybrid, releasing the transcript
from the template.
plate, while the 3 end of the gene is still being copied. The lag time between transcrip-
Wikipedia
756
Transcription in
eukaryotes
Although the process of RNA synthesis is the same in eukaryotes as in prokaryotes, there are
some additional considerations in
eukaryotes. One is that in
eukaryotes, the DNA template exists as chromatin, where the
DNA is tightly associated with histones and other proteins. The
"packaging" of the DNA must
therefore be opened up to allow
the RNA polymerase access to
the template in the region to be
YouTube Lectures
by Kevin
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All three eukaryotic RNA polymerases need additional proteins to help them get transcription started. In prokaryotes, RNA
factors.
757
Eukaryotic promoters
Like genes in prokaryotes, eukaryotic
genes also have promoters that determine
where transcription will begin. As with prokaryotes, there are specific sequences in the
promoter regions that are recognized and
bound by proteins involved in the initiation
of transcription. We will focus primarily on
the genes encoding proteins that are transcribed by RNA polymerase II. Such promoters commonly have a TATA box, a sequence similar to the -10 sequence in prokaryotic promoters. The TATA box is a sequence about 25-35 basepairs upstream of the
start of transcription (+1). (Some eukaryotic
promoters lack TATA boxes, and have, instead, other recognition sequences, known as
DPE, or downstream promoter elements.) Interestingly, the TATA box is not
directly recognized and bound by RNA polymerase II. Instead, this sequence is bound
by other proteins that, together with the RNA
polymerase, form the transcription initiation complex.
Eukaryotic promoters also have, in addition,
several other short stretches of sequences,
that affect transcription, within about 100
to 200 base-pairs upstream of the transcription start site. These sequences, which are
sometimes called upstream elements or
Figure 7.64 - Region surrounding the transcriptional start site in eukaryotic DNA
758
(Figure 7.64).
sis are termed general transcription factors. We will focus on the transcription factors that assist RNA po-
Wikipedia
is suitable for the binding of additional transcription factors and RNA polymerase.
scription factors).
759
up a DNA double helix) as well as kinase activity. The kinase activity of TFIIH adds
phosphates onto the C-terminal domain
(CTD) of the RNA polymerase II. This
760
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by Kevin
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761
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
763
Transcription
To the tune of "Frosty the Snowman"
Metabolic Melodies Website HERE
Phos-pho-di-esters
Are the bonds of RNA
That support a ribopolymer
Made of G,C,U and A
IN-i-ti-a-tion
Of transcription thus proceeds
From the closed to open complexing
In the DNA it reads
In elongation
The polymerizing spree
Moves along the way in fits and starts
Synthesizing five to three
Then termination
Fin-ish-ES the RNAs
Thanks to protein rho or hairpin forms
That release polymerase
764
Chromatin
To the tune of Sunshine on My Shoulders
Metabolic Melodies Website HERE
765
mRNA processing
The major difference in RNA
processing, however, between
prokaryotes and eukaryotes,
is in the processing of messenger
766
Capping
As might be expected, the addition of
767
Intron removal
nounced snurps).
end of the mRNA from degradation by nucleases and also helps to position the mRNA cor-
Splice junctions
thesis.
Splicing
Interactive Learning
Module
HERE
quence at the 5 exon-intron junction (also called the 5 splice site) is AG768
Spliceosome
cleotide).
Splicing mechanism
There are two main steps in splicing. The
first step is the nucleophilic attack by the
769
scribed earlier.
Alternative splicing
branch site.
relatively few genes, since a single RNA with many exons can,
by combining different exons dur-
Figure 7.72 - Alternative splicing leads to different forms of a protein from the
same gene sequence
template-independent enzyme,
Polyadenylation
The 3' end of a processed
eukaryotic mRNA typically
has a poly(A) tail consisting of about 200
adenine-containing nu-
771
lated.
tion machinery have been shown to be associated with the CTD of the RNA po-
RNA editing
(Figure 7.73).
Interactive Learning
Module
HERE
the edited transcript is translated. It is interesting that the editing of this transcript occurs
772
tRNA synthesis
& processing
tRNAs are synthesized by RNA polymerase III,
which makes precurFigure 7.75 - Template guided - one mechanism of RNA editing
Insertion/deletion
Another kind of RNA editing involves the insertion or deletion of one or more nucleotides. One example of this sort of editing is
seen in the mitochondrial RNAs of trypanosomes. Small guide RNAs indicate the sites at
which nucleotides are inserted or deleted to
produce the mRNA that is eventually translated (Figure 7.75).
773
and numerous proteins. The 3 trailer sequence (extra nucleotides at the 3 end of
Introns
As mentioned earlier, some tRNA precursors
contain an intron located in the anticodon
arm. In eukaryotes, this intron is typically
found immediately 3 to the anticodon. The
introns is spliced out with the help of a tRNA
splicing endonuclease and a ligase.
Base modifications
Mature tRNAs contain a high proportion of
bases other than the usual adenine (A), guanine (G), cytidine (C) and uracil (U).
Figure 7.78 - Sequence of a mature tRNA
Wikipedia
These unusual bases are produced by modifying the bases in the tRNA to form variants,
774
YouTube Lectures
by Kevin
HERE & HERE
28S rRNA, and is transcribed by RNA polymerase I into a single long transcript
(47S). The 5S rRNA is separately transcribed.
775
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
777
the ribosome.
YouTube Lectures
by Kevin
HERE & HERE
778
779
them.
tifiers for each airport and people who can decode the identifiers correctly. That is, PDX
Degeneracy
nix, instead.
they encode?
780
protein synthesis.
How do these tRNAs, carrying specific amino acids assist the ribosome
in stringing together the
correct amino acids, as
specified by the sequence
of the mRNA?
Codon recognition
Figure 7.84 - Charging of a tRNA by aminoacyl tRNA
synthetase
some.
t-RNA specificity
A given transfer RNA is specific for a par-
782
5 CCA 3
priate charged tRNAs. The amino acid tryptophan, as we noted, is specified by the codon
UGG in the mRNA. This codon must
YouTube Lectures
by Kevin
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5 UGG 3
3 ACC 5
Figure 7.85 - Codons in mRNA pair with anticodons on tRNA to bring the
appropriate amino acid to the ribosome for polypeptide assembly
783
(Figure 7.86).
Making a polypeptide
With an idea of the various components necessary for translation and how they work, we can
Interactive Learning
Module
HERE
action be-
second tRNA
carrying the
dons in the
dipeptide (and
mRNA and
the codon it
the antico-
is base paired
dons on
charged
tRNAs.
the P-site.
Ribosomes
now is ready
(P-site and
A-site) for
binding and
The A-site
next incoming
charged tRNA.
784
rRNA
Name
Prokaryotes
Eukaryotes
Function
5S
5.8S
16S
tRNA binding?
Large Subunit
Translocation?
Small Subunit
18S
23S
mRNA alignment
Large Subunit
Large Subunit
28S
mRNA alignment
Peptide bond formation
Large Subunit
Three steps
Having considered the steps of translation
in broader terms, we can now look at them in
greater detail. We will consider the three
steps of translation (bel0w) individually.
785
Initiation
Initiator tRNA
Initiation also requires the binding of the first
tRNA to the ribosome. As we have noted earlier, the initiation, or start codon is usually
AUG, which codes for the amino acid methionine. Thus, the initiator tRNA is one that
carries methionine and is designated as
tRNAmet or methionyl tRNAmet. In bacteria,
the methionine on the initiator tRNA is
modified by the addition of a formyl group,
and is designated tRNAfmet. The initiator
tRNA carrying methionine to the AUG is different from the tRNAs that carry methionine
786
Shine-Dalgarno sequence
Examination of the sequences upstream of the
start codon in prokaryotic mRNAs reveals
that there is a short purine-rich sequence
ahead of the start codon that is crucial to recognition and binding by the small ribosomal subunit (Figure 7.89). This sequence, called the Shine-Dalgarno sequence, is complementary to a stretch of pyrimidines at the 3 end of the 16S rRNA component of the small ribosomal subunit
Movie 7.2 - Large ribosomal subunit
Wikipedia
ferred to as tRNAimet.
site.
Prokaryotic initiation
Initiation factors
the messenger
RNA in order to
initiate translation. How does
the ribosome
know exactly
where to bind in
the 5UTR of the
mRNA?
787
Eukaryotic initiation
In eukaryotes, initiation follows a similar
pattern, although the order of
YouTube Lectures
by Kevin
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788
Kozak
sequences
Specific sequences
surrounding the
AUG, called Kozak
sequences for the
scientist who defined them, have
been shown to be
necessary for the
Figure 7.92 - Kozak sequence plot showing relative abundance of
bases surrounding the AUG (ATG) start codon of human genes
IFs that are known as eIFs (eukaryotic initiation factors). These initiation factors are in-
Ribosome assembly
The assembly of the translation machinery in
eukaryotes begins with the binding of the
initiator tRNA to the 40S (small)
subunit. This step requires the assistance of
eIF2 and eIF3. Next the small subunit with
the initiator tRNA binds to the 7-methyl G
cap on the 5'end of the mRNA. The 40S
subunit then moves along the mRNA, scanning for a a start codon. Binding of the ribosomal subunit to the mRNA is dependent not
just on finding an AUG, but on the sequences
surrounding the codon.
789
Elongation
After the ribosome is assembled with the initiator
tRNA positioned at the
AUG in the P-site, the addition of further amino acids
can begin. In both prokaryotes and eukaryotes,
the elongation of the
polypeptide chain requires
the assistance of elongation
factors. In bacteria, the binding of the second charged
tRNA at the A-site requires
the elongation factor EF-Tu
complexed with GTP (Figure 7.93). When the
charged tRNA has been
loaded at the A-site, EF-Tu
hydrolyzes the GTP to GDP
and dissociates from the ribosome. The free EF-Tu
can then work with another
charged tRNA to help position it at the A-site (Figure
7.94), after exchanging its
790
along the mRNA in bacteria, while in eukaryotes, this role is played by eEF2.GTP. Repeated cycles of these steps result in the elon-
Wikipedia
is in the A-site.
Termination
When a stop codon is in the A-
Interactive Learning
Module
HERE
the stop codon and cleave and release the newly made polypeptide.
In bacteria, RF1 is a release factor that can
recognize the stop codon UAG, while RF2 rec-
Ribozyme
791
792
Delivery
Each of the thousands of
proteins made in the cytoFigure 7.97 - Another perspective of translation. The 3
end of the mRNA is on the left and the ribosome is moving
from right to left
Polypeptide processing
What happens to the newly synthesized
polypeptide after it is released from the ribosome? As you know, functional proteins
are not simply strings of amino acids. The
polypeptide must fold properly in order to
perform its function in the cell. It may also undergo a variety of modifications such as the addition of phosphate groups, sugars, lipids,
etc. Some proteins are produced as inactive
precursors that must be cleaved by proteases to be functional.
An additional challenge in eukaryotic cells is
the presence of internal, membrane-bounded
compartments. Each compartment contains
different proteins with different functions.
793
ments post-translationally. But, with the exception of cytosolic proteins, all proteins must
cross membrane barriers, through membrane
channels or other "gates", or by transport
within membrane vesicles that fuse with the
membrane of the target organelle to deliver
their contents.
cell.
Proper folding may also involve the interaction of regions of the polypeptide that are
distant from each other, so that por-
YouTube Lectures
by Kevin
HERE & HERE
794
cule.
Protein sorting
sent?
795
Signal sequences
bels".
Signal se-
in the mem-
quences may
branes of these
be found at the
organelles, to
N-terminal or
be folded at
Figure 7.100 - N-terminal signal sequence (green) emerging from the ribosome.
may be within
their destination.
Proteins that
amino acids.
brane.
the ER lumen.
797
798
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Translation
To the tune of Maria (from West Side Story)
Metabolic Melodies Website HERE
Translation
The most intricate thing I ever saw
From five prime to three prime, translation, translation
The final step that we know about the central dog-ma
Amino, carboxyl, translation, translation. . . .
Translation, translation, translation . .
Translation!
800
Elongation happens in
Ribosomic insides
Where rRNA creates
Bonds for polypeptides
801
YouTube Lectures
by Kevin
HERE & HERE
meet their changing needs. Regulating gene expression is, therefore, crucial. Given that there are
multiple steps involved in gene ex-
802
(sequences of DNA
on the same DNA
DNA sequences and bind to them. The binding of such proteins to the DNA can regulate
Regulation of transcription
Transcriptional regulation in
prokaryotes
Let us first consider some examples from prokaryotes. In bacteria, genes are often clustered in groups, such that genes that need to
be expressed at the same time are next to each
other and all of them are controlled as a single
unit by the same promoter. Groups of genes
that are coordinately regulated by a single promoter are referred to as operons. The entire
set of genes in an operon can be controlled
through the action of DNA binding proteins
803
Interactive Learning
Module
HERE
Removing a repressor
804
allolactose
(Figure
805
cAMP binding
CAP binds to its site only when glucose levWhat makes this an especially effective con-
of lactose. Turning on
these genes requires lactose to be present. Once
the lactose has been broken down, the lac repressor binds to the operator once more and
the lac genes are no
longer expressed. This
allows the genes to be
expressed only when
they are needed.
Recruiting RNA
polymerase
But how do glucose lev-
806
YouTube Lectures
by Kevin
HERE & HERE
RNA polymerase
transcribes the downstream genes.
807
Attenuation
Another mechanism that
regulates the expression
of the trp operon is attenuation. Attenuation is a process by
which the expression of
an operon is controlled
by termination of
transcription before
the first gene of the
operon (Figure 7.111).
In the trp operon, this
functions as follows:
Transcription begins
some distance upstream
of the first gene in the
operon, producing what
is termed a 5 leader sequence. This leader sequence contains an inFigure 7.111 - Attenuation in regulation of the trp operon
Wikipedia
trinsic terminator
that can form a hairpin
structure that stops tran-
XX AUG AAA GCA AUU UUC GUA CUG AAA GGU UGG UGG CGC ACU UCC UGA -XX
MET LYS ALA ILE PHE VAL LEU LYS GLY TRP TRP ARG THR SER STOP
808
operon.
Riboswitches
Features
Riboswitches have two characteristic
features that are important for their
function. One is a region of the sequence called an aptamer, which
folds into a three-dimensional shape
Figure 7.113 - Riboswitch features
809
to the effector.
expressed as needed.
Regulation of transcription in
eukaryotes
810
Figure 7.115 - DNA looping allows contact between activator bound at a distant
enhancer and the basal transcription complex
Image by Martha Baker
transcription?
Transcriptional activators
Distant regulatory sequences
811
YouTube Lectures
by Kevin
HERE & HERE
Silencers
In addition to enhancers, there
are also negative regulatory se-
812
factors that combine the DNA binding domain of one activator with the
activation domain of another. Such
proteins retain the specificity dictated
duce transcription.
813
natorial nature of
such regulation provides great versatility, with different
combinations of
regulatory elements
and proteins working together in response to a wide variety of conditions
and signals.
The mechanisms described so far have
focused on the seFigure 7.119 - Transcriptional activation (right) and deactivation
(left) by histone modification
Wikipedia
quence elements in
DNA that regulate
transcription
through the activa-
Following transcription, alternative splicing (see HERE) and editing of the transcripts
Multiple factors
is modulated in cells.
repressor to a particular enhancer or silencer site. However, it turns out that the
transcription of any given gene may be simultaneously regulated by a combination of
proteins, both activators and repressors,
bound at multiple regulatory sites on the
DNA, all of which interact with the transcription initiation complex. The combi-
First, we will consider some so-called epigenetic mechanisms that affect gene expression.
The term epigenetics derives from epi (above,
or on top of) and genetic (of genes) and refers
to the fact that these mechanisms act in addition to, or overlaid on, the information in the
gene sequences. Two such epigenetic mechanisms are the covalent modifications of his-
814
DNA sequences.
Histone modification
Interactive Learning
Module
HERE
enzyme is histone acetyl transferase (HAT) that works to acetylate specific amino acid residues in
The opposite effect may be achieved if the enzymes recruited are histone deacetylases
815
DNA methylation
Gene expression can also
be regulated by methyla-
tin.
sion.
Regulatory RNAs
One of the most unexpected discoveries in the
817
Small regulatory
RNAs
MicroRNAs (miRNAs)
818
stranded RNAs.
complex.
RISC assembly
819
and siRNAs are, at this point doublestranded. One strand of the RNA is referred
to as the guide RNA, while the other is called
the passenger RNA.
sion of translation of the mRNA (for miRNAs). The extent to which these processes
Regulation of translation
gene regulation.
820
fore, be regulated
YouTube Lectures
by Kevin
HERE & HERE
by mechanisms
of mRNA degrada-
tion. Regulation of
translation is used to control the production
of many proteins. Two examples, ferritin
and the transferrin receptor, are important for iron storage and transport in cells.
Ferritin is an iron-binding protein that sequesters iron atoms in cells to keep them from reacting. When iron levels are high, there is a
need for more ferritin than when iron levels
a 28-nucleotide se-
script (Figure
IRE-binding pro-
the IRE-binding
IRE-binding protein,
which dissociates
blocks translation of
ceptible to attack by
RNases, leading to
Figure 7.127 -Regulation of ferritin mRNA
translation
Image by Aleia Kim
degradation of the
transferrin receptor
821
Gene expression is
controlled at many
steps
As can be seen from the examples in this section, regulation of gene expression in
eukaryotic cells is a function of multiple mechanisms
that act at different stages in
the flow of information from
DNA to protein, responding to the internal state of
the cell as well as external
conditions and signals.
822
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
All information in
Cells DNA
Just increases
With pieces
Mixed and matched in the mRNAs
Linking exons
All together
Using snurps in
Complex-ES
God bless the spliceosomes
And trans-crip-tomes
(slow and loud) God bless the spliceosomes
And my ge-nome
Instrumental
Pyrimidines
Paired to purines
The book of life
Cellular communication
among themselves.
Coordination
Since different cells take on specialized functions in a multicellular organism, they must
be able to coordinate activities. Cells grow, divide, or differentiate in response to specific
YouTube Lectures
by Kevin
HERE & HERE
826
Signal properties
The chemical properties of the signal determine whether its receptors are on the
cell surface or intracellular. If the signal is small and hydrophobic it can
cross the cell membrane and bind a
receptor inside the cell. If, on the other
hand, the signal is charged, or very
large, it would not be able to diffuse
through the plasma membrane.
Such signals need receptors on the cell
surface, typically transmembrane
Figure 7.129 - Some examples of signal molecules
proteins that have an extracellular portion that binds the signal and an intra-
827
cells have different sets of receptors, they respond to different signals or combinations of
signals. The binding of a signal molecule to a
receptor sets off a chain of events in the target
cell. These events could cause change in various ways, including, but not limited to, alterations in metabolic pathways or gene expression in the target cell.
828
ated by a different
kind of receptor.
Ligand-gated
ion channel
receptors
The simplest and
fastest of signal
pathways is seen
in the case of signals whose receptors are gated ion
channels (Figure
7.132). Gated ion
channels are made
up of multiple
transmembrane
proteins that create a pore, or channel, in the cell
membrane. Depending upon its
type, each ion
channel is specific
829
their receptors on
the membrane of
the muscle cell. The
binding of the acetylcholine to its receptor, an ion channel
on the membrane of
the muscle cell, causes
the gate in the ion
channel to open. The
resulting ion flow
through the channel
can immediately
change the membrane
potential of the cell.
This, in turn, can trigger other changes in
of the cell are thus brought about in microseconds and in a single step.
the cell.
The speed with which
changes are brought about in neurotransmitter signaling is evident when you think
Swift response
the synaptic cleft, which is the space between the nerve cell and the muscle cell it is
Figure 7.135 - Steroid hormones structures, with the names of their receptors
Wikipedia
tors.
YouTube Lectures
by Kevin
HERE & HERE
Glucocorticoid receptor
Examples of such signaling path-
831
832
pies.
The steroid receptor pathways are relatively simple and have only a couple of steps
(Figure 7.138). Most other signaling pathways involve multiple steps in which the original signal is passed on and amplified through
833
G-protein coupled
receptors
G-protein coupled receptors (GPCRs) are involved in
responses of cells to many different kinds of signals, from
epinephrine, to odors, to
light. In fact, a variety of
physiological phenomena including vision, taste, smell,
and the fight-or-flight response
Figure 7.139 - Structure of a G-protein linked receptor
Wikipedia
G-protein coupled receptors are cell surface receptors that pass on the signals that
they receive with the help of guanine nucleotide binding proteins (a.k.a. G-proteins).
Before thinking any further about the signaling pathways downstream of GPCRs, it is necessary to know a few important facts about
these receptors and the G-proteins that assist them.
GPCR structure
and amplification of the signal through a variable number of intermediate molecules, with
membrane. For this reason, they are sometimes called seven-pass transmembrane
834
plasma membrane, where they are ideally situated to interact with the tail of the
GPCR, when a signal binds to the GPCR.
There are many different G-proteins, all of
which share a characteristic structurethey are composed of three subunits called
, and (Figure 7.140). Because of
this, they are sometimes called heterotrimeric G proteins (hetero=different, trimeric= having three parts).
Ligand binding
The guanine nucleotide binding site is on
the subunit of the G-protein. This site
it into GDP.
the cell.
lar domain of a GPCR, the receptor undergoes a conformational change, on its cytoplasmic side, that allows it to interact with a Gprotein that will then pass the
signal on to other intermediates
in the signaling pathway.
Interactive Learning
Module
HERE
G-proteins
What is a G-protein? As noted
above, a G-protein is a guanine
nucleotide-binding protein that can interact
with a G-protein linked receptor. G-proteins
are associated with the cytosolic side of the
835
YouTube Lectures
by Kevin
HERE & HERE
836
Enzyme activation
The interaction of G-proteins with their target enzymes can regulate the activity of the
Figure 7.142 - 2 -adrenergic
receptor embedded in
membrane (gray)
Wikipedia
Ion channels
channels can be opened or closed by the direct binding of neurotransmitters to a receptor that is an ion-channel protein. In
other cases, ion channels are regulated by the
binding of G-proteins. That is, instead of
the signal directly binding to the ion channel,
it binds to a GPCR, which activates a Gprotein that then may cause opening of the
837
838
accomplish this?
cAMP molecules bind to, and activate an enzyme, protein kinase A (PKA - Figure
7.145). PKA is composed of two catalytic and
two regulatory subunits that are bound tightly
together. Upon binding of cAMP, the cata-
cogen synthase, phosphorylation inactivates it, and prevents free glucose from being used up for glycogen synthesis, ensuring
that your cells are amply supplied with glucose (Figure 7.146).
Common pattern
839
cules!
finally, PKA)
Phosphorylation of target proteins by
there must be
mechanisms to
turn the pathway
ceptor itself. A
kinase called G-
to activate glyco-
protein recep-
gen phosphory-
lase to break
phosphorylates the
tion with a G-
protein.
The next point of
of the G-protein is
a tyrosine kinase activity. The signal binding domain of the receptor tyrosine kinase is
YouTube Lectures
by Kevin
HERE & HERE
841
842
Figure 7.152 - Effects of insulin binding to its receptor tyrosine kinase: 1) insulin
binding; 2) activation of protein activation cascades. These include: 3)
translocation of Glut-4 transporter to plasma membrane and influx of glucose; 4)
glycogen synthesis; 5) glycolysis; and 6) fatty acid synthesis.
Wikipedia
tyrosine kinases.
tyrosine kinase domains also phosphorylate intracellular proteins called Insulin Re-
Insulin receptor
Interactive Learning
Module
HERE
serves to activate yet another kinase, PDK1, which in turn, activates the Akt group of kinases. It
is this group of enzymes that appears to increase the translocation
EGFR pathway
Epidermal growth factor, EGF, is an
important signaling molecule involved
in growth, proliferation and differentiation in mammalian cells. EGF acts
through the EGF receptor, EGFR, a receptor tyrosine kinase (Figure 7.153).
Because of its role in stimulating cell proliferation and because overexpression of
EGFR is associated with some kinds of
cancers, EGFR is the target for many
anti-cancer therapies. We can trace the
signal transduction pathway from
the binding of EGF to its receptor to the
stimulation of cell division.
EGF binding to the EGFR is followed by
receptor dimerization and stimulation of
the tyrosine kinase activity of the cytosolic domains of the EGFR. Autophosphorylation of the receptor tails is followed by the assembly of a signaling
844
2. Receptor dimerization
plasma membrane
(in fact, it is a lot like the
Ras activation
Activation of Ras accompanies the exchange
of the GDP bound to the inactive Ras for a
GTP. Activated Ras triggers a phos-
YouTube Lectures
by Kevin
HERE & HERE
bers of a group called the MAP kinases (Mitogen Activated Protein Kinases).
The final kinase in this cascade phosphorylates various target proteins, including enzymes and transcriptional activators
that regulate gene expression.
845
ries of kinases. The terminal kinase in the cascade acts on target proteins and brings about
846
The pathways described above show a considerable degree of "cross-talk" and the response
to any given signal is affected by the other signals that the cell receives simultaneously. The
multitude of different receptors, signals, and
the combinations thereof are the means by
which cells are able to respond to an enormous variety of different circumstances.
and other growth factors, that stimulates mitosis or cell division. The final kinase in the
MAP kinase cascade phosphorylates a number of target proteins, many of them transcription factors, that when activated, increase the expression of genes associated with
cell proliferation.
Given that the EGF-receptor pathway normally functions to stimulate cell division, it
is not surprising that malfunctions in the pathway could lead to uncontrolled cell proliferation, or cancer. Next, we will take a brief look
at some examples of such defects.
HER2
The human EGF receptor (HER) family
has four members, HER1, HER2, HER3 and
HER4. These are all receptor tyrosine ki-
847
Figure 7.157 - The extracellular domains of the four members of the HER (ErbB) family
tion.
A crucial step in the signal transduction pathway is the dimerization of the receptors following binding of the signal, EGF, to the receptor. While HER1, HER3 and HER4 must
bind the signal to dimerize, the structure of
the HER2 receptor can, apparently, allow the
receptor monomers to dimerize independently of EGF binding.
This means that the downstream events of the
signaling pathway can be triggered even in
the absence of a growth signal. In normal
cells, only a few HER2 receptors are expressed at the cell surface, so this property of
848
Bcr-abl
Another example of a cancer caused by defects in an RTK signaling pathway is
chronic myeloid leukemia (CML). Patients
with CML have an abnormal receptor tyrosine kinase that is the product of a hybrid
gene called bcr-abl, formed by the breakage
and rejoining of chromosomes 9 and 22.
Figure 7.159 - Normal chromosomes (left)
and altered chromosomes giving rise to
the bcr-abl fusion (right)
Wikipedia
849
As with HER2, the problem in CML is a receptor tyrosine kinase that dimerizes in
the absence of a growth signal. The approach
in this case was to target the next step in the
signaling pathway. As you know, dimerization of RTKs activates the tyrosine kinase domain of the receptor, which results in the autophosphorylation of the cytoplasmic domains
of both monomers. The phosphorylated tyrosines serve to recruit a number of other
signaling proteins that pass the signal on
within the cell.
In the case of the bcr-abl RTK, the drug
Gleevec (imatinib) was designed to bind near
the ATP-binding site of the tyrosine kinase
domain. This "locks" the site in a conformation that inhibits the enzymatic activity of the
tyrosine kinase and thus blocks downstream
signaling. With no "grow" signal passed on,
cells stop proliferating.
850
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
851
Biochemistry my friend
It's time to study you again
Mechanisms that I need to know
Are the things that really stress me so
"Get these pathways planted firmly in your head,"
Ahern said
Let's start with ep-inephrine
Membrane proteins are well known
Changed on binding this hormone
Rearranging selves without protest
Stimulating a G alpha S
To go open up and displace its GDP
With GTP
Because of ep-inephrine
Active G then moves a ways
Stimulating ad cyclase
So a bunch of cyclic AMP
Binds to kinase and then sets it free
All the active sites of the kinases await
Triphosphate
Because of ep-inephrine
Muscles are affected then
Breaking down their glycogen
So they get a wad of energy
In the form of lots of G-1-P
And the synthases that could make a glucose chain
All refrain
Because of ep-inephrine
Now I've reached the pathway end
Going from adrenalin
Here's a trick I learned to get it right
Linking memory to flight or fright
So the mechanism that's the source of anxious fears
Reappears
When I make ep-inephrine
852
Obtaining a substrate
All of them burn
Thanks to this you have energy
853
8
Toolbox
The pace of discovery in biochemistry is astounding. It is hard to believe that the first
Basic Techniques
Introduction
YouTube Lectures
by Kevin
HERE & HERE
Mechanical disruption
Mechanical agitation may be employed in the form of beads that are
shaken with a mixture of cells. In
this method, cells are bombarded
with tiny, glass beads that break the
cells open. Sonication (20-50 kHz
sound waves) provides an alternative
type of agitation that can be effective.
The method is noisy, however, and
generates heat that can be problematic for heat-sensitive compounds.
Pressure disruption
Another means of disrupting cells involves using a cell bomb. In this
method, cells are placed under very
high pressure (up to 25,000 psi) and
then the pressure is rapidly released.
The rapid pressure change causes dissolved gases in cells to be released as
bubbles which, in turn, break open
cells.
Figure 8.1 - A sonicator in use
Wikipedia
Cryopulverization
Cryopulverization is often employed
856
compartment. The
tough extracellular
ous methods.
Column
chromatography
grinder) is performed.
The powder so ob-
Wikipedia
buffer.
Fractionation
Fractionation of samples, as the name suggests, is a process of separating out the components or fractions of the lysate. Fractionation
typically begins with centrifugation of the
lysate. Using low-speed centrifugation, one
can remove cell debris, leaving a supernatant
containing the contents of the cell. By using
successively higher centrifugation speeds (and
resulting g forces) it is possible to separate out
different cellular components, like nuclei, mi-
Ion exchange
chromatography
In ion exchange chromatography, the support consists of tiny beads to
which are attached chemi-
Supports are composed of tiny beads suspended in buffer (Figure 8.4) and are designed to exploit the chemistry or size differences of the components of the samples and
thus provide a means of separation. Columns
are packed or filled with the support, and a
buffer or solvent carries the mixture of compounds to be separated through the support.
Molecules in the sample interact differentially
with the support and, consequently, travel
through it at different speeds, thus enabling
separation.
Exchanges
Thus, a cation exchange column will have
858
Uses
Anion exchange
On the other hand, in anion exchange chroma-
to release them.
Size exclusion
chromatography
Interactive Learning
Module
HERE
859
Affinity chromatography
Affinity chromatography is a very powerful and selective technique that ex-
860
Interactive Learning
Module
HERE
trix.
Histidine tagging
861
encoded protein.
by treatment with a
This His-Tag is
useful in purifying
tidines, allowing
because histidine
desired protein
quence.
tion of His-tagged
proteins from a cell
HPLC
lysate is relatively
High performance
liquid chromatogra-
a column with
Wikipedia
phy (HPLC) is a
powerful tool for
separating a variety
of molecules based
862
cally produces.
Gel electrophoresis
Electrophoresis uses an electric field applied
863
Because electrophoresis uses an electric current as a force to drive the molecules through
the matrix, the molecules being
Interactive Learning
Module
HERE
migrate from the cathode (-) towards the anode (+). The rate of
All fragments of a given size will migrate the same distance on the gel,
forming the so-called bands on the
gel. Visualization of the DNA fragments in the gel is made possible by
addition of a dye, such as ethidium
bromide, which intercalates between
the bases and fluoresces when
viewed under ultraviolet light (Figure 8.13) By running reference
DNAs of known sizes alongside the
samples, it is possible to determine
the sizes of the DNA fragments in
864
Gel matrix
First, a matrix made by polymerizing and
cross-linking acrylamide units is employed.
A monomeric acrylamide (Figure 8.14) is polymerized and the polymers are cross-linked
Figure 8.14 - Acrylamide
monomer
Polyacrylamide gel
electrophoresis (PAGE)
Wikipedia
one nucleotide.)
eral modifications.
865
Stacking gel
A third consideration is that a
stacking gel may be employed
at the top of a polyacrylamide gel
866
Isoelectric focusing
Proteins vary considerably in their charges and,
consequently, in their pI
values (pH at which their
charge is zero). This can
be exploited to separate
proteins in a mixture. Separating proteins by isoelectric focusing requires establishment of a pH gradient
in a tube containing an acrylamide gel matrix. The
pore size of the gel is adjusted to be large, to reduce the effect of sieving
based on size. Molecules
867
2D gel electrophoresis
units.
The mixture of proteins is first applied to a
868
Interactive Learning
Module
HERE
Protein profiles
comparison
Comparison of 2-D gels of proteins
from non-cancerous tissue and pro-
869
However, if we wanted to know whether a specific protein was present, we could not tell by
cleic acid or protein is dependent on transferring the separated molecules from the gels
onto a membrane made of nitrocellulose or ny-
Protein detection usually employs two antibodies, the first of which is not labeled. The
label is on the second antibody, which is de-
Western blots
Proteins cannot, for obvious reasons, be detected through base-pairing with a DNA
probe, but protein blots, made by transferring
The second antibody commonly carries an enzyme or reagent which can cause a reaction
to produce a color upon further treatment. In
the end, if the molecule of interest is in the
original mixture, it will light up and reveal
itself on the blot. This variation on the blotting theme was dubbed a western blot (Figure 8.22).
871
Microarrays
2-D gels are a way of surveying a broad
spectrum of protein molecules simultaneously. One approach to doing something
similar with DNA or RNA involves what
are called microarrays. Microarrays are
especially useful for monitoring the expressions of thousands of genes, simultaneously. Where a northern blot would al-
872
Adding samples
Transcriptomics
Interactive Learning
Module
HERE
The presence/absence/abundance
873
874
875
RNA-Seq
mRNA present in
scripts in a given
non-cancerous tis-
sample. This
method relies on
boxes correspond
recently devel-
to an mRNA pre-
oped sequencing
technologies
cancerous tissue,
called next-
generation se-
quencing, or deep
sequencing.
spond to mRNAs
These techniques
present in equal
abundance in the
two tissues (Fig-
parallel sequencWikipedia
ing of millions of
DNA fragments
each tissue.
Protein microarrays
tics.
876
ment of molecular cloning was dependent on the discovery of restriction endonucleases, described below.
by the probes on a chip. RNA-Seq is more sensitive than microarrays and offers a much
Restriction enzymes
be measured accurately.
ases, are enzymes made by bacteria. These enzymes protect bacteria by degrading foreign
Isolating genes
The utility and importance of restriction enzymes lies in their ability to recognize specific
sequences in DNA and cut near or (usually)
at the site they recognize. Over 3000 such enzymes are known. Sequences recognized by
these enzymes are typically 4-8 base pairs
long and the most commonly used enzymes
877
Consider cutting a DNA sequence that contains the Hind III recognition site, which is
Wikipedia
Palindrome
In molecular biology, the term palindrome
means that the sequence of the recognition
site when read in the 5 to 3 direction for the
top strand is exactly the same as that of the
bottom strand. Consider the sequence recognized by the restriction enzyme known as
Hind III (pronounced hin-dee-three). It is
5 -A-A-G-C-T-T-3
3 -T-T-C-G-A-A-5
878
5 -A-A-G-C-T-T-3
3 -T-T-C-G-A-A-5
5 -N-N-N-C-T-G-C-A 3
5G-N-N-N-N 3
3 -N-N-N-G 5
3 A-C-G-T-C-N-N-N-N 5
III sequence would look like this (Ns correspond to any base and represent all of the
DNA around the recognition site).
5 -N-N-N-A-A-G-C-T-T-NN-N-3
3 -N-N-N-T-T-C-G-A-A-NN-N-5
After cutting with Hind III,
it would look as follows:
5 -N-N-N-A 3
G-C-T-T-N-N-N-N-3
3 -N-N-N-T-T-C-G-A-5
3 A-N-N-N-N-5
5A-
where gaps have been inserted to illustrate where cutting has occurred. Hind III
cuts between the two A containing nucleotides near the
5 end of the recognition sequence and thus leaves 5
overhangs (Figure 8.31).
5 -N-N-N-C-T-G-C-A-G-N-N-N-N-3
3 -N-N-N-G-A-C-G-T-C-N-N-N-N-5
Making recombinant
DNAs
Joining together of DNA fragments from different sources creates recombinant DNA. The ability to cut and paste DNA might
seem like purely a technical feat,
but one key application that arose
out of this is molecular cloning.
In molecular cloning a gene of interest can be inserted into a vector, usually a plasmid, by cutting
plish this goal, cloned DNAs remain very useful. For example, it is possible to clone a gene
that encodes a protein of interest so that it can
be expressed at high levels in the cells into
which the recombinant plasmid is introduced.
Whatever the purpose for which the recombinant plasmid is made, it typically carries an
antibiotic resistance gene (or genes), called a
selectable marker. Cells that take up the plasmid will be able to grow in the presence of the
antibiotic. If bacterial cells to which the plasmid has been added are plated on agar containing the antibiotic, the cells which took up
the plasmid will be able to grow, while the others will not.
880
Expression cloning
Expression vectors
881
Selective replication
chromatography.
replicate their DNA before they divide, and in doing so, double the
amount of the cells DNA. PCR
essentially mimics cellular DNA
each cycle.
dNTPs (DNA nucleotides to build
the new DNA strands).
replication in the test tube, repeatedly copying the target DNA over and over, to
882
stranded DNA
molecules whose
sequence
matches a region
get sequence. It
mentary se-
is possible to
chemically syn-
thesize DNA
molecules of any
paired to the
primers. These
quence, to use as
primers. To
synthesis of DNA.
make primers of
Only where a
primer anneals to
Extension
In the third step in the process, the DNA polymerase replicates DNA by extension from
Interactive Learning
Module
HERE
molecules, just as in cellular replication. But in PCR, the process is repeated, usually for between 25 and
883
scene.)
PCR can also be used to measure gene expresThe temperature cycles are controlled in a
in a couple of min-
tion of product is
because real-time
analyzed on a gel to
els of a fluorescent
pending on what it is
also be sequenced, to
be certain that it is
the desired fragment.
Mutagenesis
PCR is frequently used to obtain gene sequences to be cloned into vectors for protein
expression, for example. Besides simplicity
and speed, PCR also has other advantages. Because primers can be synthesized that differ
from the template sequence at any given position, it is possible to use PCR for site-directed
mutagenesis. That is, PCR can be used to mu-
product over the cycles it is possible to calculate the amount of starting template. To measure gene expression, the template used is
mRNA reverse-transcribed into cDNA (see below). This coupling of reverse transcription
with quantitative real-time PCR is called qRTPCR.
Reverse transcription
which codes for protein. One known exception to the central dogma is exhibited by retroviruses. These RNA-encoded viruses have a
phase in their life cycle in which their genomic RNA is converted back to DNA by a
virally-encoded enzyme known as reverse transcriptase. The ability to convert RNA to DNA
is a method that is desirable in the laboratory
for numerous reasons. For example, converting RNAs of interest to cDNA is used in RTPCR as well as in other applications like microarray analysis.
Process
First, one creates a DNA oligonucleotide to
serve as a primer for reverse transcriptase
to use on a target RNA. The primer must, of
course, be complementary to a segment (near
the 3 end) of the RNA to be amplified. The
RNA, reverse transcriptase, the primer,
885
Figure 8.39 - Four scenarios for the yeast two-hybrid system. UAS = Upstream Activator Sequences - acts like a promoter. Scenario A shows that the two transcription factors start out as one protein
Wikipedia
886
Figure 8.39 (A) shows the normal yeast transcriptional activator, GAL4, with both the DNAbinding (DBD) and Activation
activation domain.
FRET
nance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET).
The technique is based on the observation
that a molecule excited by the absorption of
light can transfer energy to a nearby molecule
if the emission spectrum of the first molecule
overlaps with the excitation spectrum of the
second (Figure 8.40) This transfer of energy can only take place if the two molecules
are sufficiently close together (no more than a
The experiment begins in the cell with one protein with a donor fluorophore and the other
protein with an acceptor fluorophore. Light of
a wavelength that excites the donor fluorophore is shined on the cell. If a protein with
a donor interacts with the protein carrying an
acceptor, then energy transfer occurs from the
donor fluorophore to the acceptor and the
Design
acceptor is detected.
Genome editing
The development of tools
that would allow scientists
to make specific, targeted
changes in the genome
has been the Holy Grail of
molecular biology. An ingenious new tool that is
both simple and effective
in making precise changes
is poised to revolutionize
the field, much as PCR did
in the 1980s. Known as
the CRISPR/Cas9 system,
and often abbreviated simply as CRISPR, it is based
on a sort of bacterial immune system that allows
bacteria to recognize and
inactivate viral invaders.
CRISPR stands for Clustered Regularly Inter-
associated.)
guide RNA that homes in on the target sequence and a nuclease that can make a cut
889
function.
Interactive Learning
gene, it is possible to target the nuModule
clease to cleave within that gene.
HERE
double-strand
break that the
cell attempts to
repair.
As you may remember,
double-strand
breaks in DNA
can be repaired
by simple, non-
890
Scientists have also come up with some creative variations on the CRISPR/Cas9 system.
For instance, one variant inactiCas9. The guide RNA in this
quence, but the Cas9 does not
cleave it. Instead, the Cas9
Trp)
next to proline)
sequence.
amino acid
891
CRISPR has already been used to edit genomes in a wide variety of species (and in human cell cultures). It may not be long before
the technique is approved for clinical use. In
the meanwhile, CRISPR is transforming molecular biology.
Protein cleavage
Because of their large size, intact proteins can
be difficult to study using analytical techniques, such as mass spectrometry. Consequently, it is often desirable to break a large
polypeptide down into smaller pieces. Proteases are enzymes that typically break peptide
bonds by binding to specific amino acid sequences in a protein and catalyzing their hydrolysis.
Chemical reagents, such as cyanogen bromide, which cleaves peptide bonds on the Cterminal side of a methionine residue can also
be used to cut larger proteins into smaller pep-
tides. Common proteins performing this activity are found in the digestive system and are
ized molecule to move from its point of ionization to the detector will depend on both its
mass and its charge and is termed its time of
flight (TOF).
MALDI-TOF
and a charge of +2. Thus, by precisely determining the time it takes for an ion to go from
Membrane dynamics
termined.
894
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
On binding to A-A-G-C-T-T
The site recognition sites bent easily
Phosphodiester attacking meanwhile
Has water behaving as nucleophile
Crawling.
Im almost bawling
The boss is calling to follow through
I just loaded all Ive got to make this final western blot
My fingers are both crossed for sure
I hope my protein products pure. I do
Then my thesis is through
Hating.
All of the waiting
Im contemplating what I should do
Staining.
My eyes are straining
Theres no complaining. I say wahoo
Writing so unexciting.
But no more biting. My nails again.
Writing is coinciding.
With reference citing. Im at the end.
9
Point by Point
in your studies.x
899
Basic Biology
Cells are the fundamental units of life
Three main branches of cells - prokaryotes, eukaryotes, and archaeans
All cells have 1) plasma membrane; 2) ribosomes; 3) cytoplasm
The plasma membrane has a lipid bilayer, proteins, and cholesterol
Phototrophs get energy from light
900
Basic Chemistry
Single bonds can rotate. Double bonds cannot
Double-bonded carbons create a planar
structure with angles of 120
Single-bonded carbons create tetrahedral
structures with angles of 109.5
Important organic structures needed to understand biochemistry include alkanes, alkenes, alcohols, esters, amines, thiols, aldehydes, ketones, carboxylic acids, amides,
and esters.
Molecules or chemical groups that mix or interact well with water are called hydrophilic.
Molecules or chemical groups that do not
mix or interact well with water are called hydrophobic.
901
G = G + RTlnKeq
902
903
904
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Amino Acids
20 amino acids comprise 99% of the proteins on this planet.
The genetic code specifies the incorporation of the 20 amino acids into a protein during protein synthesis (translation). Specifications are via codons, which are three
base sequences in tRNAs.
Two amino acids, selenocysteine and pyrrolysine, are not encoded by the genetic
code, but are put into proteins by unusual
mechanisms in rare proteins involving stop
codons during translation.
908
910
Proteins I
Proteins are the workhorses of cells. They
are enzymes for catalysis, mediators of
signaling, give structure to cells and control the proteome.
There are four distinct levels of protein structure - primary (amino acid sequence), secondary (interactions between close amino
acids that affect local protein shape), tertiary (interactions between amino acids not
close in primary structure that affect fold-
911
A 310 helix is the fourth most abundant secondary structure in proteins - about 10% of
all helices. It contains 10 amino acids in 3
right-handed turns. Hydrogen bonds form
between amino acids that are three apart.
-helices are thought of as a special type of
-helix, as if an extra amino acid were
placed in the middle. They are right-handed
and have 22 amino acids in 5 turns of the helix. Most are only 7 amino acids long and occur in the middle of -helices.
The peptide bond has characteristics of a
double bond and creates a planar structure.
A polypeptide chain then can be thought
of as a set of unrotatable planar structures
separated by rotatable single bonds.
Sequentially in the amino to carboxyl direction they are 1) a rotatable bond () between the -carbon and -carboxyl preceding the peptide bond, 2) an un-rotatable peptide bond () between -carboxyl and amine), and 3); a rotatable bond () between the -amine and -carbon following
the peptide bond. Note that in Figures
2.32 and 2.33 that the amino end is on the
right and the carboxyl end is on the left.
Ramachandran and colleagues performed
theoretical calculations to determine the
steric stability of the rotatable bonds on either side of the planar structures.
Their results ( shown in Ramachandran
plots) identified three primary groups of stable rotatable angles and these correspond to
the angles found in right handed -helices,
left handed -helices, and -strands.
The amino acid sequence and secondary structure of thousands of proteins
are known. By analyzing these sequences, it
is possible to determine the frequency (likeli912
Breaking tertiary structure involves breaking the stabilizing forces. This can be accomplished by heat, pH change, detergents,
urea, and mercaptoethanol. These treatments unfold proteins and destroy their
function.
Hydrogen bonds are weaker than covalent bonds. They are readily broken with
boiling water or urea.
Proteins embedded in non-polar lipid bilayers have stretches of hydrophobic sequence (called transmembrane domains) that can be seen in a KyteDoolittle plot.
Regions of proteins that have no regular, discernible structure are referred to as random coils. They may have fluid structures
and exist in multiple stable forms. These
may be metamorphic proteins or intrinsically disorder proteins and can be
characterized by spectroscopic methods that
include circular dichroism or nuclear magnetic resonance (NMR).
Ionic interactions are important for structural stability and also in catalysis. pH
can have a strong influence on ionization.
van der Waals forces are forces of attraction and repulsion caused by correlations in
the fluctuating polarizations of nearby particles.
Post-translational modifications alter amino
acids after a protein is made.
There are two popular protein folding
models. The first (diffusion collision model)
involves a nucleation even followed by secondary structure formation. By contrast,
the nucleation condensation model proposes that secondary and tertiary structures
form together.
913
914
Proteins II
Fibrous proteins have a strong structural
component and mostly have primary and
secondary structure - little tertiary
structure.
Fibrous proteins constitute hair, nails, hard
substances like horns, and connective tissues. They include keratins, fibroin,
elastin, and collagen.
Keratins are found in hair, nails, beaks,
scales, feathers, and claws. There are over
50 in the human genome. Keratins comprise the intermediate filaments of the
cytoskeleton. -keratins often have intertwined -helices in coiled-coil structures. Disulfide bonds between chains
add strength. Curling/uncurling hair involves breaking these bonds.
915
structures. Structural domains are selfsustaining and can fold independently of the
rest of the protein.
Actin is a structural globular protein comprising as much as 20% of the mass of muscles. Polymerization of actin leads to microfilaments (also called thin filaments)- a major component of the cytoskeleton. Thin filaments of actin are acted on by myosin in
muscular contraction.
The src oncoprotein has a structural domain called SH2 that binds to phosphorylated tyrosines in target proteins. The domain plays a role in signaling and is found
in over 100 human proteins.
The helix-turn-helix domain is commonly found in DNA binding proteins and
contains two -helices separated by a
small number of amino acids. The helix
parts of the domain interact with bases in
the major groove of DNA.
Pleckstrin homology domains bind to
phosphorylated inositol residues (PIP2
and PIP3) in cell membranes. Proteins
with this domain can also bind to Gproteins and protein kinase C. They
play important roles in cellular signaling.
The basement membrane is a glue that
holds tissues together. It is a layered extracellular matrix of tissue comprised of protein fibers (type IV collagen) and glycosaminoglycans that separates the epithelium from other tissues.
Integrins are important transmembrane proteins for connecting cells together. They bind to collagen, fibronectin, laminin, and vitronectin and
also play roles in communication, migration, viral attachments, and blood clotting.
They are a bridge between the extracellular matrix and the cytoskeleton. The are
important in focal adhesions.
Syndecans are transmembrane proteins that facilitate G-protein coupled receptors interaction with ligands. Syndecans typically have 3-5 heparan sulfate
and chondroitin sulfate chains attached
to them and cleavage of those chains at the
site of a wound can help stimulate the healing process. Syndecans play a role in cellcell adhesion. The syndecan 1 ectodomain
can suppress growth of tumor cells without
affecting normal epithelial cells.
Defensins are small cationic proteins that
act as ionophores to protect against infection by various bacteria, fungi, and viruses.
Focal adhesions are structures with multiple proteins that link the cytoskeleton to
the extracellular matrix. Over 100 proteins are involved. Since they are connected
to the extracellular matrix, focal adhesions
can communicate its status to cells containing them.
Ankyrins are a family of membrane adaptor proteins that anchor integral membrane proteins to the spectrin-actin
membrane cytoskeleton. Ankyrins are anchored to the plasma membrane by
palmitoyl-CoA.
917
may not get removed from hemoglobin before the returning to the lung, leaving hemoglobin in the T-state with a lower capacity
for binding oxygen. Smokers have high 2,3
BPG concentrations in the blood and this is
why smokers have a reduced oxygen carrying capacity.
Smokers also have higher levels of carbon
monoxide in their blood and this competes
with oxygen for binding iron on the heme
group, also reducing oxygen carrying capacity.
Carbon dioxide moves from tissues to
lungs in the blood by two mechanisms - 1)
carried by hemoglobin and 2) dissolved as
bicarbonate.
Fetal hemoglobin is slightly different
from adult hemoglobin, with two -chains
replacing the -chains of adult hemoglobin.
The result is a hemoglobin that can bind oxygen cooperatively, but cant bind 2,3 BPG,
resulting in a hemoglobin more frequently
in the R-state. Fetal hemoglobin thus has a
higher affinity for oxygen than adult hemoglobin so the fetus can take oxygen from the
mother.
Sickle cell disease arises from mutations in hemoglobin that cause aggregates to form under low oxygen conditions.
This, in turn, causes blood cells containing
the mutated hemoglobin to form sickle
shapes, making it harder for them to pass
through capillaries. The condition can be
very painful under conditions of high exertion and may be fatal if too severe.
People heterozygous for the sickle cell
gene (one copy of the mutant and one unmutated) appear to have a selective advantage
in being better able to survive malaria infections.
Sickle cell anemia is treated with hydroxyurea, which induces expression of the fetal
hemoglobin gene in adults to replace the
defective mutant copy.
Oxygen is needed more by plants than animals due to rapidly changing needs arising
from muscular contraction.
This is because oxygen is the terminal electron acceptor of electron transport, so
when it and oxidative phosphorylation
are running, ATP generation is much more
efficient.
Besides hemoglobin, two other oxygen
binding proteins are of note - myoglobin
(muscles of higher animals) and hemocyanin (molluscs and arthropods).
Insects and unicellular organisms have
other means of managing oxygen
Myoglobin is the primary oxygen-storage
protein found in animal muscle tissues. It
has high affinity for oxygen and only releases it when the oxygen concentration is
very low.
Red meat gets its color from ferrous iron
(Fe++), which oxidizes to ferric iron (Fe+++),
causing browning when meat is cooked.
Myoglobin has higher affinity for oxygen
than hemoglobin.
Mammals that dive deeply in the ocean,
such as whales and seals, have muscles with
particularly high abundance of myoglobin.
Hemocyanin is a copper-containing protein that transports oxygen in the bodies of
molluscs and arthropods.
919
F-actin binds to structural proteins at adherens junctions, such as -actinin, vinculin, catenins, and cadherins.
The Arp 2/3 complex mimics an actin dimer and helps to initiate the process of actin
polymerization. Thymosin at the end of actin filaments helps control growth of the filaments. The protein known as profilin acts
to exchange ADP for ATP within actin monomers.
Proteins III
Actin is a structural globular protein that
exists in monomer and polymeric forms. Polymerization of actin leads to microfilaments - a major component of the cytoskeleton.
Actin is essential for muscular contraction, cell signaling, and maintenance of
cell junctions. -actin is in the muscles,
whereas the and forms are components
of the cytoskeleton.
Tubulins are monomeric units of microtubules. The -tubulin and -tubulin proteins
polymerize to make microtubule structures
in the cytoplasm of cells. Microtubules
only grow in one direction. The end of
growth is called the plus end and the other
is referred to as the minus end.
Microtubules are major components of the
cytoskeleton. Stable microtubules contain
tubulin units bound to GTP. Those bound
to GDP are unstable and fall apart.
Microtubules are found in the cytoplasm, the inner structure of cillia and flagella and provide rail-like structures for the
movement of materials within cells. The proteins navigating these rails are dynein and
kinesin, which operate in opposite directions. Centrosomes are focal points of connection of microtubules.
Motor proteins act as their name suggests the provide movement inside of cells. In
their action, they carry cellular cargo from
one location to another.
During polymerization of actin, its weak ATPase activity is stimulated to convert ATP
to ADP.
The monomeric unit of actin is called Gactin and the polymer is known as F-actin.
920
Myosin proteins use ATP to enable movement along actin thin filaments. Myosin
proteins form aggregated structures are
called thick filaments.
At the ends of muscle fibers, the sacrolemma is fused with a tendon fiber and
the latter is adhered to bones.
921
Nucleic Acids
In the race to discover the structure of
DNA, Watson and Crick combined observations of Erwin Chargaff with the data of
Rosalind Franklin to determine the structure of B-DNA.
At the core of DNA, bases are hydrogen
bonded together - guanine (G) to cytosine (C) and thymine (T) to adenine (A).
In RNA, uracil (U) replaces thymine (T).
The interior of DNA is relatively hydrophobic and the exterior is hydrophilic.
The DNA molecule is a polymer of nucleoside monophosphates with phosphodiester bonds between the phosphate on
the 5 end of one deoxyribose and the 3
end of the next one.
922
Nucleoside diphosphokinase (NDPK) allows interchange of all diphosphate and triphosphate nucleotides
ATP + NDP <=> ADP + NTP
Deoxyribonucleotides are made from nucleoside diphosphates by catalysis with ribonucleotide reductase.
DNA strands of a double helix are antiparallel - the 5 end of one strand is paired
to the 3 end of the other strand.
923
In RNA, G-U base pairs are not unstable, allowing for more base-pairing possibilities.
Single-stranded RNA therefore has many
more ways to base-pair with itself than
single-stranded DNA.
There are five main types of eukaryotic histones - H1, H2a, H2b, H3, and H4. Pairs
of each of the last four are found as octamers in the core particle of the nucleosome - the fundamental repeating unit of
chromatin. H1 binds to the DNA in the
regions between core particles.
924
The Ames test works by using a biological assay to measure the frequency with which a
specific mutation occurs in a plasmid. By
comparing the mutation rate for bacteria
treated with a compound compared to the
mutation rate of bacteria not treated with
the compound, the mutagenicity of the
compound is determined.
Carbohydrates
Carbohydrates are molecules that are literally hydrates of carbon. They are also
known as sugars or saccharides and polymers of them are known as polysaccharides. Monosaccharides contain one
sugar. Disaccharides contain two. Oligosaccharides contain several.
Glucose is a monosaccharide, sucrose is a
disaccharide, and glycogen is a polysaccharide.
Sugars are names with the -ose suffix.
Some sugars are modified, such as deoxyribose or glucose-6-phosphate.
The most common monosaccharides include
glucose, fructose, galactose, ribose,
and mannose. All but fructose are sugars
containing an aldehyde (aldoses). Fructose contains a ketone group (ketose).
Glucose, fructose, galactose, and mannose
all contain six carbons (hexoses). Ribose
contains five carbons (pentose).
Names can be combined. Fructose is a
keto-hexose. Ribose is an aldo-pentose.
925
926
927
most primary plant cell walls and abundant in non-woody parts of terrestrial
plants.
Pectins in the diet may reduce cholesterol due to its tendency to bind it and reduce absorption of cholesterol from food.
Lectins are proteins that have high specificity of binding for certain sugars. They facilitate attached of bacteria and viruses to
cellular targets. Some, such as ricin, are
highly toxic.
In the immune system, a mannan binding
lectin (MBL) helps mediate the first defenses against microorganisms and may
modulate inflammatory processes.
Biofuels are fuels derived from biological
sources. Most commonly, they are ethanol
or methane and may be made by cellulase digestion of plant cellulose followed
by fermentation or by native metabolism
of methane producing organisms.
Agar/agarose is a polysaccharide with
laboratory applications. It is a polysaccharide polymer of D-galactose and 3,6anhydro-L-galactopyranose extracted
from seaweed. Agarose used to make laboratory gels for separation of DNAs. Agar,
which is made by adding agaropectin to agarose, is used to make growth media for plating microorganisms or other cells.
Glycosaminoglycans are polymers of unbranched repeating disaccharides. The
repeating units of the disaccharide core of
the molecules typically have an amino sugar
(N-acetylglucosamine or Nacetylgalactosamine) and a uronic
sugar (glucuronic acid or iduronic
acid) or galactose.
928
Hyaluronic acid is abundant in the granulation tissue matrix that replaces a fibrin clot
during the healing of wounds.
Breakdown of hyaluronic acid is catalyzed
by enzymes known as hyaluronidases.
Humans have seven types of such enzymes,
some of which act as tumor suppressors.
Proteoglycans are made by linking glycosaminoglycans to proteins. Proteoglycans are made by glycosylation of target
proteins in the Golgi apparatus.
Lipids
Lipids are molecules that are significantly
hydrophobic
Many are important for energy storage or
for functions in membranes
Some, like fats are purely hydrophobic.
Others, like glycerophospholipids and
sphingolipids are amphipathic/
amphiphilic.
Fatty acids are components of fats and
they store a lot of energy.
They can be saturated (no double bonds),
unsaturated (at least one double bond), or
polyunsaturated (more than one double
bond).
Double bonds in biologically produced fatty
acids are almost exclusively in the cis configuration. Partial hydrogenation of vegetable oil produces trans fats containing fatty
acids with trans double bonds.
Trans fat increases LDL levels and lowers
HDL levels.
929
The numbering system for fatty acids labels #1 as the carboxyl group whereas the
numbering system calls the methyl
group as #1.
Animals lack the ability to make double
bonds beyond position -9, so those fatty acids are essential and must be in the diet.
-3 and -6 fatty acids have important
health considerations.
Glycerophospholipids are components
of the lipid bilayer of membranes.
They are derived from phosphatidic acid,
just as fats are.
Glycerophospholipids often are esterified
to ethanolamine, serine, choline, or
inositol. These are phosphatidyl compounds.
Phosphatidyl ethanolamine is found in
all living cells and makes up 25% of the phosphatidyl compounds - up to 45% of brain tissue.
Phosphatidyl serine is preferentially
found on the inner leaflet of the plasma
membrane. In apoptosis (programmed
cell death), it appears on the outer leaflet
and serves as a signal to macrophages to
destroy the cell.
Phosphatidly choline tends to be found
more on the outer leaflet of the plasma membrane. It is positioned there by phosphatidylcholine transfer protein.
Cardiolipin is an unusual glycerophospholipid containing two diacylglycerol
backbones separated by a diphosphoglycerol. It occupies about 20% of the inner
mitochondrial membrane and plays
930
931
Movement of lipids in the body is problematic due to their hydrophobic nature and
the aqueous environment in which they
must travel. This occurs in lipoprotein
complexes made mostly in the liver and
lymph system. They include chylomicrons (from small intestine), VLDLs,
IDLs, LDLs, and HDLs. The last four are
made in the liver.
LDLs contain the highest concentration of
cholesterol and they enter the cell via
receptor-mediated endocytosis.
Cholesterol is made into bile acids by the
liver for excretion in the bile. Bile acids also
help with emulsification of fats.
Levels of trans fats in the diet correlate
with incidence of coronary artery disease.
Cholesterol is recycled through the digestive system. Plant equivalents of cholesterol
called phytosterols compete with cholesterol in the recycling system and may lower
body levels of cholesterol.
LDLs are referred to as bad cholesterol because they are associated with atherosclerosis. HDLs are called good cholesterol because their levels correlate with removal of
arterial debris (including cholesterol). They
also help to reduce inflammation.
Cholesterol acts an insulator for the transmission of signals in nerve tissue. It helps
to manage fluidity of membranes over a
wide range of temperatures and reduces the
membranes permeability. It also helps with
the structure of lipid rafts in the membrane.
Vitamin A is a fat soluble vitamin that
comes in three forms - retinol (alcohol),
932
Steroid hormones are all made from cholesterol and are grouped into five categories - mineralocorticoids (water/
electrolyte balance), glucocorticoids
(modulating immune system), progestagens (pregnancy maintenance), androgens (male sex hormones), and estrogens
(female sex hormones).
Deficiency of vitamin E reduces the efficiency of nerve signals, can lead to low birth
weights and premature deliveries.
Excess vitamin E can reduce vitamin K levels, thus reducing the ability of the body to
clot blood.
933
934
936
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Basic Concepts
Cell membranes contain cholesterol,
proteins, glycolipids, glycerophospholipids, and sphingolipids.
Lipid bilayers form spontaneously when
glycerophospholipids, and sphingolipids are
mixed in an aqueous solution.
Water, CO2, CO, and O2 move efficiently
across the lipid bilayer. Other molecules
dont move so readily and require
proteins/energy to assist their movement.
Cells need energy, export of wastes, and osmotic balance. They create chemical/ion
gradients for energy purposes.
When energy is required to move a substance across a membrane, the process is
called active transport.
Facilitated diffusion is driven by the process of diffusion and occurs through specific cellular channels made of protein.
Surrounding cells are plasma membranes and (in some cases) cell walls.
Bacteria, fungi, and plants all have cell
walls in addition to plasma membranes.
939
line and sphingomyelin are predominantly found in the outer leaflet of the bilayer and others like phosphatidylserine
and phosphatidylethanolamine predominate in the inner leaflet.
Such specific arrangements are important in
apoptosis (programmed cell death). Movement of biased lipids from one leaflet to another occurs during this process and may be
a signal.
Molecules with sugars attached almost always have the sugars arranged on the outside of the cell.
Cellular organelles in eukaryotes also
have biases of composition of their membrane lipids. Cardiolipin, for example,
isnt commonly found in the plasma membrane or that of the endoplasmic reticulum, but is common in other organelle membranes.
Lipids typically move freely within the
layer in which they are found (called lateral
diffusion), but rarely flip from one side
to the other (transverse diffusion) without the assistance of an enzyme.
Enzymes catalyzing transverse diffusion of
membrane lipids include flippases (move
from outer leaflet to inner leaflet); floppases (move from inner leaflet to outer leaflet), and scramblases (move both directions).
Cholesterol and proteins are other important components of the lipid bilayer.
Cholesterol is also a metabolic precursor of
bile acids, and steroid hormones.
Cholesterol influences membrane fluidity.
940
If two molecules are moved in opposite directions across the bilayer, the protein is
called an antiport.
Transporters have high specificity and transfer rates that are orders of magnitude slower
than channels. An example is the Na+/K+
ATPase.
Membrane Transport
942
943
944
Lactose permease facilitates the movement of the sugar lactose across the lipid
bilayer of the cell membrane.
Glucose Transport Proteins (GLUTs) are
uniport, type III integral membrane
proteins that facilitate transport of glucose
into cells.
The one in red blood cells is known as GLUT
1 and has 12 membrane-spanning hydrophobic helices.
GLUT 4 is regulated by insulin and is
found primarily in adipose and striated
muscle tissue.
Insulin acts to stimulate uptake of glucose
by cells by favoring movement of various
GLUT proteins (including GLUT 4) from intracellular vesicles to the cell membrane.
Once inside the cell, phosphorylation of
glucose by hexokinase prevents it from
exiting via GLUTs.
Other Considerations
Another means of getting material into cells
is by endocytosis. This method tends to
move particles, some of which are larger
than could be transferred via a transporter protein.
Materials entering this way include LDLs,
iron packaged in transferrin, vitamins,
hormones, proteins, and some viruses.
Receptor mediated endocytosis uses a
specific cell receptor called clathrin that
binds to particles with a binding site for it.
Cellular structures lined with clathrin are
called coated pits.
945
946
948
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Basic Principles
At equilibrium, the concentration of products and reactants will not be equal unless
the value of G is zero.
At equilibrium, the concentration of products and reactants will not change over
time.
The part of an enzyme where catalysis occurs is called the active site.
In metabolic pathways, the product of
one reaction is the substrate of the next reaction.
951
952
Vmax is limiting for describing reaction velocities, since it depends on the quantity of
enzyme used in a reaction. If one doubles
the amount of enzyme, one will double Vmax.
Consequently, for comparing rates of reaction, the quantity Kcat is used. Kcat (also
called turnover number) is calculated by dividing Vmax by the concentration of enzyme
used in a reaction. The numerical value obtained has units of inverse time (for example, seconds-1) and corresponds to the number of molecules of product made per molecule of enzyme per second.
As noted above, not all enzymes obey
Michaelis-Menten kinetics. Examples
include multi-subunit enzymes that change
in such a way upon binding the first substrate molecule that binding of further substrate molecules by the same enzyme is affected (positively or negatively).
953
Kd = [J]x[K]y/[JxKy]
Another way of analyzing enzyme kinetic
data is to plot velocity/substrate data by the
Lineweaver-Burk method. In these plots,
the inverse of V0 is plotted against the inverse of the [S].
These so-called double reciprocal plots (1/V0
vs 1/[S]) give straight lines for enzymes following Michaelis Menten kinetics. The
line of these plots, when extrapolated to the
X-axis, give the value of 1/Vmax as Yintercept and the value of -1/Km as the Xintercept.
The term molecularity refers to the number of molecules that must come together in
order for a reaction to take place. Unimolecular reactions are when there is only one
reactant molecule.
For a bimolecular reaction where A + B <=>
C, the reaction depends on the concentration of both A and B and its rate will be related to the product of the concentration of
A and of B.
where [L], [P], and [LP] are the molar concentrations of the protein, ligand and the complex when they are joined together.
Coenzymes are molecules that help enzymes to perform catalysis. These include
both inorganic ions and organic molecules.
If the latter is covalently or tightly bound to
the enzyme, it is referred to as a prosthetic
group.
JxKy <=> xJ + yK
Not all biological catalysts are proteins. Ribozymes are catalytic RNA molecules.
The most prominent of these are the 23S
rRNA of prokaryotes and the 28S rRNA
of eukaryotes. Each of these functions in
the ribosome to catalyze the formation of
peptide bonds in protein synthesis.
Kd = [L][P]/[LP]
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Control of Enzyme
Activity
The inhibition of specific enzymes by drugs
can be medically useful.
There are four types of inhibition that are of
interest - competitive, noncompetitive, uncompetitive, and suicide inhibition.
Only suicide inhibition is not reversible.
Competitive inhibition occurs when the
inhibitor resembles the natural substrate
of an enzyme and competes with it for binding at the active site.
An example is methotrexate that resembles the folate normally acted on by the enzyme dihydrofolate reductase (DHFR).
When methotrexate binds to DHFR, the enzyme is inhibited and wont function.
However, since methotrexate and folate
compete for binding to DHFR, the more one
increases the amount of folate, the less
methotrexate will be able to bind, meaning
that the amount of inhibition will decrease.
At infinite amounts of folate, the inhibition
of methotrexate disappears. Thus,
methotrexate has no effect on the Vmax of
the DHFR reaction though it can affect velocities at lower concentrations.
On the other hand, at lower concentrations,
methotrexate does have effects and thus
causes an increase in the amount of substrate necessary to reach Vmax/2. Since
this is known as the Km for an enzyme, it
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Enzymes - Mechanism
Chymotrypsin is a serine protease - a
class of enzymes with several members.
Some examples of serine proteases include
trypsin, chymotrypsin, elastase, subtilisin, and signal peptidase I.
Proteases catalyze the cleavage of peptide
bonds.
Serine proteases use a serine in their active site as part of the catalytic process.
Serine is one of three amino acids in the
protein that play critical roles in the catalysis. The three amino acids make up what is
called the catalytic triad and they are serine, histidine, and aspartic acid.
Activation of serine in the catalytic process
creates a nucleophile called an alkoxide
ion which attacks the peptide bond, causing it to be broken.
Some examples of cysteine proteases include papain, caspases, hedgehog protein, calpain, and cathepsin K.
Protease inhibitors stop the catalytic action of proteases. Mechanisms of their action include suicide inhibition, transition
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Blood Clotting
Blood clotting is a process in which liquid
blood is converted into a gelatinous substance which hardens.
Steps in the process include 1) activation
(wounding); 2) a cellular response (aggregation of blood platelets) and 3) a
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urokinase plasminogen activator (using urokinase plasminogen activator receptor as a co-factor), kallikrein (plasma serine protease with many forms and blood
functions), and FXIa and FXIIa of the blood
clotting pathway.
Conversion of plasminogen to plasmin
can be inhibited by plasminogen activator inhibitor (inactivated tPA and urokinase plasminogen activator).
Active plasmin can be inhibited by 2antiplasmin and 2-macroglobulin. Thrombin also can play a role in plasmin inhibition.
Fibronectin is a large glycoprotein
found in the extracellular matrix that
binds to integral cellular proteins called
integrins and to extracellular proteins, including collagen, fibrin, and heparan
sulfate. It is important in the healing process and in blood clot formation.
In the repair of the wound, the damaged
area is acted on by fibroblasts and macrophages, which degrade blood clot matrix
proteins and replace them with a new matrix like the undamaged, surrounding tissue.
Fibroblasts release proteases that cleave
the fibronectin from the plasma, causing
wound contraction. Then, fibroblasts release cellular fibronectin and integrate it
with the matrix.
Fibronectin is also essential for embryogenesis.
Platelet Activating Factor (PAF) is a
host defense chemical produced in greater
quantities in inflammatory cells upon
proper stimulation. It acts like a hormone
and can transmit signals between cells to
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Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Enzymes
Might powerhouse peptides
Cause reactions to go faster
In the cells insides
Tiny substrates
Bring about an induced fit
Enzyme structure is affect-ed
By what binds to it
Folding
Gives the mechanistic might
To three-D arrangement
Of the active site
(Additional stanza)
Enzymes
Have a bias they cant hide
Hydrophobic side chains are
Mostly found inside
Energy Basics
Maintaining and creating order in cells
takes the input of energy.
Oxidation is the main form of nonphotosynthetic energy in organisms.
Carbon is the most commonly oxidized biological material.
Energy released during the oxidative steps is
captured in ATP.
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ATP is made by three distinct types of phosphorylation oxidative phosphorylation (in mitochondria), photophosphorylation (in chloroplasts of plants), and
substrate level phosphorylation (in enzymatically catalyzed reactions).
For a reaction aA bB
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G = G + RTln([B]b/[A]a)
For multiple substrate reactions, such as
aA + cC bB + dD
G = G + RTln{([B]b[D]d)/([A]a[C]c)}
The G term is the change in Standard
Gibbs Free energy, which is the change in energy that occurs when all of the products
and reactants are at standard conditions
and the pH is 7.0. It is a constant for a given
reaction.
If we collect all of the terms of the numerator together and call them {Products} and
all of the terms of the denominator together
and call them {Reactants}, then
G = G + RTln({Products}/{Reactants})
A negative G indicates an energetically favorable reaction, whereas a positive G corresponds to an unfavorable one. This is not
absolute. The actual direction of a reaction
is given ONLY by the value.
Le Chateliers Principle states that a system responds to stress by acting to alleviate
the stress.
reactions that increase entropy. The hydrophobic effect, described in protein folding, is favorable, for example, because the
exclusion of water arising from interacting
hydrophobic amino acids internal to a protein actually increases the entropy of the
process.
Whenever there is a difference in concentration of molecules across a membrane,
there is said to be a concentration gradient across it.
A difference in concentration of ions across
a membrane creates an ionic (or electrical)
gradient. When both are present, then we
refer to it as an electrochemical gradient.
Such gradients function like batteries and
contain potential energy.
For two solutions of uncharged material
separated by a lipid bilayer (say inside a
cell versus outside a cell, where C1 is the concentration inside and C2 is the concentration
outside), The Gibbs free energy associated with moving material in the direction
of C2 is given by
G = RTln[C2/C1]
Here, Z refers to the charge of the transported species (+1 for a potassium or -1 for a
chloride, for example), F is the Faraday con-
G = RTln[C1/C2]
The last two equations assume the molecules have no charge. If they have charge,
this must be taken into account with another term -> ZF.
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Thus, the concentration of a product decreases and this helps to pull the reaction
forward.
From an energy perspective, removal of
product (pulling a reaction) and/or increasing the concentration of reactant
(pushing a reaction) decreases G because these have the effect of making the
fraction in the term below smaller and its Ln
value more negative, thus reducing G
G = G + RTln({Products}/{Reactants})
Electron Transport
and Oxidative Phosphorylation
The vast majority of ATP synthesis in
eukaryotes occurs in the mitochondria
in a process called oxidative phosphorylation.
Oxidative phosphorylation is preceded in
the mitochondria by another process known
as electron transport.
NADH and FADH2 donate their electrons
to the electron transport system and become
NAD+ and FAD, respectively.
Peter Mitchell proposed the chemiosmotic hypothesis to explain oxidative
phosphorylation.
Mitchell proposed that mitochondrial
ATP synthesis results from an electrochemical gradient across its inner membrane that arises ultimately from the energy of reduced electron carriers, NADH
and FADH2
Mitchell said further that electron carriers transfer electrons to an electron transport system (ETS) in the inner mitochondrial membrane and movement of
the electrons causes protons to be pumped
out of the mitochondrial matrix across
the inner mitochondrial membrane, creating
a proton gradient. Flow of the electrons
back into the matrix through a transmembrane ATP synthase is the driving force
for synthesis of ATP from ADP and Pi.
Tight coupling of electron transport and
oxidative phosphorylation exists when
the two processes are interdependent - stopping of one stops the other. This is the basis
of metabolic control.
Uncoupling of electron transport occurs
when the integrity of the inner mitochondrial membrane is compromized, allowing protons to re-enter the matrix without
passing through the ATP synthase. When
this occurs, the proton gradient is destroyed
and no ATP is made.
In the electron transport system, electrons
flow through the system via complexes and
shuttles. The order of movement for electrons from NADH is NADH -> Complex I
-> CoQ -> Complex III -> Cytochrome c
-> Complex IV. The order of movement
for electrons from FADH2 is FADH2 ->
Complex II -> CoQ -> Complex III ->
Cytochrome c -> Complex IV.
Electrons enter the system in pairs and
travel in pairs until CoQ, which passes them
off singly to Complex III. CoQ is called a
traffic cop for electrons.
Movement of electrons through complexes I,
III, and IV cause protons to be pumped
from the mitochondrial matrix to the intermembrane space, creating the pro971
Electron movement through complex I is reversible and can result in production of reactive oxygen species.
Complex II is a membrane bound enzyme
of the citric acid cycle (succinate dehydrogenase). It also transfers electrons to
CoQ.
The oxidized form of CoQ is known as
ubiquinone and the fully reduced form
(gain of two electrons) is ubiquinol. An intermediate form (gain of one electron) is
known as either ubisemiquinone or just
semiquinone. The three forms of CoQ allow
it to function as a traffic cop - accepting up
to two electrons and passing them off one at
a time.
Inhibitors of complex II include carboxin,
malonate, malate, and oxaloacetate.
The last two are thought to function as inhibitors of the production of reactive oxygen species.
Complex III contains 11 subunits, a 2-iron
ferredoxin, cytochromes b and c1 and
belongs to the family of oxidoreductase enzymes.
Complex III accepts electrons from coenzyme Q in electron transport and passes
them off to cytochrome c in the Q cycle.
Movement of electrons through the complex
can be inhibited by antimycin A, myxothiazol, and stigmatellin.
In the Q-cycle, electrons are passed from
ubiquinol (QH2) to cytochrome c using
Complex III as a docking station.
The process starts with a ubiquinol
(CoQH2), a ubiquinone (CoQ), and a cyto-
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ATP made in oxidative phosphorylation is released in the mitochondrial matrix, but is needed in the rest of the cell. To
get it out, an ADP-ATP translocase (antiport) in the inner membrane of the mitochondrion is used for the transfer.
Phosphate is moved into the mitochondrial matrix by a proton-phosphate translocase symport.
Movement of protons through the ATP Synthase c-ring causes it and the - stalk attached to it to spin. It is this action that is
necessary for making ATP.
The - stalk projects into the F1 head and
its rotation affects the and units, which
are a set of three dimers. The subunits
slightly change configuration as the - stalk
rotates, moving from configurations called
loose (L) to tight (T) to open (O). The L
form binds and holds ADP and Pi. The T
form squeezes them together to make ATP
and the O form opens to release the ATP.
Inhibiting electron transport and/or oxidative phosphorylation with exogenous
chemicals is dangerous and can be fatal.
ATP synthase can be physically stopped
with an inhibitor known as oligomycin A.
Oxidative phosphorylation can be also
stopped by destroying the proton gradient. This can be accomplished with an uncoupling agent, such as 2,4 dinitrophenol
(2,4 DNP), which pokes holes in the mitochondrial inner membrane, allowing an
alternate way for protons to enter the matrix
from the intermembrane space that does not
involve ATP synthase.
When an uncoupling agent is used, oxidative phosphorylation stops because
there is no proton gradient, but electron
transport, on the other hand operates rap974
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Catalase catalyzes the breakdown of hydrogen peroxide into water and oxygen.
Catalase converts up to 40,000,000 molecules of hydrogen peroxide to water and oxygen per enzyme per second. It is abundantly
found in peroxisomes.
There is evidence that reduced levels of catalase with aging may allow higher levels of
H2O2 that are responsible for bleaching that
produces gray hair.
Superoxide dismutase (SOD) is found,
like catalase, in virtually all organisms living
in an oxygen environment.
Like catalase, superoxide dismutase has a
very high Kcat value and has the highest
Kcat/Km known for any known enzyme.
over-expression of the gene is linked to neural disorders associated with Down syndrome.
Mixed function oxidases use molecular
oxygen for two different purposes in one reaction.
Monooygenases are one type of mixed
function oxidase that catalyze reactions like
the one shown below
AH + BH2 + O2 <=> AOH + B + H2O
Cytochrome P450 enzymes (called CYPs)
are family of heme-containing mixed function oxidase enzymes. The type of reaction catalyzed by them is shown below
RH + O2 + NADPH + H+ <=> ROH + H2O +
NADP+
It operates by ping-pong (double displacement) mechanism, shuffling between reactions 1 and 2 below
There are six different classes of P450 enzymes based on how they get electrons
1. O2- + Enzyme-Cu++
O2 + Enzyme-Cu+
2. O2- + Enzyme-Cu+ + 2 H+
H2O2 + Enzyme-Cu++
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Photophosphorylation
Photophosphorylation is the third general mechanism for synthesizing ATP (substrate level phosphorylation and oxidative phosphorylation are the others). It
is a mechanism of photosynthesis, a process which occurs only in plants and some microbes.
Photophosphorylation is similar to oxidative phosphorylation in relying on a proton gradient for making ATP, having a proton gradient being made by an electron
transport system, and using an ATP syn-
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The light reactions of photosynthesis occur inside chloroplasts in specialized structures called thylakoids. In the membranes of the thylakoids are contained the
electron transporting system and the
ATP synthase.
Light energy is used to excite electrons
(which ultimately come from water), thus beginning a series of electron transporting
steps and releasing O2 from the oxidized
water.
There are two photosystems for harvesting light in the membranes of the thylakoid. Chlorophyll is the most common
pigment used for this purpose in plants, but
carotenes and xanthophylls are also
used.
The thylakoid membrane does its magic
using four major protein complexes - photosystem II (PS II), cytochrome b6f complex (Cb6f), photosystem I (PS I), and
ATP synthase.
The process of photosynthesis begins in
PS II with the absorption of a photon of
light at a reaction center, which excites an
electron to a high energy. This electron
must be replaced as it will pass through the
electron transport system.
The electron replacing the excited electron
ultimately comes from water, but first is replaced by one from the oxygen evolving
complex with four manganese centers (the
source of the initial replacement electrons).
After four electrons have been replaced, the
oxygen evolving complex extracts four electrons from two water molecules, liberating
oxygen and dumping four protons into the
thylakoid space.
The excited electron transfers to pheophytin and then to protein bound plastoquinones (in order - PQA to PQ). PQ
waits and accepts two electrons and two protons to become PQH2.
When PQH2 donates the electrons to the
next acceptor (Cytochrome b6f, - Cb6f), it
pumps the protons into the thylakoid
space. Thus, the proton gradient is growing a a result of the splitting of water and
the movement of electrons. Cb6f passes off
one electron at a time to plastocyanin. At
this point the electron is ready to replace an
excited electron in photosystem I (PS I).
Also in the thylakoid membrane at this
time, ATP synthase makes ATP from the
proton gradient.
Absorption of light by photosystem I begins a similar process to what occurred in PS
II. Loss of an electron by absorption of light
creates a positive charge in PS I and it is neutralized by the electron from PS II in plastocyanin. Meanwhile, the excited electron
moves through an iron-sulfur protein,
then to ferredoxin, then to the last protein
in the system known as
Ferredoxin:NADP+ oxidoreductase,
which gives the electron and a proton to the
terminal electron acceptor, NADP+, creating NADPH. At this point, the light cycle
is complete - water has been oxidized,
ATP has been created, and NADPH has
been produced.
Plants also have an alternate route electrons
can take. It is known as cyclic photophosphorylation. It primarily involves PS I.
in it, excited electrons of PS I are not passed
to the route leading to NADP+. Instead,
they pass off to the proton-pumping Cb6f
complex. The electrons take the route they
would have taken from PS II through Cb6f
to plastocyanin, pumping protons along
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Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Student Nightmares
To the tune of Norwegian Wood
Metabolic Melodies Website HERE
I answered 3 b.
But then I thought. It might be c
Or was the false true?
I cant undo. It makes me blue
I suffered no harm,
'Cuz I awoke, to my alarm
Oh nothing compares
To deadly scares, of student nightmares
Sugar Metabolism
Glycolysis is the breakdown of sugars.
It is a catabolic process where the oxidation of sugars begins and it occurs in the cytoplasm of cells.
The end product of glycolysis is pyruvate.
The reversal is the synthesis of glucose and
that is called gluconeogenesis. It is reductive.
Complete oxidation of glucose yields carbon dioxide.
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The reason for the different paths depending on oxygen is because NAD+ is needed to
keep reaction 6 of glycoslysis going. In the
absence of oxygen, the electron transport
system (producer of NAD+) is not operating
very much. Formation of lactate from pyruvate produces NAD+ as does conversion
of pyruvate to ethanol.
Pyruvate is readily interconverted with alanine by transamination.
Pyruvate metabolism enzymes include include pyruvate dehydrogenase (makes
acetyl-CoA), lactate dehydrogenase
(makes lactate), transaminases (make
alanine), pyruvate carboxylase (makes
oxaloacetate), and pyruvate decarboxylase
(a part of pyruvate dehydrogenase that
makes acetaldehyde in bacteria and
yeast).
Gluconeogenesis occurs mostly in liver
and kidney.
Seven gluconeogenesis reactions are reversals of glycolysis reactions. Four gluconeogenesis reactions replace three essentially
irreversible reactions of glycolysis.
The four enzymes unique to gluconeogenesis are pyruvate carboxylase and PEP
carboxykinase - PEPCK (catalyze reactions that bypass pyruvate kinase),
F1,6BPase (bypasses PFK-1) and G6Pase
(bypasses hexokinase).
Pyruvate carboxylase and G6Pase are
found in the mitochondria and endoplasmic reticulum, respectively. All of the
other enzymes are found in the cytoplasm.
Biotin (vitamin B7) is a coenzyme used in
carboxylation reactions, such as by pyruvate carboxylase.
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When muscles are exercising, they use oxygen faster than the blood can deliver it, causing them to go anaerobic. This causes pyruvate to be converted to lactate (to make
NAD+ for glycolysis), which is dumped
into the blood. It travels to the liver where
there is plenty of oxygen and is converted to
pyruvate and then back to glucose, which is
dumped into the blood for the muscles.
This is the Cori cycle.
The glucose-alanine cycle is a sort of parallel cycle to the Cori cycle for amines. Instead of reduction to make lactate, pyruvate is transaminated in tissues to make
alanine, which travels in the blood to the
liver where the amine is removed to make
urea and the pyruvate is converted back
to glucose.
GPa converts from the R-state to the Tstate in the presence of glucose.
GPb converts to the R-state in the presence of AMP and to the T-state in the presence of ATP or G6P.
Epinephrine or glucagon can activate a
signaling cascade to favor phosphorylation of GPb to make GPa.
The sequence of signaling steps are 1) hormone binding; 2) activation of a Gprotein; 3) activation of adenylate cyclase to make cAMP; 4) activation of protein kinase A to phosphorylate phosphorylase kinase, activating it; 5) phosphorylation of GPb to make GPa.
Phosphorylase kinase can be activated
both by phosphorylation and by calcium.
Phosphorylation of GPb to make GPa favors glycogen breakdown. Phosphorylation of glycogen synthase by protein kinase A inhibits glycogen synthesis (converts glycogen synthase A to glycogen synthase B).
The G protein in the signaling cascade is activated by the hormone receptor by binding
GTP. The G protein is active with GTP and
over time slowly dephosphorylates GTP to
make GDP, which inactivates itself.
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phopentose epimerase similarly converts Xu-5P to Ru5P. Finally, phosphoribulokinase transfers a phosphate to
Ru5P (from ATP) to yield Ru1,5BP.
Ribulose-1,5-bisphosphate carboxylase (RUBISCO) catalyzes the addition of
carbon dioxide to ribulose-1,5bisphosphate (Ru1,5BP) to create two
molecules of 3-phosphoglycerate.
Bacterial cell walls contain a layer of protection known as the peptidoglycan layer.
The multi-step process for its synthesis begins with a modified sugar (glucosamine6-P) and after converting it to UDP-Nacetylmuramic acid, a pentapeptide sequence of L-Ala-D-Glu-L-Lys-D-Ala-DAla is attached and it is linked to another
pentapeptide of the same sequence. These
The hypoxia response allows cells to 1) import more glucose and 2) metabolize it
when it arrives. This is important, since anaerobic glucose metabolism is only 1/15 as
efficient as aerobic glucose metabolism.
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The process begins with formation of a nucleophilic carbanion on the TPP that attacks the electrophilic ketone carbon on the
pyruvate, releasing carbon dioxide in a
non-oxidative decarboxylation.
The remaining two carbon piece is known as
an activated acetaldehyde (or hydroxyethyl unit) attached to TPP.
Next, acetylation occurs as the 2-carbon
hydroxyethyl unit is transferred to lipoamide on E2. This is an oxidation of
the hydroxyethyl (to form an acetyl
group) and a reduction for the lipoamide
to which the unit is transferred.
Lipoamide is a lipoic acid covalently attached to a lysine of E2.
Prokaryotes have the option to release the
acetyl group as acetaldehyde (and form
ethanol in fermentation when oxygen is
limiting), but animals cannot.
993
In animals and prokaryotes with abundant oxygen, the acetyl group is then transferred from lipoamide to coenzyme A in
E2 to form acetyl-CoA, which is released.
The lipoamide is left with sulfhydryl
groups and these must be converted back to
disulfides to complete the cycle.
Lipoamide transfers electrons to FAD in E3,
forming FADH2 and a disulfide bond on
lipoamide. FADH2 transfers electrons to
NAD+, forming NADH, which is released.
Pyruvate deyhdrogenase is regulated
both allosterically and by covalent modification - phosphorylation / dephosphorylation.
ATP, acetyl-CoA, NADH, and fatty acids
(indicators of high energy) inhibit the enzyme.
AMP, coenzyme A, NAD+, and calcium
stimulate it.
Phosphorylation by pyruvate dehydrogenase kinase (PDK) inhibits the enzyme.
PDK is itself inhibited by pyruvate.
Dephosphorylation by pyruvate dehydrogenase phosphatase (PDP) activates
it.
Low concentrations of NADH and acetylCoA are necessary for PDP to dephosphorylate the enzyme and remain on it. When
those concentrations rise, PDP dissociates
and PDK gains access to a serine for phosphorylation.
Insulin and calcium can also activate the
PDP.
In the citric acid cycle, acetyl-CoA combines with oxaloacetate (OAA) to form citrate (catalyzed by citrate synthase).
The G is fairly negative and helps to
pull the reaction preceding it in the cycle
catalyzed by malate dehydrogenase.
In the next reaction, citrate is isomerized
to isocitrate by action of the enzyme
called aconitase.
Isocitrate is a branch point for the glyoxylate cycle, which occurs in plants and bacteria.
Oxidative decarboxylation of isocitrate
by isocitrate dehydrogenase produces
NADH and -ketoglutarate.
-ketoglutarate is a branch point for synthesis of glutamate (by transamination).
Decarboxylation of -ketoglutarate yields
succinyl-CoA and is catalyzed by ketoglutarate dehydrogenase, an enzyme similar to pyruvate dehydrogenase
- employs the same five coenzymes.
Succinyl-CoA is a branch point for the synthesis of heme.
Succinyl-CoA is converted to succinate in a
substrate level phosphorylation reaction catalyzed by succinyl-CoA synthetase. Cleavage of the thioester Co-A
bond provide the energy for the formation of
GTP.
Succinate is also produced by metabolism
of odd-chain fatty acids.
Oxidation of succinate to fumarate is
catalyzed by succinate dehydrogenase
and produces FADH2.
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ATP and NADH will tend to inhibit the cycle and NAD+, AMP, and ADP will tend to
activate the cycle.
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bon unit from the three carbon malonylACP in the first step of the elongation process; 3) a reductase (KR) to reduce the ketone; 4) a dehydrase (DH) to catalyze removal of water; 5) a reductase (ER) to reduce the trans double bond and 6) a thioesterase (TE) to cleave the finished palmitoylACP into palmitic acid and ACP.
The process of making a fatty acid in the
cytoplasm starts with two acetyl-CoA
molecules. One is converted to malonylCoA by adding a carboxyl group (catalyzed by acetyl-CoA carboxylase - the
only regulated enzyme of fatty acid synthesis and the only one separate from fatty
acid synthase).
Next, both acetyl-CoA and malonyl-CoA
have their CoA-SH portions replaced by acyl
carrier protein (ACP).
In the next step, a fatty acyl-ACP (in this
case, acetyl-ACP) is joined to malonylACP which splits out the carboxyl group
from malonyl-ACP and creates the
acetoacyl-ACP intermediate.
The ketone is then reduced to a hydroxyl
(D-configuration) using NADPH.
Next, water is removed from carbons 2 and
3 of the hydroxyl intermediate to form a
trans intermediate.
Last, the double bond is hydrogenated to
yield a saturated intermediate. This completes the first round of synthesis.
The acyl group produced at the end of the
first round is the substrate for the second
round of synthesis and this cycling continues until a 16-carbon acyl-ACP is produced palmitoyl-ACP. At this point, a thioesterase
on the fatty acid synthase cleaves the ACP
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Other Lipids
Acetyl-CoA is the building block of most
lipids.
Isoprenoids are molecules built from isoprene building blocks which, in turn, are
built from acetyl-CoA.
The two isoprene building blocks are
isopentenyl pyrophosphate and dimethylallyl pyrophosphate.
The pathway to make isoprene building
blocks overlaps with that of ketone body
synthesis.
The first step begins with joining of two
acetyl-CoAs by thiolase to make
acetoacetyl-CoA.
HMG-CoA synthase catalyzes addition of
a third acetyl-CoA to form the six carbon
compound known as hydroxymethyl
glutaryl-CoA (HMG-CoA).
HMG-CoA is a branch point with ketone
body synthesis.
In the direction of isoprene synthesis,
HMG-CoA reductase acts on HMG-CoA
to produce mevalonate
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Amino Acid
Metabolism
Amino acid metabolism is not a single
pathway
Nitrogen moves in cells through the process
of transamination
-ketoglutarate, glutamate, and glutamine play major roles in transamination,
differing by one amine each.
A common transamination is -ketoacid
+ glutamate <=> amino acid + ketoglutarate
Transamination reactions occur by a pingpong mechanism and involve swaps of
amines and oxygens in Schiff base reactions.
1006
Glutamine and asparagine are the products of gaining an amine in their respective
R-groups from ammonium ion.
Essential amino acids cannot be made by
an organism and must be in the diet.
Amino acids with common metabolic
pathways are grouped in families.
The -ketoglutarate family includes glutamate, arginine, glutamine, and proline.
Glutamate can be made by transamination of -ketoglutarate or by addition of ammonium ion to -ketoglutarate in a reaction catalyzed by glutamate dehydrogenase. Reversing the reaction releases ammonium ions, which can be important for
the urea cycle and glutamine metabolism.
Any citric acid cycle intermediate can
be a precursor of glutamate.
Glutamine can be made from glutamate via
catalysis by glutamine synthetase,
Glutamine synthetase is one of the most
important regulatory enzymes in all of
amino acid metabolism. It can be regulated
by many allosteric effectors and by adenylylation of a tyrosine residue in the enzyme.
The reaction catalyzed by glutamine synthetase is
Glutamine + ADP + Pi
The last means of making arginine is by reversing the methylation of asymmetric dimethylarginine (ADMA). ADMA is a meta-
1007
Aspartate + NH4+
Like glutamate metabolism, this reaction
be used to use or produce ammonium ion depending on cell needs.
1008
Dimethylglycine + Methionine
Melatonin is a hormone signaling the onset of darkness each day and affecting the
timing of sleep, seasonal responses, and
blood pressure, among other physiological
phenomena. It is used sometimes to help in
treatment of sleep disorders.
Phenylalanine is a component of the artificial sweetener known as aspartame (Nutrasweet) and is dangerous for people suffering from phenylketonuria, due to their deficiency of the enzyme phenylalanine hydroxylase.
Synthesis of phenylalanine begins the chorismate and proceeds through a molecular
rearrangement, decarboxylation / loss of
water, and transamination from either
glutamate or alanine to produce the final
product.
Tyrosine is made from phenylalanine by
hydroxylation by phenylalanine hydroxylase. Plants can synthesize tyrosine
by oxidation of prephenate followed by
transamination of the resulting 4hydroxyphenylpyruvate
Tyrosine is a phosphorylation target for
protein kinase enzymes involved in signal transduction pathways.
1010
Tyrosine forms a stable radical in the catalytic action of the enzyme ribonucleotide
reductase.
Tyrosine is a precursor of catecholamines, such as L-dopa, dopamine, norepinephrine, and epinephrine and thyroid hormones - triiodothyronine (T3)
and thyroxine (T4).
Thyroid hormone formation involves a
series of iodinations to tyrosines bound on
a protein known as thyroglobulin.
Oxidation and polymerization of tyrosine
occurs in synthesis of the family of melanin pigments and the benzoquinone ring of
coenzyme Q is derived from it. Metabolism of CoQ depends on HMG-CoA reductase of cholesterol metabolism.
Dopamine is a neurotransmitter made
in brain and kidney (also in plants) that
plays a major role in the brains rewardmediated behavior. It is also involved in motor control and in managing the release of
various hormones. In blood vessels, dopamine inhibits norepinephrine release
and causes vasodilation. In the kidneys, it
increases sodium excretion and urine output. In the pancreas, it reduces insulin production.
Epinephrine (adrenalin) is used to treat
anaphylaxis, cardiac arrest, croup, and, in
some cases, asthma, when other treatments
are not working, due to its ability to favor
bronchodilation.
The pyruvate family of amino acids includes alanine, leucine, isoleucine, and
valine. The last three are known as the
branched chain amino acids (BCAAs).
Transamination catalyzed by alanine
transaminase produces alanine from pyruvate.
Glutamate + Pyruvate
Alanine + -ketoglutarate
Alanine can also be produced by catabolism of valine, leucine, and isoleucine.
The glucose alanine cycle is an important
means of moving amines in the body. In
amine-rich tissue, pyruvate is converted to
alanine, which travels in the blood to the
liver where it is converted back to pyruvate,
which is used to make glucose for export
back to the blood. The amine from alanine is put on -ketoglutarate to make
glutamate, which can be used to make
urea for excretion.
1011
1012
Human proteins known to contain selenocysteine include five glutathione peroxidases, three thioredoxin reductases,
and a protein known as selenoprotein P
with 10 selenocysteine residues.
Urea-excreting organisms are called ureotelic. Those that excrete uric acid are uricotelic and those that excrete ammonia
are ammonotelic.
1013
Glutamate + NADP+
Glutamine + ADP + Pi
These reactions reduct the concentrations of
glutamate (brain neurotransmitter), ketoglutarate (energy source), and ammonia (toxic substance), so while removing
the toxic substance is good, loss of an energy
source and a neurotransmitter may be
problematic in the brain.
The urea cycle is even or generates a small
amount of energy, if one includes the energy
produced in releasing ammonia from glutamate (one NADH). The cycle either
breaks even in the worst case or generates 2
ATPs in the best case.
Amino acids whose catabolic products
yield intermediates in the glycolysis pathway are called glucogenic and those that
produce intermediates of acetyl-CoA or
acetoacetate are called ketogenic. Some
are both.
Citric acid cycle intermediates and glycolysis intermediates are common degradation products of amino acids.
Amino acids like tryptophan, phenylalanine, and tyrosine yield hormones
or neurotransmitters on further metabolism.
Cysteine and methionine must dispose of
their sulfur and all of the amino acids
must rid themselves of nitrogen, which can
1014
Nucleotide
Metabolism
Nucleotide metabolism is organized by metabolism of 1) purines; 2) pyrimidines;
and 3) deoxyribonucleotides.
These pathways can make nucleotides from
simple precursors (de novo pathways).
Others use pieces of nucleotides to reassemble full ones (salvage pathways).
De novo synthesis pathways for all nucleotides begins with synthesis of ribonucleotides.
Deoxyribonucleotides are made from the
ribonucleotides.
Purines are made by building the purine
rings on a ribose.
AMP + ATP
2 ADP
In reverse, this reaction is used to generate
ATP when the cells ATP concentration is
low. When ATP is made in reverse reaction,
AMP levels increase and this is one way the
cell senses that it is low on energy.
GMP has its own monophosphate kinase and it catalyzes this reaction
GMP + ATP
GDP + ADP
To make triphosphates, NDPK catalyzes reactions of the form
(d)XTP + (d)YDP
(d)XDP + (d)YTP
where X and Y refer to any base.
Salvage reactions to make purine nucleotides start with attachment of ribose to purine bases using phosphoribosylpyrophosphate.
Hypoxanthine/guanine phosphoribosyltransferase (HGPRT) catalyzes the following reactions
1016
Hypoxanthine + PRPP
IMP + PPi
and
Guanine + PRPP
GMP + PPi
Reduction in levels of HGPRT leads to hyperuricemia, a condition where uric acid
concentration increases in the body, causing
gout. Complete lack of HGPRT is linked to
Lesch-Nyhan syndrome.
Adenine phosphoribosyltransferase
(APRT) catalyzes the reaction corresponding
to HGPRT for salvaging adenine bases.
Adenine + PRPP
AMP + PPi
De novo synthesis of pyrimidine bases
occurs apart from the ribose and then they
are attached later. The first reaction is catalyzed by carbamoyl phosphate synthetase. It is the rate limiting step in pyrimidine biosynthesis. The enzyme is activated by ATP and PRPP and is inhibited by
UMP.
The second reaction is catalyzed by ATCase, a classic enzyme exhibiting allosteric regulation and feedback inhibi-
1017
1018
At the activity control site, ATP activates catalysis, dATP inactivates it.
In Severe Combined Immunodeficiency Disease (SCID), the salvage enzyme adenosine deaminase is deficient, leading to a
rise in concentration of dATP in cells of the
immune system, resulting in little or no immune cells for fighting infection.
1019
Dephosphorylation of IMP yields inosine. Ribose is removed from it by purine nucleotide phosphorylase to release hypoxanthine. Hypoxanthine is oxidized to xanthine in a hydrogen
peroxide-generating reaction catalyzed by
xanthine oxidase.
For GMP, phosphate is removed by nucleotidase to yield guanosine. Guanosine is cleaved from ribose to yield a free
guanine base, which is deaminated by
guanine deaminase (also called guanase)
to produce xanthine.
Xanthine can be oxidized by xanthine
oxidase (same enzyme as above) to yield
uric acid and H2O2.
Uric acid is problematic because it is only
not very soluble in water. Consequently it
precipitates out of solution, forming crystals
in joints and (frequently) in the big toe, causing gout.
There may be a negative correlation between gout and contracting multiple sclerosis.
Gout is treated with allopurinol. It inhibits xanthine oxidase, which favors an increase in the concentration of hypoxanthine and purine salvage synthesis.
Uric acid can be excreted into the urine (in
humans) or broken down into allantoin by
the uricase enzyme.
Uracil and thymine reduction gives dihydrothymine and dihydrouracil respectively. Addition of water to these creates 3ureidoisobutyrate and 3ureidopropionate respectively. Hydrolysis of these yields ammonia and carbon
dioxide for both (which are made into
urea) plus 3-aminoisobutyrate for the
thymine pathway and -alanine for the
products of the uracil pathway. 3aminoisobutyrate is produced during exercise and activates expression of thermogenic
genes in white fat cells.
-alanine is a rate-limiting precursor of
carnosine, a dipeptide of histidine and alanine. Carnosine functions as an antioxidant that scavenges reactive oxygen species and may play a role in aging.
Ribose and deoxyribose can be recycled
(ribose) or catabolized (ribose and deoxyribose).
Ribose an be reattached to bases by phosphorylase enzymes, such as uridine phosphorylase, or converted into PRPP for the
same purpose to create nucleosides.
Ribose-5-phosphate can be metabolized
to other sugars in the pentose phosphate pathway.
Deoxyribose-5-phosphate can be broken
into glyceraldehyde-3-phosphate and
acetaldehyde by deoxyribose-5-phosphate
aldolase.
1020
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Distance Ed
To the tune of Mr. Ed
Metabolic Melodies Website HERE
Bridge
A classroomclass meets every week the same time every day
But DistanceEd is most unique - its flexible schedules okay
The Global Genome Initiative is a collaborative effort to sequence at least one species
from each of the 9,500 described invertebrate, vertebrate, and plant families.
1023
Introns can vary in size from several hundred base-pairs to many thousands of base
pairs versus only a few hundred bases for
most exons.
Intron sequences account for roughly a quarter of the entire genome in humans.
Other non-coding DNA in genomes specifies
when and to what extent a gene is used, or
expressed - these are called regulatory sequences.
Almost half of the human genome appears
to consist of several kinds of repetitive sequences.
Many of the repetitive sequences are transposons - sections of DNA that can move
around within the genome.
Some transposon movements are simple
cut and paste events that cut the sequence
out of one region of the DNA and inserts it
into another location. Others move via a
process called retrotransposition involving an RNA intermediate.
There are two major classes of such transposable elements, the LINEs (Long Interspersed Elements) and SINEs (Short Interspersed Elements) in our genomes.
LINEs and SINEs are both a kind of transposable element called retrotransposons, sequences that are copied into RNA,
then reverse transcribed back into DNA
before being inserted into new locations.
Transposons tend to be inserted randomly
in the genome, in many cases within coding regions, causing problems.
1024
Transposons are a major cause of mutation in genomes and play a role in evolution.
DNA Replication
Each time a cell divides, all of its DNA must
be copied faithfully - a process called DNA
replication.
Watson and Cricks DNA structure suggested a mechanism by which doublestranded DNA could be copied to give two
identical copies.
Meselson and Stahl demonstrated that
DNA replication was semiconservative - resulting in two DNA molecules each made up of one old strand and
one new strand.
In DNA replication, a parental DNA molecule serves as the template and a new
strand is assembled across from it. Base
pairing rules dictate joining together of nucleotides to make the new strand.
Nucleotides used in DNA synthesis are deoxyribonucleoside triphosphates
(dNTPs).
1025
A replication bubble is made up of two replication forks that "move" or open up, in opposite directions.
Local unwinding of the double helix causes
over-winding (increased positive supercoiling) ahead of the unwound region
Enzymes called topoisomerases relieve
the topological stress caused by local unwinding of of the double helix.
Topoisomerases cut one or both strands
of the DNA and strands to swivel around
each other to release the tension before rejoining the ends.
A topoisomerase in E. coli that does this
is called gyrase.
When the two strands of the parental DNA
molecule are separated, they must be
blocked from re-forming double-stranded
DNA with each other.
To prevent this, separated strands of the parental DNA are bound by many molecules of
a protein called single-strand DNA binding protein (SSB).
DNA polymerases cannot begin synthesis
of a complementary strand de novo and can
only add new nucleotides on to the 3' end
of a pre-existing chain.
Some enzyme other than a DNA polymerase must first make a small region of
nucleic acid, complementary to the parental strand to provide a free 3' OH.
Primase is an enzyme which makes a short
base-paired region, called the RNA
primer, with a free 3'OH group to which a
DNA polymerase can add the first new
DNA nucleotide.
1026
clease site. The mispair at the end is removed followed by repositioning of the 3
end in the polymerase active site to continue synthesis.
In bidirectional, circular bacterial chromosome replication, binding of a protein
called Tus, at a Ter (termination) site on the
chromosome prevents further movement of
the replication fork *at a site opposite the
origin) and ends replication.
There is no fixed site for termination in linear eukaryotic chromosomes. Leading
strand synthesis goes all the way to the end
of its template strand. On the lagging
strand, the RNA primer at the end
(needed to start synthesis) creates a challenge. When it is removed, there is a small
stretch of the template strand that cannot
be copied (no primer). As a result, in each
round of replication a short sequence at the
ends of linear chromosomes will be lost.
Over time, chromosomes can become noticeably shorter.
The ends of linear chromosomes are characterized by structures called telomeres.
Telomeres contain many copies of short
repeated sequences and special proteins
that bind to them. Losing some of the repeats does not lead to loss of important coding information. Thus, the repeats act as a
buffer zone, where the loss of non-coding sequence does not doom the cell.
Shortening of the telomeres may act like a
clock, with the extent of shrinkage of the
chromosomes serving as a measure of aging.
At the end of a chromosome, the original
template strand has a 3 overhang result-
1028
After replication, both the original nucleosomes and new nucleosomes must be reassembled behind the replication fork.
DNA Repair
DNA is the master copy of instructions for
an organism so it is important not to make
mistakes when copying it to pass on to new
cells.
Minor changes in DNA sequence, such as
point mutations can sometimes have farreaching consequences.
Damage caused by radiation, environmental chemicals or even normal cellular
chemistry can interfere with the accurate
transmission of information in DNA.
1029
Base excision repair (BER) is a repair system dealing with damage that does not typically distort the DNA helix - for example, deamination of cytosine to uracil or the
methylation of a purine base.
In base excision repair a single damaged
base is first removed from the DNA, followed by removal of a region of the DNA surrounding the missing base. The gap is then
repaired by DNA polymerase and DNA
ligase.
Removal of uracil from DNA is catalyzed by
uracil-DNA glycosylase. It recognizes
uracil in DNA and breaks the glycosidic
bond between the uracil and the sugar in
the nucleotide, leaving an apyrimidinic
site (AP site).
Next, an AP endonuclease cuts the strand
with the AP site 5 to the AP site and then a
DNA polymerase uses its exonuclease
and polymerase activities to remove and replace nucleotides around the damage site.
DNA ligase seals the strands at the end.
Double strand breaks (DSB) in DNA are a
potentially lethal form of damage that, in addition to blocking replication and transcription, can also lead to chromosomal
translocations.
Two cellular mechanisms exist to help repair DSBs - 1) homologous recombination (HR) and 2) non-homologous end
joining (NHEJ).
Homologous recombination repair
commonly occurs in the late S and G2
phases of the cell after chromosome replication.
Here, a sister chromatid can be used as a
template to achieve error-free repair.
1031
Detection of the double-strand break triggers nuclease activity that chews back one
strand on each end of the break, resulting in
the production of single-stranded 3 overhangs on each end.
These single-stranded ends are bound by
several proteins, creating a nucleoprotein
filament that can then search for homologous (matching) sequences on a sister chromatid.
When homologous sequences are found, the
nucleoprotein filament invades the undamaged sister chromatid, forming a crossover
and creating heteroduplexes made up of
DNA strands from different chromatids.
Branch migration follows, during which the
Holliday junction moves along the DNA,
extending the heteroduplex away from the
original site of the crossover.
Branch migration in E.coli depends on the
activity of two proteins, RuvA and RuvB.
RuvC resolves the structure, giving complete, error-free strands.
Non-homologous end joining (NHEJ) is
error-prone. It does not use or require a homologous template to copy, and works by
simply chewing back the broken ends of
DSBs and ligating them together.
NHEJ introduces deletions in the DNA as a
result.
Translesion synthesis occurs when a DNA
polymerase encounters DNA damage on
the template strand, but instead of stalling
or skipping past the damage, replication
switches to an error-prone mode, ignoring
the template and incorporating random nucleotides into the new strand.
1032
Transcription
The flow of information from DNA to RNA
to protein is the central dogma of molecular biology.
tors between mRNA and amino acids during translation; Small RNAs that regulate
gene expression and control splicing, including miRNAs and siRNAs; 4) other small
RNAs that have a variety of functions, including the small nuclear RNAs that are part
of the splicing machinery; and 5) Long noncoding RNAs (lncRNAs)
Cells with identical DNA can turn out different because of differences that arise in gene
expression.
Each different cell type uses a different subset of the genes in that DNA to direct the
synthesis of a distinctive set of RNAs and
proteins.
1033
1034
Folding of the end of the RNA into the hairpin causes the RNA polymerase to pause.
The run of Us at the end of the hairpin permits the RNA-DNA duplex in this region to
come apart and the transcript to be released
from the DNA template and from the RNA
polymerase.
Rho is a helicase that separates the transcript from the template it is paired with.
Rho-dependent termination also requires the formation of a hairpin structure
in the RNA that causes pausing of the RNA
polymerase.
Rho binds to a region of the transcript
called the rho utilization site (rut) and
moves along the RNA till it reaches the
paused RNA polymerase where it unwinds the RNA-DNA duplex and releases
the transcript and RNA polymerase from
the DNA.
All eukaryotic RNA polymerases need additional proteins called transcription factors to help get transcription started.
Transcription happens in the nucleus in
eukaryotes, and the mRNAs produced
are processed further before they are sent
into the cytoplasm for translation.
Transcription starts about 25 bp downstream of the eukaryotic TATA box, and
creates a transcript that begins with a 5 untranslated region (5 UTR) followed by the
coding region which may include multiple
introns and ending in a 3 untranslated region or 3 UTR.
1035
The first step in the formation of the complex is binding by TFIID to the TATA box.
TFIID has several proteins, one of which is
called the TATA Binding Protein or TBP.
Binding of the TBP causes the DNA to bend
at this spot and favor binding of additional
transcription factors and RNA polymerase.
Binding of TBP is a necessary step in forming a transcription initiation complex
even when the promoter lacks a TATA box.
The order of binding of additional proteins
appears to be TFIIB, followed by TFIIF
and RNA polymerase II, then TFIIE. The
final step in the assembly of the basal transcription complex is binding of a general
transcription factor called TFIIH.
The presence of all of these general transcription factors and RNA Polymerase
II at the promoter is necessary for the initiation of transcription.
In order for RNA polymerase II to move
down the template and elongate the transcript, TFIIH must act. It is a multifunctional protein with a helicase activity and a
kinase activity. The kinase activity of
TFIIH adds phosphates onto the Cterminal domain of the RNA polymerase II. This phosphorylation by
TFIIH appears to be the signal releasing the
RNA polymerase II from the transcrip1036
RNA Processing
In bacterial cells, the mRNA is translated directly as it comes off the DNA template.
1037
1038
1039
Each transcription unit contains rRNA sequences coding for 18S, 5.8S and 28S
rRNA, and it is transcribed by RNA polymerase I into a single long transcript.
Translation
Translation is the process by which information in mRNAs is used to direct the synthesis of proteins.
tRNAs are extensively modified posttranscriptionally and contain a large number of unusual bases.
tRNAs have several self complementary regions, where the single-stranded tRNA folds
on itself and base-pairs to form what is
1040
1041
IF2 brings the initiator tRNA to the partial P-site of the small ribosomal
subunit.
Ribosomes assemble at the 5 end of a transcript by the stepwise binding of the small
and large subunits.
The small subunit binds first at specific sequences in the 5 UTR. Binding of the first
tRNA to the ribosome occurs next and
then the large subunit binds to the complex of the mRNA, initiator tRNA, and
small subunit, to form the complete ribosome.
In bacteria, the methionine on the initiator tRNA is modified by the addition of a
formyl group, and is designated tRNAfmet.
it is different from the tRNAs carrying methionine intended for other places in the
protein.
The Shine-Dalgarno sequence in the
mRNA helps to properly orient the 5 end
of the mRNA on the small subunit of the
ribosome. This happens as a result of complementarity between the Shine-Dalgarno
sequence and a separate sequence on the
16S rRNA of the small ribosomal
subunit.
When this pairing occurs, the AUG start codon is properly positioned at the P-site.
Three initiation factors, IF1, IF2, and IF3
facilitate the initial ribosome/mRNA complex.
IF3 facilitates binding of the small subunit
to the mRNA.
1042
The released polypeptide must fold properly in order to function. It may also undergo modifications such as the addition of
phosphates, sugars, lipids,and/or may
be cleaved by proteases to remove inactivating precursor sequences.
Proteins made in the cytoplasm must be
delivered to the appropriate cellular compartment in which it functions.
Some proteins are delivered to their destinations in an unfolded state, and are folded
within the compartment in which they function. Others are fully folded and may be
post-translationally modified before
they are sent to their cellular (or extracellular) destinations.
Some proteins are delivered as they are being synthesized. Others are sent posttranslationally. With the exception of cytosolic proteins, all proteins must cross membrane barriers, through membrane channels or other "gates", or by transport within
membrane vesicles that fuse with the
membrane of the target organelle to deliver their contents.
Folding of a protein is largely influenced
by hydrophobic interactions that position
hydrophobic residues in the interior of the
protein.
As a polypeptide emerges from the ribosome, the N-terminal region may begin
to fold on itself, with adjacent parts of the
chain interacting in inappropriate ways, before the entire protein has been made. This
can result in misfolding of the protein and
consequent malfunction.
Protein chaperones bind to and shield regions of polypeptides as they emerge from
1043
the ribosome to keep them from improperly interacting until they can fold properly.
Some chaperones sequester proteins to
permit unfolding and refolding of misfolded
polypeptides.
Protein sorting is the process by which
proteins are identified and delivered to a
proper compartment.
Proteins have "address labels" or sorting signals (also called signal sequences) in
their amino acid sequences that indicate
which cellular compartment they are destined for.
Signal sequences may be found at the Nterminal or C-terminal region of proteins, or they may be within the amino
acid sequence of the proteins.
Signal sequences targeting proteins to the
endoplasmic reticulum, mitochondrion, or chloroplast are at the Nterminus of a protein. Nuclear proteins,
by contrast, have the signal internal to the
polypeptide.
Proteins are synthesized by ribosomes in
the cytoplasm or by those that associate
with membranes temporarily (membranebound ribosomes). The latter make proteins that are destined for the nucleus, as
well as those going to chloroplasts, mitochondria and peroxisomes.
Nuclear proteins are delivered in their
folded state, while chloroplast and mitochondrial proteins are folded at their destination.
Proteins destined for the ER, the Golgi
apparatus, lysosomes and those that are
to be secreted from the cell are first deliv-
1044
Gene Expression
Gene expression is the process by which
information in DNA directs the production
of the proteins needed by the cell.
The first step in gene expression is transcription.
The basic mechanism by which transcription is regulated depends on highly specific
interactions between transcription regulating proteins and regulatory sequences
on DNA.
Besides the promoter, genes have additional cis regulatory sequences that control when it is transcribed.
The lac repressors binding here physically blocks the RNA polymerase from
transcribing the genes.
1045
When the lac repressor is gone, the roadblock to transcription is gone. Only when
lactose is present can transcription of the
operon to make proteins to break down
lactose be activated. Thus, these genes
are not expressed unless they are needed.
Glucose too is a factor - if it is present, lactose will not be used.
A second protein involved in lac operon
regulation is the Catabolite Activator Protein (CAP).
It binds on the side of the promoter opposite that of the lac repressor and its binding is necessary for RNA polymerase to
begin transcription of the operon.
CAP binds to its site only when glucose levels are low.
When glucose levels are low, adenylate cyclase makes a molecule called cyclic AMP
(cAMP), which can bind to CAP. CAP
binds to its site ahead of the lac promoter
only when bound to cAMP. Thus, only
when glucose levels are low will CAP bind
and favor RNA polymerase to bind and
start transcription of the lac operon.
For genes whose default state is ON, they
are expressed unless conditions turn the signal OFF. An example is the trp operon.
The trp operon makes proteins that allow
the cell to synthesize tryptophan. Unless
tryptophan is available from the cell's surroundings, the genes in the trp operon are
always expressed. When tryptophan is abundant, the trp operon is turned off. This is
achieved by a repressor protein that will
bind to the operator only in the presence
of tryptophan. Tryptophan is a corepressor of the operon.
The trp operon has two systems of regulation. The second is called attenuation.
Attenuation is a process by which the expression of an operon is controlled by termination of transcription before the
first gene of the operon.
This functions as follows: Transcription
begins upstream of the first gene in the
operon, producing what is termed a 5
leader sequence. This leader sequence
contains an intrinsic terminator that can
form a transcriptional terminator when high
levels of tryptophan are available to the
cells. It can also form a different structure
that permits continued transcription of
the genes in the operon when tryptophan
levels are low.
The 5 end of the mRNA is the first part of
the transcript to be made and since bacterial
translation is linked to transcription,
the 5 end of the RNA begins to be translated
before the entire transcript is made.
The 5 leader sequence of the trp
operon mRNA encodes a short peptide that
contains two tryptophan codons. When
tryptophan is abundant, the leader sequence is easily translated and it forms a
transcriptional terminator, which stops
transcription immediately - long before the
entire transcript is made.
If tryptophan levels are low, the ribosome stalls at the tryptophan codons. In
this case, the leader sequence adopts a different structure that allows transcription
to continue.
Thus, when tryptophan levels are high, transcription of the trp operon is stopped
quickly and when tryptophan levels are
low, transcription of the complete
1046
1047
1048
exported to the cytoplasm where the enzyme known as Dicer cuts them to
20-30 nucleotides are the sizes of mature
double-stranded miRNAs. The RNAs contain loops and mismatches.
siRNAs also derive from double-stranded
RNAs, but they may arise from either endogenous or exogenous (viral) sources
These double-stranded RNAs are also processed in the cytoplasm by Dicer to generate mature miRNAs - 20-30 nucleotide
double-stranded RNAs. Mature siRNAs
are perfectly base-paired along their lengths.
Both miRNAs and siRNAs then are assembled with Argonaute proteins to form a silencing complex called RISC (RNA-induced
silencing complex).
One strand of each of these double-stranded
RNAs is referred to as the guide RNA,
while the other is called the passenger
RNA.
During the process of loading the RNA onto
the Argonaute protein, the guide strand
of the RNA remains associated with the protein, while the passenger strand is removed.
The guide RNA associated with the Argonaute protein is the functional gene silencing complex.
Sequence specific base-pairing of the
guide RNA with a complementary mRNA
sequence leads to either the degradation of
the mRNA by the Argonaute protein (in
the case of the siRNAs) or in suppression of
translation of the mRNA (for miRNAs).
1049
The expression of at least a third of all human genes has already been shown to be
modulated by miRNAs.
Long noncoding RNAs (lncRNAs) are
RNAs of greater than 200 nucleotides that
do not code for proteins. Some come from
introns or antisense transcripts of coding
genes. Others from intergenic sequences.
The last ones are called lincRNAs.
lncRNAs appear to affect gene expression
by 1) modification of chromatin structure,
2) regulation of splicing, 3) serving as structural scaffolds for the assembly of nucleoprotein complexes or 4) other unknown ways.
Gene expression can also be regulated by
mechanisms that alter the rate of mRNA
degradation.
Regulation of translation is used to control the production of many proteins. Examples are ferritin and the transferrin
receptor.
Ferritin is an iron-binding protein that sequesters iron atoms in cells to keep them
from reacting. When iron levels are high,
there is a need for more ferritin than when
iron levels are low.
The 5'UTR of the ferritin mRNA contains
a sequence called the Iron Response Element (IRE). When iron levels are low, the
IRE is bound by a protein. The presence of
the IRE-binding protein at the 5'UTR
blocks translation of the ferritin mRNA.
When iron levels are high, it binds to the
IRE-binding protein, which undergoes a
conformational change and dissociates from
the IRE. This frees up the 5' end of the ferritin mRNA for ribosome assembly and
translation, producing more ferritin.
Signaling
Cells must know when to divide, when to undergo apoptosis (programmed cell death),
when to store food, and when to break it
down.
Signaling is dependent on molecular recognition.
In signaling, a molecule, sent by a signaling cell, is recognized and bound by a receptor protein in (or on the surface of) a target cell.
Signals may be proteins, short peptides,
lipids, nucleotides or catecholamines,
to name a few.
1050
Signal molecules that are small and hydrophobic can cross the cell membrane and
bind a receptor inside the cell.
In the transmembrane receptor proteins, the extracellular portion binds the signal and an intracellular part passes on the
message within the cell.
Different cells have different sets of receptors, so they respond to different signals or
combinations of signals.
Binding of a signal molecule to a receptor
sets off a chain of events (called signal
transduction) in the target cell that include, but are not limited to, alterations in
metabolic pathways or gene expression.
Signal transduction pathways all have
some features in common - 1) binding of a
signal to its receptor is usually followed by
the generation of a new signal(s) within the
cell; 2) most have multiple steps involving a
series of molecular messengers that amplify
and distribute the message to various parts
of the cell; and 3) the last of the messengers
usually interacts with a target protein(s)
and changes its activity, often by phosphorylation.
When a signal sets a particular pathway in
motion, it is acting like an ON switch. This
means that once the desired result has been
obtained, the cell must have a mechanism
that acts as an OFF switch.
1051
G-proteins are associated with the cytosolic side of the plasma membrane,
where they interact with the tail of the
GPCR
1052
All G-proteins share a characteristic structure- they are composed of three subunits
called , and .
Binding of a signal molecule by the extracellular part of the GPCR causes its cytosolic
tail alter the conformation of a G-protein
on the inner face of the plasma membrane. The subunit then swaps GDP for
GTP and it splits into the GTP-bound part
and the - part.
The now activated subunit can diffuse
freely along the cytosolic face of the
plasma membrane and act upon its targets.
G-proteins interact with different kinds of
target proteins.
Some targets for G-proteins are gated ion
channels. The change in the distribution
of ions across the plasma membrane
causes a change in the membrane potential.
G-proteins also interact and affect the activity of specific enzymes. The change in
activity of the target enzyme resulting from
G-protein interaction causes downstream
changes in other proteins in the cell, and
alters the metabolic state of the cell.
1054
1055
1056
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
Online Movie
To the tune of Feelin Groovy
Metabolic Melodies Website HERE
Doctor Kevins
Always blowin
Tellin me I should be knowin
All that biochemistry
I hope there is a
Online Movie
Techniques
To separate compounds from cellular environments, one must first burst open (lyse)
the cells. There are several ways to do this.
Variables to consider include 1) sample size;
2) number of samples; 3) toughness of cells;
Sonication (20-50 kHz sound waves) provides an alternative type of agitation that
can be effective, but it generates heat that
can be problematic for heat-sensitive compounds.
Molecules in the sample interact differentially with the support and travel through it
consequently at different speeds, thus enabling separation.
Whatever method is employed, crude fractions obtained from it must be further processed via fractionation.
Fractionation of samples is typically initiated with steps involving centrifugation. Using a centrifuge, one can remove cell debris,
and fractionate organelles, and cytoplasm.
Separating the item of interest from the milieu of other materials is where chromatography comes into play.
1060
1061
Chemical reagents can also be used. A protein sample treated with cyanogen bromide,
for example will have fragments of proteins each one terminating at a methionine, since cyanogen bromide breaks proteins uniformly at that amino acid.
Fluorescence Recovery After Photobleaching (FRAP) is used to measure the
two dimensional lateral diffusion of molecules in thin films, like membranes, using
fluorescently labeled probes.
In the method, a lipid bilayer is uniformly
labeled with a fluorescent tag and then a portion of the tag is bleached using a laser. The
spread of the bleached molecules is followed
using a microscope. Information obtained
in this manner provides data about the rate
of lateral diffusion occurring in a lipid bilayer.
Fluorescence resonance energy transfer (FRET - also called Frster resonance energy transfer, resonance energy transfer
(RET) or electronic energy transfer (EET))
is a method for determining interactions between biomolecules.
In the technique, a donor chromophore
or an acceptor chromophore is covalently attached to separate molecules of interest. The acceptor chromophore is designed to accept energy through from the donor molecule and fluoresce at a unique
wavelength when it receives that energy
from the donor. Only if the proteins containing the donor and acceptor chromophores are physically close in the cell will
the unique fluorescence resulting from the
transfer occur and be detected.
Microarrays employ a matrix of boxes
on a glass slide containing support materials, each box containing thousands of copies
1063
Labeled probes are designed to be complementary to (DNA/RNA) or have binding affinity for (proteins) the desired target sequence bound to the membrane.
Labels in probes can be radioactive or chemical reagents that give colored light. For
DNA/RNA, a probe might be a complementary nucleic acid sequence that is labeled in
some fashion (32P in DNA, for example).
For a protein, a probe would typically involve an antibody that specifically binds to
the target protein of interest. Protein analysis usually employs two antibodies and the
first one is not labeled. The label is on the
second antibody, which is designed to recognize only the first antibody in a piggyback
fashion. The first antibody specifically
binds to the protein of interest on the blot
and the second antibody recognizes the first
antibody.
The second antibody commonly carries an
enzyme or reagent which can cause a reaction to produce a color upon further treatment. So, if the molecule of interest is in the
original mixture, it will light up and reveal
itself. The utility and importance of restriction enzymes for making recombinant DNAs
lies in their ability to recognize sequences in
DNA and cut near or (usually) at the site
they recognize. Over 3000 such enzymes
are known. Sequences recognized by these
enzymes are typically 4-8 base pairs long
and the most commonly used enzymes recognize sequences described as palindromic.
5 -A-A-G-C-T-T-3
3 -T-T-C-G-A-A-5
There are four categories of restriction enzymes:
Type I - cut at sites a random distance away
from the recognition site
Type II - cut within or near the recognition
site.
Type III - cut a short distance away from the
recognition site and must bind ATP for action
Type IV - cut modified DNAs
The cut sites of Type II enzymes vary from
enzyme to enzyme. They are grouped into
three categories - 1) those that leave a staggered sequence after cutting that has an
overhang at the 5 end of one strand of the
duplex; 2) those that leave a staggered sequence after cutting that has an overhang at
the 3 end; and 3) those that cut both
strands in the same place, leaving no overhanging sequence - called blunt end cutters.
HindIII is a type 2 restriction enzyme in
the first category. It cuts and leaves a 5
overhang
5 -N-N-N-A 3
3 -N-N-N-T-T-C-G-A-5
5A-G-C-T-T-N-N-N-N-3
3 A-N-N-N-N-5
1065
Ssp I is a type 2 enzyme of the third category. It cuts and leaves a blunt end
5 -N-N-N-A-A-T 3
3 -N-N-N-T-T-A 5
5 A-T-T-N-N-N-N 3
3 T-A-A-N-N-N-N 5
1066
1067
1068
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats (short
repeated sequences found in prokaryotic
DNA)
The short repeats are separated by spacer sequences derived from past encounters with,
for example, a bacteriophage.
Inserted into the bacterial genome, these
sequences can be transcribed into a guide
RNA that matches, and base-pairs with,
sections of the viral genome if it is encountered again.
A nuclease associated with the guide
RNA cleaves the sequence base-paired with
the guide RNA. (The nucleases are named
Cas for CRISPR-associated.)
The essential elements of this system are a
guide RNA that homes in on the target sequence and a nuclease that can make a cut
in the sequence that is bound by the guide
RNA.
In the CRISPR/Cas9 system, the Cas9 endonuclease cuts both strands of the gene sequence targeted by the guide RNA. This
generates a double-strand break that the cell
attempts to repair.
Double-strand breaks in DNA can be repaired by simple, nonhomologous end
joining (NHEJ) or by homologous recombination. When a break is fixed by
NHEJ, there is good chance that there will
be deletions or insertions that will inactivate
the gene they are in.
Targeted cleavage of a site by CRISPR/
Cas9 can easily and specifically inactivate a
gene, making it easy to characterize the
gene's function.
1070
If a homologous sequence bearing the specific mutation is provided with the CRISPR
system, homologous recombination can
repair the break, and at the same time insert
the exact mutation desired.
In the second part of the process, a laser focused on the matrix volatilizes the sample,
causing the molecules within it to vaporize
and, in the process, to form ions by either
gaining or losing protons.
One variant inactivates the nuclease activity of Cas9. The guide RNA in this system
pairs with the target sequence, but the Cas9
does not cleave it. Instead, the Cas9 blocks
the transcription of the downstream gene,
allowing specific genes to be turned off without actually altering the DNA sequence.
Another variation also uses a disabled Cas9,
but this time, the Cas9 is fused to a transcriptional activation domain.
Here, the guide RNA positions the Cas9activator domain in a place where it can
enhance transcription from a specific promoter.
Other variations on this theme attach histone modifying enzymes or DNA methylases to the inactive Cas9. Again, the
guide RNA positions the Cas9 in the desired spot, and the enzyme attached to
Cas9 can methylate the DNA or modify
the histones in that region.
MALDI-TOF (Matrix-assisted Laser Desorption Ionization - Time of Flight) is an
analytical technique allowing one to determine the molecular masses of molecules
with great precision.
The MALDI-TOF process involves three basic steps. First, the material to be analyzed
is embedded in solid support material (matrix) that can be volatilized in a vacuum
chamber by a laser beam.
1071
1072
Graphic images in this book were products of the work of several talented students.
Links to their Web pages are below
(Male voice)
450 is the course for me
With all its biochemistry
I soak up what this course provides
Structure and function and info about peptides
(Female voice)
451s the choice for me
Mo-lec-u-lar biology
I love the way it gets risque
Exposing the bases inside of the DNA
Enzymes (Male)
5 primes (Female)
Histones (Male)
The clones (Female)
10
Appendix
Permissions for Main Book Figures
Format as follows
Figure ID
Description
Source/Creator Info
License type
Creator (if known)
License types
WCCA = Wikipedia/Wikimedia Creative Commons Attribution (followed by relevant number)
https://en.wikipedia.org/wiki/Creative_Commons_license
WCCSA = Wikipedia/Wikimedia Creative Commons Share
Alike (followed by relevant number)
https://en.wikipedia.org/wiki/Creative_Commons_license
GFDL = Gnu Free Document License https://en.wikipedia.org/wiki/GNU_Free_Documentation_
License
__________________________________________
Figure # 1.1
Tardigrade
https://commons.wikimedia.org/wiki/File:Water_bear.jpg
WCCSA 3.0
Aditya Sainiarya
Figure # 1.2
Cork cells
http://commons.wikimedia.org/wiki/File:Cork_Micrographi
a_Hooke.png
Public Domain
Figure # 1.3
Bacteria
https://commons.wikimedia.org/wiki/File:Staphylococcus_a
ureus,_50,000x,_USDA,_ARS,_EMU.jpg
Public Domain
Figure # 1.4
Metabolic Types
https://en.wikipedia.org/wiki/Metabolism
WCCSA 3.0
Wikipedia table
Figure # 1.5
Phyogenetic Tree of Life
https://commons.wikimedia.org/wiki/File:Tree_of_Living_
Organisms_2.png
WCCSA 3.0
Maulucioni y Doridi
Figure # 1.6
Autotroph/Heterotroph
https://commons.wikimedia.org/wiki/File:Auto-and_heterot
rophs.svg
WCCSA 3.0
Derivative by Mikael Hggstrm, using originals by Laghi
l,BorgQueen, Benjah-bmm27, Rkitko, Bobisbob, Jacek
FH,Laghi L and Jynto
Figure # 1.7
Cell types
https://commons.wikimedia.org/wiki/File:Celltypes.svg
Public Domain
Figure # 1.8
Archaeans
https://commons.wikimedia.org/wiki/File:Rio_tinto_river_
CarolStoker_NASA_Ames_Research_Center.jpg
Public Domain
Figure # 1.9
Methanobrevibacter Cell Wall
https://commons.wikimedia.org/wiki/File:Methanobrevibac
ter_smithii_cell_wall_and_membrane.png
WCCA 4.0
K. Gottlieb, V. Wacher, J. Sliman and M. Pimentel / Review
article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders - DOI: 10.1111/apt.13469
1075
Figure # 1.10
Paramecium
https://commons.wikimedia.org/wiki/File:Paramecium.jpg
WCCSA 3.0
Barfooz at the English Wikipedia
Figure # 1.11
Animal Cell
https://commons.wikimedia.org/wiki/File:Cell_animal.jpg
WCCSA 4.0
Zaldua I., Equisoain J.J., Zabalza A., Gonzalez E.M., Marzo
A., Public University of Navarre
Figure # 1.12
Nucleus
https://commons.wikimedia.org/wiki/File:Diagram_human
_cell_nucleus.svg
Public Domain
Figure # 1.13
Intermediate Filaments
https://commons.wikimedia.org/wiki/File:Hep2Intermediat
eFilaments2.JPG
WCCSA 3.0
J3D3
https://commons.wikimedia.org/wiki/File:Ammonium-fluor
ide-3D-balls-ionic.png
Public Domain
Figure # 1.20
Hydrogen Bonds
https://commons.wikimedia.org/wiki/File:3D_model_hydro
gen_bonds_in_water.svg
WCCSA 3.0
User Qwerter at Czech wikipedia: Qwerter. Transferred from
cs.wikipedia; Transfer was stated to be made by
User:sevela.p. Translated to English by by Michal Ma_as
(User:snek01). Vectorized by Magasjukur2
Figure # 1.21
Lactic Acid Enantiomers
https://commons.wikimedia.org/wiki/File:Milchsure_Enan
tiomerenpaar.svg
Public Domain
Figure # 1.22
Glyceraldehyde-3-P DH
https://commons.wikimedia.org/wiki/File:GAPDH_with_la
bels.png
WCCSA 3.0
Vossman
Figure # 1.14
Beta Tubulin
https://commons.wikimedia.org/wiki/File:Tetrachimena_Be
ta_Tubulin.png
WCCSA 3.0
Pawel Jasnos
Figure # 1.23
Water Structure
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 1.15
Cytoskeleton
https://commons.wikimedia.org/wiki/File:FluorescentCells.j
pg
Public Domain
Figure # 1.24
Soap
https://commons.wikimedia.org/wiki/File:Soap%26Deterge
nts.png
Public Domain
Figure # 1.16
Epithelia Types
https://commons.wikimedia.org/wiki/File:Illu_epithelium.j
pg
Public Domain
Figure # 1.25
Lipid Bilayers
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 1.17
Nerve Cell Anatomy
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 1.26
Glycerophospholipid
https://commons.wikimedia.org/wiki/File:Phospholipid.svg
Public Domain
Figure # 1.18
Organic Functional Groups
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 1.19
Tetrahedron
Figure # 1.27
Oil and Vinegar
https://commons.wikimedia.org/wiki/File:Olive_oil_with_B
alsamic_Vinegar.jpg
WCCA 2.0
Leon Brocard
Figure # 1.28
Hydration of Lipid Bilayer
http://www.aleiakim.com/
1076
Public Domain
Aleia Kim
Figure # 1.29
Protein Folding
https://commons.wikimedia.org/wiki/File:Protein_folding_
schematic.png
Public Domain
Figure # 1.30
Hydrogen Bonds
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 1.31
Hydrogen bonds in water
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 1.32
Dipole Interactions
Wikipedia Table
Figure # 2.3
Aliphatic Amino Acids
Numerous Wikipedia
Public Domain
Figure # 2.4
Asp and Glu
Numerous Wikipedia
Public Domain
Figure # 2.5
Amine Amino Acids
Numerous Wikipedia
Public Domain
Figure # 2.6
Aromatics
Numerous Wikipedia
Public Domain
Public Domain
Aleia Kim
Figure # 2.7
Hydroxyls
Numerous Wikipedia
Public Domain
Figure # 1.33
H Bonds in GC Bse Pair
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.8
AA Properties
https://en.wikipedia.org/wiki/Proteinogenic_amino_acid
WCCSA 3.0
Wikipedia Table
Figure # 1.34
Weak Acid Dissociation
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.9
Other Aas
Numerous Wikipedia
Public Domain
http://www.aleiakim.com/
Figure # 1.35
Buffering Region
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 1.36
Titration of Aspartate
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.1
Amino acid schematic
http://commons.wikimedia.org/wiki/File:AminoAcidball.svg
Public Domain
Figure # 2.2
Amino Acid Side chain properties
https://en.wikipedia.org/wiki/Proteinogenic_amino_acid
WCCSA 3.0
Figure # 2.10
Titration Curve
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 2.11
Enzyme Activity pH
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.12
L-Carnitine
https://commons.wikimedia.org/wiki/File:L-carnitine.svg
Public Domain
Figure # 2.13
Ketogenic Glucogenic
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
1077
Figure # 2.14
Modified Amino Acids
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 2.15
Phosphorylated amino acids
KGA/Wikipedia
Public Domain
WCCA 3.0
Dcrjsr / From PDB file 1HLO, displayed in KiNG
Figure # 2.24
Pauiing alpha helix
https://commons.wikimedia.org/wiki/File:AlphaHelixForLin
usPauling.jpg
WCCSA 3.0
Julianva at en.wikipedia
Figure # 2.16
Peptide Bond Formation
http://commons.wikimedia.org/wiki/File:Peptidformationba
ll.svg
Public Domain
Figure # 2.25
Helical wheel alpha helix
https://commons.wikimedia.org/wiki/File:Helical_Wheel_2
NRL_77-92_KaelFischer.jpg
WCCSA 3.0
Dcrjsr / modified from an image at
http://kael.net/helical.htm
Figure # 2.17
Four Levels Protein Structure
http://commons.wikimedia.org/wiki/File:Main_protein_str
ucture_levels_en.svg
Public Domain
Figure # 2.26
Beta Strand
https://commons.wikimedia.org/wiki/File:Beta_sheet_bond
ing_antiparallel-color.svg
Public Domain
Figure # 2.18
Short polypeptide
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.27
Supersecondary Structure
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.19
Peptide Bond Formation
http://commons.wikimedia.org/wiki/File:Peptidformationba
ll.svg
Public Domain
Figure # 2.28
Beta Strands Parallel
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.20
Cis-Trans R groups
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.29
Beta turn
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.21
RNA Genetic Code
https://commons.wikimedia.org/wiki/File:RNA-codons.png
WCCSA 3.0
TransControl /
http://en.wikipedia.org/skins-1.5/common/images/magnifyclip.png
Figure # 2.30
310 Helix
https://commons.wikimedia.org/wiki/File:310_helix_topvie
w.png
WCCSA 3.0
WillowW at English Wikipedia
Figure # 2.22
Alpha Helix
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.23
Leucine zipper
https://commons.wikimedia.org/wiki/File:Coiled-coil_TF_
Max_on_DNA.jpg
Figure # 2.31
Peptide bond resonance
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 2.32
Pi Helix
https://commons.wikimedia.org/wiki/File:Pi-helix_within_
an_alpha-helix.jpg
WCCSA 3.0
1078
http://commons.wikimedia.org/wiki/File:Disulfide-bond.pn
g
Public Domain
Figure # 2.43
Cystine
https://commons.wikimedia.org/wiki/File:Cystine-skeletal.p
ng
Public Domain
Figure # 2.44
Protein folding funnel
https://commons.wikimedia.org/wiki/File:Folding_funnel_s
chematic.svg
WCCSA 3.0
Thomas Splettstoesser (www.scistyle.com)
Figure # 2.45
Prions Aggregating
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 2.46
Mad Cow
https://commons.wikimedia.org/wiki/File:Aphis.usda.gov_B
SE_3.jpg
Public Domain
Figure # 2.47
Amyloidosis
https://commons.wikimedia.org/wiki/File:Amyloidosis,_diff
use_(5030992590).jpg
WCCSA 2.0
Yale Rosen
Figure # 2.48
Prion replication cycle
https://commons.wikimedia.org/wiki/File:Prion_Replicatio
n.png
WCCSA 3.0
Joannamasel at English Wikipedia
Figure # 2.49
Huntingtin
https://commons.wikimedia.org/wiki/File:PDB_3io4_EBI.p
ng
Public Domain
Figure # 2.50
HSP 70 Chaperonin
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.51
GroEL
https://commons.wikimedia.org/wiki/File:Chaperonin_1AO
N.png
WCCSA 3.0
1079
Thomas Splettstoesser
Figure # 2.52
Proteasome
https://commons.wikimedia.org/wiki/File:26S_proteasome
_structure.jpg
WCCSA 3.0
FridoFoe
Figure # 2.53
Ubiquitin
https://en.wikipedia.org/wiki/Proteasome#/media/File:Ubi
quitin_cartoon.png
Public Domain
Figure # 2.54
Ubituitination
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.55
RNA denaturation
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Unnumbered p. 99
Protein structure
http://commons.wikimedia.org/wiki/File:Main_protein_str
ucture_levels_en.svg
Public Domain
Unnumbered p. 104
Hemoglobin
https://commons.wikimedia.org/wiki/File:1GZX_Haemoglo
bin.png
WCCSA 3.0
Zephyris at English Wikipedia
Figure # 2.56
Impala
https://commons.wikimedia.org/wiki/File:Male_impala_pr
ofile.jpg
GFDL
Muhammad Mahdi Karim
Figure # 2.57
Fibroin Structure
https://commons.wikimedia.org/wiki/File:Male_impala_pr
ofile.jpg
Public Domain
Figure # 2.58
Silk Sari
https://commons.wikimedia.org/wiki/File:Silk_Sari_Weavi
ng_at_Kanchipuram,_Tamil_Nadu.jpg
WCCA 2.0
McKay Savage
Figure # 2.59
Desmosine
https://commons.wikimedia.org/wiki/File:Desmosine_Struc
tural_Formulae_V.1.svg
WCC0 1.0
J
Figure # 2.60
Collagen
https://commons.wikimedia.org/wiki/File:Collagentripleheli
x.png
WCCSA 3.0
Vossman
Figure # 2.61
Collagen sequence
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.62
Collagen srands cross-linked
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.63
Leucine zipper
https://commons.wikimedia.org/wiki/File:Coiled-coil_TF_
Max_on_DNA.jpg
WCCA 3.0
Dcrjsr
Figure # 2.64
Leucine zipper
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 2.65
SH2 Domain
https://commons.wikimedia.org/wiki/File:1lkkA_SH2_dom
ain.png
WCCSA 3.0
Original uploader was WillowW at en.wikipedia
Figure # 2.66
Helix turn helix
https://commons.wikimedia.org/wiki/File:Lambda_represso
r_1LMB.png
WCCSA 3.0
Zephyris at English Wikipedia / By Richard Wheeler (Zephyris) 2007
Figure # 2.67
Pleckstrin Domains
https://commons.wikimedia.org/wiki/File:1bwn_opm.png
WCCSA 3.0
Andrei Lomize
1080
Figure # 2.68
Basement membrane
https://commons.wikimedia.org/wiki/File:Extracellular_Ma
trix.png
Public Domain
https://commons.wikimedia.org/wiki/File:Spectrin_localizat
ion_under_the_neuronal_plasme_membrane..jpg
WCCSA 3.0
GerryShaw
Figure # 2.69
Intermediate Filaments
https://commons.wikimedia.org/wiki/File:Intermediate_fila
ment.svg
Public Domain
Figure # 2.77
Integrin
https://commons.wikimedia.org/wiki/File:Integrin.png
WCCSA 3.0
The original uploader was Juergen Bode at German Wikipedia
Figure # 2.70
Vimentin
https://commons.wikimedia.org/wiki/File:VIMENTIN.jpg
WCCSA 3.0
Simon Caulton
Figure # 2.78
Cadherin
https://commons.wikimedia.org/wiki/File:ECadherin_repea
ting_unit.png
Public Domain
Figure # 2.71
Focal adhesion
https://commons.wikimedia.org/wiki/File:Focaladhesiondet
ail.jpg
WCCSA 2.5
Description Fluorescence double staining of a fibroblast red:
Vinculin green: Actin Source: own work Author: Christoph
Moehl Date: 07.07.06 Permission: This picture is for free use.
You have to cite the author by his full name
Figure # 2.79
Selectin
https://commons.wikimedia.org/wiki/File:Pselectin.PNG
WCCSA 3.0
Neveu,Curtis
Figure # 2.72
Vinculin
https://commons.wikimedia.org/wiki/File:Protein_VCL_PD
B_1qkr.png
WCCSA 2.5
Emw / PyMOL rendering of PDB 1qkr
Figure # 2.73
Defensin
https://commons.wikimedia.org/wiki/File:Monomeric_and
_dimeric_representations_of_HBD-2.jpg
WCCSA 2.0
Suresh, A.; Verma, C. (2006). "Modelling study of dimerization in mammalian defensins". BMC Bioinformatics 7: S17.
DOI:10.1186/1471-2105-7-S5-S17. Anita Suresh and Chandra
Verma
Figure # 2.74
Ankyrin
https://commons.wikimedia.org/wiki/File:Ankyrin_R_mem
brane-binding_domain_1N11.png
Public Domain
Figure # 2.75
Spectrin
https://commons.wikimedia.org/wiki/File:Cytoskeleton_(Ell
iptocytosis).png
WCCA 3.0
The original uploader was Kupirijo at English Wikipedia
Figure # 2.76
Spectrin localization
Figure # 2.80
Glycophorin A
https://commons.wikimedia.org/wiki/File:PDB_1afo_EBI.jp
g
Public Domain
Figure # 2.81
Quaternary Structure
https://commons.wikimedia.org/wiki/File:Quaternary_struc
ture.png
WCCSA 3.0
Holger87
Figure # 2.82
Hemoglobin Heme
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.83
Hemoglobin Myoglobin
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.84
Oxygenating Hemoglobin
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.85
Sequential Model
http://www.aleiakim.com/
Public Domain
Aleia Kim
1081
Figure # 2.86
Bohr effect pH
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.87
pO2 in Tissues and Lungs
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.88
Bohr effect O2 saturation
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.89
2,3 BPG
https://commons.wikimedia.org/wiki/File:D-1,3-Bisphospho
glycerat2.svg
Public Domain
Figure # 2.90
Heme and Binding Site
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.91
Hemoglobin hole of the Donut
https://commons.wikimedia.org/wiki/File:1GZX_Haemoglo
bin.png
WCCSA 3.0
Zephyris at English Wikipedia / PDB; PDB ENZYME; Released under the GNU Free Documentation License
Figure # 2.92
Carbonic acid formation
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.93
Globin O2 saturation
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.94
Sickld Cells
https://commons.wikimedia.org/wiki/File:1911_Sickle_Cells
.jpg
WCCA 3.0
OpenStax College / Anatomy & Physiology, Connexions Web
site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013
Figure # 2.95
1082
Microtubules
https://commons.wikimedia.org/wiki/File:Comparison_of_
bacterial_and_eukaryotic_microtubules.jpg
WCCSA 4.0
Pilhofer, M., Ladinsky, M.S., McDowall, A.W., Petroni, G.,
Jensen, G.J. / Pilhofer, M., Ladinsky, M.S., McDowall, A.W.,
Petroni, G. & Jensen, G.J. Microtubules in bacteria: Ancient
tubulins build a five-protofilament homolog of the eukaryotic
cytoskeleton. PLoS Biol 9, e1001213 (2011)
Figure # 2.105
Microtubules Structure
https://commons.wikimedia.org/wiki/File:Microtubule_stru
cture.png
WCCSA 4.0
Thomas Splettstoesser (www.scistyle.com)
Figure # 2.106
Kinesin and Dynein
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.107
Kinesin
https://commons.wikimedia.org/wiki/File:PDB_3kin_EBI.j
pg
Public Domain
Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute /
http://www.ebi.ac.uk/Information/termsofuse.html
Figure # 2.108
Dynein
https://commons.wikimedia.org/wiki/File:Cytoplasmic_dyn
ein.svg
WCCA 3.0
User:Delldot
Figure # 2.109
Eukaryotic Flagellum
https://commons.wikimedia.org/wiki/File:Eukaryotic_flagel
lum.svg
WCCSA 3.0
en:User:Smartse / File:Axoneme.JPG and Figure 19.28 on
page 819 of "Molecular Cell Biology, 4th edition, Lodish and
Berk" ISBN 0-7167-3706-X
Figure # 2.110
Actin Filament Anatomy
https://commons.wikimedia.org/wiki/File:1003_Thick_and
_Thin_Filaments.jpg
WCCSA 3.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 2.111
Myosin Molecule
https://commons.wikimedia.org/wiki/File:1003_Thick_and
_Thin_Filaments.jpg
WCCSA 3.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 2.112
Sarcomere Thick thin filaments
https://commons.wikimedia.org/wiki/File:Sarcomere.gif
Public Domain
Figure # 2.113
Skeletal muscle
https://commons.wikimedia.org/wiki/File:Skeletal_muscle_
-_longitudinal_section.jpg
WCCSA 3.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 2.114
Skeletal muscle anatomy
https://commons.wikimedia.org/wiki/File:Blausen_0801_S
keletalMuscle.png
WCCA 3.0
BruceBlaus. When using this image in external sources it can
be cited as: Blausen.com staff. "Blausen gallery 2014". Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010.
ISSN 20018762
Figure # 2.115
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.116
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.117
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.118
Muscle contraction 1
1083
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.119
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.120
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.121
Muscle contraction 1
https://commons.wikimedia.org/wiki/File:Muscle_Contracti
on.svg
WCCA 4.0
James.mcd.nz / SVG reproduction of PNG
image:Muskel-molekular.png created by user:Hank van Helvete
Figure # 2.122
Sarcomere Assembly
https://commons.wikimedia.org/wiki/File:1003_Thick_and
_Thin_Filaments.jpg
WCCA 4.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 2.123
Sarcomere
https://commons.wikimedia.org/wiki/File:Sarcomere.svg
WCCSA 3.0
Slashme at English Wikipedia / Richfield, David. "Medical
gallery of David Richfield 2014". Wikiversity Journal of Medicine 1 (2). DOI:10.15347/wjm/2014.009. ISSN 2001-8762
Figure # 2.124
Muscle fiber
https://commons.wikimedia.org/wiki/File:Skeletal_muscle.j
pg
WCCSA 3.0
Raul654
Figure # 2.125
Troponin Structure
http://commons.wikimedia.org/wiki/File:Troponin_Ribbon
_Diagram.png
Public Domain
Figure # 2.126
Creatine phosphate phosphorylation
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.127
DNA Nucleotides
https://en.wikipedia.org/wiki/File:0322_DNA_Nucleotides.j
pg
WCCA 4.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 2.128
Nucleotides
http://en.wikipedia.org/wiki/File:Nucleotides_1.svg
Public Domain
Figure # 2.129
Cytidine
https://commons.wikimedia.org/wiki/File:Cytidin.svg
Public Domain
Figure # 2.130
DNA-nucleobases
https://commons.wikimedia.org/wiki/File:DNA-Nucleobase
s.svg
Public Domain
Figure # 2.131
Base pairing DNA duplex
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.132
Major/minor groove
https://commons.wikimedia.org/wiki/File:DNA-ligand-by-A
balone.png
WCCSA 3.0
P99am
Figure # 2.133
ABZ DNA
http://commons.wikimedia.org/wiki/File:A-B-Z-DNA_Side_
View.png
Public Domain
Figure # 2.134
Supercoils
https://commons.wikimedia.org/wiki/File:(%2B%26-)superc
oils2.png
WCCSA 3.0
Ascendinglotus
1084
Darekk2
Figure # 2.135
Plasmids
https://commons.wikimedia.org/wiki/File:Plasmid_em.jpg
WCCSA 3.0
The original uploader was Sec11 at German Wikipedia
Figure # 2.136
Circular DNA supercoiling
https://commons.wikimedia.org/wiki/File:Circular_DNA_S
upercoiling.png
WCCSA 3.0
Richard Wheeler (Zephyris)
Figure # 2.137
RNA Chemical Structure
https://commons.wikimedia.org/wiki/File:RNA_chemical_s
tructure.GIF
WCCSA 3.0
en:User:Narayanese
Figure # 2.138
tRNA structure
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_1ehz.png
WCCSA 3.0
Yikrazuul
Figure # 2.139
miRNA
http://commons.wikimedia.org/wiki/File:Examples_of_mic
roRNA_stem-loops.jpg
WCCSA 4.0
VTD
Figure # 2.140
50S ribosomal subunit
https://commons.wikimedia.org/wiki/File:50S-subunit_of_t
he_ribosome_3CC2.png
WCCSA 3.0
Yikrazuul
Figure # 2.141
Hyperchromic effect
https://commons.wikimedia.org/wiki/File:Hyperchromicity.
svg
WCCSA 3.0
Fdardel
Figure # 2.142
Prokaryotic cell
http://commons.wikimedia.org/wiki/File:Average_prokaryo
te_cell-_en.svg
Public Domain
Figure # 2.143
Nucleosome structure
https://commons.wikimedia.org/wiki/File:Nucleosome_orga
nization.png
WCCSA 3.0
Figure # 2.144
Nucleosome detailed structure
https://en.wikipedia.org/wiki/File:Nucleosome_core_particl
e_1EQZ_large.gif
WCCSA 3.0
Darekk2 using information at
http://www.rcsb.org/pdb/explore/explore.do?structureId=1
EQZ
Figure # 2.145
Histone H3 sequence
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.146
DNA to nucleosomes
https://www.genome.gov/dmd/img.cfm?node=Photos/Grap
hics&id=85212
Public Domain
Figure # 2.147
Ames Test
https://commons.wikimedia.org/wiki/File:Ames_test.svg
WCCSA 3.0
Histidine
Unnumbered p. 188
Sugars
https://commons.wikimedia.org/wiki/File:Sucre_blanc_cass
onade_complet_rapadura.jpg
Public Domain
Figure # 2.148
Sugar Structures
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.149
Diastereomers
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.150
Epimers
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.151
Enantiomers
https://commons.wikimedia.org/wiki/File:D-L-_Glucose_fa
rbig_V1.png
Public Domain
Figure # 2.152
1085
Fructose isomers
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.153
Anomers
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.154
Fructose & Pyranose
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.155
Boat and Chair
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.156
Modified Sugars
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.157
Glycosidic Bond Formation
http://commons.wikimedia.org/wiki/File:Ethyl-glucoside.pn
g
Public Domain
Figure # 2.158
Benedict's Test
https://commons.wikimedia.org/wiki/File:Trommer%27s_te
st.jpg
WCCSA 4.0
Kubawlo
Figure # 2.159
Reducing/Non-reducing sugars
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.160
Glucuronic Acid
https://commons.wikimedia.org/wiki/File:Alpha-D-Glucuro
nat.svg
Public Domain
Figure # 2.161
Sorbitol
https://commons.wikimedia.org/wiki/File:D-Sorbitol.svg
Public Domain
Sucralose
https://commons.wikimedia.org/wiki/File:Sucralose.svg
Public Domain
Figure # 2.163
Disaccharides
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.164
Oligosaccharide branched
https://commons.wikimedia.org/wiki/File:Branched_oligosa
ccharide_struct.svg
Public Domain
Figure # 2.165
N-glycosylation
https://commons.wikimedia.org/wiki/File:Variety_of_glyca
ns.svg
WCCSA 3.0
Dna 621
Figure # 2.166
N-linked glycosylation processing
https://commons.wikimedia.org/wiki/File:Glycan_processin
g_in_the_ER_and_Golgi.png
WCCSA 3.0
Dna 621
Figure # 2.167
N-Glycan Types
https://commons.wikimedia.org/wiki/File:Types_of_glycans
.svg
WCCSA 3.0
Dna 621
Figure # 2.168
Sugars in Glycosylation
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.169
Modified Sugars in Glycosylation
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.170
Erythropoitin
https://commons.wikimedia.org/wiki/File:Erythropoietin.pn
g
Public Domain
Figure # 2.171
Amylose
http://commons.wikimedia.org/wiki/File:Amylose2.svg
Public Domain
Figure # 2.162
1086
Figure # 2.172
Amylose
http://commons.wikimedia.org/wiki/File:Amylose_3Dproje
ction.corrected.png
Public Domain
Figure # 2.173
Glycogen
http://commons.wikimedia.org/wiki/File:Glykogen.svg
Public Domain
Figure # 2.174
Cellulose
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.175
Xylose
https://commons.wikimedia.org/wiki/File:Beta-D-Xylofuran
ose.svg
Public Domain
Figure # 2.176
Chitin
https://commons.wikimedia.org/wiki/Category:Chitin#/me
dia/File:Chitin_Haworth.svg
Public Domain
Figure # 2.177
Chitin in Wasp Wing
https://commons.wikimedia.org/wiki/File:Glanzkaefer.jpg
WCCSA 3.0
zituba / http://www.seppl-mikroskopie.de.vu (selbst fotografiert)
Figure # 2.178
Pectin
https://commons.wikimedia.org/wiki/File:Pectin.jpg
Public Domain
Figure # 2.179
Galacturonic Acid
https://commons.wikimedia.org/wiki/File:Galacturonic_aci
d.png
Public Domain
Figure # 2.180
Hemagglutinin
https://commons.wikimedia.org/wiki/File:Hemagglutinin_l
ateral.jpg
Public Domain
Figure # 2.181
Biofueled Bus
https://commons.wikimedia.org/wiki/File:Soybeanbus.jpg
Public Domain
Figure # 2.182
Agarose Polymer repeat
https://commons.wikimedia.org/wiki/File:Agarose_polymer
e.svg
Public Domain
Figure # 2.183
Agar plates
https://commons.wikimedia.org/wiki/File:Agarplate_redblo
odcells_edit.jpg
Public Domain
Figure # 2.184
Agarose Gel
https://commons.wikimedia.org/wiki/File:Two_percent_Ag
arose_Gel_in_Borate_Buffer_cast_in_a_Gel_Tray_(Front,
_angled).jpg
WCCA 2.0
Joseph Elsbernd /
https://www.flickr.com/photos/codonaug/6125594775/
Figure # 2.185
Chondroitin Sulfate
https://commons.wikimedia.org/wiki/File:Chondroitin_Sulf
ate_Structure_NTP.png
Public Domain
Figure # 2.186
Heparin forms
https://commons.wikimedia.org/wiki/File:Heparin-3D-struc
tures.png
Public Domain
Figure # 2.187
Heparin structure
http://commons.wikimedia.org/wiki/File:Heparin-2D-skelet
al.png
Public Domain
Figure # 2.188
Hyaluronic acid
http://commons.wikimedia.org/wiki/File:Hyaluronan.png
Public Domain
Figure # 2.189
Synovial Fluid
https://commons.wikimedia.org/wiki/File:Joint.svg
WCCSA 3.0
Madhero88
Figure # 2.190
Saturated and Unsaturated Fatty acids
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Unnunmbered p. 219
Fat mice
https://commons.wikimedia.org/wiki/File:Fatmouse.jpg
Public Domain
Figure # 2.191
1087
Arachidonic acid
https://commons.wikimedia.org/wiki/File:Arachidonic_acid
.svg
WCCSA 4.0
Edward the Confessor
Figure # 2.201
Phosphatidylcholine
https://commons.wikimedia.org/wiki/File:Phosphatidyl-Cho
line.svg
Public Domain
Figure # 2.192
Fatty acid summary
https://en.wikipedia.org/wiki/Fatty_acid
WCCSA 3.0
Wikipedia Table
Figure # 2.202
Cardiolipin
https://commons.wikimedia.org/wiki/File:Diphosphatidyl-G
lycerol.png
Public Domain
Figure # 2.193
Unsaturated fatty acid table
https://en.wikipedia.org/wiki/Fatty_acid
WCCSA 3.0
Wikipedia Table
Figure # 2.203
Cardiolipin in apoptosis
https://commons.wikimedia.org/wiki/File:Apotosis.jpg
Public Domain
Figure # 2.194
Fatty acid models
https://commons.wikimedia.org/wiki/File:Rasyslami.jpg
WCCSA 3.0
The original uploader was (Automated conversion) at English
Wikipedia
Figure # 2.195
Delta and Omega Numbering of fatty acids
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.196
Fat/oil
https://commons.wikimedia.org/wiki/File:Fat_triglyceride_
shorthand_formula.PNG
Public Domain
Figure # 2.197
Fat/lipase action
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.198
Pancreatic lipase
https://commons.wikimedia.org/wiki/File:Lipase_PLRP2.pn
g
Public Domain
Figure # 2.199
Phosphatidic Acid
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.200
Phosphatide add-ons
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.204
Diacylglycerol
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.205
Inositol
https://commons.wikimedia.org/wiki/File:Myo-Inositol.svg
Public Domain
Figure # 2.206
Phytic acid
https://commons.wikimedia.org/wiki/File:Phytic_acid.svg
Public Domain
Figure # 2.207
PIP2
https://commons.wikimedia.org/wiki/File:Phosphatidylinosi
tol-4,5-bisphosphate.svg
Public Domain
Figure # 2.208
Phosphatidylinositol-4-phosphate
https://commons.wikimedia.org/wiki/File:Phosphatidylinosi
tol-4-phosphate.png
Public Domain
Figure # 2.209
Plasmalogen
https://commons.wikimedia.org/wiki/File:Plasmalogen-ethe
rlipd.png
WCCSA 3.0
Phaeton1
Figure # 2.210
Sphingosine & Ceramide
https://commons.wikimedia.org/wiki/File:Sphingolipids_ge
neral_structures.png
WCCSA 3.0
LHcheM
Figure # 2.211
1088
Sphingolipid schematic
https://commons.wikimedia.org/wiki/File:Sphingolipid.png
Public Domain
https://commons.wikimedia.org/wiki/File:Sitosterol_structu
re.svg
Public Domain
Figure # 2.212
Sphingolipid generalstructures
https://commons.wikimedia.org/wiki/File:Sphingolipids_ge
neral_structures.png
WCCSA 3.0
LHcheM
Figure # 2.222
Margarine
https://commons.wikimedia.org/wiki/File:Margarine.jpg
WCCSA 2.0
SpooSpa / http://flickr.com/photos/spoospa/68758014/
Figure # 2.213
Arachidonic acid straight and bent
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.214
Prostaglanding H2
https://commons.wikimedia.org/wiki/File:Prostaglandin_H
2_skeletal.svg
Public Domain
Figure # 2.215
Prostaglandin E2
https://commons.wikimedia.org/wiki/File:Prostaglandin_E2
.svg
Public Domain
Figure # 2.216
Prostaglandin F2alpha
https://commons.wikimedia.org/wiki/File:Dinoprost.svg
Public Domain
Figure # 2.217
Thromboxane A2
https://commons.wikimedia.org/wiki/File:Thromboxane_A
2_acsv.svg
Public Domain
Figure # 2.218
Prostacyclin
http://commons.wikimedia.org/wiki/File:Prostacyclin-2D-sk
eletal.png
Public Domain
Figure # 2.219
Leukotriene A4
https://commons.wikimedia.org/wiki/File:Leukotriene_A4.s
vg
Public Domain
Figure # 2.220
Cholesterol
http://commons.wikimedia.org/wiki/File:Cholesterol.svg
Public Domain
Figure # 2.221
Sitosterol
Figure # 2.223
Cholsterol model
https://commons.wikimedia.org/wiki/File:Cholesterol_mole
cule_ball.png
Public Domain
Figure # 2.224
Ezetemibe
https://commons.wikimedia.org/wiki/File:Ezetimibe.svg
Public Domain
Figure # 2.225
Retinol all trans
https://commons.wikimedia.org/wiki/File:All-trans-Retinol
2.svg
Public Domain
Figure # 2.226
Retinal 11-cis
https://commons.wikimedia.org/wiki/File:11-cis-Retinal2.sv
g
Public Domain
Figure # 2.227
Beta-Carotene
https://commons.wikimedia.org/wiki/File:Beta-carotene.svg
Public Domain
Figure # 2.228
Color sensitivity cones
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.229
Cholecalciferol
https://commons.wikimedia.org/wiki/Category:Cholecalcifer
ol#/media/File:Cholecalciferol.svg
Public Domain
Figure # 2.230
Skin layers
https://commons.wikimedia.org/wiki/File:Skinlayers.png
Public Domain
Figure # 2.231
Calcitriol
https://commons.wikimedia.org/wiki/File:Calcitriol2DACS.s
vg
Public Domain
1089
Figure # 2.232
Tocotrienols
https://commons.wikimedia.org/wiki/File:Tocotrienols.svg
Public Domain
Figure # 2.233
Alpha tocopherol
https://commons.wikimedia.org/wiki/File:Tocopherol,_alph
a-.svg
Public Domain
Figure # 2.234
Lipid peroxidation
https://commons.wikimedia.org/wiki/File:Lipid_peroxidatio
n.svg
Public Domain
Figure # 2.235
Vitamin K forms
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.236
Vitamin K recycling
https://commons.wikimedia.org/wiki/File:K1_vitamin_Mec
hanism_of_Action.svg
WCCSA 4.0
RicHard-59
Figure # 2.237
Steroid numbering PJ
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 2.238
Aldosterone
https://commons.wikimedia.org/wiki/File:Aldosterone-2D-s
keletal.svg
Public Domain
Figure # 2.239
Cortisol
https://commons.wikimedia.org/wiki/File:Cortisol2.svg
Public Domain
Figure # 2.240
Progesterone
https://commons.wikimedia.org/wiki/File:Progesteron.svg
Public Domain
Figure # 2.241
Testosterone
https://commons.wikimedia.org/wiki/File:Testosteron.svg
Public Domain
Figure # 2.242
Estradiol
https://commons.wikimedia.org/wiki/File:Estradiol.svg
Public Domain
Figure # 2.243
Tetrahydrocannibinol
https://commons.wikimedia.org/wiki/File:Tetrahydrocanna
binol.svg
Public Domain
Figure # 2.244
Anandamide
https://commons.wikimedia.org/wiki/File:Anandamide_ske
letal.svg
Public Domain
Figure # 2.245
Lipoxin A4
http://commons.wikimedia.org/wiki/File:Lipoxin_A4.svg
Public Domain
Figure # 2.246
Heme b
https://commons.wikimedia.org/wiki/File:Heme_b.svg
Public Domain
Figure # 2.247
Heme in Succinate dehydrogenase
https://commons.wikimedia.org/wiki/File:Succinate_Dehyg
rogenase_1YQ3_Haem_group.png
WCCSA 3.0
The original uploader was Zephyris at English Wikipedia
Figure # 2.248
Porphobilinogen
https://commons.wikimedia.org/wiki/File:Porphobilinogen.
png
Public Domain
Figure # 2.249
Dolichol pyrophosphate
https://commons.wikimedia.org/wiki/File:Dolicholpyrophos
phat.svg
Public Domain
Figure # 2.250
Pine tree resin
https://commons.wikimedia.org/wiki/File:Rsine.jpg
WCCSA 3.0
Meanos (2004)
Figure # 2.251
Monoterpenes
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.252
Dimethylallylpyrophosphate
https://commons.wikimedia.org/wiki/File:Dimethylallyl_di
phosphate.svg
Public Domain
1090
Figure # 2.253
Isopentenylpyrophosphate
https://commons.wikimedia.org/wiki/File:Isopentenyl_pyro
phosphate.svg
Public Domain
Figure # 2.254
Lycopene
https://commons.wikimedia.org/wiki/File:Likopen_007.svg
Public Domain
Figure # 2.255
Caffeine
https://commons.wikimedia.org/wiki/File:Koffein_-_Caffei
ne.svg
Public Domain
Figure # 2.256
Apoliporotein table
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 2.257
Apo A1
https://commons.wikimedia.org/wiki/File:PBB_Protein_AP
OA1_image.jpg
Public Domain
Figure # 2.258
Chylomicron
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.259
Chylomicron
https://commons.wikimedia.org/wiki/File:2512_Chylomicro
ns_Contain_Triglycerides_Cholesterol_Molecules_and_Oth
er_Lipids.jpg
WCCA 3.0
OpenStax College / Anatomy & Physiology, Connexions Web
site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013
Figure # 2.260
Lipid Movement in body
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.261
Receptor mediated endocytosis
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 2.262
Foam Cells
https://commons.wikimedia.org/wiki/File:Gastric_Xanthela
sma,_CD68.jpg
WCCSA 3.0
Patho
Figure # 2.263
Atherosclerosis
https://commons.wikimedia.org/wiki/File:Endo_dysfunctio
n_Athero.PNG
WCCSA 3.0
Author information lacking
Figure # 2.264
Carotid artery plaque
https://commons.wikimedia.org/wiki/File:Carotid_Plaque.j
pg
WCCA 2.0
Ed Uthman, MD. /
http://flickr.com/photos/euthman/121061911/in/set-720575
94114099781/
Figure # 3.1
Lipid bilayer
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.2
Lipid bilayer organization and charges
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.3
Glycerophospholipid schematic
https://commons.wikimedia.org/wiki/File:Phospholipid.svg
Public Domain
Figure # 3.4
Glucocerebroside
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.5
Phosphoglyceride and Sphingolipid
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.6
Lipid bilayer types
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.7
Membrane lipid composition
http://pehrjac.wix.com/pehrjacobson
Public Domain
1091
Pehr Jacobson
Figure # 3.8
Membrane components
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.9
Organelle membrane lipids
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.10
FRAP
https://commons.wikimedia.org/wiki/File:Frap_diagram.sv
g
Public Domain
Figure # 3.11
Flippases
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Public Domain
Pehr Jacobson
Figure # 3.18
Membrane protein types
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.19
Integral and Anchored membrane proteins
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.20
Integral membrane protein types
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.21
ABO Blood types
https://commons.wikimedia.org/wiki/File:ABO_blood_type.
svg
Public Domain
Figure # 3.12
Flippase
https://commons.wikimedia.org/wiki/File:Flippase_pglK_p
db_5c73.png
WCCSA 3.0
Opabinia regalis
Figure # 3.22
Osmotic pressure sugar
https://commons.wikimedia.org/wiki/File:Osmosis_diagra
m.svg
Public Domain
Figure # 3.13
Cholesterol in membrane
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.23
Hypertonic, hypotonie Red Blood cells
https://commons.wikimedia.org/wiki/File:Osmotic_pressur
e_on_blood_cells_diagram.svg
Public Domain
Figure # 3.14
Membrane transition temperature
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.24
Hypertonic, hypotonic plant cells
https://commons.wikimedia.org/wiki/File:Turgor_pressure
_on_plant_cells_diagram.svg
Public Domain
Figure # 3.15
Lipid raft
https://commons.wikimedia.org/wiki/File:Lipid_raft_organ
isation_scheme.svg
Public Domain
Unnnumbered, p. 285
Diffusion across cell meembrane
https://commons.wikimedia.org/wiki/File:Blausen_0213_C
ellularDiffusion.png
WCCSA 3.0
BruceBlaus / Blausen.com staff. "Blausen gallery 2014".
Wikiversity Journal of Medicine.
DOI:10.15347/wjm/2014.010. ISSN 20018762
Figure # 3.16
Cholesterol with Sphingolipid
https://commons.wikimedia.org/wiki/File:Space-Filling_Mo
del_Sphingomyelin_and_Cholesterol.jpg
Public Domain
Figure # 3.17
Lipid bilayer ion barrier
http://pehrjac.wix.com/pehrjacobson
Figure # 3.25
Uniport antiport symport
https://commons.wikimedia.org/wiki/File:Porters.PNG
Public Domain
Figure # 3.26
1092
WCCA 3.0
David Goodsell / RCSB PDB Molecule of the Month
Figure # 3.36
Transport protein
https://commons.wikimedia.org/wiki/File:Blausen_0213_C
ellularDiffusion.png
WCCSA 3.0
BruceBlaus / Blausen.com staff. "Blausen gallery 2014".
Wikiversity Journal of Medicine.
DOI:10.15347/wjm/2014.010. ISSN 20018762.
Figure # 3.37
Active transport
https://commons.wikimedia.org/wiki/File:Scheme_sodiumpotassium_pump-en.svg
Public Domain
Figure # 3.38
NaK ATPase
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.39
V-type ATPase
https://en.wikipedia.org/wiki/File:VATPase-en.png
WCCSA 3.0
NOchotny at English Wikipedia
Figure # 3.40
Neuron
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.41
Nerves in muscular contraction
https://commons.wikimedia.org/wiki/File:The_Muscle_Con
traction_Process.png
WCCSA 4.0
Elliejellybelly13
Figure # 3.42
Depolarization/Repolarization
https://commons.wikimedia.org/wiki/File:1221_Action_Pot
ential.jpg
WCCSA 4.0
OPenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 3.43
Voltage-gated ion channels
https://commons.wikimedia.org/wiki/File:1218_Voltage-gat
ed_Channels.jpg
WCCA 4.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
1093
Public Domain
Figure # 3.44
Ion movement in nerve signal
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.45
Pre-synaptic vesicle
https://commons.wikimedia.org/wiki/File:Synapse_diag1.sv
g
WCCSA 3.0
vectorization: Mouagip (talk) / Synapse_diag1.png: Drawn by
fr:Utilisateur:Dake / Corrections of original PNG by
en:User:Nrets
Figure # 3.46
Na-Glucose Pump
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.47
ABC Importer
https://commons.wikimedia.org/wiki/File:Abc_importer.jpg
Public Domain
Figure # 3.48
ABC Exporter
https://commons.wikimedia.org/wiki/File:Abc_exporter.jpg
Public Domain
Figure # 3.49
Lactose Permease
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.50
Lactose permease structure WCCSA 3.0
https://en.wikipedia.org/wiki/File:2y5y.png
WCCSA 3.0
A2-33
Figure # 3.51
Lactose permease secondary transport
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.52
Glucose transporters
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.53
Endocytosis types
https://commons.wikimedia.org/wiki/File:Endocytosis_type
s.svg
Figure # 3.54
Receptor mediated endocytosis
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.55
Clathrin endocytosis
https://commons.wikimedia.org/wiki/File:Itrafig2.jpg
WCCA 2.5
Copyright: 2006 Barth D. Grant and Miyuki Sato. This is
an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted / Grant, B. D. and Sato, M /
http://www.wormbook.org/chapters/www_intracellulartraffi
cking/intracellulartrafficking.html (Transferred from
en.wikipedia to Commons by Vojtech.dostal.)
use, distribution, and reproduction in any medium, provided
the original author and source are credited."
Figure # 3.56
Macropinocytosis
https://commons.wikimedia.org/wiki/File:Pinocytosis.svg
Public Domain
Figure # 3.57
Phagocytosis
https://commons.wikimedia.org/wiki/File:(zh)Phagocytosis
2.png
WCCA 3.0
GrahamColm / hagocytosis2.png
Figure # 3.58
Phagocytosis neutrophil
https://commons.wikimedia.org/wiki/File:Neutrophil_with
_anthrax_copy.jpg
WCCA 3.0
Volker Brinkmann / (November 2005). "Neutrophil engulfing Bacillus anthracis". PLoS Pathogens 1 (3): Cover page.
DOI:10.1371. Retrieved on 2009-01-04.
Figure # 3.59
EGFR internalization
https://commons.wikimedia.org/wiki/File:HeLa_cell_endoc
ytic_pathway_labeled_for_EGFR_and_transferrin.jpg#mwjump-to-license
WCCA 3.0
Matthew R G Russell / Doyotte, A., Russell, M.R.G., Hopkins,
C.R., Woodman, P.G. (2005) Depletion of TSG101 forms a
mammalian Class E compartment: a multicisternal early
endosome with multiple sorting defects. J. Cell Sci,
118:3003-3017
Figure # 3.60
Cell membrane fusions
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
1094
Figure # 3.61
Pre-synaptic vesicle
https://en.wikipedia.org/wiki/Synaptic_vesicle#/media/File
:Synapse_diag1.svg
WCCSA 3.0
vectorization: Mouagip (talk) / Synapse_diag1.png: Drawn by
fr:Utilisateur:Dake / Corrections of original PNG by
en:User:Nrets
Figure # 3.62
Membrane fusion SNARE
https://commons.wikimedia.org/wiki/File:Exocytosis-machi
nery.jpg
WCCSA 3.0
Danko Dimchev Georgiev, M.D. /
http://en.wikipedia.org/wiki/Image:Exocytosis-machinery.jp
g
Figure # 3.70
Liposome formation
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.71
Hydropathy index
https://en.wikipedia.org/wiki/Amino_acid
WCCSA 3.0
Wikipedia Table
Figure # 3.72
Hydropathy Plot
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.63
Glycerol phosphate shuttle
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.73
Plant Cell wall
https://commons.wikimedia.org/wiki/File:Plant_cell_wall_
diagram-en.svg
Public Domain
Figure # 3.64
Malate Aspartate Shuttle
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 3.74
Gram Cell Wall
https://commons.wikimedia.org/wiki/File:Gram-Cell-wall.sv
g
WCCSA 3.0
Graevemoore (talk)
Figure # 3.65
Connexon
https://commons.wikimedia.org/wiki/File:Connexon_and_c
onnexin_structure.svg
Public Domain
Figure # 3.66
Plasmodesma
https://commons.wikimedia.org/wiki/File:Apoplast_and_sy
mplast_pathways.svg
Public Domain
Figure # 3.67
Adherens Junction
https://commons.wikimedia.org/wiki/File:Adherens_Juncti
ons_structural_proteins.svg
Public Domain
Figure # 3.68
Tight Junctions
https://commons.wikimedia.org/wiki/File:Cellular_tight_ju
nction-en.svg
Public Domain
Figure # 3.69
Glypiated protein
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 3.75
Diatoms Cell Wall
https://commons.wikimedia.org/wiki/File:Diatoms.png
WCCSA 3.0
Images courtesy of Mary Ann Tiffany, San Diego State University / Bradbury J: Nature's Nanotechnologists: Unveiling the
Secrets of Diatoms. PLoS Biol 2/10/2004: e306.
doi:10.1371/journal.pbio.0020306
Figure # 4.1
Rate Enhancement of Enzymes
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Public Domain
Aleia Kim
Figure # 4.2
Energy change no enzyme
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.3
Energy change enzyme
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.4
1095
Figure # 4.14
Enzyme Reaction Summary
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Public Domain
Kevin Ahern
Figure # 4.5
Active Site
https://commons.wikimedia.org/wiki/File:Enzyme_structur
e.svg
WCCA 4.0
Thomas Shafee
Figure # 4.15
Concentration Versus Time E,S,P,ES
https://commons.wikimedia.org/wiki/File:Michaelis_Mente
n_S_P_E_ES.svg
Public Domain
Figure # 4.6
Fischer vs Koshland
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Public Domain
Aleia Kim
Figure # 4.16
Concentration Versus Time E,S,P,ES Labeled
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Kevin Ahern
Figure # 4.7
Types of Displacement reactions
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Figure # 4.17
Steady State Considerations
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Figure # 4.8
Double Displacement Transaminase
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Public Domain
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Figure # 4.18
V vs [S]
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Public Domain
Aleia Kim
Figure # 4.9
Enzyme Binding Substrates
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Public Domain
Kevin Ahern
Figure # 4.19
Product vs Time
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Kevin Ahern
Figure # 4.10
ES Complex Formation
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Public Domain
Kevin Ahern
Figure # 4.20
Michaelis Menten Kinetics
https://commons.wikimedia.org/wiki/File:Michaelis-Mente
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Public Domain
Figure # 4.11
ES Complex Reaction
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Public Domain
Kevin Ahern
Figure # 4.21
Kcat Values
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Public Domain
Aleia Kim
Figure # 4.12
EP Complex
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 4.22
Kcat/Km
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.13
E+P Product Release
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Public Domain
Kevin Ahern
Figure # 4.23
Triose phosphate isomerase
https://commons.wikimedia.org/wiki/File:TriosePhosphateI
somerase_Ribbon_pastel_trans.png
WCCA 3.0
Jane Richardson (user:Dcrjsr)
1096
Figure # 4.24
Triose phosphate isomerase reaction
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Public Domain
Kevin Ahern
Figure # 4.25
Methyl glyoxal avoidance reaction
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Public Domain
Aleia Kim
Figure # 4.26
Lineweaver Burk Plot
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Public Domain
Aleia Kim
Figure # 4.27
Cofactors and Coenzymes
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Public Domain
Aleia Kim
Figure # 4.28
Coenzyme A
https://commons.wikimedia.org/wiki/File:Coenzym_A.svg
Public Domain
Figure # 4.29
Burst Phase
https://commons.wikimedia.org/wiki/File:Burst_phase.svg
Public Domain
Figure # 4.30
Stopped Flow Instrument
https://commons.wikimedia.org/wiki/File:Stop_flow_appar
atus.jpg
WCCSA 2.0
Wladimir Labeikovsky /
https://www.flickr.com/photos/nucho/2504889837
Figure # 4.31
Ribozyme cleavage of RNA
https://commons.wikimedia.org/wiki/File:Ribozyme.jpg
WCCA 2.5
Robinson R / RNAi Therapeutics: How Likely, How Soon?
Robinson R PLoS Biology Vol. 2, No. 1, e28
doi:10.1371/journal.pbio.0020028
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.34
Methotrexate/dihydrofolate
ben.carson@oregonstate.edu
Public Domain
Ben Carson
Figure # 4.35
V vs S competitive
https://commons.wikimedia.org/wiki/File:Michaelis-Mente
n_plot_competitive_inhibition.svg
Public Domain
Figure # 4.36
Lineweaver Burk
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.37
Non-competitive inhib diagram
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Public Domain
Aleia Kim
Figure # 4.38
Non-comp. V vs S
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 4.39
Non-comp. Lineweaver Burk
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Public Domain
Aleia Kim
Figure # 4.40
Uncom inhib diag
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Public Domain
Aleia Kim
Figure # 4.41
Uncom V vs S
https://commons.wikimedia.org/wiki/File:Michaelis-Mente
n_plot_uncompetitive_inhibition.svg
Public Domain
Figure # 4.32
Hammerhead Ribozyme
https://commons.wikimedia.org/wiki/File:Full_length_ham
merhead_ribozyme.png
WCCSA 3.0
William G. Scott / From Protein Data Bank ID 2GOZ
Figure # 4.42
Uncomp Lineweaver Burk
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.33
Competitive Inhibition
Figure # 4.43
Penicillin action
1097
https://commons.wikimedia.org/wiki/File:Penicillin_inhibit
ion.svg
WCCA 3.0
Mcstrother
Figure # 4.44
Allosteric enzyme kinetics
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.45
ATCase structure
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.46
ATCase kinetic plots
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 4.47
Sequential model
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 4.48
MWC model
https://commons.wikimedia.org/wiki/File:Morpheein_dice.
PNG
WCCSA 4.0
Eileen Jaffe,Trevor Selwood,Debra Foster,Bear919506
Figure # 4.49
Morpheein model
https://commons.wikimedia.org/wiki/File:Morpheein_dice.
PNG
WCCSA 4.0
Eileen Jaffe,Trevor Selwood,Debra Foster,Bear919506
Aleia Kim
Figure # 4.53
Catalytic Triad
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Public Domain
Kevin Ahern
Figure # 4.54
Substrate binding
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Kevin Ahern
Figure # 4.55
Alkoxide ion formation
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Kevin Ahern
Figure # 4.56
ucleophilic attack
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Kevin Ahern
Figure # 4.57
Peptide bond breakage
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Public Domain
Kevin Ahern
Figure # 4.58
Peptide 1 released
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Public Domain
Kevin Ahern
Figure # 4.59
Activation of water
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Public Domain
Kevin Ahern
Figure # 4.50
Protease activation
https://commons.wikimedia.org/wiki/File:Zymogen_activati
on.png
WCCSA 3.0
Joyjiang at English Wikibooks
Figure # 4.60
Serine bond breaks
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Public Domain
Kevin Ahern
Figure # 4.51
Kinase cascade GPCR
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Public Domain
Kevin Ahern
Figure # 4.61
Peptide 2 released end of cycle
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Public Domain
Kevin Ahern
Figure # 4.52
S1 Pockets
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Public Domain
Figure # 4.62
Subtilisin
https://commons.wikimedia.org/wiki/File:1st2.png
Public Domain
1098
Figure # 4.63
Protease mechanisms
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Public Domain
Aleia Kim
Figure # 4.64
Carboxypeptidase
https://commons.wikimedia.org/wiki/File:Carboxypeptidase
_A.png
Public Domain
Figure # 4.65
Aspartate protease
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 4.66
Alpha-1-antitrypsin
https://commons.wikimedia.org/wiki/File:Antitrypsin_1HP7
.png
Public Domain
Figure # 4.67
Alpha-1-antitrypsin in Europe
https://commons.wikimedia.org/wiki/File:PiMZ_Europe.pn
g
WCCSA 2.5
Based on extrapolated data from Worldwide racial and ethnic distribution of __-antitrypsin deficiency : summary of an
analysis of published genetic epidemiologic surveys by Frederick J. de Serres. (Orig. publ. in Chest, Nov. 2002
Figure # 4.68
Blood coagulation in vivo
https://commons.wikimedia.org/wiki/File:Coagulation_in_v
ivo.png
WCCSA 3.0
Dr Graham Beards
Figure # 4.69
Intrinsic/extrinsic pathwys
https://commons.wikimedia.org/wiki/File:Coagulation_full.
svg
WCCSA 3.0
Joe D
Figure # 4.70
Blood coagulation pathway
https://commons.wikimedia.org/wiki/File:Coagulation_in_v
ivo.png
WCCSA 3.0
Dr Graham Beards
Figure # 4.71
Transglutaminase reaction
https://commons.wikimedia.org/wiki/File:Transamidation_
and_deamidation_mechanisms_of_tissue_transglutaminase
.jpg
Public Domain
Figure # 4.72
Alpha thrombin
https://commons.wikimedia.org/wiki/File:2HPQ_Alpha-Thr
ombin02.png
WCCSA 3.0
Nevit Dilmen / Self created from PDB entry with Cn3D Data
Source: http://www.ncbi.nlm.nih.gov/Structure/
Figure # 4.73
Transglutaminase product
https://commons.wikimedia.org/wiki/File:Stabilisation_de_
la_fibrine_par_le_factor_XIII.png
WCCSA 3.0
Rupr du wikipdia anglais. (User:Jfdwolff, dcembre
2004)
Figure # 4.74
Fibrin dimer
https://commons.wikimedia.org/wiki/File:Fibrinandligand.p
ng
WCCSA 3.0
amolinski
Figure # 4.75
Blood clot
https://commons.wikimedia.org/wiki/File:Blood_clot_in_sc
anning_electron_microscopy.jpg
Public Domain
Figure # 4.76
Queen Victoria
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nterhalter_Queen_Victoria.jpg
Public Domain
Figure # 4.77
Gamma carboxyglutamic aci
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Public Domain
Kevin Ahern
Figure # 4.78
Warfarin
https://commons.wikimedia.org/wiki/File:Warfarin.svg
Public Domain
Figure # 4.79
Menetetrenone (Vitamin K MK 4)
https://commons.wikimedia.org/wiki/File:Menatetrenone.P
NG
Public Domain
Figure # 4.80
Plasminogen activation
https://commons.wikimedia.org/wiki/File:Fibrinolysis.png
1099
WCCSA 3.0
Jfdwolff / drawn by Jfdwolff in OpenOffice.org 10.0
Figure # 4.81
Plasmin
https://commons.wikimedia.org/wiki/File:Plasmin2.png
Public Domain
Figure # 4.82
Fibronectin
https://commons.wikimedia.org/wiki/File:Protein_FN1_PD
B_1e88.png
WCCSA 3.0
Emw / Structure of the FN1 protein. Based on PyMOL rendering of PDB 1e88
Mitochondrion
https://commons.wikimedia.org/wiki/File:Animal_mitocho
ndrion_diagram_en.svg
Public Domain
Figure # 5.8
Lipid bilayer ion barrier
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 5.9
Chemical Gradient
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Public Domain
Aleia Kim
Figure # 4.83
Platelet activating factor
https://commons.wikimedia.org/wiki/File:PAF-platelet_acti
vating_factor.png
WCCSA 3.0
Image created in ChemDraw by en user Roadnottaken
Figure # 5.10
Ion Gradient
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Public Domain
Aleia Kim
Figure # 5.1
Carbon oxidation states
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Public Domain
Pehr Jacobson
Figure # 5.11
Standard Reduction Electrode
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Public Domain
Pehr Jacobson
Figure # 5.2
Photosynthesis energy
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Public Domain
Aleia Kim
Figure # 5.12
ATP
https://commons.wikimedia.org/wiki/File:ATP_(chemical_s
tructure).svg
Public Domain
Figure # 5.3
Biological energy movement
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Public Domain
Aleia Kim
Figure # 5.13
Nucleotides nucleosides bases
https://commons.wikimedia.org/wiki/File:Nucleotides_1.svg
Public Domain
Figure # 5.4
Worldwide photosynthesis
https://commons.wikimedia.org/wiki/File:Seawifs_global_b
iosphere.jpg
Public Domain
Figure # 5.5
Anabolic vs Catabolic
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 5.6
Anabolic catabolic cycling
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 5.7
Figure # 5.14
Electron Transport chain
https://commons.wikimedia.org/wiki/File:Mitochondrial_el
ectron_transport_chainEtc4.svg
Public Domain
Figure # 5.15
NAD to NADH
https://commons.wikimedia.org/wiki/File:NAD%2BtoNAD
H.png
Public Domain
Figure # 5.16
ETS 1
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Public Domain
Aleia Kim
Figure # 5.17
ETS 2
1100
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Public Domain
Aleia Kim
Figure # 5.18
Complex I in Membrane
https://commons.wikimedia.org/wiki/File:NADH_Dehydrog
enase_2FUG_Electron_Carriers_Labeled.png
WCCSA 3.0
Richard Wheeler (Zephyris)
Figure # 5.19
Complex II in membrane
https://commons.wikimedia.org/wiki/File:Succinate_Dehyd
rogenase_1YQ3_and_Membrane.png
WCCSA 3.0
Zephyris at English Wikipedia
Figure # 5.20
Complex I reactions
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Public Domain
Aleia Kim
Figure # 5.21
Complex II reactions
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Public Domain
Aleia Kim
Figure # 5.22
Complex II electron flow
https://commons.wikimedia.org/wiki/File:Succinate_Dehyd
rogenase_1YQ3_Electron_Carriers_Labeled.png
WCCSA 3.0
Richard Wheeler (Zephyris) / Based on PDB 1YQ3. Labeled
version of en:Image:Succinate Dehydrogenase Electron Carriers Unlabeled.png
Figure # 5.23
Coenzyme Q
https://commons.wikimedia.org/wiki/File:Ubiquinone.png
Public Domain
Figure # 5.24
Complex III structure
https://commons.wikimedia.org/wiki/File:Cytochrome1ntz.
PNG
WCCSA 3.0
Neveu, Curtis
Figure # 5.25
Q-cycle
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Public Domain
Aleia Kim
Figure # 5.26
Complex IV
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 5.27
Cytochrome c
https://commons.wikimedia.org/wiki/File:Cytochrome_C.p
ng
WCCSA 3.0
Vossman / Three-dimensional structure of cytochrome c
(green) with a heme molecule coordinating a central Iron
atom (orange). PDB id, 1HRC, Bushnell et al., Highresolution three-dimensional structure of horse heart cytochrome c. J Mol Biol. 1990 Jul 20;214(2):585-95. PubMed
PMID: 2166170
Figure # 5.28
Mitochondrial summary
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Public Domain
Aleia Kim
Figure # 5.29
ATP synthase
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 5.30
ATP synthase labeled
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 5.31
ATP synthase LTO
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 5.32
Respiration Eukaryotes
https://commons.wikimedia.org/wiki/File:CellRespiration.s
vg
WCCSA 3.0
RegisFrey
Figure # 5.33
ETS Iniibitors
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Public Domain
Aleia Kim
Figure # 5.34
Oligomycin
https://commons.wikimedia.org/wiki/File:Oligomycin.png
Public Domain
Figure # 5.35
2,4 DNP
1101
https://commons.wikimedia.org/wiki/File:2,4-Dinitrophenol
.svg
Public Domain
Figure # 5.36
Alternative oxidase
https://commons.wikimedia.org/wiki/File:AOX.png
Public Domain
Figure # 5.37
Oxygen free radical
https://commons.wikimedia.org/wiki/File:Free-radicals-oxy
gen.jpg
WCCSA 3.0
Healthvalue
Figure # 5.38
ROS Sources
https://commons.wikimedia.org/wiki/File:Major_cellular_s
ources_of_Reactive_Oxygen_Species_in_living_cells.jpg
WCCA 2.0
Erica Novo and Maurizio Parola 2008 Novo et al; licensee
BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly
cited. Major cellular sources of ROS in living cells. Novo and
Parola Fibrogenesis & Tissue Repair 2008 1:5
doi:10.1186/1755-1536-1-5
Figure # 5.39
Hydroxyl Radical
https://commons.wikimedia.org/wiki/File:HydroxideVsHyd
roxyl.png
WCCSA 4.0
Attys
Figure # 5.40
Catalase
https://commons.wikimedia.org/wiki/File:PDB_4cat_EBI.jp
g
Public Domain
Figure # 5.41
ROS species
https://commons.wikimedia.org/wiki/File:Antioxidant_path
way.svg
Public Domain
Figure # 5.42
Human SOD2
https://commons.wikimedia.org/wiki/File:Superoxide_dism
utase_2_PDB_1VAR.png
Public Domain
Figure # 5.43
Peroxynitrite ion
https://commons.wikimedia.org/wiki/File:Peroxynitrite-ion2D.png
Public Domain
Figure # 5.44
Human SOD 1
https://commons.wikimedia.org/wiki/File:2c9v_CuZn_rib_
n_site.png
WCCA 4.0
Dcrjsr / Ribbon schematic with active-site ligand side chains,
for human Cu,Zn superoxide dismutase (SOD1). Made in
KiNG from PDB 2C9V
Figure # 5.45
Peroxynitrite actions
https://commons.wikimedia.org/wiki/File:Reactions_of_per
oxynitrite_leading_to_either_apoptotic_or_necrotic_cell_d
eath.jpg
WCCA 2.0
Erica Novo and Maurizio Parola / 2008 Novo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly
cited
Figure # 5.46
Human SOD 3
https://commons.wikimedia.org/wiki/File:SOD3_2JLP.png
Public Domain
Figure # 5.47
Cytochrome c heme
https://commons.wikimedia.org/wiki/File:Cytochrome_c.pn
g
Public Domain
Figure # 5.48
Fe2S2
https://commons.wikimedia.org/wiki/File:Fe2S2.png
Public Domain
Figure # 5.49
Fe4S4
https://commons.wikimedia.org/wiki/File:FdRedox.png
Public Domain
Figure # 5.50
Tyramine
https://commons.wikimedia.org/wiki/File:Tyramine.svg
Public Domain
Figure # 5.51
Phenthylamine
https://commons.wikimedia.org/wiki/File:Phenethylamine2
DCSD.svg
Public Domain
Figure # 5.52
Guanine and 8-oxoguanine
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1102
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Kevin Ahern
Figure # 5.53
Adenine 8-oxoguanine base pair
https://commons.wikimedia.org/wiki/File:8-oxoG_forming
_Hoogsten_base_pair_with_dA.svg
Public Domain
Figure # 5.54
Antioxidant sources
https://commons.wikimedia.org/wiki/File:Vegetarian_diet.j
pg
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Figure # 5.55
Glutathiones
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Kevin Ahern
Figure # 5.56
Glutathione Oxidized
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one-skeletal.svg
WCCSA 3.0
NEUROtiker
Figure # 5.57
Resveretrol
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Public Domain
Figure # 5.58
Chloroplasts in plant cells
https://commons.wikimedia.org/wiki/File:Plagiomnium_aff
ine_laminazellen.jpeg
WCCSA 3.0
Kristian Peters -- Fabelfroh
Figure # 5.59
Chloroplast view
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Public Domain
Aleia Kim
Figure # 5.60
Photosynthesis overview
https://commons.wikimedia.org/wiki/File:Simple_photosyn
thesis_overview.svg
WCCSA 4.0
Daniel Mayer (mav) - original image
Figure # 5.61
Chloroplast anatomy
https://commons.wikimedia.org/wiki/File:Chloroplast_mini
.svg
WCCA 3.0
Vector version by Yerpo / Vector version by Yerpo
Figure # 5.62
Thylakoids
https://en.wikipedia.org/wiki/File:Helical_granum.png
WCCSA 3.0
Kelvinsong
Figure # 5.63
Photosystems in Chloroplast
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Public Domain
Aleia Kim
Figure # 5.64
Photosynthesis steps
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Public Domain
Aleia Kim & Pehr Jacobson
Figure # 5.65
Electron movement in chloroplast
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Public Domain
Aleia Kim
Figure # 5.66
Photosystem II
https://commons.wikimedia.org/wiki/File:Photosystem-II_2
AXT.PNG
WCCSA 3.0
Neveu,Curtis (C31004)
Figure # 6.1
Metabolic Pathway overview
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Public Domain
Aleia Kim
Figure # 6.2
Glucose Metabolism
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Public Domain
Aleia Kim
Figure # 6.3
Glycolysis Scheme
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Public Domain
Ben Carson
Figure # 6.4
Hexokinase Reaction
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Kevin Ahern
Figure # 6.5
Centrality of G6P
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Aleia Kim
1103
Figure # 6.6
Phosphoglucoisomerase intermediates
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Figure # 6.16
Pyruvate Kinase Reaction
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Figure # 6.7
PFK Reaction
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Figure # 6.17
Lactase Reaction
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Figure # 6.8
Aldolase Reaction
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Kevin Ahern
Figure # 6.18
Galactokinase Reaction
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Figure # 6.9
Triose Phosphate Isomerase Reaction
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Public Domain
Ben Carson
Figure # 6.19
Gal-1P to G6P
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Public Domain
Aleia Kim
Figure # 6.10
GLAY3PDH Reaction
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Kevin Ahern
Figure # 6.20
Fructose entry into glycolysis
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Penelope Irving
Figure # 6.11
Phosphoglycerate Kinase Reaction
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Figure # 6.21
Other Sugars Entry into Glycolysis
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Penelope Irving
Figure # 6.12
Phosphoglycerate Mutase
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Figure # 6.22
Glycerol Metabolism
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Figure # 6.13
2,3 BPG Formation Routes
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Figure # 6.23
Pyruvate Metabolism
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Figure # 6.14
2,3 BPG
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Kevin Ahern
Figure # 6.24
Fermentation in Animals
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Ben Carson
Figure # 6.15
Enolase Reaction
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Kevin Ahern
Figure # 6.25
Fermentation in Yeast
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Ben Carson
1104
Figure # 6.26
Glycolysis and Gluconeogenesis
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Public Domain
Aleia Kim
Figure # 6.27
Biotin and CO2
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svg
Public Domain
Figure # 6.28
Glycolysis / Gluconeogenesis
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Aleia Kim
Figure # 6.29
Futile Cycle
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Public Domain
Aleia Kim
Figure # 6.30
Pyruvate Kinase Regulation
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Figure # 6.31
FBPase regulation
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Figure # 6.32
Cori Cycle
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Aleia Kim
Figure # 6.33
Glucose Alanine Cycle
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Figure # 6.34
Amylose Structure
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Glycogen Breakdown
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Aleia Kim
Figure # 6.37
Debranching Enzyme
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Kevin Ahern
Figure # 6.38
Glycogen Phosphorylase Regulatoin
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Aleia Kim
Figure # 6.39
Gpa Allosteric Regulation
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Public Domain
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Figure # 6.40
GPb Regulation
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Public Domain
Aleia Kim
Figure # 6.41
Kinase Cascade
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Penelope Irving
Figure # 6.42
PP1 Inactivation
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Public Domain
Pehr Jacobson
Figure # 6.43
Gpa regulation by Glucose
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Penelope Irving
Figure # 6.44
Glycogen Synthase Reaction
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Penelope Irving
Figure # 6.35
Glycogen Structure
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Public Domain
Figure # 6.45
Branching Enzyme Action
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Penelope Irving
Figure # 6.36
Figure # 6.46
1105
https://commons.wikimedia.org/wiki/File:Zea_mays_-_Ko
_hlers_Medizinal-Pflanzen-283.jpg
Public Domain
Figure # 6.57
C4 Photosynthesis
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Public Domain
Aleia Kim
Figure # 6.58
Peptidoglycan layer of cell wall
https://commons.wikimedia.org/wiki/File:Gram-positive_ce
llwall-schematic.png
WCCSA 3.0
Twooars at English Wikipedia
Figure # 6.59
Penicillin
https://commons.wikimedia.org/wiki/File:Penicillin_core.sv
g
Public Domain
Figure # 6.60
DD Transpeptidase
https://commons.wikimedia.org/wiki/File:PBP_catalysis.svg
WCCA 3.0
Mcstrother
Figure # 6.61
HIF-1
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pg
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Figure # 6.62
HIF induced proteins
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Figure # 6.63
Amino acid links to citric acid cycle
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Aleia Kim
Figure # 6.64
E1 Subunit of Pyr. DH
https://commons.wikimedia.org/wiki/File:Pyruvate_dehydr
ogenase_E1_subunit_of_E._coli_(2000_pixels).png
WCCSA 3.0
FontanaCG / Created using PyMol. The full reference for the
paper that described this structure is: Arjunan P., Nemeria,
N., Brunskill, A., Chandrasekhar, K., Sax, M., Yan, Y., Jordan,
F., Guest, J.R., and W. Furey. 2002. Structure of the pyruvate
dehydrogenase multienzyme complex E1 component from
Escherichia coli at 1.85 resolution. Biochemistry 41: 52135221
1106
Figure # 6.65
Pyruvate DH mechanism
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g
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Figure # 6.66
Lipoamide oxidized and reduced
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Kevin Ahern
Figure # 6.67
Pyruvate dehydrogenase regulation
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Aleia Kim
Figure # 6.68
Pyruvate DH
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ogenase_phosphorylation_sites.png
WCCSA 3.0
Jonathanmott09
Figure # 6.69
Citric Acid Cycle
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Public Domain
Aleia Kim
Figure # 6.70
Succinyl-CoA synthetase mechanism
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nthetase_Mechanism_Revised.png
Public Domain
Figure # 6.71
Succinate DH in membrane
https://commons.wikimedia.org/wiki/File:Succinate_Dehyd
rogenase_1YQ3_and_Membrane.png
WCCSA 3.0
Zephyris at English Wikipedia
Figure # 6.72
Complex II electron pathway
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Public Domain
Aleia Kim
Figure # 6.73
Arnon Buchanan Cytle
https://commons.wikimedia.org/wiki/File:Reductive_TCA_
cycle.png
WCCSA 3.0
Andrewrgross
Figure # 6.74
Glyoxylate Cycle
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Public Domain
Aleia Kim
Figure # 6.75
Glyoxylate Cycle
https://commons.wikimedia.org/wiki/File:Glyoxylate_cyclefr.svg
WCCSA 3.0
Original : Agrotman, vector version : Flappiefh
Figure # 6.76
Gingko Seed
https://commons.wikimedia.org/wiki/File:Ginkgo_embryo_
and_gametophyte.jpg
WCCSA 2.5
Photography and copyright by Curtis Clark
Figure # 6.77
Acetyl-CoA Metabolism
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Public Domain
Aleia Kim
Figure # 6.78
Ketone Body Metabolism
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Public Domain
Pehr Jacobson
Figure # 6.79
Ketone Bodies
https://commons.wikimedia.org/wiki/File:Ketone_bodies.p
ng
Public Domain
Figure # 6.80
Ketone body metab vs. Cholesterol
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Penelope Irving
Figure # 6.81
Acidosis
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idosis.png
Public Domain
Figure # 6.82
Trimyristin
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dW.png
Public Domain
Figure # 6.83
Fat movement in digestion
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Public Domain
Aleia Kim
Figure # 6.84
Triacylglycerol lipase regulation
1107
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Public Domain
Pehr Jacobson
Figure # 6.85
Fat synthesis from phosphatidic acid
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Penelope Irving
Figure # 6.86
Mitochondria
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Public Domain
Figure # 6.87
Carnitine translocase
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Aleia Kim
Figure # 6.88
Fatty acid oxidation steps
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Public Domain
Aleia Kim
Figure # 6.89
FA Oxidation vs Citric acid oxidation
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Aleia Kim
Figure # 6.90
Propionyl-CoA Metabolism
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Public Domain
Pehr Jacobson
Figure # 6.91
Cerotic Acid
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Figure # 6.92
Unsaturated fatty acid oxidation
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Kevin Ahern
Figure # 6.93
Phytanic acid
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g
Public Domain
Figure # 6.94
Omega Faty Acid Oxidation
https://commons.wikimedia.org/wiki/File:Omega-oxidation
_1.svg
WCCSA 3.0
Xvazquez
Figure # 6.94
Omega Faty Acid Oxidation
https://commons.wikimedia.org/wiki/File:Omega-oxidation
_2.svg
WCCSA 3.0
Xvazquez
Figure # 6.94
Omega Faty Acid Oxidation
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WCCSA 3.0
Xvazquez
Figure # 6.95
Fatty acid oxidation vs synthesis
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Figure # 6.96
Fatty acid synthesis
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Aleia Kim
Figure # 6.97
Fatty acid Synthase
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Public Domain
Figure # 6.98
Fatty acid numbering
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Public Domain
Pehr Jacobson
Figure # 6.99
Elaidic acid
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keletal.png
Public Domain
Figure # 6.100
Eicosanoid synthesis
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Public Domain
Pehr Jacobson
Figure # 6.101
Phospholipase cleavage sites
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png
Public Domain
1108
Figure # 6.102
Protaglandin synthesis
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Public Domain
Pehr Jacobson
Figure # 6.103
Cyclooxygenase action
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Public Domain
Pehr Jacobson
Figure # 6.104
Aspirin and ibuprofen
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Kevin Ahern
Figure # 6.105
Diacylglycerol
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Kevin Ahern
Figure # 6.106
Obesity worldwide females
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Female_Obesity,_2008.svg
WCCSA 2.5
Vector map from BlankMap-World6, compact.svg by Canuckguy et al. / Data from IOTF Report for December 2008
(2009-01-26) / Combined by Lokal_Profil. / Author - Lokal_Profil
Figure # 6.106
Obesity worldwide males
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Male_Obesity,_2008.svg
WCCSA 2.5
Vector map from BlankMap-World6, compact.svg by Canuckguy et al. / Data from IOTF Report for December 2008
(2009-01-26) / Combined by Lokal_Profil. / Author - Lokal_Profil
Figure # 6.107
Leptin
https://commons.wikimedia.org/wiki/File:Leptin.png
WCCSA 3.0
Vossman / Structure of w:Leptin, PDB id 1AX8, generated
with w:UCSF Chimera
Figure # 6.108
Neuropeptide Y
https://commons.wikimedia.org/wiki/File:Neuropeptide_Y.
png
Public Domain
Figure # 6.109
Preproghrelin
https://commons.wikimedia.org/wiki/File:Preproghrelin_1P
7X.png
Public Domain
Figure # 6.110
Acetyl-CoA carbons in Cholesterol
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.111
Isoprenoid synthesis
https://commons.wikimedia.org/wiki/File:Mevalonate_path
way.svg
Public Domain
Figure # 6.112
Acetyl-CoA to Isoprenes
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.113
Lovastatin
https://commons.wikimedia.org/wiki/File:Lovastatin.svg
WCCSA 3.0
Panoramix303
Figure # 6.114
Isoprenes to Cholesterol
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.115
Isoprenes
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.116
Lanosterol synthesis
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.117
7-dehydrocholsterol
https://en.wikipedia.org/wiki/7-Dehydrocholesterol#/media
/File:7-Dehydrocholesterol.svg
Public Domain
Figure # 6.118
Calcitriol synthesis
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.119
Steroid hormone synthesis
1109
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.120
Estradiol and Testosterone Synthesis
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.121
Exemestane
https://commons.wikimedia.org/wiki/File:Exemestane.svg
Public Domain
Figure # 6.122
Steroid synthesis
https://commons.wikimedia.org/wiki/File:Steroidogenesis.s
vg
WCCSA 3.0
David Richfield (User:Slashme) and Mikael Hggstrm. Derived from previous version by Hoffmeier and Settersr. /
Hggstrm M, Richfield D (2014). "Diagram of the pathways
of human steroidogenesis". Wikiversity Journal of Medicine 1
(1). DOI:10.15347/wjm/2014.005. ISSN 20018762
Figure # 6.123
Bile Acids
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.124
Beta carotene synthesis
https://commons.wikimedia.org/wiki/File:Carotenoid_synth
etic_pathway.svg
WCCSA 4.0
Jeff Dahl
Figure # 6.125
Dihydrosphingosine synthesis
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.126
Dihydrosphingosine to ceramide
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.127
Ceramide to Sphingolipids
ben.carson@oregonstate.edu
Public Domain
Ben Carson
Figure # 6.128
Spingolipid metabolism enzymes
https://commons.wikimedia.org/wiki/File:Sphingolipidoses.
svg
WCCSA 3.0
Ebuxbaum, Sav_vas
Figure # 6.129
Phosphatidic Acid Synthesis
https://commons.wikimedia.org/wiki/File:Phosphatidic_aci
d_synthesis_en.svg
WCCSA 3.0
Xvazquez
Figure # 6.130
Heme C
https://commons.wikimedia.org/wiki/File:Heme_c.svg
Public Domain
Figure # 6.131
Heme Synthesis
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.132
Hydroxymethylbilane
https://commons.wikimedia.org/wiki/File:Hydroxymethylbil
ane.svg
Public Domain
Figure # 6.133
Heme to biliverdin and bilirubin
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.134
Transaminase
http://www.aleiakim.com/
Public Domain
Aleia Kim
Unnumbered p. 618
Glutamate Amino Acids
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.135
Essential non-essential
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.136
Glutamine Synthetase
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.137
1110
Figure # 6.138
Glutamate-5-semialdehyde cyclization
http://www.aleiakim.com/
Public Domain
Aleia Kim
Unnumbered p. 630
Aromatic amino acid biosynthesis
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.139
Citrulline
https://commons.wikimedia.org/wiki/File:L-Citrullin2.svg
Public Domain
Figure # 6.146
PEP to Shikimic acid
https://commons.wikimedia.org/wiki/File:Shikimate_pathw
ay_1.svg
Public Domain
Figure # 6.140
Asymmetric Dimethyl Arginine (ADMA)
https://commons.wikimedia.org/wiki/File:Asymmetric_dim
ethylarginine.svg
Public Domain
Unnumbered p. 622
Serine Amino Acids
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.141
Methionine biosynthesis
https://en.wikipedia.org/wiki/File:Met_biosynthesis.gif
WCCSA 3.0
Inositol
Unnumbered p. 625
Aspartate Amino Acids
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.142
N-formyl methionine
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.143
Threonine biosynthesis
https://commons.wikimedia.org/wiki/File:Threonine_biosy
nthesis.svg
WCCSA 3.0
Carel.jonkhout
Figure # 6.144
Lysine biosynthesis
https://en.wikipedia.org/wiki/Lysine#/media/File:Lysine_B
iosynthesis.png
Public Domain
Figure # 6.147
Shikimate to Chorismate
https://commons.wikimedia.org/wiki/File:Chorismate_path
way_1.png
WCCSA 3.0
No machine-readable author provided. Physchim62 assumed
(based on copyright claims)
Figure # 6.148
Chorismate to Tryptophan
https://commons.wikimedia.org/wiki/File:Tryptophan_bios
ynthesis_(en).svg
Public Domain
Figure # 6.149
Tryptophan to Hormone metabolism
https://commons.wikimedia.org/wiki/File:Tryptophan_met
abolism.svg
Public Domain
Figure # 6.150
Melatonin and Circadian Rhythms
https://commons.wikimedia.org/wiki/File:Biological_clock_
human.svg
WCCSA 3.0
Addicted04 / The work was done with Inkscape by YassineMrabet. Informations were provided from "The Body Clock
Guide to Better Health" by Michael Smolensky and Lynne
Lamberg; Henry Holt and Company, Publishers (2000). Landscape was sampled from Open Clip Art Library (Ryan, Public
domain). Vitruvian Man and the clock were sampled from
Image:P human body.svg (GNU licence) and Image:Nuvola
apps clock.png, respectively.
Figure # 6.151
Auxin
https://commons.wikimedia.org/wiki/File:Indol-3-ylacetic_
acid.svg
Public Domain
Figure # 6.152
Gall on a Rose
Figure # 6.145
1111
https://commons.wikimedia.org/wiki/File:Crown_gall_on_r
ose_(a).JPG
WCCSA 4.0
PaleCloudedWhite
Figure # 6.153
Arabidopsis auxin mutant
https://commons.wikimedia.org/wiki/File:Auxin.jpg
WCCA 2.5
William M. Gray / Gray WM (2004) Hormonal Regulation of
Plant Growth and Development. PLoS Biol 2(9): e311.
doi:10.1371/journal.pbio.0020311
Figure # 6.154
Aspartame
https://commons.wikimedia.org/wiki/File:Aspartame.svg
Public Domain
Figure # 6.155
Tyrosine frm prephenate
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.156
Phosphotyrosine
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.157
PHE & TYR to Catecholamine Hormones
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.158
Thyroid hormone synthesis
https://commons.wikimedia.org/wiki/File:Thyroid_hormon
e_synthesis.png
Public Domain
Figure # 6.159
Pheomelanin
https://en.wikipedia.org/wiki/Melanin#/media/File:Pheome
lanine.svg
Public Domain
Figure # 6.160
Catecholamines
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.161
Hyroxyethyl on TPP
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Unnumbered p. 642
Pyruvate Family Metabolism
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.162
BCAA Synthesis regulation
https://commons.wikimedia.org/wiki/File:Regulation_of_T
D.png
WCCSA 3.0
Stevenq4
Figure # 6.163
Selenocysteine
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Unnumbered p. 647
Histidine synthesis
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.164
Selenomethionine
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.165
Pyrrolysine
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.166
Urea Cycle
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.167
Glucogenic and Ketogenic Aas
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.168
Ketogenic and glucogenic Aas in TCA
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.169
Tyrosine Catabolism
https://commons.wikimedia.org/wiki/File:Tyrosinedegradat
ion2.png
Public Domain
1112
Pehr Jacobson
Figure # 6.170
Purine Atom Origins
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.171
Purine Metabolism Overview
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.172
Purine Metabolism
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.173
PRPP Amidotransferase
https://commons.wikimedia.org/wiki/File:ATase_crystal_st
ructure.png
WCCSA 4.0
Jjcantu
Figure # 6.174
IMP to AMP/GMP
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.175
HGPRT
https://commons.wikimedia.org/wiki/File:Hypoxanthine-gu
anine_phosphoribosyltransferase_1BZY.png
Public Domain
Figure # 6.176
Carbamoyl Phosphate Synthesis
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.177
Pyrimidine Atom Sources
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.178
Pyrimidine de novo synthesis
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.179
Pyrimidine Metabolism Regulation
http://pehrjac.wix.com/pehrjacobson
Public Domain
Figure # 6.180
OMP Decarboxylase Mechanism
https://commons.wikimedia.org/wiki/File:OMPDC_Carbani
on_Mechanism.png
WCCA 3.0
Shareef164
Figure # 6.181
OMP Decarboxylase
https://commons.wikimedia.org/wiki/File:BMP_Bound_to_
the_Active_Site_of_OMP_Carboxylase_from_M_thermoaut
otrophicum.png
WCCA 3.0
Michael
Figure # 6.182
OMP to UMP
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.183
CTP Synthase Dimer
https://en.wikipedia.org/wiki/File:CTP_synthase_dimer.jpg
Public Domain
Figure # 6.184
CTP Synthase Mechanism
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 6.185
Nucleic acid catabolism and salvage
https://commons.wikimedia.org/wiki/File:Nuc_acid_deg.pn
g
WCCSA 4.0
Dsrapp
Figure # 6.186
Pyrimidine salvage
https://commons.wikimedia.org/wiki/File:Pyrimidine_Ribo
nucleotide_Salvage.png
Public Domain
Figure # 6.187
RNR Regulation Sites
mailto:I.penelopekay@gmail.com
Public Domain
Penelope Irving
Figure # 6.188
RNR Reaction Mechanism
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 6.189
1113
Figure # 6.199
Hypoxanthine and Allopurinol
https://commons.wikimedia.org/wiki/File:Hypoxanthin.svg
Public Domain
Figure # 6.190
dUMP to dTTP
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.200
Pyrimidine Catabolism
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.191
Thymidylate Synthase mechanism
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.201
Carnosine
https://commons.wikimedia.org/wiki/File:Carnosine-2D-ske
letal.png
Public Domain
Figure # 6.192
DHFR to THF Methtrexate
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.1
Mitochondrial DNA
https://www.genome.gov/dmd/img.cfm?node=Photos/Grap
hics&id=85203
Public Domain
Figure # 6.193
Folate Metabolism
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.2
Human Mitochondrial DNA
https://commons.wikimedia.org/wiki/File:Mitochondrial_D
NA_en.svg
WCCSA 3.0
derivative work: Shanel (talk) / Mitochondrial DNA de.svg:
translation by Knopfkind; layout by jhc
Figure # 6.194
Methotrexate vs DHF
ben.carson@oregonstate.edu
Public Domain
Ben Carson
Figure # 6.195
5-fluorouracil
https://commons.wikimedia.org/wiki/File:Fluorouracil2DA
CS.svg
Public Domain
Figure # 6.196
Purine Catabolism
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.197
Purine Catabolism 2
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 6.198
Uric Acid Crystals
https://commons.wikimedia.org/wiki/File:Fluorescent_uric
_acid.JPG
WCCSA 4.0
Bobjgalindo
Figure # 7.3
Genome to Genes
https://commons.wikimedia.org/wiki/File:Human_genome
_to_genes.png
WCCA 2.0
Plociam
Figure # 7.4
Human Genome by Function
https://commons.wikimedia.org/wiki/File:Human_genome
_by_functions.svg
Public Domain
Figure # 7.5
Genome sizes
https://commons.wikimedia.org/wiki/File:Genome_Sizes.pn
g
WCCSA 3.0
Abizar at English Wikipedia
Figure # 7.6
Components of the Human Genome WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Components_of_
the_Human_Genome.jpg
WCCSA 3.0
Alglascock
Figure # 7.7
5S rRNA
1114
https://commons.wikimedia.org/wiki/File:5S-rRNA-topologi
es.tiff
WCCSA 4.0
Valach m a
Figure # 7.8
Watson Crick DNA
https://commons.wikimedia.org/wiki/File:DNA_Structure%
2BKey%2BLabelled.pn_NoBB.png
WCCSA 3.0
Zephyris
Figure # 7.9
Semiconservative Replication
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.10
Building blocks of DNA
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.11
DNA Replication
https://commons.wikimedia.org/wiki/File:DNA_replication
_split.svg
WCCSA 3.0
Madprime
Figure # 7.12
Human Chromosomes
https://commons.wikimedia.org/wiki/File:UCSC_human_c
hromosome_colours.png
Public Domain
Figure # 7.13
Replication Bubble
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.14
Prokaryotic vs Eukaryotic Replication
https://en.wikipedia.org/wiki/Eukaryotic_DNA_replication
WCCSA 3.0
Wikipedia Table
Figure # 7.15
Base Pairs
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.16
Multiple Replication Bubbles
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.17
DNA Replication
https://commons.wikimedia.org/wiki/File:0323_DNA_Repl
ication.jpg
WCCA 4.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 7.18
Replication fork
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.19
Sliding Clamp
https://it.wikipedia.org/wiki/File:Sliding_clamp_dna_comp
lex.png
Public Domain
Figure # 7.20
Sliding clamp side view
https://commons.wikimedia.org/wiki/File:Sliding_clamp_d
na_complex_side.png
Public Domain
Figure # 7.21
DNA Chain Growth
https://commons.wikimedia.org/wiki/File:DNA_synthesis_
EN.png
WCCA 3.0
Micha_ Sobkowski
Figure # 7.22
Replication Fork Okazaki
https://commons.wikimedia.org/wiki/File:Replication_fork.
svg
WCCSA 3.0
Created by: Masur based on Gluon
Figure # 7.23
RNA Primers Okazaki Fragments
https://commons.wikimedia.org/wiki/File:RNA_primer.png
WCCSA 3.0
Boumphreyfr
Figure # 7.24
Proofreading
https://commons.wikimedia.org/wiki/File:DNA_polymerase
.svg
Public Domain
Figure # 7.25
DNA Polymerase Hand
https://commons.wikimedia.org/wiki/File:PDB_5ktq_EBI.j
pg
Public Domain
1115
Figure # 7.26
Proofreading DNA Polymerase
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.27
Mammalian DNA polymerases
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.28
Chromosomes with Telomere caps
http://commons.wikimedia.org/wiki/File:Telomere_caps.gif
Public Domain
Figure # 7.29
Linear Chromosome Problem
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.30
Telomerase Structure
https://commons.wikimedia.org/wiki/File:Tibolium_castane
um_TERT_structure.png
WCCSA 3.0
Emskorda
Figure # 7.31
Telomerase illustration
https://commons.wikimedia.org/wiki/File:Telomerase_illust
ration.jpg
WCCA 3.0
Sierra Sciences, LLC
Figure # 7.32
Telomerase in action
https://commons.wikimedia.org/wiki/File:Working_principl
e_of_telomerase.png
WCCSA 3.0
Fatma Uzbas
Figure # 7.33
DNA replication through nucleosomes
https://commons.wikimedia.org/wiki/File:Replication_thro
ugh_Nucleosomes.JPG
WCCSA 3.0
Azackta1
Figure # 7.34
Broken chromosomes
https://commons.wikimedia.org/wiki/File:Brokechromo.jpg
WCCSA 3.0
Author info not available
Figure # 7.35
DNA Damage
https://commons.wikimedia.org/wiki/File:Ssvsds.jpg
WCCSA 3.0
Author info not available
Figure # 7.36
Hemimethylation
https://commons.wikimedia.org/wiki/File:Hemimethylation
.svg
WCCSA 3.0
Histidine
Figure # 7.37
Mismatch Repair
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.38
Thymine dimer structures
https://commons.wikimedia.org/wiki/File:Thymine_photodi
mer.svg
Public Domain
Figure # 7.39
DNA Adduct
https://commons.wikimedia.org/wiki/File:Benzopyrene_DN
A_adduct_1JDG.png
WCCSA 3.0
Zephyris at the English language Wikipedia
Figure # 7.40
Thymine Dimers
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.41
Thymine Dimer Repair
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.42
Nucleotide Excision Repair
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.43
Cytosine deamination to Uracil
https://commons.wikimedia.org/wiki/File:DesaminierungCt
oU.png
Public Domain
Figure # 7.44
DNA Excision Repair
https://commons.wikimedia.org/wiki/File:Uracil_base_glyc
osidase.jpg
Public Domain
Figure # 7.45
1116
Figure # 7.46
Homologous Recombination
https://commons.wikimedia.org/wiki/File:HR_in_meiosis.s
vg
WCCSA 3.0
Emw - Products of meiotic recombination for human chromosome 1. The process shuffles genetic material between homologous chromosomes (i.e., between non-sister chromatids)
as shown. Graphic uses an adapted version of
File:Chromosome_1.svg. Inspired by Figure 10-18 in Watson,
JD et al (2003) Molecular Biology of the Gene (5th ed.),
Pearson/Benjamin Cummings, p. 283 ISBN: 9780805346350
Figure # 7.54
Ribonucleotides
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.47
Strand invasion
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.48
Holliday structure resolution
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.49
Lex A structure
https://commons.wikimedia.org/wiki/File:PDB_1jhf_EBI.jp
g
Public Domain
Figure # 7.50
Lex A gene activation
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.51
SOS Response Antibiotic Resistance
https://en.wikipedia.org/wiki/File:SOS_response_antibiotic
_resistance.png
WCCA 2.5
Michel B (2005). "After 30 Years of Study, the Bacterial SOS
Response Still Surprises Us". PLoS Biology 3 (7): e255.
DOI:10.1371/journal.pbio.0030255
Figure # 7.52
Transcriptioni
https://commons.wikimedia.org/wiki/File:MRNA.svg
WCCA 3.0
Kelvinsong
Figure # 7.53
Figure # 7.55
RNA being synthesized
https://commons.wikimedia.org/wiki/File:RNA_pol.jpg
Public Domain
Figure # 7.56
Central Dogma Genetic Code
https://commons.wikimedia.org/wiki/File:Genetic_code.svg
WCC0 1.0
Madprime
Figure # 7.57
Transcription Start Sites
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.58
RNA Polymerase on Promoter
https://commons.wikimedia.org/wiki/File:Rnap_k.png
WCCSA 4.0
Eliaspty
Figure # 7.59
Bacterial RNA Polymerase
https://commons.wikimedia.org/wiki/File:PDB_1hqm_EBI.j
pg
Public Domain
Figure # 7.60
Transcription elongation
https://commons.wikimedia.org/wiki/File:Simple_transcrip
tion_elongation1.svg
Public Domain
Figure # 7.61
Promoter and Terminator sequences
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.62
Transcription termination
https://commons.wikimedia.org/wiki/File:Prokaryotic_term
inators-en.svg
WCCSA 3.0
Prokaryotic terminators.png: Oalnefo1 / derivative
work:Miguelferig (vector version; content unchanged)
1117
BCSteve
Figure # 7.63
Chromatin Organization
https://en.wikipedia.org/wiki/File:Sha-Boyer-Fig1-CCBy3.0.
jpg
WCCA 3.0
Citation: Sha, K. and Boyer, L. A. The chromatin signature of
pluripotent cells (May 31, 2009), StemBook, ed. The Stem
Cell Research Community, StemBook,
doi/10.3824/stembook.1.45.1.
http://www.stembook.org/node/585 This is an open-access
article distributed under the terms of the Creative Commons
Attribution License (CC By 3.0), which permits unrestricted
use, distribution, and reproduction in any medium, provided
the original work is properly cited.
http://creativecommons.org/licenses/by/3.0/
Figure # 7.71
Spliceosome Assembly
https://commons.wikimedia.org/wiki/File:Spliceosome_ball
_cycle_new2.jpg
WCCSA 2.0
Jbrain /
http://de.wikipedia.org/w/index.php?title=Datei:Spliceosom
e_ball_cycle_new2.jpg&filetimestamp=20070123110615
Figure # 7.72
Alternative Splicing
https://commons.wikimedia.org/wiki/File:DNA_alternative
_splicing.gif
Public Domain
Figure # 7.64
Transcription start site
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.73
Alternative polyadenylation
https://commons.wikimedia.org/wiki/File:Alternative_polya
denylation.svg
Public Domain
Figure # 7.65
Eu transcription initiation complex
https://commons.wikimedia.org/wiki/File:Preinitiation_co
mplex.png
WCCSA 3.0
ArneLH
Figure # 7.74
Mature eukaryotic mRNA
https://commons.wikimedia.org/wiki/File:MRNA_structure.
svg
Public Domain
Figure # 7.66
Eukaryotic transcription initiation
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.67
RNA Processing
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.68
Capping mRNA
https://commons.wikimedia.org/wiki/File:5%27_cap_struct
ure.png
WCCSA 3.0
Zephyris
Figure # 7.69
Splicing of introns
https://commons.wikimedia.org/wiki/File:DNA_exons_intr
ons.gif
Public Domain
Figure # 7.70
Splicing of introns
https://commons.wikimedia.org/wiki/File:RNA_splicing_re
action.svg
WCCSA 3.0
Figure # 7.75
RNA Editing
https://commons.wikimedia.org/wiki/File:Insertion.PNG
Public Domain
Figure # 7.76
5S rRNA
https://commons.wikimedia.org/wiki/File:RF00010.jpg
Public Domain
Figure # 7.77
Pseudouridine synthesis
https://commons.wikimedia.org/wiki/File:Synthesis_of_Pse
udouridine-CS.svg
Public Domain
Figure # 7.78
tRNA sequence
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_en.svg
WCCSA 3.0
Yikrazuul
Figure # 7.79
rRNA processing
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.80
Bacterial Central Dogma
1118
https://commons.wikimedia.org/wiki/File:Bacterial_Protein
_synthesis.png
WCCSA 3.0
Joan L. Slonczewski, John W. Foster / Microbiology: An
Evolving Science
Figure # 7.81
Standard Genetic Code
https://en.wikipedia.org/wiki/Genetic_code
WCCSA 3.0
Wikipedia Table
Figure # 7.82
mRNA with codons
https://www.genome.gov/dmd/img.cfm?node=Photos/Grap
hics&id=85284
Public Domain
Figure # 7.83
tRNA structure
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_1ehz.png
WCCSA 3.0
Yikrazuul
Figure # 7.84
tRNA Charging
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_1ehz.png
WCCSA 3.0
Yikrazuul
Figure # 7.85
Translation with codons, anticodons
https://www.genome.gov/dmd/img.cfm?node=Photos/Grap
hics&id=85225
Public Domain
Figure # 7.86
A,P,E sites on Ribosome
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.87
Elongation of Translation
https://commons.wikimedia.org/wiki/File:Peptide_syn.png
WCCSA 3.0
Boumphreyfr
Figure # 7.88
5S rRNA
https://commons.wikimedia.org/wiki/File:PDB_1c2x_EBI.p
ng
Public Domain
Figure # 7.89
Shine Dalgarno
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.90
Shine Dalgarno
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.91
Initiation of Translation
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.92
Kozak sequences in humans
https://en.wikipedia.org/wiki/File:Human_Kozak_context._
Version_2.png
Public Domain
Figure # 7.93
EF-Tu
https://commons.wikimedia.org/wiki/File:81_1ttt.jpg
Public Domain
Figure # 7.94
Elongation of Translation
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.95
50S ribosome subunit
https://commons.wikimedia.org/wiki/File:50S-subunit_of_t
he_ribosome_3CC2.png
WCCSA 3.0
Yikrazuul / large ribosomal subunit (50S) of Haloarcula marismortui, facing the 30S subunit. The ribosomal proteins are
shown in blue, the rRNA in ochre, the active site (A 2486) in
red. Data were taken from PDB 3CC2, redered with PyMOL
Figure # 7.96
Translation
https://commons.wikimedia.org/wiki/File:Protein_synthesis
_(editors_version).svg
WCCA 3.0
Kelvinsong
Figure # 7.97
Translation
https://commons.wikimedia.org/wiki/File:Ribosome_mRN
A_translation_it.svg#/media/File:Ribosome_mRNA_transla
tion_en.svg
Public Domain
Figure # 7.98
Chaperonins
http://www.aleiakim.com/
Public Domain
Aleia Kim
1119
Figure # 7.99
ER Rough and Smooth
https://commons.wikimedia.org/wiki/File:0313_Endoplasm
ic_Reticulum.jpg
WCCA 3.0
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Figure # 7.100
N-terminal signal sequence
https://commons.wikimedia.org/wiki/File:Cotranslational_
membrane_insertion_type1_step1.png
WCCSA 3.0
Self made by Foobar 16:04, 14 July 2006 (UTC)
Figure # 7.101
Ribosome protein delivery
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.102
Multiple levels of gene regulation
https://en.wikipedia.org/wiki/File:Gene_Regulation.svg
Public Domain
Figure # 7.103
Prokaryotic Gene Structure
https://commons.wikimedia.org/wiki/File:Gene_structure_
prokaryote_2_annotated.svg
WCCA 4.0
Thomas Shafee
Figure # 7.104
CAP region of Lac Operator
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.105
Lac Operon
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.106
Lac Repressor binding
http://www.mjbakerartist.com
Public Domain
Martha Baker
Figure # 7.107
Allolactose and Lactose
http://www.davincipress.com/professional.html
Public Domain
Kevin Ahern
Figure # 7.108
1120
https://commons.wikimedia.org/wiki/File:C-Myc-DNA_com
plex.png
WCCSA 3.0
Mark 'AbsturZ' / I created this work entirely by myself from
the coordinates in the PDB (1nkp) by using Pymol
Figure # 7.118
Eukaryotic Combinatorial control
https://cnx.org/contents/7Ry3oRse@5/Eukaryotic-Transcri
ption-GeneWCCA 3.0
OpenStax ID #ed1cb7a1-1b1e-4426-9e90-4c7ee7cd1841@5
Figure # 7.119
Histones and Transc. Activation & Deactivation
http://www.mdpi.com/2072-6643/6/10/4273/htm
WCCA 4.0
Bassett, SA and Barnett, MPG Nutrients 2014, 6(10), 42734301; doi:10.3390/nu6104273
Figure # 7.120
Chromatin Remodeling
https://en.wikipedia.org/wiki/File:Luong_LD_SA_F2.jpg
WCCA 3.0
Figure is adapted from Luong, P. Basic Principles of Genetics,
Connexions Web site (2009) under a Creative Commons Attribution License (CC-BY 3.0). Further modification of the figure is performed by the image uploader with reference from
Davis PK, Brackmann RK. Chromatin remodeling and cancer.
Cancer Biol Ther. 2:22 (2003). PMID: 12673113
Figure # 7.121
Methylation
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.122
Epigenetics
https://commons.wikimedia.org/wiki/File:Epigenetic_mech
anisms.jpg
Public Domain
Figure # 7.123
miRNA
https://commons.wikimedia.org/wiki/File:MiRNA.svg
WCCA 3.0
Kelvinsong
Figure # 7.124
pre-miRNAs miRNAs
https://commons.wikimedia.org/wiki/File:Examples_of_mi
croRNA_stem-loops.jpg
WCCSA 4.0
VTD
Figure # 7.125
siRNA and RNAi
http://pehrjac.wix.com/pehrjacobson
Public Domain
Pehr Jacobson
Figure # 7.126
siRNA Duplex
https://commons.wikimedia.org/wiki/File:SiRNA_Structure
2.svg
Public Domain
Figure # 7.127
Ferritin regulation
http://www.aleiakim.com/
Public Domain
Aleia Kim
Figure # 7.128
Transferrin regulation
http://www.aleiakim.com/
Public Domain
Aleia Kim & Indira Rajagopal
Figure # 7.129
Signal Molecules Table
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.130
Transmembrane receptor
https://commons.wikimedia.org/wiki/File:Transmembrane_
receptor.svg
WCCSA 3.0
Mouagip (talk)
Figure # 7.131
Signal transduction pathway features
rajagopi@oregonstate.edu
Public Domain
Indira Rajagopal
Figure # 7.132
Ligand gated ion channels
https://commons.wikimedia.org/wiki/File:LGIC.png
Public Domain
Figure # 7.133
Neuromuscular signaling
https://commons.wikimedia.org/wiki/File:The_Muscle_Con
traction_Process.png
WCCSA 4.0
Elliejellybelly13
Figure # 7.134
Nerve System function
https://commons.wikimedia.org/wiki/File:Nervous_system
_organization_en.svg
WCCSA 3.0
Nervous_system_organization_fr.svg: Jdifool / derivative
work: Looie496 (talk)
Figure # 7.135
1121
1122
ElaineMeng / Ribbon diagram of H-ras, w:PDB ID 121p, generated with w:UCSF Chimera. Strands are purple, helices
aqua, loops gray. Also shown are the bound ligand (GTP analog) and magnesium ion. UCSF Chimera development is
funded by the NIH (grant P41-RR01081)
Figure # 7.155
Signaling pathway overview
http://commons.wikimedia.org/wiki/File:Signal_transductio
n_pathways.png
Public Domain
Figure # 7.156
EGFR signaling
https://commons.wikimedia.org/wiki/File:EGFR_signaling_
pathway_de.svg
Public Domain
https://commons.wikimedia.org/wiki/File:Ion_exchange_co
lumn.jpg
Public Domain
Figure # 8.4
Ion exchange beads
https://commons.wikimedia.org/wiki/File:Ion_exchange_re
sin_beads.jpg
Public Domain
Figure # 8.5
Polystyrolsulfonate
https://commons.wikimedia.org/wiki/File:Polystyrolsulfonat
.svg
Public Domain
Figure # 7.157
Erb-B family (HER)
https://commons.wikimedia.org/wiki/File:Erb_fig.jpeg
Public Domain
Figure # 8.6
Ca removal by cation exchange
https://commons.wikimedia.org/wiki/File:CationExchCarto
on.png
WCCSA 3.0
Smokefoot
Figure # 7.158
Herceptin bound to HER2
https://commons.wikimedia.org/wiki/File:Trastuzumab_Fa
b-HER2_complex_1N8Z.png
Public Domain
Figure # 8.7
Gel Filtration
rajagopi@oregonstate.edu
Public Domain
IR
Figure # 7.159
bcr-abl fusion
https://en.wikipedia.org/wiki/File:Schematic_of_the_Phila
delphia_Chromosome.svg
WCCSA 4.0
Aryn89
Figure # 8.8
Size exclusion
https://commons.wikimedia.org/wiki/File:Chrom_SephG-5
0.tif
WCCSA 3.0
Bernd Kastenholz / Open Biochem J. 2008; 2: 4448;doi:
10.2174/1874091X00802010044
Figure # 7.160
Gleevec complexed with abl
https://commons.wikimedia.org/wiki/File:1IEP.png
WCCSA 3.0
Boghog / Crystallographic structure of Imatinib (STI-571)
complexed with the proto-oncogene tyrosine-protein kinase
ABL based on PDB 1IEP
Figure # 8.1
Sonicator
https://commons.wikimedia.org/wiki/File:Sonicator.jpg
WCCSA 3.0
Eyal Bairey
Figure # 8.2
Ultracentrifuge
https://commons.wikimedia.org/wiki/File:Ultracentrifuge.jp
g
WCCSA 2.5
Nmnogueira at English Wikipedia
Figure # 8.3
Ion exchange column
Figure # 8.9
Affinity Chromatography
http://www.aleiakim.com/
Public Domain
AK
Figure # 8.1
HPLC
https://commons.wikimedia.org/wiki/File:Hplc.JPG
Public Domain
Figure # 8.11
Agarose structure
https://commons.wikimedia.org/wiki/File:Agarose_polymer
e.svg
Public Domain
Figure # 8.12
Agarose gel
https://commons.wikimedia.org/wiki/File:Two_percent_Ag
arose_Gel_in_Borate_Buffer_cast_in_a_Gel_Tray_(Front,
_angled).jpg
WCCA 2.0
1123
Joseph Elsbernd
Figure # 8.13
Gel electrophoresis
https://commons.wikimedia.org/wiki/File:Gel_electrophore
sis_2.jpg
WCCSA 3.0
Mnolf
Figure # 8.14
Acrylamide monitor
https://commons.wikimedia.org/wiki/File:Polyacrylamide.sv
g
Public Domain
Figure # 8.15
N,N'-Methylenebisacrylamide
https://commons.wikimedia.org/wiki/File:Methylenebisacry
lamide.png
Public Domain
Figure # 8.16
Disulfide bond reduction
Public Domain
KGA
Figure # 8.17
SDS-PAGE
https://commons.wikimedia.org/wiki/File:Gel_Blue_Cooma
ssie.jpg
WCCSA 2.0
Stephen Helms from Dallas, TX, United States
Figure # 8.18
Isoelectric focusing
rajagopi@oregonstate.edu
Public Domain
IR
Figure # 8.19
2-D gel
http://www.aleiakim.com/
Public Domain
AK
Figure # 8.2
2-D gel image
https://commons.wikimedia.org/wiki/File:2D_gel1.jpg
WCCSA 3.0
Itayba at Hebrew Wikipedia
Figure # 8.21
Northern/Souther Blot
https://commons.wikimedia.org/wiki/File:Northern_Blot_S
cheme.PNG
Public Domain
Figure # 8.22
Western blot
https://commons.wikimedia.org/wiki/File:Anti-lipoic_acid_
immunoblot.png
WCCSA 3.0
TimVickers
Figure # 8.23
Microarray setup
http://www.davincipress.com/bffa/tanwebpagebounce.html
Public Domain
TT
Figure # 8.24
Microarray
https://commons.wikimedia.org/wiki/File:Mouse_cdna_mic
roarray.jpg
Public Domain
Figure # 8.25
Fluorescent Probe
https://commons.wikimedia.org/wiki/File:Microarray_Com
parative_Genomic_Hybridisation.jpg
Public Domain
Figure # 8.26
Labeling mRNAs
http://www.davincipress.com/bffa/tanwebpagebounce.html
Public Domain
TT
Figure # 8.27
Add sample to microarray
http://www.davincipress.com/bffa/tanwebpagebounce.html
Public Domain
TT
Figure # 8.28
Simple microarray
https://en.wikipedia.org/wiki/DNA_microarray#/media/Fil
e:Heatmap.png
Public Domain
Figure # 8.29
Illumina Hi-Seq
https://commons.wikimedia.org/wiki/File:Illumina_HiSeq_
2500.jpg
Public Domain
Figure # 8.3
Restriction Enzyme
https://commons.wikimedia.org/wiki/File:1fok.png
WCCSA 3.0
Figure # 8.31
Restriction enzyme
https://commons.wikimedia.org/wiki/File:HindIII_Restricti
on_site_and_sticky_ends_vector.svg
WCCSA 3.0
Helixitta
1124
Figure # 8.32
Recombinant DNA construction
https://commons.wikimedia.org/wiki/File:Recombinant_for
mation_of_plasmids.svg
WCCSA 3.0
Minestrone Soup at English Wikipedia
Figure # 8.33
pUC 18/19 Map
http://davincipress.com/bffa/kgafreebies.html
Public Domain
KGA
Figure # 8.34
PCR
http://www.aleiakim.com/
Public Domain
AK
Figure # 8.35
PCR Tubes
https://commons.wikimedia.org/wiki/File:PCR_tubes.png
Public Domain
Figure # 8.36
Thermocycler
https://commons.wikimedia.org/wiki/File:G-Storm_thermal
_cycler.jpg
WCCSA 3.0
Rror
Figure # 8.37
Reverse Transcriptase
https://commons.wikimedia.org/wiki/File:Reverse_transcri
ptase_3KLF_labels.png
WCCSA 3.0
Thomas Splettstoesser (www.scistyle.com) / Surface representation of the crystal structure of wild-type HIV-1 Reverse
Transcriptase, based on PDB 3KLF. The active sites of polymerase and RNase are highlighted
Conditions_du_FRET_(de).png:
*Conditions_du_FRET.png: Maurel Damien / derivative
work: S. Jhnichen (talk) / derivative work: S. Jhnichen
(talk)
Figure # 8.41
FRET
http://pehrjac.wix.com/pehrjacobson
Public Domain
PJ
Figure # 8.42
Crispr Guide RNA to Target
http://pehrjac.wix.com/pehrjacobson
Public Domain
PJ
Figure # 8.43
Crispr 2
http://pehrjac.wix.com/pehrjacobson
Public Domain
PJ
Figure # 8.44
Crispr 3
http://pehrjac.wix.com/pehrjacobson
Public Domain
PJ
Figure # 8.45
Protease specificity
http://davincipress.com/bffa/kgafreebies.html
Public Domain
KGA
Unnumbered p. 833
Protein cleavage agents
http://davincipress.com/bffa/kgafreebies.html
Public Domain
KGA
Figure # 8.38
Transcription factor schematic
https://commons.wikimedia.org/wiki/File:Transcription_fac
tor_schematic_2.png
Public Domain
Figure # 8.46
MALDI-TOF
https://commons.wikimedia.org/wiki/File:MALDITOF.jpg
GNU GPL
Figure # 8.39
Yeast Two Hybrid Screen
https://commons.wikimedia.org/wiki/File:Two_hybrid_assa
y.svg
WCCSA 3.0
Anna
Figure # 8.47
FRAP
https://commons.wikimedia.org/wiki/File:Frap_diagram.sv
g
Public Domain
Figure # 8.4
FRET fluorescence
https://commons.wikimedia.org/wiki/File:FRET-Spektren
berlappung.png
WCCSA 3.0
Glossary Figures
All glossary figures are public domain images except the ones noted below.
1125
Format as follows
Description
Source/Creator Info
License type
Creator info (if known)
License types
WCCA = Wikipedia/Wikimedia Creative Commons Attribution (followed by relevant number)
https://en.wikipedia.org/wiki/Creative_Commons_license
WCCSA = Wikipedia/Wikimedia Creative Commons Share
Alike (followed by relevant number)
https://en.wikipedia.org/wiki/Creative_Commons_license
GFDL = Gnu Free Document License https://en.wikipedia.org/wiki/GNU_Free_Documentation_
License
__________________
Alpha Helix
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Alpha_helix.png
Zsolt Bikadi / en:User:Bikadi
Alpha Helix
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Alpha_helix_neg
60_neg45_sideview.png
No machine-readable author provided. WillowW assumed
(based on copyright claims)
Ames Test
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Ames_test.svg
Histidine
Amyloid Plaque
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Small_bowel_du
odenum_with_amyloid_deposition_20X.jpg
Michael Feldman, MD, PhD University of Pennsylvania
School of Medicine /
http://www.healcentral.org/healapp/showMetadata?metada
taId=38715
https://commons.wikimedia.org/wiki/File:Hapop.jpg
Org1012
AT Base Pair
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:AT_DNA_base_p
air.png
Originally uploaded by Roadnottaken (Transferred by Edgar181)
Atherosclerosis
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Endo_dysfunctio
n_Athero.PNG
No author information
ATP Synthase
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Atp_synthase.PN
G
Alex.X
Autoheterotrophs
WCCSA 4
https://commons.wikimedia.org/wiki/File:AutoHeteroTroph
s_flowchart.png
Cactus0
Azide Anion
WCCSA 4
https://commons.wikimedia.org/wiki/File:Azide_Anion.tif
Pwnsey
Bacteriophage
WCCSA 2.5
https://commons.wikimedia.org/wiki/File:Tevenphage.svg
Adenosine (original); en:User:Pbroks13 (redraw) /
http://commons.wikimedia.org/wiki/Image:Tevenphage.png
Beta Barrel
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Sucrose_porin_1
a0s.png
Opabinia regalis
Beta Carotene
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:BetaCarotene-3d.
png
Sbrools
Anticodon
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_en.svg
Yikrazuul
Beta Turn
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Beta_turn.svg
Muskid / Scheme of beta turns after D. E. Metzler: Biochemistry. The Chemical Reactions of Living Cells. Volume 1. Elsevier Science, 2003; S. 74
Apoptosome
WCCSA 3.0
Beta-galactosidase
WCCSA 3.0
1126
https://commons.wikimedia.org/wiki/File:Beta-galactosidas
e.png
Jonathan A Jones at English Wikipedia / Transferred from
en.wikipedia to Commons by Ronhjones using CommonsHelper
Bruce Ames
WCCA 2.5
https://commons.wikimedia.org/wiki/File:Bruce_Ames.jpg
The original uploader was Italianscallion at English Wikipedia
Calcidiol
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Calcidiol2.svg
JaGa
Cardiolipin
WCCSA 3.0
https://en.wikipedia.org/wiki/File:Cardiolipin.png
Roadnottaken (talk) (Uploads)
Catalytic Triad
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Triad_chemical_
mech.png
Thomas Shafee
Cell Cycle
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Cell_Cycle_2-2.sv
g
Cell_Cycle_2.svg: *Cell_Cycle_2.png: Original uploader was
Zephyris at en.wikipedia / derivative work: Beao / derivative
work: Histidine (talk)
Central Nervous System
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:1201_Overview_o
f_Nervous_System.jpg
OpenStax /
https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Pr
eface
Chemokine Attraction
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Chemokine_conc
entration_chemotaxis.svg
Pen1234567. Derivative of image by Kohidai, L.
Chlorophyll in Chloroplasts
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Plagiomnium_aff
ine_laminazellen.jpeg
Kristian Peters -- Fabelfroh
Chromosomes in Metaphase
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:HumanChromoso
mesChromomycinA3.jpg
Steffen Dietzel
Clathrin and Endocytosis
WCCA 2.5
https://commons.wikimedia.org/wiki/File:Itrafig2.jpg
Grant, B. D. and Sato, M /
http://www.wormbook.org/chapters/www_intracellulartraffi
cking/intracellulartrafficking.html (Transferred from
en.wikipedia to Commons by Vojtech.dostal.)
Coiled coil
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:GCN4_coiled_coi
l_dimer_1zik_rainbow.png
No machine-readable author provided. WillowW assumed
(based on copyright claims).
Complex II
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Succinate_Dehyd
rogenase_1YQ3_and_Membrane.png
Zephyris at English Wikipedia
Conserved sequence alignment
WCCSA 4
https://commons.wikimedia.org/wiki/File:Histone_Alignme
nt.png
Thomas Shafee
Cytokinesis
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Unk.cilliate.jpg
TheAlphaWolf
Diffusion
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Diffusion.svg
JrPol
DNA Binding Cro Protein
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Cro_protein_com
plex_with_DNA.png
P99am
DNA Ligase Action
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Ligation.svg
Madprime
DNA Polymerase Action
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:DNA_polymerase
.svg
Madprime
DNA Replication
WCCSA 3.0
1127
https://commons.wikimedia.org/wiki/File:DNA_replication
_split.svg
Madprime
Eicosanoid Pathway
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Eicosanoid_synth
esis.svg
Jfdwolff, whitespace removed by Fvasconcellos
Endoplasmic Reticulum
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Blausen_0350_E
ndoplasmicReticulum.png
BruceBlaus. When using this image in external sources it can
be cited as: Blausen.com staff. "Blausen gallery 2014". Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010.
ISSN 20018762.
Endothelium
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:2104_Three_Maj
or_Capillary_Types.jpg
OpenStax College / Anatomy & Physiology, Connexions Web
site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013.
Exocytosis
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Synapse_diag1.sv
g
vectorization: Mouagip (talk) / Synapse_diag1.png: Drawn by
fr:Utilisateur:Dake / Corrections of original PNG by
en:User:Nrets
Exons
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Gene_structure.s
vg
en:User:Daycd, traced by User:Stannered
Expression Vector
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:PGEX-3X_clonin
g_vector.png
Magnus Manske
Extrinsic Factor
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Classical_blood_
coagulation_pathway.png
Dr Graham Beards
F2,6BP
WCCSA 4
https://commons.wikimedia.org/wiki/File:A-D-fructose-2,6bisphosphate.tif
Austinprince
FAD
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:FAD.png
UMcrc14
FADH2
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:FADH2.png
UMcrc14
Fibroblasts
WCCA 2.5
https://commons.wikimedia.org/wiki/File:NIH_3T3.jpg
SubtleGuest at English Wikipedia
Folding Funnel
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Folding_funnel_s
chematic.svg
Thomas Splettstoesser (www.scistyle.com)
Francis Crick
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Francis_Crick_cr
op.jpg
Photo: Marc Lieberman
Free Radical
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Hydroxyl_radical
.png
SmokeyJoe
Gangliosides
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Structure_of_GM
1,_GM2,_GM3.png
LHcheM
GAR Transformylase Reaction
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Overall_Reaction
_of_GAR_transformylase.jpg
Ikghansah
Gated ion channels
WCCSA 4
https://commons.wikimedia.org/wiki/File:Open_and_close
d_conformations_of_ion_channels.png
Efazzari
Gene Expression
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Genetic_code.svg
Madprime
Glycolipid
WCCSA 4
https://commons.wikimedia.org/wiki/File:Glycolipid.svg
Wpcrosson
Glycolysis Metabolic Pathway
1128
WCCSA 4
https://en.wikipedia.org/wiki/File:Glycolysis_metabolic_pat
hway_3_annotated.svg
Thomas Shafee
GMP
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:GMP_chemical_s
tructure.png
cacycle, 12 April 2005
Golden Rice
WCCA 2.5
https://commons.wikimedia.org/wiki/File:Golden_Rice.jpg
International Rice Research Institute (IRRI) /
http://www.flickr.com/photos/ricephotos/5516789000/in/s
et-72157626241604366
Gram Stain
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Gram_stain_01.j
pg
Y tambe
Gramicidins A,B,C
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Structure_of_Gra
micidins_A_B_C.png
Danielchemik
Heparan Sulfate
WCCSA 4
https://commons.wikimedia.org/wiki/File:Heparan_Sulfate.
svg
J3D3
Hyperforin
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Hyperforin2DAC
S.svg
Fuse809
miRNA
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Examples_of_mi
croRNA_stem-loops.jpg
VTD
MWC Model
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Allostery.png
Nicolas Le Novere (talk)
Nucleic Acids
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Difference_DNA
_RNA-EN.svg
Difference_DNA_RNA-DE.svg: Sponk (talk)
Nucleolus
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Blausen_0212_C
ellNucleus.png
BruceBlaus. When using this image in external sources it can
be cited as: Blausen.com staff. "Blausen gallery 2014". Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010.
ISSN 20018762
Nucleosome
WCCSA 3.0
https://en.wikipedia.org/wiki/File:Nucleosome_core_particl
e_1EQZ_large.gif
Darekk2 using the following Protein Data Bank (PDB) structural data - PDB ID: 1EQZ / Harp, J.M., Hanson, B.L., Timm,
D.E., Bunick, G.J. (2000) Asymmetries in the nucleosome
core particle at 2.5 A resolution. Acta Crystallogr., Sect.D 56:
1513-1534.
Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J. (2000)
Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr., Sect.D 56: 1513-1534.
PDB reference:
Harp, J.M., Hanson, B.L., Timm, D.E., Bunick, G.J. X-ray
structure of the nucleosome core particle at 2.5 A resolution.
http://www.rcsb.org/pdb/explore/explore.do?structureId=1
EQZ
Nucleosome Assembly
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Nucleosome_stru
cture.png
Richard Wheeler (Zephyris)
Olive Oil
WCCA 2.5
https://commons.wikimedia.org/wiki/File:Italian_olive_oil
_2007.jpg
my friend
Palmitate
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Palmitic_acid.svg
Mrgreen71
Phi Psi Angles
WCCA 3.0
https://commons.wikimedia.org/wiki/File:Protein_backbon
e_PhiPsiOmega_drawing.svg
Dcrjsr, vectorised Adam Rdzikowski
Phosphodiesters
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Phosphodiester_
Bond_Diagram.svg
Original uploader was User:G3pro at en.wikipedia.org
Phosphoserine
WCCA 3.0
https://commons.wikimedia.org/wiki/File:L-Phosphoserine.
png
Physchim62
1129
Phylloquinone
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Vitamin_K1.png
Tony27587
Phytol
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Phytol.png
No author information
Pi Helix
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Pi-helix_within_
an_alpha-helix.jpg
Rbcooley
Pinene
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Alpha-pinen.svg
Rbcooley
Plasmid
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Plasmid_(english
).svg
Spaully on English wikipedia
Platelet Activating Factor
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:PAF-platelet_acti
vating_factor.png
Roadnottaken
https://commons.wikimedia.org/wiki/File:Prostaglandin_D
2_structure.png
Gareth CHEBI
Quaternary structure
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Quaternary_struc
ture.png
Holger87
Ramachandran
WCCSA 3.0
https://en.wikipedia.org/wiki/File:G_N_Ramachandran.jpg
No author
Recombinant DNA Construction
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Recombinant_for
mation_of_plasmids.svg
Minestrone Soup at English Wikipedia
Recombination
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Chromosomal_Cr
ossover.svg
Abbyprovenzano
Ribosome Peptide Synthesis
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Peptide_syn.png
Boumphreyfr
Platelet Clumps
WCCA 3.0
https://commons.wikimedia.org/wiki/File:Platelets.jpg
Tleonardi
Rosalind Franklin
WCCSA 3.0
https://en.wikipedia.org/wiki/File:Rosalind_Franklin.jpg
Jewish Chronicle Archive/Heritage-Images /
http://www.britannica.com/EBchecked/topic-art/217394/99
712/Rosalind-Franklin
Platelets
WCCSA 4
https://commons.wikimedia.org/wiki/File:Platelets2.JPG
No machine-readable author provided. Graham Beards assumed (based on copyright claims)
Rotavirus
WCCA 3.0
https://commons.wikimedia.org/wiki/File:Rotavirus_Recon
struction.jpg
Dr Graham Beards
Prokaryotic Cell
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Prokaryote_cell.s
vg
Ali Zifan
Sarcolemma
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Blausen_0801_S
keletalMuscle.png
BruceBlaus. When using this image in external sources it can
be cited as: Blausen.com staff. "Blausen gallery 2014". Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010.
ISSN 20018762
Proline
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:L-Proline_(At_ph
ysiological_pH).svg
Linnikh
Prostaglandin D2
WCCSA 3.0
Sarcomere
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Sarcomere.svg
Slashme at English Wikipedia - Richfield, David. "Medical
gallery of David Richfield 2014". Wikiversity Journal of Medicine 1 (2). DOI:10.15347/wjm/2014.009. ISSN 2001-8762
1130
Tautomers
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Tautomers.gif
Andervik
Terpineols
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Terpineols.png
V8rik at English Wikipedia
Tertiary Structure
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Protein_structure
.png
Holger87
Tetrahedron
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Tetrahedron.jpg
Created by en:User:Cyp and copied from the English Wikipedia
Thromboxane A2
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Thromboxane_A
2.png
Self made by Foobar 17:27, 12 July 2006 (UTC)
Thylakoid Membrane
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Chloroplast_mini
.svg
Kelvinsong
Titration Curve
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Oxalic_acid_titra
tion_grid.png
JWSchmidt at English Wikipedia
TLC
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Chromatography
_of_chlorophyll_-_Step_7.jpg
No machine-readable author provided. Flo~commonswiki
assumed (based on copyright claims)
Triiodothyronine
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:(S)-Triiodthyroni
ne_Structural_Formulae_V2.svg
J
tRNA
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast
_1ehz.png
Yikrazuul
1131
Troponin activation
WCCSA 3.0
https://en.wikipedia.org/wiki/File:Troponin-activation.png
Original drawing by RMB Hoffman (Copyleft 2010). Based on
Proteins 2008 Nov 1;73(2):338-50
Trp Operon
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Trp_operon_atte
nuation.svg
Histidine
Tubulin
WCCA4.0
https://commons.wikimedia.org/wiki/File:Comparison_of_
bacterial_and_eukaryotic_microtubules.jpg
Pilhofer, M., Ladinsky, M.S., McDowall, A.W., Petroni, G.,
Jensen, G.J. / Pilhofer, M., Ladinsky, M.S., McDowall, A.W.,
Petroni, G. & Jensen, G.J. Microtubules in bacteria: Ancient
tubulins build a five-protofilament homolog of the eukaryotic
cytoskeleton. PLoS Biol 9, e1001213 (2011)
Turnips
WCCA2.0
https://commons.wikimedia.org/wiki/File:Turnip_2622027.
jpg
thebittenword.com /
http://www.flickr.com/photos/galant/2622027467/
Urobilinogen
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Structure_of_uro
bilinogen.png
LHcheM
Vitamin K cycle
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Carboxylation_re
action_vitamin_K_cycle.png
Lomeloth
Vitamin K1
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Vitamin_K1.png
Tony27587
Vitamin K2 subtypes
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Vitamin_K_struc
tures.jpg
Lomeloth
Western Blot
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Anti-lipoic_acid_
immunoblot.png
TimVickers
Wombat
WCCSA 3.0
https://commons.wikimedia.org/wiki/File:Vombatus_ursinu
s_-Maria_Island_National_Park.jpg
JJ Harrison (jjharrison89@facebook.com)
Metabolic Melodies
All song lyrics and recordings in the book Copyright Kevin
Ahern or Kevin Ahern and Indira Rajagopal (as noted below).
These materials have also been published in BAMBED (Biochemistry and Molecular Biology). Recording artist(s) noted
on the lyrics page of each Metabolic Melody.
Relevant BAMBED reference information follows.
Around the Nucleus
Ahern, Kevin - Biochemistry and Molecular Biology Education (2012), 40, 216.
B-DNA
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 115.
Biochemistry Pie
Ahern, Kevin - Biochemistry and Molecular Biology Education (2008), 36, 380-381.
Biochemistry, Biochemistry
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 427
Catalyze
Ahern, Kevin - Biochemistry and Molecular Biology Education (2010), 38, 355.
Cell's Lament
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 351
Central Dogma Zen
Rajagopal, Indira and Ahern, Kevin - Biochemistry and Molecular Biology Education (2009) 37, p. 68.
Chromatin
Ahern, Kevin - Biochemistry and Molecular Biology Education (2012), 40, 156.
Citric Acid Cycle
Ahern, Kevin - Biochemistry and Molecular Biology Education (2014), 42, 510.
Codon Song
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 288.
En-er-gy
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 35.
Enzymes
1132
Ahern, Kevin - Biochemistry and Molecular Biology Education (2009), 37, 260.
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 114.
Tao of Hormones
Ahern, Kevin - Biochemistry and Molecular Biology Education (2007) 35, p. 226
Gluconeogenesis
Ahern, Kevin - Biochemistry and Molecular Biology Education (2008), 36, 443.
God Rest Ye Merry Lipoproteins
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 425
The Ribosome
Ahern, Kevin - Biochemistry and Molecular Biology Education (2006) 34, p. 288.
Verses
Photosynthesis is Divine
Ahern, Kevin - Biochemistry and Molecular Biology Education (2010), 38, p. 58.
Sound of Glucose
1133
Ahern, Kevin - Biochemistry and Molecular Biology Education (2013), 41, 362.
Pentose Phosphate Pathway
Ahern, Kevin.- Biochemistry and Molecular Biology Education (2012), 40, p. 288.
Two verses in the book are Copyright Indira Rajagopal and
were also published in BAMBED. Their information follows:
Rajagopal, Indira (2013) Gee, what an amazing protein, Biochemistry and Molecular Biology Education 41 (2): 128
Rajagopal, Indira, (2013) The Students Guide To A Perfect
Transcript, Biochemistry and Molecular Biology Education 41
(1): 62
Tables
Many tables in the book were given figure numbers and credits for them are shown in the permissions section on Figures.
Other Table credits follow.
Table 1.1
Aleia Kim
Prokaryotes and Eukaryotes Traits
http://www.aleiakim.com/
Table 1.2
Aleia Kim
Electronegativities
http://www.aleiakim.com/
Table 1.3
Aleia Kim
Hydrophilic vs. Hydrophobic
http://www.aleiakim.com/
Table 1.4
Aleia Kim
Bond Energies
http://www.aleiakim.com/
Table 1.5
Aleia Kim
Weak pKa acid values
http://www.aleiakim.com/
Table 1.6
Aleia Kim
Salt Acid Ratio
http://www.aleiakim.com/
Kevin Ahern
Amino acid categories
http://www.davincipress.com/professional.html
Table 2.3
Penelope Irving
Secondary structure tendencies
mailto:I.penelopekay@gmail.com
Table 7.1
Kevin Ahern
Location/function rRNAs
http://www.davincipress.com/professional.html
Animations
Permission information for animations in the book is formatted as follows:
Animation Number
Description
Relevant link
License type
Author info
2.1
Cytochrome C
https://commons.wikimedia.org/wiki/File:Protein_Dynamic
s_Cytochrome_C_2NEW_smaller.gif
WCCSA 3.0
Original uploader was Zephyris at en.wikipedia
2.2
SUMO
https://commons.wikimedia.org/wiki/File:1a5r_SUMO-1_pr
otein.gif
WCCSA 4.0
Lukasz Kozlowski / Majorek, Karolina; Kozlowski, Lukasz;
Jakalski, Marcin; Bujnicki Janusz M. (2008) First Steps of
Protein Structure Prediction. In: Prediction of Protein Structures, Functions, and Interactions Pages: 39-62. DOI:
10.1002/9780470741894.ch2
2.3
Hemoglobin
https://commons.wikimedia.org/wiki/File:Hemoglobin_t-r_
state_ani.gif
WCCSA 3.0
BerserkerBen
Table 2.1
Pehr Jacobson
Essential/non-essential Aas
http://pehrjac.wix.com/pehrjacobson
2.4
Kinesin Walking
https://commons.wikimedia.org/wiki/File:Kinesin_walking.
gif
WCC0
Jzp706
Table 2.2
2.5
1134
DNA rotating
https://commons.wikimedia.org/wiki/File:ADN_animation.
gif
Public Domain
brian0918
2.6
Glucose Fischer to Haworth
https://commons.wikimedia.org/wiki/File:Glucose_Fisher_t
o_Haworth.gif
WCCSA 3.0
Wikimuzg
3.1
Gramicidin
https://commons.wikimedia.org/wiki/File:Gramicidin_A.gif
Public Domain
Lomize, A.L., Orekhov, V.I.u., Arsen`ev, A.S. Refinement of
the spatial structure of the gramicidin A ion channel
Biol.Membr.(USSR) v18 pp.182-200, 1992
3.2
Action Potential
https://commons.wikimedia.org/wiki/File:Action_Potential.
gif
WCCSA 3.0
Laurentaylorj
5.1
ATP rotating
https://commons.wikimedia.org/wiki/File:MgATP2-small.gi
f
WCCSA 4.0
Someone1939
5.2
Q-cycle
https://commons.wikimedia.org/wiki/File:Theqcycle.gif
WCCSA 3.0
Neveu,Curtis (C31004) / Nicholls, David and Stuart Ferguson. Bioenergetics3. Academic Press: San Diego, California.
2002.pg 115.
5.3
ATP Synthase
http://commons.wikimedia.org/wiki/File:ATPsyn.gif
Public Domain
No author information
6.1
Lovastatin
https://commons.wikimedia.org/wiki/File:Lovastatin3Dan.g
if
WCCSA 3.0
Fuse809
6.2
Calcitriol
https://commons.wikimedia.org/wiki/File:Calcitriol3Dan.gif
Public Domain
Fuse809 (talk)
6.3
5-Fluorouracil
https://commons.wikimedia.org/wiki/File:Fluorouracil3Dan
Z.gif
Public Domain
Fuse809 (talk)
7.1
30S ribosome
http://commons.wikimedia.org/wiki/File:10_small_subunit.
gif
WCCSA 4.0
David S. Goodsell, RCSB Protein Data Bank /
http://pdb101.rcsb.org
7.2
50S ribosome subunit
https://commons.wikimedia.org/wiki/File:10_large_subunit
.gif
WCCSA 4.0
David S. Goodsell, RCSB Protein Data Bank /
http://pdb101.rcsb.org
7.3
Translation in ER
https://commons.wikimedia.org/wiki/File:Protein_translati
on.gif
WCCA 3.0
User:Bensaccount. Original uploader was Bensaccount at
en.wikipedia
Interactive 3D Models
Permission information for interactive 3D models in the book
is formatted as follows:
Description
PDB ID Number
License Type
URL for Download
Bacterial Ribosome
4GD2
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=4
V9D
Hexokinase Closed
1BDG
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=1
BDG
Hexokinase Open
1IG8
PDB Public Domain
1135
http://www.rcsb.org/pdb/explore/explore.do?structureId=1I
G8
Human Deoxyhemoglobin
2HHB
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=2
HHB
Human Insulin
3E7Y
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=3
E7Y
Human Oxyhemoglobin
1HHO
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=1
HHO
Klenow Fragment
2KZZ
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=2
KZZ
Oxymyoglobin
1MBO
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=1
MBO
Phenylalanine tRNA
4TNA
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=4
TNA
Sliding clamp on DNA
3BEP
PDB Public Domain
http://www.rcsb.org/pdb/explore/explore.do?structureId=3
BEP
1136
My 'A'
To the tune of "My Way"
jji
I thought it up
And wrote it down
I fought the fight
I hope its right
B-B three fif-ty
The End
-10 sequence
The Pribnow box (also known as the Pribnow-Schaller box or the -10 sequence) is the
sequence TATAAT of six nucleotides (thymine-adenine-thymine-etc.) that is an essential part of a promoter site on DNA for transcription to occur in bacteria. It is an idealized or consensus sequencethat is, it shows the most frequently occurring base at
each position in a large number of promoters analyzed. Individual promoters often
vary from the consensus at one or more positions. It is also commonly called the -10 sequence, because it is centered roughly 10 base pairs upstream from the site of initiation
of transcription.
The Pribnow box has a function similar to the TATA box that occurs in promoters in
eukaryotes and archaea: it is recognized and bound by a subunit of RNA polymerase
during initiation of transcription. This region of the DNA is also the first place where
base pairs separate during prokaryotic transcription to allow access to the template
strand. The AT-richness is important to allow this separation, since adenine and
thymine are easier to break apart (not due to the hydrogen bond count ).
It is named after David Pribnow and Heinz Schaller. The frequency of occurrence of
each nucleotide in the Pribnow box is shown below.
https://en.wikipedia.org/wiki/Pribnow_box
Index
Find Term
-35 sequence
In bacterial transcription, RNA polymerase (RNAP) binds to one of several
moter regions in the DNA. The -35 region and the -10 ("Pribnow box") regio
the core prokaryotic promoter. The DNA on the template strand between th
and the terminator sequence at the 3 end is transcribed into RNA, which is
lated into protein. At this stage, the DNA is double-stranded ("closed"). Thi
holoenzyme/wound-DNA structure is referred to as the closed complex.
https://en.wikipedia.org/wiki/Bacterial_transcription
Index
Find Term
(Cis-3-)Enoyl-CoA Isomerase
Since the key step in the degradation of fatty acids with double bonds at eve
3-Enoyl-CoA Isomerase
Enoyl-CoA isomerase is involved in the -oxidation, one of the most frequently used
pathways in fatty acid degradation, of unsaturated fatty acids with double bonds at
odd-numbered carbon positions. It does so by shifting the position of the double bonds
in the acyl-CoA intermediates and converting 3-cis or trans-enoyl-CoA to 2-transenoyl-CoA. Since the key step in the degradation of fatty acids with double bonds at
even-numbered carbon positions also produces 3-trans-enoyl-CoA in mammals and
yeasts, enoyl-CoA isomerase is technically required for their metabolism as well.
As it functions in the step immediately preceding the actual -oxidation and forms a
double bond extending from the -carbon (position 2), enoyl-CoA isomerase is involved in both the NADPH-dependent and NADPH-independent pathways of oxidation. The double bond serves as the target of oxidation and carbon-to-carbon
bond cleavage, thereby shortening the fatty acid chain.
https://en.wikipedia.org/wiki/Enoyl_CoA_isomerase
Index
Find Term
In thermodynamics, the Gibbs free energy (IUPAC recommended name: Gibbs energy
or Gibbs function - also known as free enthalpy to distinguish it from Helmholtz free
energy) is a thermodynamic potential that measures the maximum or reversible work
free energy (kJ in SI units) is the maximum amount of non-expansion work that can b
extracted from a thermodynamically closed system (one that can exchange heat and
work with its surroundings, but not matter). This maximum can be attained only in a
completely reversible process.
https://en.wikipedia.org/wiki/Gibbs_free_energy
Index
Find Term
1-alkyl-dihydroxyacetone-3-phosphate
Index
Find Term
1-pyrroline-5-carboxylic Acid
1-pyrroline-5-carboxylic acid is an intermediate in the synthesis of proline.
1,3-bisphosphoglycerate
1,3-bisphosphoglyceric acid (1,3-bisphosphoglycerate or 1,3BPG) is a 3-carbon organic
molecule present in most, if not all, living organisms. It primarily exists as a metabolic
intermediate in both glycolysis during respiration and the Calvin cycle during photosynthesis. 1,3BPG is a transitional stage between glycerate 3-phosphate and glyceraldehyde 3-phosphate during the fixation/reduction of CO2. 1,3BPG is also a precursor to
2,3-bisphosphoglycerate which in turn is a reaction intermediate in the glycolytic pathway.
https://en.wikipedia.org/wiki/1,3-Bisphosphoglyceric_acid
Index
Find Term
Index
Find Term
2-phosphoglycerate
https://en.wikipedia.org/wiki/2-Phosphoglyceric_acid
Index
Find Term
2,3-BPG
2,3-bisphosphoglyceric acid (2,3-bisphosphoglycerate or 2,3-BPG, also known as 2,3diphosphoglycerate or 2,3-DPG) is a three-carbon isomer of the glycolytic intermediate
1,3-bisphosphoglyceric acid (1,3-BPG). 2,3-BPG is present in human red blood cells
(RBC/erythrocyte) at approximately 5mmol/L. It binds with greater affinity to deoxygenated hemoglobin (e.g. when the red blood cell is near respiring tissue) than it does
to oxygenated hemoglobin (e.g., in the lungs) due to spatial changes: 2,3-BPG (with an
estimated size of about 9 angstroms) fits in the deoxygenated hemoglobin configuration (11 ), but not as well in the oxygenated (5 ). It interacts with deoxygenated hemoglobin subunits by decreasing their affinity for oxygen, so it allosterically promotes the release of the remaining oxygen molecules bound to the hemoglobin, thus
enhancing the ability of RBCs to release oxygen near tissues that need it most. 2,3-BPG
is thus an allosteric effector.
Its function was discovered in 1967 by Reinhold Benesch and Ruth Benesch.
https://en.wikipedia.org/wiki/2,3-Bisphosphoglyceric_acid
2,3-trans-enoyl-ACP Dehydrase
Index
Find Term
2,3-trans-enoyl-ACP Reductase
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate Nsuccinyltransferase
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) is an
enzyme that catalyzes the chemical reaction:
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O
<->
CoASH + N-succinyl-L-2-amino-6-oxoheptanedioate
The reaction is the fifth step in the metabolic synthesis of lysine from arginine.
This enzyme belongs to the family of transferases, specifically those acyltransferases
transferring groups other than aminoacyl groups. The systematic name of this enzyme
class is succinyl-CoA:(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate Nsuccinyltransferase. Other names in common use include tetrahydropicolinate succinylase, tetrahydrodipicolinate N-succinyltransferase, tetrahydrodipicolinate succinyltransferase, succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase,
succinyl-CoA:2,3,4,5-tetrahydropyridine-2,6-dicarboxylate, and N-succinyltransferase.
This enzyme participates in lysine biosynthesis.
https://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succin
yltransferase
CoA of equivalent length. Unlike the breakdown of saturated fat, cis and tra
uct compatible with the standard beta oxidation pathway. DECR is the seco
zyme (The others being Enoyl CoA isomerase and Dienoyl CoA isomerase) a
rate limiting step in this auxiliary flow. DECR is capable of reducing both 2-
at odd carbon positions, with equal efficiency. At this time, there is no clear
tion for this of lack of stereo-specificity.
https://en.wikipedia.org/wiki/2,4_Dienoyl-CoA_reductase
Index
Find Term
2,4 DNP
2,4-dinitrophenol (2,4-DNP or simply DNP) is an organic compound with the formula
HOC6H3(NO2)2. It is a yellow, crystalline solid that has a sweet, musty odor. It sublimes, is volatile with steam, and is soluble in most organic solvents as well as aqueous
alkaline solutions. It is a precursor to other chemicals and is biochemically active, inhibiting energy (adenosine triphosphate, ATP) production in cells with mitochondria.
Its use in high doses as a dieting aid has been identified with severe side-effects, including a number of deaths.
In living cells, DNP acts as a proton ionophore, an agent that can shuttle protons (hydrogen cations) across biological membranes. It dissipates the proton gradient across
mitochondria and chloroplast membranes, collapsing the proton motive force that the
cell uses to produce most of its ATP chemical energy. Instead of producing ATP, the energy of the proton gradient is lost as heat.
DNP is often used in biochemistry research to help explore the bioenergetics of
chemiosmotic and other membrane transport processes.
https://en.wikipedia.org/wiki/2,4-Dinitrophenol
3-hydroxy-3-methyl-2-oxobutanoate
3-hydroxy-3-methyl-2-oxobutanoate is an intermediate in synthesis of valine and leucine. Relevant reactions are shown below.
-acetolactate
3-hydroxy-3-methyl-2-oxobutanoate
3-hydroxy-3-methyl-2-oxobutanoate + NADP(P)H
,-dihydroxyisovalerate + NAD(P)+
Index
Find Term
G-G
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
3-hydroxyacyl-CoA Dehydrogenase
3-hydroxyacyl-CoA dehydrogenase is an enzyme that catalyzes the third reaction int he
-oxidation of fatty acids. It catalyzes the chemical reaction:
(S)-3-hydroxyacyl-CoA + NAD+ <-> 3-oxoacyl-CoA + NADH + H+
3-hydroxyacyl CoA dehydrogenase is classified as an oxidoreductase. It is involved in
fatty acid metabolic processes. Specifically it catalyzes the third step of oxidation the oxidation of L-3-hydroxyacyl CoA by NAD+. The reaction converts the hydroxyl
group into a keto group.
https://en.wikipedia.org/wiki/3-hydroxyacyl-CoA_dehydrogenase
Index
Find Term
3-PG Dehydrogenase
3-phosphohydroxypyruvate + NADH + H+
Index
Find Term
3-phosphoglycerate
3-phosphoglyceric acid (3PG), or glycerate 3-phosphate (GP), is a biochemically significant 3-carbon molecule that is a metabolic intermediate in both glycolysis and the Calvin cycle. This chemical is often termed PGA when referring to the Calvin cycle. In the
Calvin cycle, 3-phosphoglycerate is the product of the spontaneous split of an unstable
6-carbon intermediate formed by CO2 fixation. Thus, two 3-phosphoglycerate molecules are produced for each molecule of CO2 fixed.
https://en.wikipedia.org/wiki/3-Phosphoglyceric_acid
Index
Find Term
G-G
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
3-phosphohydroxypyruvate
Phosphohydroxypyruvic acid is an intermediate in the synthesis of serine.
https://en.wikipedia.org/wiki/Phosphohydroxypyruvic_acid
Index
Find Term
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
3-ureidoisobutyrate
3-ureidopropionate
In the reduction pathway of pyrimidine catabolism, uracil and thymine reduction by
NADPH gives dihydrothymine and dihydrouracil respectively. Addition of water to
these creates 3-ureidoisobutyrate and 3-ureidopropionate respectively, shown in the
figure below.
Index
Find Term
3,6-anhydro-L-galactopyranose
Index
Find Term
In bacteria, all three DNA polymerases (I, II and III) have the ability to proo
ing 3 5 exonuclease activity. When an incorrect base pair is recognized,
lymerase reverses its direction by one base pair of DNA and excises the mis
base. Following base excision, the polymerase can re-insert the correct base
cation can continue.
In eukaryotes only the polymerase that deal with the elongation (, and ) h
reading ability (3 5 exonuclease activity).
https://en.wikipedia.org/wiki/Proofreading_(biology)
3' UTR
The three prime untranslated region (3'-UTR) is the section of messenger RNA
(mRNA) that immediately follows the translation termination codon. An mRNA molecule is transcribed from the DNA sequence and is later translated into protein. Several
regions of the mRNA molecule are not translated into protein including the 5' cap, 5'
untranslated region, 3' untranslated region, and the poly(A) tail. The 3'-UTR often contains regulatory regions that post-transcriptionally influence gene expression.
Regulatory regions within the 3'-untranslated region can influence polyadenylation,
translation efficiency, localization, and stability of the mRNA. The 3'-UTR contains
both binding sites for regulatory proteins as well as microRNAs (miRNAs). By binding
to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various
mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3'-UTR also has silencer regions which bind to repressor proteins and will
inhibit the expression of the mRNA.
Many 3'-UTRs also contain AU-rich elements (AREs). Proteins bind AREs to affect the
stability or decay rate of transcripts in a localized manner or affect translation initiation. Furthermore, the 3'-UTR contains the sequence AAUAAA that directs addition of
several hundred adenine residues called the poly(A) tail to the end of the mRNA transcript. Poly(A) binding protein (PABP) binds to this tail, contributing to regulation of
mRNA translation, stability, and export. For example, poly (A) tail bound PABP interacts with proteins associated with the 5' end of the transcript, causing a circularization
of the mRNA that promotes translation. The 3'-UTR can also contain sequences that
attract proteins to associate the mRNA with the cytoskeleton, transport it to or from
the cell nucleus, or perform other types of localization. In addition to sequences within
the 3'-UTR, the physical characteristics of the region, including its length and secondary structure, contribute to translation regulation. These diverse mechanisms of gene
regulation ensure that the correct genes are expressed in the correct cells at the appropriate times.
https://en.wikipedia.org/wiki/Three_prime_untranslated_region
3 end
The 3 end of a nucleotide or nucleic acid is a position determined by the numbering
system for the sugars of the nucleotides composing it. The 3 end of a nucleotide has a
hydroxyl to which phosphate can be linked in the formation of a nucleic acid.
Index
Find Term
4-hydroxy-tetrahydrodipicolinate Reductase
4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) is an enzyme that catalyzes
the fourth reaction in the biosynthesis of lysine from aspartate.
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O <-> (2S,4S)-4hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH
or CH2 groups with NAD+ or NADP+ as acceptor. The systematic name of this enzyme
class is (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate:NAD(P)+ 4-oxidoreductase.
Other names in common use include:
dihydrodipicolinate reductase,
dihydrodipicolinic acid reductase, and
2,3,4,5-tetrahydrodipicolinate:NAD(P)+ oxidoreductase.
This enzyme participates in lysine biosynthesis.
https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase
Index
Find Term
4-hydroxy-tetrahydrodipicolinate Synthase
4-hydroxy-tetrahydrodipicolinate synthase is an enzyme that catalyzes the third reaction in the synthesis of lysine from aspartate.
This enzyme catalyzes the following chemical reaction:
Pyruvate + L-aspartate-4-semialdehyde <-> (2S,4S)-4-hydroxy-2,3,4,5tetrahydrodipicolinate + H2O
https://en.wikipedia.org/wiki/Dihydrodipicolinate_synthase
Index
Find Term
5-Aminoimidazole Ribotide
5'-Phosphoribosyl-5-aminoimidazole (or aminoimidazole ribotide) is an intermediate
in the formation of purines. Thus, it is an intermediate in the adenine pathway, and is
synthesized from 5'-phosphoribosylformylglycinamidine by AIR synthetase.
https://en.wikipedia.org/wiki/5-Aminoimidazole_ribotide
Index
Find Term
Chapter 6 - Metabolism:
Chapter 6 - Metabolism:
Chapter 6 - Metabolism:
Chapter 6 - Metabolism:
Nucleotides
Nucleotides
Nucleotides
Nucleotides
5-fluorouracil
tion of thymidylate synthase. It belongs to the family of drugs called the anti
lites. It is also a pyrimidine analog.
https://en.wikipedia.org/wiki/Fluorouracil
Index
Find Term
5-phosphoribosylamine
Phosphoribosylamine (5PRA) is an intermediate in purine metabolism. It is a
sor to IMP and is generated from phosphoribosyl pyrophosphate (PRPP).
https://en.wikipedia.org/wiki/Phosphoribosylamine
Index
Find Term
5.8S rRNA
The 5.8S ribosomal RNA (5.8S rRNA) is a non-coding RNA component of the large
subunit of the eukaryotic ribosome and so plays an important role in protein translation. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Its function is thought to be in ribosome translocation. It is
also known to form covalent linkage to the p53 tumor suppressor protein.
https://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
https://en.wikipedia.org/wiki/RNA_splicing
Index
Find Term
5' to 3
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical
convention of naming carbon atoms in the nucleotide sugar-ring means that there will
be a 5-end, which frequently contains a phosphate group attached to the 5 carbon of
the ribose ring, and a 3-end (usually pronounced "five prime end" and "three prime
end"), which typically is unmodified from the ribose -OH substituent. In a DNA double
helix, the strands run in opposite directions to permit base pairing between them,
which is essential for replication or transcription of the encoded information.
Nucleic acids can only be synthesized in vivo in the 5-to-3 direction, as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to the 3-hydroxyl (-OH) group, via a phosphodiester bond. The relative positions of structures along a strand of nucleic acid, including genes and various protein
binding sites, are usually noted as being either upstream (towards the 5-end) or downstream (towards the 3-end). (See also upstream and downstream.)
Directionality is related to, but independent from sense. Transcription of singlestranded RNA from a double-stranded DNA template requires the selection of one
strand of the DNA template as the template strand that directly interacts with the nascent RNA due to complementary sequence. The other strand is not copied directly, but
necessarily its sequence will be similar to that of the RNA. Transcription initiation sites
generally occur on both strands of an organism's DNA, and specify the location, direction, and circumstances under which transcription will occur. If the transcript encodes
one or (rarely) more proteins, translation of each protein by the ribosome will proceed
in a 5 to 3 direction, and will extend the protein from its N terminus toward its C terminus. For example, in a typical gene a start codon (5-ATG-3) is a DNA sequence
within the sense strand.
Transcription begins at an upstream site (relative to the sense strand), and as it proceeds through the region it copies the 3-TAC-5 from the template strand to produce
5-AUG-3 within a messenger RNA. The mRNA is scanned by the ribosome from the
5 end, where the start codon directs the incorporation of a methionine (in eukaryotes)
at the N terminus of the protein. By convention, single strands of DNA and RNA sequences are written in a 5-to-3 direction except as needed to illustrate the pattern of
base pairing.
https://en.wikipedia.org/wiki/Directionality_(molecular_biology)
Index
Find Term
5' UTR
The 5' untranslated region (5 UTR) (also known as a Leader Sequence or Leader RNA)
is the region of an mRNA that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5 UTR or
a portion of it is sometimes translated into a protein product. This product can then
regulate the translation of the main coding sequence of the mRNA. In many other organisms, however, the 5 UTR is completely untranslated, instead forming complex secondary structure to regulate translation. The 5 UTR has been found to interact with
proteins relating to metabolism and proteins translate sequences within the 5 UTR. In
addition, this region has been involved in transcription regulation, such as the sexlethal gene in Drosophila. Regulatory elements within 5' UTRs have also been linked
to mRNA export.
https://en.wikipedia.org/wiki/Five_prime_untranslated_region
Index
Find Term
5'-Phosphoribosyl-4-carboxy-5-aminoimidazole
https://en.wikipedia.org/wiki/5%27-Phosphoribosyl-4-carboxy-5-aminoim
Index
Find Term
5'-Phosphoribosylformylglycinamidine
https://en.wikipedia.org/wiki/5%27-Phosphoribosylformylglycinamidine
5 End
The 5 end of a nucleotide or nucleic acid is a position determined by the numbering
system for the sugars of the nucleotides composing it. The 5 end of a nucleotide has
phosphate can be linked to a 3 hydroxyl in the formation of a nucleic acid.
Index
Find Term
6-4PP
https://en.wikipedia.org/wiki/(6-4)DNA_photolyase
Index
Find Term
6-O-methylguanine
6-O-methylguanine (also called O6-methylguanine) is a derivative of the nucleobase
guanine in which a methyl group is attached to the oxygen atom. It base-pairs to
thymine rather than cytidine, causing a G:C to A:T transition in DNA.
6-O-methylguanine is formed in DNA by alkylation of the oxygen atom of guanine,
most often by N-nitroso compounds (NOC) and sometimes due to methylation by
other compounds such as endogenous S-adenosyl methionine. NOC are alkylating
agents formed by the reaction of nitrite or other nitrogen oxides with secondary
amines and N-alkylamides, yielding N-alkylnitrosamines and N-alkylnitrosamides.
NOC are found in some foods (bacon, sausages, cheese) and tobacco smoke, and are
formed in the gastrointestinal tract, especially after consumption of red meat. In addition, endogenous nitric oxide levels were found to be enhanced under chronic inflammatory conditions, and this could favor NOC formation in the large intestine.
https://en.wikipedia.org/wiki/6-O-Methylguanine
6-phosphogluconate
https://en.wikipedia.org/wiki/6-Phosphogluconic_acid
Index
Find Term
6-phosphogluconate Dehydrogenase
6-Phosphoglucono--lactone
https://en.wikipedia.org/wiki/6-Phosphogluconolactone
6-phosphogluconolactonase
7-dehydrocholesterol
min D3 from ultraviolet rays in the sun light, via an intermediate isomer pre-vitam
D3.
https://en.wikipedia.org/wiki/7-Dehydrocholesterol
Transmembrane proteins are of several types. The most common ones hav
(domains) that cross the membrane repeatedly. One of the most common t
brane proteins is the group of them that crosses the membrane precisely se
8-oxo-guanine
DNA lesions resulting from reactive oxygen species and can result in a mismatch
https://en.wikipedia.org/wiki/8-Oxoguanine
In the B-form the DNA helix has a repeat of 10.5 base pairs per turn, with su
adenine, guanine, cytosine, and thymine bases oriented in the middle wher
the now familiar base pairs that look like the rungs of a ladder. DNA with s
sity of base pairs per turn is referred to as relaxed. Altering that density o
sults in supercoiling of the DNA molecule.
15R-hydroxyeicosatetraenoic acid
15-Hydroxyicosatetraenoic acid (also termed 15-HETE, 15(S)-HETE, and 15S-HETE) is
an endogenous eicosanoid, i.e. a metabolite of arachidonic acid. Various cell types and
tissues first produce 15-Hydroperoxyicosatetraenoic acid (15-HpETE). These initial hydroperoxy products are extremely short lived in cells. If not otherwise metabolized,
they are reduced to 15-HETE. Both these molecules are are hormone-like autocrine
and paracrine signaling agents, involved in inflammation response, but often are further metabolized to a wide range of products that are much more potent, including eoxins.
The production and actions of these molecules and their metabolites often differ
greatly depending on cell-type or tissue-type studied. In many ways they are analogous
to the more abundant 5-HETE and 5-HPETE.
https://en.wikipedia.org/wiki/15-Hydroxyicosatetraenoic_acid
16S rRNA
16S ribosomal RNA (or 16S rRNA) is a component of the 30S small subunit of prokaryotic ribosomes. The genes coding for it are referred to as 16S rRNA gene and are used
in reconstructing phylogenies, due to the slow rates of evolution of this region of the
gene. Carl Woese and George E. Fox were two of the people who pioneered the use of
16S rRNA in phylogenies
The 16S rRNA has several functions:
Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins.
The 3' end contains the anti-Shine-Dalgarno sequence, which binds upstream to the
AUG start codon on the mRNA. The 3'-end of 16S RNA binds to the proteins S1 and
S21 known to be involved in initiation of protein synthesis
Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S)
Stabilizes correct codon-anticodon pairing in the A site, via a hydrogen bond formation between the N1 atom of Adenine residues 1492 and 1493 and the 2'OH group of
the mRNA backbone.
https://en.wikipedia.org/wiki/16S_ribosomal_RNA
Index
Find Term
18S rRNA
18S ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA. The S in
18S represents Svedberg units. 18S rRNA is a component of the small eukaryotic ribosomal subunit (40S). 18S rRNA is the structural RNA for the small component of
eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells.
It is the eukaryotic nuclear homologue of 16S ribosomal RNA in Prokaryotes and mitochondria. The genes coding for 18S rRNA are referred to as 18S rDNA. Sequence data
from these genes is widely used in molecular analysis to reconstruct the evolutionary
history of organisms, especially in vertebrates, as its slow evolutionary rate makes it
suitable to reconstruct ancient divergences.
The small subunit (SSU) 18S rRNA gene is one of the most frequently used genes in
phylogenetic studies and an important marker for random target polymerase chain reaction (PCR) in environmental biodiversity screening. In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the
use of universal primers. Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in the smallest organisms. The 18S
gene is part of the ribosomal functional core and is exposed to similar selective forces
in all living beings. Thus, when the first large-scale phylogenetic studies based on 18S
sequences were published - first and foremost phylogeny of the animal kingdom by
Field et al. (1988) - the gene was celebrated as the prime candidate for reconstructing
the metazoan tree of life. And in fact, 18S sequences later provided evidence for the
splitting of Ecdysozoa and Lophotrochozoa, thus contributing to the most recent revolutionary change in our understanding of metazoan relationships.
https://en.wikipedia.org/wiki/18S_ribosomal_RNA
Index
Find Term
20-HETE
20-Hydroxyeicosatetraenoic acid, also known as 20-HETE or 20-hydroxy5Z,8Z,11Z,14Z-eicosatetraenoic acid, is an eicosanoid metabolite of arachidonic acid
that has a wide range of effects on the vascular system including the regulation of vascular tone, blood flow to specific organs, sodium and fluid transport in the kidney, and
vascular pathway remodeling. These vascular and kidney effects of 20-HETE have
been shown to be responsible for regulating blood pressure and blood flow to specific
organs in rodents. Genetic and preclinical studies suggest that 20-HETE may similarly
regulate blood pressure and contribute to the development of stroke and heart attacks.
Additionally the loss of its production appears to be one cause of the human neurological disease, Hereditary spastic paraplegia. Preclinical studies also suggest that the overproduction of 20-HETE may contribute to the progression of certain human cancers,
particularly those of the breast.
https://en.wikipedia.org/wiki/20-Hydroxyeicosatetraenoic_acid
Index
Find Term
22-Dihydroergocalciferol
https://en.wikipedia.org/wiki/22-Dihydroergocalciferol
Index
Find Term
23S rRNA
The 23S rRNA is a 2904 nucleotide long (in E. coli) component of the large subunit
(50S) of the bacterial ribosome. The ribosomal peptidyl transferase activity resides in
domain V of this rRNA, and this domain is the most common binding site for antibiotics that inhibit translation. A well-known member of this antibiotic class, Chloramphenicol, acts by inhibiting peptide bond formation, with recent 3D-structural studies
showing two different binding sites depending on the species of ribosome. Linezolid
and quinupristin-dalfopristin also bind to the 23S rRNA, and cross-resistance has been
demonstrated between these antibiotics.
https://en.wikipedia.org/wiki/23S_ribosomal_RNA
25-hydroxycholecalciferol
Calcifediol (INN), also known as calcidiol, 25-hydroxycholecalciferol, or 25-
https://en.wikipedia.org/wiki/Calcifediol
Index
Find Term
25-hydroxyergocalciferol
25-hydroxyergocalciferol is an important metabolite in vitamin D metabolism in the
body. In the liver, cholecalciferol (vitamin D3) is converted to calcidiol, which is also
known as calcifediol (INN), 25-hydroxycholecalciferol (aka 25-hydroxyvitamin D3
abbreviated 25(OH)D3). Ergocalciferol (vitamin D2) is converted in the liver to 25hydroxyergocalciferol (aka 25-hydroxyvitamin D2 abbreviated 25(OH) D2). These
two specific vitamin D metabolites are measured in serum to determine a person's vitamin D status. Part of the calcidiol is converted by the kidneys to calcitriol, the biologically active form of vitamin D. Calcitriol circulates as a hormone in the blood, regulating the concentration of calcium and phosphate in the bloodstream and promoting the
healthy growth and remodeling of bone. Calcitriol also affects neuromuscular and immune function. The structure of ergocalciferol follows.
https://en.wikipedia.org/wiki/Vitamin_D
25-hydroxyvitamin D2
25-hydroxyvitamin D2 is an important metabolite in vitamin D metabolism in the
body.
In the liver, cholecalciferol (vitamin D3) is converted to calcidiol, which is also known
as calcifediol (INN), 25-hydroxycholecalciferol (aka 25-hydroxyvitamin D3 abbreviated 25(OH)D3). Ergocalciferol (vitamin D2) is converted in the liver to 25hydroxyergocalciferol (aka 25-hydroxyvitamin D2 abbreviated 25(OH) D2). These
two specific vitamin D metabolites are measured in serum to determine a person's vitamin D status. Part of the calcidiol is converted by the kidneys to calcitriol, the biologically active form of vitamin D. Calcitriol circulates as a hormone in the blood, regulating the concentration of calcium and phosphate in the bloodstream and promoting the
healthy growth and remodeling of bone. Calcitriol also affects neuromuscular and immune function. The structure of ergocalciferol follows.
https://en.wikipedia.org/wiki/Vitamin_D
Index
Find Term
25(OH)D2
25(OH)D2 is an important metabolite in vitamin D metabolism in the body. In the
liver, cholecalciferol (vitamin D3) is converted to calcidiol, which is also known as calcifediol (INN), 25-hydroxycholecalciferol (aka 25-hydroxyvitamin D3 abbreviated
25(OH)D3). Ergocalciferol (vitamin D2) is converted in the liver to 25hydroxyergocalciferol (aka 25-hydroxyvitamin D2 abbreviated 25(OH) D2). These
two specific vitamin D metabolites are measured in serum to determine a person's vitamin D status. Part of the calcidiol is converted by the kidneys to calcitriol, the biologically active form of vitamin D. Calcitriol circulates as a hormone in the blood, regulating the concentration of calcium and phosphate in the bloodstream and promoting the
healthy growth and remodeling of bone. Calcitriol also affects neuromuscular and immune function. The structure of ergocalciferol follows.
https://en.wikipedia.org/wiki/Vitamin_D
Index
Find Term
28S rRNA
28S ribosomal RNA is the structural RNA for the large component, or large
(LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic comp
The genes coding for 28S rRNA are referred to as 28S rDNA. The sequences
Index
Find Term
30S Subunit
Ribosomes contain two subunits, a large subunit and a small subunit. In bacteria, the
large subunit has a size of 50S and the small subunit has a size of 30S. It is the 30S
subunit that holds the 16S rRNA and also the one that is the first one to bind mRNA in
the initiation phase of translation. The small subunit below is shown in blue.
The 30S subunit is the site of inhibition for antibiotics such as tetracycline and aminoglycosides.
https://commons.wikimedia.org/wiki/File:Ribosome_shape.png
40S Subunit
The eukaryotic small ribosomal subunit (40S) is the smaller subunit of the eukaryo
80S ribosomes, with the other major component being the large ribosomal subunit
(60S). The "40S" and "60S" names originate from the convention that ribosomal p
structurally and functionally related to the 30S subunit of 70S prokaryotic ribosom
However, the 40S subunit is much larger than the prokaryotic 30S subunit and con
tains many additional protein segments, as well as rRNA expansion segments.
The 40S subunit contains the decoding center which monitors the complementarit
tRNA and mRNA in protein translation. It is the largest component of several tran
tion initiation complexes, including the 43S and 48S preinitiation complexes (PICs
being bound by several eukaryotic initiation factors, including eIF1, eIF1A, and eIF
https://en.wikipedia.org/wiki/Eukaryotic_small_ribosomal_subunit_(40S)
Index
Find Term
50S Subunit
50S is the larger subunit of the 70S ribosome of prokaryotes. It is the site of inhibition
for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA and 23S ribosomal RNA.
50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the Gprotein factors (assists initiation, elongation, and termination), and helps protein folding after synthesis.
https://en.wikipedia.org/wiki/50S
60S Subunit
The 60S subunit is the large subunit of eukaryotic 80S ribosomes. It is structurally and
functionally related to the 50S subunit of 70S prokaryotic ribosomes. However, the
60S subunit is much larger than the prokaryotic 50S subunit and contains many additional protein segments, as well as ribosomal RNA expansion segments.
There are three binding sites for tRNA, the A-site, P-site and E-site (see article on protein translation for details). The core of the 60S subunit is formed by the 28S ribosomal RNA (abbreviated 28S rRNA), which is homologous to the prokaryotic 23S
rRNA, which also contributes the active site (peptidyl transferase center, PTC) of the
ribosome. The rRNA core is decorated with dozens of proteins.
https://en.wikipedia.org/wiki/Eukaryotic_large_ribosomal_subunit_(60S)
Index
Find Term
310 helix
A 310 helix is a type of secondary structure found in proteins and polypeptides.Of the
countless protein secondary structures present, the 310-helix is the fourth most common type observed, following -helices, -sheets and reverse turns. 310-helices constitute nearly 10-15% of all helices in protein secondary structures, and are typically observed as extensions of -helices found at either their N- or C- termini. Because of the
-helices tendency to consistently fold and unfold, it has been proposed that the 310helix serves as an intermediary conformation of sorts, and provides insight into the initiation of -helix folding.
https://en.wikipedia.org/wiki/310_helix
Index
Find Term
22
22 is known as the adult form of hemoglobin. Various forms of hemoglobin are described below.
In the embryo:
Gower 1 (22)
Gower 2 (22) (PDB: 1A9W )
Hemoglobin Portland I (22)
Hemoglobin Portland II (22).
In the fetus:
Hemoglobin F (22) (PDB: 1FDH ).
After birth:
Hemoglobin A (22) (PDB: 1BZ0 ) The most common with a normal amount over
95%
Hemoglobin A2 (22) chain synthesis begins late in the third trimester and, in
adults, it has a normal range of 1.53.5%
Hemoglobin F (22) In adults hemoglobin F is restricted to a limited population of
red cells called F-cells. However, the level of Hb F can be elevated in persons with
sickle-cell disease and -thalassemia.
https://en.wikipedia.org/wiki/Hemoglobin
Index
Find Term
22
22 is a description of the subunit composition of fetal hemoglobin. In contrast to the
adult form of hemoglobin, the 22 form holds oxygen more tightly.
Various forms of hemoglobin are described below.
In the embryo:
Gower 1 (22)
Gower 2 (22) (PDB: 1A9W )
Hemoglobin Portland I (22)
Hemoglobin Portland II (22).
In the fetus:
Hemoglobin F (22) (PDB: 1FDH ).
After birth:
Hemoglobin A (22) (PDB: 1BZ0 ) The most common with a normal amount over
95%
Hemoglobin A2 (22) chain synthesis begins late in the third trimester and, in
adults, it has a normal range of 1.53.5%
Hemoglobin F (22) In adults hemoglobin F is restricted to a limited population of
red cells called F-cells. However, the level of Hb F can be elevated in persons with
sickle-cell disease and -thalassemia.
https://en.wikipedia.org/wiki/Hemoglobin
Index
Find Term
lpha Carbon
The carbon (C) in organic molecules refers to the first carbon atom that atta
a functional group, such as a carbonyl. The second carbon atom is called the c
(C), and the system continues naming in alphabetical order with Greek letters
https://en.wikipedia.org/wiki/Alpha_and_beta_carbon
Index
Find Term
lpha Helix
The helix (alpha-helix) is a common secondary structure of proteins and is a
righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding). This secondary structure is also sometimes called a classic
PaulingCoreyBranson -helix (see below). The name 3.613-helix is also used for this
type of helix, denoting the number of residues per helical turn, and 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the -helix is the most regular and the most predictable from sequence, as well
as the most prevalent.
The amino acids in an -helix are arranged in a right-handed helical structure where
each amino acid residue corresponds to a 100 turn in the helix (i.e., the helix has 3.6
residues per turn), and a translation of 1.5 (0.15nm) along the helical axis. Pauling's
first article on the theme in fact shows a left-handed helix, the enantiomer of the true
structure. Short pieces of left-handed helix sometimes occur with a large content of
achiral glycine amino acids, but are unfavorable for the other normal, biological Lamino acids. The pitch of the -helix (the vertical distance between consecutive turns
of the helix) is 5.4 (0.54nm), which is the product of 1.5 and 3.6. What is most important is that the N-H group of an amino acid forms a hydrogen bond with the C=O
group of the amino acid four residues earlier; this repeated hydrogen bonding is the
most prominent characteristic of an -helix. Official international nomenclature specifies two ways of defining -helices, rule 6.2 in terms of repeating , torsion angles
and rule 6.3 in terms of the combined pattern of pitch and hydrogen bonding. The helices can be identified in protein structure using several computational methods, one
of which being DSSP (Dictionary of Protein Secondary Structure).
Similar structures include the 310 helix and the -helix. The -helix can be described as
a 3.613 helix, since the i + 4 spacing adds 3 more atoms to the H-bonded loop compared to the tighter 310 helix, and on average, 3.6 amino acids are involved in one ring
of -helix. The subscripts refer to the number of atoms (including the hydrogen) in the
closed loop formed by the hydrogen bond.
https://en.wikipedia.org/wiki/Alpha_helix
https://en.wikipedia.org/wiki/Alpha_helix
Index
Find Term
lpha Subunit
change in the receptor that allows the receptor to function as a guanine nucleot
change factor (GEF) that exchanges GDP for GTP - thus turning the GPCR "on"
GTP (or GDP) is bound to the G subunit in the traditional view of heterotrime
GPCR activation. This exchange triggers the dissociation of the G subunit (wh
bound to GTP) from the G dimer and the receptor as a whole. However, mod
Both G-GTP and G can then activate different signaling cascades (or second
senger pathways) and effector proteins, while the receptor is able to activate the
protein.
Index
Find Term
lpha-1-Anti-trypsin
-1 ntitrypsin (A1AT) is a protease inhibitor belonging to the serpin superfamily. It is
generally known as serum trypsin inhibitor. 1-antitrypsin is also referred to as -1
proteinase inhibitor (A1PI) because it inhibits a wide variety of proteases. It protects
tissues from enzymes of inflammatory cells, especially neutrophil elastase, and has a
reference range in blood of 1.5 - 3.5 gram/liter (in US the reference range is generally
expressed as mg/dL or micromoles), but the concentration can rise manyfold upon
acute inflammation. In its absence (such as in 1-antitrypsin deficiency), neutrophil
elastase is free to break down elastin, which contributes to the elasticity of the lungs,
resulting in respiratory complications such as emphysema, or COPD (chronic obstructive pulmonary disease) in adults and cirrhosis in adults or children.
Disorders of this protein include 1-antitrypsin deficiency, an autosomal codominant
hereditary disorder in which a deficiency of 1-antitrypsin leads to a chronic uninhibited tissue breakdown. This causes the degradation especially of lung tissue, and eventually leads to characteristic manifestations of pulmonary emphysema. Evidence has
shown that cigarette smoke can lead to oxidation of methionine 358 of 1-antitrypsin
(382 in the pre-processed form containing the 24 amino acid signal peptide), a residue
essential for binding elastase. This is thought to be one of the primary mechanisms by
which cigarette smoking (or second-hand smoke) can lead to emphysema. Because
A1AT is expressed in the liver, certain mutations in the gene encoding the protein can
cause misfolding and impaired secretion, which can lead to liver cirrhosis.
An extremely rare form of Pi, termed PiPittsburgh, functions as an antithrombin (a related serpin), due to a mutation (Met358Arg). One person with this mutation has been
reported to have died of a lethal bleeding diathesis.
https://en.wikipedia.org/wiki/Alpha-1_antitrypsin
lpha-aceto--hydroxybutyrate
-aceto--hydroxybutyrate + Pyruvate
,-dihydroxy--methylvalerate + CO2
Index
Find Term
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
lpha-acetolactate
chain amino acids valine and leucine. -cetolactic acid is produced from two mo
cules of pyruvic acid by acetolactate synthase. -cetolactic acid can also be deca
lated by -acetolactate decarboxylase to produce acetoin.
https://en.wikipedia.org/wiki/Acetolactic_acid
lpha-amine
The carbon of every amino acid has four groups attached to it - a hydrogen
carboxyl group, an -amine group, and an R-group.
lpha-carboxyl
The carbon of every amino acid has four groups attached to it - a hydrogen
carboxyl group, an -amine group, and an R-group.
lpha-helix Duplicate
The helix (alpha-helix) is a common secondary structure of proteins and is a
righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding). This secondary structure is also sometimes called a classic
PaulingCoreyBranson -helix (see below). The name 3.613-helix is also used for this
type of helix, denoting the number of residues per helical turn, and 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the -helix is the most regular and the most predictable from sequence, as well
as the most prevalent.
The amino acids in an -helix are arranged in a right-handed helical structure where
each amino acid residue corresponds to a 100 turn in the helix (i.e., the helix has 3.6
residues per turn), and a translation of 1.5 (0.15nm) along the helical axis. Pauling's
first article on the theme in fact shows a left-handed helix, the enantiomer of the true
structure. Short pieces of left-handed helix sometimes occur with a large content of
achiral glycine amino acids, but are unfavorable for the other normal, biological Lamino acids. The pitch of the -helix (the vertical distance between consecutive turns
of the helix) is 5.4 (0.54nm), which is the product of 1.5 and 3.6. What is most important is that the N-H group of an amino acid forms a hydrogen bond with the C=O
group of the amino acid four residues earlier; this repeated hydrogen bonding is the
most prominent characteristic of an -helix. Official international nomenclature specifies two ways of defining -helices, rule 6.2 in terms of repeating , torsion angles
and rule 6.3 in terms of the combined pattern of pitch and hydrogen bonding. The helices can be identified in protein structure using several computational methods, one
of which being DSSP (Dictionary of Protein Secondary Structure).
Similar structures include the 310 helix and the -helix. The -helix can be described as
a 3.613 helix, since the i + 4 spacing adds 3 more atoms to the H-bonded loop compared to the tighter 310 helix, and on average, 3.6 amino acids are involved in one ring
of -helix. The subscripts refer to the number of atoms (including the hydrogen) in the
closed loop formed by the hydrogen bond.
https://en.wikipedia.org/wiki/Alpha_helix
lpha-isopropylmalate
-isopropylmalate is an intermediate in the biosynthesis of leucine.
-isopropylmalate + CoA-SH
-isopropylmalate
-isopropylmalate.
Index
Find Term
G-G
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
lpha-keto--methylvalerate
Branched chain aminotransferases in mammals catalyze the first step in branchedchain amino acid metabolism, a reversible transamination followed by the oxidative decarboxylation of the transamination products -ketoisocaproate, -keto-methylvalerate, and -ketoisovalerate to isovaleryl-CoA, 3-methylbutyryl-CoA, and
isobutyryl-CoA, respectively. This reaction regulates metabolism of amino acids and is
a crucial step in nitrogen shuttling throughout the whole body.
https://en.wikipedia.org/wiki/Branched_chain_aminotransferase
The mechanism of threonine ammonia-lyase is analogous to other deaminating PLP enzymes in its use of Schiff base intermediates. Initially, the amine group of threonine attacks the lysine/PLP Schiff base, displacing lysine. After deprotonation of the amino
acid alpha carbon and subsequent dehydration (hence the common name threonine dehydratase), a new Schiff base is formed. This Schiff base is replaced by lysine attack, reforming the catalytically active PLP and releasing an initial alkene-containing product.
This product tautomerizes, and after hydrolysis of the Schiff base, the final products
are generated. After the final -ketobutyrate product is generated, isoleucine is synthesized by progressing through the intermediates -acetohydroxybutyrate to -dihydroxy--methylvalerate, then to -keto--methylvalerate.
https://en.wikipedia.org/wiki/Threonine_ammonia-lyase
lpha-ketobutyrate
-ketobutyric acid is a product of the lysis of cystathionine. It is also one of the degradation products of threonine, produced by the catabolism of the amino acid by threonine
dehydratase. It is also produced by the degradation of homocysteine and the metabolism of methionine.
-ketobutyric acid is transported into the mitochondrial matrix, where it is converted
to propionyl-CoA by branched-chain -keto acid dehydrogenase complex. Further mitochondrial reactions produce succinyl CoA.
Index
Find Term
lpha-ketoglutarate
-etoglutaric acid is one of two ketone derivatives of glutaric acid.
Its anion, -ketoglutarate (-KG, also called oxo-glutarate) is an important biological
compound. It is the keto acid produced by deamination of glutamate, and is an intermediate in the citric acid cycle.
-ketoglutarate is a key intermediate in the citric acid cycle, coming after isocitrate and
before succinyl CoA. Anaplerotic reactions can replenish the cycle at this juncture by
synthesizing -ketoglutarate from transamination of glutamate, or through action of
glutamate dehydrogenase on glutamate.
Index
Find Term
lpha-ketoglutarate Dehydrogenase
complex is an enzyme complex, most commonly known for its role in the citri
cle.
by its products, succinyl CoA and NADH. A high energy charge in the cell will
inhibitive. ADP and calcium ions are allosteric activators of the enzyme.
By controlling the amount of available reducing equivalents generated by the
Index
Find Term
lpha-ketoisovalerate
-ketoisovaleric acid is a metabolite of valine. This molecule is a branch point for synthesis of leucine and valine. Addition of an acetyl group from acetyl-CoA yields isopropylmalate (catalyzed by -isopropylmalate synthase).
,-dihydroxyisovalerate
-ketoisovalerate + H2O
-isopropylmalate + CoA-SH
https://en.wikipedia.org/wiki/Alpha-Ketoisovaleric_acid
Index
Find Term
G-G
G-G
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
lpha-oxidation
dependent reaction to form pristanal and formyl-CoA (in turn later broken down
formate and eventually CO2).
Index
Find Term
lpha-synuclein
found in the heart, muscles, and other tissues. In the brain, -synuclein is f
lpha-tocopherol
-tocopherol is a type of tocopherol or vitamin E. -tocopherol is a form of vitamin E
that is preferentially absorbed and accumulated in humans.
There are three stereocenters in -tocopherol, so this is a chiral molecule. The eight
stereoisomers of -tocopherol differ in the arrangement of groups around these stereocenters. In the image of RRR--tocopherol, all three stereocenters are in the R form.
However, if the middle of the three stereocenters were changed (so the hydrogen was
now pointing down and the methyl group pointing up), this would become the structure of RSR--tocopherol. RSR--tocopherol and RRR--tocopherol are diastereomers
of each other. These stereoisomers can also be named in an alternative older nomenclature, where the stereocenters are either in the d or l form.
https://en.wikipedia.org/wiki/Alpha-Tocopherol
lpha-tubulin
Tubulin in molecular biology can refer either to the tubulin protein superfamily of
globular proteins, or one of the member proteins of that superfamily. - and -tubulins
polymerize into microtubules, a major component of the eukaryotic cytoskeleton. Microtubules function in many essential cellular processes, including mitosis. Tubulinbinding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.
- and -tubulin polymerize into dynamic microtubules. In eukaryotes, microtubules
are one of the major components of the cytoskeleton, and function in many processes,
including structural support, intracellular transport, and DNA segregation.
Microtubules are assembled from dimers of - and -tubulin. These subunits are
slightly acidic with an isoelectric point between 5.2 and 5.8. Each has a molecular
weight of approximately 50,000 Daltons.
To form microtubules, the dimers of - and -tubulin bind to GTP and assemble onto
the (+) ends of microtubules while in the GTP-bound state. The -tubulin subunit is exposed on the plus end of the microtubule while the -tubulin subunit is exposed on the
minus end. After the dimer is incorporated into the microtubule, the molecule of GTP
bound to the -tubulin subunit eventually hydrolyzes into GDP through inter-dimer
contacts along the microtubule protofilament.
Whether the -tubulin member of the tubulin dimer is bound to GTP or GDP influences the stability of the dimer in the microtubule. Dimers bound to GTP tend to assemble into microtubules, while dimers bound to GDP tend to fall apart. Thus, this
GTP cycle is essential for the dynamic instability of the microtubule.
https://en.wikipedia.org/wiki/Tubulin
lpha-turns
urns are elements of secondary structure in proteins where the polypeptide chain reverses its overall direction and they are classified according to the separation between
the two end residues.
In an -turn the end residues are separated by four peptide bonds
(i --> i +/- 4).
Pictured below is a -turn
https://en.wikipedia.org/wiki/Turn_(biochemistry)
Index
Find Term
lpha,beta-dihydroxy--methylvalerate
,-dihydroxy--methylvalerate + CO2
,-dihydroxy--methylvalerate
-keto--methylvalerate + 2
Index
Find Term
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
lpha,beta-dihydroxyisovalerate
Valine is produced by a four-enzyme pathway. It begins with the reaction of two pyruvate molecules catalyzed by acetohydroxy acid synthase yielding -acetolactate. Step
two is the NADPH+ + H+ - dependent reduction of -acetolactate and migration of the
methane groups to produce , -dihydroxyisovalerate. This is catalyzed by acetohydroxy isomeroreductase. The third reaction is the dehydration reaction of , dihydroxyisovalerate catalyzed by dihydroxy acid dehydrase resulting in ketoisovalerate. Finally, a transamination catalyzed either by an alanine-valine transaminase or a glutamate-valine transaminase results in valine.
3-hydroxy-3-methyl-2-oxobutanoate + NADP(P)H
,-dihydroxyisovalerate + NAD(P)+
,-dihydroxyisovalerate
-ketoisovalerate + H2O
https://en.wikipedia.org/wiki/Amino_acid_synthesis
Index
Find Term
eta Strands
The supersecondary protein structure known as sheets consist of strands connected
laterally by at least two or three backbone hydrogen bonds, forming a generally
twisted, pleated sheet. A -strand is a stretch of polypeptide chain typically 3 to 10
amino acids long with backbone in an extended conformation. Shown below are two
-strands interacting as part of a -sheet.
https://en.wikipedia.org/wiki/Beta_sheet
Index
Find Term
eta-adrenergic Receptor
The adrenergic receptors (or adrenoceptors) are a class of G protein-coupled receptors
that are targets of the catecholamines, especially norepinephrine (noradrenaline) and
epinephrine (adrenaline).
Many cells possess these receptors, and the binding of a catecholamine to the receptor
will generally stimulate the sympathetic nervous system. The sympathetic nervous system is responsible for the fight-or-flight response, which includes widening the pupils
of the eye, mobilizing energy, and diverting blood flow from non-essential organs to
skeletal muscle.
There are two main groups of adrenergic receptors, and , with several subtypes.
receptors have the subtypes 1 (a Gq coupled receptor) and 2 (a Gi coupled receptor). Phenylephrine is a selective agonist of the receptor.
receptors have the subtypes 1, 2 and 3. All three are linked to Gs proteins (although 2 also couples to Gi), which in turn are linked to adenylate cyclase.
Agonist binding thus causes a rise in the intracellular concentration of the second messenger cAMP. Downstream effectors of cAMP include cAMP-dependent protein kinase
(PKA), which mediates some of the intracellular events following hormone binding. Isoprenaline is a non-selective agonist.
https://en.wikipedia.org/wiki/Adrenergic_receptor
Index
Find Term
eta-alanine
-alanine (or beta-alanine) is a naturally occurring amino acid, which is an amino
acid in which the amino group is at the -position from the carboxylate group. The
IUPAC name for -alanine is 3-aminopropanoic acid. Unlike its counterpart -alanine,
-alanine has no stereocenter.
-alanine is not used in the biosynthesis of any major proteins or enzymes. It is formed
in vivo by the degradation of dihydrouracil and carnosine. It is a component of the
naturally occurring peptides carnosine and anserine and also of pantothenic acid (vitamin B5), which itself is a component of coenzyme A. Under normal conditions, alanine is metabolized into acetic acid.
-alanine is the rate-limiting precursor of carnosine, which is to say carnosine levels
are limited by the amount of available -alanine, not histidine. Supplementation with
-alanine has been shown to increase the concentration of carnosine in muscles, decrease fatigue in athletes and increase total muscular work done. Simply supplementing with carnosine is not as effective as supplementing with -alanine alone since carnosine, when taken orally, is broken down during digestion to its components, histidine and -alanine. Hence, by weight, only about 40% of the dose is available as alanine.
https://en.wikipedia.org/wiki/Beta-Alanine
Index
Find Term
eta-aminoisobutyrate
reaches the white fat tissue, it activates the expression of thermogenic gene
PPAR receptors, resulting in a browning of white fat cells. One of the cons
It has recently been postulated to play a role in cell metabolism, how body b
and regulates insulin, triglycerides, and total cholesterol.
https://en.wikipedia.org/wiki/3-Aminoisobutyric_acid
Index
Find Term
early branch point in the metabolic pathway forming lysine, methionine, leucine and
isoleucine from aspartate. This pathway also produces diaminopimelate which plays
an essential role in bacterial cell wall formation. There is particular interest in ASAD
as disabling this enzyme proves fatal to the organism giving rise to the possibility of a
new class of antibiotics, fungicides, and herbicides aimed at inhibiting it.
The enzyme catalyzes the reversible chemical reaction:
L-aspartate 4-semialdehyde + Phosphate + NADP+ <---> L-4-aspartyl phosphate +
NADPH + H+
This enzyme participates in glycine, serine and threonine metabolism and lysine biosynthesis.
https://en.wikipedia.org/wiki/Aspartate-semialdehyde_dehydrogenase
eta-barrel
A barrel is a large -sheet that twists and coils to form a closed structure in which the
first strand is hydrogen bonded to the last. -strands in -barrels are typically arranged in an antiparallel fashion. Barrel structures are commonly found in porins and
other proteins that span cell membranes and in proteins that bind hydrophobic ligands
in the barrel center, as in lipocalins. Porin-like barrel structures are encoded by as
many as 23% of the genes in Gram-negative bacteria.
https://en.wikipedia.org/wiki/Beta_barrel
eta-carotene
-Carotene is an organic, strongly colored red-orange pigment abundant in plants and
fruits. It is a member of the carotenes, which are terpenoids (isoprenoids), synthesized
biochemically from eight isoprene units and thus having 40 carbons. Among the carotenes, -carotene is distinguished by having -rings at both ends of the molecule. Carotene is biosynthesized from geranylgeranyl pyrophosphate.
Plant carotenoids are the primary dietary source of provitamin A worldwide, with carotene as the most well-known provitamin A carotenoid. Others include -carotene
and -cryptoxanthin. Carotenoid absorption is restricted to the duodenum of the small
intestine and dependent on Class B scavenger receptor (SR-B1) membrane protein,
which are also responsible for the absorption of vitamin E (-tocopherol). One molecule of -carotene can be cleaved by the intestinal enzyme ,-carotene 15,15'monooxygenase into two molecules of vitamin A.
Absorption efficiency is estimated to be between 922%. The absorption and conversion of carotenoids may depend on the form that the -carotene is in (e.g., cooked vs.
raw vegetables, or in a supplement), the intake of fats and oils at the same time, and
the current stores of vitamin A and -carotene in the body.
https://en.wikipedia.org/wiki/Beta-Carotene
Index
Find Term
eta-galactosidase
-galactosidase, also called -gal or -gal, is a glycoside hydrolase enzyme that catalyzes the hydrolysis of -galactosides into monosaccharides through the breaking of a
glycosidic bond. -galactosides include carbohydrates containing galactose where the
glycosidic bond lies above the galactose molecule. Substrates of different galactosidases include ganglioside GM1, lactosylceramides, lactose, and various glycoproteins.
The -galactosidase assay is used frequently in genetics, molecular biology, and other
life sciences. An active enzyme may be detected using X-gal, which forms an intense
blue product after cleavage by -galactosidase, and is easy to identify and quantify. It is
used, for example, in blue white screen. Its production may be induced by a nonhydrolyzable analog of allolactose, IPTG, which binds and releases the lac repressor
from the lac operator, thereby allowing the initiation of transcription to proceed.
It is commonly used in molecular biology as a reporter marker to monitor gene expression. It also exhibits a phenomenon called -complementation which forms the basis
for the blue/white screening of recombinant clones. This enzyme can be split in two
peptides, LacZ and LacZ, neither of which is active by itself but when both are present together, spontaneously reassemble into a functional enzyme. This property is exploited in many cloning vectors where the presence of the LacZ gene in a plasmid can
complement in trans another mutant gene encoding the LacZ in specific laboratory
strains of E. coli. However, when DNA fragments are inserted in the vector, the production of LacZ is disrupted, the cells therefore show no -galactosidase activity. The presence or absence of an active -galactosidase may be detected by X-gal, which produces
a characteristic blue dye when cleaved by -galactosidase, thereby providing an easy
means of distinguishing the presence or absence of cloned product in a plasmid.
https://en.wikipedia.org/wiki/Beta-galactosidase
Index
Find Term
eta-hairpin
The hairpin (sometimes also called -ribbon or - unit) is a simple protein structural motif involving two strands that look like a hairpin. The motif consists of two
strands that are adjacent in primary structure, oriented in an antiparallel direction
(the N-terminus of one sheet is adjacent to the C-terminus of the next), and linked by a
short loop of two to five amino acids. hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a sheet.
https://en.wikipedia.org/wiki/Beta_hairpin
Index
Find Term
eta-hydroxyacl-ACP Reductase
Index
Find Term
eta-Hydroxybutyrate
-Hydroxybutyric acid (also known as -hydroxybutyrate, 3-hydroxybutyric acid or 3hydroxybutyrate) is an organic compound with the formula CH3CH(OH)CH2CO2H. It
is a hydroxy acid and a keto acid. It is a chiral compound having two enantiomers, D3-hydroxybutyric acid and L-3-hydroxybutyric acid. Its oxidized and polymeric derivatives occur widely in nature.
In humans, -hydroxybutyrate is synthesized in the liver from acetoacetate, the first ketone produced in the fasting state. The biosynthesis is catalyzed by the enzyme hydroxybutyrate dehydrogenase.
Although not a ketone itself, the concentration of -hydroxybutyrate, like that of other
ketone bodies, is raised in ketosis. This elevated -hydroxybutyrate level seen in ketosis is naturally expected due to the fact that, as mentioned above, it is formed from acetoacetate. The compound can be used as an energy source by the brain when blood glucose is low. Diabetic patients can have their keto acid levels tested via urine or blood to
indicate diabetic ketoacidosis. In alcoholic ketoacidosis, this ketone body is produced
in greatest concentration. Both types of ketoacidosis result in an increase hydroxybutyrate to oxaloacetate ratio, resulting in TCA cycle stalling and shifting of glucose towards ketone body production.
https://en.wikipedia.org/wiki/Beta-Hydroxybutyric_acid
eta-isopropylmalate
https://en.wikipedia.org/wiki/Isopropylmalic_acid
Index
Find Term
G-G
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
eta-ketoacyl-ACP Synthase
eta-ketobutyrate
Keto acids or ketoacids (also called oxo acids or oxoacids) are organic compounds that
contain a carboxylic acid group and a ketone group. The -keto acids are especially important in biology as they are involved in the citric acid cycle and in glycolysis.
-keto acids, or 3-oxoacids, such as acetoacetic acid, have the ketone group at the second carbon from the carboxylic acid. They can be formed by the Claisen condensation.
Three different keto acids are shown below.
https://en.wikipedia.org/wiki/Keto_acid
eta-lactam
is named as such because the nitrogen atom is attached to the -carbon ato
https://en.wikipedia.org/wiki/-Lactam
Index
Find Term
eta-mercaptoethanol
2-ercaptoethanol (also -mercaptoethanol, BME, 2BME, 2-ME or -met) is the
cal compound with the formula HOCH2CH2SH.
widely used because the hydroxyl group confers solubility in water and lowers th
tility.
Due to its diminished vapor pressure, its odor, while unpleasant, is less objection
than related thiols.
https://en.wikipedia.org/wiki/2-Mercaptoethanol
eta-oxidation
In metabolism, -oxidation is the catabolic process by which fatty acid molecules are
broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to
generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which
are co-enzymes used in the electron transport chain. It is named as such because the
carbon of the fatty acid undergoes oxidation to a carbonyl group. Various mechanisms
have evolved to handle the large variety of fatty acids.
The process of -oxidation consists of 4 steps.
1 - A long-chain fatty acid is dehydrogenated to create a trans double bond between C2
and C3. This is catalyzed by acyl CoA dehydrogenase to produce trans-2-enoyl CoA. It
uses FAD as an electron acceptor and it is reduced to FADH2.
2 - Trans-2-enoyl CoA is hydrated at the double bond to produce L-3-hydroxyacyl
CoA by enoyl-CoA hydratase.
3 - L-3-hydroxyacyl CoA is dehydrogenated again to create 3-ketoacyl CoA by 3hydroxyacyl CoA dehydrogenase. This enzyme uses NAD+ as an electron acceptor.
4 - Thiolysis occurs between C2 and C3 ( and carbons) of 3-ketoacyl CoA. Thiolase
enzyme catalyzes the reaction when a new molecule of coenzyme A breaks the bond by
nucleophilic attack on C3. This releases the first two carbon units, as acetyl CoA, and a
fatty acyl CoA minus two carbons. The process continues until all of the carbons in the
fatty acid are turned into acetyl CoA.
Fatty acids are oxidized by most of the tissues in the body. However, some tissues such
as the red blood cells (which do not contain mitochondria), and cells of the central
nervous system (because fatty acids cannot cross the blood-brain barrier into the interstitial fluids that bathe these cells) do not use fatty acids for their energy requirements,
but instead use carbohydrates.
Because many fatty acids are not fully saturated or do not have an even number of carbons, several different mechanisms have evolved, described below.
https://en.wikipedia.org/wiki/Beta_oxidation
Index
Find Term
eta-secretase
-secretase 1 (BACE1) is an enzyme that in humans is encoded by the BACE1 gene. BACE1 is an aspartic-acid protease important in the formation of myelin sheaths in peripheral nerve cells. The transmembrane protein contains two active site aspartate residues
in its extracellular protein domain and may function as a dimer.
Generation of the 40 or 42 amino acid-long amyloid- peptides that aggregate in the
brain of Alzheimer's patients requires two sequential cleavages of the amyloid precursor protein (APP). Extracellular cleavage of APP by BACE1 creates a soluble extracellular fragment and a cell membrane-bound fragment referred to as C99. Cleavage of C99
within its transmembrane domain by -secretase releases the intracellular domain of
APP and produces amyloid-. Since -secretase cleaves APP closer to the cell membrane than BACE1 does, it removes a fragment of the amyloid- peptide. Initial cleavage of APP by -secretase rather than BACE1 prevents eventual generation of amyloid.
Unlike APP and the presenilin proteins important in -secretase, no known mutations
in the gene encoding BACE1 cause early-onset, familial Alzheimer's disease, which is a
rare form of the disorder. However, levels of this enzyme have been shown to be elevated in the far more common late-onset sporadic Alzheimer's. The physiological purpose of BACE's cleavage of APP and other transmembrane proteins is unknown. BACE2 is a close homolog of BACE1 with no reported APP cleavage in vivo. However a single residue mutation in APP reduces the ability of BACE1 to cleave it to produce
amyloid- and reduces the risk of Alzheimers and other cognitive declines.
https://en.wikipedia.org/wiki/Beta-secretase_1
Index
Find Term
eta-strand
In protein structure, the -sheet (also -pleated sheet) is the second form of regular secondary structure in proteins. sheets consist of strands (also -strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted,
pleated sheet. A -strand is a stretch of polypeptide chain typically 3 to 10 amino acids
long with backbone in an extended conformation. The higher-level association of sheets has been implicated in formation of the protein aggregates and fibrils observed
in many human diseases, notably the amyloidoses such as Alzheimer's disease.
Shown below are two -strands aligned antiparallel to form part of a -sheet.
https://commons.wikimedia.org/wiki/File:Beta_sheet_bonding_antiparallel-color.sv
g
Index
Find Term
eta-tubulin
In molecular biology, tubulin can refer either to the tubulin protein superfamily of
globular proteins, or one of the member proteins of that superfamily. - and -tubulins
polymerize into microtubules, a major component of the eukaryotic cytoskeleton. Microtubules function in many essential cellular processes, including mitosis. Tubulinbinding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division. Tubulin was long thought to be
specific to eukaryotes. More recently, however, several prokaryotic proteins have been
shown to be related to tubulin.
- and -tubulin polymerize into dynamic microtubules. In eukaryotes, microtubules
are one of the major components of the cytoskeleton, and function in many processes,
including structural support, intracellular transport, and DNA segregation.
Microtubules are assembled from dimers of - and -tubulin. These subunits are
slightly acidic with an isoelectric point between 5.2 and 5.8. Each has a molecular
weight of approximately 50,000 Daltons.
To form microtubules, the dimers of - and -tubulin bind to GTP and assemble onto
the (+) ends of microtubules while in the GTP-bound state. The -tubulin subunit is exposed on the plus end of the microtubule while the -tubulin subunit is exposed on the
minus end. After the dimer is incorporated into the microtubule, the molecule of GTP
bound to the -tubulin subunit eventually hydrolyzes into GDP through inter-dimer
contacts along the microtubule protofilament. Whether the -tubulin member of the
tubulin dimer is bound to GTP or GDP influences the stability of the dimer in the microtubule. Dimers bound to GTP tend to assemble into microtubules, while dimers
bound to GDP tend to fall apart. Thus, this GTP cycle is essential for the dynamic instability of the microtubule.
https://en.wikipedia.org/wiki/Tubulin
Index
Find Term
eta-turns
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
Turns are classified according to the separation between the two end residues:
In an -turn the end residues are separated by four peptide bonds
(i --> i +/- 4).
In a -turn (the most common form), by three bonds
(i --> i +/- 3).
Shown below is a turn
https://en.wikipedia.org/wiki/Turn_(biochemistry)
Index
Find Term
A-form DNA
A-DNA (A-form DNA) is one of the possible double helical structures which DNA can
adopt. A-DNA is thought to be one of three biologically active double helical structures
along with B-DNA and Z-DNA. It is a right-handed double helix fairly similar to the
more common B-DNA form, but with a shorter, more compact helical structure whose
base pairs are not perpendicular to the helix-axis as in B-DNA. It was discovered by
Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven
into the A form when under dehydrating conditions. Such conditions are commonly
used in to form crystals, and many DNA crystal structures are in the A form. The same
helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.
https://en.wikipedia.org/wiki/A-DNA
https://upload.wikimedia.org/wikipedia/commons/thumb/1/14/Adna3.ogv/200px-Adna3.ogv.jpg
Index
Find Term
A-ketoisocaproate
-Ketoisocaproic acid is an intermediate in the metabolism of leucine.
-isopropylmalate + NAD+
-ketoisocaproate + Glu
-ketoisocaproate + NADH
Leucine + -ketogluta
https://en.wikipedia.org/wiki/Alpha-Ketoisocaproic_acid
Index
Find Term
G-G
G-G
G-G
G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
A-site
The A-site is the location in a ribosome where incoming charged tTRNAs enter the ribosome in preparation for incorporating the amino acid they carry into a growing
polypeptide chain. After peptide bond synthesis, the tRNA in the A-site, now carrying
the growing polypeptide chain, translocates to the P site so that a new charge tRNA can
enter the A-site. When a STOP codon enters the A-site, release factors factilitate dissassembly of the translational complex and release of the completed polypeptide chain.
https://en.wikipedia.org/wiki/Prokaryotic_translation
Index
Find Term
ABC Transporters
ATP-binding cassette transporters (ABC transporters) are members of a transport system superfamily that is one of the largest and is possibly one of the oldest families with
representatives in all extant phyla from prokaryotes to humans.
ABC transporters often consist of multiple subunits, one or two of which are transmembrane proteins and one or two of which are membrane-associated ATPases. The ATPase subunits that utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to energize the translocation of various substrates across membranes, either
for uptake or for export of the substrate.
Most but not all uptake systems also have an extracytoplasmic receptor, a solute binding protein. Some homologous ATPases function in non-transport-related processes
such as translation of RNA and DNA repair. ABC transporters are considered to be
with the ABC superfamily based on the sequence and organization of their ATPbinding cassette (ABC) domains, even though the integral membrane proteins may
have evolved independently several times, and thus comprise different protein families. The integral membrane proteins of ABC exporters appear to have evolved independently at least three times. ABC1 exporters evolved by intragenic triplication of a 2
TMS precursor to give 6 TMS proteins. ABC2 exporters evolved by intragenic duplication of a 3 TMS precursor, and ABC3 exporters evolved from a 4 TMS precursor which
duplicated either extragenicly to give two 4 TMS proteins, both required for transport
function, or intragenicly to give 8 or 10 TMS proteins. The 10 TMS proteins appear to
have two extra TMSs between the two 4 TMS repeat units. Similarly, it is possible that
the integral membrane proteins of ABC uptake systems evolved at least 3 times independently, based on their high resolution 3-dimensional structures. ABC uptake porters take up a large variety of nutrients, biosynthetic precursors, trace metals and vitamins, while exporters transport lipids, sterols, drugs, and a large variety of primary
and secondary metabolites. Some of these exporters in humans are involved in tumor
resistance, cystic fibrosis and a range of other inherited human diseases. High level expression of the genes encoding some of these exporters in both prokaryotic and eukaryotic organisms (including human) result in the development of resistance to multiple
drugs such as antibiotics and anti-cancer agents.
https://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
Index
Find Term
ABCA-1
from inside the cell to the plasma membrane where it is taken up into the H
almost totally absent because they remain empty as a result of not being ab
cholesterol from foam cells, so they are destroyed by the body.
Index
Find Term
Acceptor Chromophore
Index
Find Term
Acesulfame Potassium
https://en.wikipedia.org/wiki/Acesulfame_potassium
Acetaldehyde
one of the most important aldehydes, occurring widely in nature and being produce
on a large scale in industry.
https://en.wikipedia.org/wiki/Acetaldehyde
Index
Find Term
Acetate
An acetate is a salt formed by the combination of acetic acid with an alkaline, earthy, o
metallic base. Acetate also describes the conjugate base or ion (specifically, the neg
tively charged ion called an anion) typically found in the aqueous solution and written
with the chemical formula C2H3O2.
https://en.wikipedia.org/wiki/Acetate
Acetoacetate
Acetoacetic acid is a weak acid. It is of biochemical importance in various animals, including humans, as one of the endogenous ketone bodies produced by the liver when it
breaks down fatty acids for ATP production. It can be viewed as the product of joining
two acetic acid molecules via a condensation reaction that ejects a water molecule in
the process, although that is only one of the ways of forming it.
https://en.wikipedia.org/wiki/Acetoacetic_acid
Index
Find Term
Acetoacetate Decarboxylase
Index
Find Term
Acetoacetyl-CoA
Acetoacetyl CoA is the precursor of HMG-CoA in the mevalonate pathway, which is essential for cholesterol biosynthesis. It also takes a similar role in the ketone bodies synthesis (ketogenesis) pathway of the liver. In the ketone bodies digestion pathway (in
the tissue), it is no longer associated with having HMG-CoA as a product or as a reactant.
https://en.wikipedia.org/wiki/Acetoacetyl-CoA
Index
Find Term
Acetoacyl-ACP
Joining of a fatty acyl-ACP (in this case, acetyl-ACP) with malonyl-ACP spli
carboxyl group from malonyl-ACP that was added to it and creates an ace
Index
Find Term
3-hydroxy-3-methyl-2-oxobutanoate + NADP(P)H
,-dihydroxyisovalerate + NAD(P)+
Acetolactate Mutase
Acetolactate Synthase
The acetolactate synthase (ALS) enzyme (also known as acetohydroxy acid
the synthesis of the branched-chain amino acids (valine, leucine, and isoleu
Acetone
Acetone is miscible with water and serves as an important solvent in its own
cally for cleaning purposes in the laboratory.
https://en.wikipedia.org/wiki/Acetone
Acetyl
In organic chemistry, acetyl is a functional group, the acyl with chemical formula
CH3CO. It is sometimes represented by the symbol Ac (not to be confused with the element actinium). The acetyl group contains a methyl group single-bonded to a carbonyl.
The carbonyl center of an acyl radical has one non-bonded electron with which it forms
a chemical bond to the remainder R of the molecule. In IUPAC nomenclature, acetyl is
called ethanoyl, although this term is rarely heard.
https://en.wikipedia.org/wiki/Acetyl
Index
Find Term
Acetyl-ACP
Acetyl-ACP is a starting point for synthesis of a fatty acid. The acetyl group
linked to two carbons of malonyl-CoA in the first step of the process. Aceto
and carbon dioxide are products of the reaction.
Index
Find Term
Acetyl-CoA
Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in
many biochemical reactions. Its main function is to convey the carbon atoms within
the acetyl group to the citric acid cycle to be oxidized for energy production. The structure of coenzyme A (CoASH or CoA) consists of a -mercaptoethylamine group linked
to the vitamin pantothenic acid through an amide linkage. The acetyl group (indicated
in blue in the structural diagram on the right) of acetyl-CoA is linked by a "high energy" thioester bond to the sulfhydryl substituent of the -mercaptoethylamine group.
Acetyl-CoA is an allosteric effector for pyruvate dehydrogenase.
https://en.wikipedia.org/wiki/Acetyl-CoA
Index
Find Term
G-G
G-G
Chapter 2 - Structure & Function
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Lipids
Chapter 3 - Membranes: Other Considerations
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Membranes
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
the process is to activate acetyl CoA for reaction with malonyl-ACP. This is
step in making a fatty acid. The reaction it catalyzes is below.
https://en.wikipedia.org/wiki/Fatty_acid_synthesis
Index
Find Term
Acetyl-CoA Carboxylase
strate for the biosynthesis of fatty acids. The activity of ACC can be controlled
Index
Find Term
Acetyl-lysine
https://en.wikipedia.org/wiki/Acetyllysine
Acetylation
Index
Find Term
Acetylcarnitine
Acetylcholine
Acetylcholine is an organic chemical that functions in the brain and body of many
types of animals, including humans, as a neurotransmittera chemical released by
nerve cells to send signals to other cells. Its name is derived from its chemical structure: it is an ester of acetic acid and choline. Parts in the body that use or are affected
by acetylcholine are referred to as cholinergic. Substances that interfere with acetylcholine activity are called anticholinergics.
Acetylcholine is the neurotransmitter used at the neuromuscular junctionin other
words, it is the chemical that motor neurons of the nervous system release in order to
activate muscles. This property means that drugs that affect cholinergic systems can
have very dangerous effects ranging from paralysis to convulsions. Acetylcholine is
also used as a neurotransmitter in the autonomic nervous system, both as an internal
transmitter for the sympathetic nervous system and as the final product released by
the parasympathetic nervous system.
Inside the brain acetylcholine functions as a neuromodulatora chemical that alters
the way other brain structures process information rather than a chemical used to
transmit information from point to point. The brain contains a number of cholinergic
areas, each with distinct functions. They play an important role in arousal, attention,
and motivation.
Partly because of its muscle-activating function, but also because of its functions in the
autonomic nervous system and brain, a large number of important drugs exert their effects by altering cholinergic transmission. Numerous venoms and toxins produced by
plants, animals, and bacteria, as well as chemical nerve agents such as Sarin, cause
harm by inactivating or hyperactivating muscles via their influences on the neuromuscular junction. Drugs that act on muscarinic acetylcholine receptors, such as atropine,
can be poisonous in large quantities, but in smaller doses they are commonly used to
treat certain heart conditions and eye problems. Scopolamine, which acts mainly on
muscarinic receptors in the brain, can cause delirium and amnesia. The addictive qualities of nicotine derive from its effects on nicotinic acetylcholine receptors in the brain.
https://en.wikipedia.org/wiki/Acetylcholine
Acetylcholinesterase
is the primary cholinesterase in the body. It is an enzyme that catalyzes the brea
ron into the synaptic cleft and binds to ACh receptors on the post-synaptic mem
relaying the signal from the nerve. AChE, also located on the post-synaptic mem
terminates the signal transmission by hydrolyzing ACh. The liberated choline is
Index
Find Term
Acetylglutamate Synthetase
N-acetylglutamate synthase (NAGS) is an enzyme that catalyzes the production of NAcetylglutamate (NAG) from glutamate and acetyl-CoA.
It catalyzes the following reaction:
Acetyl-CoA + L-glutamate CoA + N-acetyl-L-glutamate
Most prokaryotes (bacteria) and lower eukaryotes (fungi, green algae, plants, etc.) produce NAG through orinithine acetyltransferase (OAT), which is part of a cyclic ornithine production pathway. NAGS is therefore used in a supportive role, replenishing
NAG reserves as required. In some plants and bacteria, however, NAGS catalyzes the
first step in a linear arginine production pathway.
The protein sequences of NAGS between prokaryotes, lower eukaryotes and higher
eukaryotes have shown a remarkable lack of similarity. Sequence identity between prokaryotic and eukaryotic NAGS is largely <30%, while sequence identity between lower
and higher eukaryotes is ~20%.
Enzyme activity of NAGS is modulated by L-arginine, which acts as an inhibitor in
plant and bacterial NAGS, but an effector in vertebrates. While the role of arginine as
an inhibitor of NAG in ornithine and arginine synthesis is well understood, there is
some controversy as to the role of NAG in the urea cycle. The currently accepted role of
NAG in vertebrates is as an essential allosteric cofactor for CPS1, and therefore it acts
as the primary controller of flux through the urea cycle. In this role, feedback regulation from arginine would act to signal NAGS that ammonia is plentiful within the cell,
and needs to be removed, accelerating NAGS function. As it stands, the evolutionary
journey of NAGS from essential synthetic enzyme to primary urea cycle controller is
yet to be fully understood.
https://en.wikipedia.org/wiki/N-Acetylglutamate_synthase
Acid
The term acid refers to a molecule that donates a proton in solution or to a
that has a pH lower than 7. Chemists use the term acid to refer to a subst
has protons that can dissociate (come off) when dissolved in water. There a
acids, such as HCl that completely dissociate when placed in water. Weak a
the the amount of ionization (proton loss) and the pH and the pKa of the ac
For an acid HA, which dissociates as
HA <=> H+ + A-,
pH = pKa + Log {[A-]/[HA]}
Index
Find Term
Acidosis
Acidosis is an increased acidity in the blood and other body tissue (i.e. an in
The rate of cellular metabolic activity affects and, at the same time, is affect
pH of the body fluids. In mammals, the normal pH of arterial blood lies bet
tween 7.35 and 7.45). Blood pH values compatible with life in mammals are
a pH range between 6.8 and 7.8. Changes in the pH of arterial blood (and th
extracellular fluid) outside this range result in irreversible cell damage.
https://en.wikipedia.org/wiki/Acidosis
Aconitase
Citrate
Isocitrate
https://en.wikipedia.org/wiki/Aconitase
ACP
The acyl carrier protein (ACP) is an important component in both fatty acid
etide biosynthesis with the growing chain bound during synthesis as a thiol
Acrylamide
Acrylamide is a compound formed from asparagine in foods cooked at high temperatures (deep frying) when it reacts with reducing sugars or other molecules with carbonyl groups. From Wikipedia - Acrylamide is a white odorless crystalline solid, soluble in water, ethanol, ether, and chloroform. Acrylamide decomposes in the presence
of acids, bases, oxidizing agents, iron, and iron salts. It decomposes non-thermally to
form ammonia, and thermal decomposition produces carbon monoxide, carbon dioxide, and oxides of nitrogen.
Acrylamide was discovered in foods in April 2002 by Eritrean scientist Eden Tareke in
Sweden when she found the chemical in starchy foods, such as potato chips (potato
crisps), French fries (chips), and bread that had been heated higher than 120C
(248F) (production of acrylamide in the heating process was shown to be
temperature-dependent). It was not found in food that had been boiled or in foods that
were not heated.
Acrylamide levels appear to rise as food is heated for longer periods of time. Although
researchers are still unsure of the precise mechanisms by which acrylamide forms in
foods, many believe it is a byproduct of the Maillard reaction. In fried or baked goods,
acrylamide may be produced by the reaction between asparagine and reducing sugars
(fructose, glucose, etc.) or reactive carbonyls at temperatures above 120C (248F).
https://en.wikipedia.org/wiki/Acrylamide
Actin
Actin is a globular multi-functional protein that forms microfilaments. It is found in essentially all eukaryotic cells (the only known exception being nematode sperm), where
it may be present at concentrations of over 100 M. An actin protein's mass is roughly
42-kDa and it is the monomeric subunit of two types of filaments in cells: microfilaments, one of the three major components of the cytoskeleton, and thin filaments, part
of the contractile apparatus in muscle cells. It can be present as either a free monomer
called G-actin (globular) or as part of a linear polymer microfilament called F-actin
(filamentous), both of which are essential for such important cellular functions as the
mobility and contraction of cells during cell division.
https://en.wikipedia.org/wiki/Actin
Index
Find Term
Actinin
filaments to the Z-lines in skeletal muscle cells, and to the dense bodies in s
cle cells. The functional protein is an anti-parallel dimer, which cross-links
Index
Find Term
Action Potential
brane potential of a cell rapidly rises and falls, following a consistent traject
potentials occur in several types of animal cells, called excitable cells, which
neurons, muscle cells, and endocrine cells, as well as in some plant cells. In
tential is the first step in the chain of events leading to muscular contraction
https://en.wikipedia.org/wiki/Action_potential
Index
Find Term
Activated Intermediate
ergy from that bond to transfer a part of itself to another molecule. An exam
UDP-Glucose. The energy of the bond between the UDP and glucose is use
bonds between acyl groups and coenzyme A are also high energy, which ma
CoA an activated intermediate as well.
Activation Domain
An activation domain is a part of a protein that interacts with transcription
facilitate transcription of a eukaryotic gene.
https://en.wikipedia.org/wiki/Transcription_factor
Index
Find Term
Activation Energy
Enzymes lower activation energy for reactions and this is the way they spee
https://en.wikipedia.org/wiki/Activation_energy
Index
Find Term
Activators
A transcriptional activator is a protein (transcription factor) that increases gene transcription of a gene or set of genes. Most activators are DNA-binding proteins that bind
to enhancers or promoter-proximal elements.
Most activators function by binding sequence-specifically to a DNA site located in or
near a promoter and making proteinprotein interactions with the general transcription machinery (RNA polymerase and general transcription factors), thereby facilitating the binding of the general transcription machinery to the promoter. The DNA site
bound by the activator is referred to as an "activator site." The part of the activator that
makes proteinprotein interactions with the general transcription machinery is referred to as an "activating region." The part of the general transcription machinery that
makes proteinprotein interactions with the activator is referred to as an "activation
target."
The catabolite activator protein (CAP; also known as cAMP receptor protein, CRP) activates transcription at the lac operon of the bacterium Escherichia coli. Cyclic adenosine monophosphate (cAMP) is produced during glucose starvation, binds to CAP,
causes a conformational change that allows CAP to bind to a DNA site located adjacent
to the lac promoter. CAP then makes a direct proteinprotein interaction with RNA polymerase that recruits RNA polymerase to the lac promoter.
https://en.wikipedia.org/wiki/Activator_(genetics)
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Active Site
The active site of an enzyme is the region where substrate molecules bind and undergo
a chemical reaction. The active site consists of residues that form temporary bonds
with the substrate (binding site) and residues that catalyze a reaction of that substrate
(catalytic site). The active site is usually a groove or pocket of the enzyme which can be
located in a deep tunnel within the enzyme, or between the interfaces of multimeric enzymes. An active site can catalyze a reaction repeatedly as its residues are not altered at
the end of the reaction (they may change during the reaction, but are regenerated by
the end).
Usually, an enzyme molecule has only one active site, and the active site fits with one
specific type of substrate. An active site contains a binding site that binds the substrate
and orients it for catalysis. Residues in the binding site form hydrogen bonds, hydrophobic interactions, or temporary covalent interactions (van der Waals) with the substrate to make an enzyme-substrate complex. In order to function, the active site needs
to be in a specific conformation and so denaturation of the protein by high temperatures or extreme pH values will destroy its catalytic activity. A tighter fit between an active site and the substrate molecule is believed to increase efficiency of a reaction. Most
enzymes have deeply buried active sites, which can be accessed by a substrate via access channels.
https://en.wikipedia.org/wiki/Active_site
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Active Transport
Active transport is the movement of molecules across a cell membrane from a region of
their lower concentration to a region of their higher concentration in the direction
against some gradient or other obstructing factor (often a concentration gradient). Unlike passive transport, which uses the kinetic energy and natural entropy of molecules
moving down a gradient, active transport uses cellular energy to move them against a
gradient, polar repulsion, or other resistance. Active transport is usually associated
with accumulating high concentrations of molecules that the cell needs, such as ions,
glucose and amino acids. If the process uses chemical energy, such as from adenosine
triphosphate (ATP), it is termed primary active transport. Secondary active transport
involves the use of an electrochemical gradient. Examples of active transport include
the uptake of glucose in the intestines in humans and the uptake of mineral ions into
root hair cells of plants.
https://en.wikipedia.org/wiki/Active_transport
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The activity control site is an allosteric control site found on the ribonucleo
zyme). Students sometimes confuse the active site of RNR with the activity
(sometimes called the activity site). The active site is where the reaction is c
and could better be called the catalytic site.
https://en.wikipedia.org/wiki/Ribonucleotide_reductase
Index
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Acyclovir
used for the treatment of herpes simplex virus infections, chickenpox, and s
https://en.wikipedia.org/wiki/Aciclovir
Acyl-carnitine
side the mitochondrial matrix, a similar enzyme reverses the reaction to replace
nitine with a CoASH so -oxidation can proceed.
https://en.wikipedia.org/wiki/Carnitine
Acyl-CoA
side living cells. The compound undergoes oxidation, forming one or mor
of acetyl-CoA. This, in turn, enters the citric acid cycle, eventually forming A
https://en.wikipedia.org/wiki/Acyl-CoA
Acyl-CoA Dehydrogenase
Acyl-CoA dehydrogenases (ACADs) are a class of enzymes that function to catalyze the
initial step in each cycle of fatty acid -oxidation in the mitochondria of cells. Their action results in the introduction of a trans double-bond between C2 () and C3 () of the
acyl-CoA thioester substrate. Flavin adenine dinucleotide (FAD) is a required co-factor
in addition to the presence of an active site glutamate in order for the enzyme to function.
Deficiencies in acyl-CoA dehydrogenases result in decreased ability to oxidize fatty ac-
ids, thereby causing metabolic dysfunction. Medium-chain acyl-CoA dehydrogenase deficiencies (MCADD) are well known and characterized because they occur most commonly among acyl-CoA dehydrogenases, leading to fatty acid oxidation disorders and
the potential of life-threatening metabolic diseases. Some problems associated with
medium-chain acyl-CoA dehydrogenase deficiency include intolerance to fasting, hypoglycemia, and sudden infant death syndrome.
https://en.wikipedia.org/wiki/Acyl_CoA_dehydrogenase
Adenine
Adenine is a nucleobase (a purine derivative). Its derivatives have a variety of roles in
biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD)
and flavin adenine dinucleotide (FAD). It also has functions in protein synthesis and as
a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.
The image right shows pure adenine, as an independent molecule. When connected
into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen. The remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose as used in
RNA and ATP. Deoxyadenosines adenine is attached to deoxyribose, as is used to
form DNA.
https://en.wikipedia.org/wiki/Adenine
Index
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ATP out of the matrix in exchange for ADP moving into the matrix. This transport
tem, which does not require input of energy is driven by the concentration of ADP
ATP.
the inner mitochondrial membrane. The dimer was thought to be a gated pore thr
which ADP and ATP were exchanged between the mitochondrial matrix and the cy
plasm. The dimer hypothesis was first challenged when the three-dimensional stru
ture of ANT was discovered to be a monomer. Further work has shown that ANT f
tions a monomer in detergents and in mitochondrial membranes.
Index
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Adenine Phosphoribosyltransferase
Adenine phosphoribosyltransferase (APRTase) is an enzyme encoded by the APRT
gene, found in humans on chromosome 16. It is part of the Type I PRTase family and is
involved in the nucleotide salvage pathway, which provides an alternative to nucleotide
biosynthesis de novo in humans and most other animals.
In organisms that can synthesize purines de novo, the nucleotide salvage pathway provides an alternative that is energetically more efficient. It can salvage adenine from the
polyamine biosynthetic pathway or from dietary sources of purines. Although APRTase is functionally redundant in these organisms, it becomes more important during
periods of rapid growth, such as embryogenesis and tumor growth. It is constitutively
expressed in all mammalian tissue.
In protozoan parasites, the nucleotide salvage pathway provides the sole means for nucleotide synthesis. Since the consequences of APRTase deficiency in humans is comparatively mild and treatable, it may be possible to treat certain parasitic infections by
targeting APRTase function.
In plants, as in other organisms, ARPTase functions primarily for the synthesis of
adenylate. It has the unique ability to metabolize cytokininsa plant hormone that can
exist as a base, nucleotide, or nucleosideinto adenylate nucleotides.
APRT is functionally related to hypoxanthine-guanine phosphoribosyltransferase
(HPRT).
https://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase
Adenosine
Adenosine is a purine nucleoside composed of a molecule of adenine attached to a ribose sugar molecule (ribofuranose) moiety via a -N9-glycosidic bond. Adenosine is
widely found in nature and plays an important role in biochemical processes, such as
energy transfer as adenosine triphosphate (ATP) and adenosine diphosphate (ADP)
as well as in signal transduction as cyclic adenosine monophosphate (cAMP). It is
also a neuromodulator, believed to play a role in promoting sleep and suppressing
arousal. Adenosine also plays a role in regulation of blood flow to various organs
through vasodilation.
https://en.wikipedia.org/wiki/Adenosine
Index
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Adenosine Deaminase
zyme (EC 3.5.4.4) involved in purine metabolism. It is needed for the break
adenosine from food and for the turnover of nucleic acids in tissues. Its prim
Index
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Adenylate Cyclase
Adenylyl cyclase (EC 4.6.1.1, also commonly known as adenyl cyclase and adenylate cyclase, abbreviated AC) is an enzyme with key regulatory roles in essentially all cells. It
is the most polyphyletic known enzyme. Six distinct classes have been described, all
catalyzing the same reaction but representing unrelated gene families with no known
sequence or structural homology. The best known class of adenylyl cyclases is class III
or AC-III (Roman numerals are used for classes). AC-III occurs widely in eukaryotes
and has important roles in many human tissues.
All classes of adenylyl cyclases catalyze the conversion of adenosine triphosphate
(ATP) to 3',5'-cyclic AMP (cAMP) and pyrophosphate. Magnesium ions are generally
required and appears to be closely involved in the enzymatic mechanism. The cAMP
produced by AC then serves as a regulatory signal via specific cAMP-binding proteins,
either transcription factors, enzymes (e.g., cAMP-dependent kinases), or ion transporters.
https://en.wikipedia.org/wiki/Adenylyl_cyclase
Index
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Adenylate Kinase
The equilibrium constant varies with condition, but is close to 1.Thus, the
reaction is close to zero.
https://en.wikipedia.org/wiki/Adenylate_kinase
Index
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Adenylosuccinate
Adenylosuccinate is an intermediate in the interconversion of purine nucleotides inosine monophosphate (IMP) and adenosine monophosphate (AMP). The enzyme adenylosuccinate synthase carries out the reaction by the addition of aspartate to IMP and
requires the input of energy from a phosphoanhydride bond in the form of guanosine
triphosphate (GTP). GTP is used instead of adenosine triphosphate (ATP), so the reaction is not dependent on its products.
https://en.wikipedia.org/wiki/Adenylosuccinate
Adenylosuccinate Lyase
Adenylosuccinate lyase (or adenylosuccinase) is an enzyme that in humans
marate as part of the purine nucleotide cycle. ASL catalyzes two reactions in
biosynthetic pathway that makes AMP. ASL cleaves adenylosuccinate into
fumarate, and cleaves SAICAR into AICAR and fumarate.
https://en.wikipedia.org/wiki/Adenylosuccinate_lyase
Index
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Adenylosuccinate Synthetase
Adenylosuccinate synthase (or adenylosuccinate synthetase) (EC 6.3.4.4.) is an enzyme
that plays an important role in purine biosynthesis, by catalyzing the guanosine triphosphate (GTP)-dependent conversion of inosine monophosphate (IMP) and aspartic
acid to guanosine diphosphate (GDP), phosphate and N(6)-(1,2-dicarboxyethyl)-AMP.
Adenylosuccinate synthetase has been characterized from various sources ranging
from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes
are present: one involved in purine biosynthesis and the other in the purine nucleotide
cycle.
The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central -sheet of 10
strands. The first nine strands of the sheet are mutually parallel with right-handed
crossover connections between the strands. The 10th strand is antiparallel with respect
to the first nine strands. In addition, the enzyme has two antiparallel -sheets, composed of two strands and three strands each, 11 -helices and two short 310-helices. Further, it has been suggested that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct
families of GTP-binding proteins. Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana when compared with the known structures
from E. coli reveals that the overall fold is very similar to that of the E. coli protein.
https://en.wikipedia.org/wiki/Adenylosuccinate_synthase
Adenylylation
(i.e. adenylic acid). This process can occur to molecules such as tyrosine res
zymes that are capable of catalyzing this process are called AMPylators.
https://en.wikipedia.org/wiki/Adenylylation
Index
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Adherens Junction
Adherens junctions (or zonula adherens, intermediate junction, or "belt desmosome")
are protein complexes that occur at cellcell junctions in epithelial and endothelial tissues, usually more basal than tight junctions. An adherens junction is defined as a cell
junction whose cytoplasmic face is linked to the actin cytoskeleton. They can appear as
bands encircling the cell (zonula adherens) or as spots of attachment to the extracellular matrix (adhesion plaques). A similar cell junction in non-epithelial, nonendothelial cells is the fascia adherens. It is structurally the same, but appears in ribbonlike patterns that do not completely encircle the cells. One example is in cardiomyocytes.
https://en.wikipedia.org/wiki/Adherens_junction
Adherens Junctions
Adherens junctions (or zonula adherens, intermediate junction, or "belt desmosome")
are protein complexes that occur at cellcell junctions in epithelial and endothelial tissues, usually more basal than tight junctions. An adherens junction is defined as a cell
junction whose cytoplasmic face is linked to the actin cytoskeleton. They can appear as
bands encircling the cell (zonula adherens) or as spots of attachment to the extracellular matrix (adhesion plaques). A similar cell junction in non-epithelial, nonendothelial cells is the fascia adherens. It is structurally the same, but appears in ribbonlike patterns that do not completely encircle the cells. One example is in cardiomyocytes.
https://en.wikipedia.org/wiki/Adherens_junction
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Adipocytes
Adipocytes, also known as lipocytes and fat cells, are the cells that primarily compose
adipose tissue, specialized in storing energy as fat. There are two types of adipose tissue, white adipose tissue (WAT) and brown adipose tissue (BAT), which are also
known as white fat and brown fat, respectively, and comprise two types of fat cells.
Most recently, the presence of beige adipocytes with a gene expression pattern distinct
from either white or brown adipocytes has been described.
White fat cells or monovacuolar cells contain a large lipid droplet surrounded by a
layer of cytoplasm. The nucleus is flattened and located on the periphery. A typical fat
cell is 0.1mm in diameter with some being twice that size and others half that size. The
fat stored is in a semi-liquid state, and is composed primarily of triglycerides and cholesteryl ester. White fat cells secrete many proteins acting as adipokines such as resistin, adiponectin, leptin and apelin. An average human adult has 30 billion fat cells
with a weight of 30lbs or 13.5kg. If excess weight is gained as an adult, fat cells increase in size about fourfold before dividing and increasing the absolute number of fat
cells present.
Brown fat cells or plurivacuolar cells are polygonal in shape. Unlike white fat cells,
these cells have considerable cytoplasm, with lipid droplets scattered throughout. The
nucleus is round, and, although eccentrically located, it is not in the periphery of the
cell. The brown color comes from the large quantity of mitochondria. Brown fat, also
known as "baby fat," is used to generate heat.
https://en.wikipedia.org/wiki/Adipocyte
Index
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Adipokines
The adipokines, or adipocytokines (Greek adipo-, fat; cytos-, cell; and -kinos, movement) are cytokines (cell signaling proteins) secreted by adipose tissue. The first adipokine to be discovered was leptin in 1994.
Members include:
Leptin
Adiponectin
Apelin
chemerin
interleukin-6 (IL-6)
visfatin
In addition, interleukin 8 (IL-8), interleukin 10 (IL-10), interferon (IFN-) and inducible protein 10 (IP-10 or CXCL10) have been shown to be associated with excessive
body weight.
https://en.wikipedia.org/wiki/Adipokine
Index
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Adiponectin
from adipose tissue (and also from the placenta in pregnancy) into the blood
and is very abundant in plasma relative to many hormones. Levels of the hor
inversely correlated with body fat percentage in adults. However, a meta ana
not able to confirm this association in healthy adults. The association in infan
sue. However, a recent study suggests that adipose tissue within bone marro
Index
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ADP
Adenosine diphosphate (ADP) (Adenosine pyrophosphate (APP)) is an important organic compound in metabolism and is essential to the flow of energy in living cells. A
molecule of ADP consists of three important structural components: a sugar backbone
attached to a molecule of adenine and two phosphate groups bonded to the 5 carbon
atom of ribose. The carbon molecules that make up the ring structure of a sugar can be
named in a way that more specifically designates the location of the phosphate and
adenosine attachments: The sugar backbone of ADP is known as a pentose sugar and
consists of five carbon molecules. The two phosphate groups of ADP are added in series to the 5 carbon of the sugar backbone, while the adenosine molecule attaches to
the 1 carbon.
ADP is the precursor of dADP in the reaction catalyzed by ribonucleotide reductase.
https://en.wikipedia.org/wiki/Adenosine_diphosphate
Index
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G-G
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 3 - Membranes: Transport
Chapter 4 - Catalysis: Basic Principles
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
ADP-ribose
poly ADP ribose polymerase. It binds to and activates the TRPM2 ion chann
https://en.wikipedia.org/wiki/Adenosine_diphosphate_ribose
Index
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Adrenodoxin
different tissues but all forms have been shown to be identical and are not t
cific.
ADSL
tion below in purine biosynthesis. ADSL is the eighth enzyme in this metab
way.
Adult Hemoglobin
Hemoglobin A (HbA), also known as adult hemoglobin or 22, is the most
man hemoglobin tetramer, comprising over 97% of the total red blood cell h
It consists of two chains and two chains.
https://en.wikipedia.org/wiki/Hemoglobin_A
Advantame
Drug Administration has approved advantame for general use in foods and be
https://en.wikipedia.org/wiki/Advantame
Aerobic
Aerobic means "requiring air," in which "air" usually means oxygen. Aerobic respiration requires oxygen (O2) in order to create ATP. Although carbohydrates, fats, and proteins are consumed as reactants, it is the preferred method of pyruvate breakdown in
glycolysis and requires that pyruvate enter the mitochondria in order to be fully oxidized by the citric acid cycle. The products of this process are carbon dioxide and water, but the energy transferred is used to break strong bonds in ADP as the third phosphate group is added to form ATP (adenosine triphosphate), by substrate-level phosphorylation, NADH and FADH2
Simplified reaction:
C6H12O6 (s) + 6 O2 (g) 6 CO2 (g) + 6 H2O (l) + heat
G = 2880 kJ per mol of C6H12O6
The negative G indicates that the reaction can occur spontaneously. The potential of
NADH and FADH2 is converted to more ATP through an electron transport chain with
oxygen as the "terminal electron acceptor". Most of the ATP produced by aerobic cellular respiration is made by oxidative phosphorylation. This works by the energy released in the consumption of pyruvate being used to create a chemiosmotic potential
by pumping protons across a membrane. This potential is then used to drive ATP synthase and produce ATP from ADP and a phosphate group. Biology textbooks often
state that 38 ATP molecules can be made per oxidized glucose molecule during cellular
respiration (2 from glycolysis, 2 from the citric acid cycle, and about 34 from the electron transport system). However, this maximum yield is never quite reached because
of losses due to leaky membranes as well as the cost of moving pyruvate and ADP into
the mitochondrial matrix, and current estimates range around 29 to 30 ATP per glucose.
Aerobic metabolism is up to 15 times more efficient than anaerobic metabolism (which
yields 2molecules ATP per 1molecule glucose). However some anaerobic organisms,
such as methanogens are able to continue with anaerobic respiration, yielding more
ATP by using other inorganic molecules (not oxygen) as final electron acceptors in the
electron transport chain. They share the initial pathway of glycolysis but aerobic metabolism continues with the citric cycle and oxidative phosphorylation. The postglycolytic reactions take place in the mitochondria in eukaryotic cells, and in the cytoplasm in prokaryotic cells.
https://en.wikipedia.org/wiki/Aerobic
Affinity
The interaction of most ligands with their binding sites can be characterized in term
of a binding affinity. In general, high-affinity ligand binding results from greater int
molecular force between the ligand and its receptor while low-affinity ligand binding
involves less intermolecular force between the ligand and its receptor. In general, hi
affinity binding involves a longer residence time for the ligand at its receptor bindin
site than is the case for low-affinity binding. High-affinity binding of ligands to recep
tors is often physiologically important when some of the binding energy can be used
https://en.wikipedia.org/wiki/Ligand_(biochemistry)#Receptor.2Fligand_binding
finity
Index
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Affinity Chromatography
Affinity chromatography is a method of separating biochemical mixtures based on a
highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.
For example, if one wanted to separate all of the proteins in a sample that bound to
ATP from proteins that do not bind ATP, one could covalently link ATP to support
beads and then elute the sample through column. All proteins that bind ATP will
stick to the column, whereas those that do not bind ATP will pass quickly through it.
The proteins are then released from the column by adding ATP.
The stationary phase is typically a gel matrix, often of agarose, a linear sugar molecule
derived from algae. Usually the starting point is an undefined heterogeneous group of
molecules in solution, such as a cell lysate, growth medium or blood serum. The molecule of interest will have a well known and defined property, and can be exploited during the affinity purification process. The process itself can be thought of as an entrapment, with the target molecule becoming trapped on a solid or stationary phase or medium. The other molecules in the mobile phase will not become trapped as they do not
possess this property. The stationary phase can then be removed from the mixture,
washed and the target molecule released from the entrapment in a process known as
elution. Possibly the most common use of affinity chromatography is for the purification of recombinant proteins.
https://en.wikipedia.org/wiki/Affinity_chromatography
Agarose
Agarose is a polysaccharide polymer material, generally extracted from seaweed. Agarose is a linear polymer made up of the repeating unit of agarobiose, which is a disac-
https://en.wikipedia.org/wiki/Agarose
Index
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https://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
Index
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Aggrecan
tein modified with large carbohydrates. The human form of the protein is 2
acids long and can be expressed in multiple isoforms due to alternative spli
https://en.wikipedia.org/wiki/Aggrecan
Index
Find Term
AICAR
5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) is an intermediate in the
generation of inosine monophosphate. AICAR is an analog of adenosine monophosphate (AMP) that is capable of stimulating AMP-dependent protein kinase (AMPK) activity. AICAR has been used clinically to treat and protect against cardiac ischemic injury. The drug was first used in the 1980s as a method to preserve blood flow to the
heart during surgery. Currently, the drug has also been shown as a potential treatment
for diabetes by increasing the metabolic activity of tissues by changing the physical
composition of muscle.
https://en.wikipedia.org/wiki/AICA_ribonucleotide
AIR Synthetase
AIR synthetase is the fifth enzyme in the de novo synthesis of purine nucleotides. It
catalyzes the reaction to form 5-aminoimidizole ribonucleotide (AIR) from
a 5-membered imidazole ring of the purine nucleus (AIR). AIR synthetase catalyzes th
transfer of the oxygen of the formyl group to phosphate. It is a sequential mechanism
in which ATP binds first to the enzyme and ADP is released last. This enzyme hydro-
lyzes ATP to activate the oxygen of the amide in order to carry out a nucleophilic attac
by a nitrogen. In humans and many other organisms, this enzyme is contained within
the trifunctional purine biosynthetic protein adenosine-3 polypeptide.
https://en.wikipedia.org/wiki/AIR_synthetase_(FGAM_cyclase)
Index
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Akt
Protein kinase B (PKB), also known as Akt, is a serine/threonine-specific protein kinase that plays a key role in multiple cellular processes such as glucose metabolism,
apoptosis, cell proliferation, transcription and cell migration.
Akt1 is involved in cellular survival pathways, by inhibiting apoptotic processes. Akt1 is
also able to induce protein synthesis pathways, and is therefore a key signaling protein
in the cellular pathways that lead to skeletal muscle hypertrophy, and general tissue
growth. Mouse model with complete deletion of Akt1 manifests growth retardation and
increased spontaneous apoptosis in tissues such as testes and thymus. Since it can
block apoptosis, and thereby promote cell survival, Akt1 has been implicated as a major factor in many types of cancer. Akt (now also called Akt1) was originally identified
as the oncogene in the transforming retrovirus, AKT8.
Akt2 is an important signaling molecule in the insulin signaling pathway. It is required
to induce glucose transport. In a mouse which is null for Akt1 but normal for Akt2, glucose homeostasis is unperturbed, but the animals are smaller, consistent with a role for
Akt1 in growth. In contrast, mice which do not have Akt2, but have normal Akt1, have
mild growth deficiency and display a diabetic phenotype (insulin resistance), again consistent with the idea that Akt2 is more specific for the insulin receptor signaling pathway. Akt isoforms are overexpressed in a variety of human tumors, and, at the genomic
level, are amplified in gastric adenocarcinomas (Akt1), ovarian (Akt2), pancreatic
(Akt2) and breast (Akt2) cancer.
The role of Akt3 is less clear, though it appears to be predominantly expressed in the
brain. It has been reported that mice lacking Akt3 have small brains.
https://en.wikipedia.org/wiki/Protein_kinase_B
AKT
Protein kinase B (PKB), also known as Akt, is a serine/threonine-specific protein kinase that plays a key role in multiple cellular processes such as glucose metabolism,
apoptosis, cell proliferation, transcription and cell migration.
Akt1 is involved in cellular survival pathways, by inhibiting apoptotic processes. Akt1 is
also able to induce protein synthesis pathways, and is therefore a key signaling protein
in the cellular pathways that lead to skeletal muscle hypertrophy, and general tissue
growth. Mouse model with complete deletion of Akt1 manifests growth retardation and
increased spontaneous apoptosis in tissues such as testes and thymus. Since it can
block apoptosis, and thereby promote cell survival, Akt1 has been implicated as a major factor in many types of cancer. Akt (now also called Akt1) was originally identified
as the oncogene in the transforming retrovirus, AKT8.
Akt2 is an important signaling molecule in the insulin signaling pathway. It is required
to induce glucose transport. In a mouse which is null for Akt1 but normal for Akt2, glucose homeostasis is unperturbed, but the animals are smaller, consistent with a role for
Akt1 in growth. In contrast, mice which do not have Akt2, but have normal Akt1, have
mild growth deficiency and display a diabetic phenotype (insulin resistance), again consistent with the idea that Akt2 is more specific for the insulin receptor signaling pathway. Akt isoforms are overexpressed in a variety of human tumors, and, at the genomic
level, are amplified in gastric adenocarcinomas (Akt1), ovarian (Akt2), pancreatic
(Akt2) and breast (Akt2) cancer.
The role of Akt3 is less clear, though it appears to be predominantly expressed in the
brain. It has been reported that mice lacking Akt3 have small brains.
https://en.wikipedia.org/wiki/Protein_kinase_B
Index
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Alanine
Alanine (abbreviated as Ala or A; encoded by the codons GCU, GCC, GCA, and GCG) is
an -amino acid that is used in the biosynthesis of proteins. It contains an -amino
group (which is in the protonated NH3+ form under biological conditions), an carboxylic acid group (which is in the deprotonated COO form under biological conditions), and a side chain methyl group, classifying it as a nonpolar (at physiological
pH), aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it. The L-isomer (left-handed) of alanine is one of the 20 amino acids encoded by
the human genetic code. L-Alanine is second only to leucine in rate of occurrence, accounting for 7.8% of the primary structure in a sample of 1,150 proteins. The righthanded form, D-Alanine occurs in bacterial cell walls and in some peptide antibiotics.
https://en.wikipedia.org/wiki/Alanine
Index
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Alanine Aminotransferase
Index
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Alanine Transaminase
Alanine transaminase (ALT) catalyzes the transfer of an amino group from L-alanine
to -ketoglutarate, the products of this reversible transamination reaction being pyruvate and L-glutamate.
L-glutamate + Pyruvate -ketoglutarate + L-alanine
ALT (and all transaminases) require the coenzyme pyridoxal phosphate, which is converted into pyridoxamine in the first phase of the reaction, when an amino acid is converted into a keto acid.
When elevated ALT levels are found in the blood, the possible underlying causes can
be further narrowed down by measuring other enzymes. For example, elevated ALT levels due to hepatocyte damage can be distinguished from bile duct problems by measuring alkaline phosphatase. Also, myopathy-related elevations in ALT should be suspected when the aspartate transaminase (AST) is greater than ALT. The possibility of
muscle disease causing elevations in liver tests can be further explored by measuring
muscle enzymes, including creatine kinase. Many drugs may elevate ALT levels, including Zileuton, -3-acid ethyl esters (Lovaza), anti-inflammatory drugs, antibiotics, cholesterol medications, some antipsychotics such as risperidone, and anticonvulsants..
Paracetamol may also elevate ALT levels.
https://en.wikipedia.org/wiki/Alanine_transaminase
Alcohol
Index
Find Term
Alcohol Dehydrogenase
NADH). In humans and many other animals, they serve to break down alco
otherwise are toxic, and they also participate in generation of useful aldehy
Aldehyde
An aldehyde is an organic compound containing a formyl group, a functional group
with the structure -CHO, consisting of a carbonyl center (a carbon double bonded to
oxygen) bonded to hydrogen that is bonded to an R group, which is any generic alkyl or
side chain. The group without R is the aldehyde group or formyl group. Aldehydes differ from ketones in that the carbonyl is placed at the end of a carbon skeleton rather
than between two carbon atoms. Aldehydes are common in organic chemistry. Many
fragrances are aldehydes.
https://en.wikipedia.org/wiki/Aldehyde
Index
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Aldolase
verse (cleaving an aldol). The word often refers to any type of fructose-bisph
dolase, but can also refer to other enzymes, such as the one that forms sialic
glycolysis, aldolase catalyzes the following reaction:
F1,6BP <=> Glyal3P + DHAP
https://en.wikipedia.org/wiki/Aldolase
Index
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Aldose
An aldose, like a ketose, is a monosaccharide (a simple sugar) that contains only one
aldehyde (CH=O) group per molecule, whereas ketose contains a ketone group. The
chemical formula takes the form Cn(H2O)n. The simplest possible aldose is the diose
glycolaldehyde, which only contains two carbon atoms.
Because they have at least one asymmetric carbon center, aldoses with three or more
carbon atoms exhibit stereoisomerism. Aldoses containing stereogenic centers can exist in either a d- form or l- form. The determination is made based on the chirality of
the penultimate carbon (the second-furthest from the aldehyde), where alcohol groups
on the right of the Fischer projection result in d-aldoses, and epimers with alcohols on
the left result in l-aldoses. Biological systems tend to recognize d-aldoses more than laldoses.
Examples of aldose include glycolaldehyde, glyceraldehyde, erythrose, threose, ribose,
arabinose, xylose, lyxose, allose, altrose, glucose, mannose, gulose, idose, talose, and
galactose. All of these examples contain one group of aldehyde. They only differ in numbers of carbons in carbon skeleton. All of these complex sugars serve an important role
in biochemistry.
An aldose differs from a ketose in that it has a carbonyl group at the end of the carbon
chain instead of in the middle. This allows ketoses and aldoses to be chemically differentiated through Seliwanoff's test. In Seliwanoff's test, aldoses tend to react in a slow
pace, and produce a light pink color, while ketoses react with resorcinol to produce a
dark red color. With different color of production, aldoses can be differentiate from the
ketoses. An aldose may isomerize to a ketose through the Lobry-de Bruyn-van Ekenstein transformation. Aldose and ketose, also perform in different roles. Aldoses tend
to isomerise into ketoses.
https://en.wikipedia.org/wiki/Aldose
Aldosterone
Aldosterone is a steroid hormone, "the main mineralocorticoid hormone", produced by
the outer section (zona glomerulosa) of the adrenal cortex in the adrenal gland. It plays
a central role in the regulation of blood pressure mainly by acting on the distal tubules
and collecting ducts of the nephron, increasing reabsorption of ions and water in the
kidney, to cause the conservation of sodium, secretion of potassium, increase in water
retention, and increase in blood pressure and blood volume. When dysregulated, aldosterone is pathogenic and contributes to the development and progression of cardiovascular and renal disease. Aldosterone has exactly the opposite function of the atrial
natriuretic hormone secreted by the heart.
https://en.wikipedia.org/wiki/Aldosterone
Index
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Aliphatic
pounds contain an especially stable ring of atoms, such as benzene. Aliphatic com
pounds can be saturated, like hexane, or unsaturated, like hexene. Open-chain com
pounds (whether straight or branched) contain no rings of any type, and are thus
phatic. An example of an aliphatic compound is shown below.
https://en.wikipedia.org/wiki/Aliphatic_compound
Index
Find Term
Alkaline
the sensitivity of the stream to acid inputs. There can be long-term changes
linity of streams and rivers in response to human disturbances.
https://en.wikipedia.org/wiki/Alkalinity
Alkaloid
Alkaloids are a group of naturally occurring chemical compounds that contain mostly
basic nitrogen atoms. This group also includes some related compounds with neutral
and even weakly acidic properties. Some synthetic compounds of similar structure are
also termed alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may
also contain oxygen, sulfur and, more rarely, other elements such as chlorine, bromine,
and phosphorus.
Alkaloids are produced by a large variety of organisms including bacteria, fungi, plants,
and animals. They can be purified from crude extracts of these organisms by acid-base
extraction. Alkaloids have a wide range of pharmacological activities including antimalarial (e.g. quinine), antiasthma (e.g. ephedrine), anticancer (e.g. homoharringtonine),
cholinomimetic (e.g. galantamine), vasodilatory (e.g. vincamine), antiarrhythmic (e.g.
quinidine), analgesic (e.g. morphine), antibacterial (e.g. chelerythrine), and antihyperglycemic activities (e.g. piperine).
Many have found use in traditional or modern medicine, or as starting points for drug
discovery. Other alkaloids possess psychotropic (e.g. psilocin) and stimulant activities
(e.g. cocaine, caffeine, nicotine, theobromine), and have been used in entheogenic rituals or as recreational drugs. Alkaloids can be toxic too (e.g. atropine, tubocurarine). Although alkaloids act on a diversity of metabolic systems in humans and other animals,
they almost uniformly evoke a bitter taste.
The boundary between alkaloids and other nitrogen-containing natural compounds is
not clear-cut. Compounds like amino acid peptides, proteins, nucleotides, nucleic acid,
amines, and antibiotics are usually not called alkaloids. Natural compounds containing
nitrogen in the exocyclic position (mescaline, serotonin, dopamine, etc.) are usually
classified as amines rather than as alkaloids. Some authors, however, consider alkaloids a special case of amines.
https://en.wikipedia.org/wiki/Alkaloid
Alkoxide
An alkoxide is the conjugate base of an alcohol and therefore consists of an
group bonded to a negatively charged oxygen atom. They can be written as
R is the organic substituent. Alkoxides are strong bases and, when R is not
An alkoxide ion of serine plays an important role the the catalytic mechanis
proteases.
https://en.wikipedia.org/wiki/Alkoxide
Index
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Allantoin
Named after the allantois (an amniote embryonic excretory organ in which it concentrates during development in most mammals except humans and higher apes[vague]),
allantoin is a product of oxidation of uric acid by purine catabolism. After birth, it is
the predominant means by which nitrogenous waste is excreted in the urine of these
animals. In humans and higher apes, the metabolic pathway for conversion of uric acid
to allantoin is not present, so the former is excreted. Recombinant rasburicase is sometimes used as a drug to catalyze this metabolic conversion in patients. In fish, allantoin
is broken down further (into ammonia) before excretion. Allantoin is a major metabolic intermediate in many other organisms including plants and bacteria.
Allantoin has been shown to improve insulin resistance when administered to rats and
increased lifespan when administered to the nematode worm C.elegans.
https://en.wikipedia.org/wiki/Allantoin
Allolactose
Allolactose is a disaccharide similar to lactose. It consists of the monosaccharides Dgalactose and D-glucose linked through a 1-6 glycosidic linkage instead of the 1-4
linkage of lactose. It may arise from the occasional transglycosylation of lactose by galactosidase. It is the isomer of spermatiglogen.
Allolactose is an inducer of the lac operon in Escherichia coli. It binds to a subunit of
the tetrameric lac repressor, which results in conformational changes and reduces the
binding affinity of the lac repressor to the lac operator, thereby dissociating it from the
lac operator. The absence of the repressor allows the transcription of the lac operon to
proceed. A non-hydrolyzable analog of allolactose, isopropyl -D-1thiogalactopyranoside (IPTG), is normally used in molecular biology to induce the lac
operon.
https://en.wikipedia.org/wiki/Allolactose
Index
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Allopurinol
Allopurinol, sold under the brand name Zyloprim and generics, is a medication us
primarily to treat excess uric acid in the blood and its complications, including chr
gout. It is a xanthine oxidase inhibitor which is administered orally.
Allopurinol is used in chronic gout to prevent future attacks. It does not alleviate a
attacks of gout and there is currently controversy over the issue of whether it can a
ally make acute gout attacks worse initially.
https://en.wikipedia.org/wiki/Allopurinol
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Allosteric
Allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an
effector molecule. Effectors that bind at the active site are known as homotropic effectors, whereas those that bind elsewhere are known as heterotropic effectors.
The site to which the effector binds is termed the allosteric site. Allosteric sites allow
effectors to bind to the protein, often resulting in a conformational change involving
protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
Allosteric regulations are a natural example of control loops, such as feedback from
downstream products or feedforward from upstream substrates. Long-range allostery
is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity.
Most allosteric effects can be explained 1) by the concerted MWC model put forth by
Monod, Wyman, and Changeux, 2) by the sequential model described by Koshland, Nemethy, and Filmer or 3) by the dossociative concerted Morpheein model. All models
postulate that enzyme subunits exist in one of two conformations, tensed (T) or relaxed (R), and that relaxed subunits bind substrate more readily than those in the
tense state.
https://en.wikipedia.org/wiki/Allosteric_regulation
Index
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Allosteric Control
In biochemistry, allosteric regulation (or allosteric control) is the regulation of a protein by binding an effector molecule at a site other than the enzyme's active site.
The site to which the effector binds is termed the allosteric site. Allosteric sites allow
effectors to bind to the protein, often resulting in a conformational change involving
protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
Allosteric regulations are a natural example of control loops, such as feedback from
downstream products or feedforward from upstream substrates. Long-range allostery
is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity.
The term allostery comes from the Greek allos (), "other," and stereos (),
"solid (object)." This is in reference to the fact that the regulatory site of an allosteric
protein is physically distinct from its active site.
https://en.wikipedia.org/wiki/Allosteric_regulation
Index
Find Term
Allosterism
In biochemistry, allosteric regulation (or allosteric control) is the regulation of a protein by binding an effector molecule at a site other than the enzyme's active site.
The site to which the effector binds is termed the allosteric site. Allosteric sites allow
effectors to bind to the protein, often resulting in a conformational change involving
protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
Allosteric regulations are a natural example of control loops, such as feedback from
downstream products or feedforward from upstream substrates. Long-range allostery
is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity.
The term allostery comes from the Greek allos (), "other," and stereos (),
"solid (object)." This is in reference to the fact that the regulatory site of an allosteric
protein is physically distinct from its active site.
https://en.wikipedia.org/wiki/Allosteric_regulation
Index
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Alternative Oxidase
The alternative oxidase (AOX) is an enzyme that forms part of the electron transport
chain in mitochondria of different organisms. Proteins homologous to the mitochondrial oxidase have also been identified in bacterial genomes.
The oxidase provides an alternative route for electrons passing through the electron
transport chain to reduce oxygen. However, as several proton-pumping steps are bypassed in this alternative pathway, activation of the oxidase reduces ATP generation.
This enzyme was first identified as a distinct oxidase pathway from cytochrome c oxidase as the alternative oxidase is resistant to inhibition by the poison cyanide.
https://en.wikipedia.org/wiki/Alternative_oxidase
Index
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Alternative Splicing
Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be
included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. Consequently, the proteins translated from alternatively spliced
mRNAs will contain differences in their amino acid sequence and, often, in their biological functions. Notably, alternative splicing allows the human genome to direct the
synthesis of many more proteins than would be expected from its 20,000 proteincoding genes. Alternative splicing is sometimes termed differential splicing.
Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the biodiversity of proteins that can be encoded by the genome. In humans,
~95% of multi-exonic genes are alternatively spliced. There are numerous modes of alternative splicing observed, of which the most common is exon skipping. In this mode,
a particular exon may be included in mRNAs under some conditions or in particular tissues, and omitted from the mRNA in others.
The production of alternatively spliced mRNAs is regulated by a system of trans-acting
proteins that bind to cis-acting sites on the primary transcript itself. Such proteins include splicing activators that promote the usage of a particular splice site, and splicing
repressors that reduce the usage of a particular site. Mechanisms of alternative splicing
are highly variable, and new examples are constantly being found, particularly through
the use of high-throughput techniques. Researchers hope to fully elucidate the regulatory systems involved in splicing, so that alternative splicing products from a given
gene under particular conditions could be predicted by a "splicing code".
Abnormal variations in splicing are also implicated in disease. A large proportion of
human genetic disorders result from splicing variants. Abnormal splicing variants are
also thought to contribute to the development of cancer, and splicing factor genes are
frequently mutated in different types of cancer.
https://en.wikipedia.org/wiki/Alternative_splicing#/media/File:DNA_alternative_sp
licing.gif
Index
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Alzheimers Disease
that usually starts slowly and gets worse over time. The most common early
ily getting lost), mood swings, loss of motivation, not managing self care, an
ioral issues. As a person's condition declines, they often withdraw from fam
ety. Gradually, bodily functions are lost, ultimately leading to death. Althou
speed of progression can vary, the average life expectancy following diagnos
to nine years.
https://en.wikipedia.org/wiki/Alzheimer%27s_disease
Index
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Ames Test
The Ames test is a widely employed method that uses bacteria to test whether a given
chemical can cause mutations in the DNA of the test organism. More formally, it is a
biological assay to assess the mutagenic potential of chemical compounds. A positive
test indicates that the chemical is mutagenic and therefore may act as a carcinogen, because cancer is often linked to mutation. The test serves as a quick and convenient assay to estimate the carcinogenic potential of a compound because standard carcinogen
assays on mice and rats are time-consuming (taking two to three years to complete)
and expensive. However, false-positives and false-negatives are known.
The Ames test uses several strains of the bacterium Salmonella typhimurium that
carry mutations in genes involved in histidine synthesis. These strains are auxotrophic
mutants, i.e. they require histidine for growth, but cannot produce it. The method tests
the capability of the tested substance in creating mutations that result in a return to a
"prototrophic" state, so that the cells can grow on a histidine-free medium.
The tester strains are specially constructed to detect either frameshift (e.g. strains TA1537 and TA-1538) or point (e.g. strain TA-1531) mutations in the genes required to
synthesize histidine, so that mutagens acting via different mechanisms may be identified. Some compounds are quite specific, causing reversions in just one or two strains.
The tester strains also carry mutations in the genes responsible for lipopolysaccharide
synthesis, making the cell wall of the bacteria more permeable, and in the excision repair system to make the test more sensitive. Rat liver extract is optionally added to
simulate the effect of metabolism, as some compounds, like benzo[a]pyrene, are not
mutagenic themselves but their metabolic products are.
The bacteria are spread on an agar plate with small amount of histidine. This small
amount of histidine in the growth medium allows the bacteria to grow for an initial
time and have the opportunity to mutate. When the histidine is depleted only bacteria
that have mutated to gain the ability to produce its own histidine will survive. The
plate is incubated for 48 hours. The mutagenicity of a substance is proportional to the
number of colonies observed.
The procedure was described in a series of papers in the early 1970s by Bruce Ames
and his group at the University of California, Berkeley.
https://en.wikipedia.org/wiki/Ames_test
Amine
In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia,
wherein one or more hydrogen atoms have been replaced by a substituent such as an
alkyl or aryl group.
An aliphatic amine has no aromatic ring attached directly to the nitrogen atom. Aromatic amines have the nitrogen atom connected to an aromatic ring as in the various
anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents. The presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect.
Amines are organized into four subcategories:
Primary amines Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include methylamine, ethanolamine (2-aminoethanol), and the buffering agent tris, while primary aromatic amines include aniline.
Secondary amines Secondary amines have two organic substituents (alkyl, aryl or
both) bound to N together with one hydrogen (or no hydrogen if one of the substituent
bonds is double). Important representatives include dimethylamine and methylethanolamine, while an example of an aromatic amine would be diphenylamine.
Tertiary amines In tertiary amines, all three hydrogen atoms are replaced by organic substituents. Examples include trimethylamine, which has a distinctively fishy
smell, or triphenylamine.
Cyclic amines Cyclic amines are either secondary or tertiary amines. Examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring
piperidine. N-methylpiperidine and N-phenylpiperidine are examples of cyclic tertiary
amines.
It is also possible to have four organic substituents on the nitrogen. These species are
not amines but are quaternary ammonium cations and have a charged nitrogen center.
Quaternary ammonium salts exist with many kinds of anions.
https://en.wikipedia.org/wiki/Amine
Index
Find Term
Amine Group
In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia,
wherein one or more hydrogen atoms have been replaced by a substituent such as an
alkyl or aryl group.
An aliphatic amine has no aromatic ring attached directly to the nitrogen atom. Aromatic amines have the nitrogen atom connected to an aromatic ring as in the various
anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents. The presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect.
Amines are organized into four subcategories:
Primary amines Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include methylamine, ethanolamine (2-aminoethanol), and the buffering agent tris, while primary aromatic amines include aniline.
Secondary amines Secondary amines have two organic substituents (alkyl, aryl or
both) bound to N together with one hydrogen (or no hydrogen if one of the substituent
bonds is double). Important representatives include dimethylamine and methylethanolamine, while an example of an aromatic amine would be diphenylamine.
Tertiary amines In tertiary amines, all three hydrogen atoms are replaced by organic substituents. Examples include trimethylamine, which has a distinctively fishy
smell, or triphenylamine.
Cyclic amines Cyclic amines are either secondary or tertiary amines. Examples of
cyclic amines include the 3-membered ring aziridine and the six-membered ring
piperidine. N-methylpiperidine and N-phenylpiperidine are examples of cyclic tertiary amines.
It is also possible to have four organic substituents on the nitrogen. These species are
not amines but are quaternary ammonium cations and have a charged nitrogen center.
Quaternary ammonium salts exist with many kinds of anions.
https://en.wikipedia.org/wiki/Amine
Index
Find Term
Amino Acid
Amino acids are biologically important organic compounds containing amine (-NH2)
and carboxylic acid (-COOH) functional groups, usually along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino
acids.
In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (-) carbon atom have particular importance. They are known as 2-,
-, or -amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side-chain"). Often the term "amino acid" is used to refer specifically to these. They include the 23 proteinogenic ("protein-building") amino
acids, which combine into peptide chains ("polypeptides") to form the building-blocks
of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.
Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the
genetic code and are known as "standard" amino acids. The other three ("nonstandard" or "non-canonical") are selenocysteine (present in many noneukaryotes as
well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in
some archea and one bacterium) and N-formylmethionine (which is often the initial
amino acid of proteins in bacteria, mitochondria, and chloroplasts). Pyrrolysine and
selenocysteine are encoded via variant codons. For example, selenocysteine is encoded
by a stop codon and SECIS element which allows the stop codon to be read instead of
protein synthesis stopping. CodontRNA combinations not found in nature can also be
used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.
Many important proteinogenic and non-proteinogenic amino acids also play critical
non-protein roles within the body. For example, in the human brain, glutamate (standard glutamic acid) and -amino-butyric acid ("GABA", non-standard -amino acid)
are, respectively, the main excitatory and inhibitory neurotransmitters. Hydroxyproline (a major component of the connective tissue collagen) is synthesized from proline.
The standard amino acid glycine is used to synthesize porphyrins used in red blood
cells. The non-standard carnitine is used in lipid transport.
Nine proteinogenic amino acids are called "essential" for humans because they cannot
be created from other compounds by the human body and so must be taken in as food.
Others may be conditionally essential for certain ages or medical conditions. Essential
amino acids may also differ between species.
https://en.wikipedia.org/wiki/Amino_acid
Index
Find Term
Amino Acids
Amino acids are biologically important organic compounds containing amine (-NH2)
and carboxylic acid (-COOH) functional groups, usually along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino
acids.
In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (-) carbon atom have particular importance. They are known as 2-,
-, or -amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side-chain"). Often the term "amino acid" is used to refer specifically to these. They include the 23 proteinogenic ("protein-building") amino
acids, which combine into peptide chains ("polypeptides") to form the building-blocks
of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.
Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the
genetic code and are known as "standard" amino acids. The other three ("nonstandard" or "non-canonical") are selenocysteine (present in many noneukaryotes as
well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in
some archea and one bacterium) and N-formylmethionine (which is often the initial
amino acid of proteins in bacteria, mitochondria, and chloroplasts). Pyrrolysine and
selenocysteine are encoded via variant codons. For example, selenocysteine is encoded
by a stop codon and SECIS element which allows the stop codon to be read instead of
protein synthesis stopping. CodontRNA combinations not found in nature can also be
used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.
Many important proteinogenic and non-proteinogenic amino acids also play critical
non-protein roles within the body. For example, in the human brain, glutamate (standard glutamic acid) and -amino-butyric acid ("GABA", non-standard -amino acid)
are, respectively, the main excitatory and inhibitory neurotransmitters. Hydroxyproline (a major component of the connective tissue collagen) is synthesized from proline.
The standard amino acid glycine is used to synthesize porphyrins used in red blood
cells. The non-standard carnitine is used in lipid transport.
Nine proteinogenic amino acids are called "essential" for humans because they cannot
be created from other compounds by the human body and so must be taken in as food.
Others may be conditionally essential for certain ages or medical conditions. Essential
amino acids may also differ between species.
https://en.wikipedia.org/wiki/Amino_acid
Index
Find Term
Amino Terminus
charge) associated with them. The end of the protein that has the free -am
is referred to as the amino terminus.
Index
Find Term
Aminopeptidases
Aminopeptidases are enzymes that catalyze the cleavage of amino acids from
throughout the animal and plant kingdoms and are found in many subcellu
elles, in cytosol, and as membrane components. Aminopeptidases are used
cellular functions. Many, but not all, of these peptidases are zinc metalloenz
Index
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Aminopterin
Aminopterin (or 4-aminopteroic acid), the 4-amino derivative of folic acid, is an antineoplastic drug with immunosuppressive properties often used in chemotherapy.
Aminopterin is a synthetic derivative of pterin. Aminopterin works as an enzyme inhibitor by competing for the folate binding site of the enzyme dihydrofolate reductase. Its
binding affinity for dihydrofolate reductase effectively blocks tetrahydrofolate synthesis. This results in the depletion of nucleotide precursors and inhibition of DNA, RNA,
and protein synthesis.
Discovered by Dr. Yellapragada Subbarow, the drug was first used by Sidney Farber in
1947 to induce remissions among children with leukemia. Aminopterin was later marketed by Lederle Laboratories (Pearl River, New York) in the United States from 1953
to 1964 for the indication of pediatric leukemia. The closely related antifolate
methotrexate was simultaneously marketed by the company during the same period.
Aminopterin was discontinued by Lederle Laboratories in favor of methotrexate due to
manufacturing difficulties of the former.
During the period Aminopterin was marketed, the agent was used off-label to safely
treat over 4,000 patients with psoriasis in the United States, producing dramatic clearing of lesions. The use of aminopterin in cancer treatment was supplanted in the
1950s by methotrexate due to the latter's better therapeutic index in a rodent tumor
model. Now in a more pure preparation and supported by laboratory evidence of superior tumor cell uptake in vitro, aminopterin is being investigated in clinical trials in leukemia as a potentially superior antifolate to methotrexate.
https://en.wikipedia.org/wiki/Aminopterin
Ammonia
Ammonia or azane is a compound of nitrogen and hydrogen with the formula NH3. In
water, ammonia readily forms the ammonium ion (NH4+) It is a colorless gas with a
characteristic pungent smell. Ammonia contributes significantly to the nutritional
needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or indirectly, is also a building block for the synthesis of many pharmaceuticals and is used in many commercial cleaning products. Although common in
nature and in wide use, ammonia is both caustic and hazardous in its concentrated
form.
Ammonia is both a metabolic waste and a metabolic input throughout the biosphere. It
is an important source of nitrogen for living systems. Although atmospheric nitrogen
abounds (more than 75%), few living creatures are capable of using this atmospheric
nitrogen in its diatomic form, N2 gas. Therefore, nitrogen fixation is required for the
synthesis of amino acids, which are the building blocks of protein. Some plants rely on
ammonia and other nitrogenous wastes incorporated into the soil by decaying matter.
Others, such as nitrogen-fixing legumes, benefit from symbiotic relationships with rhizobia that create ammonia from atmospheric nitrogen.
In certain organisms, ammonia is produced from atmospheric nitrogen by enzymes
called nitrogenases. The overall process is called nitrogen fixation. Although it is unlikely that biomimetic methods that are competitive with the Haber process will be developed, intense effort has been directed toward understanding the mechanism of biological nitrogen fixation. The scientific interest in this problem is motivated by the unusual structure of the active site of the enzyme, which consists of an Fe7MoS9 ensemble.
Ammonia is also a metabolic product of amino acid deamination catalyzed by enzymes
such as glutamate dehydrogenase 1. Ammonia excretion is common in aquatic animals.
In humans, it is quickly converted to urea, which is much less toxic, particularly less basic. This urea is a major component of the dry weight of urine. Most reptiles, birds, insects, and snails excrete uric acid solely as nitrogenous waste.
Ammonia also plays a role in both normal and abnormal animal physiology. It is biosynthesized through normal amino acid metabolism and is toxic in high concentrations. The liver converts ammonia to urea through a series of reactions known as the
urea cycle. Liver dysfunction, such as that seen in cirrhosis, may lead to elevated
amounts of ammonia in the blood (hyperammonemia). Likewise, defects in the enzymes responsible for the urea cycle, such as ornithine transcarbamylase, lead to hyperammonemia. Hyperammonemia contributes to the confusion and coma of hepatic
encephalopathy, as well as the neurologic disease common in people with urea cycle defects and organic acidurias.
Ammonia is important for normal animal acid/base balance. After formation of ammonium from glutamine, -ketoglutarate may be degraded to produce two molecules of
bicarbonate, which are then available as buffers for dietary acids. Ammonium is excreted in the urine, resulting in net acid loss. Ammonia may itself diffuse across the renal tubules, combine with a hydrogen ion, and thus allow for further acid excretion.
Ammonium ions are a toxic waste product of metabolism in animals. In fish and
aquatic invertebrates, it is excreted directly into the water. In mammals, sharks, and
amphibians, it is converted in the urea cycle to urea, because it is less toxic and can be
stored more efficiently. In birds, reptiles, and terrestrial snails, metabolic ammonium
is converted into uric acid, which is solid, and can therefore be excreted with minimal
water loss.
https://en.wikipedia.org/wiki/Ammonia
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Ammonotelic
ammonia levels in the excretory fluid below the level in body fluids, otherw
Index
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AMP
Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide that
is used as a monomer in RNA. It is an ester of phosphoric acid and the nucleoside
adenosine. AMP consists of a phosphate group, the sugar ribose, and the nucleobase
adenine. As a substituent it takes the form of the prefix adenylyl-.
AMP can also be cylized to form a structure known as cyclic AMP (or cAMP). Within
certain cells the enzyme adenylate cyclase makes cAMP from ATP, and typically this reaction is regulated by hormones such as adrenaline or glucagon. cAMP plays an important role in intracellular signaling.
https://en.wikipedia.org/wiki/Adenosine_monophosphate
Image https://en.wikipedia.org/wiki/Adenosine_monophosphate#/media/File:Adenosinmo
nophosphat_protoniert.svg
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G-G
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
AMP Deaminase
skeletal muscle and plays an important role in the purine nucleotide cycle. T
genes have been identified, AMPD2 and AMPD3, for the liver- and erythroc
A new research report shows that the widely prescribed diabetes medication
Index
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AMP Kinase
5' AMP-activated protein kinase or AMPK or 5' adenosine monophosphate-activated
(AMP) protein kinase is an enzyme that plays a role in cellular energy homeostasis. It
consists of three proteins (subunits) that together make a functional enzyme, conserved from yeast to humans. It is expressed in a number of tissues, including the liver,
brain, and skeletal muscle. The net effect of AMPK activation is stimulation of hepatic
fatty acid oxidation and ketogenesis, inhibition of cholesterol synthesis, lipogenesis,
and triglyceride synthesis, inhibition of adipocyte lipolysis and lipogenesis, stimulation
of skeletal muscle fatty acid oxidation and muscle glucose uptake, and modulation of
insulin secretion by pancreatic -cells.
AMPK acts as a metabolic master switch regulating several intracellular systems including the cellular uptake of glucose, the -oxidation of fatty acids and the biogenesis of
glucose transporter 4 (GLUT4) and mitochondria. The energy-sensing capability of
AMPK can be attributed to its ability to detect and react to fluctuations in the
AMP:ATP ratio that take place during rest and exercise (muscle stimulation). During
muscle stimulation, AMP increases while ATP decreases, which changes AMPK into a
good substrate for activation via an upstream kinase complex, AMPKK, or better,
where binding of AMP renders activated AMPK that is phosphorylated at Thr-172 a
worse substrate for protein phosphatase 2C.
AMPKK is a complex of three proteins, STE-related adaptor (STRAD), mouse protein
25 (MO25), and LKB1 (a serine/threonine kinase). During a bout of exercise, AMPK activity increases while the muscle cell experiences metabolic stress brought about by an
extreme cellular demand for ATP. Upon activation, AMPK increases cellular energy levels by inhibiting anabolic energy consuming pathways (fatty acid synthesis, protein synthesis, etc.) and stimulating energy producing, catabolic pathways (fatty acid oxidation, glucose transport, etc.).
https://en.wikipedia.org/wiki/AMP-activated_protein_kinase
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Amphipathic
Amphiphile (from the Greek , amphis: both and , philia: love, friendship) is
a term describing a chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat-loving) properties. Such a compound is called amphiphilic or
amphipathic.
Phospholipids, a class of amphiphilic molecules, are the main components of biological
membranes. The amphiphilic nature of these molecules defines the way in which they
form membranes. They arrange themselves into bilayers, by positioning their polar
groups towards the surrounding aqueous medium, and their lipophilic chains towards
the inside of the bilayer, defining a non-polar region between two polar ones.
Although phospholipids are principal constituents of biological membranes, there are
other constituents, such as cholesterol and glycolipids, which are also included in these
structures and give them different physical and biological properties.
Many other amphiphilic compounds, such as pepducins, strongly interact with biological membranes by insertion of the hydrophobic part into the lipid membrane, while exposing the hydrophilic part to the aqueous medium, altering their physical behavior
and sometimes disrupting them.
Shown below an amphipathic/amphiphilic compound - a glycerophospholipid
https://en.wikipedia.org/wiki/Amphiphile
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Amphiphilic
Amphiphile (from the Greek , amphis: both and , philia: love, friendship) is
a term describing a chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat-loving) properties. Such a compound is called amphiphilic or
amphipathic.
Phospholipids, a class of amphiphilic molecules, are the main components of biological
membranes. The amphiphilic nature of these molecules defines the way in which they
form membranes. They arrange themselves into bilayers, by positioning their polar
groups towards the surrounding aqueous medium, and their lipophilic chains towards
the inside of the bilayer, defining a non-polar region between two polar ones.
Although phospholipids are principal constituents of biological membranes, there are
other constituents, such as cholesterol and glycolipids, which are also included in these
structures and give them different physical and biological properties.
Many other amphiphilic compounds, such as pepducins, strongly interact with biological membranes by insertion of the hydrophobic part into the lipid membrane, while exposing the hydrophilic part to the aqueous medium, altering their physical behavior
and sometimes disrupting them.
Shown below an amphipathic/amphiphilic compound - a glycerophospholipid
https://en.wikipedia.org/wiki/Amphiphile
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Amyloid
Amyloid (A or Abeta) denotes peptides of 3643 amino acids that are crucially involved in Alzheimer's disease as the main component of the amyloid plaques found in
the brains of Alzheimer patients. The peptides result from the amyloid precursor protein (APP), which is cleaved by secretase and secretase to yield A.
A molecules can aggregate to form flexible soluble oligomers which may exist in several forms. It is now believed that certain misfolded oligomers (known as "seeds") can
induce other A molecules to also take the misfolded oligomeric form, leading to a
chain reaction akin to a prion infection. The seeds or the resulting amyloid plaques are
toxic to nerve cells. The other protein implicated in Alzheimer's disease, tau protein,
also forms such prion-like misfolded oligomers, and there is some evidence that misfolded A can induce tau to misfold.
The normal function of A is not well understood. Though some animal studies have
shown that the absence of A does not lead to any loss of physiological function, several potential activities have been discovered for A, including activation of kinase enzymes, protection against oxidative stress, regulation of cholesterol transport, functioning as a transcription factor, and anti-microbial activity (potentially associated with
A's pro-inflammatory activity).
The glymphatic system clears metabolic waste from the mammalian brain, and in particular amyloids. The rate of removal is significantly increased during sleep. However
the significance of the glymphatic system is unknown in clearance of A.
https://en.wikipedia.org/wiki/Amyloid_beta
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Amyloid Plaques
Amyloids are aggregates of proteins that become folded into the wrong shape, allowing
many copies of that protein to stick together. These previously healthy proteins most
often lose their normal function and form large fibrils. These fibrils disrupt the healthy
physiological function of nearby tissues and organs.
Amyloids have been known to arise from at least 18 different proteins and polypeptides, and have been associated with more than 20 human diseases, known as amyloidosis, and may play a role in some neurodegenerative disorders.
The reasons for amyloid association disease are unclear. In some cases, the deposits
physically disrupt tissue architecture, suggesting disruption of function by some bulk
process. An emerging consensus implicates prefibrillar intermediates rather than mature amyloid fibers in causing cell death.
Calcium dysregulation has been observed in cells exposed to amyloid oligomers. These
small aggregates can form ion channels planar lipid bilayer membranes. Channel formation has been hypothesized to account for calcium dysregulation and mitochondrial
dysfunction by allowing indiscriminate leakage of ions across cell membranes. Studies
have shown that amyloid deposition is associated with mitochondrial dysfunction and
a resulting generation of reactive oxygen species (ROS), which can initiate a signalling
pathway leading to apoptosis.
There are reports that indicate amyloid polymers (such as those of huntingtin, associated with Huntington's disease) can induce the polymerization of essential amyloidogenic proteins, which should be deleterious to cells. Also, interaction partners of these
essential proteins can also be sequestered.
https://en.wikipedia.org/wiki/Amyloid
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Index
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Amyloids
Amyloids are aggregates of proteins that become folded into the wrong shape, allowing
many copies of that protein to stick together. These previously healthy proteins most
often lose their normal function and form large fibrils. These fibrils disrupt the healthy
physiological function of nearby tissues and organs.
Amyloids have been known to arise from at least 18 different proteins and polypeptides, and have been associated with more than 20 human diseases, known as amyloidosis, and may play a role in some neurodegenerative disorders.
The reasons for amyloid association disease are unclear. In some cases, the deposits
physically disrupt tissue architecture, suggesting disruption of function by some bulk
process. An emerging consensus implicates prefibrillar intermediates rather than mature amyloid fibers in causing cell death.
Calcium dysregulation has been observed in cells exposed to amyloid oligomers. These
small aggregates can form ion channels planar lipid bilayer membranes. Channel formation has been hypothesized to account for calcium dysregulation and mitochondrial
dysfunction by allowing indiscriminate leakage of ions across cell membranes. Studies
have shown that amyloid deposition is associated with mitochondrial dysfunction and
a resulting generation of reactive oxygen species (ROS), which can initiate a signalling
pathway leading to apoptosis.
There are reports that indicate amyloid polymers (such as those of huntingtin, associated with Huntington's disease) can induce the polymerization of essential amyloidogenic proteins, which should be deleterious to cells. Also, interaction partners of these
essential proteins can also be sequestered.
https://en.wikipedia.org/wiki/Amyloid
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Amylopectin
Amylopectin is a soluble polysaccharide and branched polymer of glucose found in
plants. It is one of the two components of starch, the other being amylose.
Glucose units are linked in a linear way with (14) glycosidic bonds. Branching takes
place with (16) bonds occurring every 24 to 30 glucose units, resulting in a soluble
molecule that can be quickly degraded as it has many end points onto which enzymes
can attach. In contrast, amylose contains very few (16) bonds, or even none at all.
This causes amylose to be hydrolyzed more slowly, but have higher density and be insoluble.
Its counterpart in animals is glycogen, which has the same composition and structure,
but with more extensive branching that occurs every eight to 12 glucose units.
Plants store starch within specialized organelles called amyloplasts. When energy is
needed for cell work, the plant hydrolyzes the starch, releasing the glucose subunits.
Humans and other animals that eat plant foods also use amylase, an enzyme that assists in breaking down amylopectin.
Starch is made of about 70% amylopectin by weight, though it varies depending on the
source (higher in medium-grain rice to 100% in glutinous rice, waxy potato starch, and
waxy corn, and lower in long-grain rice, amylomaize, and russet potatoes, for example). Amylopectin is highly branched, being formed of 2,000 to 200,000 glucose units.
Its inner chains are formed of 20-24 glucose subunits.
https://en.wikipedia.org/wiki/Amylopectin
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Amylose
Amylose is a helical polymer made of -D-glucose units, bound to each other through
(14) glycosidic bonds. This polysaccharide is one of the two components of starch,
making up approximately 20-30% of the structure. The other component is amylopectin, which makes up 7080% of the structure.
Because of its tightly packed structure, amylose is more resistant to digestion than
other starch molecules and is therefore an important form of resistant starch, which
has been found to be an effective prebiotic.
Amylose is important in plant energy storage. It is less readily digested than amylopectin; however, because it is more linear than amylopectin, it takes up less space. As a result, it is the preferred starch for storage in plants. It makes up about 30% of the stored
starch in plants, though the specific percentage varies by species. The digestive enzyme
-amylase is responsible for the breakdown of the starch molecule into maltotriose and
maltose, which can be used as sources of energy.
Amylose is also an important thickener, water binder, emulsion stabilizer, and gelling
agent in both industrial and food-based contexts. Loose helical amylose chains have a
hydrophobic interior that can bind to hydrophobic molecules such as lipids and aromatic compounds. The one problem with this is that, when it crystallizes or associates,
it can lose some stability, often releasing water in the process (syneresis). When amylose concentration is increased, gel stickiness decreases but gel firmness increases.
When other things including amylopectin bind to amylose, the viscosity can be affected, but incorporating -carrageenan, alginate, xanthan gum, or low-molecularweight sugars can reduce the loss in stability. The ability to bind water can add substance to food, possibly serving as a fat replacement. For example, amylose is responsible for causing white sauce to thicken, but, upon cooling, some separation between the
solid and the water will occur.
In a laboratory setting, it can act as a marker. Iodine molecules fit neatly inside the helical structure of amylose, binding with the starch polymer that absorbs certain known
wavelengths of light. Hence, a common test is the iodine test for starch. Mix starch
with a small amount of yellow iodine solution. In the presence of amylose, a blue-black
color will be observed. The intensity of the color can be tested with a colorimeter, using
a red filter to discern the concentration of starch present in the solution. It is also possible to use starch as an indicator in titrations involving iodine reduction. It is also used
in amylose magnetic beads and resin to separate maltose-binding protein.
https://en.wikipedia.org/wiki/Amylose
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Amytal
Amobarbital (formerly known as amylobarbitone or sodium amytal) is a drug that is a
barbiturate derivative. It has sedative-hypnotic properties. It is a white crystalline powder with no odor and a slightly bitter taste. It was first synthesized in Germany in 1923.
If amobarbital is taken for extended periods of time, physical and psychological dependence can develop. Amobarbital withdrawal mimics delirium tremens and may be
life-threatening.
Amobarbital has been used in a study to inhibit mitochondrial electron transport in the
rat heart as it is an inhibitor of the movement of electrons through complex I.
https://en.wikipedia.org/wiki/Amobarbital
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Anabolic
Anabolism (from Greek: "upward" and "to throw") is the set of metabolic
pathways that construct molecules from smaller units. These reactions require energy.
One way of categorizing metabolic processes, whether at the cellular, organ or organism level, is as "anabolic", or as "catabolic" which is the opposite. Anabolism is powered by catabolism, where large molecules are broken down into smaller parts and
then used up in respiration. Many anabolic processes are powered by the hydrolysis of
adenosine triphosphate (ATP).
Anabolic processes tend toward "building up" organs and tissues. These processes produce growth and differentiation of cells and increase in body size, a process that involves synthesis of complex molecules. Examples of anabolic processes include the
growth and mineralization of bone and increases in muscle mass. Endocrinologists
have traditionally classified hormones as anabolic or catabolic, depending on which
part of metabolism they stimulate. The classic anabolic hormones are the anabolic steroids, which stimulate protein synthesis, muscle growth, and insulin. The balance between anabolism and catabolism is also regulated by circadian rhythms, with processes
such as glucose metabolism fluctuating to match an animal's normal periods of activity
throughout the day.
https://en.wikipedia.org/wiki/Anabolism
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Anaerobic
Anaerobic means "living without air", as opposed to aerobic which means "living in the
presence of air".
An anaerobic organism or anaerobe is any organism that does not require oxygen for
growth. It may react negatively or even die if oxygen is present. (In contrast, an aerobic
organism (aerobe) is an organism that can survive and grow in an oxygenated environment.)
An anaerobic organism may be unicellular (e.g. protozoans, bacteria) or multicellular.
For practical purposes, there are three categories of anaerobe: obligate anaerobes,
which are harmed by the presence of oxygen; aerotolerant organisms, which cannot
use oxygen for growth but tolerate its presence; and facultative anaerobes, which can
grow without oxygen but use oxygen if it is present.
Some obligate anaerobes use fermentation, while others use anaerobic respiration.
Aerotolerant organisms are strictly fermentative. In the presence of oxygen, facultative
anaerobes use aerobic respiration. Without oxygen, some of them ferment. Some use
anaerobic respiration.
https://en.wikipedia.org/wiki/Anaerobic
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Anandamide
Anandamide, also known as N-arachidonoylethanolamine or AEA, is a fatty acid neurotransmitter derived from the non-oxidative metabolism of eicosatetraenoic acid (arachidonic acid) an essential -6 polyunsaturated fatty acid. The name is taken from the
Sanskrit word ananda, which means "joy, bliss, delight", and amide. It is synthesized
from N-arachidonoyl phosphatidylethanolamine by multiple pathways. It is degraded
primarily by the fatty acid amide hydrolase (FAAH) enzyme, which converts anandamide into ethanolamine and arachidonic acid. As such, inhibitors of FAAH lead to
elevated anandamide levels and are being pursued for therapeutic use.
Anandamide's effects can occur in either the central or peripheral nervous system.
These distinct effects are mediated primarily by CB1 cannabinoid receptors in the central nervous system, and CB2 cannabinoid receptors in the periphery. The latter are
mainly involved in functions of the immune system. Cannabinoid receptors were originally discovered as being sensitive to 9-tetrahydrocannabinol (9-THC, commonly
called THC), which is the primary psychoactive cannabinoid found in cannabis. The discovery of anandamide came from research into CB1 and CB2, as it was inevitable that a
naturally occurring (endogenous) chemical would be found to affect these receptors.
Anandamide has been shown to impair working memory in rats. Studies are under way
to explore what role anandamide plays in human behavior, such as eating and sleep
patterns, and pain relief.
Anandamide plays a role in the regulation of feeding behavior, and the neural generation of motivation and pleasure. In addition, anandamide injected directly into the forebrain reward-related brain structure nucleus accumbens enhances the pleasurable responses of rats to a rewarding sucrose taste, and enhances food intake as well. Moreover, the acute beneficial effects of exercise (termed as runner's high) seem to be mediated by anandamide in mice. In 1996, researchers discovered anandamide in chocolate. They also detected the presence of two substances that might mimic the effects of
anandamide, N-oleoylethanolamine and N-linoleoylethanolamine.
https://en.wikipedia.org/wiki/Anandamide
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Anaplerotic
Anaplerotic reactions (from the Greek = 'up' and = 'to fill') are c
the citric acid cycle (TCA cycle). In normal function of this cycle for respirat
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Anastrozole
ity of breast cancer can be increased by estrogen, as sex hormones cause hyp
https://en.wikipedia.org/wiki/Anastrozole
Anchored Protein
Lipid-anchored proteins (also known as lipid-linked proteins or anchored proteins) are
proteins located on the surface of the cell membrane that are covalently attached to lipids embedded within the cell membrane. These lipids insert and assume a place in the
bilayer structure of the membrane alongside the similar fatty acid tails. The lipidanchored protein can be located on either side of the cell membrane.Thus, the lipid
serves to anchor the protein to the cell membrane.
The lipid groups plays a role in protein interaction and can contribute to the function
of the protein to which it is attached. Furthermore, the lipid serves as a mediator of
membrane associations or as a determinant for specific protein-protein interactions.
For example, lipid groups can play an important role in increasing molecular hydrophobicity. This allows for the interaction of proteins with cellular membranes and protein
domains.
Overall, there are three main types of lipid-anchored proteins which include prenylated proteins, fatty acylated proteins and glycosylphosphatidylinositol-linked proteins
(GPI). A protein can have multiple lipid groups covalently attached to it, but the site
where the lipid binds to the protein depends both on the lipid group and protein.
https://en.wikipedia.org/wiki/Lipid-anchored_protein
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Androgens
Androgen (from Greek andro meaning male), also called androgenic hormone or testoid, is any natural or synthetic compound, usually a steroid hormone, that stimulates
or controls the development and maintenance of male characteristics in vertebrates by
binding to androgen receptors. This includes the activity of the primary male sex organs and development of male secondary sex characteristics. Androgens were first discovered in 1936. Androgens increase in both boys and girls during puberty. Androgens
are also the original anabolic steroids and the precursor of all estrogens. The primary
and most well-known androgen is testosterone. Dihydrotestosterone (DHT) and androstenedione are less known generally, but are of equal importance in male development. DHT in the embryo life causes differentiation of penis, scrotum and prostate.
Later in life DHT contributes to male balding, prostate growth and sebaceous gland activity. Although androgens are described as male sex hormones, both males and females have them to varying degrees, as is also true of estrogens.
Testosterone is the best known androgen. Besides testosterone, other androgens include:
Dehydroepiandrosterone (DHEA) is a steroid hormone produced in the adrenal cortex from cholesterol. It is the primary precursor of natural estrogens. DHEA is also
called dehydroisoandrosterone or dehydroandrosterone.
Androstenedione (Andro) is an androgenic steroid produced by the testes, adrenal
cortex, and ovaries. While androstenediones are converted metabolically to testosterone and other androgens, they are also the parent structure of estrone. Use of androstenedione as an athletic or bodybuilding supplement has been banned by the International Olympic Committee, as well as other sporting organizations.
Androstenediol is the steroid metabolite thought to act as the main regulator of gonadotropin secretion.
Androsterone is a chemical byproduct created during the breakdown of androgens, or
derived from progesterone, that also exerts minor masculinizing effects, but with oneseventh the intensity of testosterone. It is found in approximately equal amounts in the
plasma and urine of both males and females.
Dihydrotestosterone (DHT) is a metabolite of testosterone, and a more potent androgen than testosterone in that it binds more strongly to androgen receptors. It is produced in the skin and reproductive tissue.
Show below - testosterone
https://en.wikipedia.org/wiki/Androgen
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Androstenedione
stances, and is therefore banned from use by athletes in most major sports.
https://en.wikipedia.org/wiki/1-Androstenedione
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Anemia
Anemia, also spelled anaemia, is usually defined as a decrease in the amount of red
blood cells (RBCs) or hemoglobin in the blood. It can also be defined as a lowered ability of the blood to carry oxygen. When anemia comes on slowly, the symptoms are often vague and may include: feeling tired, weakness, shortness of breath or a poor ability to exercise. Anemia that comes on quickly often has greater symptoms, which may
include: confusion, feeling like one is going to pass out, loss of consciousness, or increased thirst. Anemia must be significant before a person becomes noticeably pale. Additional symptoms may occur depending on the underlying cause.
There are three main types of anemia: that due to blood loss, that due to decreased red
blood cell production, and that due to increased red blood cell breakdown. Causes of
blood loss include trauma and gastrointestinal bleeding, among others. Causes of decreased production include iron deficiency, a lack of vitamin B12, thalassemia, and a
number of neoplasms of the bone marrow. Causes of increased breakdown include a
number of genetic conditions such as sickle cell anemia, infections like malaria, and
certain autoimmune diseases. It can also be classified based on the size of red blood
cells and amount of hemoglobin in each cell. If the cells are small, it is microcytic anemia. If they are large, it is macrocytic anemia while if they are normal sized, it is normocytic anemia. Diagnosis in men is based on a hemoglobin of less than 130 to 140g/L
(13 to 14g/dL), while in women, it must be less than 120 to 130g/L (12 to 13g/dL).
Further testing is then required to determine the cause.
https://en.wikipedia.org/wiki/Anemia
Angiogenic
Angiogenesis is the physiological process through which new blood vessels form from
pre-existing vessels. This is distinct from vasculogenesis, which is the de novo formation of endothelial cells from mesoderm cell precursors. The first vessels in the developing embryo form through vasculogenesis, after which angiogenesis is responsible for
most, if not all, blood vessel growth during development and in disease.
Angiogenesis is a normal and vital process in growth and development, as well as in
wound healing and in the formation of granulation tissue. However, it is also a fundamental step in the transition of tumors from a benign state to a malignant one, leading
to the use of angiogenesis inhibitors in the treatment of cancer.
Tumors induce blood vessel growth (angiogenesis) by secreting various growth factors
(e.g. VEGF). Growth factors such as bFGF and VEGF can induce capillary growth into
the tumor, which some researchers suspect supply required nutrients, allowing for tumor expansion. Unlike normal blood vessels, tumor blood vessels are dilated with an
irregular shape. In 2007, it was discovered that cancerous cells stop producing the
anti-VEGF enzyme PKG. In normal cells (but not in cancerous ones), PKG apparently
limits beta-catenin, which solicits angiogenesis. Other clinicians believe angiogenesis
really serves as a waste pathway, taking away the biological end products secreted by
rapidly dividing cancer cells. In either case, angiogenesis is a necessary and required
step for transition from a small harmless cluster of cells, often said to be about the size
of the metal ball at the end of a ball-point pen, to a large tumor.
Angiogenesis is also required for the spread of a tumor, or metastasis. Single cancer
cells can break away from an established solid tumor, enter the blood vessel, and be
carried to a distant site, where they can implant and begin the growth of a secondary
tumor. Evidence now suggests the blood vessel in a given solid tumor may, in fact, be
mosaic vessels, composed of endothelial cells and tumor cells. This mosaicity allows
for substantial shedding of tumor cells into the vasculature, possibly contributing to
the appearance of circulating tumor cells in the peripheral blood of patients with malignancies. The subsequent growth of such metastases will also require a supply of nutrients and oxygen and a waste disposal pathway.
https://en.wikipedia.org/wiki/Angiogenesis
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Angiostatin
cell surface ATP synthase but also integrins, annexin II, C-met receptor, NG2
been proposed that angiostatin activity is related, among other things, to the
of its mechanical and redox properties.
https://en.wikipedia.org/wiki/Angiostatin
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Ankyrins
binding sites for the beta subunit of spectrin and at least 12 families of integ
brane proteins. This linkage is required to maintain the integrity of the plas
branes and to anchor specific ion channels, ion exchangers and ion transpo
plasma membrane.
dem ankyrin repeats, a central domain that binds to spectrin, a death doma
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Annealing
is often used to describe the binding of a DNA probe, or the binding of a pri
DNA strand during a polymerase chain reaction. The term is also often used
Anomeric
An anomer is a type of stereoisomer and epimer found in carbohydrate chemistry.
While an epimer is a stereoisomer that differs in configuration at any single stereogenic center, an anomer is a cyclic saccharide and an epimer that differs in configuration, specifically at the hemiacetal/acetal carbon, also called the anomeric carbon. The
anomeric carbon is the carbon derived from the carbonyl carbon (the ketone or aldehyde functional group) of the open-chain form of the carbohydrate molecule. Anomerization is the process of conversion of one anomer to the other.
Show below - anomers of glucose
https://en.wikipedia.org/wiki/Anomer
Anomers
An anomer is a type of stereoisomer and epimer found in carbohydrate chemistry.
While an epimer is a stereoisomer that differs in configuration at any single stereo-
genic center, an anomer is a cyclic saccharide and an epimer that differs in configura-
tion, specifically at the hemiacetal/acetal carbon, also called the anomeric carbon. Th
anomeric carbon is the carbon derived from the carbonyl carbon (the ketone or alde-
hyde functional group) of the open-chain form of the carbohydrate molecule. Anomer
zation is the process of conversion of one anomer to the other.
Show below - anomers of glucose
https://en.wikipedia.org/wiki/Anomer
Index
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Antenna Proteins
Little light reaches algae that reside at a depth of one meter or more in seawater, as
light is absorbed by seawater. A phycobilisome is a light-harvesting protein complex
present in cyanobacteria, glaucocystophyta, and red algae and is structured like a real
antenna. The pigments, such as phycocyanobilin and phycoerythrobilin, are the chromophores that bind through a covalent thioether bond to their apoproteins at cysteins
residues. The apoprotein with its chromophore is called phycocyanin, phycoerythrin,
and allophycocyanin, respectively. They often occur as hexamers of and subunits
(33)2. They enhance the amount and spectral window of light absorption and fill the
"green gap", which occur in higher plants.
The antenna pigments are predominantly chlorophyll b, xanthophylls, and carotenoids. Chlorophyll a is known as the core pigment. Their absorption spectra are nonoverlapping in order to broaden the range of light that can be absorbed in photosynthesis. The carotenoids have another role as an antioxidant to prevent photo-oxidative
damage of chlorophyll molecules. Each antenna complex has between 250 and 400 pigment molecules and the energy they absorb is shuttled by resonance energy transfer to
a specialized chlorophyll-protein complex known as the reaction center of each photosystem. The reaction center initiates a complex series of chemical reactions that capture energy in the form of chemical bonds.
https://en.wikipedia.org/wiki/Light-harvesting_complex
Anthranilate
Anthranilic acid (or o-amino-benzoic acid) is an aromatic acid with the formu
acid is a white solid when pure, although commercial samples may appear yel
sometimes referred to as vitamin L1 and has a sweetish taste. The anion
https://en.wikipedia.org/wiki/Anthranilic_acid
Index
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Anti-clotting
Anticoagulants are a class of drugs that work to prevent blood coagulation (clotting).
Such substances occur naturally in leeches and blood-sucking insects. A group of pharmaceuticals called anticoagulants can be used as an injection as a medication for
thrombotic disorders. Oral anticoagulants are also available. Some anticoagulants are
used in medical equipment, such as test tubes, blood transfusion bags, and renal dialysis equipment.
Anticoagulants are closely related to antiplatelet drugs and thrombolytic drugs by manipulating the various pathways of blood coagulation. Specifically, anticoagulants manipulate the coagulation cascade that builds upon the initial platelet thrombus.
A number of anticoagulants are available. The traditional ones (warfarin, other coumarins and heparins) are in widespread use. Since the 2000s a number of new agents
have been introduced that are collectively referred to as the novel oral anticoagulants
(NOACs) or directly acting oral anticoagulants (DOACs).
These agents include inhibitors of factor IIa (dabigatran) and factor Xa (rivaroxaban,
apixaban and edoxaban) and they have been shown to be as good or possibly better
than the coumarins with less serious side effects. The newer anticoagulants (NOACs/
DOACs), are more expensive than the traditional ones and should be used with care in
patients with kidney problems. Additionally, there is no antidote for the factor Xa inhibitors, so it is difficult to stop their effects in the body in cases of emergency (accidents, urgent surgery).
Anti-parallel
Index
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Antibiotic Resistance
Antimicrobial resistance (AMR) is when a microbe evolves to become more or fully resistant to antimicrobials which previously could treat it. This broader term also covers
antibiotic resistance, which applies to bacteria and antibiotics. Resistance arises
through one of three ways: natural resistance in certain types of bacteria, genetic mutation, or by one species acquiring resistance from another. Resistance can appear spontaneously due to random mutations, or more commonly following gradual buildup
over time, and because of misuse of antibiotics or antimicrobials. Resistant microbes
are increasingly difficult to treat, requiring alternative medications or higher doseswhich may be more costly or more toxic. Microbes resistant to multiple antimicrobials are called multidrug resistant (MDR) - or sometimes superbugs. Antimicrobial resistance is on the rise with millions of deaths every year. A few infections are now completely untreatable due to resistance. All classes of microbes develop resistance (fungi,
antifungal resistance; viruses, antiviral resistance; protozoa, antiprotozoal resistance;
bacteria, antibiotic resistance).
Rising drug resistance can be attributed to three causes use of antibiotics: in the human population, in the animal population, and spread of resistant strains between human or non-human sources. Antibiotics increase selective pressure in bacterial populations, causing vulnerable bacteria to diethis increases the percentage of resistant bacteria which continue growing. With resistance to antibiotics becoming more common
there is greater need for alternative treatments. Calls for new antibiotic therapies have
been issued, but new drug-development is becoming rarer. There are multiple national
and international monitoring programs for drug-resistant threats. Examples of drugresistant bacteria included in this program are: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant S. aureus (VRSA), extended spectrum betalactamase (ESBL), vancomycin-resistant Enterococcus (VRE), multidrug-resistant A.
baumannii (MRAB).
https://en.wikipedia.org/wiki/Antimicrobial_resistance
Antibiotics
Antibiotics, also called antibacterials, are a type of antimicrobial drug used in the treatment and prevention of bacterial infection. They may either kill or inhibit the growth
of bacteria. A limited number of antibiotics also possess antiprotozoal activity. Antibiotics are not effective against viruses such as the common cold or influenza, and may be
harmful when taken inappropriately.
Antibacterial antibiotics are commonly classified based on their mechanism of action,
chemical structure, or spectrum of activity. Most target bacterial functions or growth
processes. Those that target the bacterial cell wall (penicillins and cephalosporins) or
the cell membrane (polymyxins), or interfere with essential bacterial enzymes (rifamycins, lipiarmycins, quinolones, and sulfonamides) have bactericidal activities. Those
that target protein synthesis (macrolides, lincosamides and tetracyclines) are usually
bacteriostatic (with the exception of bactericidal aminoglycosides). Further categorization is based on their target specificity. "Narrow-spectrum" antibacterial antibiotics target specific types of bacteria, such as Gram-negative or Gram-positive bacteria,
whereas broad-spectrum antibiotics affect a wide range of bacteria. Following a 40year hiatus in discovering new classes of antibacterial compounds, four new classes of
antibacterial antibiotics have been brought into clinical use in the late 2000s and early
2010s: cyclic lipopeptides (such as daptomycin), glycylcyclines (such as tigecycline),
oxazolidinones (such as linezolid), and lipiarmycins (such as fidaxomicin).
Antibiotics effectiveness and easy access has led to overuse, especially in livestock raising, prompting bacteria to develop resistance. This has led to widespread problems
with antimicrobial and antibiotic resistance, so much as to prompt the World Health
Organization to classify antimicrobial resistance as a "serious threat [that] is no longer
a prediction for the future, it is happening right now in every region of the world and
has the potential to affect anyone, of any age, in any country".
https://en.wikipedia.org/wiki/Antibiotics
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Antibodies
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein
produced mainly by plasma cells that is used by the immune system to identify and
neutralize pathogens such as bacteria and viruses. The antibody recognizes a unique
molecule of the harmful agent, called an antigen, via the variable region. Each tip of
the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one
particular epitope (similarly analogous to a key) on an antigen, allowing these two
structures to bind together with precision. Using this binding mechanism, an antibody
can tag a microbe or an infected cell for attack by other parts of the immune system, or
can neutralize its target directly (for example, by blocking a part of a microbe that is essential for its invasion and survival). Depending on the antigen, the binding may impede the biological process causing the disease or may recruit macrophages to destroy
the foreign substance. The ability of an antibody to communicate with the other components of the immune system is mediated via its Fc region (located at the base of the
"Y"), which contains a conserved glycosylation site involved in these interactions. The
production of antibodies is the main function of the humoral immune system.
Antibodies are secreted by B cells of the adaptive immune system, mostly by differentiated B cells called plasma cells. Antibodies can occur in two physical forms, a soluble
form that is secreted from the cell to be free in the blood plasma, and a membranebound form that is attached to the surface of a B cell and is referred to as the B-cell receptor (BCR). The BCR is found only on the surface of B cells and facilitates the activation of these cells and their subsequent differentiation into either antibody factories
called plasma cells or memory B cells that will survive in the body and remember that
same antigen so the B cells can respond faster upon future exposure. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the
B cell and, therefore, antibody generation following antigen binding. Soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue
to survey for invading microorganisms.
https://en.wikipedia.org/wiki/Antibody
Index
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Antibody
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein
produced mainly by plasma cells that is used by the immune system to identify and
neutralize pathogens such as bacteria and viruses. The antibody recognizes a unique
molecule of the harmful agent, called an antigen, via the variable region. Each tip of
the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one
particular epitope (similarly analogous to a key) on an antigen, allowing these two
structures to bind together with precision. Using this binding mechanism, an antibody
can tag a microbe or an infected cell for attack by other parts of the immune system, or
can neutralize its target directly (for example, by blocking a part of a microbe that is essential for its invasion and survival). Depending on the antigen, the binding may impede the biological process causing the disease or may recruit macrophages to destroy
the foreign substance. The ability of an antibody to communicate with the other components of the immune system is mediated via its Fc region (located at the base of the
"Y"), which contains a conserved glycosylation site involved in these interactions. The
production of antibodies is the main function of the humoral immune system.
Antibodies are secreted by B cells of the adaptive immune system, mostly by differentiated B cells called plasma cells. Antibodies can occur in two physical forms, a soluble
form that is secreted from the cell to be free in the blood plasma, and a membranebound form that is attached to the surface of a B cell and is referred to as the B-cell receptor (BCR). The BCR is found only on the surface of B cells and facilitates the activation of these cells and their subsequent differentiation into either antibody factories
called plasma cells or memory B cells that will survive in the body and remember that
same antigen so the B cells can respond faster upon future exposure. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the
B cell and, therefore, antibody generation following antigen binding. Soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue
to survey for invading microorganisms.
https://en.wikipedia.org/wiki/Antibody
Index
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Anticoagulation
Anticoagulants are a class of drugs that work to prevent blood coagulation (clotting).
Such substances occur naturally in leeches and blood-sucking insects. A group of pharmaceuticals called anticoagulants can be used as an injection as a medication for
thrombotic disorders. Oral anticoagulants are also available. Some anticoagulants are
used in medical equipment, such as test tubes, blood transfusion bags, and renal dialysis equipment.
Anticoagulants are closely related to antiplatelet drugs and thrombolytic drugs by manipulating the various pathways of blood coagulation. Specifically, anticoagulants manipulate the coagulation cascade that builds upon the initial platelet thrombus.
A number of anticoagulants are available. The traditional ones (warfarin, other coumarins and heparins) are in widespread use. Since the 2000s a number of new agents
have been introduced that are collectively referred to as the novel oral anticoagulants
(NOACs) or directly acting oral anticoagulants (DOACs).
These agents include inhibitors of factor IIa (dabigatran) and factor Xa (rivaroxaban,
apixaban and edoxaban) and they have been shown to be as good or possibly better
than the coumarins with less serious side effects. The newer anticoagulants (NOACs/
DOACs), are more expensive than the traditional ones and should be used with care in
patients with kidney problems. Additionally, there is no antidote for the factor Xa inhibitors, so it is difficult to stop their effects in the body in cases of emergency (accidents, urgent surgery).
Shown below is warfarin (coumadin)
https://en.wikipedia.org/wiki/Anticoagulant
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Anticodon
An anticodon is a unit made up of three nucleotides that correspond to the three bases
of the codon on the mRNA. Each tRNA contains a specific anticodon triplet sequence
that can base-pair to one or more codons for an amino acid. Some anticodons can pair
with more than one codon due to a phenomenon known as wobble base pairing. Frequently, the first nucleotide of the anticodon is one not found on mRNA: inosine,
which can hydrogen bond to more than one base in the corresponding codon position.
In the genetic code, it is common for a single amino acid to be specified by all four
third-position possibilities, or at least by both pyrimidines and purines. For example,
the amino acid glycine is coded for by the codon sequences GGU, GGC, GGA, and
GGG. Other modified nucleotides may also appear at the first anticodon position sometimes known as the "wobble position" - resulting in subtle changes to the genetic
code, as for example in mitochondria.
To provide a one-to-one correspondence between tRNA molecules and codons that
specify amino acids, 61 types of tRNA molecules would be required per cell. However,
many cells contain fewer than 61 types of tRNAs because the wobble base is capable of
binding to several, though not necessarily all, of the codons that specify a particular
amino acid. A minimum of 31 tRNA are required to translate, unambiguously, all 61
sense codons of the standard genetic code.
Shown below - tRNA with anticodon. The antocodon is in red in the bottom loop.
https://en.wikipedia.org/wiki/Transfer_RNA#Anticodon
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Antimycin A
Antimycins are a group of secondary metabolites produced by Streptomyces bacteria.
Antimycin A binds to the Qi site of cytochrome c reductase in Complex III, thereby inhibiting the oxidation of ubiquinone in the Qi site thereby disrupting the Q-cycle of the
electron transport system.
Cytochrome c reductase is a central enzyme in the electron transport chain of oxidative
phosphorylation. The inhibition of this reaction disrupts the formation of the proton
gradient across the inner membrane. The production of ATP is subsequently inhibited,
as protons are unable to flow through the ATP synthase complex in the absence of a
proton gradient. This inhibition also results in the formation of quantities of the toxic
free radical superoxide.
Fungus-growing attine ants have been shown to use antimycins - produced by symbiotic Streptomyces bacteria - in their fungiculture, to inhibit non-cultivar (i.e. pathogenic) fungi.
https://en.wikipedia.org/wiki/Antimycin_A
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Antioxidants
An antioxidant is a molecule that inhibits the oxidation of other molecules. Oxidation
is a chemical reaction that can produce free radicals, leading to chain reactions that
may damage cells. Antioxidants such as thiols or ascorbic acid (vitamin C) terminate
these chain reactions.
To balance the oxidative state, plants and animals maintain complex systems of overlapping antioxidants, such as glutathione and enzymes (e.g., catalase and superoxide
dismutase) produced internally or the dietary antioxidants, vitamin A, vitamin C and
vitamin E.
Although certain levels of antioxidant vitamins in the diet are required for good health,
there is considerable doubt as to whether antioxidant-rich foods or supplements have
anti-disease activity. If they are actually beneficial, it is unknown which antioxidant(s)
are needed from the diet and in what amounts beyond typical dietary intake.
The reactive oxygen species produced in cells include hydrogen peroxide (H2O2), hypochlorous acid (HClO), and free radicals such as the hydroxyl radical (OH) and the superoxide anion (O2). The hydroxyl radical is particularly unstable and will react rapidly and non-specifically with most biological molecules. This species is produced from
hydrogen peroxide in metal-catalyzed redox reactions such as the Fenton reaction.
These oxidants can damage cells by starting chemical chain reactions such as lipid peroxidation, or by oxidizing DNA or proteins. Damage to DNA can cause mutations and
possibly cancer, if not reversed by DNA repair mechanisms, while damage to proteins
causes enzyme inhibition, denaturation and protein degradation.
The use of oxygen as part of the process for generating metabolic energy produces reactive oxygen species. In this process, the superoxide anion is produced as a by-product
of several steps in the electron transport chain. Particularly important is the reduction
of coenzyme Q in complex III, since a highly reactive free radical is formed as an intermediate (Q). This unstable intermediate can lead to electron "leakage", when electrons jump directly to oxygen and form the superoxide anion, instead of moving
through the normal series of well-controlled reactions of the electron transport chain.
Peroxide is also produced from the oxidation of reduced flavoproteins, such as complex I. However, although these enzymes can produce oxidants, the relative importance of the electron transfer chain to other processes that generate peroxide is unclear. In plants, algae, and cyanobacteria, reactive oxygen species are also produced
during photosynthesis, particularly under conditions of high light intensity. This effect
is partly offset by the involvement of carotenoids in photoinhibition, and in algae and
cyanobacteria, by large amount of iodide and selenium, which involves these antioxidants reacting with over-reduced forms of the photosynthetic reaction centers to prevent the production of reactive oxygen species.
https://en.wikipedia.org/wiki/Antioxidant
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Antiparallel
In biochemistry, two biopolymers are antiparallel if they run parallel to each oth
Nucleic acid molecules have a phosphoryl (5') end and a hydroxyl (3') end. This
tion follows from organic chemistry nomenclature, and can be used to define th
ment of enzymes such as DNA polymerases relative to the DNA strand in a non
arbitrary manner. In DNA, the 5' carbon is located at the top of the leading stra
the 3' carbon is located at the lower section of the lagging strand. The nucleic ac
quences are complementary and parallel, but they go in opposite directions, hen
way. During DNA replication the leading strand is replicated continuously wher
lagging strand is replicated in segments known as Okazaki fragments.
https://en.wikipedia.org/wiki/Antiparallel_(biochemistry)
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Antiport
An antiporter/antiport (also called exchanger or counter-transporter) is a cotransporter and integral membrane protein involved in transport of two or more different
molecules or ions (i.e., solutes) across a phospholipid membrane such as the plasma
membrane in opposite directions.
https://en.wikipedia.org/wiki/Antiporter
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Antisense
In molecular biology and genetics, sense is a concept used to compare the polarity of
nucleic acid molecules, such as DNA or RNA, to other nucleic acid molecules. Depending on the context within molecular biology, sense may have slightly different meanings.
Molecular biologists call a single strand of DNA sense (or positive (+)) if an RNA version of the same sequence is translated or translatable into protein. Its complementary
strand is called antisense (or negative (-) sense). Sometimes the phrase coding strand
is encountered. However, protein coding and non-coding RNAs can be transcribed
similarly from both strands, in some cases being transcribed in both directions from a
common promoter region, or being transcribed from within introns, on both strands.
https://commons.wikimedia.org/wiki/File:Antisense_DNA_oligonucleotide.png
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Antithrombin
of 432 amino acids. It contains three disulfide bonds and a total of four pos
Index
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AP Endonuclease
Apurinic/apyrimidinic (AP) endonuclease (BRENDA = 4.2.99.18) is an enzyme that is
involved in the DNA base excision repair pathway (BER). Its main role in the repair of
damaged or mismatched nucleotides in DNA is to create a nick in the phosphodiester
backbone of the AP site created when DNA glycosylase removes the damaged base.
There are four types of AP endonucleases that have been classified according to their
sites of incision. Class I and class II AP endonucleases incise DNA at the phosphate
groups 3 and 5 to the baseless site leaving 3-OH and 5-phosphate termini. Class
III and class IV AP endonucleases also cleave DNA at the phosphate groups 3 and
5to the baseless site, but they generate a 3-phosphate and a 5-OH.
Humans have two AP endonucleases, APE1 and APE2. APE1 exhibits robust APendonuclease activity, which accounts for >95% of the total cellular activity, and APE1
is considered to be the major AP endonuclease in human cells. Human AP Endonuclease (APE1), like most AP endonucleases, is of class II and requires an Mg2+ in its active site in order to carry out its role in base excision repair. The yeast homolog of this
enzyme is APN1.
Human AP Endonuclease 2 (APE2), like most AP endonucleases, is also of class II. The
exonuclease activity of APE2 is strongly dependent upon metal ions. However, APE2
was more than 5-fold more active in the presence of manganese than of magnesium
ions. The conserved domains involved in catalytic activity are located at the N-terminal
part of both APE1 and APE2. In addition, the APE2 protein has a C-terminal extension,
which is not present in APE1, but can also be found in homologs of human APE2 such
as APN2 proteins of S.cerevisiae and S.pombe.
AP Site
An AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in
DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine
base, either spontaneously or due to DNA damage. It has been estimated that under
physiological conditions 10,000 apurinic sites and 500 apyrimidinic may be generated
in a cell daily.
AP sites can be formed by spontaneous depurination, but also occur as intermediates
in base excision repair. In this process, a DNA glycosylase recognizes a damaged base
and cleaves the N-glycosidic bond to release the base, leaving an AP site. A variety of
glycosylases that recognize different types of damage exist, including oxidized or methylated bases, or uracil in RNA. The AP site can then be cleaved by an AP endonuclease,
leaving 3' hydroxyl and 5' deoxyribosephosphate termini. In alternative fashion, bifunctional glycosylase-lyases can cleave the AP site, leaving a 5' phosphate adjacent to a 3'
,-unsaturated aldehyde. Both mechanisms form a single-strand break, which is then
repaired by either short-patch or long-patch base excision repair.
If left unrepaired, AP sites can lead to mutation during semiconservative replication.
They can cause replication fork stalling and are bypassed by translesion synthesis. In
E. coli, adenine is preferentially inserted across from AP sites, known as the "A rule".
The situation is more complex in higher eukaryotes, with different nucleotides showing
a preference depending on the organism and experimental conditions.
https://en.wikipedia.org/wiki/AP_site
Index
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Apelin
gene. Apelin is the endogenous ligand for the G-protein-coupled APJ recept
such as the heart, lung, kidney, liver, adipose tissue, gastrointestinal tract, b
nal glands, endothelium, and human plasma.
Index
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ApoA-I
Apolipoprotein A1 (ApoA-I) is a protein that in humans is encoded by the APOA1 gene.
Apolipoprotein A1 is the major protein component of high density lipoprotein (HDL)
in plasma. Chylomicrons secreted from the intestinal enterocyte also contain apo A1,
but it is quickly transferred to HDL in the bloodstream. The protein promotes fat ef-
flux, including cholesterol, from tissues to the liver for excretion. It is a cofactor for lecithin cholesterolacyltransferase (LCAT) which is responsible for the formation of most
plasma cholesteryl esters. Apo A1 was also isolated as a prostacyclin (PGI2) stabilizing
factor, and thus may have an anticlotting effect. Defects in the gene encoding it are associated with HDL deficiencies, including Tangier disease, and with systemic nonneuropathic amyloidosis. ApoA1 is often used as a biomarker for prediction of cardiovascular diseases and the ratio apoB- 100/apoA1 has been reported as a stronger predictor for the risk of myocardial infarction than any other lipid measurement.
As a major component of the high-density lipoprotein complex (protective "fat removal" particles), apo A1 helps to clear fats, including cholesterol, from white blood
cells within artery walls, making the WBCs less likely to become fat overloaded, transform into foam cells, die and contribute to progressive atheroma.
https://en.wikipedia.org/wiki/Apolipoprotein_A1
ApoB-48
Apolipoprotein B is the primary apolipoprotein of chylomicrons, VLDL, IDL, and LDL
particles (LDL - known commonly by the misnomer "bad cholesterol" when in reference to both heart disease and vascular disease in general), which is responsible for carrying fat molecules (lipids), including cholesterol, around the body (within the water
outside cells) to all cells within all tissues. While all the functional roles of ApoB within
the LDL (and all larger) particles remains somewhat unclear, it is the primary organizing protein (of the entire complex shell enclosing/carrying fat molecules within) component of the particles and is absolutely required for the formation of these particles.
What is also clear is that the ApoB on the LDL particle acts as a ligand for LDL receptors in various cells throughout the body (i.e., less formally, ApoB indicates fat carrying
particles are ready to enter any cells with ApoB receptors and deliver fats carried
within into the cells).
The protein occurs in the plasma in 2 main isoforms, ApoB-48 and ApoB-100. The first
is synthesized exclusively by the small intestine, the second by the liver. ApoB-100 is
the largest of the apoB group of proteins, consisting of 4563 amino acids. Both isoforms are coded by APOB and by a single mRNA transcript larger than 16 kb. ApoB-48
is generated when a stop codon (UAA) at residue 2153 is created by RNA editing. There
appears to be a trans-acting tissue-specific splicing gene that determines which isoform is ultimately produced. Alternatively, there is some evidence that a cis-acting element several thousand bp upstream determines which isoform is produced.
As a result of the RNA editing, ApoB-48 and ApoB-100 share a common N-terminal sequence, but ApoB-48 lacks ApoB-100's C-terminal LDL receptor binding region. In
fact, ApoB-48 is so called because it constitutes 48% of the sequence for ApoB-100.
ApoB-48 is a unique protein to chylomicrons from the small intestine. After most of
the lipids in the chylomicron have been absorbed, ApoB-48 returns to the liver as part
of the chylomicron remnant, where it is endocytosed and degraded.
Through mechanisms only partially understood, high levels of ApoB, especially associated with the higher LDL particle concentrations, are the primary drivers of plaque formation that causes vascular disease (atherosclerosis), commonly first becoming obviously symptomatic as heart disease, stroke & many other body wide complications after decades of progression. There is considerable evidence that concentrations of ApoB
and especially the NMR assay (specific for LDL-particle concentrations) are superior
indicators of vascular/heart disease driving physiology than either total cholesterol or
LDL-cholesterol (as long promoted by the NIH starting in the early 1970s). However,
primarily for historic cost/complexity reasons, cholesterol, and estimated LDLcholesterol by calculation, remains the most commonly promoted lipid test for the risk
factor of atherosclerosis.
https://en.wikipedia.org/wiki/Apolipoprotein_B
Index
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ApoB-100
Apolipoprotein B is the primary apolipoprotein of chylomicrons, VLDL, IDL, and LDL
particles (LDL - known commonly by the misnomer "bad cholesterol" when in reference to both heart disease and vascular disease in general), which is responsible for carrying fat molecules (lipids), including cholesterol, around the body (within the water
outside cells) to all cells within all tissues. While all the functional roles of ApoB within
the LDL (and all larger) particles remains somewhat unclear, it is the primary organizing protein (of the entire complex shell enclosing/carrying fat molecules within) component of the particles and is absolutely required for the formation of these particles.
What is also clear is that the ApoB on the LDL particle acts as a ligand for LDL receptors in various cells throughout the body (i.e., less formally, ApoB indicates fat carrying
particles are ready to enter any cells with ApoB receptors and deliver fats carried
within into the cells).
The protein occurs in the plasma in 2 main isoforms, ApoB-48 and ApoB-100. The first
is synthesized exclusively by the small intestine, the second by the liver. ApoB-100 is
the largest of the apoB group of proteins, consisting of 4563 amino acids. Both isoforms are coded by APOB and by a single mRNA transcript larger than 16 kb. ApoB-48
is generated when a stop codon (UAA) at residue 2153 is created by RNA editing. There
appears to be a trans-acting tissue-specific splicing gene that determines which isoform is ultimately produced. Alternatively, there is some evidence that a cis-acting element several thousand bp upstream determines which isoform is produced.
As a result of the RNA editing, ApoB-48 and ApoB-100 share a common N-terminal sequence, but ApoB-48 lacks ApoB-100's C-terminal LDL receptor binding region. In
fact, ApoB-48 is so called because it constitutes 48% of the sequence for ApoB-100.
ApoB-48 is a unique protein to chylomicrons from the small intestine. After most of
the lipids in the chylomicron have been absorbed, ApoB-48 returns to the liver as part
of the chylomicron remnant, where it is endocytosed and degraded.
Through mechanisms only partially understood, high levels of ApoB, especially associated with the higher LDL particle concentrations, are the primary drivers of plaque formation that causes vascular disease (atherosclerosis), commonly first becoming obviously symptomatic as heart disease, stroke & many other body wide complications after decades of progression. There is considerable evidence that concentrations of ApoB
and especially the NMR assay (specific for LDL-particle concentrations) are superior
indicators of vascular/heart disease driving physiology than either total cholesterol or
LDL-cholesterol (as long promoted by the NIH starting in the early 1970s). However,
primarily for historic cost/complexity reasons, cholesterol, and estimated LDLcholesterol by calculation, remains the most commonly promoted lipid test for the risk
factor of atherosclerosis.
https://en.wikipedia.org/wiki/Apolipoprotein_B
Index
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ApoC-I
The protein encoded by this gene is a member of the apolipoprotein C family. This
gene is expressed primarily in the liver, and it is activated when monocytes differentiate into macrophages. A pseudogene of this gene is located 4 kb downstream in the
same orientation, on the same chromosome. This gene is mapped to chromosome 19,
where it resides within an apolipoprotein gene cluster. Alternatively spliced transcript
variants have been found for this gene, but the biological validity of some variants has
not been determined.
Apolipoprotein C1 has a length of 57 amino acids normally found in plasma and responsible for the activation of esterified lecithin cholesterol with an important role in the exchange of esterified cholesterol between lipoproteins and in removal of cholesterol
from tissues. Its main function is inhibition of CETP, probably by altering the electric
charge of HDL molecules.
During fasting (like other apolipoprotein C), it is found primarily within HDL, while after a meal it is found on the surface of other lipoproteins. When proteins rich in triglycerides like chylomicrons and VLDL are broken down, this apoprotein is transferred
again to HDL. It is one of the most positively charged proteins in the human body.
https://en.wikipedia.org/wiki/Apolipoprotein_C1
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ApoC-II
low density lipoproteins and chylomicrons. This protein activates the enzym
ids for cells. Mutations in this gene cause hyperlipoproteinemia type IB, cha
sclerosis. Lab tests will show elevated blood levels of triglycerides, cholester
lomicrons.
https://en.wikipedia.org/wiki/Apolipoprotein_C2
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ApoC-III
linked in both rat and human genomes. The A-I and A-IV genes are transcr
the same strand, while the A-1 and C-III genes are convergently transcribed
crease in apoC-III levels induces the development of hypertriglyceridemia.
namely Ala23Thr and Lys58Glu have been shown to abolish the intracellula
and secretion of triglyceride-rich VLDL particles from hepatic cells.
ApoE
Apolipoprotein E (APOE) is a class of apolipoprotein found in the chylomicron and
Intermediate-density lipoprotein (IDLs) that is essential for the normal catabolism of
triglyceride-rich lipoprotein constituents.
APOE transports lipoproteins, fat-soluble vitamins, and cholesterol into the lymph system and then into the blood. It is synthesized principally in the liver, but has also been
found in other tissues such as the brain, kidneys, and spleen. In the nervous system,
non-neuronal cell types, most notably astroglia and microglia, are the primary producers of APOE, while neurons preferentially express the receptors for APOE. There are
seven currently identified mammalian receptors for APOE which belong to the evolutionarily conserved LDLR family.
APOE was initially recognized for its importance in lipoprotein metabolism and cardiovascular disease. Defects in APOE result in familial dysbetalipoproteinemia aka type
III hyperlipoproteinemia (HLP III), in which increased plasma cholesterol and triglycerides are the consequence of impaired clearance of chylomicron, VLDL and LDL remnants. More recently, it has been studied for its role in several biological processes not
directly related to lipoprotein transport, including Alzheimer's disease (AD), immunoregulation, and cognition. Though the exact mechanisms remain to be elucidated,
isoform 4 of APOE, encoded by an APOE allele, has been associated with increased calcium ion levels and apoptosis following mechanical injury.
In the field of immune regulation, a growing number of studies point to APOE's interaction with many immunological processes, including suppressing T cell proliferation,
macrophage functioning regulation, lipid antigen presentation facilitation (by CD1) to
natural killer T cell as well as modulation of inflammation and oxidation. APOE is produced by macrophages and APOE secretion has been shown to be restricted to classical
monocytes in PBMC, and the secretion of APOE by monocytes is down regulated by inflammatory cytokines and upregulated by TGF-.[
Apoenzymes
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Apolipoproteins
Apolipoproteins are proteins that bind lipids (oil-soluble substances such as fat and
cholesterol) to form lipoproteins. They transport the lipids through the lymphatic and
circulatory systems.
The lipid components of lipoproteins are insoluble in water. However, because of their
detergent-like (amphipathic) properties, apolipoproteins and other amphipathic molecules (such as phospholipids) can surround the lipids, creating the lipoprotein particle
that is itself water-soluble, and can thus be carried through water-based circulation
(i.e., blood, lymph).
Apolipoproteins also serve as enzyme cofactors, receptor ligands, and lipid transfer carriers that regulate the metabolism of lipoproteins and their uptake in tissues. In lipid
transport, apolipoproteins function as structural components of lipoprotein particles,
cofactors for enzymes and ligands for cell-surface receptors. In particular, apoA1 is the
major protein component of high-density lipoproteins. ApoA4 is thought to act primarily in intestinal lipid absorption. Further, apoE is a blood plasma protein that mediates
the transport and uptake of cholesterol and lipid by way of its high affinity interaction
with different cellular receptors, including the low-density lipoprotein (LDL) receptor.
Recent findings with apoA-I and apoE suggest that the tertiary structures of these two
members of the human exchangeable apolipoprotein gene family are related. The
three-dimensional structure of the LDL receptor-binding domain of apoE indicates
that the protein forms an unusually elongated four-helix bundle that may be stabilized
by a tightly packed hydrophobic core that includes leucine zipper-type interactions and
by numerous salt bridges on the mostly charged surface. Basic amino acids important
for LDL receptor binding are clustered into a surface patch on one long helix.
Apolipoproteins are
enzyme coenzymes (C-II for lipoprotein lipase and A-I for lecithin-cholesterol acyltransferase)
lipid transport proteins
ligands for interaction with lipoprotein receptors in tissues ( apoB-100 and apoE for
LDL-receptors, apoA-I for HDL receptors)
https://en.wikipedia.org/wiki/Apolipoprotein
Apoptosis
Apoptosis (from Ancient Greek "falling off") is a process of programmed
cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal DNA fragmentation, and global mRNA decay. Between 50 and 70 billion cells die each day due to
apoptosis in the average human adult. For an average child between the ages of 8 and
14, approximately 20 billion to 30 billion cells die a day.
The initiation of apoptosis is tightly regulated by activation mechanisms, because once
apoptosis has begun, it inevitably leads to the death of the cell. The two bestunderstood activation mechanisms are of are the intrinsic pathway (also called the mitochondrial pathway) and the extrinsic pathway. The intrinsic pathway is activated by
intracellular signals generated when cells are stressed and depends on the release of
proteins from the intermembrane space of mitochondria. The extrinsic pathway is activated by extracellular ligands binding to cell-surface death receptors, which leads to
the formation of the death-inducing signaling complex (DISC).
A cell initiates intracellular apoptotic signaling in response to a stress, which may
bring about cell suicide. The binding of nuclear receptors by glucocorticoids, heat, radiation, nutrient deprivation, viral infection, hypoxia and increased intracellular calcium concentration, for example, by damage to the membrane, can all trigger the release of intracellular apoptotic signals by a damaged cell. A number of cellular components, such as poly ADP ribose polymerase, may also help regulate apoptosis.
Before the actual process of cell death is precipitated by enzymes, apoptotic signals
must cause regulatory proteins to initiate the apoptosis pathway. This step allows
those signals to cause cell death, or the process to be stopped, should the cell no longer
need to die. Several proteins are involved, but two main methods of regulation have
been identified: the targeting of mitochondria functionality, or directly transducing the
signal via adaptor proteins to the apoptotic mechanisms.
https://en.wikipedia.org/wiki/Apoptosis
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Apoptosome
The apoptosome is a large quaternary protein structure formed in the process of apoptosis. Its formation is triggered by the release of cytochrome c from the mitochondria
in response to an internal (intrinsic) or external (extrinsic) cell death stimulus. Stimuli
can vary from DNA damage and viral infection to developmental cues such as those
leading to the degradation of a tadpole's tail in development.
In mammalian cells, once cytochrome c is released, it binds to the cytosolic protein
Apaf-1 to facilitate the formation of apoptosome. An early biochemical study suggests a
two-to-one ratio of cytochrome c to apaf-1 for apoptosome formation. However, recent
structural studies suggest the cytochrome c to apaf-1 ratio is one-to-one. It has also
been shown that the nucleotide dATP as third component binds to apaf-1, however its
exact role is still debated. The mammalian apoptosome had never been crystallized,
but a human APAF-1/cytochrome-c apoptosome has been imaged at lower (2 nm) resolution by cryogenic transmission electron microscopy 10 years ago, revealing a wheellike particle with 7-fold symmetry.
Recently, a medium resolution (9.5 ngstrm) structure of human apoptosome was
also solved by cryo-electron microscopy, which allows unambiguous inference for positions of all the APAF-1 domains (CARD, NBARC and WD40) and cytochrome c. There
is also now a crystal structure of the monomeric, inactive Apaf-1 subunit (PDB 3SFZ).
Once formed, the apoptosome can then recruit and activate the inactive pro-caspase-9.
Once activated, this initiator caspase can then activate effector caspases and trigger a
cascade of events leading to apoptosis.
https://en.wikipedia.org/wiki/Apoptosome
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Apoptotic
Apoptosis (from Ancient Greek "falling off") is a process of programmed
cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal DNA fragmentation, and global mRNA decay. Between 50 and 70 billion cells die each day due to
apoptosis in the average human adult. For an average child between the ages of 8 and
14, approximately 20 billion to 30 billion cells die a day.
The initiation of apoptosis is tightly regulated by activation mechanisms, because once
apoptosis has begun, it inevitably leads to the death of the cell. The two bestunderstood activation mechanisms are of are the intrinsic pathway (also called the mitochondrial pathway) and the extrinsic pathway. The intrinsic pathway is activated by
intracellular signals generated when cells are stressed and depends on the release of
proteins from the intermembrane space of mitochondria. The extrinsic pathway is activated by extracellular ligands binding to cell-surface death receptors, which leads to
the formation of the death-inducing signaling complex (DISC).
A cell initiates intracellular apoptotic signaling in response to a stress, which may
bring about cell suicide. The binding of nuclear receptors by glucocorticoids, heat, radiation, nutrient deprivation, viral infection, hypoxia and increased intracellular calcium concentration, for example, by damage to the membrane, can all trigger the release of intracellular apoptotic signals by a damaged cell. A number of cellular components, such as poly ADP ribose polymerase, may also help regulate apoptosis.
Before the actual process of cell death is precipitated by enzymes, apoptotic signals
must cause regulatory proteins to initiate the apoptosis pathway. This step allows
those signals to cause cell death, or the process to be stopped, should the cell no longer
need to die. Several proteins are involved, but two main methods of regulation have
been identified: the targeting of mitochondria functionality, or directly transducing the
signal via adaptor proteins to the apoptotic mechanisms.
https://en.wikipedia.org/wiki/Apoptosis
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Aptamer
Aptamers (from the Latin aptus - fit, and Greek meros - part) are oligonucleotide or
peptide molecules that bind to a specific target molecule. Aptamers are usually created
by selecting them from a large random sequence pool, but natural aptamers also exist
in riboswitches. Aptamers can be used for both basic research and clinical purposes as
macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave in the
presence of their target molecule. These compound molecules have additional research, industrial and clinical applications.
More specifically, aptamers can be classified as:
DNA or RNA or XNA aptamers. They consist of (usually short) strands of oligonucleotides.
Peptide aptamers. They consist of a short variable peptide domain, attached at both
ends to a protein scaffold.
Nucleic acid aptamers are nucleic acid species that have been engineered through repeated rounds of in vitro selection or equivalently, SELEX (systematic evolution of
ligands by exponential enrichment) to bind to various molecular targets such as small
molecules, proteins, nucleic acids, and even cells, tissues and organisms. Aptamers are
useful in biotechnological and therapeutic applications as they offer molecular recognition properties that rival that of the commonly used biomolecule, antibodies. In addition to their discriminate recognition, aptamers offer advantages over antibodies as
they can be engineered completely in a test tube, are readily produced by chemical synthesis, possess desirable storage properties, and elicit little or no immunogenicity in
therapeutic applications.
https://en.wikipedia.org/wiki/Aptamer
Index
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Apyrase
arises directly from UTP. Since deoxyribonucleotides are made from ribonu
Index
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Aquaporins
Aquaporins are integral membrane proteins from a larger family of major intrinsic proteins (MIP) that form pores in the membrane of biological cells.
Genetic defects involving aquaporin genes have been associated with several human
diseases. The 2003 Nobel Prize in Chemistry was awarded jointly to Peter Agre for the
discovery of aquaporins, and Roderick MacKinnon for his work on the structure and
mechanism of potassium channels. The plasma membranes of a variety of different animal and plant cells contain aquaporins through which water can flow more rapidly inside the cell than by diffusing through the phospholipid bilayer.
Aquaporins selectively conduct water molecules in and out of the cell, while preventing
the passage of ions and other solutes. Also known as water channels, aquaporins are integral membrane pore proteins. Some of them, known as aquaglyceroporins, also transport other small uncharged solutes, such as glycerol, CO2, ammonia and urea across
the membrane, depending on the size of the pore. For example, the aquaporin 3 channel has a pore width of 8-10 ngstrms and allows the passage of hydrophilic molecules ranging between 150-200 Da. However, the water pores are completely impermeable to charged species, such as protons, a property critical for the conservation of the
membrane's electrochemical potential difference.
Water molecules traverse through the pore of the channel in single file. The presence
of water channels increases membrane permeability to water. Many human cell types
express them, as do certain bacteria and many other organisms, such as plants for
which it is essential for the water transport system and tolerance to drought and salt
stresses.
https://en.wikipedia.org/wiki/Aquaporin
Arabinose
For biosynthetic reasons, most saccharides are almost always more abundant in nat
is in fact more common than D-arabinose in nature and is found in nature as a com
nent of biopolymers such as hemicellulose and pectin.
https://en.wikipedia.org/wiki/Arabinose
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Arabitol
binose or lyxose. Some organic acid tests check for the presence of D-arabi
https://en.wikipedia.org/wiki/Arabitol
Arachidonate
Arachidonic acid (AA, sometimes ARA) is a polyunsaturated -6 fatty acid 20:4(-6).
It is structurally related to the saturated arachidic acid found in peanut oil (L. arachis
peanut). Arachidonic acid is a polyunsaturated fatty acid present in the phospholipids (especially phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositides) of membranes of the body's cells, and is abundant in the brain, muscles, and
liver. Skeletal muscle is an especially active site of arachidonic acid retention, accounting for roughly 10-20% of the phospholipid fatty acid content on average.
In addition to being involved in cellular signaling as a lipid second messenger involved
in the regulation of signaling enzymes, such as PLC-, PLC-, and PKC-, -, and - isoforms, arachidonic acid is a key inflammatory intermediate and can also act as a vasodilator.
Arachidonic acid is freed from a phospholipid molecule by the enzyme phospholipase
A2 (PLA2), which cleaves off the fatty acid, but can also be generated from DAG by diacylglycerol lipase.
Arachidonic acid generated for signaling purposes appears to be derived by the action
of a phosphatidylcholine-specific cytosolic phospholipase A2, whereas inflammatory
arachidonic acid is generated by the action of a low-molecular-weight secretory PLA2.
Arachidonic acid is the precursor that is metabolized by various enzymes to a wide
range of biologically and clinically important eicosanoids and metabolites of these eicosanoids:
The enzymes cyclooxygenase-1 and -2 (i.e. prostaglandin G/H synthase 1 and 2
{PTGS1 and PTGS2}) metabolize arachidonic acid to Prostaglandin G2 and prostaglandin H2, which in turn may be converted to various prostaglandins, to prostacyclin, to
thromboxanes, and to the 17-carbon product of thromboxane metabolism of prostaglandin G2/H2, 12-Hydroxyheptadecatrienoic acid (12-HHT).
The enzyme 5-lipoxygenase metabolizes arachidonic acid to 5hydroperoxyicosatetraenoic acid (5-HPETE), which in turn is metabolized to various
leukotrienes (i.e. leukotriene B4, leukotriene C4, leukotriene D4, and leukotriene E4 as
well as to 5-hydroxyicosatetraenoic acid (5-HETE) which may then be further metabolized to 5-HETE's more potent 5-keto analog, 5-oxo-eicosatetraenoic acid (5-oxo-ETE)
(also see 5-Hydroxyicosatetraenoic acid.
The enzymes 15-lipoxygenase-1 (ALOX15 and 15-lipoxygenase-2 (ALOX15B metabolize arachidonic acid to 15-hydroperoxyicosatetraemoic acid (15-HPETE) which may
then be further metabolized to 15-hydroxyicosatetraenoic acid (15-HETE) and lipoxins;. 15-Lipoxygenase-1 may also further metabolize 15-HPETE to eoxins in a pathway
analogous to (and presumably using the same enzymes as used in) the pathway which
metabolizes 5-HPETE to leukotrienes.
The enzyme 12-lipoxygenase (ALOX12) metabolizes arachidonic acid to 12hydroperoxyeicosatetraenoic acid (12-HPETE0 which may then be metabolized to 12hydroxyeicosatetraenoic acid (12-HETE) and to hepoxilins.
https://en.wikipedia.org/wiki/Arachidonic_acid
Arachidonate 5-lipoxygenase
tors were developed as asthma treatments. The only 5-LO inhibitor currently lic
for human use in asthma is zileuton.
Index
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Arachidonic Acid
Arachidonic acid (AA, sometimes ARA) is a polyunsaturated -6 fatty acid 20:4(-6).
It is structurally related to the saturated arachidic acid found in peanut oil (L. arachis
peanut). Arachidonic acid is a polyunsaturated fatty acid present in the phospholipids (especially phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositides) of membranes of the body's cells, and is abundant in the brain, muscles, and
liver. Skeletal muscle is an especially active site of arachidonic acid retention, accounting for roughly 10-20% of the phospholipid fatty acid content on average.
In addition to being involved in cellular signaling as a lipid second messenger involved
in the regulation of signaling enzymes, such as PLC-, PLC-, and PKC-, -, and - isoforms, arachidonic acid is a key inflammatory intermediate and can also act as a vasodilator.
Arachidonic acid is freed from a phospholipid molecule by the enzyme phospholipase
A2 (PLA2), which cleaves off the fatty acid, but can also be generated from DAG by diacylglycerol lipase.
Arachidonic acid generated for signaling purposes appears to be derived by the action
of a phosphatidylcholine-specific cytosolic phospholipase A2, whereas inflammatory
arachidonic acid is generated by the action of a low-molecular-weight secretory PLA2.
Arachidonic acid is the precursor that is metabolized by various enzymes to a wide
range of biologically and clinically important eicosanoids and metabolites of these eicosanoids:
The enzymes cyclooxygenase-1 and -2 (i.e. prostaglandin G/H synthase 1 and 2
{PTGS1 and PTGS2}) metabolize arachidonic acid to Prostaglandin G2 and prostaglandin H2, which in turn may be converted to various prostaglandins, to prostacyclin, to
thromboxanes, and to the 17-carbon product of thromboxane metabolism of prostaglandin G2/H2, 12-Hydroxyheptadecatrienoic acid (12-HHT).
The enzyme 5-lipoxygenase metabolizes arachidonic acid to 5hydroperoxyicosatetraenoic acid (5-HPETE), which in turn is metabolized to various
leukotrienes (i.e. leukotriene B4, leukotriene C4, leukotriene D4, and leukotriene E4 as
well as to 5-hydroxyicosatetraenoic acid (5-HETE) which may then be further metabolized to 5-HETE's more potent 5-keto analog, 5-oxo-eicosatetraenoic acid (5-oxo-ETE)
(also see 5-Hydroxyicosatetraenoic acid.
The enzymes 15-lipoxygenase-1 (ALOX15 and 15-lipoxygenase-2 (ALOX15B metabolize arachidonic acid to 15-hydroperoxyicosatetraemoic acid (15-HPETE) which may
then be further metabolized to 15-hydroxyicosatetraenoic acid (15-HETE) and lipoxins.
15-Lipoxygenase-1 may also further metabolize 15-HPETE to eoxins in a pathway analogous to (and presumably using the same enzymes as used in) the pathway which metabolizes 5-HPETE to leukotrienes.
The enzyme 12-lipoxygenase (ALOX12) metabolizes arachidonic acid to 12hydroperoxyeicosatetraenoic acid (12-HPETE0 which may then be metabolized to 12hydroxyeicosatetraenoic acid (12-HETE) and to hepoxilins.
https://en.wikipedia.org/wiki/Arachidonic_acid
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Archaeans
The Archaea constitute a domain and kingdom of single-celled microorganisms. These
microbes are prokaryotes, meaning that they have no cell nucleus or any other
membrane-bound organelles in their cells. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is outdated. The Archaea are further divided into multiple recognized phyla.
Classification is difficult because the majority have not been isolated in the laboratory
and have only been detected by analysis of their nucleic acids in samples from their environment.
Archaea and bacteria are generally similar in size and shape, although a few archaea
have very strange shapes, such as the flat and square-shaped cells of Haloquadratum
walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several
metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, such as
archaeols. Archaea use more energy sources than eukaryotes. These range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salttolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species
of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of
archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or
budding; unlike bacteria and eukaryotes, no known species forms spores.
Archaea were initially viewed as extremophiles living in harsh environments, such as
hot springs and salt lakes, but they have since been found in a broad range of habitats,
including soils, oceans, marshlands and the human colon, oral cavity, and skin. Archaea are particularly numerous in the oceans, and the archaea in plankton may be
one of the most abundant groups of organisms on the planet. Archaea are a major part
of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No
clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and enzymes from extremophile archaea that
can endure high temperatures and organic solvents are exploited in biotechnology.
https://en.wikipedia.org/wiki/Archaea
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Arginase
Arginase (EC 3.5.3.1, arginine amidinase, canavanase, L-arginase, arginine transamidinase) is a manganese-containing enzyme. The reaction catalyzed by this enzyme is:
Arginine + H2O Ornithine + Urea.
It is the final enzyme of the urea cycle and is ubiquitous to all domains of life. Mammalian arginase is active as a trimer, but some bacterial arginases are hexameric. The
enzyme requires a two-molecule metal cluster of manganese in order to maintain
proper function. These Mn++ ions coordinate with water, orientating and stabilizing
the molecule and allowing water to act as a nucleophile and attack L-arginine, hydrolyzing it into ornithine and urea.
In most mammals, two isozymes of this enzyme exist. The first, arginase I, functions
in the urea cycle, and is located primarily in the cytoplasm of the liver. The second isozyme, arginase II, has been implicated in the regulation of the arginine/ornithine concentrations in the cell. It is located in mitochondria of several tissues in the body, with
most abundance in the kidney and prostate. It may be found at lower levels in macrophages, lactating mammary glands, and brain. The second isozyme may be found in
the absence of other urea cycle enzymes.
https://en.wikipedia.org/wiki/Arginase
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Arginine
Arginine (abbreviated as Arg or R) encoded by the codons CGU, CGC, CGA, CGG, AGA,
and AGG is an -amino acid that is used in the biosynthesis of proteins. It contains an
-amino group (which is in the protonated NH3+ form under biological conditions),
an -carboxylic acid group (which is in the deprotonated COO form under biological
conditions), and a side chain of a 3-carbon aliphatic straight chain capped by a complex guanidinium, classifying it as a charged (at physiological pH), aliphatic amino
acid.
Arginine is classified as a semiessential or conditionally essential amino acid, depending on the developmental stage and health status of the individual. Preterm infants are
unable to synthesize or create arginine internally, making the amino acid nutritionally
essential for them. Most healthy people do not need to supplement with arginine because their body produces sufficient amounts.
Arginine is synthesized from citrulline in arginine and proline metabolism by the sequential action of the cytosolic enzymes argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL). In terms of energy, this is costly, as the synthesis of each molecule of argininosuccinate requires hydrolysis of adenosine triphosphate (ATP) to adenosine monophosphate (AMP), i.e., two ATP equivalents. In essence, taking an excess of
arginine gives more energy by saving ATPs that can be used elsewhere.
Citrulline can be derived from multiple sources:
from arginine via nitric oxide synthase (NOS)
from ornithine via catabolism of proline or glutamine/glutamate
from asymmetric dimethylarginine (ADMA) via DDAH
The roles of arginine include:
Precursor for the synthesis of nitric oxide (NO). Non-L-arginine derived NO can be
generated by the nitrate-nitrite-nitric oxide pathway that is monitored through saliva
testing.
Reduces healing time of injuries (particularly bone)
Quickens repair time of damaged tissue
Helps decrease blood pressure in clinical hypertensive subjects - NO-mediated decrease in blood pressure is influenced by both the L-arginine-dependent nitric oxide
synthase pathway and non-L-arginine or alternative pathway through nitrate-rich
foods such as beets and spinach.
https://en.wikipedia.org/wiki/Arginine
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Argininosuccinase
ASL (argininosuccinate lyase, also known as argininosuccinase) is an enzyme that catalyzes the reversible breakdown of argininosuccinate (ASA) producing the amino acid
arginine and dicarboxylic acid fumarate. Located in liver cytosol, ASL is the fourth enzyme of the urea cycle and involved in the biosynthesis of arginine in all species and
the production of urea in ureotelic species.
Ammonia (NH3) is a toxic substance for many aerobic organisms and must be excreted. Some aquatic organisms release the toxin right directly into their environment,
while other ureotelic species must convert their toxic nitrogen waste into non-toxic
components, like uric acid or urea, through a series of catalyzed steps better known as
the urea cycle. ASL catalyzes the fourth step in the cycle, following the action of argininosuccinate synthetase (ASS) in the liver cytosol. While ASS catalyzes the formation of
argininosuccinate from citrulline and aspartate, ASL breaks the newly formed argininosuccinate into L-arginine and fumarate. L-arginine continues through the urea cycle to
form urea and ornithine, while fumarate can enter the citric acid cycle. Urea, of
course, can be excreted, thus reducing ammonia levels.
https://en.wikipedia.org/wiki/Argininosuccinate_lyase
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Argininosuccinate
Some cells synthesize argininosuccinic acid from citrulline and aspartic acid and use it
as a precursor for arginine in the urea cycle or citrulline-NO cycle. The enzyme that
catalyzes the reaction is argininosuccinate synthetase.
Argininosuccinic acid is a precursor to fumarate in the citric acid cycle via argininosuccinate lyase.
https://en.wikipedia.org/wiki/Argininosuccinic_acid
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Argininosuccinate Lyase
ASL (argininosuccinate lyase, also known as argininosuccinase) is an enzyme that catalyzes the reversible breakdown of argininosuccinate (ASA) producing the amino acid
arginine and dicarboxylic acid fumarate. Located in liver cytosol, ASL is the fourth enzyme of the urea cycle and involved in the biosynthesis of arginine in all species and
the production of urea in ureotelic species.
Ammonia (NH3) is a toxic substance for many aerobic organisms and must be excreted. Some aquatic organisms release the toxin right directly into their environment,
while other ureotelic species must convert their toxic nitrogen waste into non-toxic
components, like uric acid or urea, through a series of catalyzed steps better known as
the urea cycle. ASL catalyzes the fourth step in the cycle, following the action of argininosuccinate synthetase (ASS) in the liver cytosol. While ASS catalyzes the formation of
argininosuccinate from citrulline and aspartate, ASL breaks the newly formed argininosuccinate into L-arginine and fumarate. L-arginine continues through the urea cycle to
form urea and ornithine, while fumarate can enter the citric acid cycle. Urea, of
course, can be excreted, thus reducing ammonia levels.
https://en.wikipedia.org/wiki/Argininosuccinate_lyase
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Argininosuccinate Synthase
Argininosuccinate synthase or synthetase (ASS; EC 6.3.4.5) is an enzyme that catalyzes
the synthesis of argininosuccinate from citrulline and aspartate. ASS is responsible for
the third step of the urea cycle and one of the reactions of the citrulline-NO cycle.
The transformation of citrulline into argininosuccinate is the rate-limiting step in arginine synthesis. The activity of argininosuccinate synthetase in arginine synthesis occurs largely in at the outer mitochondrial membrane of periportal liver cells as part of
the urea cycle, with some activity occurring in cortical kidney cells. Genetic defects that
cause incorrect localization of argininosuccinate synthetase to the outer mitochondrial
membrane cause type II citrullinemia.
In fetuses and infants, arginine is also produced via argininosuccinate synthetase activity in intestinal cells, presumably to supplement the low level of arginine found in
mothers milk. Expression of argininosuccinate synthetase in the intestines ceases after
two to three years of life. It is thought that regulation of argininosuccinate synthetase
activity in arginine synthesis occurs primarily at the transcriptional level in response to
glucocorticoids, cAMP, glucagon, and insulin. It has also been demonstrated in vitro
that arginine down-regulates argininosuccinate synthetase expression, while citrulline
up-regulates it.
Citrulline-NO cycle
The enzyme endothelial nitric oxide synthase produces nitric oxide from arginine in endothelial cells. Argininosuccinate synthetase and argininosuccinate lyase recycle citrulline, a byproduct of nitric oxide production, into arginine. Since nitric oxide is an important signaling molecule, this role of ASS is important to vascular physiology. In this
role, argininosuccinate synthetase activity is regulated largely by inflammatory cellular
signal molecules such as cytokines.
https://en.wikipedia.org/wiki/Argininosuccinate_synthase
Argonaute
The Argonaute protein family plays a central role in RNA silencing processes, as essential catalytic components of the RNA-induced silencing complex (RISC). RISC complex
is responsible for the gene silencing phenomenon known as RNA interference (RNAi).
Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs).
Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity (base pairing), which then leads to mRNA cleavage or translation inhibition.
RNA interference (RNAi) is a significant biological process, in which the RNA molecules inhibit gene expression. The typical way of this process is causing the destruction
of specific mRNA molecules. The RNA interference has a significant role in defending
cells against parasitic nucleotide sequences. In many eukaryotes, including animals,
the RNA interference pathway is found, and it is initiated by enzyme Dicer. Dicer
cleaves long double-stranded RNA molecules into short double stranded fragments of
around 20 nucleotide siRNAs. The dsRNA is then separated into two single-stranded
RNAs (ssRNA) - the passenger strand and the guide strand. Consequently, the passenger strand is degraded, while the guide strand is incorporated into the RNA-induced
silencing complex (RISC). The most well-studied outcome of the RNAi is posttranscriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute,
that lies in the core of RISC.
Argonaute proteins are the active part of RNA-induced silencing complex, cleaving the
target mRNA strand complementary to their bound siRNA. Theoretically the dicer produces short double-stranded fragments so there should be also two functional singlestranded siRNA produced. But only one of the two single-stranded RNA here will be
utilized to base pair with target mRNA. It is known as the guide strand, incorporated
into the Argonaute protein and leads gene silencing. The other single-stranded named
passenger strand is degraded during the RNA-induced silencing complex process.
Once the Argonaute is associated with the small RNA, the enzymatic activity conferred
by the PIWI domain cleaves only the passenger strand of the small interfering RNA.
RNA strand separation and incorporation into the Argonaute protein are guided by the
strength of the hydrogen bond interaction at the 5-ends of the RNA duplex, known as
the asymmetry rule. Also the degree of complementarity between the two strands of
the intermediate RNA duplex defines how the miRNA are sorted into different types of
Argonaute proteins.
https://en.wikipedia.org/wiki/Argonaute
Index
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Arnon-Buchanan Cycle
The reverse Krebs cycle (also known as the reverse tricarboxylic acid cycle, the reverse
TCA cycle, the reverse citric acid cycle, or the Arnon-Buchanan Cycle) is a sequence of
chemical reactions that are used by some bacteria to produce carbon compounds from
carbon dioxide and water.
The reaction is the citric acid cycle run in reverse: Where the Krebs cycle takes complex carbon molecules in the form of sugars and oxidizes them to CO2 and water, the
reverse cycle takes CO2 and water to make carbon compounds. This process is used by
some bacteria to synthesize carbon compounds, sometimes using hydrogen, sulfide, or
thiosulfate as electron donors. In this process, it can be seen as an alternative to the
fixation of inorganic carbon in the reductive pentose phosphate cycle which occurs in a
wide variety of microbes and higher organisms.
https://en.wikipedia.org/wiki/Reverse_Krebs_cycle
Index
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Aromatase
Aromatase, also called estrogen synthetase or estrogen synthase, is an enzyme responsible for a key step in the biosynthesis of estrogens. It is CYP19A1, a member of the cytochrome P450 superfamily (EC 1.14.14.1), which are monooxygenases that catalyze many
reactions involved in steroidogenesis. In particular, aromatase is responsible for the
aromatization of androgens into estrogens. The aromatase enzyme can be found in
many tissues including gonads, brain, adipose tissue, placenta, blood vessels, skin, and
bone, as well as in tissue of endometriosis, uterine fibroids, breast cancer, and endometrial cancer. It is an important factor in sexual development.
Aromatase is localized in the endoplasmic reticulum where it is regulated by tissuespecific promoters that are in turn controlled by hormones, cytokines, and other factors. It catalyzes the last steps of estrogen biosynthesis from androgens (specifically, it
transforms androstenedione to estrone and testosterone to estradiol). These steps include three successive hydroxylations of the 19-methyl group of androgens, followed by
simultaneous elimination of the methyl group as formate and aromatization of the Aring.
Aromatase inhibitors, which stop the production of estrogen in postmenopausal
women, have become useful in the management of patients with breast cancer whose
lesion was found to be estrogen receptor positive. Inhibitors that are in current clinical
use include anastrozole, exemestane, and letrozole. Aromatase inhibitors are also beginning to be prescribed to men on testosterone replacement therapy as a way to keep
estrogen levels from spiking once doses of testosterone are introduced to their systems.
https://en.wikipedia.org/wiki/Aromatase
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Aromatase Inhibitors
Aromatase inhibitors (AIs) are a class of drugs used in the treatment of breast cancer
and ovarian cancer in postmenopausal women and gynecomastia in men. They may
also be used off-label to reduce increase of estrogen conversion during cycle with external testosterone. They may also be used for chemoprevention in high risk women.
Aromatase is the enzyme that synthesizes estrogen. As breast and ovarian cancers require estrogen to grow, AIs are taken to either block the production of estrogen or
block the action of estrogen on receptors.
Aromatase inhibitors work by inhibiting the action of the enzyme aromatase, which
converts androgens into estrogens by a process called aromatization. As breast tissue is
stimulated by estrogens, decreasing their production is a way of suppressing recurrence of the breast tumor tissue. The main source of estrogen is the ovaries in premenopausal women, while in post-menopausal women most of the body's estrogen is produced in peripheral tissues (outside the CNS), and also a few CNS sites in various regions within the brain. Estrogen is produced and acts locally in these tissues, but any
circulating estrogen, which exerts systemic estrogenic effects in men and women, is the
result of estrogen escaping local metabolism and spreading to the circulatory system.
Anastrozole (Arimidex)
Letrozole (Femara)
Exemestane (Aromasin)
Vorozole (Rivizor)
Formestane (Lentaron)
Fadrozole (Afema)
https://en.wikipedia.org/wiki/Aromatase_inhibitor
Index
Find Term
Aromatic
Index
Find Term
Aromatic amino acid hydroxylase is the name for a group of enzymes that h
Arrestin
Arrestins are a small family of proteins important for regulating signal tran
tion specifically prepares the activated receptor for arrestin binding. Arrest
Index
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Artificial Sweetener
A sugar substitute is a food additive that provides a sweet taste like that of sugar while
containing significantly less food energy. Some sugar substitutes are natural and some
are synthetic. Those that are not natural are, in general, called artificial sweeteners.
An important class of sugar substitutes is known as high-intensity sweeteners. These
are compounds with many times the sweetness of sucrose, common table sugar. As a
result, much less sweetener is required and energy contribution is often negligible. The
sensation of sweetness caused by these compounds (the "sweetness profile") is sometimes notably different from sucrose, so they are often used in complex mixtures that
achieve the most natural sweet sensation.
If the sucrose (or other sugar) that is replaced has contributed to the texture of the
product, then a bulking agent is often also needed. This may be seen in soft drinks or
sweet tea that are labeled as "diet" or "light" that contain artificial sweeteners and often have notably different mouthfeel, or in table sugar replacements that mix maltodextrins with an intense sweetener to achieve satisfactory texture sensation.
In the United States, seven intensely sweet sugar substitutes have been approved for
use. They are stevia, aspartame, sucralose, neotame, acesulfame potassium (Ace-K),
saccharin, and advantame. Cyclamates are used outside the U.S., but have been prohibited in the U.S. since 1969. There is some ongoing controversy over whether artificial
sweetener usage poses health risks. Others, which may or may not be approved, include allulose (psicose), and monk fruit. The U.S. Food and Drug Administration regulates artificial sweeteners as food additives. Food additives must be approved by the
FDA, which publishes a Generally Recognized as Safe (GRAS) list of additives. (Stevia
is exempt under FDA's GRAS policy due to its being a natural substance in wide use
well before 1958, and has been approved by FDA). The conclusions about safety are
based on a detailed review of a large body of information, including hundreds of toxicological and clinical studies.
https://en.wikipedia.org/wiki/Sugar_substitute
Ascorbate
Vitamin C or L-ascorbic acid, or simply ascorbate (the anion of ascorbic acid), is an essential nutrient for humans and certain other animal species. Vitamin C describes several vitamers that have vitamin C activity in animals, including ascorbic acid and its
salts, and some oxidized forms of the molecule like dehydroascorbic acid. Ascorbate
and ascorbic acid are both naturally present in the body when either of these is introduced into cells, since the forms interconvert according to pH.
Vitamin C is a cofactor in at least eight enzymatic reactions, including several collagen
synthesis reactions that, when dysfunctional, cause the most severe symptoms of
scurvy. In animals, these reactions are especially important in wound-healing and in
preventing bleeding from capillaries. Ascorbate may also act as an antioxidant, protecting against oxidative stress.
Ascorbate (the anion of ascorbic acid) is required for a range of essential metabolic reactions in all animals and plants. It is made internally by almost all organisms; the
main exceptions are most bats, all guinea pigs, capybaras, and the Haplorrhini (one of
the two major primate suborders, consisting of tarsiers, monkeys, and humans and
other apes). Ascorbate is also not synthesized by many species of birds and fish. All species that do not synthesize ascorbate require it in the diet. Deficiency in this vitamin
causes the disease scurvy in humans.
The biological role of ascorbate is to act as a reducing agent, donating electrons to various enzymatic and a few non-enzymatic reactions. The one- and two-electron oxidized
forms of vitamin C, semidehydroascorbic acid and dehydroascorbic acid, respectively,
can be reduced in the body by glutathione and NADPH-dependent enzymatic mechanisms. The presence of glutathione in cells and extracellular fluids helps maintain
ascorbate in a reduced state.
https://en.wikipedia.org/wiki/Vitamin_C
Index
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Ascorbic acid
Vitamin C or L-ascorbic acid, or simply ascorbate (the anion of ascorbic acid), is an essential nutrient for humans and certain other animal species. Vitamin C describes several vitamers that have vitamin C activity in animals, including ascorbic acid and its
salts, and some oxidized forms of the molecule like dehydroascorbic acid. Ascorbate
and ascorbic acid are both naturally present in the body when either of these is introduced into cells, since the forms interconvert according to pH.
Vitamin C is a cofactor in at least eight enzymatic reactions, including several collagen
synthesis reactions that, when dysfunctional, cause the most severe symptoms of
scurvy. In animals, these reactions are especially important in wound-healing and in
preventing bleeding from capillaries. Ascorbate may also act as an antioxidant, protecting against oxidative stress.
Ascorbate (the anion of ascorbic acid) is required for a range of essential metabolic reactions in all animals and plants. It is made internally by almost all organisms. The
main exceptions are most bats, all guinea pigs, capybaras, and the Haplorrhini (one of
the two major primate suborders, consisting of tarsiers, monkeys, and humans and
other apes). Ascorbate is also not synthesized by many species of birds and fish. All species that do not synthesize ascorbate require it in the diet. Deficiency in this vitamin
causes the disease scurvy in humans.
The biological role of ascorbate is to act as a reducing agent, donating electrons to various enzymatic and a few non-enzymatic reactions. The one- and two-electron oxidized
forms of vitamin C, semidehydroascorbic acid and dehydroascorbic acid, respectively,
can be reduced in the body by glutathione and NADPH-dependent enzymatic mechanisms. The presence of glutathione in cells and extracellular fluids helps maintain
ascorbate in a reduced state.
https://en.wikipedia.org/wiki/Vitamin_C
Index
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Asparaginase
acute lymphoblastic leukemia cells and some other suspected tumor cells ar
make their own asparagine. Thus leukemic cells require high amount of asp
Index
Find Term
Asparagine
Asparagine (abbreviated as Asn or N) encoded by the codons AAU and AAC. is an amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain carboxamide, classifying it as a polar (at physiological pH), aliphatic
amino acid.
Since the asparagine side-chain can form hydrogen bond interactions with the peptide
backbone, asparagine residues are often found near the beginning of -helices as asx
turns and asx motifs, and in similar turn motifs, or as amide rings, in sheets. Its role
can be thought as "capping" the hydrogen bond interactions that would otherwise be
satisfied by the polypeptide backbone. Glutamines, with an extra methylene group,
have more conformational entropy and thus are less useful for capping.
Asparagine also provides key sites for N-linked glycosylation, modification of the protein chain with the addition of carbohydrate chains. Typically, a carbohydrate tree can
solely be added to an asparagine residue if the latter is flanked on the C side by Xserine or X-threonine, where X is any amino acid with the exception of proline.
https://en.wikipedia.org/wiki/Asparagine
Index
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G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Carbohydrates
Chapter 2 - Structure & Function: Carbohydrates
Chapter 2 - Structure & Function: Carbohydrates
Chapter 2 - Structure & Function: Carbohydrates
Chapter 2 - Structure & Function: Carbohydrates
Chapter 2 - Structure & Function: Lipids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Asparagine Synthetase
https://en.wikipedia.org/wiki/Asparagine_synthetase
Index
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Aspartame
Aspartame is an artificial, non-saccharide sweetener used as a sugar substitute in some
foods and beverages. In the European Union, it is codified as E951. Aspartame is a
methyl ester of the aspartic acid/phenylalanine dipeptide. Its breakdown products include phenylalanine, so aspartame must be avoided by people with the genetic condition phenylketonuria (PKU).
Aspartame is approximately 200 times sweeter than sucrose (table sugar). Due to this
property, even though aspartame produces four kilocalories of energy per gram (17kJ/
g) when metabolized, the quantity of aspartame needed to produce a sweet taste is so
small that its caloric contribution is negligible. The taste of aspartame and other artificial sweeteners differs from that of table sugar in the times of onset and how long the
sweetness lasts, though aspartame comes closest to sugar's taste profile among approved artificial sweeteners. The sweetness of aspartame lasts longer than that of sucrose, so it is often blended with other artificial sweeteners such as acesulfame potassium to produce an overall taste more like sugar. Aspartame can be synthesized from
its constituent amino acids, L-phenylalanine and L-aspartate.
Like many other peptides, aspartame may hydrolyze (break down) into its constituent
amino acids under conditions of elevated temperature or high pH. This makes aspartame undesirable as a baking sweetener, and prone to degradation in products hosting
a high pH, as required for a long shelf life. The stability of aspartame under heating
can be improved to some extent by encasing it in fats or in maltodextrin. The stability
when dissolved in water depends markedly on pH. At room temperature, it is most stable at pH 4.3, where its half-life is nearly 300 days. At pH 7, however, its half-life is
only a few days. Most soft-drinks have a pH between 3 and 5, where aspartame is reasonably stable. In products that may require a longer shelf life, such as syrups for fountain beverages, aspartame is sometimes blended with a more stable sweetener, such as
saccharin.
Aspartame's major decomposition products are its cyclic dipeptide (in a 2,5diketopiperazine, or DKP, form), the de-esterified dipeptide (aspartyl-phenylalanine),
and its constituent components, phenylalanine, aspartic acid, and methanol. At 180C,
aspartame undergoes decomposition to form a diketopiperazine derivative.
https://en.wikipedia.org/wiki/Aspartame
Aspartate
Aspartic acid (abbreviated as Asp or D; encoded by the codons [GAU and GAC]) is an
-amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain CH2COOH. It is listed by some as non-essential and others as semiessential in humans.
Aspartate can be produced from oxaloacetate by transamination. It can also be generated from ornithine and citrulline in the urea cycle. In plants and microorganisms, aspartate is the precursor to several amino acids, including four that are essential for humans: methionine, threonine, isoleucine, and lysine.
Aspartate is also a metabolite in the urea cycle and participates in gluconeogenesis. It
carries reducing equivalents in the malate-aspartate shuttle, which utilizes the ready
interconversion of aspartate and oxaloacetate, which is the oxidized (dehydrogenated)
derivative of malic acid. Aspartate donates one nitrogen atom in the biosynthesis of inosine, the precursor to the purine bases. In addition, aspartic acid acts as hydrogen acceptor in a chain of ATP synthase. Aspartate is also part of the catalytic triad of serine
proteases.
https://en.wikipedia.org/wiki/Aspartic_acid
Index
Find Term
G-G
G-G
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Proteins I
Chapter 3 - Membranes: Transport
Chapter 4 - Catalysis: Control of Activity
Chapter 4 - Catalysis: Mechanism
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Aspartate Transaminase
Aspartate transaminase (AST) or aspartate aminotransferase, also known as AspAT/
ASAT/AAT or serum glutamic oxaloacetic transaminase (SGOT), is a pyridoxal phosphate (PLP)-dependent transaminase enzyme (EC 2.6.1.1) that was first described by
Arthur Karmen and colleagues in 1954. AST catalyzes the reversible transfer of an amino group between aspartate and glutamate and, as such, is an important enzyme in
amino acid metabolism.
Aspartate transaminase catalyzes the interconversion of aspartate and -ketoglutarate
to oxaloacetate and glutamate.
Aspartate (Asp) + -ketoglutarate Oxaloacetate + Glutamate (Glu)
As a prototypical transaminase, AST relies on PLP (Vitamin B6) as a cofactor to transfer the amino group from aspartate or glutamate to the corresponding ketoacid. In the
process, the cofactor shuttles between PLP and the pyridoxamine phosphate (PMP)
form. The amino group transfer catalyzed by this enzyme is crucial in both amino acid
degradation and biosynthesis. In amino acid degradation, following the conversion of
-ketoglutarate to glutamate, glutamate subsequently undergoes oxidative deamination to form ammonium ions, which are excreted as urea. In the reverse reaction, aspartate may be synthesized from oxaloacetate, which is a key intermediate in the citric
acid cycle.
https://en.wikipedia.org/wiki/Aspartate_transaminase
Index
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Aspartate Transcarbamoylase
Aspartate carbamoyltransferase (also known as aspartate transcarbamoylase or ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway. ATCase is a
highly regulated enzyme that catalyzes the first committed step in pyrimidine biosynthesis, the condensation of l-aspartate and carbamoyl phosphate to form N-carbamylL-aspartate and inorganic phosphate.
ATCase controls the rate of pyrimidine biosynthesis by altering its catalytic velocity in
response to cellular levels of both pyrimidines and purines. The end-product of the pyrimidine pathway, CTP, decreases catalytic velocity, whereas ATP, the end-product of
the parallel purine pathway, increases catalytic velocity. The substrate, aspartate, is an
allosteric (homotropic) activator of the enzyme.
ATCase does not follow Michaelis-Menten kinetics, but lies between the low-activity,
low-affinity "tense" or T and the high-activity, high-affinity "relaxed" or R states. The
binding of substrate to the catalytic subunits results in an equilibrium shift towards the
R state, whereas binding of CTP to the regulatory subunits results in an equilibrium
shift towards the T state. Binding of ATP to the regulatory subunits results in an equilibrium shift towards the R state.
https://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase
Index
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Aspartate-semialdehyde Dehydrogenase
tant in the biosynthesis of amino acids in prokaryotes, fungi, and some higher pla
It forms an early branch point in the metabolic pathway leading to lysine, methio
leucine and isoleucine from aspartate.
The enzyme catalyzes the reversible chemical reaction
Index
Find Term
Aspartic Acid
Aspartic acid (abbreviated as Asp or D; encoded by the codons [GAU and GAC]) is an
-amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain CH2COOH. It is listed by some as non-essential and others as semiessential in humans.
Aspartate can be produced from oxaloacetate by transamination. It can also be generated from ornithine and citrulline in the urea cycle. In plants and microorganisms, aspartate is the precursor to several amino acids, including four that are essential for humans: methionine, threonine, isoleucine, and lysine.
Aspartate is also a metabolite in the urea cycle and participates in gluconeogenesis. It
carries reducing equivalents in the malate-aspartate shuttle, which utilizes the ready
interconversion of aspartate and oxaloacetate, which is the oxidized (dehydrogenated)
derivative of malic acid. Aspartate donates one nitrogen atom in the biosynthesis of inosine, the precursor to the purine bases. In addition, aspartic acid acts as hydrogen acceptor in a chain of ATP synthase. Aspartate is also part of the catalytic triad of serine
proteases.
https://en.wikipedia.org/wiki/Aspartic_acid
Index
Find Term
Aspartokinase
Aspartate kinase (aspartokinase, aspartic kinase) is an enzyme that catalyzes the phosphorylation of the amino acid aspartate. This reaction is the first step in the biosynthesis of three essential amino acids: methionine, lysine, and threonine, known as the "aspartate family".
The gene for aspartokinase is present only in microorganisms and plants. It is not present in animals, which must obtain aspartate-family amino acids in their diet.
In Escherichia coli, aspartokinase is present as three independently regulated isozymes, each of which is specific to one of the three downstream biochemical pathways.
This allows the independent regulation of the rates of methionine, lysine, and threonine production. The forms that produce threonine and lysine are subject to feedback
inhibition, and all three can be repressed at the level of gene expression by high concentrations of their end-products. Absence from animals makes these enzymes key targets
for new herbicides and biocides and for improvements in nutritional value of crops.
This enzyme may use the morpheein model of allosteric regulation.
https://en.wikipedia.org/wiki/Aspartate_kinase
Index
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Aspartyl Proteases
Aspartic (aspartyl) proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site
and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited
by pepstatin.
Eukaryotic aspartic proteases include pepsins, cathepsins, and renins. They have a
two-domain structure, arising from ancestral duplication. Retroviral and retrotransposon proteases (Pfam PF00077) are much smaller and appear to be homologous to a
single domain of the eukaryotic aspartyl proteases. Each domain contributes a catalytic
Asp residue, with an extended active site cleft localized between the two lobes of the
molecule. One lobe has probably evolved from the other through a gene duplication
event in the distant past. In modern-day enzymes, although the three-dimensional
structures are very similar, the amino acid sequences are more divergent, except for
the catalytic site motif, which is very conserved. The presence and position of disulfide
bridges are other conserved features of aspartic peptidases.
Aspartyl proteases are a highly specific family of proteases - they tend to cleave dipeptide bonds that have hydrophobic residues as well as a -methylene group. Unlike serine or cysteine proteases these proteases do not form a covalent intermediate during
cleavage. Proteolysis therefore occurs in a single step.
https://en.wikipedia.org/wiki/Aspartic_protease
Index
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Aspirin
Aspirin, also known as acetylsalicylic acid (ASA), is a medication, often used to treat
pain, fever, and inflammation. Aspirin is also used long-term, at low doses, to help prevent heart attacks, strokes, and blood clot formation in people at high risk of developing blood clots. Low doses of aspirin may be given immediately after a heart attack to
reduce the risk of another heart attack or the death of heart tissue. Aspirin may be effective at preventing certain types of cancer, particularly colorectal cancer.
Aspirin is part of a group of medications called nonsteroidal anti-inflammatory drugs
(NSAIDs), but differs from most other NSAIDs in the mechanism of action. The salicylates have similar effects (antipyretic, anti-inflammatory, analgesic) to the other
NSAIDs and inhibit the same enzyme cyclooxygenase (COX), but aspirin does so in an
irreversible manner and, unlike others, affects the COX-1 variant more than the COX-2
variant of the enzyme. Aspirin also has an antiplatelet effect by stopping the binding
together of platelets.
Aspirin's ability to suppress the production of prostaglandins and thromboxanes is due
to its irreversible inactivation of the cyclooxygenase (COX - officially known as
prostaglandin-endoperoxide synthase, PTGS) enzyme required for prostaglandin and
thromboxane synthesis. Aspirin acts as an acetylating agent where an acetyl group is
covalently attached to a serine residue in the active site of the PTGS enzyme. This
makes aspirin different from other NSAIDs (such as diclofenac and ibuprofen), which
are reversible inhibitors.
Low-dose aspirin use irreversibly blocks the formation of thromboxane A2 in platelets,
producing an inhibitory effect on platelet aggregation during the lifetime of the affected platelet (89 days). This antithrombotic property makes aspirin useful for reducing the incidence of heart attacks. 40mg of aspirin a day is able to inhibit a large proportion of maximum thromboxane A2 release provoked acutely, with the prostaglandin
I2 synthesis being little affected. However, higher doses of aspirin are required to attain further inhibition.
Prostaglandins, local hormones produced in the body, have diverse effects, including
the transmission of pain information to the brain, modulation of the hypothalamic thermostat, and inflammation. Thromboxanes are responsible for the aggregation of platelets that form blood clots. Heart attacks are caused primarily by blood clots, and low
doses of aspirin are seen as an effective medical intervention for acute myocardial infarction.
https://en.wikipedia.org/wiki/Aspirin
Index
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Aspirin-triggered LX4
the end of the process. Lipoxins act to attract macrophages to apoptotic cel
site of inflammation and they are engulfed. Lipoxins further act to start the
phase of the inflammation process.
At least one lipoxin (aspirin-triggered LX4) has its synthesis stimulated by
Index
Find Term
Peripheral membrane proteins interact with part of the bilayer (usually doe
volve hydrophobic interactions), but do not project through it. A good exam
they cannot embed in a portion of the lipid bilayer, but are found near mem
Asthma
and shortness of breath. These episodes may occur a few times a day or a fe
week.
https://en.wikipedia.org/wiki/Asthma
Asymmetric Center
A carbon has the ability to make four single bonds (forming a tetrahedral st
ATCase
Aspartate carbamoyltransferase (also known as aspartate transcarbamoylase or ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway. ATCase is a
highly regulated enzyme that catalyzes the first committed step in pyrimidine biosynthesis, the condensation of l-aspartate and carbamoyl phosphate to form N-carbamylL-aspartate and inorganic phosphate.
ATCase controls the rate of pyrimidine biosynthesis by altering its catalytic velocity in
response to cellular levels of both pyrimidines and purines. The end-product of the pyrimidine pathway, CTP, decreases catalytic velocity, whereas ATP, the end-product of
the parallel purine pathway, increases catalytic velocity. The substrate, aspartate, is an
allosteric (homotropic) activator of the enzyme.
ATCase does not follow Michaelis-Menten kinetics, but lies between the low-activity,
low-affinity "tense" or T and the high-activity, high-affinity "relaxed" or R states. The
binding of substrate to the catalytic subunits results in an equilibrium shift towards the
R state, whereas binding of CTP to the regulatory subunits results in an equilibrium
shift towards the T state. Binding of ATP to the regulatory subunits results in an equilibrium shift towards the R state.
https://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase
Atherosclerosis
Atherosclerosis (also known as arteriosclerotic vascular disease or ASVD) is a specific
form of arteriosclerosis in which an artery-wall thickens as a result of invasion and accumulation of white blood cells (WBCs) (foam cell) and proliferation of intimalsmooth-muscle cell creating a fibrofatty plaque.
The accumulation of the white blood cells is termed "fatty streaks" early on because of
the appearance being similar to that of marbled steak. These accumulations contain
both living, active WBCs (producing inflammation) and remnants of dead cells, including cholesterol and triglycerides. The remnants eventually include calcium and other
crystallized materials within the outermost and oldest plaque. The "fatty streaks" reduce the elasticity of the artery walls. However, they do not affect blood flow for decades because the artery muscular wall enlarges at the locations of plaque. The wall stiffening may eventually increase pulse pressure. Widened pulse pressure is one possible
result of advanced disease within the major arteries.
Atherosclerosis is therefore a syndrome affecting arterial blood vessels due to a chronic
inflammatory response of WBCs in the walls of arteries. This is promoted by lowdensity lipoproteins (LDL, plasma proteins that carry cholesterol and triglycerides)
without adequate removal of fats and cholesterol from the macrophages by functional
high-density lipoproteins (HDL). It is commonly referred to as a "hardening" or furring of the arteries. It is caused by the formation of multiple atheromatous plaques
within the arteries.
The plaque is divided into three distinct components:
1 The atheroma ("lump of gruel", from Greek (athera), meaning "gruel"), which
is the nodular accumulation of a soft, flaky, yellowish material at the center of large
plaques, composed of macrophages nearest the lumen of the artery
2 Underlying areas of cholesterol crystals
3 Calcification at the outer base of older or more advanced lesions.
Atherosclerosis is a chronic disease that remains asymptomatic for decades. Atherosclerotic lesions, or atherosclerotic plaques, are separated into two broad categories:
Stable and unstable (also called vulnerable). The pathobiology of atherosclerotic lesions is very complicated, but generally, stable atherosclerotic plaques, which tend to
be asymptomatic, are rich in extracellular matrix and smooth muscle cells. On the
other hand, unstable plaques are rich in macrophages and foam cells, and the extracellular matrix separating the lesion from the arterial lumen (also known as the fibrous
cap) is usually weak and prone to rupture. Ruptures of the fibrous cap expose thrombogenic material, such as collagen, to the circulation and eventually induce thrombus formation in the lumen. Upon formation, intraluminal thrombi can occlude arteries outright (e.g., coronary occlusion), but more often they detach, move into the circulation,
and eventually occlude smaller downstream branches causing thromboembolism.
Apart from thromboembolism, chronically expanding atherosclerotic lesions can cause
complete closure of the lumen. Chronically expanding lesions are often asymptomatic
until lumen stenosis is so severe (usually over 80%) that blood supply to downstream
tissue(s) is insufficient, resulting in ischemia.
These complications of advanced atherosclerosis are chronic, slowly progressive and
cumulative. Most commonly, soft plaque suddenly ruptures (see vulnerable plaque),
causing the formation of a thrombus that will rapidly slow or stop blood flow, leading
to death of the tissues fed by the artery in approximately five minutes. This catastrophic event is called an infarction. One of the most common recognized scenarios is
called coronary thrombosis of a coronary artery, causing myocardial infarction (a heart
attack). The same process in an artery to the brain is commonly called stroke. Another
common scenario in very advanced disease is claudication from insufficient blood supply to the legs. Atherosclerosis affects the entire artery tree, but mostly larger, highpressure vessels such as the coronary, renal, femoral, cerebral, and carotid arteries.
These are termed "clinically silent" because the person having the infarction does not
notice the problem and does not seek medical help, or when they do, physicians do not
recognize what has happened.
https://en.wikipedia.org/wiki/Atherosclerosis
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ATP
Adenosine triphosphate (ATP) is a nucleoside triphosphate used in cells as a coenzyme
often called the "molecular unit of currency" of intracellular energy transfer.
ATP transports chemical energy within cells for metabolism. It is one of the end products of photophosphorylation, aerobic respiration, and fermentation, and is used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division. One molecule of ATP contains three phosphate
groups, and it is produced by a wide variety of enzymes, including ATP synthase, from
adenosine diphosphate (ADP) or adenosine monophosphate (AMP) and various phosphate group donors. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three major mechanisms of ATP biosynthesis.
Metabolic processes that use ATP as an energy source convert it back into its precursors. ATP is therefore continuously recycled in organisms: the human body, which on
average contains only 250 grams (8.8oz) of ATP, turns over its own body weight
equivalent in ATP each day.
ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and lipids. It is also used by adenylate cyclase, which uses ATP to produce
the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used
as a way for a cell to sense how much energy is available and control the metabolic
pathways that produce and consume ATP. Apart from its roles in signaling and energy
metabolism, ATP is also incorporated into nucleic acids by polymerases in the process
of transcription. ATP is the neurotransmitter believed to signal the sense of taste.
The ATP concentration inside the cell is typically 110 mM. ATP can be produced by
redox reactions using simple and complex sugars (carbohydrates) or lipids as an energy source. For complex fuels to be synthesized into ATP, they first need to be broken
down into smaller, more simple molecules. Carbohydrates are hydrolyzed into simple
sugars, such as glucose and fructose. Fats (triglycerides) are metabolized to give fatty
acids and glycerol.
The overall process of oxidizing glucose to carbon dioxide is known as cellular respiration and can produce about 30 molecules of ATP from a single molecule of glucose.
ATP can be produced by a number of distinct cellular processes; the three main pathways used to generate energy in eukaryotic organisms are glycolysis and the citric acid
cycle/oxidative phosphorylation, both components of cellular respiration; and betaoxidation. The majority of this ATP production by a non-photosynthetic aerobic eukaryote takes place in the mitochondria, which can make up nearly 25% of the total volume
of a typical cell.
ATP production in an aerobic eukaryotic cell is tightly regulated by allosteric mechanisms, by feedback effects, and by the substrate concentration dependence of individual enzymes within the glycolysis and oxidative phosphorylation pathways. Key control
points occur in enzymatic reactions that are so energetically favorable that they are effectively irreversible under physiological conditions.
In glycolysis, hexokinase is directly inhibited by its product, glucose-6-phosphate, and
pyruvate kinase is inhibited by ATP itself. The main control point for the glycolytic
pathway is phosphofructokinase (PFK), which is allosterically inhibited by high concentrations of ATP and activated by high concentrations of AMP. The inhibition of PFK by
ATP is unusual, since ATP is also a substrate in the reaction catalyzed by PFK; the biologically active form of the enzyme is a tetramer that exists in two possible conformations, only one of which binds the second substrate fructose-6-phosphate (F6P). The
protein has two binding sites for ATP the active site is accessible in either protein
conformation, but ATP binding to the inhibitor site stabilizes the conformation that
binds F6P poorly. A number of other small molecules can compensate for the ATPinduced shift in equilibrium conformation and reactivate PFK, including cyclic AMP,
ammonium ions, inorganic phosphate, and fructose 1,6 and 2,6 biphosphate.
https://en.wikipedia.org/wiki/Adenosine_triphosphate
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G-G
G-G
Chapter 1 - Chemistry, Buffers, and Energy
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure and Function: Proteins
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Protein Function
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 3 - Membranes: Basic Concepts
Chapter 3 - Membranes: Basic Concepts
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Other Considerations
Chapter 4 - Catalysis: Basic Principles
Chapter 4 - Catalysis: Control of Activity
Chapter 4 - Catalysis: Control of Activity
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
ATP Hydrolysis
ATP hydrolysis is the reaction by which chemical energy that has been stored in the
high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released, for
example in muscles, by producing work in the form of mechanical energy. The product
is adenosine diphosphate (ADP) and an inorganic phosphate, orthophosphate (Pi).
ADP can be further hydrolyzed to give energy, adenosine monophosphate (AMP), and
another orthophosphate (Pi). ATP hydrolysis is the final link between the energy derived from food or sunlight and useful work such as muscle contraction, the establishment of electrochemical gradients across membranes, and biosynthetic processes necessary to maintain life.
The description and typical textbook labeling anhydridic bonds as "high energy . .
bonds" can be very misleading to students. These bonds are in fact relatively weak.
They do involve high energy electrons but the bonds themselves are quite easy to
break. As noted below, energy is released by the hydrolysis of ATP when these weak
bonds are broken - requiring a small input of energy, followed by the formation of new
bonds and the release of a larger amount of energy as the total energy of the system is
lowered and becomes more stable.
Hydrolysis of the phosphate groups in ATP is especially exergonic, because the resulting orthophosphate group is greatly stabilized by multiple resonance structures, making the products (ADP and Pi) much lower in energy than the reactant (ATP). The high
negative charge density associated with the three adjacent phosphate units of ATP also
destabilizes the molecule, making it higher in energy. Hydrolysis relieves some of these
electrostatic repulsions, liberating useful energy in the process by causing conformational changes in enzyme structure.
Hydrolysis of the terminal phosphoanhydridic bond is a highly exergonic process, releasing 30.5 kJ mol1 energy. This reaction can then be coupled with thermodynamically unfavorable reactions to give an overall negative (spontaneous) G for the reaction sequence. The actual value of G for ATP hydrolysis varies, primarily depending
on Mg2+ concentration, and under normal physiologic conditions is actually closer to
-50 kJ mol1.
In humans, approximately 60 percent of the energy released from the hydrolysis of one
mole of ATP produces metabolic heat rather than fuel the actual reactions taking place.
Due to the acid-base properties of ATP, ADP, and inorganic phosphate, the hydrolysis
of ATP has the effect of lowering the pH of the reaction medium. Under certain conditions, high levels of ATP hydrolysis can contribute to lactic acidosis.
https://en.wikipedia.org/wiki/ATP_hydrolysis
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ATP Synthase
ATP synthase (EC 3.6.3.14) is an important enzyme that creates the energy currency
molecule adenosine triphosphate (ATP). ATP is the most commonly used "energy currency" of cells from most organisms. It is formed from adenosine diphosphate (ADP)
and inorganic phosphate (Pi), and needs energy for its formation.
The overall reaction sequence is:
ADP + Pi + Energy ATP
where ADP and Pi are joined together by ATP synthase.
Energy used is available in the form of hydrogen ions (H+), moving down an electrochemical gradient, such as from the thylakoid lumen through the thylakoid membrane
and into the chloroplast stroma (of plants) or from the inter-membrane space and into
the matrix in mitochondria.
ATP synthase consists of two regions
the F0 portion embedded within the membrane
the F1 portion of the ATP synthase is outside the membrane, but inside the matrix of
the mitochondria.
In plants, ATP synthase is also present in chloroplasts (CF1F0-ATP synthase). The enzyme is integrated into thylakoid membrane. The CF1-part sticks into stroma, where
dark reactions of photosynthesis (also called the light-independent reactions or the Calvin cycle) and ATP synthesis take place. The overall structure and the catalytic mechanism of the chloroplast ATP synthase are almost the same as those of the mitochondrial enzyme. However, in chloroplasts, the proton motive force is generated not by respiratory electron transport chain but by primary photosynthetic proteins.
https://commons.wikimedia.org/wiki/File:Atp_synthase.PNG
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ATP-phosphoribosyltransferase
ATP phosphoribosyltransferase (EC 2.4.2.17) is an enzyme that catalyzes the chemical
reaction
1-(5-phospho-D-ribosyl)-ATP + diphosphate <-> ATP + 5-phospho-alpha-D-ribose 1diphosphate
This enzyme catalyses the first step in the biosynthesis of histidine in bacteria, fungi
and plants. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate
with nitrogenous bases in the presence of divalent metal ions.
Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is
based primarily on nutrient conditions and determines the amount of enzyme present
in the cell, while feedback inihibition rapidly modulates activity in response to cellular
conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and
ADP and AMP (which reflect the overall energy status of the cell). As this pathway of
histidine biosynthesis is present only in prokaryotes, plants and fungi, this enzyme is a
promising target for the development of novel antimicrobial compounds and herbicides.
ATP phosphoribosyltransferase is found in two distinct forms: a long form containing
two catalytic domains and a C-terminal regulatory domain, and a short form in which
the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required
for enzyme activity.
https://en.wikipedia.org/wiki/ATP_phosphoribosyltransferase
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ATPase
ATPases are a class of enzymes that catalyze the decomposition of ATP into ADP and a
free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme (in most cases) harnesses to drive other chemical reactions that would not otherwise occur. This process is widely used in all known forms of life.
Transmembrane ATPases import many of the metabolites necessary for cell metabolism and export toxins, wastes, and solutes that can hinder cellular processes. An important example is the sodium-potassium exchanger (or Na+/K+ATPase) that maintains the cell membrane potential. And another example is the hydrogen potassium ATPase (H+/K+ATPase or gastric proton pump) that acidifies the contents of the stomach.
Besides exchangers, other categories of transmembrane ATPase include cotransporters and pumps (however, some exchangers are also pumps). Some of these,
like the Na+/K+ATPase, cause a net flow of charge, but others do not. These are called
"electrogenic" and "nonelectrogenic" transporters, respectively.
There are different types of ATPases, which can differ in function (ATP synthesis and/
or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type
of ions they transport.
F-ATPases (F1FO-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).
V-ATPases (V1VO-ATPases) are primarily found in eukaryotic vacuoles, catalyzing
ATP hydrolysis to transport solutes and lower pH in organelles like proton pump of lysosome.
A-ATPases (A1AO-ATPases) are found in Archaea and function like F-ATPases
P-ATPases (E1E2-ATPases) are found in bacteria, fungi and in eukaryotic plasma
membranes and organelles, and function to transport a variety of different ions across
membranes.
E-ATPases are cell-surface enzymes that hydrolyze a range of NTPs, including extracellular ATP.
https://en.wikipedia.org/wiki/ATPase
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Attenuation
Attenuation is a means of controlling gene expression in bacteria that employs translation to help regulate transcription of operons involved in amino acid metabolism. In
this method, abundance of tryptophan (or several other amino acids) during translation of a portion of the mRNA copy of the tryptophan operon (coding sequences for enzymes necessary to make leucine) causes the mRNA to form a transcriptional termination sequence. This, in turn, causes transcription of the operon coding for the genes
necessary to synthesize tryptophan to terminate prematurely, thus stopping production of the enzymes necessary to make tryptophan. When tryptophan is in short supply, the transcription termination structure is unable to form and transcription of the
entire operon proceeds.
Attenuation is a regulatory feature found throughout Archaea and Bacteria causing premature termination of transcription. Attenuators are 5'-cis acting regulatory regions
which fold into one of two alternative RNA structures which determine the success of
transcription. The folding is modulated by a sensing mechanism producing either a
Rho-independent terminator, resulting in interrupted transcription and a nonfunctional RNA product, or an anti-terminator structure, resulting in a functional RNA
transcript. There are now many equivalent examples where the translation, not transcription, is terminated by sequestering the Shine-Dalgarno sequence (ribosomal binding site) in a hairpin-loop structure. While not meeting the previous definition of (transcriptional) attenuation, these are now considered to be variants of the same phenomena and are included in this article. Attenuation is an ancient regulatory system, prevalent in many bacterial species providing fast and sensitive regulation of gene operons
and is commonly used to repress genes in the presence of their own product (or a downstream metabolite).
https://en.wikipedia.org/wiki/Attenuator_(genetics)
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Autoimmune
healthy cells and tissues. Any disease that results from such an aberrant im
sponse is termed an autoimmune disease.
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Autosomal
appear in pairs whose members have the same form but differ from other p
loid cell, whereas members of an allosome pair may differ from one another
Autosomal Recessive
The first allele is dominant and the second allele is recessive. For genes on a
some (any chromosome other than a sex chromosome), the alleles and their
Mendelian inheritance and classical genetics. Often the dominant allele cod
functional protein whereas the recessive allele does not.
https://en.wikipedia.org/wiki/Dominance_(genetics)
Autotrophic
An autotroph ("self-feeding", from the Greek autos "self" and trophe "nouri
producer, is an organism that produces complex organic compounds (such
drates, fats, and proteins) from simple substances present in its surroundin
synthesis). They are the producers in a food chain, such as plants on land or
Autotrophs
An autotroph ("self-feeding", from the Greek autos "self" and trophe "nouri
producer, is an organism that produces complex organic compounds (such
drates, fats, and proteins) from simple substances present in its surroundin
synthesis). They are the producers in a food chain, such as plants on land or
Auxin
Auxins are a class of plant hormones (or plant growth substances) with some
morphogen-like characteristics. Auxins have a cardinal role in coordination of many
growth and behavioral processes in the plant's life cycle and are essential for plant
body development.
Auxins were the first of the major plant hormones to be discovered. They derive their
name from the Greek word (auxein "to grow/increase"). Auxin (namely IAA)
is present in all parts of a plant, although in very different concentrations. The concentration in each position is crucial developmental information, so it is subject to tight
regulation through both metabolism and transport. The result is the auxin creates "patterns" of auxin concentration maxima and minima in the plant body, which in turn
guide further development of respective cells, and ultimately of the plant as a whole.
On the cellular level, auxin is essential for cell growth, affecting both cell division and
cellular expansion. Auxin concentration level, together with other local factors, contributes to cell differentiation and specification of the cell fate.
Depending on the specific tissue, auxin may promote axial elongation (as in shoots),
lateral expansion (as in root swelling), or isodiametric expansion (as in fruit growth).
In some cases (coleoptile growth), auxin-promoted cellular expansion occurs in the absence of cell division. In other cases, auxin-promoted cell division and cell expansion
may be closely sequenced within the same tissue (root initiation, fruit growth). In a living plant, auxins and other plant hormones nearly always appear to interact to determine patterns of plant development.
Pictured below - Indol-3-ylacetic acid, an auxin
https://en.wikipedia.org/wiki/Auxin
Axon
An axon is a long, slender projection of a nerve cell, or neuron, that typically conducts
electrical impulses away from the neuron's cell body. Myelinated axons are known as
nerve fibers. The function of the axon is to transmit information to different neurons,
muscles and glands. In certain sensory neurons (pseudounipolar neurons), such as
those for touch and warmth, the electrical impulse travels along an axon from the periphery to the cell body, and from the cell body to the spinal cord along another branch
of the same axon. Axon dysfunction causes many inherited and acquired neurological
disorders which can affect both the peripheral and central neurons.
An axon is one of two types of protoplasmic protrusions that extrude from the cell
body of a neuron, the other type being dendrites. Axons are distinguished from dendrites by several features, including shape (dendrites often taper while axons usually
maintain a constant radius), length (dendrites are restricted to a small region around
the cell body while axons can be much longer), and function (dendrites usually receive
signals while axons usually transmit them). All of these rules have exceptions, however.
Some types of neurons have no axon and transmit signals from their dendrites. No neuron ever has more than one axon; however in invertebrates such as insects or leeches
the axon sometimes consists of several regions that function more or less independently of each other. Most axons branch, in some cases very profusely.
Axons make contact with other cellsusually other neurons but sometimes muscle or
gland cellsat junctions called synapses. At a synapse, the membrane of the axon
closely adjoins the membrane of the target cell, and special molecular structures serve
to transmit electrical or electrochemical signals across the gap. Some synaptic junctions appear partway along an axon as it extendsthese are called en passant ("in passing") synapses. Other synapses appear as terminals at the ends of axonal branches. A
single axon, with all its branches taken together, can innervate multiple parts of the
brain and generate thousands of synaptic terminals.
https://en.wikipedia.org/wiki/Axon
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Azide
Azide is the anion with the formula N3. It is the conjugate base of hydrazoi
(HN3). N3 is a linear anion that is isoelectronic with CO2 and N2O. Per vale
https://en.wikipedia.org/wiki/Azide
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B-form DNA
At least three DNA conformations are found in nature, A-DNA, B-DNA, and Z-DNA.
The "B" form described by James D. Watson and Francis Crick is believed to predominate in cells. It is 23.7 wide and extends 34 per 10 bp of sequence. The double helix
makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (known as the helical pitch) depends largely on stacking forces that
each base exerts on its neighbors in the chain.
A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. It was long thought that the A form only occurs in
dehydrated samples of DNA in the laboratory, such as those used in crystallographic
experiments, and in hybrid pairings of DNA and RNA strands, but DNA dehydration
does occur in vivo, and A-DNA is now known to have biological functions. Segments of
DNA that cells have been methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis the opposite way to A-DNA and BDNA. There is also evidence of protein-DNA complexes forming Z-DNA structures.
Other conformations are possible: A-DNA, B-DNA, C-DNA, E-DNA, L-DNA (the enantiomeric form of D-DNA), P-DNA, S-DNA, Z-DNA, etc. have been described so far. In
fact, only the letters F, Q, U, V, and Y are now available to describe any new DNA structure that may appear in the future. However, most of these forms have been created
synthetically and have not been observed in naturally occurring biological systems.
There are also triple-stranded DNA forms and quadruplex forms such as the Gquadruplex.
From left to right - A, B, and Z forms of DNA
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
B12
Vitamin B12 or vitamin B-12, also called cobalamin, is a water-soluble vitamin that has
a key role in the normal functioning of the brain and nervous system, and the formation of red blood cells. It is one of eight B vitamins. It is involved in the metabolism of
every cell of the human body, especially affecting DNA synthesis, fatty acid and amino
acid metabolism. No fungi, plants, nor animals (including humans) are capable of producing vitamin B12. Only bacteria and archaea have the enzymes needed for its synthesis. Some plant foods are a natural source of B12 because of bacterial symbiosis. B12 is
the largest and most structurally complicated vitamin and can be produced industrially
only through a bacterial fermentation-synthesis. This synthetic B12 is used to fortify
foods and sold as a dietary supplement.
Vitamin B12 consists of a class of chemically related compounds (vitamers), all of which
show pharmacological activity. It contains the biochemically rare element cobalt
(chemical symbol Co) positioned in the center of a planar tetra-pyrrole ring called a corrin ring. The vitamer is produced by bacteria as hydroxocobalamin, but conversion between different forms of the vitamin occurs in the body after consumption.
A common synthetic form of the vitamin is cyanocobalamin, produced by chemically
modifying bacterial hydroxocobalamin. Because of superior stability and low cost this
form is used in many pharmaceuticals and supplements as well as for fortification of
foods. In the body, it is converted into the human physiological forms methylcobalamin and 5'-deoxyadenosylcobalamin. In this process a cyanide ion, (CN), is produced,
but the amount is very, very small (20 g from 1,000 g of cyanocobalamin) compared
to what would cause a toxicity risk, and is in fact less than the amount of cyanide consumed daily from food (primarily fruit, nuts, seeds, and legumes). Cyanide-free synthetic forms of the vitaminhydroxocobalamin, methylcobalamin, and adenosylcobalaminare being used in some pharmacological products and supplements, but their
claimed superiority to cyanocobalamin is debatable.
Vitamin B12 was discovered from its relationship to the disease pernicious anemia, an
autoimmune disease in which parietal cells of the stomach responsible for secreting intrinsic factor are destroyed. These cells are also responsible for secreting acid in the
stomach. Because intrinsic factor is crucial for the normal absorption of B12, its lack in
the presence of pernicious anemia causes a vitamin B12 deficiency. Many other subtler
kinds of vitamin B12 deficiency and their biochemical effects have since been elucidated.
https://en.wikipedia.org/wiki/Vitamin_B12
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Bacteria
Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods
and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive
waste, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals.
There are typically 40 million bacterial cells in a gram of soil and a million bacterial
cells in a milliliter of fresh water. There are approximately 51030 bacteria on Earth,
forming a biomass which exceeds that of all plants and animals. Bacteria are vital in recycling nutrients, with many of the stages in nutrient cycles dependent on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide
the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy.
On 17 March 2013, researchers reported data that suggested bacterial life forms thrive
in the Mariana Trench, which with a depth of up to 11 kilometers is the deepest part of
the Earth's oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 meters below the sea floor under 2.6 kilometers of ocean off the
coast of the northwestern United States. According to one of the researchers, "You can
find microbes everywhere they're extremely adaptable to conditions, and survive
wherever they are. Shown below - cells of E. coli.
https://en.wikipedia.org/wiki/Bacteria
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Bacteriophages
A bacteriophage is a virus that infects and replicates within a bacterium. The term is derived from "bacteria" and the Greek: (phagein), "to devour". Bacteriophages are
composed of proteins that encapsulate a DNA or RNA genome, and may have relatively
simple or elaborate structures. Their genomes may encode as few as four genes, and as
many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common
and diverse entities in the biosphere.
Phages are widely distributed in locations populated by bacterial hosts, such as soil or
the intestines of animals. One of the densest natural sources for phages and other viruses is sea water, where up to 9108 virions per milliliter have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages.
They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria (see phage therapy). Nevertheless, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis, shelter the bacteria from drugs meant to eradicate disease
and promote persistent infection.
https://en.wikipedia.org/wiki/Bacteriophage
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BamH I
the capacity for recognizing short sequences (6 b.p.) of DNA and specificall
them at a target site. Specifically, BAMH I cuts duplex DNA as shown below
places of the vertical bars.
G|GATC C
C CTAG|G
https://en.wikipedia.org/wiki/BamHI
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Base
The term base has two meanings in biochemistry
1. Bases are substances that, in aqueous solution, are slippery to the touch,
gent, change the color of indicators (e.g., turn red litmus paper blue), react
Index
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https://en.wikipedia.org/wiki/Base_excision_repair
Base Pairing
A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix, and contribute to
the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the
DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a
backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well
suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base
pairs (G-C and A-U) permit the formation of short double-stranded helices, and a wide
variety of non-Watson-Crick interactions (e.g., G-U or A-A) allow RNAs to fold into a
vast range of specific three-dimensional structures. In addition, base-pairing between
transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular
recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code.
The size of an individual gene or an organism's entire genome is often measured in
base pairs because DNA is usually double-stranded. Hence, the number of total base
pairs is equal to the number of nucleotides in one of the strands (with the exception of
non-coding single-stranded regions of telomeres). The haploid human genome (23
chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000
25,000 distinct protein-coding genes. A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related
DNA base pairs on Earth is estimated at 5.0 x 1037, and weighs 50 billion tonnes. In
comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC
(trillion tons of carbon).
https://en.wikipedia.org/wiki/Base_pair
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Base Pairs
A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix, and contribute to
the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the
DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a
backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well
suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base
pairs (G-C and A-U) permit the formation of short double-stranded helices, and a wide
variety of non-Watson-Crick interactions (e.g., G-U or A-A) allow RNAs to fold into a
vast range of specific three-dimensional structures. In addition, base-pairing between
transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular
recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code.
The size of an individual gene or an organism's entire genome is often measured in
base pairs because DNA is usually double-stranded. Hence, the number of total base
pairs is equal to the number of nucleotides in one of the strands (with the exception of
non-coding single-stranded regions of telomeres). The haploid human genome (23
chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000
25,000 distinct protein-coding genes. A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related
DNA base pairs on Earth is estimated at 5.0 x 1037, and weighs 50 billion tonnes. In
comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC
(trillion tons of carbon).
https://en.wikipedia.org/wiki/Base_pair
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Basement Membrane
The basement membrane is a thin, fibrous, extracellular matrix of tissue that separates
the epithelium (skin, respiratory tract, gastrointestinal tract, etc), mesothelium (pleural cavity, peritoneal cavity, pericardial cavity, etc) and endothelium (blood vessels,
lymph vessels, etc) from underlying connective tissue.
https://en.wikipedia.org/wiki/Basement_membrane
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Bcl-2
Bcl-2 (B-cell lymphoma 2), encoded in humans by the BCL2 gene, is the founding member of the Bcl-2 family of regulator proteins that regulate cell death (apoptosis), by either inducing (pro-apoptotic) or inhibiting (anti-apoptotic) apoptosis. Bcl-2 is specifically considered an important anti-apoptotic protein and is thus classified as an oncogene.
BCL-2 is localized to the outer membrane of mitochondria, where it plays an important
role in promoting cellular survival and inhibiting the actions of pro-apoptotic proteins.
The pro-apoptotic proteins in the BCL-2 family, including Bax and Bak, normally act
on the mitochondrial membrane to promote permeabilization and release of cytochrome C and ROS, that are important signals in the apotosis cascade. These proapoptotic proteins are in turn activated by BH3-only proteins, and are inhibited by the
function of BCL-2 and its relative BCL-Xl.
There are additional non-canonical roles of BCL-2 that are being explored. BLC-2 is
known to regulate mitochondrial dynamics, and is involved in the regulation of mitochondrial fusion and fission. Additionally, in pancreatic -cells, BCL-2 and BCL-Xl are
known to be involved in controlling metabolic activity and insulin secretion, with inhibition of BCL-2/Xl showing increasing metabolic activity, but also additional ROS production. This suggests it has a protective metabolic effect in conditions of high demand.
https://en.wikipedia.org/wiki/Bcl-2
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Bcr-abl
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incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
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Beads on a String
In addition to the core histones, there is the linker histone, H1, which contacts the ex
entry of the DNA strand on the nucleosome. The nucleosome core particle, together
DNA packaging. There are, however, large DNA sequence preferences that govern nu
cleosome positioning. This is due primarily to the varying physical properties of diffe
ent DNA sequences: For instance, adenine and thymine are more favorably com-
pressed into the inner minor grooves. This means nucleosomes can bind preferential
at one position approximately every 10 base pairs (the helical repeat of DNA)- where
the DNA is rotated to maximize the number of A and T bases that will lie in the inner
minor groove.
https://en.wikipedia.org/wiki/Chromatin
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Benedicts Test
Several qualitative tests are used to detect the presence of reducing sugars. Two of
them use solutions of copper(II) ions: Benedict's reagent (Cu++ in aqueous sodium citrate) and Fehling's solution (Cu++ in aqueous sodium tartrate). The reducing sugar reduces the copper(II) ions in these test solutions to copper(I), which then forms a brick
red copper(I) oxide precipitate. Reducing sugars can also be detected with the addition
of Tollen's reagent, which consist of silver ions (Ag+) in aqueous ammonia. When Tollen's reagent is added to an aldehyde, it precipitates silver metal, often forming a silver
mirror on clean glassware.
3,5-dinitrosalicylic acid is another test reagent, one that allows quantitative detection.
It reacts with a reducing sugar to form 3-amino-5-nitrosalicylic acid, which can be
measured by spectrophotometry to determine the amount of reducing sugar that was
present.
Sugars having acetal or ketal linkages are not reducing sugars, as they do not have free
aldehyde chains. They therefore do not react with any of the reducing-sugar test solutions. However, a non-reducing sugar can be hydrolyzed using dilute hydrochloric
acid. After hydrolysis and neutralization of the acid, the product may be a reducing
sugar that gives normal reactions with the test solutions.
https://en.wikipedia.org/wiki/Reducing_sugar
Benzopyrene
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Beta Barrels
A barrel is a large beta-sheet that twists and coils to form a closed structure in which
the first strand is hydrogen bonded to the last. -strands in beta-barrels are typically
arranged in an antiparallel fashion. Barrel structures are commonly found in porins
and other proteins that span cell membranes and in proteins that bind hydrophobic
ligands in the barrel center, as in lipocalins. Porin-like barrel structures are encoded by
as many as 23% of the genes in Gram-negative bacteria.
In many cases the strands contain alternating polar and hydrophobic amino acids, so
that the hydrophobic residues are oriented into the interior of the barrel to form a hydrophobic core and the polar residues are oriented toward the outside of the barrel on
the solvent-exposed surface. Porins and other membrane proteins containing beta barrels reverse this pattern, with hydrophobic residues oriented toward the exterior where
they contact the surrounding lipids, and hydrophilic residues oriented toward the interior pore.
https://en.wikipedia.org/wiki/Beta_barrel
Betaine-homocysteine Methyltransferase
https://en.wikipedia.org/wiki/Betaine%E2%80%94homocysteine_S-meth
e
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Bicarbonate
In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogen
carbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula HCO3-.
Bicarbonate serves a crucial biochemical role in the physiological pH buffering system.
https://en.wikipedia.org/wiki/Bicarbonate
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Bile
Bile or gall is a dark green to yellowish brown fluid, produced by the liver of
brates, that aids the digestion of lipids in the small intestine. In humans, bi
duced continuously by the liver (liver bile), and stored and concentrated in
der (gallbladder bile). After eating, this stored bile is discharged into the du
The composition of gallbladder bile is 97% water, 0.7% bile salts, 0.2% bilir
fats (cholesterol, fatty acids and lecithin), and 200 meq/l inorganic salts.
https://en.wikipedia.org/wiki/Bile
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Bile Acid
Bile acids are steroid acids found predominantly in the bile of mammals and other vertebrates. Different molecular forms of bile acids can be synthesized in the liver by different species. Bile acids are conjugated with taurine or glycine in the liver, forming
bile salts. Primary bile acids are those synthesized by the liver. Secondary bile acids result from bacterial actions in the colon. In humans, taurocholic acid and glycocholic
acid (derivatives of cholic acid) and taurochenodeoxycholic acid and glycochenodeoxycholic acid (derivatives of chenodeoxycholic acid) are the major bile salts in bile and
are roughly equal in concentration.
As amphipathic molecules with hydrophobic and hydrophilic regions, conjugated bile
salts sit at the lipid/water interface and, at the right concentration, form micelles. The
added solubility of conjugated bile salts aids in their function by preventing passive reabsorption in the small intestine. As a result, the concentration of bile acids/salts in
the small intestine is high enough to form micelles and solubilize lipids. "Critical micellar concentration" refers to both an intrinsic property of the bile acid itself and amount
of bile acid necessary to function in the spontaneous and dynamic formation of micelles. Bile acid-containing micelles aid lipases to digest lipids and bring them near the
intestinal brush border membrane, which results in fat absorption.
Synthesis of bile acids is a major route of cholesterol metabolism in most species other
than humans. The body produces about 800mg of cholesterol per day and about half
of that is used for bile acid synthesis producing 400600mg daily. Human adults secrete between 12-18g of bile acids into the intestine each day, mostly after meals. The
bile acid pool size is between 46g, which means that bile acids are recycled several
times each day. About 95% of bile acids are reabsorbed by active transport in the ileum
and recycled back to the liver for further secretion into the biliary system and gallbladder. This enterohepatic circulation of bile acids allows a low rate of synthesis but with
large amounts being secreted into the intestine.
Bile acids have other functions, including eliminating cholesterol from the body, driving the flow of bile to eliminate certain catabolites (including bilirubin), emulsifying
fat-soluble vitamins to enable their absorption, and aiding in motility and the reduction of the bacteria flora found in the small intestine and biliary tract.
https://en.wikipedia.org/wiki/Bile_acid
Bile Acids
Bile acids are steroid acids found predominantly in the bile of mammals and other vertebrates. Different molecular forms of bile acids can be synthesized in the liver by different species. Bile acids are conjugated with taurine or glycine in the liver, forming
bile salts. Primary bile acids are those synthesized by the liver. Secondary bile acids result from bacterial actions in the colon. In humans, taurocholic acid and glycocholic
acid (derivatives of cholic acid) and taurochenodeoxycholic acid and glycochenodeoxycholic acid (derivatives of chenodeoxycholic acid) are the major bile salts in bile and
are roughly equal in concentration.
As amphipathic molecules with hydrophobic and hydrophilic regions, conjugated bile
salts sit at the lipid/water interface and, at the right concentration, form micelles. The
added solubility of conjugated bile salts aids in their function by preventing passive reabsorption in the small intestine. As a result, the concentration of bile acids/salts in
the small intestine is high enough to form micelles and solubilize lipids. "Critical micellar concentration" refers to both an intrinsic property of the bile acid itself and amount
of bile acid necessary to function in the spontaneous and dynamic formation of micelles. Bile acid-containing micelles aid lipases to digest lipids and bring them near the
intestinal brush border membrane, which results in fat absorption.
Synthesis of bile acids is a major route of cholesterol metabolism in most species other
than humans. The body produces about 800mg of cholesterol per day and about half
of that is used for bile acid synthesis producing 400600mg daily. Human adults secrete between 12-18g of bile acids into the intestine each day, mostly after meals. The
bile acid pool size is between 46g, which means that bile acids are recycled several
times each day. About 95% of bile acids are reabsorbed by active transport in the ileum
and recycled back to the liver for further secretion into the biliary system and gallbladder. This enterohepatic circulation of bile acids allows a low rate of synthesis but with
large amounts being secreted into the intestine.
Bile acids have other functions, including eliminating cholesterol from the body, driving the flow of bile to eliminate certain catabolites (including bilirubin), emulsifying
fat-soluble vitamins to enable their absorption, and aiding in motility and the reduction of the bacteria flora found in the small intestine and biliary tract.
https://en.wikipedia.org/wiki/Bile_acid
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Bilirubin
Bilirubin (formerly referred to as haematoidin) is the yellow breakdown product of normal heme catabolism, caused by the body's clearance of aged red blood cells which contain hemoglobin.
Bilirubin is excreted in bile and urine, and elevated levels may indicate certain diseases. It is responsible for the yellow color of bruises and the yellow discoloration in
jaundice. It is also responsible for the brown color of feces, via its conversion to stercobilin, and the background straw-yellow color of urine via its breakdown product, urobilin.
https://en.wikipedia.org/wiki/Bilirubin
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Biliverdin
Biliverdin is a green tetrapyrrolic bile pigment, and is a product of heme catabolism. It
is the pigment responsible for a greenish color sometimes seen in bruises. Biliverdin
results from the breakdown of the heme moiety of hemoglobin in erythrocytes. Macrophages break down senescent erythrocytes and break the heme down into biliverdin,
which normally rapidly reduces to free bilirubin.
While typically regarded as a mere waste product of heme breakdown, evidence that
suggests that biliverdin and other bile pigments has a physiological role in humans has been mounting.
Bile pigments such as biliverdin possess significant anti-mutagenic and antioxidant
properties and therefore may fulfill a useful physiological function. Biliverdin and bilirubin have been shown to be potent scavengers of peroxyl radicals. They have also
been shown to inhibit the effects of polycyclic aromatic hydrocarbons, heterocyclic
amines, and oxidants all of which are mutagens. Some studies have found that people with higher concentration levels of bilirubin and biliverdin in their bodies have a
lower frequency of cancer and cardiovascular disease. It has been suggested that biliverdin as well as many other tetrapyrrolic pigments may function as an HIV-1 protease inhibitor as well as having beneficial effects in asthma though further research is
needed to confirm these results. There are currently no practical implications for using
biliverdin in the treatment of any disease.
https://en.wikipedia.org/wiki/Biliverdin
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Biliverdin Reductase
Biliverdin reductase (BVR) is an enzyme (EC 1.3.1.24) found in all tissues under
https://en.wikipedia.org/wiki/Biliverdin_reductase
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Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through
biochemical signaling and the flow of chemical energy through metabolism, biochemical processes give rise to the complexity of life. Over the last decades of the 20th century, biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine to genetics are engaged in
biochemical research. Today, the main focus of pure biochemistry is on understanding
how biological molecules give rise to the processes that occur within living cells, which
in turn relates greatly to the study and understanding of tissues, organs, and whole organismsthat is, all of biology.
Biochemistry is closely related to molecular biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes
of life. Depending on the exact definition of the terms used, molecular biology can be
thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate and study molecular biology.
Much of biochemistry deals with the structures, functions and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates and lipids, which
provide the structure of cells and perform many of the functions associated with life.
The chemistry of the cell also depends on the reactions of smaller molecules and ions.
These can be inorganic, for example water and metal ions, or organic, for example the
amino acids, which are used to synthesize proteins. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism.
The findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases. In nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways
to improve crop cultivation, crop storage and pest control.
https://en.wikipedia.org/wiki/Biochemistry
Biofilms
A biofilm is any group of microorganisms in which cells stick to each other and often
these cells adhere to a surface. These adherent cells are frequently embedded within a
self-produced matrix of extracellular polymeric substance (EPS). Biofilm extracellular
polymeric substance, which is also referred to as slime (although not everything described as slime is a biofilm), is a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides. Biofilms may form on living or nonliving surfaces and can be prevalent in natural, industrial and hospital settings. A
Staphylococcus aureus biofilm is shown below.
https://en.wikipedia.org/wiki/Biofilm
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Biotin
Biotin is a water-soluble B-vitamin (vitamin B7), formerly known as vitamin H or coenzyme R.
It is composed of a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring. A valeric acid substituent is attached to one of the carbon atoms of the tetrahydrothiophene ring. Biotin is a coenzyme for carboxylase enzymes, involved in the
synthesis of fatty acids, isoleucine, and valine, and in gluconeogenesis.
Biotin deficiency can be caused by inadequate dietary intake or inheritance of one or
more inborn genetic disorders that affect biotin metabolism (see multiple carboxylase
deficiency). Subclinical deficiency can cause mild symptoms, whereas the inborn genetic disorders can have severe (even lethal) consequences. Neonatal screening for biotinidase deficiency began in the United States in 1984 and today many countries test
for this disorder at birth. Individuals born prior to 1984 are unlikely to have been
screened, thus the true prevalence of the disorder is unknown.
Biotin-thiamine-responsive basal ganglia disease is another potentially life-threatening
condition that requires biotin (and thiamine, another B vitamin) for treatment.
https://en.wikipedia.org/wiki/Biotin
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Biotinylation
In biochemistry, biotinylation is the process of covalently attaching biotin to a protein,
nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb
the natural function of the molecule due to the small size of biotin (MW = 244.31 g/
mol). Biotin binds to streptavidin and avidin with an extremely high affinity, fast onrate, and high specificity, and these interactions are exploited in many areas of biotechnology to isolate biotinylated molecules of interest. Biotin-binding to streptavidin and
avidin is resistant to extremes of heat, pH and proteolysis, making capture of biotinylated molecules possible in a wide variety of environments. Also, multiple biotin molecules can be conjugated to a protein of interest, which allows binding of multiple streptavidin, avidin or Neutravidin protein molecules and increases the sensitivity of detection of the protein of interest. There is a large number of biotinylation reagents available that exploit the wide range of possible labelling methods. Due to the strong affinity between biotin and streptavidin, the purification of biotinylated proteins has been a
widely used approach to identify protein-protein interactions and post-translational
events such as ubiquitylation in molecular biology.
https://en.wikipedia.org/wiki/Biotinylation
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Bisphophglycerate Mutase
BPG) from 1,3-bisphosphoglycerate. BPGM also has a mutase and a phosphatase fun
tion, but these are much less active, in contrast to its glycolitic cousin, phosphoglycer
ate mutase (PGM), which favors these two functions, but can also catalyze the synthe
sis of 2,3-BPG to a lesser extent.
1,3-BPG is formed as an intermediate in glycolysis. BPGM then takes this and conver
with high affinity to hemoglobin, causing a conformational change that results in the
release of oxygen. Local tissues can then pick up the free oxygen. This is also importa
in the placenta, where fetal and maternal blood come within such close proximity.
With the placenta producing 2,3-BPG, a large amount of oxygen is released from
nearby maternal hemoglobin, which can then dissociate and bind with fetal hemoglo
bin, which has a much lower affinity for 2,3-BPG.
https://en.wikipedia.org/wiki/Bisphosphoglycerate_mutase
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Blood
Blood is a bodily fluid in animals that delivers necessary substances such as nutrients
and oxygen to the cells and transports metabolic waste products away from those same
cells.
In vertebrates, it is composed of blood cells suspended in blood plasma. Plasma, which
constitutes 55% of blood fluid, is mostly water (92% by volume), and contains dissipated proteins, glucose, mineral ions, hormones, carbon dioxide (plasma being the
main medium for excretory product transportation), and blood cells themselves. Albumin is the main protein in plasma, and it functions to regulate the colloidal osmotic
pressure of blood. The blood cells are mainly red blood cells (also called RBCs or erythrocytes), white blood cells (also called WBCs or leukocytes) and platelets. The most
abundant cells in vertebrate blood are red blood cells. These contain hemoglobin, an
iron-containing protein, which facilitates oxygen transport by reversibly binding to this
respiratory gas and greatly increasing its solubility in blood. In contrast, carbon dioxide is almost entirely transported extracellularly dissolved in plasma as bicarbonate
ion.
Vertebrate blood is bright red when its hemoglobin is oxygenated and dark red when it
is deoxygenated. Some animals, such as crustaceans and mollusks, use hemocyanin to
carry oxygen, instead of hemoglobin. Insects and some mollusks use a fluid called
hemolymph instead of blood, the difference being that hemolymph is not contained in
a closed circulatory system. In most insects, this "blood" does not contain oxygencarrying molecules such as hemoglobin because their bodies are small enough for their
tracheal system to suffice for supplying oxygen.
https://en.wikipedia.org/wiki/Blood
Blood Clotting
Coagulation (also known as clotting) is the process by which blood changes from a liquid to a gel, forming a clot. It potentially results in hemostasis, the cessation of blood
loss from a damaged vessel, followed by repair. The mechanism of coagulation involves
activation, adhesion, and aggregation of platelets along with deposition and maturation of fibrin. Disorders of coagulation are disease states which can result in bleeding
(hemorrhage or bruising) or obstructive clotting (thrombosis).
Coagulation is highly conserved throughout biology - in all mammals, coagulation involves both a cellular (platelet) and a protein (coagulation factor) component. The system in humans has been the most extensively researched and is the best understood.
Coagulation begins almost instantly after an injury to the blood vessel has damaged
the endothelium lining the vessel. Exposure of blood to the space under the endothelium initiates two processes: changes in platelets, and the exposure of subendothilial
tissue factor to plasma Factor VII, which ultimately leads to fibrin formation. Platelets
immediately form a plug at the site of injury. This is called primary hemostasis. Secondary hemostasis occurs simultaneously: Additional coagulation factors or clotting factors beyond Factor VII respond in a complex cascade to form fibrin strands, which
strengthen the platelet plug.
https://en.wikipedia.org/wiki/Coagulation
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Blood Thinning
The term blood thinning refers to using an anticoagulant to reduce the clotting tendency of blood in a patient. Anticoagulants occur naturally in leeches and bloodsucking insects. A group of pharmaceuticals called anticoagulants can be used as an injection as a medication for thrombotic disorders. Oral anticoagulants are also available. Some anticoagulants are used in medical equipment, such as test tubes, blood
transfusion bags, and renal dialysis equipment.
Anticoagulants are closely related to antiplatelet drugs and thrombolytic drugs by manipulating the various pathways of blood coagulation. Specifically, anticoagulants manipulate the coagulation cascade that builds upon the initial platelet thrombus.
A number of anticoagulants are available. The traditional ones (warfarin, other coumarins and heparins) are in widespread use. Since the 2000s a number of new agents
have been introduced that are collectively referred to as the novel oral anticoagulants
(NOACs) or directly acting oral anticoagulants (DOACs). These agents include inhibitors of factor IIa (dabigatran) and factor Xa (rivaroxaban, apixaban and edoxaban) and
they have been shown to be as good or possibly better than the coumarins with less serious side effects. The newer anticoagulants (NOACs/DOACs), are more expensive than
the traditional ones and should be used with care in patients with kidney problems. Additionally, there is no antidote for the factor Xa inhibitors, so it is difficult to stop their
effects in the body in cases of emergency (accidents, urgent surgery).
https://en.wikipedia.org/wiki/Anticoagulant
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Blood-brain Barrier
The bloodbrain barrier (BBB) is a highly selective permeability barrier that separates
the circulating blood from the brain extracellular fluid in the central nervous system
(CNS). The bloodbrain barrier is formed by brain endothelial cells, which are connected by tight junctions with an extremely high electrical resistivity of at least 0.1
m. The bloodbrain barrier allows the passage of water, some gases, and lipidsoluble molecules by passive diffusion, as well as the selective transport of molecules
such as glucose and amino acids that are crucial to neural function. On the other hand,
the bloodbrain barrier may prevent the entry of lipophilic, potential neurotoxins by
way of an active transport mechanism mediated by P-glycoprotein. Astrocytes are necessary to create the bloodbrain barrier. A small number of regions in the brain, including the circumventricular organs (CVOs), do not have a bloodbrain barrier.
The bloodbrain barrier occurs along all capillaries and consists of tight junctions
around the capillaries that do not exist in normal circulation. Endothelial cells restrict
the diffusion of microscopic objects (e.g., bacteria) and large or hydrophilic molecules
into the cerebrospinal fluid (CSF), while allowing the diffusion of small or hydrophobic
molecules (O2, CO2, hormones). Cells of the barrier actively transport metabolic products such as glucose across the barrier with specific proteins. This barrier also includes
a thick basement membrane and astrocytic endfeet.
https://en.wikipedia.org/wiki/Blood%E2%80%93brain_barrier
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Blotting
A blot, in molecular biology and genetics, is a method of transferring proteins, DNA or
RNA, onto a carrier (for example, a nitrocellulose PVDF or nylon membrane). In many
instances, this is done after a gel electrophoresis, transferring the molecules from the
gel onto the blotting membrane, and other times adding the samples directly onto the
membrane.
After the blotting, the transferred proteins, DNA or RNA are then visualized by colorant staining (for example, silver staining of proteins), autoradiographic visualization of
radioactive labelled molecules (performed before the blot), or specific labelling of some
proteins or nucleic acids. The latter is done with antibodies or hybridization probes
that bind only to some molecules of the blot and have an enzyme joined to them.
After proper washing, this enzymatic activity (and so, the molecules we search in the
blot) is visualized by incubation with proper reactive, rendering either a colored deposit on the blot or a chemiluminiscent reaction which is registered by photographic
film. Three commons blots and the material separated/identified by them are Southern (DNA), Northern (RNA), and Western (proteins).
https://en.wikipedia.org/wiki/Blot_(biology)
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Blue/White Screening
The blue-white screen is a screening technique that allows for the rapid and convenient
detection of recombinant bacteria in vector-based molecular cloning experiments.
DNA of interest is ligated into a vector. The vector is then inserted into a competent
host cell viable for transformation, which are then grown in the presence of X-gal. Cells
transformed with vectors containing recombinant DNA will produce white colonies.
Cells transformed with non-recombinant plasmids (i.e. only the vector) grow into blue
colonies. This method of screening is usually performed using a suitable bacterial
strain, but other organisms such as yeast may also be used.
The correct type of vector and competent cells are important considerations when planning a blue white screen. The plasmid must contain the lacZ, and examples of such
plasmids are pUC19 and pBluescript. The E. coli cell should contain the mutant lacZ
gene with deleted sequence (i.e. lacZM15), and some of the commonly used cells with
such genotype are JM109, DH5, and XL1-Blue.
It should also be understood that the lac operon is affected by the presence of glucose.
The protein EIIAGlc, which is involved in glucose import, shuts down lactose permease
when glucose is being transported into the cell. The media used in agar plate therefore
should not include glucose.
X-gal is light-sensitive and therefore its solution and plates containing X-gal should be
stored in the dark. Isopropyl -D-1-thiogalactopyranoside (IPTG), which functions as
the inducer of the lac operon, may be used in the media to enhance the expression of
LacZ.
https://en.wikipedia.org/wiki/Blue_white_screen
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Bohr Effect
The Bohr effect is a physiological phenomenon first described in 1904 by the Danish
physiologist Christian Bohr, stating that haemoglobin's oxygen binding affinity (see
Oxygenhaemoglobin dissociation curve) is inversely related both to acidity and to the
concentration of carbon dioxide. That is, an increase in blood CO2 concentration,
which leads to a decrease in blood pH, will result in hemoglobin proteins releasing
their load of oxygen. Conversely, a decrease in carbon dioxide provokes an increase in
pH, which results in haemoglobin picking up more oxygen. Since carbon dioxide reacts
with water to form carbonic acid, an increase in CO2 results in a decrease in blood pH.
The Bohr effect facilitates oxygen transport as heemoglobin binds to oxygen in the
lungs, but then releases it in the tissues, particularly those tissues in most need of oxygen. When a tissue's metabolic rate increases, its carbon dioxide production increases.
Carbon dioxide forms bicarbonate through the following reaction:
CO2 + H2O <=> H2CO3 <=> H+ + HCO3
Although the reaction usually proceeds very slowly, the enzyme family of carbonic anhydrase, which is present in red blood cells, accelerates the formation of bicarbonate
and protons. This causes the pH of tissues to decrease, and so, promotes the dissociation of oxygen from haemoglobin to the tissue, allowing the tissue to obtain enough
oxygen to meet its demands. Conversely, in the lungs, where oxygen concentration is
high, binding of oxygen causes haemoglobin to release protons, which combine with bicarbonate to drive off carbon dioxide in exhalation. Since these two reactions are
closely matched, there is little change in blood pH.
The dissociation curve shifts to the right when carbon dioxide or hydrogen ion concentration is increased. This facilitates increased oxygen dumping. This mechanism allows
for the body to adapt the problem of supplying more oxygen to tissues that need it the
most. When muscles are undergoing strenuous activity, they generate CO2 and lactic
acid as products of cellular respiration and lactic acid fermentation. In fact, muscles
generate lactic acid so quickly that pH of the blood passing through the muscles will
drop to around 7.2. As lactic acid releases its protons, pH decreases, which causes hemoglobin to release ~10% more oxygen.
https://en.wikipedia.org/wiki/Bohr_effect
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Branch Site
Spliceosomal introns often reside within the sequence of eukaryotic protein-coding
genes. Within the intron, a donor site (5' end of the intron), a branch site (near the 3'
end of the intron) and an acceptor site (3' end of the intron) are required for splicing.
The splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3' end
of the intron terminates the intron with an almost invariant AG sequence. Upstream
(5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide involved in lariat formation. The consensus sequence for
an intron (in IUPAC nucleic acid notation) is: G-G-[cut]-G-U-R-A-G-U (donor site) ...
intron sequence ... Y-U-R-A-C (branch sequence 20-50 nucleotides upstream of acceptor site) ... Y-rich-N-C-A-G-[cut]-G (acceptor site). However, it is noted that the specific sequence of intronic splicing elements and the number of nucleotides between the
branchpoint and the nearest 3 acceptor site affect splice site selection. Also, point mutations in the underlying DNA or errors during transcription can activate a cryptic
splice site in part of the transcript that usually is not spliced. This results in a mature
messenger RNA with a missing section of an exon. In this way, a point mutation, which
might otherwise only affect a single amino acid, can manifest as a deletion or truncation in the final protein.
https://en.wikipedia.org/wiki/RNA_splicing
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Branching
Glycogen is a biopolymer consisting of linear chains of glucose residues with further
chains branching off every 8 to 12 glucoses or so. Glucoses are linked together linearly
by (14) glycosidic bonds from one glucose to the next.
Branches are linked to the chains from which they are branching off by (16) glycosidic bonds between the first glucose of the new branch and a glucose on the stem chain.
Branching is an important consideration for glycogen metabolism, since glucose units
are excised from glycogen from free ends. More branching = more ends = more glucose quickly released. Branching of glycogen is shown below. Free ends are marked in
red. Glucose units involved in branches marked in green.
https://en.wikipedia.org/wiki/Glycogen
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Branching Enzyme
Glycogen branching enzyme is an enzyme that adds branches to the growing glycogen
molecule during the synthesis of glycogen, a storage form of glucose. More specifically,
during glycogen synthesis, a glucose 1-phosphate molecule reacts with uridine triphosphate (UTP) to become UDP-glucose, an activated form of glucose. The activated glucosyl unit of UDP-glucose is then transferred to the hydroxyl group at the C-4 of a terminal residue of glycogen to form an -1,4-glycosidic linkage, a reaction catalyzed by glycogen synthase.
In glycogen, every 10 to 14 glucose units, a side branch with an additional chain of glucose units occurs. The side chain attaches at carbon atom 6 of a glucose unit, an -1,6glycosidic bond. This connection is catalyzed by a branching enzyme, generally given
the name -glucan branching enzyme. A branching enzyme attaches a string of seven
glucose units (with some minor variation to this number) to the carbon at the C-6 position on the glucose unit, forming the -1,6-glycosidic bond. The specific nature of this
enzyme means that this chain of 7 carbons is usually attached to a glucose molecule
that is in position three from the non-reducing end of another chain. Because the enzyme works with such specificity regarding the number of glucose units transferred
and the position to which they are transferred, the enzyme creates the very characteristic, highly-branched glycogen molecule.
https://en.wikipedia.org/wiki/Glycogen_branching_enzyme
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Brevican
Brevican is a proteoglycan localized to the surface of neurons in the brain.
https://en.wikipedia.org/wiki/Brevican
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Brown Fat
Brown adipose tissue (BAT) or brown fat is one of two types of fat or adipose tissue
(the other being white adipose tissue, or white fat) found in mammals.
Importantly, classification of brown fat in humans refers to at least two distinct cell
populations with similar functions. The first shares a common embryological origin
with muscle cells, found in larger "classic" deposits. The second develops from adrenergically induced adipocytes, found interspersed in white adipose tissue.
It is especially abundant in newborns and in hibernating mammals. Its primary function is to generate body heat in animals or newborns that do not shiver. In contrast to
white adipocytes (fat cells), which contain a single lipid droplet, brown adipocytes contain numerous smaller droplets and a much higher number of (iron-containing) mitochondria, which make it brown. Brown fat also contains more capillaries than white
fat, since it has a greater need for oxygen than most tissues.
The mitochondria in a eukaryotic cell utilize fuels to produce energy in the form of
adenosine triphosphate (ATP). This process involves storing energy as a proton gradient, also known as the proton motive force (PMF), across the mitochondrial inner
membrane. This energy is used to synthesize ATP when the protons flow across the
membrane (down their concentration gradient) through the ATP synthase enzyme.
This is known as chemiosmosis.
In endotherms, body heat is maintained by signaling the mitochondria to allow protons to run back along the gradient without producing ATP (proton leak). This can occur since an alternative return route for the protons exists through an uncoupling protein in the inner membrane. This protein, known as uncoupling protein 1 (thermogenin), facilitates the return of the protons after they have been actively pumped out of
the mitochondria by the electron transport chain. This alternative route for protons uncouples oxidative phosphorylation and the energy in the PMF is instead released as
heat.
To some degree, all cells of endotherms give off heat, especially when body temperature is below a regulatory threshold. However, brown adipose tissue is highly specialized for this non-shivering thermogenesis. First, each cell has a higher number of mitochondria compared to more typical cells. Second, these mitochondria have a higherthan-normal concentration of thermogenin in the inner membrane.
https://en.wikipedia.org/wiki/Brown_adipose_tissue
Bruce Ames
Bruce Nathan Ames (born December 16, 1928) is an American biochemist. He is a professor of Biochemistry and Molecular Biology Emeritus at the University of California,
Berkeley, and a senior scientist at Children's Hospital Oakland Research Institute
(CHORI). He is the inventor of the Ames test, a system for easily and cheaply testing
the mutagenicity of compounds.
In the 1970s, Bruce Ames developed the Ames test which is a cheap and convenient assay for mutagens and therefore potential carcinogens. Previous carcinogenic testing
used live animals, and the procedures are expensive and time-consuming. This made
animal testing impractical for use in screening on a wide scale, and reduced the number of compounds that could be tested. The Ames test on the other hand uses the bacteria Salmonella typhimurium to test for mutagens, and is considerably cheaper and
faster. The Ames test became widely used as an initial screen for possible carcinogens
and has been used to identify potential carcinogens previously used in commercial
products. Their identification led to some of those formulations, such as chemicals
used in hair dye, being withdrawn from commercial use. The ease with which Ames
test allows widely used chemicals to be identified as possible carcinogens made him an
early hero of environmentalism.
https://en.wikipedia.org/wiki/Bruce_Ames
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Buffer
A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa. Its pH
changes very little when a small or moderate amount of strong acid or base is added to
it and thus it is used to prevent changes in the pH of a solution. Buffer solutions are
used as a means of keeping pH at a nearly constant value in a wide variety of chemical
applications. Many life forms thrive only in a relatively small pH range so they utilize a
buffer solution to maintain a constant pH. In nature, the bicarbonate buffering system
is used to regulate the pH of blood.
Buffer solutions achieve their resistance to pH change because of the presence of an
equilibrium between the acid HA and its salt A.
HA H+ + A
When some strong acid is added to an equilibrium mixture of the weak acid and its
salt, the equilibrium is shifted to the left, in accordance with Le Chtelier's principle.
Because of this, the hydrogen ion concentration increases by less than the amount expected for the quantity of strong acid added. Similarly, if strong alkali is added to the
mixture the hydrogen ion concentration decreases by less than the amount expected
for the quantity of alkali added.
https://en.wikipedia.org/wiki/Buffer_solution
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Buffer Capacity
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Burst Phase
Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. The initial period of high velocity
product formation is referred to as the "Burst Phase". This period is observed as the enzymes become saturated with substrate up until all enzymes are saturated. Once all enzymes are saturated, the Burst Phase gives way to a linear reaction velocity. An example of a burst kinetics is observed in Step 6 of glycolysis involving glyceraldehyde-3phosphate dehydrogenase (also called GAPDH) and the reduction of NAD+ to NADH.
https://en.wikipedia.org/wiki/Burst_kinetics
C-linked Glycosylation
spondins are one of the most commonly C-modified proteins, although this
Index
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C-terminal
terminus. The convention for writing peptide sequences is to put the C-term
on the right and write the sequence from N- to C-terminus.
https://en.wikipedia.org/wiki/C-terminus
C-terminal Domain
covered first in the laboratory of C.J.Ingles at the University of Toronto and als
ing the DNA encoding the RPB1 subunit of RNA polymerase from Yeast and Mi
spectively. Other proteins often bind the C-terminal domain of RNA polymeras
Index
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C4 Plants
A C4 plant is a plant that uses C4 carbon fixation. C4 carbon fixation is one of three biochemical processes, along with C3 and CAM photosynthesis, used to fix carbon. It is
named for the 4-carbon molecule present in the first product of carbon fixation in the
small subset of plants that use that process, in contrast to the 3-carbon molecule products in C3 plants.
C4 fixation is an elaboration of the more common C3 carbon fixation and is believed to
have evolved more recently. C4 and CAM overcome the tendency of the enzyme
RuBisCO to wastefully fix oxygen rather than carbon dioxide in the process of photorespiration. This is achieved in a more efficient environment for RubisCo by shuttling CO2
via malate or aspartate from mesophyll cells to bundle-sheath cells. In these bundlesheath cells, RuBisCO is isolated from atmospheric oxygen and saturated with the CO2
released by decarboxylation of the malate.
C4 plants use PEP Carboxylase to capture more CO2 in the mesophyll cells. PEP Carboxylase (3 carbons) binds to CO2 to make oxaloacetic acid (OAA). Then OAA makes
malate (4 carbons). Malate enters bundle sheath cells and releases CO2 inside bundle
sheath for rubisco to work more efficiently. These additional steps, however, require
more energy in the form of ATP. Because of this extra energy requirement, C4 plants
are able to more efficiently fix carbon in drought, high temperatures, and limitations of
nitrogen or CO2, with the more common C3 pathway being more efficient in the other
conditions.
https://en.wikipedia.org/wiki/C4_carbon_fixation
CAAT Box
A CCAAT box (also sometimes abbreviated a CAAT box or CAT box) is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occur upstream by 60100 bases to the initial transcription site. The CAAT box signals the binding site for the
RNA transcription factor, and is typically accompanied by a conserved consensus sequence. It is an invariant DNA sequence at about minus 70 base pairs from the origin
of transcription in many eukaryotic promoters. Genes that have this element seem to
require it for the gene to be transcribed in sufficient quantities. It is frequently absent
from genes that encode proteins used in virtually all cells. This box along with the GC
box is known for binding general transcription factors. Both of these consensus se-
quences belong to the regulatory promoter. Full gene expression occurs when transcription activator proteins bind to each module within the regulatory promoter. Protein
specific binding is required for the CCAAT box activation. These proteins are known as
CCAAT box binding proteins/CCAAT box binding factors.
A CCAAT box is a feature frequently found before eukaryote coding regions, but is not
found in prokaryotes.
https://en.wikipedia.org/wiki/CAAT_box
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Cadherin
Cadherins (named for "calcium-dependent adhesion") are a class of type-1 transmembrane proteins. They play important roles in cell adhesion, forming adherens junctions
to bind cells within tissues together. They are dependent on calcium (Ca++) ions to function, hence their name.
The cadherin superfamily includes cadherins, protocadherins, desmogleins, and desmocollins, and more. In structure, they share cadherin repeats, which are the extracellular Ca++-binding domains. There are multiple classes of cadherin molecule, each designated with a prefix (in general, noting the type of tissue with which it is associated).
It has been observed that cells containing a specific cadherin subtype tend to cluster together to the exclusion of other types, both in cell culture and during development. For
example, cells containing N-cadherin tend to cluster with other N-cadherin-expressing
cells. However, it has been noted that the mixing speed in the cell culture experiments
can have an effect on the extent of homotypic specificity. In addition, several groups
have observed heterotypic binding affinity (i.e., binding of different types of cadherin
together) in various assays. One current model proposes that cells distinguish cadherin
subtypes based on kinetic specificity rather than thermodynamic specificity, as different types of cadherin homotypic bonds have different lifetimes.
https://en.wikipedia.org/wiki/Cadherin
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Caffeine
Caffeine is a central nervous system (CNS) stimulant of the methylxanthine class. It is
the world's most widely consumed psychoactive drug, but unlike many other psychoactive substances it is legal and unregulated in nearly all parts of the world.
There are several known mechanisms of action to explain the effects of caffeine. The
most prominent is that it reversibly blocks the action of adenosine on its receptor and
consequently prevents the onset of drowsiness induced by adenosine. Caffeine also
stimulates certain portions of the autonomic nervous system.
Caffeine can have both positive and negative health effects. It can be used to treat bronchopulmonary dysplasia of prematurity, and to prevent apnea of prematurity: caffeine
citrate was placed on the WHO Model List of Essential Medicines in 2007. It may confer a modest protective effect against some diseases, including Parkinson's disease and
certain types of cancer. One meta-analysis concluded that cardiovascular disease such
as coronary artery disease and stroke is less likely with 35 cups of non-decaffeinated
coffee per day but more likely with over 5 cups per day. Some people experience insomnia or sleep disruption if they consume caffeine, especially during the evening hours,
but others show little disturbance. Evidence of a risk during pregnancy is equivocal.
Some authorities recommend that pregnant women limit consumption to the equivalent of two cups of coffee per day or less. Caffeine can produce a mild form of drug dependence associated with withdrawal symptoms such as sleepiness, headache, and
irritability when an individual stops using caffeine after repeated daily intake. Tolerance to the autonomic effects of increased blood pressure and heart rate, and increased
urine output, develops with chronic use (i.e., these symptoms become less pronounced
or do not occur following consistent use).
Caffeine is classified by the Food and Drug Administration as "generally recognized as
safe" (GRAS). Toxic doses, over 10 grams per day for an adult, are much higher than
typical dose of under 500 milligrams per day. A cup of coffee contains 80175mg of
caffeine, depending on what "bean" (seed) is used and how it is prepared (e.g. drip, percolation, or espresso). Thus it requires roughly 50100 ordinary cups of coffee to reach
a lethal dose. However pure powdered caffeine, which is available as a dietary supplement, can be lethal in tablespoon-sized amounts.
https://en.wikipedia.org/wiki/Caffeine
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CAIR
Index
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G-G
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Calcidiol
Calcifediol (INN), also known as calcidiol, 25-hydroxycholecalciferol, or 25hydroxyvitamin D (abbreviated 25(OH)D), is a prehormone that is produced in the
liver by hydroxylation of vitamin D3 (cholecalciferol) by the enzyme cholecalciferol 25hydroxylase which was isolated by Michael F. Holick. Physicians worldwide measure
this metabolite to determine a patient's vitamin D status.
https://en.wikipedia.org/wiki/Calcifediol
Calcifediol
Calcifediol (INN), also known as calcidiol, 25-hydroxycholecalciferol, or 25hydroxyvitamin D (abbreviated 25(OH)D), is a prehormone that is produced in the
liver by hydroxylation of vitamin D3 (cholecalciferol) by the enzyme cholecalciferol 25hydroxylase which was isolated by Michael F. Holick. Physicians worldwide measure
this metabolite to determine a patient's vitamin D status.
https://en.wikipedia.org/wiki/Calcifediol
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Calcitriol
Calcitriol (INN), also called 1,25-dihydroxycholecalciferol or 1,25-dihydroxyvitamin
D3, is the hormonally active metabolite of vitamin D with three hydroxyl groups (abbreviated 1,25-(OH)2D3 or simply 1,25(OH)2D).
Calcitriol increases blood calcium levels ([Ca++]) by promoting absorption of dietary
calcium from the gastrointestinal tract and increasing renal tubular reabsorption of calcium, thus reducing the loss of calcium in the urine. Calcitriol also stimulates release of
calcium from bone by its action on the specific type of bone cells referred to as osteoblasts, causing them to release RANKL, which in turn activates osteoclasts.
Calcitriol acts in concert with parathyroid hormone (PTH) in all three of these roles.
For instance, PTH also indirectly stimulates osteoclasts. However, the main effect of
PTH is to increase the rate at which the kidneys excrete inorganic phosphate (Pi), the
counterion of Ca++. The resulting decrease in serum phosphate causes hydroxyapatite
(Ca5(PO4)3OH) to dissolve out of bone thus increasing serum calcium. PTH also stimulates the production of calcitriol (see below).
Many of the effects of calcitriol are mediated by its interaction with the calcitriol receptor, also called the vitamin D receptor or VDR. For instance, the unbound inactive
form of the calcitriol receptor in intestinal epithelial cells resides in the cytoplasm.
When calcitriol binds to the receptor, the ligand-receptor complex translocates to the
cell nucleus, where it acts as a transcription factor promoting the expression of a gene
encoding a calcium binding protein. The levels of the calcium binding protein increase
enabling the cells to actively transport more calcium (Ca++) from the intestine across
the intestinal mucosa into the blood.
https://en.wikipedia.org/wiki/Calcitriol
Calcium Pump
Calcium pumps are a family of ion transporters found in the cell membrane of all animal cells. They are responsible for the active transport of calcium out of the cell for the
maintenance of the steep Ca++ electrochemical gradient across the cell membrane. Calcium pumps play a crucial role in proper cell signaling by keeping the intracellular calcium concentration roughly 10,000 times lower than the extracellular concentration.
Failure to do so is one cause of muscle cramps. The plasma membrane Ca++ ATPase
and the sodium-calcium exchanger are together the main regulators of intracellular
Ca++ concentrations.
Ca++ has many important roles as an intracellular messenger. The release of a large
amount of free Ca++ can trigger a fertilized egg to develop, skeletal muscle cells to contract, secretion by secretory cells and interactions with Ca++ -responsive proteins like
calmodulin. To maintain low concentrations of free Ca++ in the cytosol, cells use membrane pumps like calcium ATPase found in the membranes of sarcoplasmic reticulum
of skeletal muscle. These pumps are needed to provide the steep electrochemical gradient that allows Ca++ to rush into the cytosol when a stimulus signal opens the Ca++
channels in the membrane. The pumps are also necessary to actively pump the Ca++
back out of the cytoplasm and return the cell to its pre-signal state.
https://en.wikipedia.org/wiki/Calcium_pump
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Calpain
A calpain (EC 3.4.22.53) is a protein belonging to the family of calcium-dependent,
non-lysosomal cysteine proteases (proteolytic enzymes) expressed ubiquitously in
mammals and many other organisms. Although the physiological role of calpains is
still poorly understood, they have been shown to be active participants in processes
such as cell mobility and cell cycle progression, as well as cell-type specific functions
such as long-term potentiation in neurons and cell fusion in myoblasts.
Although the physiological role of calpains is still poorly understood, they have been
shown to be active participants in processes such as cell mobility and cell cycle progression, as well as cell-type specific functions such as long-term potentiation in neurons
and cell fusion in myoblasts. Under these physiological conditions, a transient and localized influx of calcium into the cell activates a small local population of calpains (for
example, those close to Ca++ channels), which then advance the signal transduction
pathway by catalyzing the controlled proteolysis of its target proteins. Other reported
roles of calpains are in cell function, helping to regulate clotting and the diameter of
blood vessels, and playing a role in memory. Calpains have been implicated in apoptotic cell death, and appear to be an essential component of necrosis.
Enhanced calpain activity, regulated by CAPNS1, significantly contributes to platelet
reactivity and thrombosis under hypoxic conditions. In the brain, while -calpain is
mainly located in the cell body and dendrites of neurons and to a lesser extent in axons
and glial cells, m-calpain is found in glia and a small amount in axons. Calpain is also
involved in skeletal muscle protein breakdown due to exercise and altered nutritional
states.
https://en.wikipedia.org/wiki/Calpain
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Calvin Cycle
The light-independent reactions of photosynthesis are chemical reactions that convert
carbon dioxide and other compounds into glucose. These reactions occur in the
stroma, the fluid-filled area of a chloroplast outside of the thylakoid membranes. They
take the products (ATP and NADPH) of light-dependent reactions and perform further
chemical processes on them.
There are three phases to the light-independent reactions, collectively called the Calvin
cycle: carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.
Despite its name, this process occurs only when light is available. Plants do not carry
out the Calvin cycle during nighttime. They instead release sucrose into the phloem
from their starch reserves. This process happens when light is available independent of
the kind of photosynthesis (C3 carbon fixation, C4 carbon fixation, and Crassulacean
acid metabolism). CAM plants store malic acid in their vacuoles every night and release it by day in order to make this process work.
The enzymes in the Calvin cycle are functionally equivalent to most enzymes used in
other metabolic pathways such as gluconeogenesis and the pentose phosphate pathway, but they are to be found in the chloroplast stroma instead of the cell cytosol, separating the reactions. They are activated in the light (which is why the name "dark reaction" is misleading), and also by products of the light-dependent reaction. These regulatory functions prevent the Calvin cycle from being respired to carbon dioxide. Energy
(in the form of ATP) would be wasted in carrying out these reactions that have no net
productivity. The sum of reactions in the Calvin cycle is the following:
3 CO2 + 6 NADPH + 5 H2O + 9 ATP Glyceraldehyde-3-phosphate (Glyal-3P) + 2 H+
+ 6 NADP+ + 9 ADP + 8 Pi
Hexose (six-carbon) sugars are not a product of the Calvin cycle. Although many texts
list a product of photosynthesis as C6H12O6, this is mainly a convenience to counter the
equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin cycle are three-carbon sugar phosphate molecules, or
"triose phosphates," namely, Glyal-3P.
https://en.wikipedia.org/wiki/Light-independent_reactions
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cAMP
Cyclic adenosine monophosphate (cAMP, cyclic AMP, or 3',5'-cyclic adenosine monophosphate) is a second messenger important in many biological processes. cAMP is a
derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.
cAMP and its associated kinases function in several biochemical processes, including
the regulation of glycogen, sugar, and lipid metabolism. In eukaryotes, cyclic AMP
works by activating protein kinase A (PKA, or cAMP-dependent protein kinase). PKA
is normally inactive as a tetrameric holoenzyme, consisting of two catalytic and two
regulatory units (C2R2), with the regulatory units blocking the catalytic centers of the
catalytic units.
Cyclic AMP binds to specific locations on the regulatory units of the protein kinase,
and causes dissociation between the regulatory and catalytic subunits, thus enabling
those catalytic units to phosphorylate substrate proteins.
The active subunits catalyze the transfer of phosphate from ATP to specific serine or
threonine residues of protein substrates. The phosphorylated proteins may act directly
on the cell's ion channels, or may become activated or inhibited enzymes. Protein kinase A can also phosphorylate specific proteins that bind to promoter regions of DNA,
causing increased expression of specific genes. Not all protein kinases respond to
cAMP. Several classes of protein kinases, including protein kinase C, are not cAMPdependent.
Further effects mainly depend on cAMP-dependent protein kinase, which vary based
on the type of cell. Still, there are some minor PKA-independent functions of cAMP,
e.g., activation of calcium channels, providing a minor pathway by which growth
hormone-releasing hormone causes a release of growth hormone.
https://en.wikipedia.org/wiki/Cyclic_adenosine_monophosphate
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In cell biology, protein kinase A (PKA[N 1]) is a family of enzymes whose act
pendent on cellular levels of cyclic AMP (cAMP). PKA is also known as cAMP
dependent protein kinase (EC 2.7.11.11). Protein kinase A has several functio
cell, including regulation of glycogen, sugar, and lipid metabolism. It should
fused with AMP-activated protein kinase which, although being of similar
type to cell type, the proteins that are available for phosphorylation will depe
the cell in which PKA is present. Thus, the effects of PKA activation vary with
https://en.wikipedia.org/wiki/Protein_kinase_A
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Cancer
Cancer is a group of diseases involving abnormal cell growth with the poten
vade or spread to other parts of the body. Not all tumors are cancerous. Be
mors do not spread to other parts of the body. Possible signs and symptoms
lump, abnormal bleeding, prolonged cough, unexplained weight loss and a
bowel movements. While these symptoms may indicate cancer, they may ha
causes. Over 100 cancers affect humans.
https://en.wikipedia.org/wiki/Cancer
Cannabinoid Receptors
Cannabinoid receptors, located throughout the body, are part of the Endocannabinoid
system which is involved in a variety of physiological processes including appetite,
pain-sensation, mood, and memory.
Cannabinoid receptors are of a class of cell membrane receptors under the G proteincoupled receptor superfamily. As is typical of G protein-coupled receptors, the cannabinoid receptors contain seven transmembrane spanning domains. Cannabinoid receptors are activated by three major groups of ligands: endocannabinoids, produced by
the mammillary body; plant cannabinoids (such as cannabidiol, produced by the cannabis plant); and synthetic cannabinoids (such as HU-210). All of the endocannabinoids
and plant cannabinoids are lipophilic, such as fat soluble compounds.
There are currently two known subtypes of cannabinoid receptors, termed CB1 and
CB2. The CB1 receptor is expressed mainly in the brain (central nervous system or
"CNS"), but also in the lungs, liver and kidneys. The CB2 receptor is expressed mainly
in the immune system and in hematopoietic cells. Mounting evidence suggests that
there are novel cannabinoid receptors that is, non-CB1 and non-CB2, which are expressed in endothelial cells and in the CNS. In 2007, the binding of several cannabinoids to the G protein-coupled receptor GPR55 in the brain was described.
https://en.wikipedia.org/wiki/Cannabinoid_receptor
Cannabinoids
Cannabinoids are a class of diverse chemical compounds that act on cannabinoid receptors in cells that repress neurotransmitter release in the brain. Ligands for these receptor proteins include the endocannabinoids (produced naturally in the body by humans
and animals), the phytocannabinoids (found in cannabis and some other plants), and
synthetic cannabinoids (manufactured artificially).
The most notable cannabinoid is the phytocannabinoid tetrahydrocannabinol (THC shown below), the primary psychoactive compound in cannabis. Cannabidiol (CBD) is
another major constituent of the plant. There are at least 113 different cannabinoids isolated from cannabis, exhibiting varied effects.
Synthetic cannabinoids encompass a variety of distinct chemical classes: the classical
cannabinoids structurally related to THC, the nonclassical cannabinoids (cannabimimetics) including the aminoalkylindoles, 1,5-diarylpyrazoles, quinolines, and arylsulfonamides, as well as eicosanoids related to the endocannabinoids.
https://en.wikipedia.org/wiki/Cannabinoid
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CAP
Catabolite Activator Protein (CAP; also known as cAMP receptor protein, CRP) is a
transcriptional activator that exists as a homodimer in solution, with each subunit comprising a ligand-binding domain at the N-terminus (CAPN, residues 1-138), which is
also responsible for the dimerization of the protein, and a DNA-binding domain at the
C-terminus (DBD, residues 139-209). Two cAMP (cyclic AMP) molecules bind dimeric
CAP with negative cooperativity and function as allosteric effectors by increasing the
protein's affinity for DNA. Cytosolic cAMP levels rise when the amount of glucose transported into the cell is low.
CAP has a characteristic helix-turn-helix structure that allows it to bind to successive
major grooves on DNA. The two helices are reinforcing each, causing a 43 turn in the
structure, so overall causing a 94 degree turn in the DNA. This opens the DNA molecule up, allowing RNA polymerase to bind and transcribe the genes involved in lactose
catabolism. cAMP-CAP is required for transcription of the lac operon.
https://en.wikipedia.org/wiki/Catabolite_activator_protein
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Carbamate
tional groups that are inter-related structurally and often are interconverted
cally. Carbamate esters are also called urethanes.
https://en.wikipedia.org/wiki/Carbamate
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Carbamino
Carbamino refers to a compound created by the addition of carbon dioxide
Carbamoyl Aspartate
https://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase
Carbamoyl Phosphate
Carbamoyl phosphate is an anion of biochemical significance. In land-dwelling animals, it is an intermediary metabolite in nitrogen disposal through the urea cycle and
in the synthesis of pyrimidines. It is a substrate of the enzyme ATCase, shown below.
https://en.wikipedia.org/wiki/Carbamoyl_phosphate
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phosphate from glutamine (EC 6.3.5.5) or ammonia (EC 6.3.4.16) and bicarbonate
This enzyme catalyzes the reaction of ATP and bicarbonate to produce carboxy ph
phate and ADP. Carboxy phosphate reacts with ammonia to give carbamate. In tu
carbamate reacts with a second ATP to give carbamoyl phosphate plus ADP.
karyotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates. Mos
karyotes carry one form of CPSase that participates in both arginine and pyrimidin
biosynthesis, however certain bacteria can have separate forms.
https://en.wikipedia.org/wiki/Carbamoyl_phosphate_synthetase
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Carbanion
A carbanion is an anion in which carbon has an unshared pair of electrons and
negative charge usually with three substituents for a total of eight valence electr
https://en.wikipedia.org/wiki/Carbanion
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Carbohydrate
A carbohydrate (also called a saccharide) is a biological molecule consisting of carbon
(C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogenoxygen atom ratio
of 2:1 (as in water). Some exceptions exist. For example, deoxyribose, a sugar component of DNA, has the empirical formula C5H10O4. Carbohydrates are technically hydrates of carbon. Structurally it is more accurate to view them as polyhydroxy aldehydes and ketones.
Monosaccharides are the major source of fuel for metabolism, being used both as an
energy source (glucose - shown below - being the most important in nature) and in biosynthesis. When monosaccharides are not immediately needed by many cells they are
often converted to more space-efficient forms, often polysaccharides. In many animals,
including humans, this storage form is glycogen, especially in liver and muscle cells. In
plants, starch is used for the same purpose.
The most abundant carbohydrate, cellulose, is a structural component of the cell wall
of plants and many forms of algae. Ribose is a component of RNA. Deoxyribose is a
component of DNA. Lyxose is a component of lyxoflavin found in the human heart.
Ribulose and xylulose occur in the pentose phosphate pathway. Galactose, a component of milk sugar lactose, is found in galactolipids in plant cell membranes and in glycoproteins in many tissues. Mannose occurs in human metabolism, especially in the
glycosylation of certain proteins. Fructose, or fruit sugar, is found in many plants and
in humans, it is metabolized in the liver, absorbed directly into the intestines during digestion, and found in semen. Trehalose, a major sugar of insects, is rapidly hydrolyzed
into two glucose molecules to support continuous flight.
https://en.wikipedia.org/wiki/Carbohydrate
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Carbon
Carbon (from Latin: carbo "coal") is a chemical element with symbol C and
number 6. On the periodic table, it is the first (row 2) of six elements in colu
(group) 14, which have in common the composition of their outer electron s
cal bonds. Three isotopes occur naturally, 12C and 13C being stable while 14C
tive, decaying with a half-life of about 5,730 years.
https://en.wikipedia.org/wiki/Carbon
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Carbon Dioxide
Carbon dioxide (chemical formula CO2) is a colorless and odorless gas vital to life on
Earth. This naturally occurring chemical compound is composed of a carbon atom covalently double-bonded to two oxygen atoms.
Carbon dioxide exists in Earth's atmosphere as a trace gas at a concentration of about
0.04 percent (400 ppm) by volume. Natural sources include volcanoes, hot springs
and geysers, and it is freed from carbonate rocks by dissolution in water and acids. Because carbon dioxide is soluble in water, it occurs naturally in groundwater, rivers and
lakes, in ice caps and glaciers and also in seawater. It is present in deposits of petroleum and natural gas.
Atmospheric carbon dioxide is the primary source of carbon in life on Earth and its concentration in Earth's pre-industrial atmosphere since late in the Precambrian was regulated by photosynthetic organisms and geological phenomena. As part of the carbon cycle, plants, algae, and cyanobacteria use light energy to photosynthesize carbohydrate
from carbon dioxide and water, with oxygen produced as a waste product.
Carbon dioxide (CO2) is produced by all aerobic organisms when they metabolize carbohydrate and lipids to produce energy by respiration. It is returned to water via the gills
of fish and to the air via the lungs of air-breathing land animals, including humans.
Carbon dioxide is produced during the processes of decay of organic materials and the
fermentation of sugars in bread, beer and winemaking. It is produced by combustion
of wood, carbohydrates and fossil fuels such as coal, peat, petroleum and natural gas.
https://en.wikipedia.org/wiki/Carbon_dioxide
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Carbon Monoxide
Carbon monoxide consists of one carbon atom and one oxygen atom, connected by a
triple bond that consists of two covalent bonds as well as one dative covalent bond. It is
the simplest oxocarbon and is isoelectronic with the cyanide anion, the nitrosonium
cation and molecular nitrogen. In coordination complexes the carbon monoxide ligand
is called carbonyl.
In biology, carbon monoxide is naturally produced by the action of heme oxygenase 1
and 2 on the heme from hemoglobin breakdown. This process produces a certain
amount of carboxyhemoglobin in normal persons, even if they do not breathe any carbon monoxide. Following the first report that carbon monoxide is a normal neurotransmitter in 1993, as well as one of three gases that naturally modulate inflammatory responses in the body (the other two being nitric oxide and hydrogen sulfide), carbon
monoxide has received a great deal of clinical attention as a biological regulator. In
many tissues, all three gases are known to act as anti-inflammatories, vasodilators, and
promoters of neovascular growth. Clinical trials of small amounts of carbon monoxide
as a drug are ongoing. Nonetheless, too much carbon monoxide causes carbon monoxide poisoning. Carbon monoxide competes with oxygen for binding on hemoglobin,
thus reducing oxygen carrying capacity.
https://en.wikipedia.org/wiki/Carbon_monoxide
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Carbonic Acid
Carbonic acid is a chemical compound with the chemical formula H2CO3. It is also a
name sometimes given to solutions of carbon dioxide in water (carbonated water), because such solutions contain small amounts of H2CO3. In physiology, carbonic acid is
described as volatile acid or respiratory acid, because it is the only acid excreted as a
gas by the lungs. Carbonic acid, which is a weak acid, forms two kinds of salts, the carbonates and the bicarbonates.
When carbon dioxide dissolves in water it exists in chemical equilibrium producing carbonic acid:
CO2 + H2O H2CO3
The hydration equilibrium constant at 25C is called Kh, which in the case of carbonic
acid is [H2CO3]/[CO2] 1.7103 in pure water and 1.2103 in seawater. Hence, the
majority of the carbon dioxide is not converted into carbonic acid, remaining as CO2
molecules. In the absence of a catalyst, the equilibrium is reached quite slowly.
https://en.wikipedia.org/wiki/Carbonic_acid
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Chapter 4 - Catalysis:
Chapter 4 - Catalysis:
Chapter 4 - Catalysis:
Chapter 4 - Catalysis:
Basic Principles
Basic Principles
Basic Principles
Basic Principles
Carbonic Anhydrase
tons (or vice versa), shown below, a reversible reaction that occurs relativel
the absence of a catalyst. The active site of most carbonic anhydrases contai
base balance in blood and other tissues, and to help transport carbon dioxid
sues.
https://en.wikipedia.org/wiki/Carbonic_anhydrase
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Carbonyl
In organic chemistry, a carbonyl group is a functional group composed of a carbon
atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a
carbonyl group is often referred to as a carbonyl compound.
https://en.wikipedia.org/wiki/Carbonyl
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Carboxamide
tional groups with the general R-CO-NR'R with R, R', and R as organic s
or hydrogen.
https://en.wikipedia.org/wiki/Carboxamide
Index
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Carboxyamide
tional groups with the general R-CO-NR'R with R, R', and R as organic s
or hydrogen.
https://en.wikipedia.org/wiki/Carboxamide
Carboxyl Group
A carboxylic acid is an organic compound that contains a carboxyl group (C(O)OH).
The general formula of a carboxylic acid is RC(O)OH, with R referring to the rest of
the (possibly quite large) molecule.
https://en.wikipedia.org/wiki/Carboxylic_acid
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Carboxyl Terminus
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal
tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or
polypeptide), terminated by a free carboxyl group (-COOH).
When a protein is translated from messenger RNA, it is created from N-terminus to Cterminus. The convention for writing peptide sequences is to put the C-terminal end
on the right and write the sequence from N- to C-terminus.
https://en.wikipedia.org/wiki/C-terminus
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Carboxylated
Carboxylation in chemistry is a chemical reaction in which a carboxylic acid group is
introduced in a substrate. The opposite reaction is decarboxylation.
One example of carboxylation in biochemistry is a posttranslational modification of glutamate residues, to -carboxyglutamate, in proteins. It occurs primarily in proteins involved in the blood clotting cascade, specifically factors II, VII, IX, and X, protein C,
and protein S, and also in some bone proteins. This modification is required for these
proteins to function. Carboxylation occurs in the liver and is performed by -glutamyl
carboxylase.
The carboxylase requires vitamin K as a cofactor and performs the reaction in a processive manner. -carboxyglutamate binds calcium, which is essential for its activity. For
example, in prothrombin, calcium binding allows the protein to associate with the
plasma membrane in platelets, bringing it into close proximity with the proteins that
cleave prothrombin to active thrombin after injury.
https://en.wikipedia.org/wiki/Carboxylation
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Carboxypeptidases
The first carboxypeptidases studied were those involved in the digestion of foo
creatic carboxypeptidases A1, A2, and B). However, most of the known carboxy
dases are not involved in catabolism. They help to mature proteins (e.g., Post-
Index
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Carcinogen
A carcinogen is any substance, radionuclide, or radiation that is an agent directly involved in causing cancer. This may be due to the ability to damage the genome or to
the disruption of cellular metabolic processes. Several radioactive substances are considered carcinogens, but their carcinogenic activity is attributed to the radiation, for example rays and particles, which they emit. Common examples of non-radioactive
carcinogens are inhaled asbestos, certain dioxins, and tobacco smoke. Although the
public generally associates carcinogenicity with synthetic chemicals, it is equally likely
to arise in both natural and synthetic substances. Carcinogens are not necessarily immediately toxic, thus their effect can be insidious.
Cancer is any disease in which normal cells are damaged and do not undergo programmed cell death as fast as they divide via mitosis. Carcinogens may increase the
risk of cancer by altering cellular metabolism or damaging DNA directly in cells, which
interferes with biological processes, and induces the uncontrolled, malignant division,
ultimately leading to the formation of tumors. Usually, severe DNA damage leads to
apoptosis, but if the programmed cell death pathway is damaged, then the cell cannot
prevent itself from becoming a cancer cell.
There are many natural carcinogens. Aflatoxin B1, which is produced by the fungus Aspergillus flavus growing on stored grains, nuts and peanut butter, is an example of a
potent, naturally occurring microbial carcinogen. Certain viruses such as hepatitis B
and human papilloma virus have been found to cause cancer in humans. The first one
shown to cause cancer in animals is Rous sarcoma virus, discovered in 1910 by Peyton
Rous. Other infectious organisms which cause cancer in humans include some bacteria
(e.g. Helicobacter pylori) and helminths (e.g. Opisthorchis viverrini and Clonorchis
sinensis).
Dioxins and dioxin-like compounds, benzene, kepone, EDB, and asbestos have all been
classified as carcinogenic. As far back as the 1930s, industrial smoke and tobacco
smoke were identified as sources of dozens of carcinogens, including benzo[a]pyrene,
tobacco-specific nitrosamines such as nitrosonornicotine, and reactive aldehydes such
as formaldehydewhich is also a hazard in embalming and making plastics. Vinyl chloride, from which PVC is manufactured, is a carcinogen and thus a hazard in PVC production.
https://en.wikipedia.org/wiki/Carcinogen
Cardiac Muscle
Cardiac muscle (heart muscle) is involuntary, striated muscle that is found
These three types of muscle all form in the process of myogenesis. The cells
only one nucleus, although populations with two to four nuclei do exist. Th
dium is the muscle tissue of the heart, and forms a thick middle layer betwe
outer epicardium layer and the inner endocardium layer.
https://en.wikipedia.org/wiki/Cardiac_muscle
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Cardiolipin
Cardiolipin (IUPAC name "1,3-bis(sn-3-phosphatidyl)-sn-glycerol") is an important
component of the inner mitochondrial membrane, where it constitutes about 20% of
the total lipid composition. It can also be found in the membranes of most bacteria.
The name cardiolipin is derived from the fact that it was first found in animal hearts.
In mammalian cells, but also in plant cells, cardiolipin (CL) is found almost exclusively
in the inner mitochondrial membrane where it is essential for the optimal function of
numerous enzymes that are involved in mitochondrial energy metabolism.
Because of cardiolipins unique bicyclic structure, a change in pH and the presence of
divalent cations can induce a structural change. CL shows a great variety of forms of aggregates. It is found that in the presence of Ca++ or other divalent cations, CL can be induced to have a lamellar-to-hexagonal (La-HII) phase transition. And it is believed to
have a close connection with membrane fusion.
The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein
complex found in bacteria and the mitochondrion. It is the last enzyme in the respiratory electron transport chain of mitochondria (or bacteria) located in the mitochondrial (or bacterial) membrane. It receives an electron from each of four cytochrome c
molecules, and transfers them to one oxygen molecule, converting molecular oxygen to
two molecules of water. Complex IV has been shown to require two associated CL molecules in order to maintain its full enzymatic function. Cytochrome bc1(Complex III)
also needs cardiolipin to maintain its quaternary structure and to maintains its functional role. Complex V of the oxidative phosphorylation machinery also displays high
binding affinity for CL, binding four molecules of CL per molecule of complex V.
Cardiolipin distribution to the outer mitochondrial membrane would lead to apoptosis
of the cells, as evidenced by cytochrome c (cyt c) release, Caspase-8 activation, MOMP
induction and NLRP3 inflammasome activation. During apoptosis, cyt c is released
from the intermembrane spaces of mitochondria into the cytosol. Cyt c can then bind
to the IP3 receptor on ER, stimulating calcium release, which then reacts back to cause
the release of cyt c. When the calcium concentration reaches a toxic level, this causes
cell death. Cytochrome c is thought to play a role in apoptosis via the release of apoptotic factors from the mitochondria. A cardiolipin-specific oxygenase produces CL hydroperoxides which can result in the conformation change of the lipid. The oxidized CL
transfers from the inner membrane to the outer membrane, and then helps to form a
permeable pore which releases cyt c.
During the oxidative phosphorylation process catalyzed by Complex IV, large quantities of protons are transferred from one side of the membrane to another side causing
a large pH change. CL is suggested to function as a proton trap within the mitochondrial membranes, thereby strictly localizing the proton pool and minimizing the
changes in pH in the mitochondrial intermembrane space. This function is due to CLs
unique structure. As stated above, CL can trap a proton within the bicyclic structure
while carrying a negative charge. Thus, this bicyclic structure can serve as an electron
buffer pool to release or absorb protons to maintain the pH near the membranes.
https://en.wikipedia.org/wiki/Cardiolipin
Carnitine
Carnitine is an amino acid derivative and nutrient involved in lipid (fat) metabolism in
mammals and other eukaryotes. It is in the chemical compound classes of hydroxyacids and quaternary ammonium compounds, and because of the hydroxylsubstituent, it exists in two stereoisomers, the biologically active enantiomer Lcarnitine, and the essentially biologically inactive D-carnitine. In such eukaryotic cells,
it is specifically required for the transport of fatty acids from the intermembraneous
space in the mitochondria into the mitochondrial matrix during the catabolism of lipids, in the generation of metabolic energy.
https://en.wikipedia.org/wiki/Carnitine
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Index
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Carnosine
Carnosine (-alanyl-L-histidine) is a dipeptide of the amino acids -alanine and histidine. It is highly concentrated in muscle and brain tissues.
Carnosine acts as an antiglycating agent, reducing the rate of formation of advanced
nal failure, and Alzheimer's disease.), and ultimately reducing development of atherosclerotic plaque build-up. Chronic glycolysis is speculated to accelerate aging.
https://en.wikipedia.org/wiki/Carnosine
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Carotenes
The term carotene (also carotin, from the Latin carota, "carrot") is used for many r
lated unsaturated hydrocarbon substances having the formula C40Hx, which are sy
sized by plants but in general cannot be made by animals (with the sole known exc
tion of some aphids and spider mites which acquired the synthetic genes from fung
tain no oxygen atoms. They absorb ultraviolet, violet, and blue light and scatter ora
or red light, and (in low concentrations) yellow light.
https://en.wikipedia.org/wiki/Carotene
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Cartilage
cage, the ear, the nose, the bronchial tubes and the intervertebral discs. It is
hard and rigid as bone, but it is stiffer and less flexible than muscle. Becaus
ity, cartilage often serves the purpose of holding tubes open in the body. Ex
clude the rings of the trachea, such as the cricoid cartilage and carina, the to
Index
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Cas (9)
Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme associated with the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)
adaptive immunity system in Streptococcus pyogenes, among other bacteria. S. pyogenes utilizes Cas9 to memorize and later interrogate and cleave foreign DNA, such as
invading bacteriophage DNA or plasmid DNA. Cas9 performs this interrogation by unwinding foreign DNA and checking whether it is complementary to the 20 basepair
spacer region of the guide RNA. If the DNA substrate is complementary to the guide
RNA, Cas9 cleaves the invading DNA. In this sense, the CRISPR-Cas9 mechanism has
a number of parallels with the RNA interference (RNAi) mechanism in eukaryotes.
Apart from its original function in bacterial immunity, the Cas9 protein has been heavily utilized as a genome engineering tool to induce site-directed double strand breaks
in DNA. These breaks can lead to gene inactivation or the introduction of heterologous
genes through non-homologous end joining and homologous recombination respectively in many laboratory model organisms. Alongside zinc finger nucleases and
TALEN proteins, Cas9 is becoming a prominent tool in the field of genome editing.
Cas9 has gained traction in recent years because it can cleave nearly any sequence complementary to the guide RNA. Because the target specificity of Cas9 stems from the
guide RNA:DNA complementarity and not modifications to the protein itself (like
TALENs and Zinc-fingers), engineering Cas9 to target new DNA is straightforward.
Versions of Cas9 that bind but do not cleave cognate DNA can be used to localize transcriptional activator or repressors to specific DNA sequences in order to control transcriptional activation and repression. While native Cas9 requires a guide RNA composed of two disparate RNAs that associate to make the guide - the CRISPR RNA
(crRNA), and the trans-activating RNA (tracrRNA). Cas9 targeting has been simplified
through the engineering of a chimeric single guide RNA. Scientists have suggested that
Cas9-based gene drives may be capable of editing the genomes of entire populations of
organisms. In 2015, scientists used Cas9 to modify the genome of human embryos for
the first time. The Heroes of CRISPR are the individuals who have, since its initial discovery in the Mediterranean port of Santa Pola on Spains Costa Blanca in 1989, made
significant contributions in the elucidation of the Class 2, Type II CRISPR/Cas9 system.
Cascade
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Caspases
Caspases (cysteine-aspartic proteases, cysteine aspartases or cysteine-dependent
aspartate-directed proteases) are a family of protease enzymes playing essential roles
in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation. They are named caspases due to their specific cysteine protease activity - a
cysteine in its active site nucleophilically attacks and cleaves a target protein only at
the C-terminal of an aspartic acid amino acid.
The role of these enzymes in programmed cell death was first identified in 1993, with
their functions in apoptosis well characterized. This is a form of programmed cell
death, occurring widely during development, and throughout life to maintain cell homeostasis. Activation of caspases ensure that the cellular components are degraded in
a controlled manner, carrying out cell death with minimal effect to surrounding tissues.
Caspases have other identified roles in programmed cell death such as Pyroptosis and
Necroptosis. These forms of cell death are important for protecting an organism from
stress signals and pathogenic attack. Caspases also have a role in inflammation,
whereby it directly processes pro-inflammatory cytokines such as pro-IL1. These are
signaling molecules that allow recruitment of immune cells to an infected cell or tissue.
There are other identified roles of caspases such as cell proliferation, tumor suppression, cell differentiation, neural development and axon guidance and aging.
Caspase deficiency has been identified as a cause of tumor development. Tumor
growth can occur by a combination of factors, including a mutation in a cell cycle gene
which removes the restrains of cell growth, combined with mutations in apoptopic proteins such as caspases that would respond by inducing cell death in abnormal growing
cells. On the contrary, over activation of some caspases such as caspase-3 can lead to
excessive programmed cell death. This is seen in several neurodegenerative diseases
where neural cells are lost, such as Alzheimers disease. Caspases involved with processing inflammatory signals are also implicated in disease. Insufficient activation of these
caspases can increase the organisms susceptibility to infection as an appropriate immune response may not be activated. The integral role caspases play in cell death and
disease has led to research for using caspases as a drug target. For example, inflammatory caspase-1 has been implicated in causing autoimmune diseases. Drugs blocking
the activation of caspase-1 have been used to improve the health of patients. Additionally, scientists have used caspases as cancer therapy to kill unwanted cells in tumors.
https://en.wikipedia.org/wiki/Caspase
Catabolic
Catabolism (from Greek kato, "downward" and ballein, "to throw") is the
set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks
down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into
smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).
Cells use the monomers released from breaking down polymers to either construct new
polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia,
and urea. The creation of these wastes is usually an oxidation process involving a release of chemical free energy, some of which is lost as heat, but the rest of which is
used to drive the synthesis of adenosine triphosphate (ATP). This molecule acts as a
way for the cell to transfer the energy released by catabolism to the energy-requiring
reactions that make up anabolism. (Catabolism is seen as destructive metabolism and
anabolism as constructive metabolism). Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include glycolysis, the citric acid cycle, the breakdown of muscle protein in order
to use amino acids as substrates for gluconeogenesis, the breakdown of fat in adipose
tissue to fatty acids, and oxidative deamination of neurotransmitters by monoamine
oxidase.
There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which
part of metabolism they stimulate. The so-called classic catabolic hormones known
since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects
have been discovered, including cytokines, orexin (also known as hypocretin), and
melatonin.
https://en.wikipedia.org/wiki/Catabolism
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Catabolism
Catabolism (from Greek kato, "downward" and ballein, "to throw") is the
set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks
down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into
smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).
Cells use the monomers released from breaking down polymers to either construct new
polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia,
and urea. The creation of these wastes is usually an oxidation process involving a release of chemical free energy, some of which is lost as heat, but the rest of which is
used to drive the synthesis of adenosine triphosphate (ATP). This molecule acts as a
way for the cell to transfer the energy released by catabolism to the energy-requiring
reactions that make up anabolism. (Catabolism is seen as destructive metabolism and
anabolism as constructive metabolism). Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include glycolysis, the citric acid cycle, the breakdown of muscle protein in order
to use amino acids as substrates for gluconeogenesis, the breakdown of fat in adipose
tissue to fatty acids, and oxidative deamination of neurotransmitters by monoamine
oxidase.
There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which
part of metabolism they stimulate. The so-called classic catabolic hormones known
since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects
have been discovered, including cytokines, orexin (also known as hypocretin), and
melatonin.
https://en.wikipedia.org/wiki/Catabolism
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Catalase
Catalase is a common enzyme found in nearly all living organisms exposed to oxygen
(such as bacteria, plants, and animals). It catalyzes the decomposition of hydrogen peroxide to water and oxygen. It is a very important enzyme in protecting the cell from oxidative damage by reactive oxygen species (ROS). Likewise, catalase has one of the highest turnover numbers of all enzymes. One catalase molecule can convert approximately 5 million molecules of hydrogen peroxide to water and oxygen each minute.
The reaction of catalase in the decomposition of hydrogen peroxide in living tissue:
2 H2O2 2 H2O + O2
The presence of catalase in a microbial or tissue sample can be tested by adding a volume of hydrogen peroxide and observing the reaction. The formation of bubbles, oxygen, indicates a positive result. This easy assay, which can be seen with the naked eye,
without the aid of instruments, is possible because catalase has a very high specific activity, which produces a detectable response. Alternative splicing may result in different protein variants.
Hydrogen peroxide is a harmful byproduct of many normal metabolic processes. To
prevent damage to cells and tissues, it must be quickly converted into other, less dangerous substances. To this end, catalase is frequently used by cells to rapidly catalyze
the decomposition of hydrogen peroxide into less-reactive gaseous oxygen and water
molecules.
The true biological significance of catalase is not always straightforward to assess:
Mice genetically engineered to lack catalase are phenotypically normal, indicating this
enzyme is dispensable in animals under some conditions. A catalase deficiency may increase the likelihood of developing type 2 diabetes. Some humans have very low levels
of catalase (acatalasia), yet show few ill effects. The predominant scavengers of H2O2 in
normal mammalian cells are likely peroxiredoxins rather than catalase.
https://en.wikipedia.org/wiki/Catalase
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Catalysis
Catalysis is the increase in the rate of a chemical reaction due to the participation of an
additional substance called a catalyst. With a catalyst, reactions occur faster and require less activation energy. Because catalysts are not consumed in the catalyzed reaction, they can continue to catalyze the reaction of further quantities of reactant. Often
only tiny amounts are required.
In the presence of a catalyst, less free energy is required to reach the transition state,
but the total free energy from reactants to products does not change. A catalyst may
participate in multiple chemical transformations. The effect of a catalyst may vary due
to the presence of other substances known as inhibitors or poisons (which reduce the
catalytic activity) or promoters (which increase the activity). The opposite of a catalyst,
a substance that reduces the rate of a reaction, is an inhibitor.
Catalyzed reactions have a lower activation energy (rate-limiting free energy of activation) than the corresponding uncatalyzed reaction, resulting in a higher reaction rate
at the same temperature and for the same reactant concentrations. However, the detailed mechanics of catalysis is complex. Catalysts may affect the reaction environment
favorably, or bind to the reagents to polarize bonds, e.g. acid catalysts for reactions of
carbonyl compounds, or form specific intermediates that are not produced naturally,
such as osmate esters in osmium tetroxide-catalyzed dihydroxylation of alkenes, or
cause dissociation of reagents to reactive forms, such as chemisorbed hydrogen in catalytic hydrogenation.
Kinetically, catalytic reactions are typical chemical reactions; i.e. the reaction rate depends on the frequency of contact of the reactants in the rate-determining step. Usually, the catalyst participates in this slowest step, and rates are limited by amount of
catalyst and its "activity". In heterogeneous catalysis, the diffusion of reagents to the
surface and diffusion of products from the surface can be rate determining. A
nanomaterial-based catalyst is an example of a heterogeneous catalyst. Analogous
events associated with substrate binding and product dissociation apply to homogeneous catalysts.
https://en.wikipedia.org/wiki/Catalysis
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Catalyst
Catalysis is the increase in the rate of a chemical reaction due to the participation of an
additional substance called a catalyst. With a catalyst, reactions occur faster and require less activation energy. Because catalysts are not consumed in the catalyzed reaction, they can continue to catalyze the reaction of further quantities of reactant. Often
only tiny amounts are required.
In the presence of a catalyst, less free energy is required to reach the transition state,
but the total free energy from reactants to products does not change. A catalyst may
participate in multiple chemical transformations. The effect of a catalyst may vary due
to the presence of other substances known as inhibitors or poisons (which reduce the
catalytic activity) or promoters (which increase the activity). The opposite of a catalyst,
a substance that reduces the rate of a reaction, is an inhibitor.
Catalyzed reactions have a lower activation energy (rate-limiting free energy of activation) than the corresponding uncatalyzed reaction, resulting in a higher reaction rate
at the same temperature and for the same reactant concentrations. However, the detailed mechanics of catalysis is complex. Catalysts may affect the reaction environment
favorably, or bind to the reagents to polarize bonds, e.g. acid catalysts for reactions of
carbonyl compounds, or form specific intermediates that are not produced naturally,
such as osmate esters in osmium tetroxide-catalyzed dihydroxylation of alkenes, or
cause dissociation of reagents to reactive forms, such as chemisorbed hydrogen in catalytic hydrogenation.
Kinetically, catalytic reactions are typical chemical reactions. That is, the reaction rate
depends on the frequency of contact of the reactants in the rate-determining step. Usually, the catalyst participates in this slowest step, and rates are limited by amount of
catalyst and its "activity". In heterogeneous catalysis, the diffusion of reagents to the
surface and diffusion of products from the surface can be rate determining. A
nanomaterial-based catalyst is an example of a heterogeneous catalyst. Analogous
events associated with substrate binding and product dissociation apply to homogeneous catalysts.
https://en.wikipedia.org/wiki/Catalysis
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Catalytic Triad
A catalytic triad refers to the three amino acid residues that function together at the
center of the active site of some hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and -lactamases). An Acid-Base-Nucleophile triad is
a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolyzed to regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid,
but occasionally threonine. Because enzymes fold into complex three-dimensional
structures, the residues of a catalytic triad can be far from each other along the aminoacid sequence (primary structure), however, they are brought close together in the final fold.
In serine proteases, the triad consists of the amino acids serine, histidine, and aspartic
acid.
https://en.wikipedia.org/wiki/Catalytic_triad
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Cataplerotic
pathway. Examples of such are found in the citric acid cycle (TCA cycle). In
The TCA cycle is a hub of metabolism, with central importance in both ener
tion and biosynthesis. Therefore, it is crucial for the cell to regulate concent
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Catecholamines
A catecholamine (CA) is a monoamine, an organic compound that has a catechol (benzene with two hydroxyl side groups) and a side-chain amine.
Catecholamines are derived from the amino acid tyrosine. Catecholamines are watersoluble and are 50%-bound to plasma proteins in circulation.
Included among catecholamines are epinephrine (adrenaline), norepinephrine (noradrenaline), and dopamine (pictured below), all of which are produced from phenylalanine and tyrosine. Release of the hormones epinephrine and norepinephrine from
the adrenal medulla of the adrenal glands is part of the fight-or-flight response.
Tyrosine is created from phenylalanine by hydroxylation by the enzyme phenylalanine
hydroxylase. Tyrosine is also ingested directly from dietary protein. Catecholaminesecreting cells use several reactions to convert tyrosine serially to L-DOPA and then to
dopamine. Depending on the cell type, dopamine may be further converted to norepinephrine or even further converted to epinephrine.
Various stimulant drugs are catecholamine analogues.
https://en.wikipedia.org/wiki/Catecholamine
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Catenins
Catenins are a family of proteins found in complexes with cadherin cell adhesion molecules of animal cells. The first two catenins that were identified became known as catenin and -catenin. A-catenin can bind to -catenin and can also bind actin. Bcatenin binds the cytoplasmic domain of some cadherins. Additional catenins such as
-catenin and -catenin have been identified. The name "catenin" was originally selected ('catena' means 'chain' in Latin) because it was suspected that catenins might
link cadherins to the cytoskeleton.
Cell-cell adhesion complexes are required for simple epithelia in higher organisms to
maintain structure, function and polarity. These complexes, which help regulate cell
growth in addition to creating and maintaining epithelial layers, are known as adherens junctions and they typically include at least cadherin, -catenin, and -catenin.
Catenins play roles in cellular organization and polarity long before the development
and incorporation of Wnt signaling pathways and cadherins.
The primary mechanical role of catenins is connecting cadherins to actin filaments, specifically in these adhesion junctions of epithelial cells. Most studies investigating catenin actions focus on -catenin and -catenin. -catenin is particularly interesting as it
plays a dual role in the cell. First of all, by binding to cadherin receptor intracellular cytoplasmic tail domains, it can act as an integral component of a protein complex in adherens junctions that helps cells maintain epithelial layers. -catenin acts by anchoring
the actin cytoskeleton to the junctions, and may possibly aid in contact inhibition signaling within the cell.
https://en.wikipedia.org/wiki/Catenin
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Cathepsin K
The protein encoded by this gene is a lysosomal cysteine protease involved
modeling and resorption. This protein, which is a member of the peptidase
defined by its high specificity for kinins, that is involved in bone resorption
and cartilage. This catabolic activity is also partially responsible for the loss
ticity and recoil in emphysema.
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that separates ions and polar molecules based on their affinity to the ion ex
tides, and amino acids. It is often used in protein purification, water analys
ity control. Cation exchange chromatography is used when the desired mole
meaning that the beads in the column contain positively charged functional
attract the anions.
https://en.wikipedia.org/wiki/Ion_chromatography#Weak_and_strong_i
gers
Cationic
A cation is an ion with fewer electrons than protons, giving it a positive cha
thing that is cationic is said to me more like a cationic, that is, more positive
https://en.wikipedia.org/wiki/Ion#Anions_and_cations
Cations
A cation is an ion with fewer electrons than protons, giving it a positive cha
There are additional names used for ions with multiple charges. For examp
Caveolae-based Endocytosis
In biology, caveolae (Latin for "little caves" - singular, caveola), which are a special
type of lipid raft, are small (50100 nanometer) invaginations of the plasma membrane in many vertebrate cell types, especially in endothelial cells and adipocytes.
These flask-shaped structures are rich in proteins as well as lipids such as cholesterol
and sphingolipids and have several functions in signal transduction.
Caveolae are one source of clathrin-independent raft-dependent endocytosis. The ability of caveolins to oligomerize due to their oligomerization domains is necessary for formation of caveolar endocytic vesicles. The oligomerization leads to formation of
caveolin-rich microdomains in the plasma membrane. Increased levels of cholesterol
and insertion of scaffolding domain of caveolins to the plasma membrane then lead to
expansion of the caveolar invagination and to formation of endocytic vesicle. Fission of
the vesicle from the plasma membrane is then mediated by GTPase dynamin II which
is localized at the neck of the budding vesicle. The released caveolar vesicle can fuse
with early endosome or caveosome. The caveosome is an endosomal compartment
with neutral pH which does not have early endosomal markers, however, contains
molecules internalized by the caveolar endocytosis.
This type of endocytosis is used for example for transcytosis of albumin in endothelial
cells or for internalization of the insulin receptor in primary adipocytes.
https://en.wikipedia.org/wiki/Caveolae
Caveolin
Caveolins are a family of integral membrane proteins that are the principal components of caveolae membranes and involved in receptor-independent endocytosis. Caveolins may act as scaffolding proteins within caveolar membranes by compartmentalizing and concentrating signaling molecules. Various classes of signaling molecules, including G-protein subunits, receptor and non-receptor tyrosine kinases, endothelial nitric oxide synthase (eNOS), and small GTPases, bind Cav-1 through its 'caveolinscaffolding domain'.
The functions of caveolins are still under intensive investigation. They are best known
for their role in the formation of 50-nanometer-size invaginations of the plasma membrane, called caveolae. Oligomers of caveolin form the coat of these domains. Cells that
lack caveolins also lack caveolae. Many functions are ascribed to these domains, ranging from endocytosis and transcytosis to signal transduction.
Caveolin-1 has also been shown to play a role in the integrin signaling. The tyrosine
phosphorylated form of caveolin-1 colocalizes with focal adhesions, suggesting a role
for caveolin-1 in migration. Indeed, downregulation of caveolin-1 leads to less efficient
migration in vitro.
https://en.wikipedia.org/wiki/Caveolin
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CD36
CD36 (cluster of differentiation 36), also known as FAT (fatty acid translocase), FAT/
CD36, (FAT)/CD36, SCARB3, GP88, glycoprotein IV (gpIV), and glycoprotein IIIb
(gpIIIb), is an integral membrane protein found on the surface of many cell types in
vertebrate animals. CD36 is a member of the class B scavenger receptor family of cell
surface proteins. CD36 binds many ligands including collagen, thrombospondin, erythrocytes parasitized with Plasmodium falciparum, oxidized low density lipoprotein, native lipoproteins, oxidized phospholipids, and long-chain fatty acids.
Recent work using genetically modified rodents have identified a clear role for CD36 in
fatty acid metabolism, heart disease, taste, and dietary fat processing in the intestine.
It may be involved in glucose intolerance, atherosclerosis, arterial hypertension, diabetes, cardiomyopathy and Alzheimer's disease.
CD36s function in long-chain fatty acid uptake and signaling can be irreversibly inhibited by sulfo-N-succinimidyl oleate (SSO), which binds lysine 164 within a hydrophobic pocked shared by several CD36 ligands, e.g. fatty acid and oxLDL.
On binding a ligand the protein and ligand are internalized. This internalization is independent of macropinocytosis and occurs by an actin dependent mechanism requiring
the activation Src-family kinases, JNK and Rho-family GTPases. Unlike macropinocytosis this process is not affected by inhibitors of phosphatidylinositol 3-kinase or Na+/H+
exchange.
https://en.wikipedia.org/wiki/CD36
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cDNA
Complementary DNA (cDNA) is double-stranded DNA synthesized from a messenger
RNA (mRNA) template in a reaction catalyzed by the enzyme reverse transcriptase.
cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to
express a specific protein in a cell that does not normally express that protein (i.e., heterologous expression), they will transfer the cDNA that codes for the protein to the recipient cell.
Although there are several methods for doing so, cDNA is most often synthesized from
mature (fully spliced) mRNA using the enzyme reverse transcriptase. This enzyme,
which naturally occurs in retroviruses, operates on a single strand of mRNA, generating its complementary DNA based on the pairing of RNA base pairs (A, U, G and C) to
their DNA complements (T, A, C and G, respectively).
To obtain eukaryotic cDNA whose introns have been removed:
1 A eukaryotic cell transcribes the DNA (from genes) into RNA (pre-mRNA).
2 The same cell processes the pre-mRNA strands by removing introns, and adding a
poly-A tail and 5 Methyl-Guanine cap (this is known as post-transcriptional modification)
3 This mixture of mature mRNA strands is extracted from the cell. The Poly-A tail of
the post-transcription mRNA can be taken advantage of with oligo(dT) beads in an affinity chromatography assay.
4 A poly-T oligonucleotide primer is hybridized onto the poly-A tail of the mature
mRNA template, or random hexamer primers can be added which contain every possible 6 base single strand of DNA and can therefore hybridize anywhere on the RNA (Reverse transcriptase requires this double-stranded segment as a primer to start its operation.)
5 Reverse transcriptase is added, along with deoxynucleotide triphosphates (A, T, G,
C). This synthesizes one complementary strand of DNA hybridized to the original
mRNA strand.
6 To synthesize an additional DNA strand, traditionally one would digest the RNA of
the hybrid strand, using an enzyme like RNase H, or through alkali digestion method.
7 After digestion of the RNA, a single stranded DNA (ssDNA) is left and because single
stranded nucleic acids are hydrophobic, it tends to loop around itself. It is likely that
the ssDNA forms a hairpin loop at the 3' end.
8 From the hairpin loop, a DNA polymerase can then use it as a primer to transcribe a
complementary sequence for the ss cDNA.
9 Now, you should be left with a double stranded cDNA with identical sequence as the
mRNA of interest.
https://en.wikipedia.org/wiki/Complementary_DNA
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cDNA Library
scriptome of the organism. cDNA is produced from fully transcribed mRNA fou
the nucleus and therefore contains only the expressed genes of an organism. Si
is already spliced, hence the cDNA produced lacks introns and can be readily ex
enhancers, introns, and other regulatory elements found in a genomic DNA lib
https://en.wikipedia.org/wiki/CDNA_library
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Techniques
Techniques
Techniques
Techniques
CDP
Cytidine diphosphate, abbreviated CDP, is a nucleoside diphosphate. It is an ester of
pyrophosphoric acid with the nucleoside cytidine. CDP consists of the pyrophosphate
group, the pentose sugar ribose, and the nucleobase cytosine.
https://en.wikipedia.org/wiki/Cytidine_diphosphate
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CDP-choline
Citicoline (INN), also known as cytidine diphosphate-choline (CDP-Choline) or cytidine 5'-diphosphocholine is a psychostimulant/nootropic. It is an intermediate in the
generation of phosphatidylcholine from choline.
Studies suggest that CDP-choline supplements increase dopamine receptor densities,
and suggest that CDP-choline supplementation helps prevent memory impairment resulting from poor environmental conditions. Preliminary research has found that citicoline supplements help improve focus and mental energy and may possibly be useful in
the treatment of attention deficit disorder.
Citicoline has also been shown to elevate ACTH independently from CRH levels and to
amplify the release of other HPA axis hormones such as LH, FSH, GH and TSH in response to hypothalamic releasing factors. These effects on HPA hormone levels may be
beneficial for some individuals but may have undesirable effects in those with medical
conditions featuring ACTH or cortisol hypersecretion including PCOS, type II diabetes
and major depressive disorder.
https://en.wikipedia.org/wiki/Citicoline
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CDP-diacylglycerol
CDP-diacylglycerol is an activated intermediate found in biosynthesis of various glycerophospholipids. The high energy of the bond between the cytidine and the diacylglyerol is used to attach the phosphatidyl part of itself to another molecule, leaving behind a CMP. Several examples are shown below.
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Celebrex
Celecoxib (also known as Celebrex) is a COX-2 selective nonsteroidal antiinflammatory drug (NSAID). It is used to treat the pain and inflammation of osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, acute pain in adults, painful menstruation, and juvenile rheumatoid arthritis in people two years or older.
Side effects include a 37% increase in incidence of major vascular events, which include nonfatal myocardial infarction, nonfatal stroke, or death from a blood vesselrelated cause. Additionally, an 81% increase in incidence of upper gastrointestinal complications occurs, which include perforations, obstructions, or gastrointestinal bleeding as in all NSAIDs.
In July 2015 the FDA strengthened the warning that non-aspirin nonsteroidal antiinflammatory drugs (NSAIDs) can cause heart attacks or strokes.
https://en.wikipedia.org/wiki/Celecoxib
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Cell Cycle
The cell cycle or cell-division cycle is the series of events that take place in a cell leading to its division and duplication of its DNA (DNA replication) to produce two daughter cells.
In bacteria, which lack a cell nucleus, the cell cycle is divided into the B, C, and D periods. The B period extends from the end of cell division to the beginning of DNA replication. DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter cells.
In cells with a nucleus, as in eukaryotes, the cell cycle is also divided into three periods:
interphase, the mitotic (M) phase, and cytokinesis. During interphase, the cell grows,
accumulating nutrients needed for mitosis, preparing it for cell division and duplicating its DNA. During the mitotic phase, the cell splits itself into two distinct daughter
cells. During the final stage, cytokinesis, the new cell is completely divided. To ensure
the proper division of the cell, there are control mechanisms known as cell cycle checkpoints.
The cell-division cycle is a vital process by which a single-celled fertilized egg develops
into a mature organism, as well as the process by which hair, skin, blood cells, and
some internal organs are renewed. After cell division, each of the daughter cells begin
the interphase of a new cycle. Although the various stages of interphase are not usually
morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of cell division.
In the figure below, I is interphase and M is mitosis.
https://en.wikipedia.org/wiki/Cell_cycle
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Cell Division
Cell division is the process by which a parent cell divides into two or more daughter
cells. Cell division usually occurs as part of a larger cell cycle. In eukaryotes, there are
two distinct types of cell division: a vegetative division, whereby each daughter cell is
genetically identical to the parent cell (mitosis), and a reproductive cell division,
whereby the number of chromosomes in the daughter cells is reduced by half, to produce haploid gametes (meiosis). Meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions: homologous chromosomes are separated in the first division, and sister chromatids are separated in the second division. Both of these cell division cycles are used in sexually reproducing organisms at some point in their life cycle, and both are believed to be present in the last
eukaryotic common ancestor. Prokaryotes also undergo a vegetative cell division
known as binary fission, where their genetic material is segregated equally into two
daughter cells. All cell divisions, regardless of organism, are preceded by a single
round of DNA replication.
For simple unicellular organisms, such as the amoeba, one cell division is equivalent to
reproduction an entire new organism is created. On a larger scale, mitotic cell division can create progeny from multicellular organisms, such as plants that grow from
cuttings. Cell division also enables sexually reproducing organisms to develop from the
one-celled zygote, which itself was produced by cell division from gametes. And after
growth, cell division allows for continual construction and repair of the organism. A human being's body experiences about 10 quadrillion cell divisions in a lifetime.
The primary concern of cell division is the maintenance of the original cell's genome.
Before division can occur, the genomic information that is stored in chromosomes
must be replicated, and the duplicated genome must be separated cleanly between
cells. A great deal of cellular infrastructure is involved in keeping genomic information
consistent between "generations".
https://en.wikipedia.org/wiki/Cell_division
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Cell Junctions
A cell junction (or intercellular bridge) is a type of structure that exists within th
and the extracellular matrix. They also build up the paracellular barrier of epith
and control the paracellular transport. Cell junctions are especially abundant in
lial tissues.
https://en.wikipedia.org/wiki/Cell_junction
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Cell Membrane
The cell membrane (or plasma membrane or plasmalemma) surrounds the cytoplasm
of living cells, physically separating the intracellular components from the extracellular
environment. Fungi, bacteria and plants also have a cell wall in addition, which provides a mechanical support to the cell and precludes the passage of larger molecules.
The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to
the cell, and in attaching to the extracellular matrix and other cells to hold them together to form tissues.
The cell membrane is selectively permeable and able to regulate what enters and exits
the cell, thus facilitating the transport of materials needed for survival. The movement
of substances across the membrane can be either "passive", occurring without the input of cellular energy, or "active", requiring the cell to expend energy in transporting it.
The membrane also maintains the cell potential. The cell membrane thus works as a selective filter that allows only certain things to come inside or go outside the cell. The
cell employs a number of transport mechanisms that involve biological membranes:
Passive osmosis and diffusion: Some substances (small molecules, ions) such as carbon dioxide (CO2) and oxygen (O2), can move across the plasma membrane by diffusion, which is a passive transport process. Because the membrane acts as a barrier for
certain molecules and ions, they can occur in different concentrations on the two sides
of the membrane. Such a concentration gradient across a semipermeable membrane
sets up an osmotic flow for the water.
Transmembrane protein channels and transporters: Nutrients, such as sugars or
amino acids, must enter the cell, and certain products of metabolism must leave the
cell. Such molecules diffuse passively through protein channels such as aquaporins (in
the case of water (H2O)) in facilitated diffusion or are pumped across the membrane by
transmembrane transporters. Protein channel proteins, also called permeases, are usually quite specific, recognizing and transporting only a limited food group of chemical
substances, often even only a single substance.
Endocytosis: Endocytosis is the process in which cells absorb molecules by engulfing
them. The plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. The deformation then
pinches off from the membrane on the inside of the cell, creating a vesicle containing
the captured substance. Endocytosis is a pathway for internalizing solid particles ("cell
eating" or phagocytosis), small molecules and ions ("cell drinking" or pinocytosis), and
macromolecules. Endocytosis requires energy and is thus a form of active transport.
Exocytosis: Just as material can be brought into the cell by invagination and formation
of a vesicle, the membrane of a vesicle can be fused with the plasma membrane, extruding its contents to the surrounding medium. This is the process of exocytosis. Exocytosis occurs in various cells to remove undigested residues of substances brought in by
endocytosis, to secrete substances such as hormones and enzymes, and to transport a
substance completely across a cellular barrier. In the process of exocytosis, the undigested waste-containing food vacuole or the secretory vesicle budded from Golgi apparatus, is first moved by cytoskeleton from the interior of the cell to the surface. The vesicle membrane comes in contact with the plasma membrane. The lipid molecules of the
two bilayers rearrange themselves and the two membranes are, thus, fused. A passage
is formed in the fused membrane and the vesicles discharges its contents outside the
cell.
https://en.wikipedia.org/wiki/Cell_membrane
Cell Suicide
Apoptosis (from Ancient Greek "falling off") is a process of programmed
cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal DNA fragmentation, and global mRNA decay. Between 50 and 70 billion cells die each day due to apoptosis in the average human adult. For an average child between the ages of 8 and 14,
approximately 20 billion to 30 billion cells die a day.
In contrast to necrosis, which is a form of traumatic cell death that results from acute
cellular injury, apoptosis is a highly regulated and controlled process that confers advantages during an organism's lifecycle. For example, the separation of fingers and
toes in a developing human embryo occurs because cells between the digits undergo
apoptosis. Unlike necrosis, apoptosis produces cell fragments called apoptotic bodies
that phagocytic cells are able to engulf and quickly remove before the contents of the
cell can spill out onto surrounding cells and cause damage.
Because apoptosis cannot stop once it has begun, it is a highly regulated process. Apoptosis can be initiated through one of two pathways. In the intrinsic pathway the cell
kills itself because it senses cell stress, while in the extrinsic pathway the cell kills itself
because of signals from other cells. Both pathways induce cell death by activating caspases, which are proteases, or enzymes that degrade proteins. The two pathways both
activate initiator caspases, which then activate executioner caspases, which then kill
the cell by degrading proteins indiscriminately.
Research on apoptosis has increased substantially since the early 1990s. In addition to
its importance as a biological phenomenon, defective apoptotic processes have been implicated in a wide variety of diseases. Excessive apoptosis causes atrophy, whereas an
insufficient amount results in uncontrolled cell proliferation, such as cancer. Some factors like Fas receptors and caspases promote apoptosis, while some members of the
Bcl-2 family of proteins inhibit apoptosis.
https://en.wikipedia.org/wiki/Apoptosis
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Cell Wall
A cell wall is a structural layer that surrounds some types of cells, situated outside the
cell membrane. It can be tough, flexible, and sometimes rigid. It provides cells with
both structural support and protection, and also acts as a filtering mechanism. Cell
walls are present in plants, fungi and prokaryotic cells, where a major function is to act
as pressure vessels, preventing over-expansion when water enters the cells. Cell walls
are absent from mycoplasmas.
The composition of cell walls varies between species and may depend on cell type and
developmental stage. The primary cell wall of land plants is composed of the polysaccharides cellulose, hemicellulose and pectin. In bacteria, the cell wall is composed of
peptidoglycan. Archaean cell walls have various compositions, and may be formed of
glycoprotein S-layers, pseudopeptidoglycan, or polysaccharides. Fungi possess cell
walls made of the glucosamine polymer chitin, and algae typically possess walls made
of glycoproteins and polysaccharides. Unusually, diatoms have a cell wall composed of
biogenic silica. Often, other accessory molecules such as lignin or cutin are found anchored to the cell wall.
https://en.wikipedia.org/wiki/Cell_wall
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Cells
The cell (from Latin cella, meaning "small room") is the basic structural, functional,
and biological unit of all known living organisms. A cell is the smallest unit of life that
can replicate independently, and cells are often called the "building blocks of life". The
study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Organisms can be classified as unicellular (consisting of a single cell, including bacteria) or
multicellular (including plants and animals).
Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Organisms can be classified as unicellular
(consisting of a single cell; including bacteria) or multicellular (including plants and
animals). While the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion (1013) cells. Most plant and animal cells are
visible only under the microscope, with dimensions between 1 and 100M.
https://en.wikipedia.org/wiki/Cell_(biology)
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Cellular Response
The cellular response is one of two primary responses of the blood clotting system to
injury. The other response is known as the molecular response and is the response
that makes the blood clot.
The cellular response, by contrast, is the first response to injury. Injury to the epithelial lining of a blood vessel begins the process of coagulation almost instantly. The cellular response has an initial action followed by an amplification step. In the cellular response, the platelets bind directly to collagen using Ia/IIa collagen-binding surface receptors and glycoprotein VI to form a plug. The signal to the platelets to take this action is exposure of the underlying collagen, something that would not happen in the absence of a wound. In this overall process, platelets integrins get activated and then
bind tightly to the extracellular matrix to anchor them to the site of the wound.
The von Willebrand factor assists by forming additional links between the platelets glycoprotein Ib/IX/V and the fibrils of the collagen.
In the amplification part of the cellular response, the activated platelets release a large
number of factors, including platelet factor 4 (a cytokine stimulating inflammation and
moderating action of the heparin anticoagulant) and thromboxane A2, The latter has
the effect of increasing the stickiness of platelets, favoring their aggregation. In addition, a a Gq-linked protein receptor cascade is activated, resulting in release of calcium
in the area. This plays a role in the molecular response.
https://en.wikipedia.org/wiki/Coagulation
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Cellulase
Cellulase is any of several enzymes produced chiefly by fungi, bacteria, and protozoans
that catalyze cellulolysis, the decomposition of cellulose and of some related polysaccharides. The name is also used for any naturally occurring mixture or complex of various such enzymes, that act serially or synergistically to decompose cellulosic material.
Cellulases break down the cellulose molecule into monosaccharides ("simple sugars")
such as -glucose, or shorter polysaccharides and oligosaccharides. Cellulose breakdown is of considerable economic importance, because it makes a major constituent of
plants available for consumption and use in chemical reactions. The specific reaction
involved is the hydrolysis of the 1,4--D-glycosidic linkages in cellulose, hemicellulose,
lichenin, and cereal -D-glucans. Because cellulose molecules bind strongly to each
other, cellulolysis is relatively difficult compared to the breakdown of other polysaccharides such as starch.
Most mammals have only very limited ability to digest dietary fibers such as cellulose
by themselves. In many herbivorous animals such as ruminants like cattle and sheep
and hindgut fermenters like horses, cellulases are produced by symbiotic bacteria. Cellulases are produced by a few types of animals, such as some termites.
https://en.wikipedia.org/wiki/Cellulase
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Cellulose
Cellulose is an organic compound with the formula (C6H10O5)n, a polysaccharide consisting of a linear chain of several hundred to many thousands of (14) linked Dglucose units. Cellulose is an important structural component of the primary cell wall
of green plants, many forms of algae and the oomycetes. Some species of bacteria secrete it to form biofilms. Cellulose is the most abundant organic polymer on Earth.
Cellulose is mainly used to produce paperboard and paper. Smaller quantities are converted into a wide variety of derivative products such as cellophane and rayon. Conversion of cellulose from energy crops into biofuels such as cellulosic ethanol is under investigation as an alternative fuel source. Cellulose for industrial use is mainly obtained
from wood pulp and cotton.
Some animals, particularly ruminants and termites, can digest cellulose with the help
of symbiotic micro-organisms that live in their guts, such as Trichonympha. In humans, cellulose acts as a hydrophilic bulking agent for feces and is often referred to as
a "dietary fiber".
https://en.wikipedia.org/wiki/Cellulose
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Cellulose Synthase
Cellulose synthase (GDP-forming) (EC 2.4.1.29) is an enzyme that catalyzes the chemical reaction
UDP-glucose + (1,4--D-glucosyl)n <-> UDP + (1,4--D-glucosyl)n+1
Some forms of the enzyme can use GDP-glucose instead of UDP-glucose.
Cellulose biosynthesis is the process during which separate homogeneous -1,4-glucan
chains, ranging from 2,000 to 25,000 glucose residues in length, are synthesized and
then immediately hydrogen bonded with one another to form rigid crystalline arrays,
or microfibrils. Microfibrils in the primary cell wall are approximately 36 chains long
while those of the secondary cell wall are much larger, containing up to 1200 -1,4glucan chains. Uridine diphosphate-glucose (UDP), which is produced by the enzyme
sucrose synthase (SuSy) that produces and transports UDP-glucose to the plasma membrane is the substrate used by cellulose synthase to produce the glucan chains. The rate
at which glucose residues are synthesized per one glucan chain ranges from 300-1000
glucose residues per minute, the higher rate being more prevalent in secondary wall
particles, such as in the xylem.
https://en.wikipedia.org/wiki/Cellulose_synthase_(UDP-forming)
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Central Dogma
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system.
The central dogma has also been described as "DNA makes RNA and RNA makes protein," a positive statement which was originally termed the sequence hypothesis by
Francis Crick. However, this simplification does not make it clear that the central
dogma as stated by Crick does not preclude the reverse flow of information from RNA
to DNA, only ruling out the flow from protein to RNA or DNA.
The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 33 = 9 conceivable direct transfers of information
that can occur between these. The dogma classes these into 3 groups of 3: 3 general
transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and
3 unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA
information can be copied into mRNA (transcription), and proteins can be synthesized
using the information in mRNA as a template (translation).
Crick's use of the word dogma was unconventional, and has been controversial.
https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
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https://en.wikipedia.org/wiki/Central_nervous_system
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Ceramide
Ceramides are a family of waxy lipid molecules. A ceramide is composed of sphingosine and a fatty acid. Ceramides are found in high concentrations within the cell
membrane of cells. They are one of the component lipids that make up sphingomyelin,
one of the major lipids in the lipid bilayer.
As a bioactive lipid, ceramide has been implicated in a variety of physiological functions including apoptosis, cell growth arrest, differentiation, cell senescence, cell migration and adhesion. Roles for ceramide and its downstream metabolites have also been
suggested in a number of pathological states including cancer, neurodegeneration, diabetes, microbial pathogenesis, obesity, and inflammation.
One of the most studied roles of ceramide pertains to its function as a proapoptotic
molecule. Apoptosis, or Type I programmed cell death, is essential for the maintenance
of normal cellular homeostasis and is an important physiological response to many
forms of cellular stress. Ceramide accumulation has been found following treatment of
cells with a number of apoptotic agents including ionizing radiation, UV light, TNF-,
and chemotherapeutic agents. This suggests a role for ceramide in the biological responses of all these agents. Because of its apoptosis-inducing effects in cancer cells, ceramide has been termed the tumor suppressor lipid . Several studies have attempted
to define further the specific role of ceramide in the events of cell death and some evidence suggests ceramide functions upstream of the mitochondria in inducing apoptosis. However, owing to the conflicting and variable nature of studies into the role of ceramide in apoptosis, the mechanism by which this lipid regulates apoptosis remains
elusive. (R below in the figure is the non-polar end of a fatty acid).
https://en.wikipedia.org/wiki/Ceramide
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Cerebroside
Cerebrosides is the common name for a group of glycosphingolipids called monoglycosylceramides which are important components in animal muscle and nerve cell membranes. They consist of a ceramide with a single sugar residue at the 1-hydroxyl moiety.
The sugar residue can be either glucose or galactose. The two major types are therefore called glucocerebrosides and galactocerebrosides. Galactocerebrosides are typically found in neural tissue, while glucocerebrosides are found in other tissues.
The fundamental structure of a cerebroside is ceramide. Monoglycosyl and oligoglycosylceramides having a mono or polysaccharide bonded glycosidically to the terminal
OH group of ceramide are defined as cerebrosides. Sphingosine is the main long-chain
base present in ceramide.
Galactosylceramide (shown at bottom) is the principal glycosphingolipid in brain tissue. Galactosylceramides are present in all nervous tissues, and can compose up to 2%
dry weight of grey matter and 12% of white matter. They are major constituents of oligodendrocytes. Glucosylceramide is found at low levels in animal cells such as the
spleen, erythrocytes, and nervous tissues, especially neurons. Glucosylceramide is a
major constituent of skin lipids, where it is essential for lamellar body formation in the
stratum corneum and to maintain the water permeability barrier of the skin. Glucosylceramide is the only glycosphingolipid common to plants, fungi and animals. It is usually considered to be the principal glycosphingolipid in plants. It is a major component
of the outer layer of the plasma membrane. Galactosylceramides have not been found
in plants.
Monogalactosylceramide is the largest single component of the myelin sheath of
nerves. Cerebroside synthesis can therefore give a measurement of myelin formation
or remyelination. The sugar moiety is linked glycosidically to the C-1 hydroxyl group of
ceramide, such as in lactosylceramide. Cerebrosides containing a sulfuric ester (sulfate) group, known as sulfatides, also occur in the myelin sheath of nerves. These compounds are preferably named as sulfates of the parent glycosphingolipid.
https://en.wikipedia.org/wiki/Cerebroside
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CFTR
Cystic fibrosis transmembrane conductance regulator (CFTR) is a membrane protein
and chloride channel in vertebrates that is encoded by the CFTR gene.
CFTR is an ABC transporter-class ion channel that codes for a protein that conducts
chloride and thiocyanate ions across epithelial cell membranes. Mutations of the CFTR
gene affecting chloride ion channel function lead to dysregulation of epithelial fluid
transport in the lung, pancreas and other organs, resulting in cystic fibrosis.
The CFTR protein is a channel protein that controls the flow of H2O and Cl ions in
and out of cells inside the lungs. When the CFTR protein is working correctly, ions
freely flow in and out of the cells. However, when the CFTR protein is malfunctioning,
these ions cannot flow out of the cell due to a blocked channel. This causes cystic fibrosis, characterized by the buildup of thick mucus in the lungs.
Complications include thickened mucus in the lungs with frequent respiratory infections, and pancreatic insufficiency giving rise to malnutrition and diabetes. These conditions lead to chronic disability and reduced life expectancy. In male patients, the progressive obstruction and destruction of the developing vas deferens (spermatic cord)
and epididymis appear to result from abnormal intraluminal secretions, causing congenital absence of the vas deferens and male infertility.
https://en.wikipedia.org/wiki/Cystic_fibrosis_transmembrane_conductance_regulat
or
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Channels
Ion channels are pore-forming membrane proteins whose functions include establishing a resting membrane potential, shaping action potentials and other electrical signals
by gating the flow of ions across the cell membrane, controlling the flow of ions across
secretory and epithelial cells, and regulating cell volume. Ion channels are present in
the membranes of all cells. Ion channels are considered to be one of the two traditional
classes of ionophoric proteins, with the other class known as ion transporters (including the sodium-potassium pump, sodium-calcium exchanger, and sodium-glucose
transport proteins, amongst others).
Study of ion channels (channelomics) often includes biophysics, electrophysiology and
pharmacology, utilizing techniques including voltage clamp, patch clamp, immunohistochemistry, X-ray crystallography, fluorescence, and RT-PCR.
https://en.wikipedia.org/wiki/Ion_channel
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Chaperonin
Chaperonins are proteins that provide favorable conditions for the correct folding of
other proteins, thus preventing aggregation. Newly made proteins usually must fold
from a linear chain of amino acids into a three-dimensional form. Chaperonins belong
to a large class of molecules that assist protein folding, called molecular chaperones.
The energy to fold proteins is supplied by adenosine triphosphate (ATP).
Chaperonins undergo large conformational changes during a folding reaction as a function of the enzymatic hydrolysis of ATP as well as binding of substrate proteins and cochaperonins, such as GroES. These conformational changes allow the chaperonin to
bind an unfolded or misfolded protein, encapsulate that protein within one of the cavities formed by the two rings, and release the protein back into solution. Upon release,
the substrate protein will either be folded or will require further rounds of folding, in
which case it can again be bound by a chaperonin.
The exact mechanism by which chaperonins facilitate folding of substrate proteins is
unknown. According to recent analyses by different experimental techniques, GroELbound substrate proteins populate an ensemble of compact and locally expanded states
that lack stable tertiary interactions. A number of models of chaperonin action have
been proposed, which generally focus on two (not mutually exclusive) roles of chaperonin interior: passive and active. Passive models treat the chaperonin cage as an inert
form, exerting influence by reducing the conformational space accessible to a protein
substrate or preventing intermolecular interactions e.g. by aggregation prevention. The
active chaperonin role is in turn involved with specific chaperoninsubstrate interactions that may be coupled to conformational rearrangements of the chaperonin.
Probably the most popular model of the chaperonin active role is the iterative annealing mechanism (IAM), which focus on the effect of iterative, and hydrophobic in nature, binding of the protein substrate to the chaperonin. According to computational
simulation studies, the IAM leads to more productive folding by unfolding the substrate from misfolded conformations or by prevention from protein misfolding through
changing the folding pathway.
https://en.wikipedia.org/wiki/Chaperonin
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Chaperonins
Chaperonins are proteins that provide favorable conditions for the correct folding of
other proteins, thus preventing aggregation. Newly made proteins usually must fold
from a linear chain of amino acids into a three-dimensional form. Chaperonins belong
to a large class of molecules that assist protein folding, called molecular chaperones.
The energy to fold proteins is supplied by adenosine triphosphate (ATP).
Chaperonins undergo large conformational changes during a folding reaction as a function of the enzymatic hydrolysis of ATP as well as binding of substrate proteins and cochaperonins, such as GroES. These conformational changes allow the chaperonin to
bind an unfolded or misfolded protein, encapsulate that protein within one of the cavities formed by the two rings, and release the protein back into solution. Upon release,
the substrate protein will either be folded or will require further rounds of folding, in
which case it can again be bound by a chaperonin.
The exact mechanism by which chaperonins facilitate folding of substrate proteins is
unknown. According to recent analyses by different experimental techniques, GroELbound substrate proteins populate an ensemble of compact and locally expanded states
that lack stable tertiary interactions. A number of models of chaperonin action have
been proposed, which generally focus on two (not mutually exclusive) roles of chaperonin interior: passive and active. Passive models treat the chaperonin cage as an inert
form, exerting influence by reducing the conformational space accessible to a protein
substrate or preventing intermolecular interactions e.g. by aggregation prevention. The
active chaperonin role is in turn involved with specific chaperoninsubstrate interactions that may be coupled to conformational rearrangements of the chaperonin.
Probably the most popular model of the chaperonin active role is the iterative annealing mechanism (IAM), which focus on the effect of iterative, and hydrophobic in nature, binding of the protein substrate to the chaperonin. According to computational
simulation studies, the IAM leads to more productive folding by unfolding the substrate from misfolded conformations or by prevention from protein misfolding through
changing the folding pathway.
https://en.wikipedia.org/wiki/Chaperonin
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Chemerin
tein that in humans is encoded by the RARRES2 gene. Retinoids exert biolo
such as potent growth inhibitory and cell differentiation activities and are u
specific nuclear receptor proteins that are members of the steroid and thyro
mone receptor superfamily of transcriptional regulators.
https://en.wikipedia.org/wiki/Chemerin
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Chemiosmotic
Chemiosmosis is the movement of ions across a selectively permeable membrane,
down their electrochemical gradient. More specifically, it relates to the generation of
ATP by the movement of hydrogen ions across a membrane during cellular respiration
or photosynthesis.
Hydrogen ions (protons) will diffuse from an area of high proton concentration to an
area of lower proton concentration, and an electrochemical concentration gradient of
protons across a membrane can be harnessed to make ATP. This process is related to
osmosis, the diffusion of water across a membrane, which is why it is called chemiosmosis.
ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to
pass through the membrane and uses the kinetic energy to phosphorylate ADP, making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts as well as in
most bacteria and archaea.
Peter D. Mitchell proposed the chemiosmotic hypothesis in 1961. The theory suggests
essentially that most ATP synthesis in respiring cells comes from the electrochemical
gradient across the inner membranes of mitochondria by using the energy of NADH
and FADH2 formed from the breaking down of energy-rich molecules such as glucose.
Molecules such as glucose are metabolized to produce acetyl CoA as an energy-rich intermediate. The oxidation of acetyl CoA in the mitochondrial matrix is coupled to the
reduction of a carrier molecule such as NAD and FAD. The carriers pass electrons to
the electron transport chain (ETC) in the inner mitochondrial membrane, which in
turn pass them to other proteins in the ETC. The energy available in the electrons is
used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The protons
move back across the inner membrane through the enzyme ATP synthase. The flow of
protons back into the matrix of the mitochondrion via ATP synthase provides enough
energy for ADP to combine with inorganic phosphate to form ATP. The electrons and
protons at the last pump in the ETC are taken up by oxygen to form water.
https://en.wikipedia.org/wiki/Chemiosmosis
Chemokine
Chemokines (Greek -kinos, movement) are a family of small cytokines, or signaling proteins secreted by cells. Their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. They are chemotactic cytokines.
The major role of chemokines is to act as a chemoattractant to guide the migration of
cells. Cells that are attracted by chemokines follow a signal of increasing chemokine
concentration towards the source of the chemokine. Some chemokines control cells of
the immune system during processes of immune surveillance, such as directing lymphocytes to the lymph nodes so they can screen for invasion of pathogens by interacting with antigen-presenting cells residing in these tissues. These are known as homeostatic chemokines and are produced and secreted without any need to stimulate their
source cell(s).
Some chemokines have roles in development. They promote angiogenesis (the growth
of new blood vessels), or guide cells to tissues that provide specific signals critical for
cellular maturation. Other chemokines are inflammatory and are released from a wide
variety of cells in response to bacterial infection, viruses and agents that cause physical
damage such as silica or the urate crystals that occur in gout. Their release is often
stimulated by pro-inflammatory cytokines such as interleukin 1. Inflammatory chemokines function mainly as chemoattractants for leukocytes, recruiting monocytes,
neutrophils and other effector cells from the blood to sites of infection or tissue damage. Certain inflammatory chemokines activate cells to initiate an immune response or
promote wound healing. They are released by many different cell types and serve to
guide cells of both innate immune system and adaptive immune system.
https://en.wikipedia.org/wiki/Chemokine
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Chemotrophic
Chemotrophs are organisms that obtain energy by the oxidation of electron donors in
their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs,
which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic.
Chemoautotrophs are commonly found in ocean floors where sunlight cannot reach
them because they are not dependent on solar energy. Ocean floors often contain underwater volcanos that can provide heat to substitute sunlight for warmth.
In addition to deriving energy from chemical reactions, chemoautotrphos synthesize
all necessary organic compounds from carbon dioxide. Chemoautotrophs use inorganic
energy sources, such as hydrogen sulfide, elemental sulfur, ferrous iron, and also molecular hydrogen, and ammonia. Most are bacteria or archaea that live in hostile environments such as deep sea vents and are the primary producers in such ecosystems.
Chemoautotrophs generally fall into several groups: methanogens, halophiles, sulfur
oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. Chemolithotrophic growth could be dramatically fast, such as Thiomicrospira crunogena
with a doubling time around one hour.
https://en.wikipedia.org/wiki/Chemotroph
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Chemotrophs
Chemotrophs are organisms that obtain energy by the oxidation of electron donors in
their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs,
which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic.
Chemoautotrophs are commonly found in ocean floors where sunlight cannot reach
them because they are not dependent on solar energy. Ocean floors often contain underwater volcanos that can provide heat to substitute sunlight for warmth.
In addition to deriving energy from chemical reactions, chemoautotrphos synthesize
all necessary organic compounds from carbon dioxide. Chemoautotrophs use inorganic
energy sources, such as hydrogen sulfide, elemental sulfur, ferrous iron, and also molecular hydrogen, and ammonia. Most are bacteria or archaea that live in hostile environments such as deep sea vents and are the primary producers in such ecosystems.
Chemoautotrophs generally fall into several groups: methanogens, halophiles, sulfur
oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. Chemolithotrophic growth could be dramatically fast, such as Thiomicrospira crunogena
with a doubling time around one hour.
https://en.wikipedia.org/wiki/Chemotroph
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Chenodeoxycholic Acid
Chenodeoxycholic acid (also known as chenodesoxycholic acid, chenocholic acid and
3,7-dihydroxy-5-cholan-24-oic acid) is a bile acid. It occurs as a white crystalline
substance insoluble in water but soluble in alcohol and acetic acid, with melting point
at 165-167C. Salts of this carboxylic acid are called chenodeoxycholates. Chenodeoxycholic acid is one of the main bile acids produced by the liver.
Chenodeoxycholic acid and cholic acid are the two primary bile acids in humans. Some
other mammals have muricholic acid or deoxycholic acid rather than chenodeoxycholic acid.
Chenodeoxycholic acid is synthesized in the liver from cholesterol by a process which
involves several enzymatic steps. Like other bile acids, it can be conjugated in the liver
with taurine or glycine, forming taurochenodeoxycholate or glycochenodeoxycholate.
Conjugation results in a lower pKa. This means the conjugated bile acids are ionized at
the usual pH in the intestine and will stay in the gastrointestinal tract until reaching
the ileum where most will be reabsorbed. Bile acids form micelles which facilitate lipid
digestion. After absorption, they are taken up by the liver and resecreted, so undergoing an enterohepatic circulation. Unabsorbed chenodeoxycholic acid can be metabolized by bacteria in the colon to form the secondary bile acid known as lithocholic acid.
Choendeoxycholic acid is the most potent natural bile acid at stimulating the nuclear
bile acid receptor, farnesoid X receptor (FXR). The transcription of many genes is activated by FXR.
https://en.wikipedia.org/wiki/Chenodeoxycholic_acid
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Chirality
Chirality is a property of asymmetry important in several branches of science. The
word chirality is derived from the Greek, (kheir), "hand", a familiar chiral object.
An object or a system is chiral if it is distinguishable from its mirror image. That is, it
cannot be superposed onto it. Conversely, a mirror image of an achiral object, such as a
sphere, cannot be distinguished from the object. A chiral object and its mirror image
are called enantiomorphs (Greek opposite forms) or, when referring to molecules,
enantiomers. A non-chiral object is called achiral (sometimes also amphichiral) and
can be superposed on its mirror image. If the object is non-chiral and is imagined as being colored blue and its mirror image is imagined as colored yellow, then by a series of
rotations and translations the two can be superposed producing green with none of the
original colors remaining.
The term was first used by Lord Kelvin in 1893 in the second Robert Boyle Lecture at
the Oxford University Junior Scientific Club which was published in 1894:
I call any geometrical figure, or group of points, 'chiral', and say that it has chirality if
its image in a plane mirror, ideally realized, cannot be brought to coincide with itself.
Human hands are perhaps the most universally recognized example of chirality: The
left hand is a non-superimposable mirror image of the right hand. No matter how the
two hands are oriented, it is impossible for all the major features of both hands to coincide across all axes. This difference in symmetry becomes obvious if someone attempts
to shake the right hand of a person using their left hand, or if a left-handed glove is
placed on a right hand. In mathematics chirality is the property of a figure that is not
identical to its mirror image.
https://commons.wikimedia.org/wiki/File:Chirality_with_hands.svg
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Chitin
Chitin (C8H13O5N)n is a long-chain polymer of an N-acetylglucosamine, a derivative of
glucose, and is found in many places throughout the natural world. It is a characteristic component of the cell walls of fungi, the exoskeletons of arthropods such as crustaceans (e.g., crabs, lobsters and shrimps) and insects, the radulae of molluscs, and the
beaks and internal shells of cephalopods, including squid and octopuses and on the
scales and other soft tissues of fish and lissamphibians. The structure of chitin is comparable to the polysaccharide cellulose, forming crystalline nanofibrils or whiskers. In
terms of function, it may be compared to the protein keratin.
https://en.wikipedia.org/wiki/Chitin
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Chlorophyll
Chlorophyll (also chlorophyl) is a term used for several closely related green pigments
found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived
from the Greek words , chloros ("green") and , phyllon ("leaf"). Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows
plants to absorb energy from light. Chlorophyll absorbs light most strongly in the blue
portion of the electromagnetic spectrum, followed by the red portion. Conversely, it is
a poor absorber of green and near-green portions of the spectrum which it reflects,
hence the green color of chlorophyll-containing tissues.
Chlorophyll molecules are specifically arranged in and around photosystems that are
embedded in the thylakoid membranes of chloroplasts. In these complexes, chlorophyll serves two primary functions. The function of the vast majority of chlorophyll (up
to several hundred molecules per photosystem) is to absorb light and transfer that
light energy by resonance energy transfer to a specific chlorophyll pair in the reaction
center of the photosystems. The two currently accepted photosystem units are photosystem II and photosystem I, which have their own distinct reaction centers, named
P680 and P700, respectively. These centers are named after the wavelength (in nanometers) of their red-peak absorption maximum. The identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by
each other and the protein structure surrounding them. Once extracted from the protein into a solvent (such as acetone or methanol), these chlorophyll pigments can be
separated into chlorophyll a and chlorophyll b.
The function of the reaction center of chlorophyll is to absorb light energy and transfer
it to other parts of the photosystem. The absorbed energy of the photon is transferred
to an electron in a process called charge separation. The removal of the electron from
the chlorophyll is an oxidation reaction. The chlorophyll donates the high energy electron to a series of molecular intermediates called an electron transport chain. The
charged reaction center of chlorophyll (P680+) is then reduced back to its ground state
by accepting an electron stripped from water. The electron that reduces P680+ ultimately comes from the oxidation of water into O2 and H+ through several intermediates. This reaction is how photosynthetic organisms such as plants produce O2 gas, and
is the source for practically all the O2 in Earth's atmosphere. Photosystem I typically
works in series with Photosystem II. Thus the P700+ of Photosystem I is usually reduced as it accepts the electron, via many intermediates in the thylakoid membrane, by
electrons come, ultimately, from Photosystem II. Electron transfer reactions in the thylakoid membranes are complex, however, and the source of electrons used to reduce
P700+ can vary.
The electron flow produced by the reaction center chlorophyll pigments is used to
pump H+ ions across the thylakoid membrane, setting up a chemiosmotic potential
used mainly in the production of ATP (stored chemical energy) or to reduce NADP+ to
NADPH. NADPH is a universal agent used to reduce CO2 into sugars as well as other
biosynthetic reactions.
Reaction center chlorophyllprotein complexes are capable of directly absorbing light
and performing charge separation events without other the assistance of other chlorophyll pigments, but the probability of that happening under a given light intensity is
small. Thus, the other chlorophylls in the photosystem and antenna pigment proteins
all cooperatively absorb and funnel light energy to the reaction center. Besides chlorophyll a, there are other pigments, called accessory pigments, which occur in these pigmentprotein antenna complexes.
https://en.wikipedia.org/wiki/Chlorophyll
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Chloroplasts
Chloroplasts are organelles, specialized subunits, in plant and algal cells. Chloroplasts'
main role is to conduct photosynthesis, where the photosynthetic pigment chlorophyll
captures the energy from sunlight and converts it and stores it in the energy-storage
molecules ATP and NADPH while freeing oxygen from water. They then use the ATP
and NADPH to make organic molecules from carbon dioxide in a process known as the
Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid
synthesis, much amino acid synthesis, and the immune response in plants.
A chloroplast is one of three types of plastids, characterized by its high concentration
of chlorophyll, the other two types, the leucoplast and the chromoplast, contain little
chlorophyll and do not carry out photosynthesis.
Chloroplasts are highly dynamicthey circulate and are moved around within plant
cells, and occasionally pinch in two to reproduce. Their behavior is strongly influenced
by environmental factors like light color and intensity. Chloroplasts, like mitochondria,
contain their own DNA, which is thought to be inherited from their ancestora photosynthetic cyanobacterium that was engulfed by an early eukaryotic cell. Chloroplasts
cannot be made by the plant cell and must be inherited by each daughter cell during
cell division.
With one exception (the amoeboid Paulinella chromatophora), all chloroplasts can
probably be traced back to a single endosymbiotic event, when a cyanobacterium was
engulfed by the eukaryote. Despite this, chloroplasts can be found in an extremely wide
set of organisms, some not even directly related to each othera consequence of many
secondary and even tertiary endosymbiotic events.
https://en.wikipedia.org/wiki/Chloroplast
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Cholecalciferol
Cholecalciferol (vitamin D3) is one of the five forms of vitamin D. It is a secosteroid,
that is, a steroid molecule with one ring open. Cholecalciferol is inactive: it is converted
to its active form by two hydroxylations: the first in the liver, the second in the kidney,
to form calcitriol, whose action is mediated by the vitamin D receptor, a nuclear receptor which regulates the synthesis of hundreds of enzymes and is present in virtually
every cell in the body.
https://en.wikipedia.org/wiki/Cholecalciferol
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Cholesterol
Cholesterol, from the Ancient Greek chole- (bile) and stereos (solid) followed by the
chemical suffix -ol for an alcohol, is an organic molecule. It is a sterol (or modified steroid), a lipid molecule and is biosynthesized by all animal cells because it is an essential
structural component of all animal (not plant or bacterial) cell membranes that is required to maintain both membrane structural integrity and fluidity. Cholesterol enables animal cells to dispense with a cell wall to protect membrane integrity and cell viability, thus allowing them to change shape and move about (unlike bacteria and plant
cells which are restricted by their cell walls).
In addition to its importance for animal cell structure, cholesterol also serves as a precursor for the biosynthesis of steroid hormones and bile acids. Cholesterol is the principal sterol synthesized by all animals. In vertebrates the hepatic cells typically produce
greater amounts than other cells. It is absent among prokaryotes (bacteria and archaea), although there are some exceptions such as Mycoplasma, which require cholesterol for growth.
Cholesterol, given that it composes about 30% of all animal cell membranes, is required to build and maintain membranes; and modulates membrane fluidity over the
range of physiological temperatures. The hydroxy group on cholesterol interacts with
the polar head groups of the membrane phospholipids and sphingolipids, while the
bulky steroid and the hydrocarbon chain are embedded in the membrane, alongside
the nonpolar fatty-acid chain of the other lipids. Through the interaction with the phospholipid fatty-acid chains, cholesterol increases membrane packing, which both:
(a) alters membrane fluidity and
(b) maintains membrane integrity so that animal cells do not need to build cell walls
(like plants and most bacteria)
allowing animal cells to change shape and animals to move. The structure of the tetracyclic ring of cholesterol contributes to the fluidity of the cell membrane as the molecule is in a trans conformation making all but the side chain of cholesterol rigid and planar. In this structural role, cholesterol also reduces the permeability of the plasma
membrane to neutral solutes, hydrogen ions, and sodium ions.
Within the cell membrane, cholesterol also functions in intracellular transport, cell signaling and nerve conduction. Cholesterol is essential for the structure and function of
invaginated caveolae and clathrin-coated pits, including caveola-dependent and
clathrin-dependent endocytosis. The role of cholesterol in such endocytosis can be investigated by using methyl cyclodextrin (MCD) to remove cholesterol from the
plasma membrane. Recent studies show that cholesterol is also implicated in cell signaling processes, assisting in the formation of lipid rafts in the plasma membrane.
Lipid raft formation brings receptor proteins in close proximity with high concentrations of second messenger molecules. Cholesterol & phospholipids, both electrical insulators, in multiple layers, can facilitate speed of transmission of electrical impulses
along nerve tissue. For many neuron fibers, a myelin sheath, rich in cholesterol, since
it is derived from compacted layers of Schwann cell membrane, provides insulation for
more efficient conduction of impulses. Demyelination (loss of some of these schwann
cells) is believed to be part of the basis for multiple sclerosis.
Within cells, cholesterol is also a precursor molecule for several biochemical pathways.
For example, it is the precursor molecule for the synthesis of vitamin D and all steroid
hormones, including the adrenal gland hormones cortisol and aldosterone, as well as
the sex hormones progesterone, estrogens, and testosterone, and their derivatives.
The liver excretes cholesterol into biliary fluids, which is then stored in the gallbladder.
Bile contains bile salts, which solubilize fats in the digestive tract and aid in the intestinal absorption of fat molecules as well as the fat-soluble vitamins, A, D, E, and K.
https://en.wikipedia.org/wiki/Cholesterol
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Cholesteryl Esters
tween the carboxylate group of a fatty acid and the hydroxyl group of choles
lesteryl esters have a lower solubility in water due to their increased hydrop
Index
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Cholic Acid
Cholic acid, also known as 3,7,12-trihydroxy-5-cholan-24-oic acid is a primary
bile acid that is insoluble in water (soluble in alcohol and acetic acid), it is a white crystalline substance. Salts of cholic acid are called cholates. Cholic acid, along with chenodeoxycholic acid, is one of the two major bile acids produced by the liver, where it is
synthesized from cholesterol. These two major bile acids are roughly equal in concentration in humans. Derivatives are made from cholyl-CoA, which exchanges its CoA
with either glycine, or taurine, yielding glycocholic and taurocholic acid, respectively.
Cholic acid downregulates cholesterol-7--hydroxylase (rate-limiting step in bile acid
synthesis), and cholesterol does the opposite. This is why chenodeoxycholic acid, and
not cholic acid, can be used to treat gallstones (because decreasing bile acid synthesis
would supersaturate the stones even more).
https://en.wikipedia.org/wiki/Cholic_acid
Choline
Choline is a water-soluble nutrient. It is usually grouped within the B-complex vitamins. Choline generally refers to the various quaternary ammonium salts containing
the N,N,N-trimethylethanolammonium cation. (X on the right denotes an undefined
counteranion.) The cation appears in the head groups of phosphatidylcholine and
sphingomyelin, two classes of phospholipid that are abundant in cell membranes. Choline is the precursor molecule for the neurotransmitter acetylcholine, which is involved
in many functions including memory and muscle control.
Some animals must consume choline through their diet to remain healthy. To humans,
choline is an essential nutrient, as its role in reducing the risk of neural tube defects,
fatty liver disease, and other pathologies has been documented. Furthermore, while methionine and folate are known to interact with choline in the methylation of homocysteine to produce methionine, recent studies have shown that choline deficiency may
have adverse effects, even when sufficient amounts of methionine and folate are present. It is used in the synthesis of components in cell membranes. The 2005 National
Health and Nutrition Examination Survey stated that only 2% of postmenopausal
women consume the recommended intake for choline.
Choline and its metabolites are needed for three main physiological purposes: structural integrity and signaling roles for cell membranes, cholinergic neurotransmission
(acetylcholine synthesis), and a major source for methyl groups via its metabolite, trimethylglycine (betaine), which participates in the S-adenosylmethionine (SAMe) synthesis pathways.
https://en.wikipedia.org/wiki/Choline
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Chondroitin Sulfate
Chondroitin sulfate is a sulfated glycosaminoglycan (GAG) composed of a chain of alternating sugars (N-acetylgalactosamine and glucuronic acid). It is usually found attached to proteins as part of a proteoglycan. A chondroitin chain can have over 100 individual sugars, each of which can be sulfated in variable positions and quantities.
Chondroitin sulfate is an important structural component of cartilage and provides
much of its resistance to compression. Along with glucosamine, chondroitin sulfate has
become a widely used dietary supplement for treatment of osteoarthritis.
The effect of chondroitin sulfate in patients with osteoarthritis is likely the result of a
number of reactions including its anti-inflammatory activity, the stimulation of the synthesis of proteoglycans and hyaluronic acid, and the decrease in catabolic activity of
chondrocytes inhibiting the synthesis of proteolytic enzymes, nitric oxide, and other
substances that contribute to damage cartilage matrix and cause death of articular
chondrocytes. A recent review summarizes data from relevant reports describing the
biochemical basis of the effect of chondroitin sulfate on osteoarthritis articular tissues.
The rationale behind the use of chondroitin sulfate is based on the belief that osteoarthritis is associated with a local deficiency or degradation of natural substances, including internal chondroitin sulfate.
Recently, new mechanisms of action have been described for chondroitin sulfate. In an
in vitro study, chondroitin sulfate reduced the IL-1-induced nuclear factor-kB (NFB) translocation in chondrocytes. In addition, chondroitin sulfate has recently shown
a positive effect on osteoarthritic structural changes occurred in the subchondral bone.
https://en.wikipedia.org/wiki/Chondroitin_sulfate
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Chorismate Mutase
from tryptophan. Its role in maintaining the balance of these aromatic amin
the cell is vital. This is the single known example of a naturally occurring en
higher plants. This protein may use the morpheein model of allosteric regul
https://en.wikipedia.org/wiki/Chorismate_mutase
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Chorismic Acid
Chorismic acid, more commonly known as its anionic form chorismate, is an important biochemical intermediate in plants and microorganisms. The name chorismic acid
derives from a classical Greek word, meaning "to separate", because the compound plays a role as a branch-point in aromatic amino acid biosynthesis. It is a precursor for:
https://en.wikipedia.org/wiki/Chorismic_acid
Christian Bohr
Christian Harald Lauritz Peter Emil Bohr (18551911) was a Danish physici
of the physicist and Nobel laureate Niels Bohr, as well as the mathematician
ball player Harald Bohr and grandfather of another physicist and Nobel lau
Bohr. He married Ellen Adler in 1881.
In 1891, he was the first to characterize dead space. In 1903, Christian Boh
the phenomenon, now called the Bohr effect, whereby hydrogen ions and ca
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Chromatin
Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein,
and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin
is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region).
The structure of chromatin depends on several factors. The overall structure depends
on the stage of the cell cycle. During interphase, the chromatin is structurally loose to
allow access to RNA and DNA polymerases that transcribe and replicate the DNA. The
local structure of chromatin during interphase depends on the genes present on the
DNA: DNA coding genes that are actively transcribed ("turned on") are more loosely
packaged and are found associated with RNA polymerases (referred to as euchromatin) while DNA coding inactive genes ("turned off") are found associated with structural proteins and are more tightly packaged (heterochromatin). Epigenetic chemical
modification of the structural proteins in chromatin also alters the local chromatin
structure, in particular chemical modifications of histone proteins by methylation and
acetylation. As the cell prepares to divide, i.e. enters mitosis or meiosis, the chromatin
packages more tightly to facilitate segregation of the chromosomes during anaphase.
During this stage of the cell cycle this makes the individual chromosomes in many cells
visible by optical microscope.
In general terms, there are three levels of chromatin organization:
1 - DNA wraps around histone proteins forming nucleosomes - the "beads on a string"
structure (euchromatin).
2 - Multiple histones wrap into a 30 nm fiber consisting of nucleosome arrays in their
most compact form (heterochromatin). (Definitively established to exist in vitro, the
30-nanometer fiber was not seen in recent X-ray studies of human mitotic chromosomes.)
3 - Higher-level DNA packaging of the 30nm fiber into the metaphase chromosome
(during mitosis and meiosis).
https://en.wikipedia.org/wiki/Chromatin
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Chromatography
Chromatography (from Greek chroma which means "color" and graphein "to write") is the collective term for a set of laboratory techniques for the separation of mixtures. The mixture is dissolved in a fluid called the mobile phase, which carries it through a structure holding another material called the stationary phase. The
various constituents of the mixture travel at different speeds, causing them to separate.
The separation is based on differential partitioning between the mobile and stationary
phases. Subtle differences in a compound's partition coefficient result in differential retention on the stationary phase and thus changing the separation.
Chromatography was first employed in Russia by the Italian-born scientist Mikhail
Tsvet in 1900. He continued to work with chromatography in the first decade of the
20th century, primarily for the separation of plant pigments such as chlorophyll, carotenes, and xanthophylls. Since these components have different colors (green, orange,
and yellow, respectively) they gave the technique its name. New types of chromatography developed during the 1930s and 1940s made the technique useful for many separation processes.
Chromatography technique developed substantially as a result of the work of Archer
John Porter Martin and Richard Laurence Millington Synge during the 1940s and
1950s. They established the principles and basic techniques of partition chromatography, and their work encouraged the rapid development of several chromatographic
methods: paper chromatography, gas chromatography, and what would become
known as high performance liquid chromatography. Since then, the technology has advanced rapidly. Researchers found that the main principles of Tsvet's chromatography
could be applied in many different ways, resulting in the different varieties of chromatography described below. Advances are continually improving the technical performance of chromatography, allowing the separation of increasingly similar molecules.
Shown below - separation by thin layer chromatography.
https://en.wikipedia.org/wiki/Chromatography
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Chromosome
A chromosome (from Greek: color and body) is a packaged and organized
structure containing most of the DNA of a living organism. It is not usually found on
its own, but rather is structured by being wrapped around protein complexes called nucleosomes, which consist of proteins called histones. The DNA in chromosomes is also
associated with transcription (copying of genetic sequences) factors and several other
macromolecules. During most of the duration of the cell cycle, a chromosome consists
of one long double-stranded DNA molecule (with associated proteins).
Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the
rest of the genetic hereditary information. All act in the same way during cell division.
Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex
chromosomes), giving a total of 46 per cell. In addition to these, human cells have
many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes.
Shown below - human chromosomes in metaphase.
https://en.wikipedia.org/wiki/Chromosome
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Chromosomes
A chromosome (from Greek: color and body) is a packaged and organized
structure containing most of the DNA of a living organism. It is not usually found on
its own, but rather is structured by being wrapped around protein complexes called nucleosomes, which consist of proteins called histones. The DNA in chromosomes is also
associated with transcription (copying of genetic sequences) factors and several other
macromolecules. During most of the duration of the cell cycle, a chromosome consists
of one long double-stranded DNA molecule (with associated proteins).
Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the
rest of the genetic hereditary information. All act in the same way during cell division.
Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex
chromosomes), giving a total of 46 per cell. In addition to these, human cells have
many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes.
Shown below - human chromosomes in metaphase.
https://en.wikipedia.org/wiki/Chromosome
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Chylomicron Remnant
ity of the lipoprotein lipase, allowing the released free fatty acids to be abso
tissues. When a large portion of the triacylglycerol core has been hydrolyzed
cron remnants are formed and are taken up by the liver, hereby transferring
also to the liver.
https://en.wikipedia.org/wiki/Chylomicron
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Chylomicrons
Chylomicrons (from the Greek chylo, meaning juice or milky fluid, and micron, m
ing small particle) are lipoprotein particles that consist of triglycerides (8592%
pholipids (612%), cholesterol (13%), and proteins (12%). They transport die
ids from the intestines to other locations in the body. Chylomicrons are one of th
major groups of lipoproteins that enable fats and cholesterol to move within the
based solution of the bloodstream.
https://en.wikipedia.org/wiki/Chylomicron
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Chymotrypsin
Chymotrypsin is a digestive enzyme component of pancreatic juice acting in the duodenum where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the carboxyl side of the
amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan,
and phenylalanine).
In Vivo, chymotrypsin is a proteolytic enzyme (Serine protease) acting in the digestive
systems of many organisms. It facilitates the cleavage of peptide bonds by a hydrolysis
reaction, which despite being thermodynamically favorable occurs extremely slowly in
the absence of a catalyst. The main substrates of chymotrypsin include tryptophan, tyrosine, phenylalanine, and leucine residues in proteins. The enzyme cleaves at the carboxyl end of each of these in a substrate protein. Like many proteases, chymotrypsin
will also hydrolyze amide bonds in vitro, a virtue that enabled the use of substrate analogs such as N-acetyl-L-phenylalanine p-nitrophenyl amide for enzyme assays.
Chymotrypsin cleaves peptide bonds by attacking the unreactive carbonyl group with a
powerful nucleophile, the serine 195 residue located in the active site of the enzyme,
which briefly becomes covalently bonded to the substrate, forming an enzymesubstrate intermediate. Along with histidine 57 and aspartic acid 102, this serine residue constitutes the catalytic triad of the active site.
https://en.wikipedia.org/wiki/Chymotrypsin
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Chymotrypsinogen
Chymotrypsinogen is a proteolytic enzyme and a precursor (zymogen) of the digestive
enzyme chymotrypsin. It is a single polypetide chain consisting of 245 amino acid residues. It is synthesized in the acinar cells of the pancreas and stored inside membranebounded granules at the apex of the acinar cell. The cell is then stimulated by either a
hormonal signal or a nerve impulse and the contents of the granules spill into a duct
leading into the duodenum.
Chymotrypsinogen must be inactive until it gets to the digestive tract. This prevents
damage to the pancreas or any other organs. It is activated into its active form by another enzyme called trypsin. This active form is called -Chymotrypsin and is used to
create -Chymotrypsin. Trypsin cleaves the peptide bond in chymotrypsinogen between arginine-15 and isoleucine-16. This creates two peptides within -chymotrypsin
molecule held together by a disulfide bond. One of the -chymotrypsin acts on another
by breaking a leucine and serine peptide bond. The activated -chymotrypsin reacts
with other -chymotrypsin molecules to cleave out two dipeptides, which are, Serine14Arginine-15 and Threonine-147Asparagine-148. This reaction yields the chymotrypsin.
https://en.wikipedia.org/wiki/Chymotrypsinogen
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Cilia
A cilium (Latin for eyelash; the plural is cilia) is an organelle found in eukaryotic cells.
Cilia are thick protuberances that project from the much larger cell body. There are
two types of cilia: motile cilia and nonmotile, or primary cilia, which typically serve as
sensory organelles. In eukaryotes, motile cilia and flagella together make up a group of
organelles known as undulipodia. Eukaryotic cilia are structurally identical to eukaryotic flagella, although distinctions are sometimes made according to function and/or
length. Biologists have various ideas about how the various flagella may have evolved.
Inside cilia and flagella is a microtubule-based cytoskeleton called the axoneme. The
axoneme of primary cilia typically has a ring of nine outer microtubule doublets (called
a 9+0 axoneme), and the axoneme of a motile cilium has two central microtubule
singlets in addition to the nine outer doublets (called a 9+2 axoneme). The axonemal
cytoskeleton acts as a scaffolding for various protein complexes and provides binding
sites for molecular motor proteins such as kinesin II, that help carry proteins up and
down the microtubules.
The dynein in the axoneme forms bridges between neighboring microtubule doublets.
When ATP activates the motor domain of dynein, it attempts to walk along the adjoining microtubule doublet. This would force the adjacent doublets to slide over one another if not for the presence of Nexin between the microtubule doublets. And thus the
force generated by dyenin is instead converted into a bending motion.
Cilia are formed through the process of ciliogenesis. The building blocks of the cilia
such as tubulins and other partially assembled axonemal proteins are added to the ciliary tips which point away from the cell body. In most species bi-directional motility
called intraflagellar transport (IFT) plays an essential role to move these building materials from the cell body to the assembly site. IFT also carries the disassembled material
to be recycled from the ciliary tip back to the cell body. By regulating the equilibrium
between these two IFT processes, the length of cilia can be maintained dynamically.
Disassembly of cilia requires the action of the Aurora A kinase.
https://en.wikipedia.org/wiki/Cilium
Ciprofloxacin
Ciprofloxacin is an antibiotic used to treat a number of bacterial infections. This includes bone and joint infections, intra abdominal infections, certain type of infectious
diarrhea, respiratory tract infections, skin infections, typhoid fever, and urinary tract
infections, among others. For some infections it is used in addition to other antibiotics.
It can be taken by mouth or used intravenously.
Ciprofloxacin is used to treat a wide variety of infections, including infections of bones
and joints, endocarditis, gastroenteritis, malignant otitis externa, respiratory tract infections, cellulitis, urinary tract infections, prostatitis, anthrax, and chancroid.
Ciprofloxacin only treats bacterial infections. It does not treat viral infections such as
the common cold. For certain uses including acute sinusitis, lower respiratory tract infections and uncomplicated gonorrhea, ciprofloxacin is not considered a first-line
agent.
Ciprofloxacin occupies an important role in treatment guidelines issued by major medical societies for the treatment of serious infections, especially those likely to be caused
by Gram-negative bacteria, including Pseudomonas aeruginosa. For example, ciprofloxacin in combination with metronidazole is one of several first-line antibiotic regimens
recommended by the Infectious Diseases Society of America for the treatment of
community-acquired abdominal infections in adults. It also features prominently in
treatment guidelines for acute pyelonephritis, complicated or hospital-acquired urinary tract infection, acute or chronic prostatitis, certain types of endocarditis, certain
skin infections, and prosthetic joint infections.
https://en.wikipedia.org/wiki/Ciprofloxacin
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Circular Dichroism
Circular dichroism (CD) is dichroism involving circularly polarized light, i.e., the differential absorption of left- and right-handed light. Left-hand circular (LHC) and righthand circular (RHC) polarized light represent two possible spin angular momentum
states for a photon, and so circular dichroism is also referred to as dichroism for spin
angular momentum.
In general, this phenomenon will be exhibited in absorption bands of any optically active molecule. As a consequence, circular dichroism is exhibited by biological molecules, because of their dextrorotary and levorotary components. Even more important
is that a secondary structure will also impart a distinct CD to its respective molecules.
Therefore, the helix of proteins and the double helix of nucleic acids have CD spectral
signatures representative of their structures. The capacity of CD to give a representative structural signature makes it a powerful tool in modern biochemistry with applications that can be found in virtually every field of study.
CD is closely related to the optical rotatory dispersion (ORD) technique, and is generally considered to be more advanced. CD is measured in or near the absorption bands
of the molecule of interest, while ORD can be measured far from these bands. CD's advantage is apparent in the data analysis. Structural elements are more clearly distinguished since their recorded bands do not overlap extensively at particular wavelengths as they do in ORD. In principle these two spectral measurements can be interconverted through an integral transform (KramersKronig relation), if all the absorptions are included in the measurements.
https://en.wikipedia.org/wiki/Circular_dichroism
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Circular DNA
Circular DNA is DNA that forms a closed loop and therefore has no free end
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Citrate
Citric acid is a weak organic tribasic acid. It occurs naturally in citrus fruits. In biochemistry, it is an intermediate in the citric acid cycle, which occurs in the metabolism
of all aerobic organisms.
Citrate is an intermediate in the citric acid cycle, a central metabolic pathway for animals, plants and bacteria. Citrate synthase catalyzes the condensation of oxaloacetate
with acetyl CoA to form citrate. Citrate then acts as the substrate for aconitase and is
converted into aconitic acid. The cycle ends with regeneration of oxaloacetate. This series of chemical reactions is the source of two-thirds of the food-derived energy in
higher organisms. Hans Adolf Krebs received the 1953 Nobel Prize in Physiology or
Medicine for the discovery.
Some bacteria, notably E. coli, can produce and consume citrate internally as part of
their citric acid cycle, but are unable to use it as food because they lack the enzymes required to import it into the cell. The acquisition by these bacteria, after tens of thousands of generations, of the ability to use citrate as food was studied by Lenski et al, to
explore mechanisms of evolution under selective pressure (in this case, a citratecontaining culture medium with limited amounts of other foods). They found evidence
that in this case the innovation occurred via an accumulation of several somewhat rare
mutations, none of which by itself would confer the selective advantage, rather than by
a single extremely rare mutation.
Citrate can be transported out of the mitochondria and into the cytoplasm, then broken down into acetyl-CoA for fatty acid synthesis and into oxaloacetate. Citrate is a
positive modulator of this conversion, and allosterically regulates the enzyme acetylCoA carboxylase, which is the regulating enzyme in the conversion of acetyl-CoA into
malonyl-CoA (the commitment step in fatty acid synthesis). In short, citrate is transported to the cytoplasm, converted to acetyl CoA, which is converted into malonyl CoA
by the acetyl CoA carboxylase, which is allosterically modulated by citrate.
High concentrations of cytosolic citrate can inhibit phosphofructokinase, the catalyst
of one of the rate-limiting steps of glycolysis. This effect is advantageous: high concentrations of citrate indicate that there is a large supply of biosynthetic precursor molecules, so there is no need for phosphofructokinase to continue to send molecules of its
substrate, fructose 6-phosphate, into glycolysis. Citrate acts by augmenting the inhibitory effect of high concentrations of ATP, another sign that there is no need to carry
out glycolysis.
https://en.wikipedia.org/wiki/Citric_acid
Citrate Lyase
In the presence of ATP and Coenzyme A, citrate lyase (also called ATP citrate lyase)
catalyzes the cleavage of citrate to yield acetyl CoA, oxaloacetate, ADP, and orthophosphate:
Citrate + ATP + CoA + H2O <=> Oxaloacetate + Acetyl-CoA + ADP + Pi
ATP citrate lyase is the primary enzyme responsible for the synthesis of cytosolic
acetyl-CoA in many tissues. The enzyme is a tetramer of apparently identical subunits.
The product, acetyl-CoA, in animals serves several important biosynthetic pathways,
including lipogenesis and cholesterogenesis. It is activated by insulin signaling. In
plants, ATP citrate lyase generates the acetyl-CoA for cytosolically-synthesized metabolites. (Acetyl-CoA is not transported across subcellular membranes of plants.) These include: elongated fatty acids (used in seed oils, membrane phospholipids, the ceramide
moiety of sphingolipids, cuticle, cutin, and suberin); flavonoids; malonic acid; acetylated phenolics, alkaloids, isoprenoids, anthocyanins, and sugars; and, mevalonatederived isoprenoids (e.g., sesquiterpenes, sterols, brassinosteroids); malonyl and acylderivatives (d-amino acids, malonylated flavonoids, acylated, prenylated and malonated proteins). De novo fatty acid biosynthesis in plants is plastidic, thus ATP citrate
lyase is not important for this pathway.
https://en.wikipedia.org/wiki/ATP_citrate_lyase
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Citrate Synthase
Citrate synthase is localized within eukaryotic cells in the mitochondrial matrix, but is
encoded by nuclear DNA rather than mitochondrial. It is synthesized using cytoplasmic ribosomes, then transported into the mitochondrial matrix. Citrate synthase is
commonly used as a quantitative enzyme marker for the presence of intact mitochondria. Citrate synthase catalyzes the condensation reaction of the two-carbon acetate
residue from acetyl coenzyme A and a molecule of four-carbon oxaloacetate to form
the six-carbon citrate.
https://en.wikipedia.org/wiki/Citrate_synthase
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Citrulline
The organic compound citrulline is an -amino acid. It is a key intermediate in the
urea cycle, the pathway by which mammals excrete ammonia. In the body, citrulline is
produced as a byproduct of the enzymatic production of nitric oxide from the amino
acid arginine, catalyzed by nitric oxide synthase. This is an essential reaction in the
body because nitric oxide is an important vasodilator required for regulating blood
pressure.
Several proteins contain citrulline as a result of a posttranslational modification. These
citrulline residues are generated by a family of enzymes called peptidylarginine deiminases (PADs), which convert arginine into citrulline in a process called citrullination or
deimination. Proteins that normally contain citrulline residues include myelin basic
protein (MBP), filaggrin, and several histone proteins, whereas other proteins, such as
fibrin and vimentin are susceptible to citrullination during cell death and tissue inflammation.
Patients with rheumatoid arthritis often have detectable antibodies against proteins
containing citrulline. Although the origin of this immune response is not known, detection of antibodies reactive with citrulline (anti-citrullinated protein antibodies) containing proteins or peptides is now becoming an important help in the diagnosis of rheumatoid arthritis.
Circulating citrulline concentration is, in humans, a biomarker of intestinal functionality.
https://en.wikipedia.org/wiki/Citrulline
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Clamp Loader
Sliding clamps for DNA polymerases are loaded onto their associated DNA tem
ble the clamps after replication has completed. The binding sites for these init
teins overlap with the binding sites for the DNA polymerase, so the clamp can
taneously associate with a clamp loader and with a polymerase. Thus the clam
not be actively disassembled while the polymerase remains bound. DNA clam
associate with other factors involved in DNA and genome homeostasis, such a
some assembly factors, Okazaki fragment ligases, and DNA repair proteins. Al
proteins also share a binding site on the DNA clamp that overlaps with the cla
loader site, ensuring that the clamp will not be removed while any enzyme is s
ing on the DNA. The activity of the clamp loader requires ATP hydrolysis to "c
clamp around the DNA.
https://en.wikipedia.org/wiki/DNA_clamp#Assembly
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Clathrin
Clathrin is a protein that plays a major role in the formation of coated vesicles.
Clathrin was first isolated and named by Barbara Pearse in 1975. It forms a triskelion
shape composed of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds the vesicle. This is how
clathrin gets its name, from the Latin clatratus meaning like a lattice. Coat-proteins,
like clathrin, are used to build small vesicles in order to transport molecules within
cells. The endocytosis and exocytosis of vesicles allows cells to communicate, to transfer nutrients, to import signaling receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue inflammation. The endocytic pathway can be hijacked by viruses and other pathogens in order to
gain entry to the cell during infection.
https://en.wikipedia.org/wiki/Clathrin
Clot Formation
Coagulation (also known as blood clotting) is the process by which blood changes from
a liquid to a gel, forming a clot. It potentially results in hemostasis, the cessation of
blood loss from a damaged vessel, followed by repair. The mechanism of coagulation
involves activation, adhesion, and aggregation of platelets along with deposition and
maturation of fibrin. Disorders of coagulation are disease states which can result in
bleeding (hemorrhage or bruising) or obstructive clotting (thrombosis).
Coagulation is highly conserved throughout biology. In all mammals, coagulation involves both a cellular (platelet) and a protein (coagulation factor) component. The system in humans has been the most extensively researched and is the best understood.
Coagulation begins almost instantly after an injury to the blood vessel has damaged
the endothelium lining the vessel. Exposure of blood to the space under the endothelium initiates two processes: changes in platelets, and the exposure of subendothilial
tissue factor to plasma Factor VII, which ultimately leads to fibrin formation. Platelets
immediately form a plug at the site of injury. This is called primary hemostasis. Secondary hemostasis occurs simultaneously: Additional coagulation factors or clotting factors beyond Factor VII respond in a complex cascade to form fibrin strands, which
strengthen the platelet plug.
https://en.wikipedia.org/wiki/Coagulation
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Clotting of Blood
Coagulation (also known as blood clotting) is the process by which blood changes from
a liquid to a gel, forming a clot. It potentially results in hemostasis, the cessation of
blood loss from a damaged vessel, followed by repair. The mechanism of coagulation
involves activation, adhesion, and aggregation of platelets along with deposition and
maturation of fibrin. Disorders of coagulation are disease states which can result in
bleeding (hemorrhage or bruising) or obstructive clotting (thrombosis).
Coagulation is highly conserved throughout biology. In all mammals, coagulation involves both a cellular (platelet) and a protein (coagulation factor) component. The system in humans has been the most extensively researched and is the best understood.
Coagulation begins almost instantly after an injury to the blood vessel has damaged
the endothelium lining the vessel. Exposure of blood to the space under the endothelium initiates two processes: changes in platelets, and the exposure of subendothilial
tissue factor to plasma Factor VII, which ultimately leads to fibrin formation. Platelets
immediately form a plug at the site of injury. This is called primary hemostasis. Secondary hemostasis occurs simultaneously: Additional coagulation factors or clotting factors beyond Factor VII respond in a complex cascade to form fibrin strands, which
strengthen the platelet plug.
https://en.wikipedia.org/wiki/Coagulation
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CMP
Cytidine monophosphate, also known as 5'-cytidylic acid or simply cytidylate, and abbreviated CMP, is a nucleotide that is used as a monomer in RNA. It is an ester of phosphoric acid with the nucleoside cytidine. CMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase cytosine. Hence, a ribonucleoside monophosphate. As a substituent it takes the form of the prefix cytidylyl-.
CMP can be phosphorylated to cytidine diphosphate by the enzyme CMP kinase, with
adenosine triphosphate or guanosine triphosphate donating the phosphate group.
Since cytidine triphosphate is generated by amination of uridine triphosphate, the
main source of CMP is from RNA being decomposed by RNAse.
https://en.wikipedia.org/wiki/Cytidine_monophosphate
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CMP Kinase
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CO2
Carbon dioxide (chemical formula CO2) is a colorless and odorless gas vital to life on
Earth. This naturally occurring chemical compound is composed of a carbon atom covalently double-bonded to two oxygen atoms.
Carbon dioxide exists in Earth's atmosphere as a trace gas at a concentration of about
0.04 percent (400 ppm) by volume. Natural sources include volcanoes, hot springs
and geysers, and it is freed from carbonate rocks by dissolution in water and acids. Because carbon dioxide is soluble in water, it occurs naturally in groundwater, rivers and
lakes, in ice caps and glaciers and also in seawater. It is present in deposits of petroleum and natural gas.
Atmospheric carbon dioxide is the primary source of carbon in life on Earth and its concentration in Earth's pre-industrial atmosphere since late in the Precambrian was regulated by photosynthetic organisms and geological phenomena. As part of the carbon cycle, plants, algae, and cyanobacteria use light energy to photosynthesize carbohydrate
from carbon dioxide and water, with oxygen produced as a waste product.
Carbon dioxide (CO2) is produced by all aerobic organisms when they metabolize carbohydrate and lipids to produce energy by respiration. It is returned to water via the gills
of fish and to the air via the lungs of air-breathing land animals, including humans.
Carbon dioxide is produced during the processes of decay of organic materials and the
fermentation of sugars in bread, beer and winemaking. It is produced by combustion
of wood, carbohydrates and fossil fuels such as coal, peat, petroleum and natural gas.
https://en.wikipedia.org/wiki/Carbon_dioxide
Index
CoA-SH
Coenzyme A (CoA, CoASH, or HSCoA) is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All
genomes sequenced to date encode enzymes that use coenzyme A as a substrate, and
around 4% of cellular enzymes use it (or a thioester, such as acetyl-CoA) as a substrate.
In humans, CoA biosynthesis requires cysteine, pantothenate, and adenosine triphosphate (ATP).
Since coenzyme A is, in chemical terms, a thiol, it can react with carboxylic acids to
form thioesters, thus functioning as an acyl group carrier. It assists in transferring fatty
acids from the cytoplasm to mitochondria. A molecule of coenzyme A carrying an acetyl group is also referred to as acetyl-CoA. When it is not attached to an acyl group, it is
usually referred to as 'CoASH' or 'HSCoA'.
Coenzyme A is also the source of the phosphopantetheine group that is added as a prosthetic group to proteins such as acyl carrier protein and formyltetrahydrofolate dehydrogenase.
https://en.wikipedia.org/wiki/Coenzyme_A
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G-G
G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 5 - Energy: Basics
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Coated Pits
Caveolae (also called coated pits are a special type of lipid raft. They are small (50
100 nanometer) invaginations of the plasma membrane in many vertebrate cell types,
especially in endothelial cells and adipocytes.
These flask-shaped structures are rich in proteins as well as lipids such as cholesterol
and sphingolipids and have several functions in signal transduction. They are also believed to play a role in endocytosis, oncogenesis, and the uptake of pathogenic bacteria
and certain viruses.
Formation and maintenance of caveolae is primarily due to the protein caveolin, a 21
kD protein. There are three homologous genes of caveolin expressed in mammalian
cells: Cav1, Cav2 and Cav3. These proteins have a common topology: cytoplasmic Nterminus with scaffolding domain, long hairpin transmembrane domain and cytoplasmic C-terminus. Caveolins are synthesized as monomers and transported to the Golgi
apparatus. During their subsequent transport through the secretory pathway, caveolins
associate with lipid rafts and form oligomers (14-16 molecules). These oligomerized
caveolins form the caveolae. The presence of caveolin leads to a local change in morphology of the membrane.
Caveolae are one source of clathrin-independent raft-dependent endocytosis. The ability of caveolins to oligomerize due to their oligomerization domains is necessary for formation of caveolar endocytic vesicles. The oligomerization leads to formation of
caveolin-rich microdomains in the plasma membrane. Increased levels of cholesterol
and insertion of scaffolding domain of caveolins to the plasma membrane then lead to
expansion of the caveolar invagination and to formation of endocytic vesicle. Fission of
the vesicle from the plasma membrane is then mediated by GTPase dynamin II which
is localized at the neck of the budding vesicle. The released caveolar vesicle can fuse
with early endosome or caveosome. The caveosome is an endosomal compartment
with neutral pH which does not have early endosomal markers, however, contains
molecules internalized by the caveolar endocytosis.
https://en.wikipedia.org/wiki/Caveolae
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Coated Vesicles
coated vesicles (CCV) selectively sort cargo at the cell membrane, trans-Gol
buds into the cytoplasm, the coat rapidly disassembles, allowing the clathri
while the vesicle gets transported to a variety of locations.
https://en.wikipedia.org/wiki/Clathrin
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Coding Regions
The coding region of a gene, also known as the coding sequence or CDS (fro
for protein. The region is bounded nearer the 5' end by a start codon and ne
end with a stop codon. The coding region in mRNA is bounded by the five p
translated region (5'-UTR) and the three prime untranslated region (3'-UTR
are also parts of the exons. The CDS is that portion of an mRNA transcript t
Codon
The genome of an organism is inscribed in DNA, or, in the case of some viruses, RNA.
The portion of the genome that codes for a protein or an RNA is called a gene. Those
genes that code for proteins are composed of tri-nucleotide units called codons, each
coding for a single amino acid.
A codon is defined by the initial nucleotide from which translation starts. For example,
the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA,
and CCC. If read from the second position, it contains the codons GGA and AAC. If
read starting from the third position, GAA and ACC. Every sequence can, thus, be read
in its 5' 3' direction in three reading frames, each of which will produce a different
amino acid sequence (in the given example, Gly-Lys-Pro, Gly-Asn, or Glu-Thr, respectively). With double-stranded DNA, there are six possible reading frames, three in the
forward orientation on one strand and three reverse on the opposite strand. The actual
frame from which a protein sequence is translated is defined by a start codon, usually
the first AUG codon in the mRNA sequence.
Translation starts with a chain initiation codon or start codon. Unlike stop codons, the
codon alone is not sufficient to begin the process. Nearby sequences such as the ShineDalgarno sequence in E. coli and initiation factors are also required to start translation. The most common start codon is AUG, which is read as methionine or, in bacteria, as formylmethionine. Alternative start codons depending on the organism include
"GUG" or "UUG". These codons normally represent valine and leucine, respectively,
but as start codons they are translated as methionine or formylmethionine.
The three stop codons have been given names: UAG is amber, UGA is opal (sometimes
also called umber), and UAA is ochre. "Amber" was named by discoverers Richard Epstein and Charles Steinberg after their friend Harris Bernstein, whose last name means
"amber" in German. The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme. Stop codons are also called "termination" or "nonsense" codons. They signal release of the nascent polypeptide from the ribosome because there is no cognate tRNA that has anticodons complementary to these stop signals, and so a release factor binds to the ribosome instead.
https://en.wikipedia.org/wiki/Genetic_code#Transfer_of_information_via_the_gene
tic_code
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Codons
The genome of an organism is inscribed in DNA, or, in the case of some viruses, RNA.
The portion of the genome that codes for a protein or an RNA is called a gene. Those
genes that code for proteins are composed of tri-nucleotide units called codons, each
coding for a single amino acid.
A codon is defined by the initial nucleotide from which translation starts. For example,
the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA,
and CCC; and, if read from the second position, it contains the codons GGA and AAC.
If read starting from the third position, GAA and ACC. Every sequence can, thus, be
read in its 5' 3' direction in three reading frames, each of which will produce a different amino acid sequence (in the given example, Gly-Lys-Pro, Gly-Asn, or Glu-Thr, respectively). With double-stranded DNA, there are six possible reading frames, three in
the forward orientation on one strand and three reverse on the opposite strand. The actual frame from which a protein sequence is translated is defined by a start codon, usually the first AUG codon in the mRNA sequence.
Translation starts with a chain initiation codon or start codon. Unlike stop codons, the
codon alone is not sufficient to begin the process. Nearby sequences such as the ShineDalgarno sequence in E. coli and initiation factors are also required to start translation. The most common start codon is AUG, which is read as methionine or, in bacteria, as formylmethionine. Alternative start codons depending on the organism include
"GUG" or "UUG"; these codons normally represent valine and leucine, respectively,
but as start codons they are translated as methionine or formylmethionine.
The three stop codons have been given names: UAG is amber, UGA is opal (sometimes
also called umber), and UAA is ochre. "Amber" was named by discoverers Richard Epstein and Charles Steinberg after their friend Harris Bernstein, whose last name means
"amber" in German. The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme. Stop codons are also called "termination" or "nonsense" codons. They signal release of the nascent polypeptide from the ribosome because there is no cognate tRNA that has anticodons complementary to these stop signals, and so a release factor binds to the ribosome instead.
https://en.wikipedia.org/wiki/Genetic_code#Transfer_of_information_via_the_gene
tic_code
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Coenzyme Q
Coenzyme Q10, also known as ubiquinone, ubidecarenone, coenzyme Q, and abbreviated at times to CoQ10, CoQ, or Q10 is a coenzyme that is ubiquitous in the bodies of
most animals. It is a 1,4-benzoquinone, where Q refers to the quinone chemical group
and 10 refers to the number of isoprenyl chemical subunits in its tail. This fat-soluble
substance, which resembles a vitamin, is present in most eukaryotic cells, primarily in
the mitochondria. It is a component of the electron transport chain and participates in
aerobic cellular respiration, which generates energy in the form of ATP.
There are three redox states of CoQ10: fully oxidized (ubiquinone), semiquinone (ubisemiquinone), and fully reduced (ubiquinol). The capacity of this molecule to act as a
2 electron carrier (moving between the quinone and quinol form) and 1 electron carrier
(moving between the semiquinone and one of these other forms) is central to its role in
the electron transport chain, and as radical-scavenging antioxidant.
https://en.wikipedia.org/wiki/Coenzyme_Q10
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Coenzymes
A cofactor is a non-protein chemical compound that is required for the protein's biological activity to happen. These proteins are commonly enzymes, and cofactors can be
considered "helper molecules" that assist in biochemical transformations. Cofactors
can be subdivided into either one or more inorganic ions, or a complex organic or metalloorganic molecule called a coenzyme, most of which are derived from vitamins and
from required organic nutrients in small amounts.
Organic cofactors are often vitamins or are made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the
AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.
https://en.wikipedia.org/wiki/Cofactor_(biochemistry)
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Coiled Coil
A coiled coil is a structural motif in proteins in which 2-7 -helices are coiled together
like the strands of a rope (dimers and trimers are the most common types). Many
coiled coil-type proteins are involved in important biological functions such as the regulation of gene expression, e.g. transcription factors. Notable examples are the oncoproteins c-Fos and c-jun, as well as the muscle protein tropomyosin.
https://en.wikipedia.org/wiki/Coiled_coil
Collagen
Collagen is the main structural protein in the extracellular space in the various connective tissues in animal bodies. As the main component of connective tissue, it is the
most abundant protein in mammals, making up from 25% to 35% of the whole-body
protein content. Depending upon the degree of mineralization, collagen tissues may be
rigid (bone), compliant (tendon), or have a gradient from rigid to compliant (cartilage). Collagen, in the form of elongated fibrils, is mostly found in fibrous tissues such
as tendons, ligaments and skin. It is also abundant in corneas, cartilage, bones, blood
vessels, the gut, intervertebral discs and the dentin in teeth. In muscle tissue, it serves
as a major component of the endomysium. Collagen constitutes one to two percent of
muscle tissue, and accounts for 6% of the weight of strong, tendinous muscles. The fibroblast is the most common cell that creates collagen.
A single collagen molecule, tropocollagen, is used to make up larger collagen aggregates, such as fibrils. It is approximately 300nm long and 1.5nm in diameter, and it is
made up of three polypeptide strands (called peptides, see step 2), each of which has
the conformation of a left-handed helix this should not be confused with the righthanded helix. These three left-handed helices are twisted together into a righthanded triple helix or "super helix", a cooperative quaternary structure stabilized by
many hydrogen bonds. With type I collagen and possibly all fibrillar collagens, if not all
collagens, each triple-helix associates into a right-handed super-super-coil referred to
as the collagen microfibril. Each microfibril is interdigitated with its neighboring microfibrils to a degree that might suggest they are individually unstable, although within
collagen fibrils, they are so well ordered as to be crystalline.
Three polypeptides coil to form tropocollagen. Many tropocollagens then bind together
to form a fibril, and many of these then form a fiber. A distinctive feature of collagen is
the regular arrangement of amino acids in each of the three chains of these collagen
subunits. The sequence often follows the pattern Gly-Pro-X or Gly-X-Hyp, where X
may be any of various other amino acid residues. Proline or hydroxyproline constitute
about 1/6 of the total sequence. With glycine accounting for the 1/3 of the sequence,
this means approximately half of the collagen sequence is not glycine, proline or hydroxyproline, a fact often missed due to the distraction of the unusual GX1X2 character of collagen -peptides. The high glycine content of collagen is important with respect to stabilization of the collagen helix as this allows the very close association of the
collagen fibers within the molecule, facilitating hydrogen bonding and the formation of
intermolecular cross-links. This kind of regular repetition and high glycine content is
found in only a few other fibrous proteins, such as silk fibroin.
https://en.wikipedia.org/wiki/Collagen
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Collagenases
Collagenases are enzymes that break the peptide bonds in collagen. They ass
They are considered a virulence factor, facilitating the spread of gas gangrene
normally target the connective tissue in muscle cells and other body organs.
age of pro-collagen by collagenase once it has been secreted from the cell. Th
large structures from forming inside the cell itself.
In addition to being produced by some bacteria, collagenase can be made by
stimulate cells such as fibroblasts and osteoblasts, and can cause indirect tiss
age.
https://en.wikipedia.org/wiki/Collagenase
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Competitive Inhibition
Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor to
the active site on the enzyme prevents binding of the substrate and vice versa. Most
competitive inhibitors function by binding reversibly to the active site of the enzyme.
As a result, many sources state that this is the defining feature of competitive inhibitors. This, however, is a misleading oversimplification, as there are many possible
mechanisms by which an enzyme may bind either the inhibitor or the substrate but
never both at the same time. For example, allosteric inhibitors may display competitive, non-competitive, or uncompetitive inhibition.
In competitive inhibition, at any given moment, the enzyme may be bound to the inhibitor, the substrate, or neither, but it cannot bind both at the same time.
In virtually every case, competitive inhibitors bind in the same binding site as the substrate, but same-site binding is not a requirement. A competitive inhibitor could bind
to an allosteric site of the free enzyme and prevent substrate binding, as long as it does
not bind to the allosteric site when the substrate is bound. For example, strychnine
acts as an allosteric inhibitor of the glycine receptor in the mammalian spinal cord and
brain stem. Glycine is a major post-synaptic inhibitory neurotransmitter with a specific
receptor site. Strychnine binds to an alternate site that reduces the affinity of the
glycine receptor for glycine, resulting in convulsions due to lessened inhibition by the
glycine.
In competitive inhibition, the maximum velocity (Vmax) of the reaction is unchanged,
while the apparent affinity of the substrate to the binding site is decreased (Km increases). Any given competitive inhibitor concentration can be overcome by increasing
the substrate concentration sufficiently.
https://en.wikipedia.org/wiki/Competitive_inhibition
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Competitive Inhibitor
Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor to
the active site on the enzyme prevents binding of the substrate and vice versa. Most
competitive inhibitors function by binding reversibly to the active site of the enzyme.
As a result, many sources state that this is the defining feature of competitive inhibitors. This, however, is a misleading oversimplification, as there are many possible
mechanisms by which an enzyme may bind either the inhibitor or the substrate but
never both at the same time. For example, allosteric inhibitors may display competitive, non-competitive, or uncompetitive inhibition.
In competitive inhibition, at any given moment, the enzyme may be bound to the inhibitor, the substrate, or neither, but it cannot bind both at the same time.
In virtually every case, competitive inhibitors bind in the same binding site as the substrate, but same-site binding is not a requirement. A competitive inhibitor could bind
to an allosteric site of the free enzyme and prevent substrate binding, as long as it does
not bind to the allosteric site when the substrate is bound. For example, strychnine
acts as an allosteric inhibitor of the glycine receptor in the mammalian spinal cord and
brain stem. Glycine is a major post-synaptic inhibitory neurotransmitter with a specific
receptor site. Strychnine binds to an alternate site that reduces the affinity of the
glycine receptor for glycine, resulting in convulsions due to lessened inhibition by the
glycine.
In competitive inhibition, the maximum velocity (Vmax) of the reaction is unchanged,
while the apparent affinity of the substrate to the binding site is decreased (Km increases). Any given competitive inhibitor concentration can be overcome by increasing
the substrate concentration sufficiently.
https://en.wikipedia.org/wiki/Competitive_inhibition
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Complex I
Complex I (EC 1.6.5.3) (also referred to as NADH:ubiquinone oxidoreductase or, especially in the context of the human protein, NADH dehydrogenase (ubiquinone)) is an
enzyme of the respiratory chains of myriad organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and, in eukaryotes,
it is located in the inner mitochondrial membrane. It is one of the "entry enzymes" of
cellular respiration or oxidative phosphorylation in the mitochondria.
Complex I is the first enzyme of the mitochondrial electron transport chain. There are
three energy-transducing enzymes in the electron transport chain - NADH:ubiquinone
oxidoreductase (complex I), Coenzyme Q cytochrome c reductase (complex III), and
cytochrome c oxidase (complex IV). Complex I is the largest and most complicated enzyme of the electron transport chain.
The reaction catalyzed by complex I is:
NADH + H+ + CoQ + 4 H+in NAD+ + CoQH2 + 4 H+out
In this process, the complex translocates four protons across the inner membrane per
molecule of oxidized NADH, helping to build the electrochemical potential difference
used to produce ATP.
The reaction can be reversed - referred to as aerobic succinate-supported NAD+ reduction - in the presence of a high membrane potential, but the exact catalytic mechanism
remains unknown.
Complex I may have a role in triggering apoptosis. In fact, there has been shown to be
a correlation between mitochondrial activities and programmed cell death (PCD) during somatic embryo development.
The best-known inhibitor of complex I is rotenone (commonly used as an organic pesticide). Rotenone and rotenoids are isoflavonoids occurring in several genera of tropical
plants such as Antonia (Loganiaceae), Derris and Lonchocarpus (Faboideae, Fabaceae). There have been reports of the indigenous people of French Guiana using
rotenone-containing plants to fish - due to its ichthyotoxic effect - as early as the 17th
century. Rotenone binds to the ubiquinone binding site of complex I as well as piericidin A, another potent inhibitor with a close structural homologue to ubiquinone.
https://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H%2B-translocating)
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Complex II
Succinate dehydrogenase or succinate-coenzyme Q reductase (SQR) or respiratory
Complex II is an enzyme complex, bound to the inner mitochondrial membrane of
mammalian mitochondria and many bacterial cells. It is the only enzyme that participates in both the citric acid cycle and the electron transport chain. In step 6 of the citric acid cycle, SQR catalyzes the oxidation of succinate to fumarate with the reduction
of ubiquinone to ubiquinol. This occurs in the inner mitochondrial membrane by coupling the two reactions together.
The fundamental role of succinate-coenzyme Q reductase in the electron transfer chain
of mitochondria makes it vital in most multicellular organisms, removal of this enzyme
from the genome has also been shown to be lethal at the embryonic stage in mice.
SdhA mutations can lead to Leigh syndrome, mitochondrial encephalopathy, and optic atrophy.
SdhB mutations can lead to tumorogenesis in chromaffin cells, causing hereditary
paraganglioma and hereditary pheochromocytoma. Tumors tend to be malignant. It
can also lead to decreased life-span and increased production of superoxide ions.
SdhC mutations can lead to decreased life-span, increased production of superoxide
ions, hereditary paraganglioma and hereditary pheochromocytoma. Tumors tend to be
benign. These mutations are uncommon.
SdhD mutations can lead to hereditary paraganglioma and hereditary pheochromocytoma. Tumors tend to be benign, and occur often in the head and neck regions. These
mutations can also decrease life-span and increase production of superoxide ions.
Mammalian succinate dehydrogenase functions not only in mitochondrial energy generation, but also has a role in oxygen sensing and tumor suppression and, therefore, is
the object of ongoing research.
https://en.wikipedia.org/wiki/Succinate_dehydrogenase
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Complex III
The coenzyme Q: cytochrome c oxidoreductase, sometimes called the cytochrome
bc1 complex, and at other times complex III, is the third complex in the electron transport chain (EC 1.10.2.2), playing a critical role in biochemical generation of ATP (oxidative phosphorylation). Complex III is a multisubunit transmembrane protein encoded
by both the mitochondrial (cytochrome b) and the nuclear genomes (all other
subunits). Complex III is present in the mitochondria of all animals and all aerobic
eukaryotes and the inner membranes of most eubacteria. Mutations in Complex III
cause exercise intolerance as well as multisystem disorders.
The reaction proceeds according to the following steps:
Round 1:
1 - Cytochrome b binds a ubiquinol and a ubiquinone.
2 - The 2Fe/2S center and BL heme each pull an electron off the bound ubiquinol, releasing two hydrogens into the intermembrane space.
3 - One electron is transferred to cytochrome c1 from the 2Fe/2S centre, whilst another
is transferred from the BL heme to the BH Heme.
4 - Cytochrome c1 transfers its electron to cytochrome c (not to be confused with cytochrome c1), and the BH Heme transfers its electron to a nearby ubiquinone, resulting
in the formation of a ubisemiquinone.
5 - Cytochrome c diffuses. The first ubiquinol (now oxidized to ubiquinone) is released,
whilst the semiquinone remains bound.
Round 2:
1 - A second ubiquinol is bound by cytochrome b.
2 - The 2Fe/2S center and BL heme each pull an electron off the bound ubiquinol, releasing two hydrogens into the intermembrane space.
3 - One electron is transferred to cytochrome c1 from the 2Fe/2S centre, whilst another
is transferred from the BL heme to the BH Heme.
4 - Cytocrome c1 then transfers its electron to cytochrome c, whilst the nearby semiquinone picks up a second electron from the BH heme, along with two protons from the
matrix.
5 - The second ubiquinol (now oxidized to ubiquinone), along with the newly formed
ubiquinol are released.
Complex III inhibitors include
Antimycin A binds to the Qi site and inhibits the transfer of electrons in Complex III
from heme bH to oxidized Q (Qi site inhibitor).
Myxothiazol and stigmatellin binds to the Qo site and inhibits the transfer of electrons from reduced QH2 to the Rieske Iron sulfur protein. Myxothiazol and stigmatellin bind to distinct but overlapping pockets within the Qo site.
Myxothiazol binds nearer to cytochrome bL (hence termed a "proximal" inhibitor).
Stigmatellin binds farther from heme bL and nearer the Rieske Iron sulfur protein,
with which it strongly interacts.
https://en.wikipedia.org/wiki/Coenzyme_Q_%E2%80%93_cytochrome_c_reductase
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Complex IV
The enzyme cytochrome c oxidase or Complex IV, EC 1.9.3.1 is a large transmembrane
protein complex found in bacteria and the mitochondrion of eukaryotes. It is the last
enzyme in the respiratory electron transport chain of mitochondria (or bacteria) located in the mitochondrial (or bacterial) membrane. Complex IV receives an electron
from each of four cytochrome c molecules, and transfers them to one oxygen molecule,
converting molecular oxygen to two molecules of water. In the process, it binds four
protons from the inner aqueous phase to make water, and in addition translocates four
protons across the membrane, helping to establish a transmembrane difference of proton electrochemical potential that the ATP synthase then uses to synthesize ATP.
Summary reaction:
4 Fe++-cytochrome c + 8 H+in + O2 4 Fe+++-cytochrome c + 2 H2O + 4 H+out
Two electrons are passed from two cytochrome c's, through the CuA and cytochrome a
sites to the cytochrome a3- CuB binuclear center, reducing the metals to the Fe++ form
and Cu+. The hydroxide ligand is protonated and lost as water, creating a void between
the metals that is filled by O2. The oxygen is rapidly reduced, with two electrons coming from the Fe++cytochrome a3, which is converted to the ferryl oxo form (Fe++++=O).
The oxygen atom close to CuB picks up one electron from Cu+, and a second electron
and a proton from the hydroxyl of Tyr(244), which becomes a tyrosyl radical: The second oxygen is converted to a hydroxide ion by picking up two electrons and a proton. A
third electron arising from another cytochrome c is passed through the first two electron carriers to the cytochrome a3- CuB binuclear center, and this electron and two protons convert the tyrosyl radical back to Tyr, and the hydroxide bound to CuB++ to a water molecule. The fourth electron from another cytochrome c flows through CuA and
cytochrome a to the cytochrome a3- CuB binuclear center, reducing the Fe++++=O to
Fe+++, with the oxygen atom picking up a proton simultaneously, regenerating this oxygen as a hydroxide ion coordinated in the middle of the cytochrome a3- CuB center as it
was at the start of this cycle. The net process is that four reduced cytochrome c molecules are used, along with 4 protons, to reduce O2 to two water molecules.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase
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Complex V
ATP synthase (EC 3.6.3.14) is an important enzyme that creates the energy currency
molecule adenosine triphosphate (ATP). ATP is the most commonly used "energy currency" of cells from most organisms. It is formed from adenosine diphosphate (ADP)
and inorganic phosphate (Pi), and needs energy for its formation.
The overall reaction sequence is:
ADP + Pi + Energy ATP
where ADP and Pi are joined together by ATP synthase.
Energy used is available in the form of hydrogen ions (H+), moving down an electrochemical gradient, such as from the thylakoid lumen through the thylakoid membrane
and into the chloroplast stroma (of plants) or from the inter-membrane space and into
the matrix in mitochondria.
ATP synthase consists of two regions
the F0 portion embedded within the membrane.
the F1 portion of the ATP synthase is outside the membrane, but inside the matrix of
the mitochondria.
In plants, ATP synthase is also present in chloroplasts (CF1FO-ATP synthase). The enzyme is integrated into thylakoid membrane. The CF1-part sticks into stroma, where
dark reactions of photosynthesis (also called the light-independent reactions or the Calvin cycle) and ATP synthesis take place. The overall structure and the catalytic mechanism of the chloroplast ATP synthase are almost the same as those of the mitochondrial enzyme. However, in chloroplasts, the proton motive force is generated not by respiratory electron transport chain but by primary photosynthetic proteins.
https://commons.wikimedia.org/wiki/File:Atp_synthase.PNG
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Concentration Gradient
Index
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Concerted Model
In biochemistry, the Monod-Wyman-Changeux model (MWC model, also known as
the concerted model or symmetry model) describes allosteric transitions of proteins
made up of identical subunits. It was proposed by Jean-Pierre Changeux based on his
PhD experiments, and described by Jacques Monod, Jeffries Wyman, and Jean-Pierre
Changeux. It stands in opposition to the sequential model.
The concept of two distinct symmetric states is the central postulate of the MWC
model.The main idea of the model is that regulated proteins, such as many enzymes
and receptors, exist in different interconvertible states in the absence of any regulator.
The ratio of the different conformational states is determined by thermal equilibrium.
The ratio of the different conformational states is determined by thermal equilibrium.
This model, alternatively termed the MWC model, is defined by the following rules:
1 - An allosteric protein is an oligomer of protomers that are symmetrically related (for
hemoglobin, we shall assume, for the sake of algebraic simplicity, that all four subunits
are functionally identical).
2 - Each protomer can exist in (at least) two conformational states, designated T and R.
These states are in equilibrium whether or not ligand is bound to the oligomer.
3 - The ligand can bind to a protomer in either conformation. Only the conformational
change alters the affinity of a protomer for the ligand. The regulators merely shift the
equilibrium toward one state or another. For instance, an agonist will stabilize the active form of a pharmacological receptor. Phenomenologically, it looks as if the agonist
provokes the conformational transition.
One crucial feature of the model is the dissociation between the binding function (the
fraction of protein bound to the regulator), and the state function (the fraction of protein under the activated state). In the models said of "induced-fit", those functions are
identical.
https://en.wikipedia.org/wiki/Monod-Wyman-Changeux_model
Connective Tissue
Connective tissue (CT) is one of the four types of biological tissue that support, connect, or separate different types of tissues and organs in the body. It develops from the
mesoderm. The other three types are epithelial, muscle, and nervous tissue. Connective tissue is found in between other tissues everywhere in the body, including the nervous system. In the central nervous system, the three outer membranes (the meninges)
that envelop the brain and spinal cord are composed of connective tissue. All connective tissue apart from blood and lymph consists of three main components: fibers (elastic and collagenous fibers), ground substance and cells. (Not all authorities include
blood or lymph as connective tissue.) Blood and lymph lack the fiber component. All
are immersed in the body water. The cells of connective tissue include fibroblasts, adipocytes, macrophages, mast cells and leucocytes.
Connective tissue has a wide variety of functions that depend on the types of cells and
the different classes of fibers involved. Loose and dense irregular connective tissue,
formed mainly by fibroblasts and collagen fibers, have an important role in providing a
medium for oxygen and nutrients to diffuse from capillaries to cells, and carbon dioxide and waste substances to diffuse from cells back into circulation. They also allow organs to resist stretching and tearing forces. Dense regular connective tissue, which
forms organized structures, is a major functional component of tendons, ligaments and
aponeuroses, and is also found in highly specialized organs such as the cornea. Elastic
fibers, made from elastin and fibrillin, also provide resistance to stretch forces. They
are found in the walls of large blood vessels and in certain ligaments, particularly in
the ligamenta flava.
https://en.wikipedia.org/wiki/Connective_tissue
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Connexons
In biology, a connexon, also known as a connexin hemichannel or a pannexin channel,
is an assembly of six proteins called connexins that form the pore for a gap junction between the cytoplasm of two adjacent cells. This channel allows for bidirectional flow of
ions and signaling molecules. The connexon is the hemichannel supplied by a cell on
one side of the junction. Two connexons from opposing cells normally come together
to form the complete intercellular gap junction channel. However, in some cells, the
hemichannel itself is active as a conduit between the cytoplasm and the extracellular
space, allowing the transference of ions and small molecules lower than 1-2 KDa. Little
is known about this function of connexons besides the new evidence suggesting their
key role in intracellular signaling. Connexons made of the same type of connexins are
considered homomeric, while connexons made of differing types of connexins are heteromeric.
https://en.wikipedia.org/wiki/Connexon
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Conserved
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein
structures or polymeric carbohydrates across species (orthologous sequences) or
within different molecules produced by the same organism (paralogous sequences). In
the case of cross species conservation, this indicates that a particular sequence may
have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is
said to be. Since sequence information is normally transmitted from parents to progeny by genes, a conserved sequence implies that there is a conserved gene. It is widely
believed that mutation in a "highly conserved" region leads to a non-viable life form, or
a form that is eliminated through natural selection. What determines conserved and
non-conserved is the environment. If for example, a microorganism with antibiotic resistance genes is in the presence of antibiotic, the antibiotic resistance genes will be
highly conserved. If not in the presence of antibiotics, the genes will become nonconserved.
https://en.wikipedia.org/wiki/Conserved_sequence
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Constitutive
Index
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Convergent Evolution
Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar
form or function but were not present in the last common ancestor of those groups.
The cladistic term for the same phenomenon is homoplasy, from Greek for same form.
The recurrent evolution of flight is a classic example of convergent evolution. Flying insects, birds, and bats have all evolved the capacity of flight independently. They have
"converged" on this useful trait.
Functionally similar features arising through convergent evolution are termed analogous, in contrast to homologous structures or traits, which have a common origin but
not necessarily a similar function. The British anatomist Richard Owen was the first scientist to recognize the fundamental difference between analogies and homologies. Bat
and pterosaur wings constitute an example of analogous structures, while the bat wing
is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions. The opposite of convergent evolution is divergent evolution in which related species evolve different traits. On a molecular level, that can
happen from random mutation unrelated to adaptive changes.
Convergent evolution is similar to but different from parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and
thus independently acquire similar characteristic. For instance, gliding frogs have
evolved in parallel from multiple types of tree frog.
https://en.wikipedia.org/wiki/Convergent_evolution
Cooperative Binding
Molecular binding is an interaction between molecules that results in a stable physical
association between those molecules. Cooperative binding occurs in binding systems
containing more than one type, or species, of molecule and in which one of the partners is not mono-valent and can bind more than one molecule of the other species.
In 1904, Christian Bohr studied hemoglobin binding to oxygen under different conditions. When plotting hemoglobin saturation with oxygen as a function of the partial
pressure of oxygen, he obtained a sigmoidal (or "S-shaped") curve. This indicates that
the more oxygen is bound to hemoglobin, the easier it is for more oxygen to bind - until all binding sites are saturated. In addition, Bohr noticed that increasing CO2 pressure shifted this curve to the right - i.e. higher concentrations of CO2 make it more difficult for hemoglobin to bind oxygen. This latter phenomenon, together with the observation that hemoglobin's affinity for oxygen increases with increasing pH, is known as
the Bohr effect.
A receptor molecule is said to exhibit cooperative binding if its binding to ligand scales
non-linearly with ligand concentration. Cooperativity can be positive (if binding of a
ligand molecule increases the receptor's apparent affinity, and hence increases the
chance of another ligand molecule binding) or negative (if binding of a ligand molecule
decreases affinity and hence makes binding of other ligand molecules less likely).
The concept of cooperative binding only applies to molecules or complexes with more
than one ligand binding sites. If several ligand binding sites exist, but ligand binding to
any one site does not affect the others, the receptor is said to be non-cooperative. Cooperativity can be homotropic, if a ligand influences the binding of ligands of the same
kind, or heterotropic, if it influences binding of other kinds of ligands. In the case of hemoglobin, Bohr observed homotropic positive cooperativity (binding of oxygen facilitates binding of more oxygen) and heterotropic negative cooperativity (binding of CO2
reduces hemoglobin's facility to bind oxygen.)
https://en.wikipedia.org/wiki/Cooperative_binding
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Cooperativity
Molecular binding is an interaction between molecules that results in a stable physical
association between those molecules. Cooperative binding occurs in binding systems
containing more than one type, or species, of molecule and in which one of the partners is not mono-valent and can bind more than one molecule of the other species.
In 1904, Christian Bohr studied hemoglobin binding to oxygen under different conditions. When plotting hemoglobin saturation with oxygen as a function of the partial
pressure of oxygen, he obtained a sigmoidal (or "S-shaped") curve. This indicates that
the more oxygen is bound to hemoglobin, the easier it is for more oxygen to bind - until all binding sites are saturated. In addition, Bohr noticed that increasing CO2 pressure shifted this curve to the right - i.e. higher concentrations of CO2 make it more difficult for hemoglobin to bind oxygen. This latter phenomenon, together with the observation that hemoglobin's affinity for oxygen increases with increasing pH, is known as
the Bohr effect.
A receptor molecule is said to exhibit cooperative binding if its binding to ligand scales
non-linearly with ligand concentration. Cooperativity can be positive (if binding of a
ligand molecule increases the receptor's apparent affinity, and hence increases the
chance of another ligand molecule binding) or negative (if binding of a ligand molecule
decreases affinity and hence makes binding of other ligand molecules less likely).
The concept of cooperative binding only applies to molecules or complexes with more
than one ligand binding sites. If several ligand binding sites exist, but ligand binding to
any one site does not affect the others, the receptor is said to be non-cooperative. Cooperativity can be homotropic, if a ligand influences the binding of ligands of the same
kind, or heterotropic, if it influences binding of other kinds of ligands. In the case of hemoglobin, Bohr observed homotropic positive cooperativity (binding of oxygen facilitates binding of more oxygen) and heterotropic negative cooperativity (binding of CO2
reduces hemoglobin's facility to bind oxygen.)
https://en.wikipedia.org/wiki/Cooperative_binding
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Core Particle
The nucleosome core particle consists of approximately 147 base pairs of DNA
wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of
2 copies each of the core histones H2A, H2B, H3, and H4. Core particles are connected
by stretches of "linker DNA", which can be up to about 80 bp long. Technically, a nucleosome is defined as the core particle plus one of these linker regions. However the
word is often synonymous with the core particle. Genome-wide nucleosome positioning maps are now available for many model organisms including mouse liver and
brain.
A core particle is depicted below. Histones H2A, H2B, H3 and H4 are colored, DNA is
gray.
https://en.wikipedia.org/wiki/Nucleosome
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Cori Cycle
The Cori cycle (also known as the lactic acid cycle), named after its discoverers, Carl
Ferdinand Cori and Gerty Cori, refers to the metabolic pathway in which lactate produced by anaerobic glycolysis in the muscles moves to the liver and is converted to glucose, which then returns to the muscles and is metabolized back to lactate.
Muscular activity requires ATP, which is provided by the breakdown of glycogen in the
skeletal muscles. The breakdown of glycogen, a process known as glycogenolysis, releases glucose in the form of glucose-1-phosphate (G-1-P). The G-1-P is converted to G6-P by the enzyme phosphoglucomutase. G-6-P is readily fed into glycolysis, (or can go
into the pentose phosphate pathway if G-6-P concentration is high) a process that provides ATP to the muscle cells as an energy source. During muscular activity, the store
of ATP needs to be constantly replenished. When the supply of oxygen is sufficient,
this energy comes from feeding pyruvate, one product of glycolysis, into the citric acid
cycle.
When oxygen supply is insufficient, typically during intense muscular activity, energy
must be released through anaerobic metabolism. Lactic acid fermentation converts pyruvate to lactate by lactate dehydrogenase. Most important, fermentation regenerates
NAD+, maintaining the NAD+ concentration so that additional glycolysis reactions can
occur. The fermentation step oxidizes the NADH produced by glycolysis back to NAD+,
transferring two electrons from NADH to reduce pyruvate into lactate. Refer to the
main articles on glycolysis and fermentation for the details.
Instead of accumulating inside the muscle cells, lactate produced by anaerobic fermentation is taken up by the liver. This initiates the other half of the Cori cycle. In the liver,
gluconeogenesis occurs. From an intuitive perspective, gluconeogenesis reverses both
glycolysis and fermentation by converting lactate first into pyruvate, and finally back to
glucose. The glucose is then supplied to the muscles through the bloodstream. It is
ready to be fed into further glycolysis reactions. If muscle activity has stopped, the glucose is used to replenish the supplies of glycogen through glycogenesis.
Overall, the glycolysis part of the cycle produces 2 ATP molecules at a cost of 6 ATP
molecules consumed in the gluconeogenesis part. Each iteration of the cycle must be
maintained by a net consumption of 4 ATP molecules. As a result, the cycle cannot be
sustained indefinitely. The intensive consumption of ATP molecules indicates that the
Cori cycle shifts the metabolic burden from the muscles to the liver.
https://en.wikipedia.org/wiki/Cori_cycle
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Corticosteroid
Corticosteroids are a class of steroid hormones that are produced in the adrenal cortex
of vertebrates, as well as the synthetic analogues of these hormones. Corticosteroids
are involved in a wide range of physiological processes, including stress response, im-
https://en.wikipedia.org/wiki/Corticosteroid
Index
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Cortisol
in humans by the zona fasciculata of the adrenal cortex within the adrenal gland.
aid in the metabolism of fat, protein, and carbohydrates. It also decreases bone f
tion.
https://en.wikipedia.org/wiki/Cortisol
Index
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https://en.wikipedia.org/wiki/Coomassie_Brilliant_Blue
Covalent Bond
A covalent bond, also called a molecular bond, is a chemical bond that involves the
sharing of electron pairs between atoms. These electron pairs are known as shared
pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding.
https://en.wikipedia.org/wiki/Covalent_bond
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Covalent Modification
Post-translational modification (PTM) refers to the covalent and generally enzymatic
modification of proteins during or after protein biosynthesis. Proteins are synthesized
by ribosomes translating mRNA into polypeptide chains, which may then undergo
PTM to form the mature protein product. PTMs are important components in cell signaling.
Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini. They can extend the chemical repertoire of the 20 standard
amino acids by introducing new functional groups such as phosphate, acetate, amide
groups, or methyl groups. Phosphorylation is a very common mechanism for regulating the activity of enzymes and is the most common post-translational modification.
Many eukaryotic proteins also have carbohydrate molecules attached to them in a process called glycosylation, which can promote protein folding and improve stability as
well as serving regulatory functions. Attachment of lipid molecules, known as lipidation, often targets a protein or part of a protein to the cell membrane.
Other forms of post-translational modification consist of cleaving peptide bonds, as in
processing a propeptide to a mature form or removing the initiator methionine residue. The formation of disulfide bonds from cysteine residues may also be referred to as
a post-translational modification. For instance, the peptide hormone insulin is cut
twice after disulfide bonds are formed, and a propeptide is removed from the middle of
the chain. The resulting protein consists of two polypeptide chains connected by disulfide bonds.
Some types of post-translational modification are consequences of oxidative stress. Carbonylation is one example that targets the modified protein for degradation and can result in the formation of protein aggregates. Specific amino acid modifications can be
used as biomarkers indicating oxidative damage.
https://en.wikipedia.org/wiki/Post-translational_modification
Index
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COX-1
Cyclooxygenase (COX), officially known as prostaglandin-endoperoxide synthase
(PTGS), is an enzyme (EC 1.14.99.1) that is responsible for formation of prostanoids,
including thromboxane and prostaglandins such as prostacyclin.
The abbreviation "COX" is more often encountered in medicine. In genetics, the
"PTGS" symbol is officially used for the prostaglandin-endoperoxide synthase (cyclooxygenase) family of genes and proteins, because the stem "COX" was already used for
the cytochrome c oxidase family of genes and proteins.
Pharmacological inhibition of COX can provide relief from the symptoms of inflammation and pain. Non-steroidal anti-inflammatory drugs (NSAID), such as aspirin and
ibuprofen, exert their effects through inhibition of COX. The names "prostaglandin synthase (PHS)" and "prostaglandin endoperoxide synthetase (PES)" are still used to refer
to COX.
In terms of their molecular biology, COX-1 and COX-2 are of similar molecular weight,
approximately 70 and 72 kDa, respectively, and having 65% amino acid sequence homology and near-identical catalytic sites. COX-3 has been reported as a splice variant
of COX-1, but information about it is unclear. The most significant difference between
the isoenzymes, which allows for selective inhibition, is the substitution of isoleucine at
position 523 in COX-1 with valine in COX-2. The smaller Val523 residue in COX-2 allows access to a hydrophobic side-pocket in the enzyme (which Ile523 sterically hinders). Drug molecules, such as DuP-697 and the coxibs derived from it, bind to this alternative site and are considered to be selective inhibitors of COX-2.
https://en.wikipedia.org/wiki/Cyclooxygenase
Index
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COX-2
Cyclooxygenase (COX), officially known as prostaglandin-endoperoxide synthase
(PTGS), is an enzyme (EC 1.14.99.1) that is responsible for formation of prostanoids,
including thromboxane and prostaglandins such as prostacyclin.
The abbreviation "COX" is more often encountered in medicine. In genetics, the
"PTGS" symbol is officially used for the prostaglandin-endoperoxide synthase (cyclooxygenase) family of genes and proteins, because the stem "COX" was already used for
the cytochrome c oxidase family of genes and proteins.
Pharmacological inhibition of COX can provide relief from the symptoms of inflammation and pain. Non-steroidal anti-inflammatory drugs (NSAID), such as aspirin and
ibuprofen, exert their effects through inhibition of COX. The names "prostaglandin synthase (PHS)" and "prostaglandin endoperoxide synthetase (PES)" are still used to refer
to COX.
In terms of their molecular biology, COX-1 and COX-2 are of similar molecular weight,
approximately 70 and 72 kDa, respectively, and having 65% amino acid sequence homology and near-identical catalytic sites. COX-3 has been reported as a splice variant
of COX-1, but information about it is unclear. The most significant difference between
the isoenzymes, which allows for selective inhibition, is the substitution of isoleucine at
position 523 in COX-1 with valine in COX-2. The smaller Val523 residue in COX-2 allows access to a hydrophobic side-pocket in the enzyme (which Ile523 sterically hinders). Drug molecules, such as DuP-697 and the coxibs derived from it, bind to this alternative site and are considered to be selective inhibitors of COX-2.
https://en.wikipedia.org/wiki/Cyclooxygenase
Index
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COX-3
Cyclooxygenase (COX), officially known as prostaglandin-endoperoxide synthase
(PTGS), is an enzyme (EC 1.14.99.1) that is responsible for formation of prostanoids,
including thromboxane and prostaglandins such as prostacyclin.
The abbreviation "COX" is more often encountered in medicine. In genetics, the
"PTGS" symbol is officially used for the prostaglandin-endoperoxide synthase (cyclooxygenase) family of genes and proteins, because the stem "COX" was already used for
the cytochrome c oxidase family of genes and proteins.
Pharmacological inhibition of COX can provide relief from the symptoms of inflammation and pain. Non-steroidal anti-inflammatory drugs (NSAID), such as aspirin and
ibuprofen, exert their effects through inhibition of COX. The names "prostaglandin synthase (PHS)" and "prostaglandin endoperoxide synthetase (PES)" are still used to refer
to COX.
In terms of their molecular biology, COX-1 and COX-2 are of similar molecular weight,
approximately 70 and 72 kDa, respectively, and having 65% amino acid sequence homology and near-identical catalytic sites. COX-3 has been reported as a splice variant
of COX-1, but information about it is unclear. The most significant difference between
the isoenzymes, which allows for selective inhibition, is the substitution of isoleucine at
position 523 in COX-1 with valine in COX-2. The smaller Val523 residue in COX-2 allows access to a hydrophobic side-pocket in the enzyme (which Ile523 sterically hinders). Drug molecules, such as DuP-697 and the coxibs derived from it, bind to this alternative site and are considered to be selective inhibitors of COX-2.
https://en.wikipedia.org/wiki/Cyclooxygenase
Index
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Creatine
Creatine is a nitrogenous organic acid that occurs naturally in vertebrates and helps to
supply energy to all cells in the body, primarily muscle. This is achieved by increasing
the formation of adenosine triphosphate (ATP).
Creatine is not an essential nutrient as it is naturally produced in the human body from
the amino acids glycine and arginine. In the first step of the biosynthesis these two
amino acids are combined by the enzyme arginine:glycine amidinotransferase (AGAT,
EC:2.1.4.1) to form guanidinoacetate, this is then methylated by guanidinoacetate Nmethyltransferase (GAMT,EC:2.1.1.2), using S-adenosyl methionine as the methyl donor. Creatine itself can be phosphorylated by creatine kinase to form phosphocreatine,
which is used as an energy reserve (energy battery) in skeletal muscles and the brain.
Creatine, synthesized in the liver and kidney, is transported through the blood and
taken up by tissues with high energy demands, such as the brain and skeletal muscle,
through an active transport system. The concentration of ATP in skeletal muscle is usually 2-5 mM, which would result in a muscle contraction of only a few seconds. Fortunately, during times of increased energy demands, the phosphagen (or ATP/PCr) system rapidly resynthesizes ATP from ADP with the use of phosphocreatine (PCr)
through a reversible reaction with the enzyme creatine kinase (CK). In skeletal muscle,
PCr concentrations may reach 20-35 mM or more. Additionally, in most muscles, the
ATP regeneration capacity of CK is very high and is therefore not a limiting factor. Although the cellular concentrations of ATP are small, changes are difficult to detect because ATP is continuously and efficiently replenished from the large pools of PCr and
CK. Creatine has the ability to increase muscle stores of PCr, potentially increasing the
muscles ability to resynthesize ATP from ADP to meet increased energy demands.
https://en.wikipedia.org/wiki/Creatine
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Creatine Kinase
Creatine kinase (CK) also known as creatine phosphokinase (CPK) or phosphocreatine kinase is an enzyme (EC 2.7.3.2) expressed by various tissues and cell types.
CK catalyzes the conversion of creatine and utilizes adenosine triphosphate (ATP) to
create phosphocreatine (PCr) and adenosine diphosphate (ADP). This CK enzyme reaction is reversible and thus ATP can be generated from PCr and ADP.
In tissues and cells that consume ATP rapidly, especially skeletal muscle, but also
brain, photoreceptor cells of the retina, hair cells of the inner ear, spermatozoa and
smooth muscle, PCr serves as an energy reservoir for the rapid buffering and regeneration of ATP in situ, as well as for intracellular energy transport by the PCr shuttle or circuit. Thus creatine kinase is an important enzyme in such tissues.
Clinically, creatine kinase is assayed in blood tests as a marker of damage of CK-rich
tissue such as in myocardial infarction (heart attack), rhabdomyolysis (severe muscle
breakdown), muscular dystrophy, the autoimmune myositides and in acute renal failure.
https://en.wikipedia.org/wiki/Creatine_kinase
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Creatine Phosphate
Phosphocreatine, also known as creatine phosphate (CP) or PCr, is a phosphorylated
creatine molecule that serves as a rapidly mobilizable reserve of high-energy phosphates in skeletal muscle and the brain.
Phosphocreatine can anaerobically donate a phosphate group to ADP to form ATP during the first 2 to 7 seconds following an intense muscular or neuronal effort. Conversely, excess ATP can be used during a period of low effort to convert creatine to
phosphocreatine. The reversible phosphorylation of creatine (i.e., both the forward and
backward reaction) is catalyzed by several creatine kinases. The presence of creatine
kinase (CK-MB, MB for muscle/brain) in blood plasma is indicative of tissue damage
and is used in the diagnosis of myocardial infarction. The cell's ability to generate phosphocreatine from excess ATP during rest, as well as its use of phosphocreatine for
quick regeneration of ATP during intense activity, provides a spatial and temporal
buffer of ATP concentration. In other words, phosphocreatine acts as high-energy reserve in a coupled reaction. The energy given off from donating the phosphate group is
used to regenerate the other compound - in this case, ATP. Phosphocreatine plays a
particularly important role in tissues that have high, fluctuating energy demands such
as muscle and brain.
https://en.wikipedia.org/wiki/Phosphocreatine
Index
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CREB
CREB (cAMP response element-binding protein) is a cellular transcription factor. It
binds to certain DNA sequences called cAMP response elements (CRE), thereby increasing or decreasing the transcription of the downstream genes.
CREB has a well-documented role in neuronal plasticity and long-term memory formation in the brain and has been shown to be integral in the formation of spatial memory.
CREB downregulation is implicated in the pathology of Alzheimer's disease and increasing the expression of CREB is being considered as a possible therapeutic target
for Alzheimers disease. CREB also has a role in photoentrainment in mammals.
CREB has many functions in many different organs, and some of its functions have
been studied in relation to the brain. CREB proteins in neurons are thought to be involved in the formation of long-term memories. This has been shown in the marine
snail Aplysia, the fruit fly Drosophila melanogaster, in rats and in mice (see CREB in
Molecular and Cellular Cognition). CREB is necessary for the late stage of long-term
potentiation. CREB also has an important role in the development of drug addiction
and even more so in psychological dependence. There are activator and repressor
forms of CREB. Flies genetically engineered to overexpress the inactive form of CREB
lose their ability to retain long-term memory. CREB is also important for the survival
of neurons, as shown in genetically engineered mice, where CREB and CREM were deleted in the brain. If CREB is lost in the whole developing mouse embryo, the mice die
immediately after birth, again highlighting the critical role of CREB in promoting survival.
https://en.wikipedia.org/wiki/CREB
Index
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Creutzfeld-Jacob
CreutzfeldtJakob disease or CJD is a degenerative neurological disease that is incurable and invariably fatal. CJD is at times called a human form of mad cow disease (bovine spongiform encephalopathy or BSE). However, given that BSE is believed to be
the cause of variant CreutzfeldtJakob (vCJD) disease in humans, the two are often
confused. CJD is caused by an infectious agent called a prion. Prions are misfolded proteins that replicate by converting their properly folded counterparts, in their host, to
the same misfolded structure they possess. CJD causes the brain tissue to degenerate
rapidly, and as the disease destroys the brain, the brain develops holes and the texture
changes to resemble that of a kitchen sponge.
Transmissible spongiform encephalopathy diseases are caused by prions. Prions are
proteins that occur normally in neurons of the central nervous system (CNS). As of
2007, these proteins were thought to affect signaling processes, damaging neurons and
resulting in degeneration that causes the spongiform appearance in the affected brain.
The CJD prion is dangerous because it promotes refolding of native proteins into the
diseased state. The number of misfolded protein molecules will increase exponentially
and the process leads to a large quantity of insoluble protein in affected cells. This
mass of misfolded proteins disrupts neuronal cell function and causes cell death. Mutations in the gene for the prion protein can cause a misfolding of the dominantly helical regions into pleated sheets. This change in conformation disables the ability of
the protein to undergo digestion. Once the prion is transmitted, the defective proteins
invade the brain and are produced in a self-sustaining feedback loop.These neurodegenerative diseases are commonly called prion diseases.
People can also acquire CJD genetically through a mutation of the gene that codes for
the prion protein (PRNP). This occurs in only 5-10% of all CJD cases. An EU study determined that "87% of cases were sporadic, 8% genetic, and 5% iatrogenic."
https://en.wikipedia.org/wiki/Creutzfeldt%E2%80%93Jakob_disease
Index
Find Term
Creutzfeld-Jacob Disease
CreutzfeldtJakob disease or CJD is a degenerative neurological disease that is incurable and invariably fatal. CJD is at times called a human form of mad cow disease (bovine spongiform encephalopathy or BSE). However, given that BSE is believed to be
the cause of variant CreutzfeldtJakob (vCJD) disease in humans, the two are often
confused. CJD is caused by an infectious agent called a prion. Prions are misfolded proteins that replicate by converting their properly folded counterparts, in their host, to
the same misfolded structure they possess. CJD causes the brain tissue to degenerate
rapidly, and as the disease destroys the brain, the brain develops holes and the texture
changes to resemble that of a kitchen sponge.
Transmissible spongiform encephalopathy diseases are caused by prions. Prions are
proteins that occur normally in neurons of the central nervous system (CNS). As of
2007, these proteins were thought to affect signaling processes, damaging neurons and
resulting in degeneration that causes the spongiform appearance in the affected brain.
The CJD prion is dangerous because it promotes refolding of native proteins into the
diseased state. The number of misfolded protein molecules will increase exponentially
and the process leads to a large quantity of insoluble protein in affected cells. This
mass of misfolded proteins disrupts neuronal cell function and causes cell death. Mutations in the gene for the prion protein can cause a misfolding of the dominantly helical regions into pleated sheets. This change in conformation disables the ability of
the protein to undergo digestion. Once the prion is transmitted, the defective proteins
invade the brain and are produced in a self-sustaining feedback loop.These neurodegenerative diseases are commonly called prion diseases.
People can also acquire CJD genetically through a mutation of the gene that codes for
the prion protein (PRNP). This occurs in only 5-10% of all CJD cases. An EU study determined that "87% of cases were sporadic, 8% genetic, and 5% iatrogenic."
https://en.wikipedia.org/wiki/Creutzfeldt%E2%80%93Jakob_disease
Index
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CRISPR/Cas9
Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced
crisper) are segments of prokaryotic DNA containing short repetitions of base sequences. Each repetition is followed by short segments of "spacer DNA" from previous
exposures to a bacteriophage virus or plasmid.
The CRISPR/Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides
a form of acquired immunity. CRISPR spacers recognize and cut these exogenous genetic elements in a manner analogous to RNA interference in eukaryotic organisms.
CRISPRs are found in approximately 40% of sequenced bacterial genomes and 90% of
sequenced archaea.
By delivering the Cas9 nuclease and appropriate guide RNAs into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or
new ones added. CRISPRs have been used in concert with specific endonuclease enzymes for genome editing and gene regulation in species throughout the tree of life.
Cas9 was the first nuclease discovered, followed by Cpf1, which was discovered in the
CRISPR/Cpf1 system of Francisella novicida. Other such systems are thought to exist.
CRISPR/C2c2 from the bacterium Leptotrichia shahii is RNA-guided CRISPR system
that targets RNA rather than DNA, and can either cleave single-stranded RNA targets
or knock them down.
The CRISPR interference technique has many potential applications, including altering
the germline of humans, animals, and food crops. The use of CRISPR for genome editing was the AAAS's choice for breakthrough of the year in 2015.
https://en.wikipedia.org/wiki/CRISPR
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CTP
Cytidine triphosphate is a pyrimidine nucleoside triphosphate. CTP is a substrate in
the synthesis of RNA. CTP is a high-energy molecule similar to ATP, but its role as an
energy coupler is limited to a much smaller subset of metabolic reactions. CTP is a coenzyme in metabolic reactions like the synthesis of glycerophospholipids and glycosylation of proteins. CTP acts as an inhibitor of the enzyme Aspartate carbamoyltransferase, which is used in pyrimidine biosynthesis.
CTP acts as an inhibitor of the enzyme aspartate carbamoyltransferase, which is used
in pyrimidine biosynthesis.
https://en.wikipedia.org/wiki/Cytidine_triphosphate
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CTP Synthetase
CTP synthetase is an enzyme involved in pyrimidine biosynthesis that interconverts
UTP and CTP. Active CTP synthase exists as a homotetrameric enzyme. At low enzyme
concentrations and in the absence of ATP and UTP, CTP synthase exists as inactive
monomer. As enzyme concentration increases, it polymerizes first to a dimer (such as
the form shown to the left) and, in the presence of ATP and UTP, forms a tetramer.
The enzyme contains two major domains, responsible for the aminotransferase and
synthase activity, respectively. The amidotransferase domains are located away from
the tetramer interfaces and are not affected by the oligomeric state. The ATP-binding
site and CTP-binding site in the synthase domain are located at the tetramer interface.
It is for this reason that ATP and UTP are required for tetramerization.
CTP synthase is precisely regulated by the intracellular concentrations of CTP and
UTP, and both hCTPS1 and hCTPS2 have been seen to be maximally active at physiological concentrations of ATP, GTP, and glutamine.
The activity of human CTPS1 isozyme has been demonstrated to be inhibited by phosphorylation. One major example of this is phosphorylation of the Ser-571 residue by
glycogen synthase kinase 3 (GSK3) in response to low serum conditions. Additionally,
Ser568 has been seen to be phosphorylated by casein kinase 1, inhibiting CTP synthase
activity.
CTP is also subject to various forms of allosteric regulation. GTP acts as an allosteric
activator that strongly promotes the hydrolysis of glutamine, but is also inhibiting to
glutamine-dependent CTP formation at high concentrations. This acts to balance the
relative amounts of purine and pyrimidine nucleotides. The reaction product CTP also
serves as an allosteric inhibitor. The triphosphate binding site overlaps with that of
UTP, but the nucleoside moiety of CTP binds in an alternative pocket opposite the binding site for UTP.
The glutamine analog DON has also been seen to act as an irreversible inhibitor, and
has been used as an anti-cancer agent.
https://en.wikipedia.org/wiki/CTP_synthetase
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CuA
mals, eleven subunits are nuclear in origin, and three are synthesized in the
dria. The complex contains two hemes, a cytochrome a and cytochrome a3,
per centers, the CuA and CuB centers. In fact, the cytochrome a3 and CuB for
clear center that is the site of oxygen reduction. Cytochrome c, which is red
docks near the CuA binuclear center and passes an electron to it, being oxid
cytochrome c containing Fe+++. The reduced CuA binuclear center now pass
binuclear center. The two metal ions in this binuclear center are 4.5 apart
nate a hydroxide ion in the fully oxidized state.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase
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CuB
mals, eleven subunits are nuclear in origin, and three are synthesized in the
dria. The complex contains two hemes, a cytochrome a and cytochrome a3,
per centers, the CuA and CuB centers. In fact, the cytochrome a3 and CuB for
clear center that is the site of oxygen reduction. Cytochrome c, which is red
docks near the CuA binuclear center and passes an electron to it, being oxid
cytochrome c containing Fe+++. The reduced CuA binuclear center now pass
binuclear center. The two metal ions in this binuclear center are 4.5 apart
nate a hydroxide ion in the fully oxidized state.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase
Cyanide
A cyanide is any chemical compound that contains monovalent combining group CN.
This group, known as the cyano group, consists of a carbon atom triple-bonded to a nitrogen atom. In inorganic cyanides, such as sodium cyanide and potassium cyanide
this group is present as the negatively charged polyatomic cyanide ion (CN). These
compounds, which are regarded as salts of hydrocyanic acid, are highly toxic. The cyanide ion is isoelectronic with carbon monoxide and with molecular nitrogen. Organic
cyanides are usually called nitriles. In these, the CN group is linked by a covalent bond
to a carbon-containing group, such as methyl (CH3) in methyl cyanide (acetonitrile).
Many cyanides are highly toxic. The cyanide anion is an inhibitor of the enzyme cytochrome c oxidase (also known as aa3) in the fourth complex of the electron transport
chain (found in the membrane of the mitochondria of eukaryotic cells). It attaches to
the iron within this protein. The binding of cyanide to this enzyme prevents transport
of electrons from cytochrome c to oxygen. As a result, the electron transport chain is
disrupted, meaning that the cell can no longer aerobically produce ATP for energy.
Tissues that depend highly on aerobic respiration, such as the central nervous system
and the heart, are particularly affected. This is an example of histotoxic hypoxia.
The most hazardous compound is hydrogen cyanide, which is a gas at ambient temperatures and pressure and can therefore be inhaled. For this reason, an air respirator
supplied by an external oxygen source must be worn when working with hydrogen cyanide. Hydrogen cyanide is produced when a solution containing a labile cyanide is
made acidic, because HCN is a weak acid. Alkaline solutions are safer to use because
they do not evolve hydrogen cyanide gas. Hydrogen cyanide may be produced in the
combustion of polyurethanes. For this reason, polyurethanes are not recommended
for use in domestic and aircraft furniture. Oral ingestion of a small quantity of solid
cyanide or a cyanide solution as little as 200mg, or to airborne cyanide of 270 ppm is
sufficient to cause death within minutes.
https://en.wikipedia.org/wiki/Cyanide
Cyclic Photophosphorylation
This form of photophosphorylation occurs on the thylakoid membrane. In cyclic electron flow, the electron begins in a pigment complex called photosystem I, passes from
the primary acceptor to ferredoxin, then to cytochrome b6f (a similar complex to that
found in mitochondria), and then to plastocyanin before returning to chlorophyll. This
transport chain produces a proton-motive force, pumping H+ ions across the membrane. This produces a concentration gradient that can be used to power ATP synthase
during chemiosmosis. This pathway is known as cyclic photophosphorylation, and it
produces neither O2 nor NADPH. Unlike non-cyclic photophosphorylation, NADP+
does not accept the electrons. They are instead sent back to cytochrome b6f complex.
In bacterial photosynthesis, a single photosystem is used, and therefore is involved in
cyclic photophosphorylation. It is favored in anaerobic conditions and conditions of
high irradiance and CO2 compensation points.
In the figure below, cyclic photophosphorylation is shown by the blue dashed line.
https://en.wikipedia.org/wiki/Photophosphorylation#Cyclic_photophosphorylation
Index
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https://en.wikipedia.org/wiki/Pyrimidine_dimer
Index
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Cyclohexane
used for the industrial production of adipic acid and caprolactam, which are
https://en.wikipedia.org/wiki/Cyclohexane
Index
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Cyclooxygenase
Cyclooxygenase (COX), officially known as prostaglandin-endoperoxide synthase
(PTGS), is an enzyme (EC 1.14.99.1) that is responsible for formation of prostanoids,
including thromboxane and prostaglandins such as prostacyclin.
The abbreviation "COX" is more often encountered in medicine. In genetics, the
"PTGS" symbol is officially used for the prostaglandin-endoperoxide synthase (cyclooxygenase) family of genes and proteins, because the stem "COX" was already used for
the cytochrome c oxidase family of genes and proteins.
Pharmacological inhibition of COX can provide relief from the symptoms of inflammation and pain. Non-steroidal anti-inflammatory drugs (NSAID), such as aspirin and
ibuprofen, exert their effects through inhibition of COX. The names "prostaglandin synthase (PHS)" and "prostaglandin endoperoxide synthetase (PES)" are still used to refer
to COX.
In terms of their molecular biology, COX-1 and COX-2 are of similar molecular weight,
approximately 70 and 72 kDa, respectively, and having 65% amino acid sequence homology and near-identical catalytic sites. COX-3 has been reported as a splice variant
of COX-1, but information about it is unclear. The most significant difference between
the isoenzymes, which allows for selective inhibition, is the substitution of isoleucine at
position 523 in COX-1 with valine in COX-2. The smaller Val523 residue in COX-2 allows access to a hydrophobic side-pocket in the enzyme (which Ile523 sterically hinders). Drug molecules, such as DuP-697 and the coxibs derived from it, bind to this alternative site and are considered to be selective inhibitors of COX-2.
https://en.wikipedia.org/wiki/Cyclooxygenase
CYP3A4
small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they ca
be removed from the body.
CYP3A4 is a member of the cytochrome P450 family of oxidizing enzymes. Several
other members of this family are also involved in drug metabolism, but CYP3A4 is th
most common and the most versatile one. Like all members of this family, it is a hem
protein, i.e. a protein containing a heme group with an iron atom. In humans, the
CYP3A4 protein is encoded by the CYP3A4 gene. This gene is part of a cluster of cyto
chrome P450 genes on chromosome 7q21.1.
While many drugs are deactivated by CYP3A4, there are also some drugs which are a
vated by the enzyme. Some substances, such as grapefruit juice and some drugs, inte
fere with the action of CYP3A4. These substances will therefore either amplify or
weaken the action of those drugs that are modified by CYP3A4.
https://en.wikipedia.org/wiki/CYP3A4
Index
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Cystathionase
Cystathionine -lyase (CTH or CSE) (also known as cystathionase) is an enzyme which
breaks down cystathionine into cysteine, -ketobutyrate, and ammonia. Pyridoxal
phosphate is a prosthetic group of this enzyme.
Cystathionine
Cystathionine is an intermediate in the synthesis of cysteine. An excess in the urine is
called cystathioninuria. Biosynthetically, cystathionineis generated from homocysteine
and serine by cystathionine synthase (upper reaction in the diagram below). It is
then cleaved into cysteine and -ketobutyrate by cystathionine -lyase (lower reaction).
https://en.wikipedia.org/wiki/Cystathionine
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Cystathionine -synthase
mans is encoded by the CBS gene. It catalyzes the first step of the transsulfu
way, from homocysteine to cystathionine:
L-serine + L-homocysteine <-> L-cystathionine + H2O
Index
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Cystathionine--lyase
Cystathionine -lyase (EC 4.4.1.8) is an enzyme that catalyzes the chemical reac
L-cystathionine + H2O <-> L-homocysteine + NH3 + Pyruvate
This enzyme belongs to the family of lyases, specifically the class of carbon-sulf
Cystathionine--synthase
Cystathionine -synthase (EC 2.5.1.48) is an enzyme that catalyzes the chemical reaction
O4-succinyl-L-homoserine + L-cysteine <-> L-cystathionine + Succinate
This enzyme belongs to the family of transferases, specifically those transferring aryl or
alkyl groups other than methyl groups. The systematic name of this enzyme class is
O4-succinyl-L-homoserine:L-cysteine S-(3-amino-3-carboxypropyl)transferase. Other
names in common use include O-succinyl-L-homoserine succinate-lyase (adding cysteine), O-succinylhomoserine (thiol)-lyase, homoserine O-transsuccinylase, Osuccinylhomoserine synthase, O-succinylhomoserine synthetase, cystathionine synthase, cystathionine synthetase, homoserine transsuccinylase,
4-O-succinyl-L-homoserine:L-cysteine, and S-(3-amino-3-carboxypropyl)transferase.
This enzyme participates in 4 metabolic pathways: methionine metabolism, cysteine
metabolism, selenoamino acid metabolism, and sulfur metabolism. It employs one cofactor, pyridoxal phosphate.
https://en.wikipedia.org/wiki/Cystathionine_gamma-synthase
Cysteic Acid
Cysteic acid is an intermediate in cysteine metabolism.
L-cysteine + Sulfite
https://en.wikipedia.org/wiki/Cysteic_acid
Index
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G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Cysteine
Cysteine (abbreviated as Cys or C) is a semi-essential proteinogenic amino acid with
the formula HO2CCH(NH2)CH2SH>. It is encoded by the codons UGU and UGC. The
thiol side chain in cysteine often participates in enzymatic reactions, as a nucleophile.
The thiol is susceptible to oxidization to give the disulfide derivative cystine, which
serves an important structural role in many proteins.
The cysteine thiol group is nucleophilic and easily oxidized. The reactivity is enhanced
when the thiol is ionized, and cysteine residues in proteins have pKa values close to
neutrality, so are often in their reactive thiolate form in the cell. Because of its high reactivity, the thiol group of cysteine has numerous biological functions.
Cysteine has antioxidant properties. Cysteine's antioxidant properties are typically expressed in the tripeptide glutathione, which occurs in humans as well as other organisms. The systemic availability of oral glutathione (GSH) is negligible; so it must be biosynthesized from its constituent amino acids, cysteine, glycine, and glutamic acid. Glutamic acid and glycine are readily available in most Western diets, but the availability
of cysteine can be the limiting substrate.
Cysteine is an important source of sulfide in human metabolism. The sulfide in ironsulfur clusters and in nitrogenase is extracted from cysteine, which is converted to alanine in the process.
Beyond the iron-sulfur proteins, many other metal cofactors in enzymes are bound to
the thiolate substituent of cysteinyl residues. Examples include zinc in zinc fingers and
alcohol dehydrogenase, copper in the blue copper proteins, iron in cytochrome P450,
and nickel in the [NiFe]-hydrogenases. The thiol group also has a high affinity for
heavy metals, so that proteins containing cysteine, such as metallothionein, will bind
metals such as mercury, lead, and cadmium tightly.
https://en.wikipedia.org/wiki/Cysteine
Index
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G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure and Function: Proteins
Chapter 2 - Structure and Function: Proteins
Chapter 2 - Structure and Function: Proteins
Chapter 4 - Catalysis: Mechanism
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 7 - DNA Repair
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Information Processing
Cysteine Lyase
Cysteine lyase (EC 4.4.1.10) is an enzyme that catalyzes the chemical reactio
L-cysteine + Sulfite <-> L-cysteate + H2S
This enzyme belongs to the family of lyases, specifically the class of carbon-
Index
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Cysteine Proteases
Cysteine proteases, also known as thiol proteases, are enzymes that degrade proteins.
These proteases share a common catalytic mechanism that involves a nucleophilic cysteine thiol in a catalytic triad or dyad.
Cysteine proteases are commonly encountered in fruits including the papaya, pineapple, fig and kiwifruit. The proportion of protease tends to be higher when the fruit is unripe. In fact, dozens of latices of different plant families are known to contain cysteine
proteases. Cysteine proteases are used as an ingredient in meat tenderizers.
The first step in the reaction mechanism by which cysteine proteases catalyze the hydrolysis of peptide bonds is deprotonation of a thiol in the enzyme's active site by an
adjacent amino acid with a basic side chain, usually a histidine residue. The next step
is nucleophilic attack by the deprotonated cysteine's anionic sulfur on the substrate carbonyl carbon. In this step, a fragment of the substrate is released with an amine terminus, the histidine residue in the protease is restored to its deprotonated form, and a
thioester intermediate linking the new carboxy-terminus of the substrate to the cysteine thiol is formed. Therefore they are also sometimes referred to as thiol proteases.
The thioester bond is subsequently hydrolyzed to generate a carboxylic acid moiety on
the remaining substrate fragment, while regenerating the free enzyme.
Cysteine proteases play multi-faceted roles, virtually in every aspect of physiology and
development. In plants they are important in growth and development and in accumulation and mobilization of storage proteins such as in seeds. In addition, they are involved in signaling pathways and in the response to biotic and abiotic stresses. In humans and other animals, they are responsible for senescence and apoptosis (programmed cell death), MHC class II immune responses, prohormone processing, and
extracellular matrix remodeling important to bone development. The ability of macrophages and other cells to mobilize elastolytic cysteine proteases to their surfaces under
specialized conditions may also lead to accelerated collagen and elastin degradation at
sites of inflammation in diseases such as atherosclerosis and emphysema. Several viruses (e.g. polio, hepatitis C) express their entire genome as a singe massive polyprotein and use a protease to cleave it into functional units (e.g. Tobacco Etch Virus protease).
https://en.wikipedia.org/wiki/Cysteine_protease
Cysteine Synthase
Cysteine synthase (EC 2.5.1.47) is an enzyme that catalyzes the chemical reaction
O3-acetyl-L-serine + H2S <-> L-cysteine + Acetate
This enzyme belongs to the family of transferases, specifically those transferring aryl or
alkyl groups other than methyl groups. The systematic name of this enzyme class is
O3-acetyl-L-serine:hydrogen-sulfide 2-amino-2-carboxyethyltransferase. Other names
in common use include O-acetyl-L-serine sulfhydrylase, O-acetyl-L-serine sulfohydrolase, O-acetylserine (thiol)-lyase, O-acetylserine (thiol)-lyase A, O-acetylserine sulfhydrylase, O3-acetyl-L-serine acetate-lyase (adding hydrogen-sulfide), acetylserine sulfhydrylase, cysteine synthetase, S-sulfocysteine synthase,
3-O-acetyl-L-serine:hydrogen-sulfide, and 2-amino-2-carboxyethyltransferase.
This enzyme participates in 3 metabolic pathways: cysteine metabolism, selenoamino
acid metabolism, and sulfur metabolism. It employs one cofactor, pyridoxal phosphate.
https://en.wikipedia.org/wiki/Cysteine_synthase
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Cystic Fibrosis
Cystic fibrosis (CF) is a genetic disorder that affects mostly the lungs but also the pancreas, liver, kidneys, and intestine. Long-term issues include difficulty breathing and
coughing up mucus as a result of frequent lung infections. Other signs and symptoms
include sinus infections, poor growth, fatty stool, clubbing of the fingers and toes, and
infertility in males, among others. Different people may have different degrees of symptoms. CF is inherited in an autosomal recessive manner. It is caused by the presence of
mutations in both copies of the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Those with a single working copy are carriers and otherwise mostly normal.
CF is most common among people of Northern European ancestry and affects about
one out of every 3,000 newborns. About one in 25 people are carriers. It is least com-
mon in Africans and Asians. It was first recognized as a specific disease by Dorothy Andersen in 1938, with descriptions that fit the condition occurring at least as far back as
1595. The name cystic fibrosis refers to the characteristic fibrosis and cysts that form
within the pancreas.
https://en.wikipedia.org/wiki/Cystic_fibrosis
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Cystine
Cystine is the oxidized dimer form of the amino acid cysteine and has formula
(SCH2CH(NH2)CO2H)2. It is a white solid that is slightly soluble in water. It serves two
biological functions, a site of redox reactions and a mechanical linkage that allows proteins to retain their 3-dimensional structure.
Cystine is formed from the oxidation of two cysteine molecules, via the formation of a
disulfide bond. In cell biology, cystine (found in proteins) can only exist in nonreductive (oxidative) organelles, such as the secretory pathway (ER, Golgi, Lysosomes,
Vesicles and ECM). Meaning that in reductive conditions (Cytoplasm, Nucleus, etc.)
cysteine is favorably found. The disulfide link is readily reduced to give the corresponding thiol cysteine. Typical thiols for this reaction are mercaptoethanol and dithiothreitol:
(SCH2CH(NH2)CO2H)2 + 2 RSH 2 HSCH2CH(NH2)CO2H + RSSR
Because of the facility of the thiol-disulfide exchange, the nutritional benefits and
sources of cystine are identical to those for the more-common cysteine. Disulfide
bonds cleave more rapidly at higher temperatures.
https://en.wikipedia.org/wiki/Cystine
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Cystine Reductase
Cystine reductase (EC 1.8.1.6) is an enzyme that catalyzes the chemical reac
2 L-cysteine + NAD+ <-> L-cystine + NADH + H+
fur group of donors with NAD+ or NADP+ as acceptor. The systematic name
This enzyme participates in cysteine metabolism and is named for the rever
https://en.wikipedia.org/wiki/Cystine_reductase
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Cytidine
Cytidine is a nucleoside molecule that is formed when cytosine is attached to a ribose
ring (also known as a ribofuranose) via a -N1-glycosidic bond. Cytidine is a component of RNA.
If cytosine is attached to a deoxyribose ring, it is known as a deoxycytidine.
In addition to its role as a pyrimidine component of RNA, cytidine has been found to
control neuronal-glial glutamate cycling, with supplementation decreasing midfrontal/
cerebral glutamate/glutamine levels. As such, cytidine has generated interest as a potential glutamatergic antidepressant drug.
https://en.wikipedia.org/wiki/Cytidine
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Cytidine Deaminase
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Cytochrome a
from the CuA binuclear center of Complex IV and passes it off to the cytochr
binuclear center.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase
Cytochrome a3
mals, eleven subunits are nuclear in origin, and three are synthesized in the m
dria. The complex contains two hemes, a cytochrome a and cytochrome a3, an
per centers, the CuA and CuB centers. In fact, the cytochrome a3 and CuB form
clear center that is the site of oxygen reduction. Cytochrome c, which is reduc
docks near the CuA binuclear center and passes an electron to it, being oxidize
cytochrome c containing Fe+++. The reduced CuA binuclear center now passes
binuclear center. The two metal ions in this binuclear center are 4.5 apart a
nate a hydroxide ion in the fully oxidized state.
https://en.wikipedia.org/wiki/Cytochrome_c_oxidase
Cytochrome b
part of the electron transport chain and is the main subunit of transmembran
as the b6f complex. These complexes are involved in electron transport, pump
protons to the create a PMF. The proton gradient is finally used for the genera
ATP. Concluding, the complexes play a vital role in cells.
https://en.wikipedia.org/wiki/Cytochrome_b
Cytochrome b5
plants, fungi and purple phototrophic bacteria. The microsomal and mitochon
and fungal nitrate reductases (EC 1.7.1.1, EC 1.7.1.2, EC 1.7.1.3), and plant and
cytochrome b5/acyl lipid desaturase fusion proteins.
https://en.wikipedia.org/wiki/Cytochrome_b5
Cytochrome c
The cytochrome complex, or cyt c is a small hemeprotein found loosely associated with
the inner membrane of the mitochondrion. It belongs to the cytochrome c family of proteins. Cytochrome c is highly water-soluble, unlike other cytochromes, and is an essential component of the electron transport chain, where it carries one electron. It is capable of undergoing oxidation and reduction, but does not bind oxygen. It transfers electrons between Complexes III (Coenzyme Q Cyt C reductase) and IV (Cyt C oxidase).
In humans, cytochrome c is encoded by the CYCS gene.
Cytochrome c is a component of the electron transport chain in mitochondria. The
heme group of cytochrome c accepts electrons from the bc1 complex and transfers electrons to the complex IV. Cytochrome c is also involved in initiation of apoptosis. Upon
release of cytochrome c to the cytoplasm, the protein binds apoptotic protease activating factor-1 (Apaf-1).
Cytochrome c is also an intermediate in apoptosis, a controlled form of cell death used
to kill cells in the process of development or in response to infection or DNA damage.
Cytochrome c binds to cardiolipin in the inner mitochondrial membrane, thus anchoring its presence and keeping it from releasing out of the mitochondria and initiating
apoptosis. While the initial attraction between cardiolipin and cytochrome c is electrostatic due to the extreme positive charge on cytochrome c, the final interaction is hydrophobic, where a hydrophobic tail from cardiolipin inserts itself into the hydrophobic
portion of cytochrome c.
During the early phase of apoptosis, mitochondrial ROS production is stimulated, and
cardiolipin is oxidized by a peroxidase function of the cardiolipincytochrome c complex. The hemoprotein is then detached from the mitochondrial inner membrane and
can be extruded into the soluble cytoplasm through pores in the outer membrane.
The sustained elevation in calcium levels precedes cyt c release from the mitochondria.
The release of small amounts of cyt c leads to an interaction with the IP3 receptor
(IP3R) on the endoplasmic reticulum (ER), causing ER calcium release. The overall increase in calcium triggers a massive release of cyt c, which then acts in the positive feedback loop to maintain ER calcium release through the IP3Rs. This explains how the ER
calcium release can reach cytotoxic levels. This release of cytochrome c in turn activates caspase 9, a cysteine protease. Caspase 9 can then go on to activate caspase 3 and
caspase 7, which are responsible for destroying the cell from within.
One of the ways cell apoptosis is activated is by release of cytochrome c from the mitochondria into cytosol. A study has shown that cells are able to protect themselves from
apoptosis by block the release of cytochrome c using Bcl-xL. Another way that cells can
control apoptosis is by phosphorylation of Tyr48 which would turn cytochrome c into
an anti-apoptotic switch.
Cytochrome c is known to play a role in the electron transport chain and cell apoptosis.
However, a recent study has shown that it can also act as an antioxidative enzyme in
the mitochondria. It does so by removing superoxide (O2) and hydrogen peroxide
(H2O2) from mitochondria. Therefore, not only is cytochrome c required in the mitochondria for cell respiration, but it is also needed in the mitochondria to limit the production of O2- and H2O2.
https://en.wikipedia.org/wiki/Cytochrome_c
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Cytochrome C
The cytochrome complex, or cyt c is a small hemeprotein found loosely associated with
the inner membrane of the mitochondrion. It belongs to the cytochrome c family of proteins. Cytochrome c is highly water-soluble, unlike other cytochromes, and is an essential component of the electron transport chain, where it carries one electron. It is capable of undergoing oxidation and reduction, but does not bind oxygen. It transfers electrons between Complexes III (Coenzyme Q Cyt C reductase) and IV (Cyt C oxidase).
In humans, cytochrome c is encoded by the CYCS gene.
Cytochrome c is a component of the electron transport chain in mitochondria. The
heme group of cytochrome c accepts electrons from the bc1 complex and transfers electrons to the complex IV. Cytochrome c is also involved in initiation of apoptosis. Upon
release of cytochrome c to the cytoplasm, the protein binds apoptotic protease activating factor-1 (Apaf-1).
Cytochrome c is also an intermediate in apoptosis, a controlled form of cell death used
to kill cells in the process of development or in response to infection or DNA damage.
Cytochrome c binds to cardiolipin in the inner mitochondrial membrane, thus anchoring its presence and keeping it from releasing out of the mitochondria and initiating
apoptosis. While the initial attraction between cardiolipin and cytochrome c is electrostatic due to the extreme positive charge on cytochrome c, the final interaction is hydrophobic, where a hydrophobic tail from cardiolipin inserts itself into the hydrophobic
portion of cytochrome c.
During the early phase of apoptosis, mitochondrial ROS production is stimulated, and
cardiolipin is oxidized by a peroxidase function of the cardiolipincytochrome c complex. The hemoprotein is then detached from the mitochondrial inner membrane and
can be extruded into the soluble cytoplasm through pores in the outer membrane.
The sustained elevation in calcium levels precedes cyt c release from the mitochondria.
The release of small amounts of cyt c leads to an interaction with the IP3 receptor
(IP3R) on the endoplasmic reticulum (ER), causing ER calcium release. The overall increase in calcium triggers a massive release of cyt c, which then acts in the positive feedback loop to maintain ER calcium release through the IP3Rs. This explains how the ER
calcium release can reach cytotoxic levels. This release of cytochrome c in turn activates caspase 9, a cysteine protease. Caspase 9 can then go on to activate caspase 3 and
caspase 7, which are responsible for destroying the cell from within.
One of the ways cell apoptosis is activated is by release of cytochrome c from the mitochondria into cytosol. A study has shown that cells are able to protect themselves from
apoptosis by block the release of cytochrome c using Bcl-xL. Another way that cells can
control apoptosis is by phosphorylation of Tyr48 which would turn cytochrome c into
an anti-apoptotic switch.
Cytochrome c is known to play a role in the electron transport chain and cell apoptosis.
However, a recent study has shown that it can also act as an antioxidative enzyme in
the mitochondria. It does so by removing superoxide (O2) and hydrogen peroxide
(H2O2) from mitochondria. Therefore, not only is cytochrome c required in the mitochondria for cell respiration, but it is also needed in the mitochondria to limit the production of O2- and H2O2.
https://en.wikipedia.org/wiki/Cytochrome_c
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Cytochrome c1
Cytochrome c1 is formed in the cytosol and targeted to the mitochondrial intermem-
brane space. It is one of the constituents of complex III, which forms the third proton
bacteria and other prokaryotes. The general function of the complex is electron trans-
fer between two mobile redox carriers, ubiquinol and cytochrome c. The electron tran
fer is coupled with proton translocation across the membrane, thus generating proton
motive force in the form of an electrochemical potential difference that can drive ATP
synthesis. In its structure and functions, the cytochrome bc1 complex bears extensive
analogy to the cytochrome b6f complex of chloroplasts and cyanobacteria. Cyt c1 plays
an analogous role to cytochrome f, in spite of their different structures.
https://en.wikipedia.org/wiki/Cytochrome_C1
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Cytochrome P450
Cytochromes P450 (CYPs) belong to the superfamily of proteins containing a heme cofactor and, therefore, are hemoproteins. CYPs use a variety of small and large molecules as substrates in enzymatic reactions. They are, in general, the terminal oxidase
enzymes in electron transfer chains, broadly categorized as P450-containing systems.
The term P450 is derived from the spectrophotometric peak at the wavelength of the
absorption maximum of the enzyme (450nm) when it is in the reduced state and complexed with CO.
CYP enzymes have been identified in all domains of life - animals, plants, fungi, protists, bacteria, archaea, and even in viruses. However, the enzymes have not been
found in E. coli. Most CYPs require a protein partner to deliver one or more electrons
to reduce the iron (and eventually molecular oxygen). Based on the nature of the electron transfer proteins, CYPs can be classified into several groups:
Microsomal P450 systems in which electrons are transferred from NADPH via cytochrome P450 reductase (variously CPR, POR, or CYPOR). Cytochrome b5 (cyb5) can
also contribute reducing power to this system after being reduced by cytochrome b5 reductase (CYB5R).
Mitochondrial P450 systems, that employ adrenodoxin reductase and adrenodoxin to
transfer electrons from NADPH to P450.
Bacterial P450 systems, that employ a ferredoxin reductase and a ferredoxin to transfer electrons to P450.
CYB5R/cyb5/P450 systems in which both electrons required by the CYP come from cytochrome b5.
FMN/Fd/P450 systems originally found in Rhodococcus sp. in which a FMN-domaincontaining reductase is fused to the CYP.
P450 only systems, which do not require external reducing power. Notable ones include thromboxane synthase (CYP5), prostacyclin synthase (CYP8), and CYP74A (allene oxide synthase).
The most common reaction catalyzed by cytochromes P450 is a monooxygenase reaction, e.g., insertion of one atom of oxygen into the aliphatic position of an organic substrate (RH) while the other oxygen atom is reduced to water:
RH + O2 + NADPH + H+ ROH + H2O + NADP+
The Human Genome Project has identified 57 human genes coding for the various cytochrome P450 enzymes. Human CYPs are primarily membrane-associated proteins located either in the inner membrane of mitochondria or in the endoplasmic reticulum
of cells. CYPs metabolize thousands of endogenous and exogenous chemicals. Some
CYPs metabolize only one (or a very few) substrates, such as CYP19 (aromatase), while
others may metabolize multiple substrates. Both of these characteristics account for
their central importance in medicine. Cytochrome P450 enzymes are present in most tissues of the body, and play important roles in hormone synthesis and breakdown (including estrogen and testosterone synthesis and metabolism), cholesterol synthesis,
and vitamin D metabolism. Cytochrome P450 enzymes also function to metabolize potentially toxic compounds, including drugs and products of endogenous metabolism
such as bilirubin, principally in the liver.
https://en.wikipedia.org/wiki/Cytochrome_P450
Cytochromes
Cytochromes are iron containing hemeproteins central to which are heme groups that
are primarily responsible for the generation of ATP via electron transport. They are
found either as monomeric proteins (e.g., cytochrome c) or as subunits of larger enzymatic complexes that catalyze redox reactions.
The heme group is a highly conjugated ring system (which allows its electrons to be
very mobile) surrounding a metal ion, which readily interconverts between the oxidation states. For many cytochromes, the metal ion present is that of iron, which interconverts between Fe++ (reduced) and Fe+++ (oxidized) states (electron-transfer processes)
or between Fe++ (reduced) and Fe+++ (formal, oxidized) states (oxidative processes). Cytochromes are, thus, capable of performing oxidation and reduction. Because the cytochromes (as well as other complexes) are held within membranes in an organized way,
the redox reactions are carried out in the proper sequence for maximum efficiency.
In the process of oxidative phosphorylation, which is the principal energy-generating
process undertaken by organisms, other membrane-bound and -soluble complexes and
cofactors are involved in the chain of redox reactions, with the additional net effect
that protons (H+) are transported across the mitochondrial inner membrane. The resulting transmembrane proton gradient (protonmotive force) is used to generate ATP,
which is the universal chemical energy currency of life. ATP is consumed to drive cellular processes that require energy (such as synthesis of macromolecules, active transport of molecules across the membrane, and assembly of flagella).
https://en.wikipedia.org/wiki/Cytochrome
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Cytoglobin
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Cytokine
Cytokines are a broad and loose category of small proteins (~520 kDa) that are important in cell signaling. They are released by cells and affect the behavior of other cells.
Cytokines can also be involved in autocrine signaling. Cytokines include chemokines,
interferons, interleukins, lymphokines, and tumor necrosis factors but generally not
hormones or growth factors (despite some overlap in the terminology). Cytokines are
produced by a broad range of cells, including immune cells like macrophages, B lymphocytes, T lymphocytes and mast cells, as well as endothelial cells, fibroblasts, and
various stromal cells. A given cytokine may be produced by more than one type of cell.
Each cytokine has a matching cell-surface receptor. Subsequent cascades of intracellular signaling then alter cell functions. This may include the upregulation and/or downregulation of several genes and their transcription factors, resulting in the production
of other cytokines, an increase in the number of surface receptors for other molecules,
or the suppression of their own effect by feedback inhibition.
The effect of a particular cytokine on a given cell depends on the cytokine, its extracellular abundance, the presence and abundance of the complementary receptor on the cell
surface, and downstream signals activated by receptor binding. These last two factors
can vary by cell type. Cytokines are characterized by considerable "redundancy", in
that many cytokines appear to share similar functions.
Cytokines are often involved in several developmental processes during embryogenesis. Cytokines are crucial for fighting off infections and in other immune responses.
However, they can become dysregulated and pathological in inflammation, trauma,
and sepsis. Adverse effects of cytokines have been linked to many disease states and
conditions ranging from schizophrenia, major depression and Alzheimer's disease to
cancer. Normal tissue integrity is preserved by feedback interactions between diverse
cell types mediated by adhesion molecules and secreted cytokines. Disruption of normal feedback mechanisms in cancer, threatens tissue integrity. Over-secretion of cytokines can trigger a dangerous syndrome known as a cytokine storm. This may have
been the cause of severe adverse events during a clinical trial of TGN1412. Cytokine
storms also were the main cause of death in the 1918 "Spanish Flu" pandemic. Deaths
were weighted more heavily towards people with healthy immune systems, due to its
ability to produce stronger immune responses, likely increasing cytokine levels. Another important example of cytokine storm is seen in acute pancreatitis. Cytokines are
integral and implicated in all angles of the cascade resulting in the systemic inflammatory response syndrome and multi organ failure associated with this intra-abdominal
catastrophe.
https://en.wikipedia.org/wiki/Cytokine
Cytokinesis
Cytokinesis (from the Greek , "container" and , "motion") is the process
during cell division in which the cytoplasm of a single eukaryotic cell is divided to form
two daughter cells. It usually initiates during the late stages of mitosis, and sometimes
meiosis, splitting a mitotic cell in two, to ensure that chromosome number is maintained from one generation to the next. After cytokinesis two (daughter) cells will be
formed that are exact copies of the (parent) original cell. It is formed after cytokinesis,
each daughter cell is in the interphase portion of the cell cycle.
https://en.wikipedia.org/wiki/Cytokinesis
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Cytokinins
Cytokinins (CK) are a class of plant growth substances (phytohormones) that promote
cell division, or cytokinesis, in plant roots and shoots. They are involved primarily in
cell growth and differentiation, but also affect apical dominance, axillary bud growth,
and leaf senescence.
There are two types of cytokinins: adenine-type cytokinins represented by kinetin, zeatin, and 6-benzylaminopurine, and phenylurea-type cytokinins like diphenylurea and
thidiazuron (TDZ). Most adenine-type cytokinins are synthesized in roots. Cambium
and other actively dividing tissues also synthesize cytokinins. No phenylurea cytokinins have been found in plants. Cytokinins participate in local and long-distance signaling, with the same transport mechanism as purines and nucleosides. Typically, cytokinins are transported in the xylem.
Cytokinins act in concert with auxin, another plant growth hormone. The two are complementary, having generally opposite effects. The ratio of auxin to cytokinin plays an
important role in the effect of cytokinin on plant growth. Cytokinin alone has no effect
on parenchyma cells. When cultured with auxin but no cytokinin, they grow large but
do not divide. When cytokinin is added, the cells expand and differentiate. When cytokinin and auxin are present in equal levels, the parenchyma cells form an undifferentiated callus. More cytokinin induces growth of shoot buds, while more auxin induces
root formation.
Cytokinins are involved in many plant processes, including cell division and shoot and
root morphogenesis. They are known to regulate axillary bud growth and apical dominance. The "direct inhibition hypothesis" posits that these effects result from the cytokinin to auxin ratio. This theory states that auxin from apical buds travels down shoots
to inhibit axiliary bud growth. This promotes shoot growth, and restricts lateral branching. Cytokinin moves from the roots into the shoots, eventually signaling lateral bud
growth. Simple experiments support this theory. When the apical bud is removed, the
axillary buds are uninhibited, lateral growth increases, and plants become bushier. Applying auxin to the cut stem again inhibits lateral dominance.
https://en.wikipedia.org/wiki/Cytokinin
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Cytoplasm
The cytoplasm comprises cytosol (the gel-like substance enclosed within the cell membrane) and the organelles the cell's internal sub-structures. All of the contents of the
cells of prokaryote organisms (such as bacteria, which lack a cell nucleus) are contained within the cytoplasm. Within the cells of eukaryote organisms the contents of
the cell nucleus are separated from the cytoplasm, and are then called the nucleoplasm. The cytoplasm is about 80% water and usually colorless. It is within the cytoplasm that most cellular activities occur, such as many metabolic pathways including
glycolysis, and processes such as cell division. The concentrated inner area is called the
endoplasm and the outer layer is called the cell cortex or the ectoplasm. Movement of
calcium ions in and out of the cytoplasm is a signaling activity for metabolic processes.
https://en.wikipedia.org/wiki/Cytoplasm
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Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto
group at position 2). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.
Cytosine can be found as part of DNA, as part of RNA, or as a part of a nucleotide. As
cytidine triphosphate (CTP), it can act as a co-factor to enzymes, and can transfer a
phosphate to convert adenosine diphosphate (ADP) to adenosine triphosphate (ATP).
In DNA and RNA, cytosine is paired with guanine. However, it is inherently unstable,
and can change into uracil (spontaneous deamination). This can lead to a point mutation if not repaired by the DNA repair enzymes such as uracil glycosylase, which
cleaves a uracil in DNA.
When found third in a codon of RNA, cytosine is synonymous with uracil, as they are
interchangeable as the third base. When found as the second base in a codon, the third
is always interchangeable. For example, UCU, UCC, UCA and UCG are all serine, regardless of the third base.
Cytosine can also be methylated into 5-methylcytosine by an enzyme called DNA methyltransferase or be methylated and hydroxylated to make 5-hydroxymethylcytosine. Active enzymatic deamination of cytosine or 5-methylcytosine by the APOBEC family of
cytosine deaminases could have both beneficial and detrimental implications on various cellular processes as well as on organismal evolution. The implications of deamination on 5-hydroxymethylcytosine, on the other hand, remains less understood.
https://en.wikipedia.org/wiki/Cytosine
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Cytoskeleton
In all cells of all domains of life (archaea, bacteria, eukaryotes) a cytoskeleton is found
(notably in all eukaryotic cells, which include human, animal, fungal and plant cells).
The cytoskeleton can be referred to as a complex network of interlinking filaments and
tubules that extend throughout the cytoplasm, from the nucleus to the plasma membrane. The cytoskeletal systems of different organisms are composed of similar proteins. In eukaryotes, the cytoskeletal matrix is a dynamic structure composed of three
main proteins, which are capable of rapid growth or disassembly dependent on the
cell's requirements at a certain period of time.
However, the structure, function and dynamic behavior of the cytoskeleton can be very
different, depending on organism and cell type. Similarly, within the same cell type the
structure, dynamic behavior, and function of the cytoskeleton can change through association with other proteins and the previous history of the network.
There is a multitude of functions that the cytoskeleton can perform. Primarily, it gives
the cell shape and mechanical resistance to deformation, so that through association
with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can also actively contract, thereby deforming the cell and the cell's environment and allowing cells to migrate. Moreover, it is involved in many cell signaling pathways, in the uptake of extracellular material (endocytosis), segregates chromosomes
during cellular division, is involved in cytokinesis (the division of a mother cell into
two daughter cells), provides a scaffold to organize the contents of the cell in space and
for intracellular transport (for example, the movement of vesicles and organelles
within the cell); and can be a template for the construction of a cell wall. Furthermore,
it forms specialized structures, such as flagella, cilia, lamellipodia and podosomes.
A large-scale example of an action performed by the cytoskeleton is muscle contraction. During contraction of a muscle, within each muscle cell, myosin molecular motors collectively exert forces on parallel actin filaments. This action contracts the muscle cell, and through the synchronous process in many muscle cells, the entire muscle.
https://en.wikipedia.org/wiki/Cytoskeleton
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Cytotoxic
Cytotoxicity is the quality of being toxic to cells. Examples of toxic agents are an immune cell or some types of venom, e.g. from the puff adder (Bitis arietans) or brown
recluse spider (Loxosceles reclusa).
Treating cells with the cytotoxic compound can result in a variety of cell fates. The cells
may undergo necrosis, in which they lose membrane integrity and die rapidly as a result of cell lysis. The cells can stop actively growing and dividing (a decrease in cell viability), or the cells can activate a genetic program of controlled cell death (apoptosis).
Cells undergoing necrosis typically exhibit rapid swelling, lose membrane integrity,
shut down metabolism and release their contents into the environment. Cells that undergo rapid necrosis in vitro do not have sufficient time or energy to activate apoptotic
machinery and will not express apoptotic markers. Apoptosis is characterized by well
defined cytological and molecular events including a change in the refractive index of
the cell, cytoplasmic shrinkage, nuclear condensation and cleavage of DNA into regularly sized fragments. Cells in culture that are undergoing apoptosis eventually undergo secondary necrosis. They will shut down metabolism, lose membrane integrity
and lyse.
https://en.wikipedia.org/wiki/Cytotoxicity
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D-alanine
The amino acid L-alanine is one of the most abundant ones in proteins. The righthanded form, D-alanine occurs in the peptidoglycan bacterial cell walls and in some
peptide antibiotics.
The peptidoglycan layer in the bacterial cell wall is a crystal lattice structure formed
from linear chains of two alternating amino sugars, namely N-acetylglucosamine
(GlcNAc or NAG) and N-acetylmuramic acid (MurNAc or NAM). The alternating sugars are connected by a -(1,4)-glycosidic bond. Each MurNAc is attached to a short (4to 5-residue) amino acid chain, containing L-alanine, D-glutamic acid, mesodiaminopimelic acid, and D-alanine in the case of Escherichia coli (a Gram-negative
bacterium) or L-alanine, D-glutamine, L-lysine, and D-alanine with a 5-glycine interbridge between tetrapeptides in the case of Staphylococcus aureus (a Gram-positive
bacterium).
https://en.wikipedia.org/wiki/Alanine
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D-galactose
Galactose (galacto- + -ose, "milk sugar"), sometimes abbreviated Gal, is a monosaccharide sugar that is less sweet than glucose and fructose. It is a C-4 epimer of glucose. Galactan is a polymeric form of galactose found in hemicellulose. Galactan can be converted to galactose by hydrolysis.
Galactose is a monosaccharide. When combined with glucose (monosaccharide),
through a condensation reaction, the result is the disaccharide lactose. The hydrolysis
of lactose to glucose and galactose is catalyzed by the enzymes lactase and galactosidase. The latter is produced by the lac operon in Escherichia coli.
In nature, lactose is found primarily in milk and milk products. Consequently, various
food products made with dairy-derived ingredients, e.g. breads and cereals, can contain lactose. Galactose metabolism, which converts galactose into glucose, is carried
out by the three principal enzymes in a mechanism known as the Leloir pathway. The
enzymes are listed in the order of the metabolic pathway: galactokinase (GALK),
galactose-1-phosphate uridyltransferase (GALT), and UDP-galactose-4-epimerase
(GALE).
In the human body, glucose is changed into galactose via hexoneogenesis to enable the
mammary glands to secrete lactose. However, most lactose in breast milk is synthesized from galactose taken up from the blood, and only 356% is made from galactose
from de novo synthesis. Glycerol also contributes some to the mammary galactose production.
Depicted below are the linear form of D-galactose and four different cyclic forms of Dgalactose.
https://en.wikipedia.org/wiki/Galactose
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D-glucose
Glucose is a sugar with the molecular formula C6H12O6. The name "glucose" comes
from the Greek word , meaning "sweet wine, must". The suffix "-ose" is a chemical classifier, denoting a carbohydrate. It is also known as grape sugar. With 6 carbon
atoms, it is classed as a hexose, a sub-category of monosaccharides. D-glucose is one of
the 16 aldohexose stereoisomers. The D-isomer (D-glucose), also known as dextrose,
occurs widely in nature, but the L-isomer (L-glucose) does not. Glucose is made during
photosynthesis from water and carbon dioxide, using energy from sunlight. The reverse of the photosynthesis reaction, which releases this energy, is a very important
source of power for cellular respiration. Glucose is stored as a polymer, in plants as
starch and in animals as glycogen, for times when the organism will need it. Glucose
circulates in the blood of animals as blood sugar. Glucose can be obtained by hydrolysis of carbohydrates such as milk, cane sugar, maltose, cellulose, glycogen etc. It is however, manufactured by hydrolysis of cornstarch by steaming and diluting acid.
Glucose is the most widely used aldohexose in living organisms. One possible explanation for this is that glucose has a lower tendency than other aldohexoses to react nonspecifically with the amine groups of proteins. This reaction glycation impairs or
destroys the function of many proteins. Glucose's low rate of glycation can be attributed to it having a more stable cyclic form compared to other aldohexoses, which
means it spends less time than they do in its reactive open-chain form. The reason for
glucose having the most stable cyclic form of all the aldohexoses is that its hydroxy
groups (with the exception of the hydroxy group on the anomeric carbon of D-glucose)
are in the equatorial position. Many of the long-term complications of diabetes (e.g.,
blindness, renal failure, and peripheral neuropathy) are probably due to the glycation
of proteins or lipids. In contrast, enzyme-regulated addition of sugars to protein is
called glycosylation and is essential for the function of many proteins.
Use of glucose as an energy source in cells is by either aerobic respiration, anaerobic
respiration, or fermentation. All of these processes follow from an earlier metabolic
pathway known as glycolysis. The first step of glycolysis is the phosphorylation of glucose by a hexokinase to form glucose 6-phosphate. The main reason for the immediate
phosphorylation of glucose is to prevent its diffusion out of the cell as the charged phosphate group prevents glucose 6-phosphate from easily crossing the cell membrane. Furthermore, addition of the high-energy phosphate group activates glucose for subsequent breakdown in later steps of glycolysis. At physiological conditions this initial reaction is irreversible.
In anaerobic respiration, one glucose molecule produces a net gain of two ATP molecules (four ATP molecules are produced during glycolysis, but two are required by enzymes used during the process). In aerobic respiration, a molecule of glucose is much
more profitable in that a maximum net production of 30 or 32 ATP molecules (depending on the organism) is generated.
Shown below are the cyclic and linear forms of glucose.
https://en.wikipedia.org/wiki/Glucose
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D-Glutamic Acid
Glutamic acid (abbreviated as Glu or E; encoded by the codons GAA or GAG) is an amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain carboxylic acid, classifying it as a polar negatively charged (at physiological pH), aliphatic amino acid. It is non-essential in humans, meaning the body can
synthesize it.
Glutamate is a key compound in cellular metabolism. In humans, dietary proteins are
broken down by digestion into amino acids, which serve as metabolic fuel for other
functional roles in the body. A key process in amino acid degradation is transamination, in which the amino group of an amino acid is transferred to an -ketoacid, typically catalyzed by a transaminase. The reaction can be generalized as such:
R1-amino acid + R2--ketoacid R1--ketoacid + R2-amino acid
A very common -keto acid is -ketoglutarate, an intermediate in the citric acid cycle.
Transamination of -ketoglutarate gives glutamate. The resulting -ketoacid product
is often a useful one as well, which can contribute as fuel or as a substrate for further
metabolism processes. Examples are as follows:
Alanine + -ketoglutarate Pyruvate + Glutamate
Aspartate + -ketoglutarate Oxaloacetate + Glutamate
Both pyruvate and oxaloacetate are key components of cellular metabolism, contributing as substrates or intermediates in fundamental processes such as glycolysis, gluconeogenesis, and the citric acid cycle.
Glutamate also plays an important role in the body's disposal of excess or waste nitrogen. Glutamate undergoes deamination, an oxidative reaction catalyzed by glutamate
dehydrogenase, as follows:
Glutamate + H2O + NADP+ -ketoglutarate + NADPH + NH3 + H+
Ammonia (as ammonium) is then excreted predominantly as urea, synthesized in the
liver. Transamination can thus be linked to deamination, effectively allowing nitrogen
from the amine groups of amino acids to be removed, via glutamate as an intermediate, and finally excreted from the body in the form of urea.
Glutamate is also a neurotransmitter, which makes it one of the most abundant molecules in the brain. Malignant brain tumors known as glioma or glioblastoma exploit
this phenomenon by using glutamate as an energy source, especially when these mutations become more dependent on glutamate due to mutations in the gene IDH1.
https://en.wikipedia.org/wiki/Glutamic_acid
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D-serine
Serine (abbreviated as Ser or S) encoded by the codons UCU, UCC, UCA, UCG, AGU
and AGC is an -amino acid that is used in the biosynthesis of proteins. It contains an
-amino group (which is in the protonated NH3+ form under biological conditions), a
carboxyl group (which is in the deprotonated COO form under biological conditions), and a side chain hydroxyl group, classifying it as a polar amino acid. It is nonessential in humans, meaning the body can synthesize it.
D-Serine, synthesized in the brain by serine racemase from L-serine (its enantiomer),
serves as a neuromodulator by coactivating NMDA receptors, making them able to
open if they then also bind glutamate. D-serine is a potent agonist at the glycine site of
the NMDA-type glutamate receptor (NMDAR). For the receptor to open, glutamate
and either glycine or D-serine must bind to it. In fact, D-serine is a more potent agonist
at the glycine site on the NMDAR than glycine itself. D-serine was only thought to exist
in bacteria until relatively recently. It was the second D amino acid discovered to naturally exist in humans, present as a signaling molecule in the brain, soon after the discovery of D-aspartate. Had D amino acids been discovered in humans sooner, the
glycine site on the NMDA receptor might instead be named the D-serine site. Apart
from central nervous system, D-serine plays a signaling role in peripheral tissues and
organs such as cartilage, kidney and corpus cavernosum.
https://en.wikipedia.org/wiki/Serine
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dADP
Deoxyadenosine diphosphate (dADP) is a nucleoside diphosphate. It is related to
common nucleic acid ATP, or adenosine triphosphate, with the -OH (hydroxyl) gr
on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of th
name), and with one fewer phosphoryl group than ATP. Deoxyadenosine diphosp
is abbreviated dADP.
https://en.wikipedia.org/wiki/Deoxyadenosine_diphosphate
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DAG
A diglyceride, or diacylglycerol (DAG), is a glyceride consisting of two fatty acid chains
covalently bonded to a glycerol molecule through ester linkages. One example, shown
on the right, is 1-palmitoyl-2-oleoyl-glycerol, which contains side-chains derived from
palmitic acid and oleic acid. Diacylglycerols can also have many other combinations of
fatty acids attached at either the C-1 and C-2 positions or the C-1 and C-3 positions. 1,2
disubstituted glycerols are always chiral, 1,3 disubstituted glycerols are chiral if the substituents are different from each other.
In biochemical signaling, diacylglycerol functions as a second messenger signaling
lipid, and is a product of the hydrolysis of the phospholipid phosphatidylinositol 4,5bisphosphate (PIP2) by the enzyme phospholipase C (PLC) (a membrane-bound enzyme) that, through the same reaction, produces inositol trisphosphate (IP3). Although
inositol trisphosphate diffuses into the cytosol, diacylglycerol remains within the
plasma membrane, due to its hydrophobic properties. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, whereas DAG is a physiological activator of protein kinase C (PKC). The production of DAG in the membrane facilitates
translocation of PKC from the cytosol to the plasma membrane.
In addition to activating PKC, diacylglycerol has a number of other functions in the
cell:
a source for prostaglandins
a precursor of the endocannabinoid 2-arachidonoylglycerol
an activator of a subfamily of transient receptor potential canonical (TRPC) cation
channels, TRPC3/6/7.
https://en.wikipedia.org/wiki/Diglyceride
DAM Methylase
DAM methylase, an abbreviation for deoxyadenosine methylase, is an enzyme that
adds a methyl group to the adenine of the sequence 5'-GATC-3' in newly synthesized
DNA. Immediately after DNA synthesis, the daughter strand remains unmethylated
a short time.
insertion or deletion during DNA synthesis, the cell will repair the DNA by a pathway
called mismatch repair. However, the cell must be able to differentiate between the
template strand and the newly synthesized strand. In bacteria, DNA strands are meth
lated by Dam methylase, and therefore, immediately after replication, the DNA will b
hemimethylated. A repair enzyme, MutS, binds to mismatches in DNA and recruits
MutL, which subsequently activates the endonuclease MutH. MutH binds hemimeth
lated GATC sites and when activated will selectively cleave the unmethylated daughte
strand, allowing helicase and exonucleases to excise the nascent strand in the region
surrounding the mismatch. The strand is then re-synthesized by DNA polymerase III
https://en.wikipedia.org/wiki/Dam_methylase
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Dark Cycle
The so-called dark cycle of photosynthesis (also known as the Calvin Cycle) is better
called the light-independent cycle, because it is not require light, but actually occurs in
the light. The Calvin cycle, reductive pentose phosphate cycle or C3 cycle is a series of
biochemical redox reactions that take place in the stroma of chloroplast in photosynthetic organisms. It is also known as the light-independent reactions.
Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport
molecules ATP and NADPH. The light-independent Calvin cycle uses the energy from
short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals that feed on it).
This set of reactions is also called carbon fixation. The key enzyme of the cycle is called
RuBisCO. In the following biochemical equations, the chemical species (phosphates
and carboxylic acids) exist in equilibria among their various ionized states as governed
by the pH.
The enzymes in the Calvin cycle are functionally equivalent to most enzymes used in
other metabolic pathways such as gluconeogenesis and the pentose phosphate pathway, but they are to be found in the chloroplast stroma instead of the cell cytosol, separating the reactions. They are activated in the light (which is why the name "dark reaction" is misleading), and also by products of the light-dependent reaction. These regulatory functions prevent the Calvin cycle from being respired to carbon dioxide. Energy
(in the form of ATP) would be wasted in carrying out these reactions that have no net
productivity.
The sum of reactions in the Calvin cycle is the following:
3 CO2 + 6 NADPH + 5 H2O + 9 ATP Glyceraldehyde-3-phosphate + 2 H+ + 6 NADP+
+ 9 ADP + 8 Pi
Hexose (six-carbon) sugars are not a product of the Calvin cycle. Although many texts
list a product of photosynthesis as C6H12O6, this is mainly a convenience to counter the
equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin cycle are three-carbon sugar phosphate molecules, or
"triose phosphates," namely, glyceraldehyde-3-phosphate.
https://en.wikipedia.org/wiki/Light-independent_reactions#Calvin_Cycle
dATP
Deoxyadenosine triphosphate (dATP) is a nucleoside triphosphate used in cells for
DNA synthesis (or replication), as a substrate of DNA polymerase. It is also an allosteric inhibitor of the enzyme ribonucleotide reductase.
https://en.wikipedia.org/wiki/Deoxyadenosine_triphosphate
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dCDP
Deoxycytidine diphosphate (dCDP) is a nucleoside diphosphate. It is related to the
common nucleic acid CTP, or cytidine triphosphate, with the -OH (hydroxyl) group on
the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name),
and with one fewer phosphoryl group than CTP. 2'-deoxycytidine diphosphate is abbreviated as dCDP. dCDP is a product of action of the enzyme ribonucleotide reductase,
which makes it from CDP.
https://en.wikipedia.org/wiki/Deoxycytidine_diphosphate
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dCMP
dylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucle
tide, and one of the four monomers that make up DNA. In a DNA double helix, it w
base pair with deoxyguanosine monophosphate.
https://en.wikipedia.org/wiki/Deoxycytidine_monophosphate
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dCTP
Deoxycytidine triphosphate (dCTP) is a nucleoside triphosphate that contains the pyrimidine base cytosine. The triphosphate group contains high-energy phosphoanhydride bonds, which liberate energy when hydrolized.
DNA polymerase enzymes use this energy to incorporate deoxycytidine into a newly
synthesized strand of DNA. A chemical equation can be written that represents the
process:
(DNA)n + dCTP (DNA)n-C + PPi
That is, dCTP has the PPi (pyrophosphate) cleaved off and the dCMP is incorporated
into the DNA strand at the 3' end. Subsequent hydrolysis of the PPi drives the equilibrium of the reaction toward the right side, i.e. incorporation of the deoxyribonucleotide
in the growing DNA chain.
https://en.wikipedia.org/wiki/Deoxycytidine_triphosphate
DD Transpeptidase
The bacterial peptidoglycan cell wall network is built in a multi-step process.
The enzyme catalyzing the addition of the N-acetylmuramic acid-N-acetylglucosaminedecapeptide to the network in the last step of the construction is DD-transpeptidase.
-Lactam antibiotics inhibit the formation of peptidoglycan cross-links in the bacterial
cell wall by binding of the four-membered -lactam ring of penicillin to the enzyme
DD-transpeptidase. As a consequence, DD-transpeptidase cannot catalyze formation of
these cross-links, and an imbalance between cell wall production and degradation develops, causing the cell to rapidly die.
Bacteria constantly remodel their peptidoglycan cell walls, simultaneously building
and breaking down portions of the cell wall as they grow and divide. The enzymes that
hydrolyze the peptidoglycan cross-links continue to function in the presence of penicillin, even while those that form such cross-links do not. This weakens the cell wall of
the bacterium, and osmotic pressure becomes increasingly uncompensatedeventually causing cell death (cytolysis). In addition, the build-up of peptidoglycan precursors
triggers the activation of bacterial cell wall hydrolases and autolysins, which further digest the cell wall's peptidoglycans. The small size of the penicillins increases their potency, by allowing them to penetrate the entire depth of the cell wall. This is in contrast
to the glycopeptide antibiotics vancomycin and teicoplanin, which are both much
larger than the penicillins.
https://en.wikipedia.org/wiki/Penicillin
Index
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De novo pathways
De novo is a Latin phrase, literally translating to "from the new," but implyi
"from scratch," or "from the beginning." De novo synthesis refers to the syn
to recycling after partial degradation. For example, nucleotides are not need
diet as they can be constructed from small precursor molecules such as form
partate. Methionine, on the other hand, is needed in the diet because while
Index
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Deaminate
Deamination is the removal of an amine group from a molecule. Enzymes that catalyze
this reaction are called deaminases.
Deamination is the removal of an amine group from a molecule. Enzymes that catalyze
this reaction are called deaminases. In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination
is the process by which amino acids are broken down if there is an excess of protein intake. The amino group is removed from the amino acid and converted to ammonia.
The rest of the amino acid is made up of mostly carbon and hydrogen, and is recycled
or oxidized for energy. Ammonia is toxic to the human system, and enzymes convert it
to urea or uric acid by addition of carbon dioxide molecules (which is not considered a
deamination process) in the urea cycle, which also takes place in the liver. Urea and
uric acid can safely diffuse into the blood and then be excreted in urine.
Spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing
ammonia in the process. This can occur in vitro through the use of bisulfite, which converts cytosine, but not 5-methylcytosine. This property has allowed researchers to sequence methylated DNA to distinguish non-methylated cytosine (shown up as uracil)
and methylated cytosine (unaltered).
In DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. The resulting abasic site is then recognized by enzymes (AP endonucleases) that break a phosphodiester bond in the DNA, permitting the repair of
the resulting lesion by replacement with another cytosine. A DNA Polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5'-->3' exonuclease activity, followed by a fill-in reaction by its polymerase activity. DNA ligase
then forms a phosphodiester bond to seal the resulting nicked duplex product, which
now includes a new, correct cytosine.
Spontaneous deamination of 5-methylcytosine results in thymine and ammonia. This
is the most common single nucleotide mutation. In DNA, this reaction, if detected
prior to passage of the replication fork, can be corrected by the enzyme thymine-DNA
glycosylase, which removes the thymine base in a G/T mismatch. This leaves abasic
site that is repaired by AP endonucleases and polymerase, like with uracil-DNA glycosylase.
https://en.wikipedia.org/wiki/Deamination
Deamination
Deamination is the removal of an amine group from a molecule. Enzymes that catalyze
this reaction are called deaminases.
Deamination is the removal of an amine group from a molecule. Enzymes that catalyze
this reaction are called deaminases. In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination
is the process by which amino acids are broken down if there is an excess of protein intake. The amino group is removed from the amino acid and converted to ammonia.
The rest of the amino acid is made up of mostly carbon and hydrogen, and is recycled
or oxidized for energy. Ammonia is toxic to the human system, and enzymes convert it
to urea or uric acid by addition of carbon dioxide molecules (which is not considered a
deamination process) in the urea cycle, which also takes place in the liver. Urea and
uric acid can safely diffuse into the blood and then be excreted in urine.
Spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing
ammonia in the process. This can occur in vitro through the use of bisulfite, which converts cytosine, but not 5-methylcytosine. This property has allowed researchers to sequence methylated DNA to distinguish non-methylated cytosine (shown up as uracil)
and methylated cytosine (unaltered).
In DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. The resulting abasic site is then recognized by enzymes (AP endonucleases) that break a phosphodiester bond in the DNA, permitting the repair of
the resulting lesion by replacement with another cytosine. A DNA Polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5'-->3' exonuclease activity, followed by a fill-in reaction by its polymerase activity. DNA ligase
then forms a phosphodiester bond to seal the resulting nicked duplex product, which
now includes a new, correct cytosine.
Spontaneous deamination of 5-methylcytosine results in thymine and ammonia. This
is the most common single nucleotide mutation. In DNA, this reaction, if detected
prior to passage of the replication fork, can be corrected by the enzyme thymine-DNA
glycosylase, which removes the thymine base in a G/T mismatch. This leaves abasic
site that is repaired by AP endonucleases and polymerase, like with uracil-DNA glycosylase.
https://en.wikipedia.org/wiki/Deamination
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Debranching Enzyme
A debranching enzyme is a molecule that helps facilitate the breakdown of glycogen,
which serves as a store of glucose in the body, through glucosyltransferase and glucosidase activity. Together with phosphorylases, debranching enzymes mobilize glucose reserves from glycogen deposits in the muscles and liver. This constitutes a major source
of energy reserves in most organisms. Glycogen breakdown is highly regulated in the
body, especially in the liver, by various hormones including insulin and glucagon, to
maintain a homeostatic balance of blood-glucose levels.
When glycogen breakdown is compromised by mutations in the glycogen debranching
enzyme, metabolic diseases such as Glycogen storage disease type III can result.
Glucosyltransferase and glucosidase are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in E. coli and other bacteria, complicating nomenclature. Proteins that catalyze both functions are referred to as glycogen debranching enzymes (GDEs). When glucosyltransferase and glucosidase are catalyzed by distinct enzymes, "glycogen debranching enzyme" usually refers to the glucosidase enzyme. In some literature, an enzyme capable only of glucosidase is referred to
as a "debranching enzyme".
https://en.wikipedia.org/wiki/Glycogen_debranching_enzyme
Index
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Decanoic Acid
Decanoic acid (capric acid) is a saturated fatty acid. Its formula is CH3(CH2)8COOH.
Salts and esters of decanoic acid are called decanoates or "caprates". The term capric
acid is derived from the Latin "caper / capra" (goat) because the sweaty, unpleasant
smell of the compound is reminiscent of goats.
Decanoic acid acts as a non-competitive AMPA receptor antagonist at therapeutically
relevant concentrations, in a voltage- and subunit-dependent manner, and this is sufficient to explain its antiseizure effects. This direct inhibition of excitatory neurotransmission by decanoic acid in the brain contributes to the anticonvulsant effect of the
MCT ketogenic diet. Decanoic acid and the AMPAr antagonist drug perampanel act at
separate sites on the AMPA receptor, and so it is possible that they have a cooperative
effect at the AMPA receptor, suggesting that permapanel and the ketogenic diet could
be synergistic.
Decanoic acid may mimic the mitochondrial proliferation associated with the ketogenic diet, and that this may occur via PPAR receptor agonism and its target genes
involved in mitochondrial biogenesis.
It should however be noted that orally ingested medium chain fatty acids would be
very rapidly degraded by first-pass metabolism by being taken up in the liver via the
portal vein, and are quickly metabolized via coenzyme A intermediates through oxidation and the citric acid cycle to produce carbon dioxide, acetate and ketone bodies. It is unclear whether the ketones -hydroxybutryate and acetone have direct antiseizure activity.
https://en.wikipedia.org/wiki/Decanoic_acid
Index
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Decarboxylation
Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first
chemical step in photosynthesis, is called carboxylation, the addition of CO2 to a compound. Enzymes that catalyze decarboxylations are called decarboxylases or, the more
formal term, carboxy-lyases (EC number 4.1.1).
https://en.wikipedia.org/wiki/Decarboxylation
Index
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Defensins
tebrates. They have also been reported in plants. They are, and function as,
fense peptides. They are active against bacteria, fungi and many enveloped
veloped viruses. They consist of 18-45 amino acids including six (in vertebr
eight conserved cysteine residues. Cells of the immune system contain thes
almost all epithelial cells. Most defensins function by binding to the microb
Index
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Dehydration
chemical reaction that involves the loss of a water molecule from the reactin
droxyl group (OH) is a poor leaving group, having a Brnsted acid catalyst
helps by protonating the hydroxyl group to give the better leaving group, O
Dehydrogenation
Delta G
In thermodynamics, the change in the Gibbs free energy is a thermodynamic potential
that measures the maximum or reversible work that may be performed by a thermodynamic system at a constant temperature and pressure (isothermal, isobaric).
The Gibbs free energy (kJ in SI units) is the maximum amount of non-expansion work
that can be extracted from a thermodynamically closed system (one that can exchange
heat and work with its surroundings, but not matter); this maximum can be attained
only in a completely reversible process. When a system changes from a well-defined initial state to a well-defined final state, the Gibbs free energy change G equals the work
exchanged by the system with its surroundings, minus the work of the pressure forces,
during a reversible transformation of the system from the initial state to the final state.
The Gibbs energy (also referred to as G) is also the thermodynamic potential that is
minimized when a system reaches chemical equilibrium at constant pressure and temperature. Its derivative with respect to the reaction coordinate of the system vanishes
at the equilibrium point. As such, a reduction in G is a necessary condition for the spontaneity of processes at constant pressure and temperature.
https://en.wikipedia.org/wiki/Gibbs_free_energy
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Delta G
The change in the standard Gibbs free energy of formation of a compound (G) is the
change of Gibbs free energy that accompanies the formation of 1 mole of a substance in
its standard state from its constituent elements in their standard states (the most stable form of the element at 1 bar of pressure and the specified temperature, usually
298.15 K or 25C). In biological systems, a slightly modified G is employed. It is
known as G since it substitutes a solution of pH of 7 instead of having protons at
1M, a concentration living systems do not function at.
https://en.wikipedia.org/wiki/Standard_Gibbs_free_energy_of_formation
Index
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Delta H
nal energy, which is the energy required to create a system, and the amount o
required to make room for it by displacing its environment and establishing
and pressure.
Index
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Delta S
Delta-9-tetrahydrocannabinol
Tetrahydrocannabinol (THC, dronabinol by INN), or more precisely its main isomer
()-trans-9-tetrahydrocannabinol, is the principal psychoactive constituent (or cannabinoid) of cannabis. It can be an amber or gold colored glassy solid when cold, which
becomes viscous and sticky if warmed.
Like most pharmacologically-active secondary metabolites of plants, THC in Cannabis
is assumed to be involved in self-defense, perhaps against herbivores. THC also possesses high UV-B (280315nm) absorption properties, which, it has been speculated,
could protect the plant from harmful UV radiation exposure.
THC, along with its double bond isomers and their stereoisomers, is one of only three
cannabinoids scheduled by the UN Convention on Psychotropic Substances (the other
two are dimethylheptylpyran and parahexyl). It was listed under Schedule I in 1971,
but reclassified to Schedule II in 1991 following a recommendation from the WHO.
Based on subsequent studies, the WHO has recommended the reclassification to the
less-stringent Schedule III. Cannabis as a plant is scheduled by the Single Convention
on Narcotic Drugs (Schedule I and IV).
https://en.wikipedia.org/wiki/Tetrahydrocannabinol
Delta-aminolevulinic Acid
-Aminolevulinic acid (dALA or -ALA or 5ala or 5-aminolevulinic acid ) is the first
compound in the porphyrin synthesis pathway, the pathway that leads to heme in mammals and chlorophyll in plants.
In plants, production of -ALA is the step on which the speed of synthesis of chlorophyll is regulated. Plants that are fed by external -ALA accumulate toxic amounts of
chlorophyll precursor, protochlorophyllide, indicating that the synthesis of this intermediate is not suppressed anywhere downwards in the chain of reaction. Protochlorophyllide is a strong photosensitizer in plants.
https://en.wikipedia.org/wiki/Aminolevulinic_acid
Index
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Delta-turns
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
Turns are classified according to the separation between the two end residues:
In an -turn the end residues are separated by four peptide bonds
(i --> i +/- 4).
In a -turn, by one bond
(i --> i +/- 1).
Shown below is a turn
https://en.wikipedia.org/wiki/Turn_(biochemistry)
Dementia
Dementia, also known as senility, is a broad category of brain diseases that
long term and often gradual decrease in the ability to think and remember t
son's usual mental functioning and a greater decline than one would expect
ing. These diseases also have a significant effect on a person's caregivers.
https://en.wikipedia.org/wiki/Dementia
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Denaturation
Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state,
by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or
heat. If proteins in a living cell are denatured, this results in disruption of cell activity
and possibly cell death. Denatured proteins can exhibit a wide range of characteristics,
from conformational change and loss of solubility to aggregation due to the exposure
of hydrophobic groups.
Protein folding is key to whether a globular protein or a membrane protein can do its
job correctly. It must be folded into the right shape to function. But hydrogen bonds,
which play a big part in folding, are rather weak, and it doesn't take much heat, acidity,
or other stress to break some and form others, denaturing the protein. This is one reason why tight homeostasis is physiologically necessary in many life forms.
This concept is unrelated to denatured alcohol, which is alcohol that has been mixed
with additives to make it unsuitable for human consumption.
https://en.wikipedia.org/wiki/Denaturation_(biochemistry)
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Dendritic cells
Dendritic cells (DCs) are antigen-presenting cells (also known as accessory cells) of
the mammalian immune system. Their main function is to process antigen material
and present it on the cell surface to the T cells of the immune system. They act as messengers between the innate and the adaptive immune systems.
Dendritic cells are present in those tissues that are in contact with the external environment, such as the skin (where there is a specialized dendritic cell type called the Langerhans cell) and the inner lining of the nose, lungs, stomach and intestines. They can also
be found in an immature state in the blood. Once activated, they migrate to the lymph
nodes where they interact with T cells and B cells to initiate and shape the adaptive immune response. At certain development stages they grow branched projections, the
dendrites that give the cell its name ( or dndron being Greek for "tree").
While similar in appearance, these are structures distinct from the dendrites of neurons. Immature dendritic cells are also called veiled cells, as they possess large cytoplasmic 'veils' rather than dendrites.
Below - an artists rendering of a dendritic cell.
https://en.wikipedia.org/wiki/Dendritic_cell
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Deoxyadenosine
Deoxyadenosine (symbol dA or dAdo) is a deoxyribonucleoside. It is a derivative of the
nucleoside adenosine, differing from the latter by the replacement of a hydroxyl group
(-OH) by hydrogen (-H) at the 2' position of its ribose sugar moiety. Deoxyadenosine is
the DNA nucleoside A, which pairs with deoxythymidine (T) in double-stranded DNA.
In absence of adenosine deaminase (ADA) it accumulates in T lymphocytes and kills
these cells resulting in a genetic disorder known as adenosine deaminase severe combined immunodeficiency disease (ADA-SCID).
https://en.wikipedia.org/wiki/Deoxyadenosine
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Deoxycholic Acid
Deoxycholic acid (conjugate base deoxycholate), also known as cholanoic acid and 3,
12-dihydroxy-5-cholan-24-oic acid, is a bile acid. Deoxycholic acid is one of the secondary bile acids, which are metabolic byproducts of intestinal bacteria. The two primary bile acids secreted by the liver are cholic acid and chenodeoxycholic acid. Bacteria metabolize chenodeoxycholic acid into the secondary bile acid lithocholic acid, and
they metabolize cholic acid into deoxycholic acid. There are additional secondary bile
acids, such as ursodeoxycholic acid. Deoxycholic acid is soluble in alcohol and acetic
acid. When pure, it comes in a white to off-white crystalline powder form.
A number of factors, including diet, obesity, and exercise, affect the level of deoxycholate in the human colon. When humans were switched from their usual diet to a meat,
egg and cheese based diet for five days, deoxycholate in their feces increased by factors
of 2 to 10 fold. Rats, fed diets with either 30% beef tallow (high fat) or 5% beef tallow
(low fat) had almost 2-fold more deoxycholate in their feces on the high fat compared
to the low fat diet. In this study, adding the further dietary elements of curcumin or caffeic acid to the rats' high fat (30% beef tallow) diet reduced the deoxycholate in their
feces to levels comparable to levels seen in the rats on a low fat diet. Curcumin is a component of the spice turmeric, and caffeic acid is a component high in some fruits and
spices. Caffeic acid is also a digestive break-down product of chlorogenic acid, high in
coffee and some fruits and vegetables.
https://en.wikipedia.org/wiki/Deoxycholic_acid
Deoxycytidine
similar to the ribonucleoside cytidine, but with one hydroxyl group removed fr
https://en.wikipedia.org/wiki/Deoxycytidine
Index
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Deoxyguanosine
gen to the C1 carbon of deoxyribose. It is similar to guanosine, but with one hydro
group removed from the 2' position of the ribose sugar (making it deoxyribose). I
https://en.wikipedia.org/wiki/Deoxyguanosine
Deoxynucleotides
bonded to the 1' carbon of the deoxyribose, which is distinguished from ribo
presence of a proton on the 2' carbon rather than an -OH group. The phosp
DNA, the phosphate group from one nucleotide will bond to the 3' carbon o
are always added to the 3' carbon of the last nucleotide, so synthesis always
from 5' to 3'.
https://en.wikipedia.org/wiki/Deoxyribonucleotide
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Deoxyribonucleoside Diphosphates
phosphates are substrates for the enzyme NDPK in the synthesis of deoxyri
side triphosphates.
Deoxyribonucleoside Triphosphates
dUTP is rapidly degraded to dUMP by the enzyme dUMPase. All of the deo
cleoside triphosphates are substrates for DNA polymerases and are thus the
blocks of DNA.
Deoxyribonucleosides
Deoxyribonucleotides
A deoxyribonucleotide is the monomer, or single unit, of DNA, or deoxyribonucleic
acid. Each deoxyribonucleotide comprises three parts: a nitrogenous base, a deoxyribose sugar, and one phosphate group. The nitrogenous base is always bonded to the 1'
carbon of the deoxyribose, which is distinguished from ribose by the presence of a proton on the 2' carbon rather than an -OH group. The phosphate groups bind to the 5' carbon of the sugar.
When deoxyribonucleotides polymerize to form DNA, the phosphate group from one
nucleotide will bond to the 3' carbon on another nucleotide, forming a phosphodiester
bond via dehydration synthesis. New nucleotides are always added to the 3' carbon of
the last nucleotide, so synthesis always proceeds from 5' to 3'.
https://en.wikipedia.org/wiki/Deoxyribonucleotide
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Deoxyribose
Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H(C=O)(CH2)(CHOH)3H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom. Since the pentose
sugars arabinose and ribose only differ by the stereochemistry at C2, 2-deoxyribose
and 2-deoxyarabinose are equivalent, although the latter term is rarely used because
ribose, not arabinose, is the precursor to deoxyribose.
https://en.wikipedia.org/wiki/Deoxyribose
Index
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Deoxyribose-5-phosphate
https://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase
Index
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Deoxyuridine
to uridine, but without the 2'-hydroxyl group. Idoxuridine and Trifluridine are va
part of DNA replication, but they possess side groups on the uracil component (a
dine and a CF3 group, respectively), that prevent base pairing.
https://en.wikipedia.org/wiki/Deoxyuridine
Dephosphorylation
Dephosphorylation is the removal of a phosphate (PO43) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP and inorganic phosphate.
Dephosphorylation employs a type of hydrolytic enzyme, or hydrolase, which cleave ester bonds. The prominent hydrolase subclass used in dephosphorylation is phosphatase. Phosphatase removes phosphate groups by hydrolyzing phosphoric acid
monoesters into a phosphate ion and a molecule with a free hydroxyl (-OH) group.
The reversible phosphorylation-dephosphorylation reaction occurs in every physiological process, making proper function of protein phosphatases necessary for organism
viability. Because protein dephosphorylation is a key process involved in cell signaling,
protein phosphatases are implicated in conditions such as cardiac disease, diabetes,
and Alzheimer's disease.
https://en.wikipedia.org/wiki/Dephosphorylation
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Depolarization
Depolarization, in biology, refers to a sudden change within a cell, during which the
cell undergoes a dramatic electrical change. Most cells, especially those that compose
the tissues of highly organized animals, typically maintain an internal environment
that is negatively charged compared to the cell's surrounding environment. This difference in charge is called the cell's membrane potential. In the process of depolarization,
the negative internal charge of the cell becomes positive for a very brief time. This shift
from a negative to a positive internal cellular environment allows for the transmission
of electrical impulses both within a cell and, in certain instances, between cells. This
communicative function of depolarization is essential to the function of many cells,
communication between cells, and the overall function of an organism.
The process of depolarization is entirely dependent upon the intrinsic electrical nature
of most cells. When a cell is at rest, the cell maintains what is known as a resting potential. The resting potential generated by nearly all cells results in the interior of the cell
having a negative charge compared to the exterior of the cell. To maintain this electrical imbalance, microscopic positively and negatively charged particles called ions are
transported across the cell's plasma membrane. The transport of the ions across the
plasma membrane is accomplished through several different types of transmembrane
proteins embedded in the cell's plasma membrane that function as pathways for ions
both into and out of the cell, such as ion channels, sodium potassium pumps, and voltage gated ion channels.
https://en.wikipedia.org/wiki/Depolarization
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Dermatan Sulfate
https://en.wikipedia.org/wiki/Dermatan_sulfate
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Desaturase
A fatty acid desaturase is an enzyme that removes two hydrogen atoms from a fatty
acid, creating a carbon/carbon double bond. These desaturases are classified as
- indicating that the double bond is created at a fixed position from the carboxyl
group of a fatty acid (for example, 9desaturase creates a double bond at the 9th position from the carboxyl end).
(e.g. 3desaturase) - indicating the double bond is created between the third and
fourth carbon from the methyl end of the fatty acid.
In the biosynthesis of essential fatty acids, an elongase alternates with different desaturases (for example, 6desaturase) repeatedly inserting an ethyl group, then forming a
double bond.
Four desaturases occur in humans: 9desaturase, 6desaturase, 5desaturase, and
4desaturase. 9desaturase, also known as stearoyl-CoA desaturase-1, is used to synthesize oleic acid, a monounsaturated, ubiquitous component of all cells in the human
body. 9desaturase produces oleic acid by desaturating stearic acid, a saturated fatty
acid either synthesized in the body from palmitic acid or ingested directly.
6 and 5 desaturases are required for the synthesis of highly unsaturated fatty acids
such as eicosopentaenoic and docosahexaenoic acids (synthesized from -linolenic
acid), and arachidonic acid (synthesized from linoleic acid). This is a multi-stage process requiring successive actions by elongase and desaturase enzymes. The genes coding
for 6 and 5desaturase production have been located on human chromosome 11.
https://en.wikipedia.org/wiki/Fatty_acid_desaturase
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Desaturation
of carbon atoms all linked together by single bonds. Alkanes are saturated h
double bonds or triple bonds, such as those found in alkenes or alkynes, res
They can form straight chain, branched chain, or ring arrangements. They c
functional groups, as well. It is in this sense that fatty acids are classified as
Index
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Desmosine
A desmosine cross-link is formed from three allysyl side chains plus one unaltered lysyl side chain from the same or neighboring polypeptides. Detection of desmosine in
urine, plasma or sputum samples can be a marker for elastin breakdown due to high
elastase activity related to certain diseases.
Desmosine causes a yellow color in elastin and is responsible for its rubbery properties.
https://en.wikipedia.org/wiki/Desmosine
Dexamethasone
Dexamethasone is a type of steroid medication. It is used in the treatment of rheumatic
problems, a number of skin diseases, severe allergies, asthma, chronic obstructive lung
disease, croup, brain swelling, and along with antibiotics in tuberculosis, among others. In adrenocortical insufficiency it should be used together with a medication that
has greater mineralocorticoid effects such as fludrocortisone. In preterm labor, it may
be used to improve outcomes in the baby. It may be taken by mouth, as an injection
into a muscle, or intravenously. The effects of dexamethasone are frequently seen
within a day and last for about three days.
Dexamethasone is used to treat many inflammatory and autoimmune conditions, such
as rheumatoid arthritis and bronchospasm. Idiopathic thrombocytopenic purpura, a
decrease in numbers of platelets due to an immune problem, responds to 40mg daily
for four days. It may be administered in 14-day cycles. It is unclear whether dexamethasone in this condition is significantly better than other glucocorticoids.
It is also given in small amounts before and/or after some forms of dental surgery,
such as the extraction of the wisdom teeth, an operation which often leaves the patient
with puffy, swollen cheeks.
Dexamethasone is injected into the heel when treating plantar fasciitis, sometimes in
conjunction with triamcinolone acetonide. It is useful to counteract allergic anaphylactic shock, if given in high doses.
Dexamethasone is present in certain eye drops particularly after eye surgery and as
a nasal spray (trade name Dexacort), and certain ear drops (Sofradex, when combined
with an antibiotic and an antifungal). Dexamethasone intravitreal steroid implants
(trade name Ozurdex) have been approved by the FDA to treat ocular conditions such
as diabetic macular edema, central retinal vein occlusion, and uveitis.
https://en.wikipedia.org/wiki/Dexamethasone
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dGDP
Deoxyguanosine diphosphate (dGDP) is a nucleoside diphosphate. It is related to
common nucleic acid guanosine triphosphate (GTP), with the -OH group on the 2
bon on the nucleotide's pentose removed (hence the deoxy- part of the name), and
one fewer phosphoryl group than GTP. dGDP is a product of action of ribonucleo
reductase, which uses GDP as a substrate.
https://en.wikipedia.org/wiki/Deoxyguanosine_diphosphate
Index
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dGTP
precursor used in cells for DNA synthesis. The substance is used in the poly
https://en.wikipedia.org/wiki/Deoxyguanosine_triphosphate
DHFR
Dihydrofolate reductase, or DHFR, is an enzyme that reduces dihydrofolic acid to tetrahydrofolic acid, using NADPH as electron donor, which can be converted to the kinds
of tetrahydrofolate cofactors used in 1-carbon transfer chemistry.
Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group
shuttle required for the de novo synthesis of purines, thymidylic acid, and certain
amino acids. While the functional dihydrofolate reductase gene has been mapped to
chromosome 5, multiple intronless processed pseudogenes or dihydrofolate reductaselike genes have been identified on separate chromosomes.
The reaction catalyzed by DHFR is shown below.
https://en.wikipedia.org/wiki/Dihydrofolate_reductase
Diabetes
eases in which there are high blood sugar levels over a prolonged period. Sy
high blood sugar include frequent urination, increased thirst, and increased
tions include cardiovascular disease, stroke, chronic kidney failure, foot ulc
damage to the eyes. Diabetes is due to either the pancreas not producing en
lin (type I) or the cells of the body not responding properly to the insulin pr
(type II).
https://en.wikipedia.org/wiki/Diabetes_mellitus
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Diacylglyceride Lipase
catalyzes the hydrolysis of diacylglycerol, releasing a free fatty acid and mon
erol.
Two separate genes encoding DGL enzymes have been cloned, termed DGL
and DGL (DAGLB), that share 33% sequence identity.
https://en.wikipedia.org/wiki/Diacylglycerol_lipase
Diacylglycerol
A diglyceride, or diacylglycerol (DAG), is a glyceride consisting of two fatty acid chains
covalently bonded to a glycerol molecule through ester linkages. One example, shown
on the right, is 1-palmitoyl-2-oleoyl-glycerol, which contains side-chains derived from
palmitic acid and oleic acid. Diacylglycerols can also have many other combinations of
fatty acids attached at either the C-1 and C-2 positions or the C-1 and C-3 positions. 1,2
disubstituted glycerols are always chiral, 1,3 disubstituted glycerols are chiral if the substituents are different from each other.
In biochemical signaling, diacylglycerol functions as a second messenger signaling
lipid, and is a product of the hydrolysis of the phospholipid phosphatidylinositol 4,5bisphosphate (PIP2) by the enzyme phospholipase C (PLC) (a membrane-bound enzyme) that, through the same reaction, produces inositol trisphosphate (IP3). Although
inositol trisphosphate diffuses into the cytosol, diacylglycerol remains within the
plasma membrane, due to its hydrophobic properties. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, whereas DAG is a physiological activator of protein kinase C (PKC). The production of DAG in the membrane facilitates
translocation of PKC from the cytosol to the plasma membrane.
In addition to activating PKC, diacylglycerol has a number of other functions in the
cell:
a source for prostaglandins
a precursor of the endocannabinoid 2-arachidonoylglycerol
an activator of a subfamily of transient receptor potential canonical (TRPC) cation
channels, TRPC3/6/7.
https://en.wikipedia.org/wiki/Diglyceride
Diaminopimelate Decarboxylase
ucts, L-lysine and CO2. This enzyme belongs to the family of lyases, specifically th
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Diaminopimelate Epimerase
Diaminopimelate epimerase (EC 5.1.1.7) is an enzyme that catalyzes the chemical rea
tion
LL-2,6-diaminoheptanedioate <-> Meso-diaminoheptanedioate
rase is a monomeric protein of about 30 kDa consisting of two domains which are sim
lar in structure though they share little Sequence alignment. Each domain consists o
mixed -sheets which fold into a barrel around the central helix. The active site cleft
formed from both domains and contains two conserved cysteines thought to function
as the acid and base in the catalysis. Other PLP-independent racemases such as gluta
mate racemase have been shown to share a similar structure and mechanism of catal
sis.
https://en.wikipedia.org/wiki/Diaminopimelate_epimerase
Diastereomers
Diastereomers (sometimes called diastereoisomers) are a type of a stereoisomer. Diastereomerism occurs when two or more stereoisomers of a compound have different
configurations at one or more (but not all) of the equivalent (related) stereocenters and
are not mirror images of each other. When two diastereoisomers differ from each other
at only one stereocenter they are epimers. Each stereocenter gives rise to two different
configurations and thus increases the number of stereoisomers by a factor of two.
Diastereomers differ from enantiomers in that the latter are pairs of stereoisomers that
differ in all stereocenters and are therefore mirror images of one another. Enantiomers
of a compound with more than one stereocenter are also diastereomers of the other
stereoisomers of that compound that are not their mirror image. Diastereomers have
different physical properties (unlike enantiomers) and different chemical reactivity.
Diastereoselectivity is the preference for the formation of one or more than one diastereomer over the other in an organic reaction.
If a molecule contains two asymmetric carbons, there are up to 4 possible configurations, and they cannot all be non-superimposable mirror images of each other. The possibilities continue to multiply as there are more asymmetric centers in a molecule. In
general, the number of configurational isomers of a molecule can be determined by calculating 2n, where n=the number of chiral centers in the molecule. This holds true except in cases where the molecule has meso forms.
For n = 3, there are eight stereoisomers. There are four pairs of enantiomers: R,R,R
and S,S,S; R,R,S and S,S,R; R,S,S and S,R,R; and R,S,R and S,R,S. There are four diastereomers, because each of the pairs of enantiomers is a diastereomer with respect to
the other three. For n = 4, there are sixteen stereoisomers, or eight pairs of enantiomers. The four aldopentoses and the eight aldohexoses (subsets of the five- and sixcarbon sugars) are examples of sets of compounds that differ in this way.
Pictured below are two diastereomers.
https://en.wikipedia.org/wiki/Diastereomer
Dicer
Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, is an enzyme that in humans is encoded by the DICER1 gene. Being part of the RNase III family, Dicer cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into
short double-stranded RNA fragments called small interfering RNA and microRNA, respectively. These fragments are approximately 20-25 base pairs long with a two-base
overhang on the 3' end. Dicer facilitates the activation of the RNA-induced silencing
complex (RISC), which is essential for RNA interference. RISC has a catalytic component argonaute, which is an endonuclease capable of degrading messenger RNA
(mRNA).
RNA interference is a process where the breakdown of RNA molecules into miRNA inhibits gene expression of specific host mRNA sequences. miRNA is produced within
the cell starting from primary miRNA (pri-miRNA) in the nucleus. These long sequences are cleaved into smaller precursor miRNA (pre-miRNA), which are usually 70
nucleotides with a hairpin structure. Pri-miRNA are identified by DGCR8 and cleaved
by Drosha to form the pre-miRNA. These pre-miRNA are then cleaved by Dicer to
form mature miRNA.
Small interfering RNA (siRNA) are produced and function in a similar manner to
miRNA by cleaving double-stranded RNA with Dicer into smaller fragments 21 to 23
nucleotides in length. Both miRNAs and siRNAs activate the RNA-induced silencing
complex (RISC), which finds the complementary target mRNA sequence and cleaves
the RNA using RNase. This in turn silences the particular gene by RNA interference.
siRNAs and miRNAs differ in the fact that siRNAs are typically specific to the mRNA
sequence while miRNAs arent completely complementary to the mRNA sequence.
MiRNAs can interact with targets that have similar sequences, which inhibits translation of different genes. In general, RNA interference is an essential part of normal processes within organisms such as humans, and it is an area being researched as a diagnostic and therapeutic tool for cancer targets.
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Diffusion
Diffusion is the net movement of molecules or atoms from a region of high concentration (or high chemical potential) to a region of low concentration (or low chemical potential). This is also referred to as the movement of a substance down a concentration
gradient. A gradient is the change in the value of a quantity (e.g., concentration, pressure, temperature) with the change in another variable (usually distance). For example, a change in concentration over a distance is called a concentration gradient, a
change in pressure over a distance is called a pressure gradient, and a change in temperature over a distance is a called a temperature gradient.
https://en.wikipedia.org/wiki/Diffusion
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Digitalis
A group of medicines extracted from digitalis plants are called digitalin. The use of D.
purpurea extract containing cardiac glycosides for the treatment of heart conditions
was first described in the English-speaking medical literature by William Withering, in
1785, which is considered the beginning of modern therapeutics. It is used to increase
cardiac contractility (it is a positive inotrope) and as an antiarrhythmic agent to control the heart rate, particularly in the irregular (and often fast) atrial fibrillation. Digitalis is hence often prescribed for patients in atrial fibrillation, especially if they have
been diagnosed with congestive heart failure.
Digoxin was approved for heart failure in 1998 under current regulations by the Food
and Drug Administration on the basis of prospective, randomized study and clinical trials. It was also approved for the control of ventricular response rate for patients with
atrial fibrillation. American College of Cardiology/American Heart Association guidelines recommend digoxin for symptomatic chronic heart failure for patients with reduced systolic function, preservation of systolic function, and/or rate control for atrial
fibrillation with a rapid ventricular response. Heart Failure Society of America guidelines for heart failure provide similar recommendations. Despite its relatively recent approval by the Food and Drug Administration and the guideline recommendations, the
therapeutic use of digoxin is declining in patients with heart failurelikely the result of
several factors. Safety concerns regarding a proposed link between digoxin therapy and
increased mortality in women may be contributing to the decline in therapeutic use of
digoxin.
https://en.wikipedia.org/wiki/Digoxin
Dihomo--linolenic acid
ture, it is given the name 20:3 (6). DGLA is a carboxylic acid with a 20-carb
and three cis double bonds. The first double bond is located at the sixth carbon
the end. DGLA is the elongation product of -linolenic acid (GLA - 18:3, 6
body by the elongation of GLA, by an efficient enzyme which does not appear t
https://en.wikipedia.org/wiki/Dihomo-%CE%B3-linolenic_acid
Index
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Dihydrofolate
https://en.wikipedia.org/wiki/Dihydrofolic_acid
Dihydroorotase
Carbamoyl Aspartate
3
Dihydroorotate + H2O
https://en.wikipedia.org/wiki/Dihydroorotase
Dihydroorotate
https://en.wikipedia.org/wiki/4,5-Dihydroorotic_acid
Dihydroorotate Dehydrogenase
Dihydroorotate dehydrogenase (DHODH) is an enzyme that in humans is encoded by
the DHODH gene on chromosome 16. The protein encoded by this gene catalyzes the
fourth enzymatic step, the ubiquinone-mediated oxidation of dihydroorotate to orotate, in de novo pyrimidine biosynthesis. This protein is a mitochondrial protein located on the outer surface of the inner mitochondrial membrane (IMM). Inhibitors of
this enzyme are used to treat autoimmune diseases such as rheumatoid arthritis.
In mammalian species, DHODH catalyzes the fourth step in de novo pyrimidine biosynthesis, which involves the ubiquinone-mediated oxidation of dihydroorotate to orotate and the reduction of FMN to dihydroflavin mononucleotide (FMNH2)
Human DHODH is a ubiquitous FMN flavoprotein. In bacteria (gene pyrD), it is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1), it is a cytosolic protein, whereas, in other eukaryotes, it
is found in the mitochondria. It is also the only enzyme in the pyrimidine biosynthesis
pathway located in the mitochondria rather than the cytosol.
Dihydroorotate + NAD+
4
Orotate + NADH + H+
https://en.wikipedia.org/wiki/Dihydroorotate_dehydrogenase
Dihydrotestosterone
Dihydrotestosterone (commonly abbreviated to DHT), or 5-dihydrotestosterone (5DHT), also known as 5-androstan-17-ol-3-one, is a sex steroid and androgen hormone. The enzyme 5-reductase synthesizes DHT from testosterone in the prostate,
testes, hair follicles, and adrenal glands. This enzyme reduces the 4,5 double-bond of
the testosterone. Relative to testosterone, DHT is much more potent as an agonist of
the androgen receptor.
DHT is also known as androstanolone (INN) and stanolone (BAN), and under brand
names including Anabolex, Anaprotin, Andractim, Androlone, Gelovit, Neoprol, Pesomax, and Stanaprol, is used clinically as an androgen and anabolic steroid. Unlike testosterone and some anabolic steroids, DHT cannot be aromatized, and hence, has no
risk of producing estrogenic effects such as gynecomastia.
https://en.wikipedia.org/wiki/Dihydrotestosterone
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Dihydrothymine
Dihydrothymine is an intermediate in the reductive pathway of pyrimidine
It is produced by reduction of thymine by NADPH.
https://en.wikipedia.org/wiki/Dihydrothymine
Index
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Dihydrouracil
https://en.wikipedia.org/wiki/Dihydrouracil
Dihydroxyacetone Phosphate
Dihydroxyacetone phosphate (DHAP) is an intermediate in the glycolysis metabolic
pathway, and is one of the two products of breakdown of fructose 1,6-bisphosphate,
along with glyceraldehyde 3-phosphate. It is rapidly and reversibly isomerized to glyceraldehyde 3-phosphate.
In the Calvin cycle, DHAP is one of the products of the sixfold reduction of 1,3bisphosphoglycerate by NADPH. It is also used in the synthesis of sedoheptulose 1,7bisphosphate and fructose 1,6-bisphosphate, both of which are used to reform ribulose
5-phosphate, the 'key' carbohydrate of the Calvin cycle.
DHAP is also the product of the dehydrogenation of L-glycerol-3-phosphate, which is
part of the entry of glycerol (sourced from triglycerides) into the glycolytic pathway.
Conversely, reduction of glycolysis-derived DHAP to L-glycerol-3-phosphate provides
adipose cells with the activated glycerol backbone they require to synthesize new triglycerides. Both reactions are catalyzed by the enzyme glycerol 3-phosphate dehydrogenase with NAD+/NADH as cofactor.
DHAP also has a role in the ether-lipid biosynthesis process in the protozoan parasite
Leishmania mexicana.
https://en.wikipedia.org/wiki/Dihydroxyacetone_phosphate
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https://en.wikipedia.org/wiki/Dihydroxyacetone_phosphate
Index
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Dihydroxyacid Dehydratase
Dihydroxy-acid dehydratase (EC 4.2.1.9) is an enzyme that catalyzes the chemical reaction
2,3-dihydroxy-3-methylbutanoate <-> 3-methyl-2-oxobutanoate + H2O
Hence, this enzyme has one substrate, 2,3-dihydroxy-3-methylbutanoate, and two
products, 3-methyl-2-oxobutanoate (-ketoisovaleric acid) and H2O. This enzyme participates in valine, leucine and isoleucine biosynthesis and pantothenate and coenzyme
A (CoA) biosynthesis.
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave
carbon-oxygen bonds. The systematic name of this enzyme class is 2,3-dihydroxy-3methylbutanoate hydro-lyase (3-methyl-2-oxobutanoate-forming). Other names in
common use include
acetohydroxyacid dehydratase,
,-dihydroxyacid dehydratase,
2,3-dihydroxyisovalerate dehydratase,
,-dihydroxyisovalerate dehydratase,
DHAD,
https://en.wikipedia.org/wiki/Dihydroxy-acid_dehydratase
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Dihyrouridine
Dihydrouridine (abbreviated as D, DHU, or UH2) is a pyrimidine which is the result of
adding two hydrogen atoms to a uridine, making it a fully saturated pyrimidine ring
with no remaining double bonds. D is found in tRNA and rRNA molecules as a nucleoside. The corresponding nucleobase is 5,6-dihydrouracil.
Because it is non-planar, D disturbs the stacking interactions in helices and destabilizes the RNA structure. D also stabilizes the C2-endo sugar conformation, which is
more flexible than the C3-endo conformation, and this effect is propagated to the 5neighboring residue. Thus, while pseudouridine and 2-O-methylations stabilize the local RNA structure, D does the opposite.
tRNA of organisms that grow at low temperatures (psychrophiles) have high 5,6dihydrouridine levels (40-70% more on average) which provides the necessary, local,
flexibility of the tRNA at or below the freezing point.
https://en.wikipedia.org/wiki/Dihydrouridine#/media/File:Dihydrouridine.svg
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Dimerization
In biochemistry, a dimer is a macromolecular complex formed by two, usually noncovalently bound, macromolecules such as proteins or nucleic acids. (The word dimer
has roots meaning "two parts", di- + -mer.) It is a quaternary structure of a protein. A
homodimer is formed by two identical molecules (a process called homodimerization).
A heterodimer is formed by two different macromolecules (called heterodimerization).
https://en.wikipedia.org/wiki/Protein_dimer
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Dimethylallyl Pyrophosphate
Dimethylallyl pyrophosphate (DMAPP) is an intermediate product of both mevalonic
acid (MVA) pathway and DOXP/MEP pathway. It is an isomer of isopentenyl pyrophosphate (IPP) and exists in virtually all life forms. The enzyme isopentenyl pyrophosphate isomerase catalyzes the isomerization of DMAPP from IPP. Precursor of DMAPP
in the MVA pathway is mevalonic acid, and HMBPP in the MEP/DOXP pathway.
The precursor of DMAPP in the MVA pathway is mevalonic acid, and HMBPP in the
MEP/DOXP pathway. At present, it is believed that there is crossover between the two
pathways in organisms that use both pathways to create terpenes and terpenoids, such
as in plants, and that DMAPP is the crossover product.
https://en.wikipedia.org/wiki/Dimethylallyl_pyrophosphate
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Dimethylglycine
Dimethylglycine is a derivative of the amino acid glycine with the structural
ylglycine upon the loss of one of its methyl groups. It is also a byproduct of th
lism of choline. When DMG was first discovered, it was referred to as Vitami
unlike true B vitamins, deficiency of DMG in the diet does not lead to any ill-
and it is synthesized by the human body in the citric acid cycle meaning it do
meet the definition of a vitamin.
https://en.wikipedia.org/wiki/Dimethylglycine
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Dioxygenase
Dioxygenases (EC 1.13.11) are oxidoreductase enzymes. Aerobic life, from simple
single-celled bacteria species to complex eukaryotic organisms, has evolved to depend
on the oxidizing power of dioxygen in various metabolic pathways. From energetic
adenosine triphosphate (ATP) generation to xenobiotic degradation, the use of dioxygen as a biological oxidant is widespread and varied in the exact mechanism of its use.
Enzymes employ many different schemes to use dioxygen, and this largely depends on
the substrate and reaction at hand.
In the monooxygenases, only a single atom of dioxygen is incorporated into a substrate
with the other being reduced to a water molecule. The dioxygenases catalyze the oxidation of a substrate without the reduction of one oxygen atom from dioxygen into a water molecule. However, this definition is ambiguous because it does not take into account how many substrates are involved in the reaction. The majority of dioxygenases
fully incorporate dioxygen into a single substrate, and a variety of cofactor schemes are
utilized to achieve this. For example, in the -ketoglutarate-dependent enzymes, one
atom of dioxygen is incorporated into two substrates, with one always being ketoglutarate, and this reaction is brought about by a mononuclear iron center.
https://en.wikipedia.org/wiki/Dioxygenase
Dipole
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Disaccharide
A disaccharide (also called a double sugar or biose) is the sugar formed when two
monosaccharides (simple sugars) are joined. Like monosaccharides, disaccharides are
soluble in water. Three common examples are sucrose, lactose, and maltose.
The joining of simple sugars into a double sugar happens by a condensation reaction,
which involves the elimination of a water molecule from the functional groups only.
Breaking apart a double sugar into its two simple sugars is accomplished by hydrolysis
with the help of a type of enzyme called a disaccharidase. As building the larger sugar
ejects a water molecule, breaking it down consumes a water molecule. These reactions
are vital in metabolism. Each disaccharide is broken down with the help of a corresponding disaccharidase (sucrase, lactase, and maltase).
The formation of a disaccharide molecule from two monosaccharide molecules proceeds by displacing a hydroxyl radical from one molecule and a hydrogen nucleus (a
proton) from the other, so that the now vacant bonds on the monosaccharides join the
two monomers together. The vacant bonds on the hydroxyl radical and the proton
unite in their turn, forming a molecule of water, that then goes free. Because of the removal of the water molecule from the product, the term of convenience for such a process is "dehydration reaction" (also "condensation reaction" or "dehydration synthesis"). For example, milk sugar (lactose) is a disaccharide made by condensation of one
molecule of each of the monosaccharides glucose and galactose, whereas the disaccharide sucrose in sugar cane and sugar beet, is a condensation product of glucose and
fructose. Maltose, another common disaccharide, is condensed from two glucose molecules.
The dehydration reaction that bonds monosaccharides into disaccharides (and also
bonds monosaccharides into more complex polysaccharides) forms what are called glycosidic bonds.
https://en.wikipedia.org/wiki/Disaccharide
Dissociation
such as atoms, ions or radicals. For instance, when an acid dissolves in wate
lent bond between an electronegative atom and a hydrogen atom is broken
lytic fission, which gives a proton (H+) and a negative ion. Dissociation is th
of recombination.
https://en.wikipedia.org/wiki/Dissociation_(chemistry)
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Disulfide
In chemistry and biology a disulfide refers to a functional group with the general structure RSSR. The linkage is also called an SS-bond or a disulfide bridge and is usually derived by the coupling of two thiol groups. In formal terms, the connection is a
persulfide, in analogy to its congener, peroxide (ROOR), but this terminology is
rarely used, except in reference to hydrodisulfides (RSSH or HSSH compounds).
The disulfide bone of cystine below is shown in yellow.
https://en.wikipedia.org/wiki/Disulfide
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Diterpenes
Diterpenes are a class of chemical compounds composed of two terpene units with the
molecular formula C20H32. They may also be thought of as consisting of four isoprene
units. They are biosynthesized by plants, animals and fungi via the HMG-CoA reduc-
penes form the basis for biologically important compounds such as retinol, retinal, an
phytol. Diterpenes are known to be antimicrobial and antiinflammatory.
Starting material for diterpene synthesis, geranylpyrophosphate, is shown below.
https://en.wikipedia.org/wiki/Diterpene
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Dithiothreitol
Dithiothreitol (DTT) is the common name for a small-molecule redox reagent also
known as Cleland's reagent. DTT's formula is C4H10O2S2 and the chemical structure of
one of its enantiomers in its reduced form is shown at the right. Its oxidized form is a
disulfide bonded 6-membered ring (shown below). The reagent is commonly used in
its racemic form, as both enantiomers are reactive. Its name derives from the fourcarbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol
(DTE).
DTT is a reducing agent. Once oxidized, it forms a stable six-membered ring with an
internal disulfide bond. It has a redox potential of -0.33 V at pH 7. The reduction of a
typical disulfide bond proceeds by two sequential thiol-disulfide exchange reactions
and is illustrated below. The reduction usually does not stop at the mixed-disulfide species because the second thiol of DTT has a high propensity to close the ring, forming
oxidized DTT and leaving behind a reduced disulfide bond. The reducing power of DTT
is limited to pH values above 7, since only the negatively charged thiolate form -S is
reactive (the protonated thiol form -SH is not). The pKa of the thiol groups is 9.2 and
10.1.
Reduction of a disulfide bond by DTT is shown below.
https://en.wikipedia.org/wiki/Dithiothreitol
DNA
Deoxyribonucleic acid (DNA) is a molecule that carries most of the genetic instructions
used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids; alongside proteins and
complex carbohydrates, they comprise the three major types of macromolecule that
are essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are
known as polynucleotides since they are composed of simpler units called nucleotides.
DNA stores biological information. The DNA backbone is resistant to cleavage, and
both strands of the double-stranded structure store the same biological information.
Biological information is replicated as the two strands are separated. A significant portion of DNA (more than 98% for humans) is non-coding, meaning that these sections
do not serve as patterns for protein sequences.
The two strands of DNA run in opposite directions to each other and are therefore
anti-parallel. Attached to each sugar is one of four types of nucleobases (informally,
bases). It is the sequence of these four nucleobases along the backbone that encodes
biological information. Under the genetic code, RNA strands are translated to specify
the sequence of amino acids within proteins. These RNA strands are initially created
using DNA strands as a template in a process called transcription.
Within cells, DNA is organized into long structures called chromosomes. During cell
division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals,
plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of
their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes
(bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
DNA was first isolated by Friedrich Miescher in 1869. Its molecular structure was identified by James Watson and Francis Crick in 1953, whose model-building efforts were
guided by X-ray diffraction data acquired by Rosalind Franklin. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic
theorem and the theory of elasticity. The unique material properties of DNA have
made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and
DNA-based hybrid materials.
https://en.wikipedia.org/wiki/DNA
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DNA Adducts
A DNA adduct is a segment of DNA bound to a cancer-causing chemical. This process
could be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as biomarkers of exposure and as such are themselves measured to
reflect quantitatively, for comparison, the amount of carcinogen exposure to the subject organism, for example rats or other living animals. Under experimental conditions
for study, such DNA adducts are induced by known carcinogens, of which commonly
used is DMBA (7,12-dimethylbenz(a)anthracene). For example, the term "DMBA-DNA
adduct" in a scientific journal refers to a piece of DNA that has DMBA attached to it.
The presence of such an adduct indicates prior exposure to a potential carcinogen, but
does not by itself indicate the presence of cancer in the subject animal.
When a chemical binds to DNA, the DNA becomes damaged, and proper and complete
replication cannot occur to make the normal intended cell. This could be the start of a
mutation, or mutagenesis. Without effective DNA repair, which happens naturally under normal circumstances, this can lead to carcinogenesis, the beginnings of cancer.
Chemicals that form DNA adducts include:
acetaldehyde, a significant constituent of tobacco smoke
cisplatin, which binds to DNA and causes crosslinking, leading to death of the cell
DMBA (7,12-dimethylbenz(a)anthracene)
malondialdehyde, a naturally occurring product of lipid peroxidation
DNA adducts include:
etheno-DNA adducts: 1,N(6)-etheno-2'-deoxyadenosine (epsilondA) and 3,N(4)etheno-2'-deoxycytidine (epsilondC)
https://en.wikipedia.org/wiki/DNA_adduct
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DNA Binding
DNA-binding proteins are proteins that contain DNA-binding domains and thus have
a specific or general affinity for either single or double stranded DNA.
Sequence-specific DNA-binding proteins generally interact with the major groove of BDNA, because it exposes more functional groups that identify a base pair.
DNA-binding proteins include transcription factors which modulate the process of
transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. DNA-binding proteins can incorporate such domains as the zinc finger, the
helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to
nucleic acid. There are also more unusual examples such as transcription activator like
effectors.
Below - binding of DNA by Cro protein
https://en.wikipedia.org/wiki/DNA-binding_protein
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DNA damage
DNA damage, due to environmental factors and normal metabolic processes inside the
cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. While
this constitutes only 0.000165% of the human genome's approximately 6 billion bases
(3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor
genes) can impede a cell's ability to carry out its function and appreciably increase the
likelihood of tumor formation and contribute to tumor heterogeneity.
The vast majority of DNA damage affects the primary structure of the double helix.
That is, the bases themselves are chemically modified. These modifications can in turn
disrupt the molecules' regular helical structure by introducing non-native chemical
bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins
and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance
does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable
to the effects of DNA damage.
DNA damage can be subdivided into two main types:
1
endogenous damage such as attack by reactive oxygen species produced from nor-
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DNA Damage
DNA damage, due to environmental factors and normal metabolic processes inside the
cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. While
this constitutes only 0.000165% of the human genome's approximately 6 billion bases
(3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor
genes) can impede a cell's ability to carry out its function and appreciably increase the
likelihood of tumor formation and contribute to tumor heterogeneity.
The vast majority of DNA damage affects the primary structure of the double helix.
That is, the bases themselves are chemically modified. These modifications can in turn
disrupt the molecules' regular helical structure by introducing non-native chemical
bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins
and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance
does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable
to the effects of DNA damage.
DNA damage can be subdivided into two main types:
1
endogenous damage such as attack by reactive oxygen species produced from nor-
Index
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DNA Glycosylase
DNA glycosylases are a family of enzymes involved in base excision repair, classified
under EC number EC 3.2.2. Base excision repair is the mechanism by which damaged
bases in DNA are removed and replaced. DNA glycosylases catalyze the first step of
this process. They remove the damaged nitrogenous base while leaving the sugarphosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred
to as an AP site. This is accomplished by flipping the damaged base out of the double
helix followed by cleavage of the N-glycosidic bond.
Glycosylases were first discovered in bacteria, and have since been found in all kingdoms of life. In addition to their role in base excision repair DNA glycosylase enzymes
have been implicated in the repression of gene silencing in A. thaliana, N. tabacum
and other plants by active demethylation. 5-methylcytosine residues are excised and
replaced with unmethylated cytosines allowing access to the chromatin structure of the
enzymes and proteins necessary for transcription and subsequent translation.
Uracil-DNA glycosylase (UDG) is an enzyme that reverts mutations in DNA. The most
common mutation is the deamination of cytosine to uracil. UDG repairs these mutations. UDG is crucial in DNA repair, without it these mutations may lead to cancer.
This entry represents various uracil-DNA glycosylases and related DNA glycosylases
(EC), such as uracil-DNA glycosylase, thermophilic uracil-DNA glycosylase, G:T/U
mismatch-specific DNA glycosylase (Mug), and single-strand selective monofunctional
uracil-DNA glycosylase (SMUG1).
Uracil DNA glycosylases remove uracil from DNA, which can arise either by spontaneous deamination of cytosine or by the misincorporation of dU opposite dA during DNA
replication. The prototypical member of this family is E. coli UDG, which was among
the first glycosylases discovered. Four different uracil-DNA glycosylase activities have
been identified in mammalian cells, including UNG, SMUG1, TDG, and MBD4. They
vary in substrate specificity and subcellular localization. SMUG1 prefers singlestranded DNA as substrate, but also removes U from double-stranded DNA. In addition to unmodified uracil, SMUG1 can excise 5-hydroxyuracil, 5-hydroxymethyluracil
and 5-formyluracil bearing an oxidized group at ring C5. TDG and MBD4 are strictly
specific for double-stranded DNA.
TDG can remove thymine glycol when present opposite guanine, as well as derivatives
of U with modifications at carbon 5. Current evidence suggests that, in human cells,
TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs
caused by spontaneous cytosine deamination, whereas uracil arising in DNA through
dU misincorporation is mainly dealt with by UNG. MBD4 is thought to correct T:G mismatches that arise from deamination of 5-methylcytosine to thymine in CpG sites.
MBD4 mutant mice develop normally and do not show increased cancer susceptibility
or reduced survival. But they acquire more C T mutations at CpG sequences in epithelial cells of the small intestine.
The structure of human UNG in complex with DNA revealed that, like other glycosylases, it flips the target nucleotide out of the double helix and into the active site
pocket. UDG undergoes a conformational change from an open unbound state to a
closed DNA-bound state.
https://en.wikipedia.org/wiki/DNA_glycosylase
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DNA ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that
facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair doublestrand breaks (i.e. a break in both complementary strands of DNA). Single-strand
breaks are repaired by DNA ligase using the complementary strand of the double helix
as a template, with DNA ligase creating the final phosphodiester bond to fully repair
the DNA.
DNA ligase is used in both DNA repair and DNA replication. In addition, DNA ligase
has extensive use in molecular biology laboratories for recombinant DNA experiments.
Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA.
https://en.wikipedia.org/wiki/DNA_ligase
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DNA Ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that
facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair doublestrand breaks (i.e. a break in both complementary strands of DNA). Single-strand
breaks are repaired by DNA ligase using the complementary strand of the double helix
as a template, with DNA ligase creating the final phosphodiester bond to fully repair
the DNA.
DNA ligase is used in both DNA repair and DNA replication. In addition, DNA ligase
has extensive use in molecular biology laboratories for recombinant DNA experiments.
Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA.
https://en.wikipedia.org/wiki/DNA_ligase
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DNA Methyltransferases
The DNA methyltransferase (DNA MTase) family of enzymes catalyzes the transfer of a
methyl group to DNA. DNA methylation serves a wide variety of biological functions.
All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the
methyl donor.
MTases can be divided into three different groups on the basis of the chemical reactions they catalyze:
m6A and m4C methyltransferases are found primarily in prokaryotes. m5C methyltransfereases are found in some lower eukaryotes, in most higher plants, and in animals beginning with the echinoderms. The m6A methyltransferases (N-6 adenine-specific
DNA methylase) (A-Mtase) are enzymes that specifically methylate the amino group at
the C-6 position of adenines in DNA. They are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the
hsdM gene, and in type III it is the product of the mod gene). These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host
from digesting its own genome via its restriction enzymes.
https://en.wikipedia.org/wiki/DNA_methyltransferase
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DNA Polymerase
DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and
usually work in pairs to create two identical DNA strands from a single original DNA
molecule. During this process, DNA polymerase reads the existing DNA strands to
create two new strands that match the existing ones. It catalyzes DNA-templatedirected extension of the 3'- end of a DNA strand by one nucleotide at a time.
These enzymes catalyze the following chemical reaction
Deoxynucleoside triphosphate + DNAn <+> PPi + DNAn+1
Every time a cell divides, DNA polymerases are required to help duplicate the cells
DNA, so that a copy of the original DNA molecule can be passed to each daughter cell.
In this way, genetic information is passed down from generation to generation.
Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form. This opens up or unzips the double-stranded DNA
to give two single strands of DNA that can be used as templates for replication.
https://en.wikipedia.org/wiki/DNA_polymerase
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DNA Polymerase
Eukaryotic DNA polymerases Pol (alpha), Pol (delta), and Pol (epsilon) are members of Family B Polymerases and are the main polymerases involved with nuclear
DNA replication. Pol complex (pol -DNA primase complex) consists of four
subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the small
and the large primase subunits PRIM1 and PRIM2 respectively. Once primase has created the RNA primer, Pol starts replication elongating the primer with ~20 nucleotides.
Due to its high processivity, Pol takes over the leading and lagging strand synthesis
from Pol . Pol is expressed by genes POLD1, creating the catalytic subunit, POLD2,
POLD3, and POLD4 creating the other subunits that interact with Proliferating Cell Nuclear Antigen (PCNA), which is a DNA clamp that allows Pol to possess processivity.
Pol is encoded by the POLE1, the catalytic subunit, POLE2, and POLE3 gene. It has
been reported that the function of Pol is to extend the leading strand during replication, while Pol primarily replicates the lagging strand. However, recent evidence suggested that Pol might have a role in replicating the leading of DNA as well. Pol 's Cterminus region is thought to be essential to cell vitality as well. The C-terminus region
is thought to provide a checkpoint before entering anaphase, provide stability to the
holoenzyme, and add proteins to the holoenzyme necessary for initiation of replication.
https://en.wikipedia.org/wiki/DNA_polymerase
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DNA Polymerase
Eukaryotic DNA polymerases Pol (alpha), Pol (delta), and Pol (epsilon) are members of Family B Polymerases and are the main polymerases involved with nuclear
DNA replication. Pol complex (pol -DNA primase complex) consists of four
subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the small
and the large primase subunits PRIM1 and PRIM2 respectively. Once primase has created the RNA primer, Pol starts replication elongating the primer with ~20 nucleotides.
Due to its high processivity, Pol takes over the leading and lagging strand synthesis
from Pol . Pol is expressed by genes POLD1, creating the catalytic subunit, POLD2,
POLD3, and POLD4 creating the other subunits that interact with Proliferating Cell Nuclear Antigen (PCNA), which is a DNA clamp that allows Pol to possess processivity.
Pol is encoded by the POLE1, the catalytic subunit, POLE2, and POLE3 gene. It has
been reported that the function of Pol is to extend the leading strand during replication, while Pol primarily replicates the lagging strand. However, recent evidence suggested that Pol might have a role in replicating the leading of DNA as well. Pol 's Cterminus region is thought to be essential to cell vitality as well. The C-terminus region
is thought to provide a checkpoint before entering anaphase, provide stability to the
holoenzyme, and add proteins to the holoenzyme necessary for initiation of replication.
https://en.wikipedia.org/wiki/DNA_polymerase
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DNA Polymerase
Eukaryotic DNA polymerases Pol (alpha), Pol (delta), and Pol (epsilon) are members of Family B Polymerases and are the main polymerases involved with nuclear
DNA replication. Pol complex (pol -DNA primase complex) consists of four
subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the small
and the large primase subunits PRIM1 and PRIM2 respectively. Once primase has created the RNA primer, Pol starts replication elongating the primer with ~20 nucleotides.
Due to its high processivity, Pol takes over the leading and lagging strand synthesis
from Pol . Pol is expressed by genes POLD1, creating the catalytic subunit, POLD2,
POLD3, and POLD4 creating the other subunits that interact with Proliferating Cell Nuclear Antigen (PCNA), which is a DNA clamp that allows Pol to possess processivity.
Pol is encoded by the POLE1, the catalytic subunit, POLE2, and POLE3 gene. It has
been reported that the function of Pol is to extend the leading strand during replication, while Pol primarily replicates the lagging strand. However, recent evidence suggested that Pol might have a role in replicating the leading of DNA as well. Pol 's Cterminus region is thought to be essential to cell vitality as well. The C-terminus region
is thought to provide a checkpoint before entering anaphase, provide stability to the
holoenzyme, and add proteins to the holoenzyme necessary for initiation of replication.
https://en.wikipedia.org/wiki/DNA_polymerase
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DNA Polymerase I
DNA Polymerase I (or Pol I) is an enzyme that participates in the process of DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase
(and, indeed, the first known of any kind of polymerase). It was initially characterized
in E. coli and is ubiquitous in prokaryotes. In E. coli and many other bacteria, the gene
that encodes Pol I is known as polA. The E. coli form of the enzyme is composed of 928
amino acids, and is an example of a processive enzymeit can sequentially catalyze
multiple polymerizations.
Pol I possesses four enzymatic activities:
1 A 5'3' (forward) DNA-Dependent DNA polymerase activity, requiring a 3' primer
site and a template strand
2 A 3'5' (reverse) exonuclease activity that mediates proofreading
3 A 5'3' (forward) exonuclease activity mediating nick translation during DNA repair.
4 A 5'3' (forward) RNA-Dependent DNA polymerase activity. Pol I operates on RNA
templates with considerably lower efficiency (0.10.4%) than it does DNA templates,
and this activity is probably of only limited biological significance.
In the replication process, RNase H removes the RNA primer (created by Primase)
from the lagging strand and then Polymerase I fills in the necessary nucleotides between the Okazaki fragments (see DNA replication) in a 5'3' direction, proofreading
for mistakes as it goes. It is a template-dependent enzymeit only adds nucleotides
that correctly base pair with an existing DNA strand acting as a template. DNA ligase
then joins the various fragments together into a continuous strand of DNA.
https://en.wikipedia.org/wiki/DNA_polymerase_I
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DNA Polymerase II
DNA polymerase II (also known as DNA Pol II or Pol II) is a prokaryotic DNADependent DNA polymerase encoded by the PolB gene. DNA Polymerase II is an
89.9-kDa protein and is a member of the B family of DNA polymerases. It was originally isolated by Thomas Kornberg in 1970, and characterized over the next few years.
The in vivo functionality of Pol II is under debate, yet consensus shows that Pol II is
primarily involved as a backup enzyme in prokaryotic DNA replication. The enzyme
has 5 3 DNA synthesis capability as well as 3 5 exonuclease proofreading activity. DNA Pol II interacts with multiple binding partners common with DNA Pol III in
order to enhance its fidelity and processivity.
DNA Polymerase II is a member of the polymerase B family and supports Polymerase
III in DNA replication moving from the 3 end to the 5 end. In the case when Polymerase III stalls during a replication error, Polymerase II can interrupt and excise
the mismatched bases. Polymerase II has a much higher fidelity factor than Polymerase III, meaning that it is much less likely to create mispairings. Without Polymerase IIs proofreading step, Polymerase III would extend the mispairings and thus
create a mutation.
In addition to protecting from mutations that could be caused by Polymerase III, Polymerase II functions to protect against mutations caused by Polymerase IV. Polymerase IV is much more error prone than Polymerase II but also functions to repair
mismatched base pairings starting from the 3 end. Polymerase II protects the 3 end
from Polymerase IV and blocks it from acting. This protection will prevent the formation of mutations while the Polymerase II is functioning normally. If the Polymerase II
is knocked out by a mutation or disabled by other factors, Polymerase IV will take its
place to fix the mispaired bases.
https://en.wikipedia.org/wiki/DNA_polymerase_II
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DNA Polymerase IV
Y polymerase expressed by the dinB gene that is switched on via SOS induc
tion is increased tenfold and one of the functions during this time is to inter
lows time to repair DNA lesions via the appropriate repair pathway. Anothe
aged DNA. Cells lacking dinB gene have a higher rate of mutagenesis caused
damaging agents.
https://en.wikipedia.org/wiki/DNA_polymerase_IV
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DNA Polymerase V
DNA Polymerase V (Pol V) is a polymerase enzyme involved in DNA repair mechanisms in the bacteria Escherichia coli. It is composed of a UmuD homodimer and a
UmuC monomer, forming the UmuD2C protein complex. It is part of the Y-family of
DNA Polymerases, which are capable of performing DNA translesion synthesis (TLS).
Translesion polymerases bypass DNA damage lesions during DNA replication, if a lesion is not repaired or bypassed the replication fork can stall and lead to cell death.
However, Y polymerases have low sequence fidelity during replication (prone to add
wrong nucleotides). When the UmuC and UmuD proteins were initially discovered in
E. coli, they were thought to be agents that inhibit faithful DNA replication and caused
DNA synthesis to have high mutation rates after exposure to UV-light. The polymerase
function of Pol V was not discovered until the late 1990s when UmuC was successfully
extracted, consequent experiments unequivocally proved UmuD2C is a polymerase.
This finding lead to the detection of many Pol V orthologs and the discovery of the Yfamily of polymerases.
Pol V functions as a TLS polymerase in E. coli as part of the SOS response to DNA damage. When DNA is damaged regular DNA synthesis polymerases are unable to add
dNTPs onto the newly synthesized strand. DNA Polymerase III (Pol III) is the regular
DNA polymerase in E. coli. As Pol III stalls unable to add nucleotides to the nascent
DNA strand, the cell becomes at risk of having the replication fork collapse and apoptosis to take place. Pol V TLS function depends on association with other elements of the
SOS response, most importantly Pol V translesion activity is tightly dependent on the
formation of RecA nucleoprotein filaments. Pol V can use TLS on lesions that block replication or miscoding lesions, which modify bases and lead to wrong base pairing. However, it is unable to translate through 5 3 backbone nick errors. Pol V also lacks exonuclease activity, thus rendering unable to proofread synthesis causing it to be error
prone.
https://en.wikipedia.org/wiki/DNA_polymerase_V
DNA Repair
DNA repair is a collection of processes by which a cell identifies and corrects damage
to the DNA molecules that encode its genome. In human cells, both normal metabolic
activities and environmental factors such as UV light and radiation can cause DNA
damage, resulting in as many as 1 million individual molecular lesions per cell per day.
Many of these lesions cause structural damage to the DNA molecule and can alter or
eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other
lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair
process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA
damage may occur, including double-strand breaks and DNA crosslinkages (interstrand crosslinks or ICLs).
The rate of DNA repair is dependent on many factors, including the cell type, the age of
the cell, and the extracellular environment. A cell that has accumulated a large amount
of DNA damage, or one that no longer effectively repairs damage incurred to its DNA,
can enter one of three possible states:
1 an irreversible state of dormancy, known as senescence
2 cell suicide, also known as apoptosis or programmed cell death
3 unregulated cell division, which can lead to the formation of a tumor that is cancerous
When only one of the two strands of a double helix has a defect, the other strand can
be used as a template to guide the correction of the damaged strand. In order to repair
damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand.
1 Base excision repair (BER) repairs damage to a single nitrogenous base by deploying
enzymes called glycosylases. These enzymes remove a single nitrogenous base to create
an apurinic or apyrimidinic site (AP site). Enzymes called AP endonucleases nick the
damaged DNA backbone at the AP site. DNA polymerase then removes the damaged
region using its 5 to 3 exonuclease activity and correctly synthesizes the new strand
using the complementary strand as a template.
2 Nucleotide excision repair (NER) repairs damaged DNA which commonly consists of
bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light.
Damaged regions are removed in 12-24 nucleotide-long strands in a three-step process
which consists of recognition of damage, excision of damaged DNA both upstream and
downstream of damage by endonucleases, and resynthesis of removed DNA region.
NER is a highly evolutionarily conserved repair mechanism and is used in nearly all
eukaryotic and prokaryotic cells. In prokaryotes, NER is mediated by Uvr proteins. In
eukaryotes, many more proteins are involved, although the general strategy is the
same.
3 Mismatch repair systems are present in essentially all cells to correct errors that are
not corrected by proofreading. These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli, the proteins involved are
the Mut class proteins. This is followed by removal of damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase.
https://en.wikipedia.org/wiki/DNA_repair
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DNA Replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living
organisms and is the basis for biological inheritance. DNA is made up of a double helix
of two strands, and each strand of the original DNA molecule serves as a template for
the production of the complementary strand, a process referred to as semiconservative
replication. Cellular proofreading and error-checking mechanisms ensure near perfect
fidelity for DNA replication.
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DNA Synthesis
DNA synthesis is the natural or artificial creation of deoxyribonucleic acid (DNA) molecules. The term DNA synthesis can refer to any of the following in various contexts:
DNA replication - DNA biosynthesis (in vivo DNA amplification)
Polymerase chain reaction - enzymatic DNA synthesis (in vitro DNA amplification)
Gene synthesis - physically creating artificial gene sequences
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DNA-protein Complexes
Biomolecular complexes, also called macromolecular complexes or biomacromolecular
complexes, refer to any biological complexes made of more than one molecule of pro-
tein, RNA, DNA, lipids, or carbohydrates. The interactions between these biomolecules
are non-covalent.
Examples:
Protein complexes: proteasome, DNA polymerase III holoenzyme, RNA polymerase II
holoenzyme, symmetric viral capsids, complex of GroEL and GroES, photosystem I,
ATP synthase
RNA-protein complexes: ribosome, spliceosome, vault, SnRNP. Such complexes in cell
nucleus are called ribonucleoproteins (RNPs).
DNA-protein complexes: nucleosome
Protein-lipid complexes: lipoproteins
https://en.wikipedia.org/wiki/Biomolecular_complex
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dNTPs
The dNTPs are the building blocks for DNA (they lose two of the phosphate
the process of incorporation).
https://en.wikipedia.org/wiki/Nucleoside_triphosphate
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Dolichol
Dolichols play a role in the co-translational modification of proteins known as Nglycosylation in the form of dolichol phosphate. Dolichols function as a membrane anchor for the formation of the oligosaccharide Glc3-Man9-GlcNAc2 (where Glc is glucose, Man is mannose, and GlcNAc is N-acetylglucosamine). This oligosaccharide is
transferred from the dolichol donor onto certain asparagine residues (onto a specific
sequence that is "Asn-X-Ser/Thr") of newly forming polypeptide chains. Dolichol is
also involved in transfer of the monosaccharides to the forming Glc3-Man9-GlcNAc2Dolichol carrier.
In addition, dolichols can be adducted to proteins as a posttranslational modification,
a process in which branched carbohydrate trees are formed on a dolichol moiety and
then transferred to an assembly of proteins to form a large glycoprotein in the rough
endoplasmic reticulum.
Dolichols are the major lipid component (14% by mass) of human substantia nigra
(SN) neuromelanin. Dolichol phosphate was discovered at the University of Liverpool
in the 1960s, although researchers did not know its function at the time of discovery.
Dolichol has been suggested to be used as a biomarker for aging. During aging, the human brain shows a progressive increase in levels of dolichol, a reduction in levels of
ubiquinone, but relatively unchanged concentrations of cholesterol and dolichyl phosphate. In the neurodegenerative disease Alzheimer's disease, the situation is reversed,
with decreased levels of dolichol and increased levels of ubiquinone. The concentrations of dolichyl phosphate are also increased, while cholesterol remains unchanged.
This study shows that the isoprenoid changes in Alzheimer's disease differ from those
occurring during normal aging, and, therefore, this disease cannot be regarded as a result of premature aging. The increase in the sugar carrier dolichyl phosphate may reflect an increased rate of glycosylation in the diseased brain, and the increase in the endogenous anti-oxidant ubiquinone an attempt to protect the brain from oxidative
stress, for instance, induced by lipid peroxidation.
https://en.wikipedia.org/wiki/Dolichol
Dolichol Phosphate
Dolichol monophosphate is a fatty alcohol that plays a role synthesis of the
can cell wall of bacteria.
https://en.wikipedia.org/wiki/Dolichol_monophosphate
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Dolichol Pyrophosphate
https://en.wikipedia.org/wiki/Dolichol
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Donor Chromophore
Fluorescence resonance energy transfer (FRET - also called Frster resonance energy
transfer, resonance energy transfer (RET) or electronic energy transfer (EET)) is a
method for determining interactions between biomolecules. In the technique, a donor
chromophore and an acceptor chromophore are covalently attached to molecules of interest.
The acceptor chromophore is designed to accept energy through nonradiative dipoledipole coupling from the donor molecule and fluoresce at a unique wavelength
(red arrow) when it receives that energy from the donor.
Further, the wavelength of light that causes the donor to transfer energy (blue arrow)
to the acceptor has no effect on the acceptor chromophore. The only way the acceptor
can fluoresce is if it receives energy transferred from the donor. If the two are not
close enough together, the donor fluoresces and emits light corresponding to the green
or black arrow.
The experiment begins with donors and acceptors in a cell. Light of a wavelength that
excites the donor chromophore is shined on the cell. In order for the acceptor chromophore to receive the energy from the donor molecule, the acceptor must be physically
very close to it. Thus, if a protein with a donor binds with a protein with an acceptor,
then energy transfer from the donor chromophore to the acceptor fluorescence can occur and the unique fluorescence of the acceptor is detected. If the two proteins do not
interact together, then little or no fluorescence from the acceptor is detected.
https://en.wikipedia.org/wiki/Frster_resonance_energy_transfer
Dopamine
Dopamine (contracted from 3,4-dihydroxyphenethylamine) is an organic chemical of
the catecholamine and phenethylamine families that plays several important roles in
the brain and body. It is an amine synthesized by removing a carboxyl group from a
molecule of its precursor chemical L-DOPA, which is synthesized in the brain and kidneys. Dopamine is also synthesized in plants and most multicellular animals. In the
brain, dopamine functions as a neurotransmittera chemical released by neurons
(nerve cells) to send signals to other nerve cells. The brain includes several distinct dopamine pathways, one of which plays a major role in reward-motivated behavior. Most
types of reward increase the level of dopamine in the brain, and most addictive drugs
increase dopamine neuronal activity. Other brain dopamine pathways are involved in
motor control and in controlling the release of various hormones. These pathways and
cell groups form a dopamine system which is neuromodulatory.
Outside the central nervous system, dopamine functions in several parts of the peripheral nervous system as a local chemical messenger. In blood vessels, it inhibits norepinephrine release and acts as a vasodilator (at normal concentrations); in the kidneys, it
increases sodium excretion and urine output; in the pancreas, it reduces insulin production; in the digestive system, it reduces gastrointestinal motility and protects intestinal mucosa; and in the immune system, it reduces the activity of lymphocytes. With
the exception of the blood vessels, dopamine in each of these peripheral systems is synthesized locally and exerts its effects near the cells that release it.
Several important diseases of the nervous system are associated with dysfunctions of
the dopamine system, and some of the key medications used to treat them work by altering the effects of dopamine. Parkinson's disease, a degenerative condition causing
tremor and motor impairment, is caused by a loss of dopamine-secreting neurons in
an area of the midbrain called the substantia nigra. Its metabolic precursor L-DOPA
can be manufactured, and in its pure form marketed as Levodopa is the most widely
used treatment for the condition. There is evidence that schizophrenia involves altered
levels of dopamine activity, and most antipsychotic drugs used to treat this are dopamine antagonists which reduce dopamine activity. Similar dopamine antagonist drugs
are also some of the most effective anti-nausea agents. Restless legs syndrome and attention deficit hyperactivity disorder (ADHD) are associated with decreased dopamine
activity. Dopaminergic stimulants can be addictive in high doses, but some are used at
lower doses to treat ADHD. Dopamine itself is available as a manufactured medication
for intravenous injection: although it cannot reach the brain from the bloodstream, its
peripheral effects make it useful in the treatment of heart failure or shock, especially in
newborn babies.
https://en.wikipedia.org/wiki/Dopamine
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Dopaminergic Neurons
Dopaminergic means "related to dopamine" (literally, "working on dopamine"), dopamine being a common neurotransmitter. Dopaminergic substances or actions increase
dopamine-related activity in the brain. Dopaminergic brain structures facilitate
dopamine-related activity. For example, certain proteins such as the dopamine transporter (DAT), vesicular monoamine transporter 2 (VMAT2), and dopamine receptors
can be classified as dopaminergic, and neurons that synthesize or contain dopamine
and synapses with dopamine receptors in them may also be labeled as dopaminergic.
Enzymes that regulate the biosynthesis or metabolism of dopamine such as aromatic
L-amino acid decarboxylase or DOPA decarboxylase, monoamine oxidase (MAO), and
catechol O-methyl transferase (COMT) may be referred to as dopaminergic as well.
Also, any endogenous or exogenous chemical substance that acts to affect dopamine receptors or dopamine release through indirect actions (for example, on neurons that
synapse onto neurons that release dopamine or express dopamine receptors) can also
be said to have dopaminergic effects, two prominent examples being opioids, which enhance dopamine release indirectly in the reward pathways, and some substituted amphetamines, which enhance dopamine release directly by binding to and inhibiting
VMAT2.
https://en.wikipedia.org/wiki/Dopaminergic
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Double Bond
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond,
that is between two carbon atoms, can be found in alkenes. Many types of double
bonds exist between two different elements. For example, in a carbonyl group with a
carbon atom and an oxygen atom. Other common double bonds are found in azo compounds (N=N), imines (C=N) and sulfoxides (S=O). In skeletal formula the double
bond is drawn as two parallel lines (=) between the two connected atoms. Typographically, the equals sign is used for this. Double bonds were first introduced in chemical
notation by prominent Russian chemist Alexander Butlerov.
Double bonds involving carbon are stronger than single bonds and are also shorter.
The bond order is two. Double bonds are also electron-rich, which makes them reactive.
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Double Bonds
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond,
that is between two carbon atoms, can be found in alkenes. Many types of double
bonds exist between two different elements. For example, in a carbonyl group with a
carbon atom and an oxygen atom. Other common double bonds are found in azo compounds (N=N), imines (C=N) and sulfoxides (S=O). In skeletal formula the double
bond is drawn as two parallel lines (=) between the two connected atoms; typographically, the equals sign is used for this. Double bonds were first introduced in chemical
notation by prominent Russian chemist Alexander Butlerov.
Double bonds involving carbon are stronger than single bonds and are also shorter.
The bond order is two. Double bonds are also electron-rich, which makes them reactive.
https://en.wikipedia.org/wiki/Double_bond
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Double Displacement
Double displacement (also called ping-pong) is a mechanism used by some enzymes
that catalyze reactions with multiple substrates. Enzymes with a ping-pong mechanism can exist in two states, E and a chemically modified form of the enzyme E*. This
modified enzyme is known as an intermediate. In such mechanisms, substrate A binds,
changes the enzyme to E* by, for example, transferring a chemical group to the active
site, and is then released. Only after the first substrate is released can substrate B bind
and react with the modified enzyme, regenerating the unmodified E form. When a set
of v by [S] curves (fixed A, varying B) from an enzyme with a pingpong mechanism
are plotted in a LineweaverBurk plot, a set of parallel lines will be produced. This is
called a secondary plot.
Enzymes with pingpong mechanisms include some oxidoreductases such as thioredoxin peroxidase, transferases such as acylneuraminate cytidylyltransferase and serine
proteases such as trypsin and chymotrypsin. Serine proteases are a very common and
diverse family of enzymes, including digestive enzymes (trypsin, chymotrypsin, and
elastase), several enzymes of the blood clotting cascade and many others. In these serine proteases, the E* intermediate is an acyl-enzyme species formed by the attack of an
active site serine residue on a peptide bond in a protein substrate.
https://en.wikipedia.org/wiki/Enzyme_kinetics#Ping.E2.80.93pong_mechanisms
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Double helix
In molecular biology, the term double helix refers to the structure formed by do
stranded molecules of nucleic acids such as DNA. The double helical structure o
mental component in determining its tertiary structure. The term entered popu
ture with the publication in 1968 of The Double Helix: A Personal Account of th
covery of the Structure of DNA, by James Watson.
The DNA double helix polymer of nucleic acid, held together by nucleotides wh
pair together. In B-DNA, the most common double helical structure, the double
right-handed with about 1010.5 base pairs per turn. This translates into abou
nucleotides per turn. The double helix structure of DNA contains a major groov
minor groove. In B-DNA the major groove is wider than the minor groove. Give
difference in widths of the major groove and minor groove, many proteins whic
to B-DNA do so through the wider major groove.
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
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Double-reciprocal Plot
The LineweaverBurk plot (or double reciprocal plot) is a graphical representation of
the LineweaverBurk equation of enzyme kinetics, described by Hans Lineweaver and
Dean Burk in 1934.
The LineweaverBurk plot was widely used to determine important terms in enzyme
kinetics, such as Km and Vmax, before the wide availability of powerful computers and
non-linear regression software. The y-intercept of such a graph is equivalent to the inverse of Vmax. The x-intercept of the graph represents 1/Km. It also gives a quick, visual impression of the different forms of enzyme inhibition.
The double reciprocal plot distorts the error structure of the data, and it is therefore unreliable for the determination of enzyme kinetic parameters. Although it is still used
for representation of kinetic data, non-linear regression or alternative linear forms of
the MichaelisMenten equation such as the Hanes-Woolf plot or EadieHofstee plot
are generally used for the calculation of parameters.
When used for determining the type of enzyme inhibition, the LineweaverBurk plot
can distinguish competitive, non-competitive and uncompetitive inhibitors. Competitive inhibitors have the same y-intercept as uninhibited enzyme (since Vmax is unaffected by competitive inhibitors the inverse of Vmax also doesn't change) but there are
different slopes and x-intercepts between the two data sets. Non-competitive inhibition produces plots with the same x-intercept as uninhibited enzyme (Km is unaffected)
but different slopes and y-intercepts. Uncompetitive inhibition causes different intercepts on both the y- and x-axes.
https://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plot
ment. Like all core promoters, the DPE plays an important role in the initiation of gene
transcription by RNA polymerase II.
Together with the initiator motif (Inr), another core promoter element, the DPE is recognized by the transcription factor II D (TFIID) subunits TAF6 and TAF9. It has been
shown that DPE-dependent basal transcription depends highly on the Inr (and vice
versa) and on correct spacing between the two elements.
The DPE consensus sequence was originally thought to be RGWCGTG, however more
recent studies have suggested it to be the similar but more general sequence
RGWYV(T). It is located about 2833 nucleotides downstream of the transcription
start site.
It has been shown that the DPE is about as widely used as the TATA box in D. melanogaster. While a DPE was found in many promoters that do not contain a TATA box,
there are also promoters that contain both a TATA box and a DPE.
https://en.wikipedia.org/wiki/Downstream_promoter_element
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Drosha
Drosha is a Class 2 ribonuclease III enzyme that in humans is encoded by the DROSHA (formerly RNASEN) gene. Members of the ribonuclease III superfamily of
double-stranded (ds) RNA-specific endoribonucleases participate in diverse RNA maturation and decay pathways in eukaryotic and prokaryotic cells. The RNase III Drosha is
the core nuclease that executes the initiation step of microRNA (miRNA) processing in
the nucleus.
The microRNAs thus generated are short RNA molecules that regulate a wide variety
of other genes by interacting with the RNA-induced silencing complex (RISC) to induce cleavage of complementary messenger RNA (mRNA) as part of the RNA interference pathway. A microRNA molecule is synthesized as a long RNA primary transcript
known as a pri-miRNA, which is cleaved by Drosha to produce a characteristic stemloop structure of about 70 base pairs long, known as a pre-miRNA. Drosha exists as
part of a protein complex called the Microprocessor complex, which also contains the
double-stranded RNA binding protein Pasha (also called DGCR8). Pasha is essential
for Drosha activity and is capable of binding single-stranded fragments of the primiRNA that are required for proper processing.
https://en.wikipedia.org/wiki/Drosha
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dTMP
Thymidine monophosphate (TMP), also known as thymidylic acid (conjugate base
thymidylate), deoxythymidine monophosphate (dTMP), or deoxythymidylic acid (conjugate base deoxythymidylate), is a nucleotide that is used as a monomer in DNA. It is
an ester of phosphoric acid with the nucleoside thymidine. dTMP consists of a phosphate group, the pentose sugar deoxyribose, and the nucleobase thymine. Unlike the
other deoxyribonucleotides, thymidine monophosphate often does not contain the "deoxy" prefix in its name. Nevertheless, its symbol often includes a "d" ("dTMP").
https://en.wikipedia.org/wiki/Thymidine_monophosphate
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dTMP Kinase
dTMP kinase (EC 2.7.4.9) is an enzyme that catalyzes the chemical reaction
ATP + dTMP <=> ADP + dTDP
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dTTP
Deoxythymidine triphosphate (dTTP) is one of the four nucleotide triphosphates that
are used in the in vivo synthesis of DNA. Unlike the other deoxyribonucleotide triphosphates, thymidine triphosphate does not always contain the "deoxy" prefix in its name.
The corresponding ribonucleoside triphosphate is called uridine triphosphate.
https://en.wikipedia.org/wiki/Thymidine_triphosphate
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dUDP
tion of the enzyme ribonucleotide reductase. dUDP is part of the metabolic pathwa
for making thymidine nucleotides. dUDP is converted next into dUTP, then to dUM
and then into dTMP.
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dUMP
Deoxyuridine monophosphate (dUMP), also known as deoxyuridylic acid or deoxyuridylate in its conjugate acid and conjugate base forms, respectively, is a deoxynucleotide.
It is an intermediate in the metabolism of thymidine nucleotides. Thymidylate synthase acts on it and converts it to dTMP.
https://en.wikipedia.org/wiki/Deoxyuridine_monophosphate
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dUTP
tides. It is made from dUDP by action of NDPK and is acted on by dUTPase (al
Index
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dUTPase
dUTP diphosphatase (also called dUTPase) (EC 3.6.1.23) is an enzyme that catalyzes
the reaction below in thymidine metabolism
dUTP + H2O <-> dUMP + PPi
This enzyme has a dual function: on one hand, it removes dUTP from the deoxynucleotide pool, which reduces the probability of this base being incorporated into DNA by
DNA polymerases, while on the other hand, it produces the dTTP precursor dUMP.
Lack or inhibition of dUTPase action leads to harmful perturbations in the nucleotide
pool resulting in increased uracil content of DNA that activates a hyperactive futile cycle of DNA repair.
This enzyme belongs to the family of hydrolases, specifically those acting on acid anhydrides in phosphorus-containing anhydrides. The systematic name of this enzyme
class is dUTP nucleotidohydrolase. Other names in common use include deoxyuridinetriphosphatase, dUTPase, dUTP pyrophosphatase, deoxyuridine 5'-triphosphate nucleotidohydrolase, and deoxyuridine 5'-triphosphatase. This enzyme participates in pyrimidine metabolism.
https://en.wikipedia.org/wiki/DUTP_diphosphatase
Dynein
Dynein is a motor protein (also called molecular motor or motor molecule) in cells
which converts the chemical energy contained in ATP into the mechanical energy of intracellular movement. Dynein transports various cellular cargo by "walking" along cytoskeletal microtubules towards the minus-end of the microtubule, which is usually oriented towards the cell center. Thus, they are called "minus-end directed motors." This
form of transport is known as retrograde transport. In contrast, kinesins, which are motor proteins that move toward the microtubules' plus end, are called plus-end directed
motors.
Axonemal dynein causes sliding of microtubules in the axonemes of cilia and flagella
and is found only in cells that have those structures.
Cytoplasmic dynein, found in all animal cells and possibly plant cells as well, performs
functions necessary for cell survival such as organelle transport and centrosome assembly. Cytoplasmic dynein moves processively along the microtubule; that is, one or the
other of its stalks is always attached to the microtubule so that the dynein can "walk" a
considerable distance along a microtubule without detaching.
Cytoplasmic dynein helps to position the Golgi complex and other organelles in the
cell. It also helps transport cargo needed for cell function such as vesicles made by the
endoplasmic reticulum, endosomes, and lysosomes. Dynein is involved in the movement of chromosomes and positioning the mitotic spindles for cell division. Dynein carries organelles, vesicles and possibly microtubule fragments along the axons of neurons toward the cell body in a process called retrograde axoplasmic transport.
https://en.wikipedia.org/wiki/Dynein
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E-site
The E-site is the third and final binding site for t-RNA in the ribosome duri
synthesis. The "E" stands for exit, and is accompanied by the P-site (for pep
which is the second binding site, and the A-site (aminoacyl), which is the fir
site.
https://en.wikipedia.org/wiki/E-site
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E1
E1 is one of three subunits of the pyruvate dehydrogenase complex. It catalyzes the decarboxylation of pyruvate within the enzyme complex and transfer of the two carbon
activated acetaldehyde to thiamine pyrophosphate (TPP).
The overall reaction to convert pyruvate to acetyl-AoA involves three steps, each occurring on one of the enzymes subunits. The steps, sequentially occurring on subunits E1,
E2, and E3, are 1) decarboxylation of pyruvate; 2) oxidation of the decarboxylated product (with transfer of the two carbon unit to CoASH to make acetyl-CoA); and 3) transfer of electrons to ultimately form NADH.
Phosphorylation of E1 by pyruvate dehydrogenase kinase (PDK) inactivates E1 and subsequently the entire complex. PDK is inhibited by dichloroacetic acid and pyruvate, resulting in a higher quantity of active, unphosphorylated PDH. Phosphorylation is reversed by pyruvate dehydrogenase phosphatase, which is stimulated by insulin, PEP,
and AMP, but competitively inhibited by ATP, NADH, and Acetyl-CoA.
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase
E2
E2 (dihydrolipoamide acetyltransferase) is one of three subunits of the enzyme pyruvate dehydrogenase. It performs the oxidation of the two carbon activated acetaldehyde (hydroxyethyl group) within the enzyme complex. Lipoamide is covalently bound
to E2 and it is during the transfer of the activated acetaldehyde to it from the TPP of E1
that the oxidation occurs. E2 also catalyzes transfer of the two carbon group from lipoamide to CoASH, forming acetyl-CoA.
The overall reaction to convert pyruvate to acetyl-AoA involves three steps, each occurring on one of the enzymes subunits. The steps, sequentially occurring on subunits E1,
E2, and E3, are 1) decarboxylation of pyruvate; 2) oxidation of the decarboxylated product (with transfer of the two carbon unit to CoASH to make acetyl-CoA); and 3) transfer of electrons to ultimately form NADH.
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase
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E3
The overall reaction to convert pyruvate to acetyl-AoA involves three steps, each
ring on one of the enzymes subunits. The steps, sequentially occurring on subu
uct (with transfer of the two carbon unit to CoASH to make acetyl-CoA); and 3)
fer of electrons to ultimately form NADH.
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase
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Eadie-Hofstee
In biochemistry, an EadieHofstee diagram (also WoolfEadieAugustinssonHofstee or EadieAugustinsson plot) is a graphical representation of enzyme kinetics in
which reaction rate is plotted as a function of the ratio between rate and substrate concentration:
where v represents reaction rate, Km is the MichaelisMenten constant, [S] is the substrate concentration, and Vmax is the maximum reaction rate.
A plot of v against v/[S] will hence yield Vmax as the y-intercept, Vmax/Km as the xintercept, and Km as the negative slope. Like other techniques that linearize the MichaelisMenten equation, the Eadie-Hofstee plot was used historically for rapid identification of important kinetic terms like Km and Vmax, but has been superseded by nonlinear regression methods that are significantly more accurate and no longer computationally inaccessible. It is also more robust against error-prone data than the LineweaverBurk plot, particularly because it gives equal weight to data points in any range of
substrate concentration or reaction rate. (The LineweaverBurk plot unevenly weights
such points.) Both plots remain useful as a means to present data graphically.
One drawback from the EadieHofstee approach is that neither ordinate nor abscissa
represent independent variables: both are dependent on reaction rate. Thus any experimental error will be present in both axes. Also, experimental error or uncertainty will
propagate unevenly and become larger over the abscissa thereby giving more weight to
smaller values of v/[S]. Therefore, the typical measure of goodness of fit for linear regression, the correlation coefficient R, is not applicable.
https://en.wikipedia.org/wiki/EadieHofstee_diagram
EcoRV
EcoRV is a type II restriction endonuclease isolated from certain strains of
coli. It has the alternative name Eco32I.
makes a cut at the vertical line. The complementary sequence is then 3'-CTA
The ends are blunt and can be ligated into a blunt cloning site easily but wit
ciency than sticky ends.
https://en.wikipedia.org/wiki/EcoRV
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EDTA
Ethylenediaminetetraacetic acid, widely abbreviated as EDTA (for other names, see Table), is an aminopolycarboxylic acid and a colorless, water-soluble solid. Its conjugate
base is named ethylenediaminetetraacetate. It is widely used to dissolve limescale. Its
usefulness arises because of its role as a hexadentate ("six-toothed") ligand and chelating agent, i.e., its ability to "sequester" metal ions such as Ca2+ and Fe3+. After being
bound by EDTA, metal ions remain in solution but exhibit diminished reactivity. EDTA
is produced as several salts, notably disodium EDTA and calcium disodium EDTA.
In the laboratory, EDTA is widely used for scavenging metal ions. In biochemistry and
molecular biology, ion depletion is commonly used to deactivate metal-dependent enzymes, either as an assay for their reactivity or to suppress damage to DNA or proteins.
In analytical chemistry, EDTA is used in complexometric titrations and analysis of water hardness or as a masking agent to sequester metal ions that would interfere with
the analyses.
EDTA finds many specialized uses in the biomedical laboratories, such as in veterinary
ophthalmology as an anticollagenase to prevent the worsening of corneal ulcers in animals. In tissue culture EDTA is used as a chelating agent that binds to calcium and prevents joining of cadherins between cells, preventing clumping of cells grown in liquid
suspension, or detaching adherent cells for passaging. In histopathology, EDTA can be
used as a decalcifying agent making it possible to cut sections using a microtome once
the tissue sample is demineralized. EDTA is also known to inhibit a range of metallopeptidases, the method of inhibition occurs via the chelation of the metal ion required for catalytic activity. EDTA can also be used to test for bioavailability of heavy
metals in sediments. However, EDTA may influence the bioavailability of metals in solution, which may pose concerns regarding its effects in the environment, especially
given its widespread uses and applications.
https://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid
EF-G
EF-G or elongation factor G (historically known as translocase) is a prokaryotic elongation factor and a GTPase responsible for catalyzing the coordinated movement of tRNA
and mRNA through the ribosome.
The factor EF-G catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation. Just like the EFTu+tRNA+GTP complex, EF-G binds to the ribosome in its GTP-bound state. When it
binds to the ribosome A-site, EF-G causes the tRNA previously occupying that site to
occupy an intermediate A/P position (bound to the A site of the small ribosomal
subunit and to the P site of the large subunit), and the tRNA in the P site is shifted to a
P/E hybrid state. EF-G hydrolysis of GTP causes a conformation change that forces the
A/P tRNA to fully occupy the P site, the P/E tRNA to fully occupy the E site (and exit
the ribosome complex), and the mRNA to shift three nucleotides down relative to the
ribosome due to its association with these tRNA molecules. The GDP-bound EF-G
molecule then dissociates from the complex, leaving another free A-site where the elongation cycle can start again.
Apart from its role in translocation, EF-G, working together with Ribosome Recycling
Factor, promotes ribosome recycling in a GTP-dependent manner.
https://en.wikipedia.org/wiki/EF-G
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EF-Tu
EF-Tu (elongation factor thermo unstable) is one of the prokaryotic elongation factors.
Elongation factors are part of the mechanism that synthesizes new proteins by translation at the ribosome. Individual amino acid links are added to the protein chain by
transfer RNA (t-RNA). Messenger RNA (mRNA) carries a codon that codes for each
amino acid. t-RNA carries the amino acid and an anticodon for that amino acid. The ribosome creates a protein chain by following the mRNA code and selecting the next tRNA and its amino acid.
The prokaryotic factor EF-Tu helps the aminoacyl-tRNA move onto a free site on the
ribosome. In the cytoplasm, EF-Tu binds an aminoacylated, or charged, tRNA molecule. This complex enters the ribosome.
There are 3 tRNA attachment sites on the ribosome: aminoacyl (A), peptidyl (P) and
exit (E). The tRNA complex first binds to the A site, then moves to the P site, and is released at the E site.
The tRNA anticodon domain associates with the mRNA codon domain in the ribosomal A site. If the codon-anticodon pairing is correct, EF-Tu hydrolyzes guanosine triphosphate (GTP) into guanosine diphosphate (GDP) and inorganic phosphate. This creates a conformational change in EF-Tu that causes EF-Tu to dissociate from the tRNA
of the ternary complex (and therefore leave the ribosome). The aminoacyl-tRNA then
fully enters the A site, where its amino acid is brought near the P site's polypeptide and
the ribosome catalyzes the covalent transfer of the polypeptide onto the amino acid .
The tRNA on the P site (without peptide) moves to the E site and is then released.
EF-Tu contributes to translational accuracy in three ways. It delays GTP hydrolysis if
the tRNA in the ribosomes A site does not match the mRNA codon, thus preferentially
increasing the likelihood for the incorrect tRNA to leave the ribosome. It also adds a
second delay (regardless of tRNA matching) after freeing itself from tRNA, before the
aminoacyl-tRNA fully enters the A site. This delay period is a second opportunity for
incorrectly paired tRNA (and their bound amino acids) to move out of the A site before
the incorrect amino acid is irreversibly added to the polypeptidic chain. A third mechanism is the less well understood function of EF-Tu to crudely check aminoacyl-tRNA
associations and reject complexes where the amino acid is not bound to the correct
tRNA coding for it.
https://en.wikipedia.org/wiki/EF-Tu
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Efflux
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EGF Receptor
The epidermal growth factor receptor (EGFR; ErbB-1; HER1 in humans) is the cellsurface receptor for members of the epidermal growth factor family (EGF-family) of extracellular protein ligands.
The epidermal growth factor receptor is a member of the ErbB family of receptors, a
subfamily of four closely related receptor tyrosine kinases: EGFR (ErbB-1), HER2/cneu (ErbB-2), Her 3 (ErbB-3) and Her 4 (ErbB-4). Mutations affecting EGFR expression or activity could result in cancer.
Mutations that lead to EGFR overexpression (known as upregulation) or overactivity
have been associated with a number of cancers, including lung cancer, anal cancers
and glioblastoma multiforme. These somatic mutations involving EGFR lead to its constant activation, which produces uncontrolled cell division. In glioblastoma a more or
less specific mutation of EGFR, called EGFRvIII is often observed. Mutations, amplifications or misregulation of EGFR or family members are implicated in about 30% of
all epithelial cancers.
https://en.wikipedia.org/wiki/Epidermal_growth_factor_receptor
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Eicosanoid
In biochemistry, eicosanoids (preferred IUPAC name icosanoids) are signaling molecules made by oxidation of 20-carbon fatty acids. They exert complex control over
many bodily systems, mainly in growth during and after physical activity, inflammation or immunity after the intake of toxic compounds and pathogens, and as messengers in the central nervous system. Many are classified as hormones. The networks of
controls that depend upon eicosanoids are among the most complex in the human
body.
Eicosanoids are derived from either omega-3 (-3) or omega-6 (-6) fatty acids. In
general, the -6 eicosanoids are pro-inflammatory. -3s are much less so. The
amounts and balance of these fats in a person's diet will affect the body's eicosanoidcontrolled functions, with effects on cardiovascular disease, triglycerides, blood pressure, and arthritis.
There are multiple subfamilies of eicosanoids, including the prostaglandins, thromboxanes, and leukotrienes, as well as the lipoxins and eoxins, and others. For each, there
are two or three separate series, derived from either an -3 or an -6 EFA. These series' different activities largely explain the health effects of -3 and -6 fats.
https://en.wikipedia.org/wiki/Eicosanoid
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Eicosapentaenoic Acid
Eicosapentaenoic acid (EPA or also icosapentaenoic acid) is an -3 fatty acid. In
physiological literature, it is given the name 20:5(n-3). It also has the trivial name timnodonic acid. In chemical structure, EPA is a carboxylic acid with a 20-carbon chain
and five cis double bonds. he first double bond is located at the third carbon from the
end.
EPA is a polyunsaturated fatty acid (PUFA) that acts as a precursor for prostaglandin-3
(which inhibits platelet aggregation), thromboxane-3, and leukotriene-5 eicosanoids.
Studies of fish oil supplements, which contain EPA, have failed to support claims of
preventing heart attacks or strokes.
The human body converts -linolenic acid (ALA) to EPA. ALA is itself an essential fatty
acid, an appropriate supply of which must be ensured. The efficiency of the conversion
of ALA to EPA, however, is much lower than the absorption of EPA from food containing it. Because EPA is also a precursor to docosahexaenoic acid (DHA), ensuring a sufficient level of EPA on a diet containing neither EPA nor DHA is harder both because of
the extra metabolic work required to synthesize EPA and because of the use of EPA to
metabolize into DHA. Medical conditions like diabetes or certain allergies may significantly limit the human body's capacity for metabolization of EPA from ALA.
https://en.wikipedia.org/wiki/Eicosapentaenoic_acid
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eIFs
Eukaryotic initiation factors (eIFs) are proteins involved in the initiation phase
eukaryotic translation. These proteins help stabilize the formation of the functio
bosome around the start codon and also provide regulatory mechanisms in tran
initiation. Several initiation factors form a complex with the small 40S ribosom
subunit and Met-tRNAiMet called the 43S preinitation complex (PIC). Addition
tors of the eIF4F complex (eIF4A, E, and G) recruit the 43S PIC to the five-prim
an AUG start codon. Recognition of the start codon by the Met-tRNAiMet prom
GTP hydrolysis (or gated phosphate release) by specific initiation factors and in
factor release, resulting in the 60S ribosomal subunit recruitment to form the 8
some. There exist many more eukaryotic initiation factors than prokaryotic init
Index
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Elastase
Elastase breaks down elastin, an elastic fiber that, together with collagen, determin
the mechanical properties of connective tissue. The neutrophil form breaks down t
uter membrane protein A (OmpA) of E. coli and other Gram-negative bacteria.
Elastase also has the important immunological role of breaking down Shigella viru
lence factors. This is accomplished through the cleavage of peptide bonds in the tar
proteins. The specific peptide bonds cleaved are those on the carboxyl side of smal
drophobic amino acids such as glycine, alanine, and valine.
most irreversibly to the active site of elastase and trypsin. A1AT is normally secrete
the liver cells into the serum. 1-antitryspin deficiency (A1AD) leads to uninhibited
struction of elastic fiber by elastase. The main result is pulmonary emphysema.
https://en.wikipedia.org/wiki/Elastase
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Elastin
Elastin is a highly elastic protein in connective tissue and allows many tissues in the
body to resume their shape after stretching or contracting. Elastin helps skin to return
to its original position when it is poked or pinched. Elastin is also an important loadbearing tissue in the bodies of vertebrates and used in places where mechanical energy
is required to be stored. In humans, elastin is encoded by the ELN gene.
Elastic fiber is composed mainly of an amorphous component, which is extensively
cross-linked elastin, and a fibrillar component, which are primarily the microfibrils
such as fibrillin, both of which are made of simple amino acids such as glycine, valine,
alanine, and proline. The total elastin ranges from 58 to 75% of the weight of the dry
defatted artery in normal canine arteries. Comparison between fresh and digested tissues shows that, at 35% strain, a minimum of 48% of the arterial load is carried by elastin, and a minimum of 43% of the change in stiffness of arterial tissue is due to the
change in elastin stiffness. Elastin is made by linking many soluble tropoelastin protein molecules, in a reaction catalyzed by lysyl oxidase, to make a massive insoluble, durable complex cross-linked by desmosine and isodesmosine in an in vivo Chichibabin
pyridine synthesis reaction. The amino acid responsible for these cross-links is lysine.
Tropoelastin is a specialized protein with a molecular weight of 64 to 66 kDa, and an
irregular or random coil conformation made up of 830 amino acids.
https://en.wikipedia.org/wiki/Elastin
Electrochemical Gradients
An electrochemical gradient is a gradient of electrochemical potential, usually for an
ion that can move across a membrane. The gradient consists of two parts, the chemical
gradient, or difference in solute concentration across a membrane, and the electrical
gradient, or membrane potential (Vm). The ions move across the membrane to achieve
the greatest amount of entropy in conformity with the second law of thermodynamics.
When there are unequal concentrations of an ion across a permeable membrane, the
ion will move across the membrane from the area of higher concentration to the area
of lower concentration through simple diffusion. Ions also carry an electric charge that
forms an electric potential across a membrane. If there is an unequal distribution of
charges across the membrane, then the difference in electric potential generates a force
that drives ion diffusion until the charges are balanced on both sides of the membrane.
In biological processes, the direction an ion moves by diffusion or active transport
across a membrane is determined by the electrochemical gradient. In mitochondria
and chloroplasts, proton gradients are used to generate a chemiosmotic potential that
is also known as a proton motive force. This potential energy is used for the synthesis
of ATP by oxidative phosphorylation.
An electrochemical gradient has two components. First, the electrical component is
caused by a charge difference across the lipid membrane. Second, a chemical component is caused by a differential concentration of ions across the membrane. The combination of these two factors determines the thermodynamically favourable direction for
an ion's movement across a membrane.
An electrochemical gradient is analogous to the water pressure across a hydroelectric
dam. Membrane transport proteins such as the sodium-potassium pump within the
membrane are equivalent to turbines that convert the water's potential energy to other
forms of physical or chemical energy, and the ions that pass through the membrane are
equivalent to water that ends up at the bottom of the dam. Also, energy can be used to
pump water up into the lake above the dam. In similar manner, chemical energy in
cells can be used to create electrochemical gradients.
https://en.wikipedia.org/wiki/Electrochemical_gradient
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Electrogenic
potassium pump, which moves three sodium ions outside of the cell in exch
two potassium ions, for example, is electrogenic.
Index
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Electron Acceptor
tron acceptor. During this process (electron transport chain) the electron accep
reduced and the electron donor is oxidized.
https://en.wikipedia.org/wiki/Electron_acceptor
Electron Carrier
Electron carriers are molecules that accept electrons from other molecules.
cules donating electrons are reduced and the carriers are, in the process, re
electron carrier can transfer electrons from itself to another carrier. This ha
rier to another until they arrive at molecular oxygen, the terminal acceptor,
cepts four electrons and four protons to form two molecules of water.
Electron Donor
An electron donor is a chemical entity that donates electrons to another compound. It
is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process.
In biology, electron donors release an electron during cellular respiration, resulting in
the release of energy. Microorganisms, such as bacteria, obtain energy in the electron
transfer processes. Through its cellular machinery, the microorganism collects the energy for its use. The final result is the electron is donated to an electron acceptor. During this process (electron transport chain) the electron donor is oxidized and the electron acceptor is reduced. Petroleum hydrocarbons, less chlorinated solvents like vinyl
chloride, soil organic matter, and reduced inorganic compounds are all compounds
that can act as electron donors.
In cells, foodstuffs are electron donors. Oxidation of glucose to carbon dioxide, for example, involves transfer of electrons from glucose through the electron transport system, ultimately resulting in synthesis of ATP by the process of oxidative phosphorylation.
https://en.wikipedia.org/wiki/Electron_donor
Electron Microscope
times shorter than that of visible light photons, the electron microscope has
resolving power than a light microscope and can reveal the structure of sma
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volved in the oxidation of fatty acids (Group I), and ETFs produced by some
tes under specific growth conditions, receiving electrons only from the oxid
cific substrates (Group II).
https://en.wikipedia.org/wiki/Electron-transferring_flavoprotein
Electron Transport
An electron transport (system) chain (ETC) is a series of compounds that transfer electrons from electron donors to electron acceptors via redox (both reduction and oxidation occurring simultaneously) reactions. They couple this electron movement with
the transfer (pumping) of protons (H+ ions) across a membrane. This creates an electrochemical proton gradient that is used to synthesize adenosine triphosphate (ATP) in
the coupled process of oxidative phosphorylation. Molecules of the chain include peptides, enzymes (which are proteins or protein complexes), cytochromes and others.
The final acceptor of electrons in the electron transport chain during aerobic respiration is molecular oxygen although a variety of acceptors other than oxygen exist in anaerobic respiration.
Electron transport chains are used for extracting energy via redox reactions from sunlight in photosynthesis or, such as in the case of the oxidation of sugars, cellular respiration. In eukaryotes, an important electron transport chain is found in the inner mitochondrial membrane where it serves as the site of oxidative phosphorylation through
the use of ATP synthase. It is also found in the thylakoid membrane of the chloroplast
in photosynthetic eukaryotes. In bacteria, the electron transport chain is located in
their cell membrane.
In chloroplasts, light drives the conversion of water to oxygen and NADP+ to NADPH
with transfer of H+ ions across chloroplast membranes. In mitochondria, it is the conversion of oxygen to water, NADH to NAD+ and succinate to fumarate that are required to generate the proton gradient.
Electron transport chains are major sites of premature electron leakage to oxygen, generating superoxide and potentially resulting in increased oxidative stress.
Pictured below - the electron transport system of mitochondria.
https://en.wikipedia.org/wiki/Electron_transport_chain
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https://en.wikipedia.org/wiki/Electron_transport_chain
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Electronegativity
atom's electronegativity is affected by both its atomic number and the dista
which its valence electrons reside from the charged nucleus. The higher the
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Electroneutral
Electrophilic
In chemistry, an electrophile (literally electron lover) is a reagent attracted
trons. Electrophiles are positively charged or neutral species having vacant
electrons, they are Lewis acids. Most electrophiles are positively charged, h
that carries a partial positive charge, or have an atom that does not have an
electrons.
https://en.wikipedia.org/wiki/Electrophile
Electrophoresis
ence of a spatially uniform electric field. The term is commonly used in bioc
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Elongases
An elongase is an enzyme that extends the length of a fatty acid beyond that
carbon product of the fatty acid synthase reaction. Elongases are found in t
plasmic reticulum and in the mitochondrial matrix.
Embryogenesis
Embryogenesis is the process by which the embryo forms and develops. In
the term refers chiefly to early stages of prenatal development, whereas the
and fetal development describe later stages. Embryogenesis starts with the
of the egg cell (ovum) by a sperm cell, (spermatozoon). Once fertilized, the
ferred to as a zygote, a single diploid cell. The zygote undergoes mitotic divi
Enantiomers
The term enantiomers refer to two stereoisomers that are mirror images of each other
that are non-superposable (not identical), much as one's left and right hands are the
same except for being reversed along one axis (the hands cannot be made to appear
identical simply by reorientation). Organic compounds that contain a chiral carbon
usually have two non-superposable structures. These two structures are mirror images
of each other and are, thus, commonly called enantiomorphs (enantio = opposite;
morph = form), hence this structural property is now commonly referred to as enantiomerism.
Shown below are the enantiomers D-glucose and L-glucose.
https://en.wikipedia.org/wiki/Enantiomer
Endocannabinoids
Cannabinoids are a class of diverse chemical compounds that act on cannabinoid receptors in cells that repress neurotransmitter release in the brain. Ligands for these receptor proteins include the endocannabinoids (produced naturally in the body by humans
and animals), the phytocannabinoids (found in cannabis and some other plants), and
synthetic cannabinoids (manufactured artificially). The most notable cannabinoid is
the phytocannabinoid tetrahydrocannabinol (THC), the primary psychoactive compound in cannabis. Cannabidiol (CBD) is another major constituent of the plant. There
are at least 113 different cannabinoids isolated from cannabis, exhibiting varied effects.
Endocannabinoids serve as intercellular 'lipid messengers', signaling molecules that
are released from one cell and activating the cannabinoid receptors present on other
nearby cells. Although in this intercellular signaling role they are similar to the wellknown monoamine neurotransmitters, such as acetylcholine and dopamine, endocannabinoids differ in numerous ways from them. For instance, they are used in retrograde signaling between neurons. Furthermore, endocannabinoids are lipophilic molecules that are not very soluble in water. They are not stored in vesicles, and exist as integral constituents of the membrane bilayers that make up cells. They are believed to
be synthesized 'on-demand' rather than made and stored for later use. The mechanisms and enzymes underlying the biosynthesis of endocannabinoids remain elusive
and continue to be an area of active research.
Anandamide is an endocannabinoid derived from arachidonic acid. It has a pharmacology similar to THC, although its chemical structure is different. Anandamide binds to
the central (CB1) and, to a lesser extent, peripheral (CB2) cannabinoid receptors, where
it acts as a partial agonist. Anandamide is about as potent as THC at the CB1 receptor.
Anandamide is found in nearly all tissues in a wide range of animals. Anandamide has
also been found in plants, including small amounts in chocolate.
Two analogs of anandamide, 7,10,13,16-docosatetraenoylethanolamide and homo-linolenoylethanolamine, have similar pharmacology. All of these are members of a family of signaling lipids called N-acylethanolamines, which also includes the noncannabimimetic palmitoylethanolamide and oleoylethanolamide, which possess antiinflammatory and orexigenic effects, respectively. Many N-acylethanolamines have
also been identified in plant seeds and in molluscs.
Shown below - anandamide.
https://en.wikipedia.org/wiki/Cannabinoid#Endocannabinoids
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Endocytosis
Endocytosis is a form of active transport in which a cell transports molecules (such as
proteins) into the cell (endo- + cytosis) by engulfing them in an energy-using process.
Endocytosis and its counterpart, exocytosis, are used by all cells because most chemical substances important to them are large polar molecules that cannot pass through
the hydrophobic plasma or cell membrane by passive means. Endocytosis includes
pinocytosis (cell drinking) and phagocytosis (cell eating).
Endocytosis pathways can be subdivided into four categories: namely, clathrin
receptor-mediated endocytosis, caveolae, macropinocytosis, and phagocytosis.
Clathrin-mediated endocytosis is mediated by small (approx. 100nm in diameter)
vesicles that have a morphologically characteristic coat made up of a complex of proteins that are mainly associated with the cytosolic protein clathrin. Clathrin-coated
vesicles (CCVs) are found in virtually all cells and form domains of the plasma membrane termed clathrin-coated pits. Coated pits can concentrate large extracellular molecules that have different receptors responsible for the receptor-mediated endocytosis
of ligands, e.g. low density lipoprotein, transferrin, growth factors, antibodies and
many others.
Caveolae are the most common reported non-clathrin-coated plasma membrane
buds, which exist on the surface of many, but not all cell types. They consist of the
cholesterol-binding protein caveolin (Vip21) with a bilayer enriched in cholesterol and
glycolipids. Caveolae are small (approx. 50nm in diameter) flask-shape pits in the
membrane that resemble the shape of a cave (hence the name caveolae). They can constitute up to a third of the plasma membrane area of the cells of some tissues, being especially abundant in smooth muscle, type I pneumocytes, fibroblasts, adipocytes, and
endothelial cells. Uptake of extracellular molecules is also believed to be specifically
mediated via receptors in caveolae.
Macropinocytosis, which usually occurs from highly ruffled regions of the plasma
membrane, is the invagination of the cell membrane to form a pocket, which then
pinches off into the cell to form a vesicle (0.55m in diameter) filled with a large volume of extracellular fluid and molecules within it (equivalent to ~100 CCVs). The filling of the pocket occurs in a non-specific manner. The vesicle then travels into the cytosol and fuses with other vesicles such as endosomes and lysosomes.
Phagocytosis is the process by which cells bind and internalize particulate matter
larger than around 0.75m in diameter, such as small-sized dust particles, cell debris,
micro-organisms and apoptotic cells. These processes involve the uptake of larger
membrane areas than clathrin-mediated endocytosis and caveolae pathway.
https://en.wikipedia.org/wiki/Endocytosis
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Endogenous Pathway
The endogenous pathway is one of three major pathways taken by lipids in the body.
(The others are the exogenous pathway and the reverse transport pathway.)
The liver plays a central role in managing the bodys needs for lipids. When lipids are
needed by the body or when the capacity of the liver to contain more lipids than is supplied by the diet, the liver packages up fats and cholesteryl esters into Very Low Density Lipoprotein (VLDL) complexes. They contain the ApoB-100, ApoC-I, ApoC-II,
ApoC-III, and ApoE apolipoproteins. VLDLs enter the blood and travel to muscles and
adipose tissue where lipoprotein lipase is activated by ApoC-II. In the muscle cells, the
released fatty acids are taken up and oxidized. By contrast, in the adipoctyes, the fatty
acids are taken up and reassembled back into triacylglycerides (fats) and stored in
droplets. Removal of fat from the VLDLs causes them to shrink, first to Intermediate
Density Lipoprotein (IDL) complexes (also called VLDL remnants) and then to Low
Density Lipoprotein (LDL) complexes.
This is accompanied by loss of apolipoproteins so that LDLs are comprised primarily
of ApoB-100. This lipoprotein complex is important because cells have receptors for it
to bind and internalize it by receptor-mediated endocytosis . Up until this point, cholesterol and cholesteryl esters have traveled in chylomicrons, VLDLs, and IDLs as fat
has been stripped stripped away. For cholesterol compounds to get into the cell from
the lipoprotein complexes, they must be internalized by cells and that is the job of
receptor-mediated endocytosis.
The endogenous pathway is shown below in blue.
https://en.wikipedia.org/wiki/Lipoprotein#Endogenous_pathway
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Endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as Deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences.
Restriction enzymes are endonucleases from eubacteria and archaea that recognize a
specific DNA sequence. The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site. Typically, a restriction site will be a palindromic sequence about four to six nucleotides long. Most restriction endonucleases cleave
the DNA strand unevenly, leaving complementary single-stranded ends. These ends
can reconnect through hybridization and are termed "sticky ends". Once paired, the
phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site.
The DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA. Such DNA is called recombinant DNA - DNA formed by
the joining of genes into new combinations. Restriction endonucleases (restriction enzymes) are divided into three categories, Type I, Type II, and Type III, according to
their mechanism of action. These enzymes are often used in genetic engineering to
make recombinant DNA for introduction into bacterial, plant, or animal cells, as well
as in synthetic biology.
https://en.wikipedia.org/wiki/Endonuclease
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Endoplasmic reticulum
The endoplasmic reticulum (ER) is a type of organelle in the cells of eukaryotic organisms that forms an interconnected network of flattened, membrane-enclosed sacs or
tube-like structures known as cisternae. The membranes of the ER are continuous with
the outer nuclear membrane. The endoplasmic reticulum occurs in most types of
eukaryotic cells, including the most primitive Giardia, but is absent from red blood
cells and spermatozoa. There are two types of endoplasmic reticulum, rough and
smooth. The outer (cytosolic) face of the rough endoplasmic reticulum is studded with
ribosomes that are the sites of protein synthesis. The smooth endoplasmic reticulum
lacks ribosomes and functions in lipid manufacture and metabolism, the production of
steroid hormones, and detoxification.
Functions of the endoplasmic reticulum include folding of proteins in sacs called cisternae and the transport of synthesized proteins in vesicles to the Golgi apparatus. Correct folding of newly made proteins is performed by several endoplasmic reticulum
chaperone proteins, including protein disulfide isomerase (PDI), ERp29, the Hsp70
family member BiP/Grp78, calnexin, calreticulin, and the peptidylpropyl isomerase
family. Only properly folded proteins are transported from the rough ER to the Golgi
apparatus unfolded proteins cause an unfolded protein response as a stress response
in the ER.
The smooth endoplasmic reticulum (abbreviated SER) synthesizes lipids, phospholipids, and steroids. It also carries out the metabolism of carbohydrates, detoxification of
natural metabolism products and of alcohol and drugs, attachment of receptors on cell
membrane proteins, and steroid metabolism. In muscle cells, it regulates calcium ion
concentration. The smooth endoplasmic reticulum also contains the enzyme glucose6-phosphatase, which converts glucose-6-phosphate to glucose, a step in gluconeogenesis. The sarcoplasmic reticulum (SR), from the Greek sarx ("flesh"), is smooth
ER found in myocytes.
The rough endoplasmic reticulum is key in:
Manufacture of lysosomal enzymes with a mannose-6-phosphate marker added in
the cis-Golgi network
Manufacture of secreted proteins, either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids in the
signal peptide.
Integral membrane proteins that stay embedded in the membrane as vesicles exit and
bind to new membranes. Rab proteins are key in targeting the membrane. SNAP and
SNARE proteins are key in the fusion event.
Initial glycosylation as assembly continues. This is N-linked (O-linking occurs in the
Golgi).
N-linked glycosylation: If the protein is properly folded, Oligosaccharyltransferase
recognizes the AA sequence NXS or NXT (with the S/T residue phosphorylated) and
adds a 14-sugar backbone (2-N-acetylglucosamine, 9-branching mannose, and 3glucose at the end) to the side-chain nitrogen of Asn.
https://en.wikipedia.org/wiki/Endoplasmic_reticulum
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Endoplasmic Reticulum
The endoplasmic reticulum (ER) is a type of organelle in the cells of eukaryotic organisms that forms an interconnected network of flattened, membrane-enclosed sacs or
tube-like structures known as cisternae. The membranes of the ER are continuous with
the outer nuclear membrane. The endoplasmic reticulum occurs in most types of
eukaryotic cells, including the most primitive Giardia, but is absent from red blood
cells and spermatozoa. There are two types of endoplasmic reticulum, rough and
smooth. The outer (cytosolic) face of the rough endoplasmic reticulum is studded with
ribosomes that are the sites of protein synthesis. The smooth endoplasmic reticulum
lacks ribosomes and functions in lipid manufacture and metabolism, the production of
steroid hormones, and detoxification.
Functions of the endoplasmic reticulum include folding of proteins in sacs called cisternae and the transport of synthesized proteins in vesicles to the Golgi apparatus. Correct folding of newly made proteins is performed by several endoplasmic reticulum
chaperone proteins, including protein disulfide isomerase (PDI), ERp29, the Hsp70
family member BiP/Grp78, calnexin, calreticulin, and the peptidylpropyl isomerase
family. Only properly folded proteins are transported from the rough ER to the Golgi
apparatus unfolded proteins cause an unfolded protein response as a stress response
in the ER.
The smooth endoplasmic reticulum (abbreviated SER) synthesizes lipids, phospholipids, and steroids. It also carries out the metabolism of carbohydrates, detoxification of
natural metabolism products and of alcohol and drugs, attachment of receptors on cell
membrane proteins, and steroid metabolism. In muscle cells, it regulates calcium ion
concentration. The smooth endoplasmic reticulum also contains the enzyme glucose6-phosphatase, which converts glucose-6-phosphate to glucose, a step in gluconeogenesis. The sarcoplasmic reticulum (SR), from the Greek sarx ("flesh"), is smooth
ER found in myocytes.
The rough endoplasmic reticulum is key in:
Manufacture of lysosomal enzymes with a mannose-6-phosphate marker added in
the cis-Golgi network
Manufacture of secreted proteins, either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids in the
signal peptide.
Integral membrane proteins that stay embedded in the membrane as vesicles exit and
bind to new membranes. Rab proteins are key in targeting the membrane; SNAP and
SNARE proteins are key in the fusion event.
Initial glycosylation as assembly continues. This is N-linked (O-linking occurs in the
Golgi).
N-linked glycosylation: If the protein is properly folded, Oligosaccharyltransferase
recognizes the AA sequence NXS or NXT (with the S/T residue phosphorylated) and
adds a 14-sugar backbone (2-N-acetylglucosamine, 9-branching mannose, and 3glucose at the end) to the side-chain nitrogen of Asn.
https://en.wikipedia.org/wiki/Endoplasmic_reticulum
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Endosome
In cell biology, an endosome is a membrane-bound compartment inside eukaryotic
cells. It is a compartment of the endocytic membrane transport pathway originating
from the trans Golgi membrane. Molecules or ligands internalized from the plasma
membrane can follow this pathway all the way to lysosomes for degradation, or they
can be recycled back to the plasma membrane. Molecules are also transported to endosomes from the trans-Golgi network and either continue to lysosomes or recycle back
to the Golgi. Endosomes can be classified as early, sorting, or late depending on their
stage post internalization. Endosomes represent a major sorting compartment of the
endomembrane system in cells.
Endosomes provide an environment for material to be sorted before it reaches the degradative lysosome. For example, LDL is taken into the cell by binding to the LDL receptor at the cell surface. Upon reaching early endosomes, the LDL dissociates from the
receptor, and the receptor can be recycled to the cell surface. The LDL remains in the
endosome and is delivered to lysosomes for processing. LDL dissociates because of the
slightly acidified environment of the early endosome, generated by a vacuolar membrane proton pump V-ATPase. On the other hand, EGF and the EGF receptor have a
pH-resistant bond that persists until it is delivered to lysosomes for their degradation.
The mannose 6-phosphate receptor carries ligands from the Golgi destined for the lysosome by a similar mechanism.
Early endosomes consist of a dynamic tubular-vesicular network (vesicles up to
1m in diameter with connected tubules of approx. 50nm diameter). Markers include
RAB5A and RAB4, transferrin and its receptor and EEA1.
Late endosomes, also known as MVBs, are mainly spherical, lack tubules, and
contain many close-packed lumenal vesicles. Markers include RAB7, RAB9, and mannose 6-phosphate receptors.
Recycling endosomes are concentrated at the microtubule organizing center and
consist of a mainly tubular network. Marker - RAB11.
https://en.wikipedia.org/wiki/Endosome
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Endosomes
In cell biology, an endosome is a membrane-bound compartment inside eukaryotic
cells. It is a compartment of the endocytic membrane transport pathway originating
from the trans Golgi membrane. Molecules or ligands internalized from the plasma
membrane can follow this pathway all the way to lysosomes for degradation, or they
can be recycled back to the plasma membrane. Molecules are also transported to endosomes from the trans-Golgi network and either continue to lysosomes or recycle back
to the Golgi. Endosomes can be classified as early, sorting, or late depending on their
stage post internalization. Endosomes represent a major sorting compartment of the
endomembrane system in cells.
Endosomes provide an environment for material to be sorted before it reaches the degradative lysosome. For example, LDL is taken into the cell by binding to the LDL receptor at the cell surface. Upon reaching early endosomes, the LDL dissociates from the
receptor, and the receptor can be recycled to the cell surface. The LDL remains in the
endosome and is delivered to lysosomes for processing. LDL dissociates because of the
slightly acidified environment of the early endosome, generated by a vacuolar membrane proton pump V-ATPase. On the other hand, EGF and the EGF receptor have a
pH-resistant bond that persists until it is delivered to lysosomes for their degradation.
The mannose 6-phosphate receptor carries ligands from the Golgi destined for the lysosome by a similar mechanism.
Early endosomes consist of a dynamic tubular-vesicular network (vesicles up to
1m in diameter with connected tubules of approx. 50nm diameter). Markers include
RAB5A and RAB4, transferrin and its receptor and EEA1.
Late endosomes, also known as MVBs, are mainly spherical, lack tubules, and
contain many close-packed lumenal vesicles. Markers include RAB7, RAB9, and mannose 6-phosphate receptors.
Recycling endosomes are concentrated at the microtubule organizing center and
consist of a mainly tubular network. Marker - RAB11.
https://en.wikipedia.org/wiki/Endosome
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Endothelium
The endothelium is a type of tissue that lines the interior surface of blood vessels and
lymphatic vessels, forming an interface between circulating blood or lymph in the lumen and the rest of the vessel wall. It is a thin layer of simple squamous cells called endothelial cells. Endothelial cells in direct contact with blood are called vascular endothelial cells, whereas those in direct contact with lymph are known as lymphatic endothelial cells.
Endothelial cells are involved in many aspects of vascular biology, including:
Barrier function - the endothelium acts as a semi-selective barrier between the vessel
lumen and surrounding tissue, controlling the passage of materials and the transit of
white blood cells into and out of the bloodstream. Excessive or prolonged increases in
permeability of the endothelial monolayer, as in cases of chronic inflammation, may
lead to tissue edema/swelling.
Blood clotting (thrombosis & fibrinolysis). The endothelium normally provides a
non-thrombogenic surface because it contains, for example, heparan sulfate which acts
as a cofactor for activating antithrombin, a protease that inactivates several factors in
the coagulation cascade.
Inflammation
Formation of new blood vessels (angiogenesis)
Vasoconstriction and vasodilation, and hence the control of blood pressure
Repair of damaged or diseased organs via an injection of blood vessel cells
Angiopoietin-2 works with VEGF to facilitate cell proliferation and migration of endothelial cells
https://en.wikipedia.org/wiki/Endothelium
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Enediol
Enediols are alkenes with a hydroxyl group on both sides of a C=C double bond. Enediols are reaction intermediates in the Lobry-de Bruyn-van Ekenstein transformation.
Enediols with a carbonyl group adjacent to the enediol group are called reductones.
The enediol structure is stabilized by the resonance resulting from the tautomerism
with the adjacent carbonyl. Therefore, the chemical equilibrium produces mainly the
enediol form rather than the keto form. Reductones are strong reducing agents, thus
efficacious antioxidants, and fairly strong acids. Examples of reductones are tartronaldehyde, reductic acid and ascorbic acid.
Shown below is aldehyde tautomerization of tartronaldehyde
https://en.wikipedia.org/wiki/Enol
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Energy Coupling
self, this process is not very energetically favorable (that is, it needs an input o
to occur). Cells overcome this energy obstacle by using ATP to drive the reac
Hydrolysis of ATP provides energy for the enzyme to stimulate the reaction on
other substance(s). Without the hydrolysis of ATP (or GTP, in some cases), the
tion would not be favorable.
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Enhancers
In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by
proteins (activators) to increase the likelihood transcription will occur at a gene. These
proteins are usually referred to as transcription factors. Enhancers are generally cisacting, located up to 1 Mbp (1,000,000 bp) away from the gene and can be upstream or
downstream from the start site, and either in the forward or backward direction. There
are hundreds of thousands of enhancers in the human genome.
In eukaryotic cells the structure of the chromatin complex of DNA is folded in a way
that functionally mimics the supercoiled state characteristic of prokaryotic DNA, so although the enhancer DNA may be far from the gene in a linear way, it is spatially close
to the promoter and gene. This allows it to interact with the general transcription factors and RNA polymerase II. The same mechanism holds true for silencers in the
eukaryotic genome. Silencers are antagonists of enhancers that, when bound to its
proper transcription factors called repressors, repress the transcription of the gene. Silencers and enhancers may be in close proximity to each other or may even be the
same region only differentiated by the transcription factor the region binds to.
An enhancer may be located upstream or downstream of the gene it regulates. Furthermore, an enhancer doesn't need to be located near the transcription initiation site to
affect transcription, as some have been found located in several hundred thousand
base pairs upstream or downstream of the start site. Enhancers do not act on the promoter region itself, but are bound by activator proteins. These activator proteins interact with the mediator complex, which recruits polymerase II and the general transcription factors which then begin transcribing the genes. Enhancers can also be found
within introns. An enhancer's orientation may even be reversed without affecting its
function. Additionally, an enhancer may be excised and inserted elsewhere in the chromosome, and still affect gene transcription. That is one reason that introns polymorphisms may have effects although they are not translated. Enhancers can also be found
at the exonic region of an unrelated gene and they may act on genes.
https://en.wikipedia.org/wiki/Enhancer_(genetics) on another chromosome
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Enol
Enols, or more formally, alkenols, are a type of reactive structure or intermediate in organic chemistry that is represented as an alkene (olefin) with a hydroxyl group attached to one end of the alkene double bond. The terms enol and alkenol are portmanteaus deriving from "-ene"/"alkene" and the "-ol" suffix indicating the hydroxyl group
of alcohols, dropping the terminal "-e" of the first term. Generation of enols often involves removal of a hydrogen adjacent (-) to the carbonyl groupi.e., deprotonation,
its removal as a proton, H+. When this proton is not returned at the end of the stepwise
process, the result is an anion termed an enolate. The enolate structures shown are
schematic. A more modern representation considers the molecular orbitals that are
formed and occupied by electrons in the enolate. Similarly, generation of the enol often
is accompanied by "trapping" or masking of the hydroxy group as an ether, such as a
silyl enol ether.
Shown below is keto-enol tautomerization. The enol is on the right.
https://en.wikipedia.org/wiki/Enol
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Enolase
vate (PEP), the ninth and penultimate step of glycolysis. The chemical react
lyzed by enolase is:
2-phospho-D-glycerate <-> Phosphoenolpyruvate + H2O
The optimum pH for the human enzyme is 6.5. Enolase belongs to the fam
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Enoyl-CoA Hydratase
Enoyl-CoA hydratase is an enzyme that hydrates the double bond between the second
and third carbons on acyl-CoA. This enzyme, also known as crotonase, is essential to
metabolizing fatty acids to produce both acetyl CoA and energy.
Enoyl-CoA hydratase catalyzes the second step (shown in the figure below) in the
breakdown of fatty acids or the second step of -oxidation in fatty acid metabolism
shown below. Fatty acid metabolism is how our bodies turn fats or lipids into energy.
When fats come into our bodies, they are generally in the form of triacyl-glycerols.
These must be broken down in order for the fats to pass into our bodies. When that
happens, three fatty acids are released.
In fatty acid metabolism, fatty acids are changed into fatty acyl-CoA. To do this, the carboxylate which occupies one end of the fatty acid is changed into a thioester by substituting coenzyme A for the hydroxyl group. Next the fatty acyl-CoA is oxidized and broken down into an acetyl-CoA molecule and another acyl-CoA. The acetyl CoA is then
sent to the citric acid cycle while the remaining acyl-CoA is broken down further into
acetyl-CoAs. The complete breakdown of a fatty acid not only generates acetyl-CoA
molecules, but it also generates energy in the form of NADH. This NADH goes on to be
converted into ATP which can be used in other reactions.
https://en.wikipedia.org/wiki/Enoyl-CoA_hydratase
Enthalpy
nal energy, which is the energy required to create a system, and the amount of e
required to make room for it by displacing its environment and establishing its
and pressure.
Enthalpy is defined as a state function that depends only on the prevailing equil
sive quantity. The unit of measurement for enthalpy in the International System
Units (SI) is the joule, but other historical, conventional units are still in use, su
the British thermal unit and the calorie.
https://en.wikipedia.org/wiki/Enthalpy
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Entropy
In thermodynamics, entropy (usual symbol S) is a measure of the number of microscopic configurations that correspond to a thermodynamic system in a state specified
by certain macroscopic variables. For example, gas in a container with known volume,
pressure, and temperature could have an enormous number of possible configurations
of the individual gas molecules, and which configuration the gas is actually in may be
regarded as random. Hence, entropy can be understood as a measure of molecular disorder within a macroscopic system. The second law of thermodynamics states that an
isolated system's entropy never decreases. Such systems spontaneously evolve towards
thermodynamic equilibrium, the state with maximum entropy. Non-isolated systems
may lose entropy, provided their environment's entropy increases by at least that increment. Since entropy is a state function, the change in entropy of a system is determined by its initial and final states. This applies whether the process is reversible or irreversible. However, irreversible processes increase the combined entropy of the system and its environment.
https://en.wikipedia.org/wiki/Entropy
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Enzyme
Enzymes are macromolecular biological catalysts. Enzymes accelerate, or catalyze,
chemical reactions. The molecules at the beginning of the process are called substrates
and the enzyme converts these into different molecules, called products. The place on
the enzyme where the reaction occurs is called the active site. Almost all metabolic
processes in the cell need enzymes in order to occur at rates fast enough to sustain life.
The set of enzymes made in a cell determines which metabolic pathways occur in that
cell. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Enzymes' specificity comes from their unique three-dimensional structures.
Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy. Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5'-phosphate decarboxylase,
which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzyme activity can be affected
by other molecules. Inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH.
Enzymes serve a wide variety of functions inside living organisms. They are indispensable for signal transduction and cell regulation, often via kinases and phosphatases.
They also generate movement, with myosin hydrolyzing ATP to generate muscle contraction, and also transport cargo around the cell as part of the cytoskeleton. Other ATPases in the cell membrane are ion pumps involved in active transport. Enzymes are
also involved in more exotic functions, such as luciferase generating light in fireflies.
Viruses can also contain enzymes for infecting cells, such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase.
An important function of enzymes is in the digestive systems of animals. Enzymes such
as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules,
for example, are too large to be absorbed from the intestine, but enzymes hydrolyze the
starch chains into smaller molecules such as maltose and eventually glucose, which can
then be absorbed. Different enzymes digest different food substances. In ruminants,
which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase, to break down the cellulose cell walls of plant fiber.
https://en.wikipedia.org/wiki/Enzyme
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Enzyme Kinetics
Enzyme kinetics is the investigation of how enzymes bind substrates and turn them
into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays. In 1913 Leonor Michaelis and Maud Leonora Menten proposed a quantitative theory of enzyme kinetics, which is referred to as MichaelisMenten kinetics. The
major contribution of Michaelis and Menten was to think of enzyme reactions in two
stages. In the first, the substrate binds reversibly to the enzyme, forming the enzymesubstrate complex. The enzyme then catalyzes the chemical step in the reaction and releases the product.
Enzyme rates depend on solution conditions and substrate concentration. To find the
maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This is shown in the saturation curve
on the right. Saturation happens because, as substrate concentration increases, more
and more of the free enzyme is converted into the substrate-bound ES complex. At the
maximum reaction rate (Vmax) of the enzyme, all the enzyme active sites are bound to
substrate, and the amount of ES complex is the same as the total amount of enzyme.
Vmax is only one of several important kinetic parameters. The amount of substrate
needed to achieve a given rate of reaction is also important. This is given by the
Michaelis-Menten constant (Km), which is the substrate concentration required for an
enzyme to reach one-half its maximum reaction rate. Generally, each enzyme has a
characteristic Km for a given substrate. Another useful constant is kcat, also called the
turnover number, which is the number of substrate molecules handled by one active
site per second.
The efficiency of an enzyme can be expressed in terms of kcat/Km. This is also called the
specificity constant and incorporates the rate constants for all steps in the reaction up
to and including the first irreversible step. Because the specificity constant reflects
both affinity and catalytic ability, it is useful for comparing different enzymes against
each other, or the same enzyme with different substrates. The theoretical maximum for
the specificity constant is called the diffusion limit and is about 108 to 109 (M1 s1). At
this point every collision of the enzyme with its substrate will result in catalysis, and
the rate of product formation is not limited by the reaction rate but by the diffusion
rate. Enzymes with this property are called catalytically perfect or kinetically perfect.
Example of such enzymes are triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, -lactamase, and superoxide dismutase. The turnover of such enzymes can reach several million reactions per second.
MichaelisMenten kinetics relies on the law of mass action, which is derived from the
assumptions of free diffusion and thermodynamically driven random collision. Many
biochemical or cellular processes deviate significantly from these conditions, because
of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects.
Shown below - Velocity versus [Substrate] for a reaction.
https://en.wikipedia.org/wiki/Enzyme
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Enzymes
Enzymes are macromolecular biological catalysts. Enzymes accelerate, or catalyze,
chemical reactions. The molecules at the beginning of the process are called substrates
and the enzyme converts these into different molecules, called products. The place on
the enzyme where the reaction occurs is called the active site. Almost all metabolic
processes in the cell need enzymes in order to occur at rates fast enough to sustain life.
The set of enzymes made in a cell determines which metabolic pathways occur in that
cell. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Enzymes' specificity comes from their unique three-dimensional structures.
Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy. Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5'-phosphate decarboxylase,
which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzyme activity can be affected
by other molecules. Inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH.
Enzymes serve a wide variety of functions inside living organisms. They are indispensable for signal transduction and cell regulation, often via kinases and phosphatases.
They also generate movement, with myosin hydrolyzing ATP to generate muscle contraction, and also transport cargo around the cell as part of the cytoskeleton. Other ATPases in the cell membrane are ion pumps involved in active transport. Enzymes are
also involved in more exotic functions, such as luciferase generating light in fireflies.
Viruses can also contain enzymes for infecting cells, such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase.
An important function of enzymes is in the digestive systems of animals. Enzymes such
as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules,
for example, are too large to be absorbed from the intestine, but enzymes hydrolyze the
starch chains into smaller molecules such as maltose and eventually glucose, which can
then be absorbed. Different enzymes digest different food substances. In ruminants,
which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase, to break down the cellulose cell walls of plant fiber.
https://en.wikipedia.org/wiki/Enzyme
Index
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EP
Index
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Index
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Epigenetics
genes on and off and affect how cells read genes. Hence, epigenetic research
may or may not be heritable, although the use of the term "epigenetic" to de
esses that are not heritable is controversial. Unlike genetics based on chang
epigenetics have other causes, thus use of the prefix epi- (Greek: - over, o
around).
https://en.wikipedia.org/wiki/Epigenetics
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Epimers
In stereochemistry, epimer refers to one of a pair of stereoisomers. The two isomers differ in configuration at only one stereogenic center. All other stereocenters in the molecules, if any, are the same in each
The sugars glucose and galactose are epimers. In glucose, the -OH group on the first
carbon is in the axial position, the direction opposite the -OH group on carbon C-4. In
galactose, the -OH group is oriented in the same direction, the equatorial position.
The stereoisomers -D-glucopyranose and -D-mannopyranose are epimers because
they differ only in the stereochemistry at the C-2 position.
https://en.wikipedia.org/wiki/Epimer
Epinephrine
Epinephrine, also known as adrenalin or adrenaline, is primarily a medication and hormone. As a medication it is used for a number of conditions including: anaphylaxis, cardiac arrest, and superficial bleeding. Inhaled epinephrine may be used to improve the
symptoms of croup. It may also be used for asthma when other treatments are not effective. It is given intravenously, by injection into a muscle, by inhalation, or by injection just under the skin.
Epinephrine is normally produced by both the adrenal glands and certain neurons. It
plays an important role in the fight-or-flight response by increasing blood flow to muscles, output of the heart, pupil dilation, and blood sugar. Epinephrine does this by its
effects on alpha and beta receptors. It is found in many animals and some one cell organisms.
As a hormone, epinephrine acts on nearly all body tissues. Its actions vary by tissue
type and tissue expression of adrenergic receptors. For example, high levels of epinephrine causes smooth muscle relaxation in the airways but causes contraction of the
smooth muscle that lines most arterioles.
Epinephrine acts by binding to a variety of adrenergic receptors. Epinephrine is a nonselective agonist of all adrenergic receptors, including the major subtypes 1, 2, 1,
2, and 3.Epinephrine's binding to these receptors triggers a number of metabolic
changes. Binding to -adrenergic receptors inhibits insulin secretion by the pancreas,
stimulates glycogenolysis in the liver and muscle, and stimulates glycolysis and inhibits insulin-mediated glycogenesis in muscle. adrenergic receptor binding triggers glucagon secretion in the pancreas, increased adrenocorticotropic hormone (ACTH) secretion by the pituitary gland, and increased lipolysis by adipose tissue. Together, these
effects lead to increased blood glucose and fatty acids, providing substrates for energy
production within cells throughout the body.
https://en.wikipedia.org/wiki/Epinephrine
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Epithelial
Epithelium (epi- + thele + -ium) is one of the four basic types of animal tissue. The
other three types are connective tissue, muscle tissue and nervous tissue. Epithelial tissues line the cavities and surfaces of blood vessels and organs throughout the body.
There are three principal shapes of epithelial cells: squamous, columnar, and cuboidal.
These can be arranged in a single layer of cells as simple epithelium, either squamous,
columnar or cuboidal, or in layers of two or more cells deep as stratified (layered), either squamous, columnar or cuboidal. All glands are made up of epithelial cells. Functions of epithelial cells include secretion, selective absorption, protection, transcellular
transport, and sensing.
Epithelium lines both the outside (skin) and the inside cavities and lumina of bodies.
The outermost layer of human skin is composed of dead stratified squamous, keratinized epithelial cells. Tissues that line the inside of the mouth, the esophagus and
part of the rectum are composed of nonkeratinized stratified squamous epithelium.
Other surfaces that separate body cavities from the outside environment are lined by
simple squamous, columnar, or pseudostratified epithelial cells. Other epithelial cells
line the insides of the lungs, the gastrointestinal tract, the reproductive and urinary
tracts, and make up the exocrine and endocrine glands. The outer surface of the cornea
is covered with fast-growing, easily regenerated epithelial cells. Endothelium (the inner lining of blood vessels, the heart, and lymphatic vessels) is a specialized form of epithelium. Another type, mesothelium, forms the walls of the pericardium, pleurae, and
peritoneum.
Epithelial tissue rests on a basement membrane, which acts as a scaffolding on which
epithelium can grow and regenerate after injuries. Epithelial tissue is innervated, but
avascular. This epithelial tissue must be nourished by substances diffusing from the
blood vessels in the underlying tissue, but they don't have their own blood supply. The
basement membrane acts as a selectively permeable membrane that determines which
substances will be able to enter the epithelium.
https://en.wikipedia.org/wiki/Epithelium
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Epithelium
Epithelium (epi- + thele + -ium) is one of the four basic types of animal tissue. The
other three types are connective tissue, muscle tissue and nervous tissue. Epithelial tissues line the cavities and surfaces of blood vessels and organs throughout the body.
There are three principal shapes of epithelial cells: squamous, columnar, and cuboidal.
These can be arranged in a single layer of cells as simple epithelium, either squamous,
columnar or cuboidal, or in layers of two or more cells deep as stratified (layered), either squamous, columnar or cuboidal. All glands are made up of epithelial cells. Functions of epithelial cells include secretion, selective absorption, protection, transcellular
transport, and sensing.
Epithelium lines both the outside (skin) and the inside cavities and lumina of bodies.
The outermost layer of human skin is composed of dead stratified squamous, keratinized epithelial cells. Tissues that line the inside of the mouth, the esophagus and
part of the rectum are composed of nonkeratinized stratified squamous epithelium.
Other surfaces that separate body cavities from the outside environment are lined by
simple squamous, columnar, or pseudostratified epithelial cells. Other epithelial cells
line the insides of the lungs, the gastrointestinal tract, the reproductive and urinary
tracts, and make up the exocrine and endocrine glands. The outer surface of the cornea
is covered with fast-growing, easily regenerated epithelial cells. Endothelium (the inner lining of blood vessels, the heart, and lymphatic vessels) is a specialized form of epithelium. Another type, mesothelium, forms the walls of the pericardium, pleurae, and
peritoneum.
Epithelial tissue rests on a basement membrane, which acts as a scaffolding on which
epithelium can grow and regenerate after injuries. Epithelial tissue is innervated, but
avascular. This epithelial tissue must be nourished by substances diffusing from the
blood vessels in the underlying tissue, but they don't have their own blood supply. The
basement membrane acts as a selectively permeable membrane that determines which
substances will be able to enter the epithelium.
https://en.wikipedia.org/wiki/Epithelium
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Equilibrium
time. There are no net changes in the concentrations of the reactant(s) and pr
at equilibrium. Such a state is known as dynamic equilibrium.
https://en.wikipedia.org/wiki/List_of_types_of_equilibrium
Index
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Equilibrium Duplicate
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Ergocalciferol
Ergocalciferol (vitamin D2) is a form of vitamin D. Ergocalciferol is a secosteroid
formed by a photochemical bond breaking of a steroid, specifically, by the action of ultraviolet light on ergosterol. Viosterol, the name given to early preparations of irradiated ergosterol, is essentially synonymous with ergocalciferol.
Conflicting evidence exists for how similarly D2 and D3 behave in the body and
whether they are equally active or efficient in production of 1,25-hydroxyvitamin D
(1,25(OH)D), the active hormone. Some preliminary studies indicate D3 is more potent, while others report equal efficacy. Both forms appear to have similar efficacy in
ameliorating rickets and reducing the incidence of falls in elderly patients.
The metabolism of each appears to be different, with the vitamin D binding protein possibly having greater affinity for 25(OH)D3 than for 25(OH)D2, as shown in one study.
Cholecalciferol (vitamin D3) is sensitive to UV radiation and rapidly, but reversibly,
forms other sterols which can further irreversibly convert to ergosterol.
https://en.wikipedia.org/wiki/Ergocalciferol
Erwin Chargaff
who immigrated to the United States during the Nazi era and was a professor
Chargaff discovered two rules that helped lead to the discovery of the double
structure of DNA.
The first rule was that in DNA the number of guanine units equals the numb
sine units, and the number of adenine units equals the number of thymine un
hinted at the base pair makeup of DNA.
The second rule was that the relative amounts of guanine, cytosine, adenine
thymine bases varies from one species to another. This hinted that DNA rath
protein could be the genetic material.
https://en.wikipedia.org/wiki/Erwin_Chargaff
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Erythropoietin
Erythropoietin is a glycoprotein hormone that controls erythropoiesis, or red blood cell
production. It is a cytokine (protein signaling molecule) for erythrocyte (red blood cell)
precursors in the bone marrow.
Erythropoietin is an essential hormone for red blood cell production. Without it, definitive erythropoiesis does not take place. Under hypoxic conditions, the kidney will produce and secrete erythropoietin to increase the production of red blood cells by targeting CFU-E, proerythroblast and basophilic erythroblast subsets in the differentiation.
Erythropoietin has its primary effect on red blood cell progenitors and precursors
(which are found in the bone marrow in humans) by promoting their survival through
protecting these cells from apoptosis.
Erythropoietin has been shown to exert its effects by binding to the erythropoietin receptor (EpoR). EPO is highly glycosylated (40% of total molecular weight), with halflife in blood around five hours. EPO's half-life may vary between endogenous and various recombinant versions. Additional glycosylation or other alterations of EPO via recombinant technology have led to the increase of EPO's stability in blood (thus requiring less frequent injections). EPO binds to the erythropoietin receptor on the red cell
progenitor surface and activates a JAK2 signaling cascade. High level erythropoietin
receptor expression is localized to erythroid progenitor cells. While there are reports
that EPO receptors are found in a number of other tissues, such as heart, muscle, kidney and peripheral/central nervous tissue, those results are confounded by nonspecificity of reagents such as anti-EpoR antibodies. In controlled experiments, EPO receptor
is not detected in those tissues. In the bloodstream, red cells themselves do not express
erythropoietin receptor, so cannot respond to EPO. However, indirect dependence of
red cell longevity in the blood on plasma erythropoietin levels has been reported, a
process termed neocytolysis.
https://en.wikipedia.org/wiki/Erythropoietin
Erythrose-4-phosphate
Erythrose-4-phosphate is a phosphate of the simple sugar erythrose. It is an intermediate in the pentose phosphate pathway and the Calvin cycle. In addition, it serves as a
precursor in the biosynthesis of the aromatic amino acids tyrosine, phenylalanine, and
tryptophan. It is used in the first step of the shikimate pathway. At this stage, phosphoenolpyruvate and erythrose-4-phosphate react to form 3-deoxy-Darabinoheptulosonate-7-phosphate (DAHP), in a reaction catalyzed by the enzyme
DAHP synthase.
https://en.wikipedia.org/wiki/Erythrose_4-phosphate
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G-G
G-G
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
ES
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Ester
Esters are chemical compounds derived from an acid (organic or inorganic) in which at
least one OH (hydroxyl) group is replaced by an Oalkyl (alkoxy) group. Usually, esters are derived from a carboxylic acid and an alcohol. Glycerides, which are fatty acid
esters of glycerol, are important esters in biology, being one of the main classes of lipids, and making up the bulk of animal fats and vegetable oils. Esters with low molecular weight are commonly used as fragrances and found in essential oils and pheromones. Phosphoesters form the backbone of DNA molecules. Nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important
plastics, with monomers linked by ester moieties.
https://en.wikipedia.org/wiki/Ester
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Estradiol
Estradiol, or more precisely, 17-estradiol, is a steroid and estrogen sex hormone, and
the primary female sex hormone. It is named for and is important in the regulation of
the estrous and menstrual female reproductive cycles. Estradiol is essential for the development and maintenance of female reproductive tissues but it also has important
effects in many other tissues including bone. While estrogen levels in men are lower
compared to women, estrogens have essential functions in men as well. Estradiol is
found in most vertebrates as well as many crustaceans, insects, fish, and other animal
species.
In the female, estradiol acts as a growth hormone for tissue of the reproductive organs,
supporting the lining of the vagina, the cervical glands, the endometrium, and the lining of the fallopian tubes. It enhances growth of the myometrium. Estradiol appears
necessary to maintain oocytes in the ovary. During the menstrual cycle, estradiol produced by the growing follicle triggers, via a positive feedback system, the
hypothalamic-pituitary events that lead to the luteinizing hormone surge, inducing ovulation. In the luteal phase, estradiol, in conjunction with progesterone, prepares the endometrium for implantation. During pregnancy, estradiol increases due to placental
production. In baboons, blocking of estrogen production leads to pregnancy loss, suggesting estradiol has a role in the maintenance of pregnancy. Research is investigating
the role of estrogens in the process of initiation of labor. Actions of estradiol are required before the exposure of progesterone in the luteal phase.
A more potent chemical derivative of estradiol, ethinyl estradiol is a major component
of hormonal contraceptives. Combined forms of hormonal contraception contain ethinyl estradiol and a progestin, which both contribute to the inhibition of gonadotropinreleasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH), which accounts for the ability of these birth control methods to prevent
ovulation and thus prevent pregnancy. Other types of hormonal birth control contain
only progestins and no ethinyl estradiol.
https://en.wikipedia.org/wiki/Estradiol
Estriol
Estriol (also oestriol or E3) is one of the three main estrogens produced by the human
body. Estriol is only produced in significant amounts during pregnancy as it is made by
the placenta from 16-hydroxydehydroepiandrosterone sulfate (16-OH DHEAS), an androgen steroid made in the fetal liver and adrenal glands.
In pregnant women with multiple sclerosis, estriol reduces the disease's symptoms noticeably, according to researchers at UCLA's Geffen Medical School. Estriol can be a
weak or strong estrogen depending on if it is given acutely or chronically when given to
immature animals, but is an antagonist when given in combination with estradiol. Estriol may play a role in the development of breast cancer, but based on in vitro research, does appear to act as an antagonist to the G-protein coupled estrogen receptor.
Though estriol is used as part of the primarily North American phenomenon of bioidentical hormone replacement therapy, it is not approved for use by the FDA or Health
Canada. Though initial research in the 1970s suggested it could be used therapeutically
as an estrogen, subsequent research failed to confirm this hypothesis.
https://en.wikipedia.org/wiki/Estriol
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Estrogen
Estrogen is the primary female sex hormone and is responsible for development and
regulation of the female reproductive system and secondary sex characteristics. Estrogen may also refer to any substance, natural or synthetic, that mimics the effects of the
natural hormone. The steroid 17-estradiol is the most potent and prevalent endogenous estrogen, although several metabolites of estradiol also have estrogenic hormonal
activity.
The three major naturally occurring forms of estrogen in women are estrone (E1), estradiol (E2), and estriol (E3). Another type of estrogen called estetrol (E4) is produced only
during pregnancy. Quantitatively, estrogens circulate at lower levels than androgens in
both men and women. While estrogen levels are significantly lower in males compared
to females, estrogens nevertheless also have important physiological roles in males.
Like all steroid hormones, estrogens readily diffuse across the cell membrane. Once inside the cell, they bind to and activate estrogen receptors (ERs) which in turn modulate
the expression of many genes. Additionally, estrogens bind to and activate rapidsignaling membrane estrogen receptors (mERs), such as GPER.
The estrogen known as estradiol is shown below.
https://en.wikipedia.org/wiki/Estrogen
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Estrogen Receptors
Estrogen receptors (ERs) are a group of proteins found inside and on cells. They are receptors that are activated by the hormone estrogen (17-estradiol). Two classes of ER
exist: nuclear estrogen receptors (ER and ER), which are members of the nuclear receptor family of intracellular receptors, and membrane estrogen receptors (mERs)
(GPER (GPR30), ER-X, and Gq-mER), which are mostly G protein-coupled receptors.
Once activated by estrogen, the intracellular ER is able to translocate into the nucleus
and bind to DNA to regulate the activity of different genes (i.e. it is a DNA-binding transcription factor). However, it also has additional functions independent of DNA binding.
In the absence of hormone, estrogen receptors are largely located in the cytosol. Hormone binding to the receptor triggers a number of events starting with migration of
the receptor from the cytosol into the nucleus, dimerization of the receptor, and subsequent binding of the receptor dimer to specific sequences of DNA known as hormone
response elements. The DNA/receptor complex then recruits other proteins that are responsible for the transcription of downstream DNA into mRNA and finally protein that
results in a change in cell function. Estrogen receptors also occur within the cell nucleus, and both estrogen receptor subtypes have a DNA-binding domain and can function as transcription factors to regulate the production of proteins.
The receptor also interacts with activator protein 1 and Sp-1 to promote transcription,
via several co-activators such as PELP-1.
https://en.wikipedia.org/wiki/Estrogen_receptor
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Estrone
Estrone (E1) is an estrogenic hormone secreted by the ovary as well as adipose tissue
with the chemical name of 3-hydroxyestra-1,3,5(10)-triene-17-one and the chemical formula C18H22O2. Estrone is an odorless, solid crystalline powder, white in color with a
melting point of 254.5 C and a specific gravity of 1.23. Estrone is one of several natural estrogens, which also include estriol and estradiol. Estrone is the least abundant of
the three hormones. Estradiol is present almost always in the reproductive female
body, and estriol is abundant primarily during pregnancy.
Estrone is known to be a carcinogen for human females as well as a cause of breast tenderness or pain, nausea, headache, hypertension, and leg cramps in the context of nonendogenous exposure. In men, estrone has been known to cause anorexia, nausea, vomiting, and erectile dysfunction. Estrone is relevant to health and disease states because
of its conversion to estrone sulfate, a long-lived derivative. Estrone sulfate acts as a reservoir that can be converted as needed to the more active estradiol. It is the predominant estrogen in postmenopausal women.
https://en.wikipedia.org/wiki/Estrone
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Ethanol
Ethanol also commonly called alcohol, ethyl alcohol, and drinking alcohol, is the principal type of alcohol found in alcoholic beverages, produced by the fermentation of sugars by yeasts. It is a neurotoxic, psychoactive drug, and one of the oldest recreational
drugs. It can cause alcohol intoxication when consumed in sufficient quantity.
Ethanol in alcoholic beverages and fuel is produced by fermentation. Certain species of
yeast (e.g., Saccharomyces cerevisiae) metabolizes sugar producing ethanol and carbon dioxide. The chemical equations below summarize the conversion:
C6H12O6 2 CH3CH2OH + 2 CO2
C12H22O11 + H2O 4 CH3CH2OH + 4 CO2
Fermentation is the process of culturing yeast under favorable thermal conditions to
produce alcohol. This process is carried out at around 3540C (95104F). Toxicity
of ethanol to yeast limits the ethanol concentration obtainable by brewing; higher concentrations, therefore, are obtained by fortification or distillation. The most ethanoltolerant yeast strains can survive up to approximately 18% ethanol by volume.
To produce ethanol from starchy materials such as cereal grains, the starch must first
be converted into sugars. In brewing beer, this has traditionally been accomplished by
allowing the grain to germinate, or malt, which produces the enzyme amylase. When
the malted grain is mashed, the amylase converts the remaining starches into sugars.
Sugars for ethanol fermentation can be obtained from cellulose. Deployment of this
technology could turn a number of cellulose-containing agricultural by-products, such
as corncobs, straw, and sawdust, into renewable energy resources. Other agricultural
residues such as sugar cane bagasse and energy crops such as switchgrass may also be
a sources of fermentable sugars.
https://en.wikipedia.org/wiki/Ethanol
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Ethanolamine
Ethanolamine, also called 2-aminoethanol or monoethanolamine (often abbreviated as
ETA or MEA), is an organic chemical compound with the formula HOCH2CH2NH2.
The molecule is both a primary amine and a primary alcohol (due to a hydroxyl group).
The ethanolamines comprise a group of amino alcohols. A class of antihistamines is
identified as ethanolamines, which includes carbinoxamine, clemastine, dimenhydrinate, diphenhydramine, and doxylamine.
Ethanolamine is biosynthesized by decarboxylation of serine:
HOCH2CH(CO2H)NH2 HOCH2CH2NH2 + CO2
Ethanolamine is the second-most-abundant head group for phospholipids, substances
found in biological membranes (particularly those of procaryotes), e.g., phosphatidylethanolamine. It is also used in messenger molecules such as palmitoylethanolamide,
which has an effect on CB1 receptors.
https://en.wikipedia.org/wiki/Ethanolamine
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Ether
again be classified into two varieties. If the alkyl groups are the same on bo
https://en.wikipedia.org/wiki/Ether
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Ethidium Bromide
Ethidium bromide is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel
electrophoresis. It is commonly abbreviated as "EtBr", which is also an abbreviation
for bromoethane. When exposed to ultraviolet light, it will fluoresce with an orange
color, intensifying almost 20-fold after binding to DNA.
Ethidium bromide is commonly used to detect nucleic acids in molecular biology laboratories. In the case of DNA this is usually double-stranded DNA from PCRs, restriction digests, etc. Single-stranded RNA can also be detected, since it usually folds back
onto itself and thus provides local base pairing for the dye to intercalate. Detection typically involves a gel containing nucleic acids placed on or under a UV lamp. Since ultraviolet light is harmful to eyes and skin, gels stained with ethidium bromide are usually
viewed indirectly using an enclosed camera, with the fluorescent images recorded as
photographs. Where direct viewing is needed, the viewer's eyes and exposed skin
should be protected. In the laboratory the intercalating properties have long been used
to minimize chromosomal condensation when a culture is exposed to mitotic arresting
agents during harvest. The resulting slide preparations permit a higher degree of resolution, and thus more confidence in determining structural integrity of chromosomes
upon microscopic analysis.
Ethidium bromide has also been used extensively to reduce mitochondrial DNA copy
number in proliferating cells. The effect of EtBr on mitochondrial DNA is used in veterinary medicine to treat trypanosomosis in cattle, as EtBr binds molecules of kinetoplastid DNA and changes their conformation to Z-DNA form. This form inhibits replication
of kinetoplastid DNA which is lethal for trypanosomas.
https://en.wikipedia.org/wiki/Ethidium_bromide
Eukaryotes
A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota. The
defining feature that sets eukaryotic cells apart from prokaryotic cells (bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which
contains the genetic material, and is enclosed by the nuclear envelope.
Eukaryotic cells also contain other membrane-bound organelles such as mitochondria
and the Golgi apparatus. In addition, plants and algae contain chloroplasts. Eukaryotic
organisms may be unicellular, or multicellular. Only eukaryotes have multicellular organisms consisting of many kinds of tissue made up of different cell types.
Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical
cells. In meiosis, DNA replication is followed by two rounds of cell division to produce
four daughter cells each with half the number of chromosomes as the original parent
cell (haploid cells). These act as sex cells (gametes each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes) resulting from genetic recombination during meiosis.
The domain Eukaryota appears to be monophyletic, and so makes up one of the three
domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and
have none of the above features. Eukaryotes represent a tiny minority of all living
things. However, due to their much larger size, eukaryotes' collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1.62.1 billion years ago.
https://en.wikipedia.org/wiki/Eukaryote
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Eukaryotic
A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota. The
defining feature that sets eukaryotic cells apart from prokaryotic cells (bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which
contains the genetic material, and is enclosed by the nuclear envelope.
Eukaryotic cells also contain other membrane-bound organelles such as mitochondria
and the Golgi apparatus. In addition, plants and algae contain chloroplasts. Eukaryotic
organisms may be unicellular, or multicellular. Only eukaryotes have multicellular organisms consisting of many kinds of tissue made up of different cell types.
Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical
cells. In meiosis, DNA replication is followed by two rounds of cell division to produce
four daughter cells each with half the number of chromosomes as the original parent
cell (haploid cells). These act as sex cells (gametes each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes) resulting from genetic recombination during meiosis.
The domain Eukaryota appears to be monophyletic, and so makes up one of the three
domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and
have none of the above features. Eukaryotes represent a tiny minority of all living
things. However, due to their much larger size, eukaryotes' collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1.62.1 billion years ago.
https://en.wikipedia.org/wiki/Eukaryote
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Eumelanin
Melanin is a broad term for a group of natural pigments found in most organisms
(arachnids are one of the few groups in which it has not been detected). Melanin is produced by the oxidation of the amino acid tyrosine, followed by polymerization. The pigment is produced in a specialized group of cells known as melanocytes.
There are three basic types of melanin: eumelanin, pheomelanin, and neuromelanin.
The most common is eumelanin, of which there are two typesbrown eumelanin and
black eumelanin. Pheomelanin is a cysteine-containing red polymer of benzothiazine
units largely responsible for red hair, among other pigmentation. Neuromelanin is
found in the brain, though its function remains obscure.
Eumelanin polymers have long been thought to comprise numerous cross-linked 5,6dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) polymers.
There are two types of eumelaninbrown eumelanin and black eumelaninwhich
chemically differ from each other in their pattern of polymeric bonds. A small amount
of black eumelanin in the absence of other pigments causes grey hair. A small amount
of brown eumelanin in the absence of other pigments causes yellow (blond) color hair.
As the body ages, it continues to produce black melanin but stops producing the brown
version, explaining the grey hair common in the elderly.
Part of the structure of eumelanin is shown below
https://en.wikipedia.org/wiki/Melanin#Eumelanin
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Exclusion Limit
tion method for separating molecules on the basis of size. It works by empl
with tiny tunnels in them that each have a precise opening. The size of the
lar weight will not typically fit into the tunnels and are therefore excluded fr
ing through them.
https://en.wikipedia.org/wiki/Size-exclusion_chromatography
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Exemestane
Exemestane (trade name Aromasin) is a drug used to treat breast cancer. It is a member of the class of drugs known as aromatase inhibitors. Some breast cancers require
estrogen to grow. Those cancers have estrogen receptors (ERs), and are called ERpositive. They may also be called estrogen-responsive, hormonally-responsive, or
hormone-receptor-positive. Aromatase is an enzyme that synthesizes estrogen. Aromatase inhibitors block the synthesis of estrogen. This lowers the estrogen level, and
slows the growth of cancers.
The main source of estrogen is the ovaries in premenopausal women, while in postmenopausal women most of the body's estrogen is produced via the conversion of androgens into estrogen by the aromatase enzyme in the peripheral tissues (i.e. adipose
tissue like that of the breast) and a number of sites in the brain. Estrogen is produced
locally via the actions of the aromatase enzyme in these peripheral tissues where it acts
locally. Any circulating estrogen in post-menopausal women as well as men is the result of estrogen escaping local metabolism and entering the circulatory system.
Exemestane is an irreversible, steroidal aromatase inactivator of type I, structurally related to the natural substrate 4-androstenedione. It acts as a false substrate for the aromatase enzyme, and is processed to an intermediate that binds irreversibly to the active site of the enzyme causing its inactivation, an effect also known as "suicide inhibition." By being structurally similar to enzyme targets, exemestane permanently binds
to the enzymes, preventing them from converting androgen into estrogen.
Type II aromatase inhibitors such as anastrozole and letrozole, by contrast, are not steroids and work by interfering with the aromatase's heme.
https://en.wikipedia.org/wiki/Exemestane
Exocytosis
Exocytosis is a form of active transport in which a cell transports molecules (such as
proteins) out of the cell (exo- + cytosis) by expelling them in an energy-using process.
Exocytosis and its counterpart, endocytosis, are used by all cells because most chemical substances important to them are large polar molecules that cannot pass through
the hydrophobic portion of the cell membrane by passive means.
In exocytosis, membrane-bound secretory vesicles are carried to the cell membrane,
and their contents (water-soluble molecules such as proteins) are secreted into the extracellular environment. This secretion is possible because the vesicle transiently fuses
with the outer cell membrane.
Exocytosis is also a mechanism by which cells are able to insert membrane proteins
(such as ion channels and cell surface receptors), lipids, and other components into the
cell membrane. Vesicles containing these membrane components fully fuse with and
become part of the outer cell membrane.
In the image below, neurotransmitters in vesicles (2) are exocytosed into the synaptic
junction between nerve cells.
https://en.wikipedia.org/wiki/Exocytosis
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Exogenous Pathway
The exogenous pathway is one of three major pathways taken by lipids in the body.
(The others are the endogenous pathway and the reverse transport pathway.)
Dietary fat entering the body from the intestinal system must be transported, as appropriate, to places needing it or storing it. This is the function of the exogenous pathway
of lipid movement in the body (shown in the figure below in green). All dietary lipids
(fats, cholesterol, fat soluble vitamins, and other lipids) are moved by it. In the case of
dietary fat, it begins its journey after ingestion first by being solubilized by bile acids in
the intestinal tract. After passing through the stomach, pancreatic lipases clip two
fatty acids from the fat, leaving a monoacyl glycerol. The fatty acids and monoacyl glycerol are absorbed by intestinal cells (enterocytes) and reassembled back into a fat, and
then this is mixed with phospholipids, cholesterol esters, and apolipoprotein B-48 and
processed to form chylomicrons in the Golgi apparatus and smooth endoplasmic reticulum.
These are exocytosed from the cell into lymph capillaries called lacteals. The chylomicrons pass through the lacteals and enter the bloodstream via the left subclavian vein.
Within the bloodstream, lipoprotein lipase breaks down the fats causing the chylomicron to shrink and become what is known as a chylomicron remnant. It retains its cholesterol and other lipid molecules.
The chylomicron remnants travel to the liver where they are absorbed. This is accomplished by receptors in the liver that recognize and bind to the ApoE of the chylomicrons. The bound complexes are then internalized by endocytosis, degraded in the lysosomes, and the cholesterol is disbursed in the cell.
https://en.wikipedia.org/wiki/Lipoprotein#Exogenous_pathway
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Exons
An exon is any part of a gene that will become a part of the final mature RNA produced
by that gene after introns have been removed by RNA splicing. The term exon refers to
both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA.
In protein-coding genes, the open reading frame (ORF) that codes for a specific portion of the complete protein are located in the exons. However, the term exon is often
misused to refer only to coding sequences for the final protein. This is incorrect, since
many noncoding exons are known in human genes. Exons can include both sequences
that code for amino acids and untranslated sequences. Stretches of unused sequence
called introns are removed, and the exons are joined together to form the final functional mRNA. Some of the exons will be wholly or part of the 5' untranslated region (5'
UTR) or the 3' untranslated region (3' UTR) of each transcript. The untranslated regions are important for efficient translation of the transcript and for controlling the
rate of translation and half-life of the transcript. Furthermore, transcripts made from
the same gene may not have the same exon structure, since parts of the mRNA could
be removed by the process of alternative splicing. Some mRNA transcripts have exons
with no ORFs and, thus, are sometimes referred to as non-coding RNA.
https://en.wikipedia.org/wiki/Exon
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Exonuclease
Exonucleases are enzymes that work by cleaving nucleotides one at a time from the
end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester
bonds at either the 3 or the 5 end occurs. Its close relative is the endonuclease, which
cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover
of mRNA: 5 to 3 exonuclease, which is a dependent decapping protein; 3 to 5 exonuclease, an independent protein; and poly(A)-specific 3 to 5 exonuclease.
In both archaebacteria and eukaryotes, one of the main routes of RNA degradation is
performed by the multi-protein exosome complex, which consists largely of 3' to 5' exoribonucleases.
DNA polymerase I also has 3' to 5' and 5' to 3' exonuclease activity, which is used in editing and proofreading DNA for errors. The 3' to 5' can only remove one mononucleotide at a time, and the 5' to 3' activity can remove mononucleotides or up to 10 nucleotides at a time.
RNA polymerase II is known to be in effect during transcriptional termination. It
works with a 5 exonuclease (human gene Xrn2) to degrade the newly formed transcript downstream, leaving the polyadenylation site and simultaneously shooting the
polymerase. This process involves the exonuclease's catching up to the pol II and terminating the transcription. Pol I then synthesizes DNA nucleotides in place of the RNA
primer it had just removed.
https://en.wikipedia.org/wiki/Exonuclease
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Expression Platform
sion platform. The aptamer directly binds the small molecule, and the expre
Index
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Expression Vector
An expression vector, otherwise known as an expression construct, is usually a plasmid
or virus designed for gene expression in cells. The vector is used to introduce a specific
gene into a target cell, and can commandeer the cell's mechanism for protein synthesis
to produce the protein encoded by the gene. Expression vectors are the basic tools in
biotechnology for the production of proteins. They typically contain at a minimum 1) a
replication origin, 2) a (marker) gene for antibiotic resistance, and 3) a promoter active
in the target cell.
The plasmid is engineered to contain regulatory sequences that act as enhancer and
promoter regions and lead to efficient transcription of the gene carried on the expression vector. The goal of a well-designed expression vector is the efficient production of
protein, and this may be achieved by the production of significant amount of stable
messenger RNA, which can then be translated into protein. The expression of protein
may be tightly controlled and protein is only produced in significant quantity when necessary through the use of an inducer, in some systems however the protein may be expressed constitutively. Escherichia coli is commonly used as the host for protein production, but other cell types may also be used. An example of the use of expression vector is the production of insulin, which is used for medical treatments of diabetes.
Shown below is the structure of the PGEX-3X expression vector.
https://en.wikipedia.org/wiki/Expression_vector
Extra-chromosomal DNA
Extrachromosomal DNA is any DNA that is found outside of the nucleus of a cell. It is
also referred to as extranuclear DNA or cytoplasmic DNA. Most DNA in an individual
genome is found in chromosomes but DNA found outside of the nucleus also serves important biological functions.
In prokaryotes, nonviral extrachromosomal DNA is primarily found in plasmids
whereas in eukaryotes extrachromosomal DNA is primarily found in organelles. Mitochondrial DNA is a main source of this extrachromosomal DNA in eukaryotes. Extrachromosomal DNA is often used in research of replication because it is easy to identify
and isolate.
Extrachromosomal DNA was found to be structurally different from nuclear DNA. Cytoplasmic DNA is less methylated than DNA found within the nucleus. It was also confirmed that the sequences of cytoplasmic DNA was different from nuclear DNA in the
same organism, showing that cytoplasmic DNAs are not simply fragments of nuclear
DNA.
Although prokaryotic organisms do not possess a membrane bound nucleus like the
eukaryotes, they do contain a nucleoid region in which the main chromosome is found.
Extrachromosomal DNA exists in prokaryotes outside of the nucleoid region as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1
kilobase (kb) to a few hundred kb segments, and contain an origin of replication which
allows the plasmid to replicate independently of the bacterial chromosome. The total
number of a particular plasmid within a cell is referred to as the copy number and can
range from as few as two copies per cell to as many as several hundred copies per cell.
https://en.wikipedia.org/wiki/Extrachromosomal_DNA
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Extracellular Matrix
In biology, the extracellular matrix (ECM) is a collection of extracellular molecules secreted by cells that provides structural and biochemical support to the surrounding
cells. Because multicellularity evolved independently in different multicellular lineages, the composition of ECM varies between multicellular structures. However, cell adhesion, cell-to-cell communication and differentiation are common functions of the
ECM.
The animal extracellular matrix includes the interstitial matrix and the basement membrane. Interstitial matrix is present between various animal cells (i.e., in the intercellular spaces). Gels of polysaccharides and fibrous proteins fill the interstitial space and
act as a compression buffer against the stress placed on the ECM. Basement membranes are sheet-like depositions of ECM on which various epithelial cells rest. Each
type of connective tissue in animals has a type of ECM: collagen fibers and bone mineral comprise the ECM of bone tissue. Reticular fibers and ground substance comprise
the ECM of loose connective tissue and blood plasma is the ECM of blood.
The plant ECM includes cell wall components, like cellulose, in addition to more complex signaling molecules. Some single-celled organisms adopt multicelluar biofilms in
which the cells are embedded in an ECM composed primarily of extracellular polymeric substances (EPS).
https://en.wikipedia.org/wiki/Extracellular_matrix
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Extremophiles
An extremophile (from Latin extremus meaning "extreme" and Greek phili ()
meaning "love") is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in
more moderate environments may be termed mesophiles or neutrophiles.
Most known extremophiles are microbes. The domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of bacteria and archaeans. Furthermore, it is erroneous to use the term extremophile to encompass all archaeans, as some are mesophilic. Neither are all extremophiles unicellular; protostome animals found in similar environments include the Pompeii worm, the
psychrophilic Grylloblattidae (insects) and Antarctic krill (a crustacean). Many would
also classify tardigrades (water bears) as extremophiles, but while tardigrades can survive in extreme environments, they are not considered extremophiles because they are
not adapted to live in these conditions. Their chances of dying increase the longer they
are exposed to the extreme environment.
Pictured below - extremophiles living in a Yellowstone hot spring
https://en.wikipedia.org/wiki/Extremophile
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Extrinsic Pathway
In blood clotting, the main role of the tissue factor (extrinsic pathway) is to generate a
"thrombin burst", a process by which thrombin, the most important constituent of the
coagulation cascade in terms of its feedback activation roles, is released very rapidly.
FVIIa circulates in a higher amount than any other activated coagulation factor. The
process includes the following steps:
1. Following damage to the blood vessel, FVII leaves the circulation and comes into
contact with tissue factor (TF) expressed on tissue-factor-bearing cells (stromal fibroblasts and leukocytes), forming an activated complex (TF-FVIIa).
2. TF-FVIIa activates FIX and FX.
3. FVII is itself activated by thrombin, FXIa, FXII and FXa.
4. The activation of FX (to form FXa) by TF-FVIIa is almost immediately inhibited by
tissue factor pathway inhibitor (TFPI).
5. FXa and its co-factor FVa form the prothrombinase complex, which activates
prothrombin to thrombin.
6. Thrombin then activates other components of the coagulation cascade, including FV
and FVIII (which forms a complex with FIX), and activates and releases FVIII from
being bound to vWF.
7. FVIIIa is the co-factor of FIXa, and together they form the "tenase" complex, which
activates FX and so the cycle continues. ("Tenase" is a contraction of "ten" and the
suffix "-ase" used for enzymes.)
https://en.wikipedia.org/wiki/Coagulation#Tissue_factor_pathway_.28extrinsic.29
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F-actin
Actin is a protein found in cells either a free monomer called G-actin (globular) or as
part of a linear polymer microfilament called F-actin (filamentous), both of which are
essential for such important cellular functions as the mobility and contraction of cells
during cell division.
The classical description of F-actin states that it has a filamentous structure that can be
considered to be a single stranded levorotatory helix with a rotation of 166 around the
helical axis and an axial translation of 27.5 , or a single stranded dextrorotatory helix
with a cross over spacing of 350-380 , with each actin surrounded by four more.
The F-actin polymer is considered to have structural polarity due to the fact that all the
microfilaments subunits point towards the same end. This gives rise to a naming convention: the end that possesses an actin subunit that has its ATP binding site exposed
is called the "(-) end", while the opposite end where the cleft is directed at a different
adjacent monomer is called the "(+) end".
https://en.wikipedia.org/wiki/Actin#F-Actin
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F0
The F0 region of ATP synthase is a proton pore that is embedded in the mitochondrial
membrane. It consists of three main subunits A, B, and C, and (in humans) six additional subunits, d, e, f, g, F6, and 8 (or A6L).
According to the current model of ATP synthesis (known as the alternating catalytic
model), the transmembrane potential created by (H+) proton cations supplied by the
electron transport chain, drives the (H+) proton cations from the intermembrane space
through the membrane via the F0 region of ATP synthase. A portion of the F0 (the ring
of c-subunits) rotates as the protons pass through the membrane.
https://en.wikipedia.org/wiki/ATP_synthase#FO-ATP_Synthase_Structure
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F1
The F1 particle of the ATP synthase complex is large and can be seen in the
that pepper the inner mitochondrial membrane. They were originally called
tary particles and were thought to contain the entire respiratory apparatus
(who first isolated the F1 particle in 1961) were able to show that this particl
lated with ATPase activity in uncoupled mitochondria and with the ATPase
Pase activity was further associated with the creation of ATP by a long serie
ments in many laboratories.
https://en.wikipedia.org/wiki/ATP_synthase#F1-ATP_Synthase_structure
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F1,6BP
Fructose 1,6-bisphosphate, also known as Harden-Young ester, is fructose sugar phosphorylated on carbons 1 and 6 (i.e., is a fructosephosphate). The -D-form of this compound is very common in cells. The vast majority of glucose and fructose entering a cell
will become converted to fructose 1,6-bisphosphate at some point.
Fructose 1,6-bisphosphate lies within the glycolysis metabolic pathway and is produced by phosphorylation of fructose 6-phosphate. It is, in turn, broken down into two
compounds: glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. It is an allosteric activator of pyruvate kinase through distinct interactions of binding and allostery at the enzyme's catalytic site.
Fructose 1,6-bis(phosphate) has also been implicated in the ability to bind and sequester Fe(II), a soluble form of iron whose oxidation to the insoluble Fe(III) is capable of
generating reactive oxygen species via Fenton chemistry. The ability of fructose 1,6bis(phosphate) to bind Fe(II) may prevent such electron transfers, and thus act as an
antioxidant within the body. Certain neurodegenerative diseases, like Alzheimer's and
Parkinson's, have been linked to metal deposits with high iron content, although it is
uncertain whether Fenton chemistry plays a substantial role in these diseases, or
whether fructose 1,6-bis(phosphate) is capable of mitigating those effects.
https://en.wikipedia.org/wiki/Fructose_1,6-bisphosphate
F1,6BPase
Fructose-1,6-bisphosphatase (F1,6BPase) is an enzyme that converts fructose-1,6bisphosphate to fructose 6-phosphate in gluconeogenesis and the Calvin cycle which
are both anabolic pathways. Fructose bisphosphatase catalyzes the reverse of the reaction which is catalyzed by phosphofructokinase in glycolysis. These enzymes only catalyze the reaction in one direction each, and are regulated by metabolites such as fructose 2,6-bisphosphate so that high activity of one of the two enzymes is accompanied
by low activity of the other. More specifically, fructose 2,6-bisphosphate allosterically
inhibits fructose 1,6-bisphosphatase, but activates phosphofructokinase-I. Fructose
1,6-bisphosphatase is involved in many different metabolic pathways and found in
most organisms. FBPase requires metal ions for catalysis (Mg++ and Mn++ being preferred) and the enzyme is potently inhibited by Li+.
https://en.wikipedia.org/wiki/Fructose_1,6-bisphosphatase
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F2,6BP
Fructose-2,6-bisphosphate abbreviated Fru-2,6-P2, is a metabolite that allosterically
affects the activity of the enzymes phosphofructokinase 1 (PFK-1) and fructose 1,6bisphosphatase (FBPase-1) to regulate glycolysis and gluconeogenesis. Fru-2,6-P2 is
synthesized and broken down by the bifunctional enzyme phosphofructokinase 2/
fructose-2,6-bisphosphatase (PFK-2/FBPase-2).
The synthesis of Fru-2,6-P2 is performed through the phosphorylation of fructose 6phosphate using ATP by the PFK-2 portion of the enzyme. The breakdown of Fru-2,6P2 is catalyzed by dephosphorylation by FBPase-2 to produce Fructose 6-phosphate
and Pi.
Fru-2,6-P2 strongly activates glucose breakdown in glycolysis through allosteric modulation of phosphofructokinase 1 (PFK-1). Elevated expression of Fru-2,6-P2 levels in
the liver allosterically activates phosphofructokinase 1 by increasing the enzymes affinity for fructose 6-phosphate, while decreasing its affinity for inhibitory ATP and citrate. At physiological concentration, PFK-1 is almost completely inactive, but interaction with Fru-2,6-P2 activates the enzyme to stimulate glycolysis and enhance breakdown of glucose.
The concentration of Fru-2,6-P2 in cells is controlled through regulation of the synthesis and breakdown by PFK-2/FBPase-2. The primary regulators of this are the hormones insulin, glucagon, and epinephrine which affect the enzyme through
phosphorlyation/dephosphorylation reactions. Release of the hormone glucagon triggers production of cyclic adenosine monophosphate (cAMP), which activates a cAMPdependent protein kinase. This kinase phosphorylates the PFK-2/FBPase-2 enzyme at
an NH2-terminal Ser residue with ATP to activate the FBPase-2 activity and inhibit the
PFK-2 activity of the enzyme, thus reducing levels of Fru-2,6-P2 in the cell. With decreasing amounts of Fru-2,6-P2, glycolysis becomes inhibited while gluconeogenesis is
activated. Insulin triggers the opposite response. As a phosphoprotein phosphatase, insulin dephosphorylates the enzyme, thus activating the PFK-2 and inhibiting the
FBPase-2 activities. With additional Fru-2,6-P2 present, activation of PFK-1 occurs to
stimulate glycolysis while inhibiting gluconeogenesis.
https://en.wikipedia.org/wiki/Fructose_2,6-bisphosphate
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Facilitated Diffusion
Facilitated diffusion (also known as facilitated transport or passive-mediated transport) is the process of spontaneous passive transport (as opposed to active transport)
of molecules or ions across a biological membrane via specific transmembrane integral
proteins. Being passive, facilitated transport does not directly require chemical energy
from ATP hydrolysis in the transport step itself. Rather, molecules and ions move
down their concentration gradient reflecting its diffusive nature.
https://en.wikipedia.org/wiki/Facilitated_diffusion
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Facultative Anaerobes
gen is absent. An obligate aerobe, by contrast, cannot make ATP in the abse
gen, and obligate anaerobes die in the presence of oxygen.
https://en.wikipedia.org/wiki/Facultative_anaerobic_organism
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FAD
In biochemistry, flavin adenine dinucleotide (FAD) is a redox cofactor, more specifically a prosthetic group, involved in several important reactions in metabolism. FAD
can exist in three (or four: flavin-N(5)-oxide) different redox states, which are the quinone, semiquinone, and hydroquinone. FAD is converted between these states by accepting or donating electrons.
FAD, in its fully oxidized form, or quinone form, accepts two electrons and two protons
to become FADH2 (hydroquinone form). The semiquinone (FADH) can be formed by
either reduction of FAD or oxidation of FADH2 by accepting or donating one electron
and one proton, respectively. See the mechanism section below for details.
A flavoprotein is a protein that contains a flavin moiety, this may be in the form of FAD
or flavin mononucleotide (FMN). There are many flavoproteins besides components of
the succinate dehydrogenase complex, including -ketoglutarate dehydrogenase and a
component of the pyruvate dehydrogenase complex.
Flavin adenine dinucleotide consists of two main portions: an adenine nucleotide
(adenosine monophosphate) and a flavin mononucleotide bridged together through
their phosphate groups. Adenine is bound to a cyclic ribose at the 1' carbon, while phosphate is bound to the ribose at the 5' carbon to form the adenine nucledotide. Riboflavin is formed by a carbon-nitrogen (C-N) bond between a isoalloxazine and a ribitol.
The phosphate group is then bound to the on the terminal ribose carbon to form a
FMN. Because the bond between the isoalloxazine and the ribitol is not considered to
be a glycosidic bond, the flavin mononucleotide is not truly a nucleotide. This makes
the dinucleotide name misleading. However, the flavin mononucleotide group is still
very close to a nucleotide in its structure and chemical properties.
FAD can be reduced to FADH2 through by the addition of two H+ and two e-. FADH2
can also be oxidized by the loss of one H+ and one e- to form FADH. The FAD form
can be recreated from another loss on one H+ and one e-. FAD formation can also occur through the reduction and dehydration of flavin-N(5)-oxide. Based on the oxidation state, flavins take specific colors when in aqueous solution. FAD (fully oxidized) is
yellow, FADH(half reduced) is either blue or red based on the pH, and the fully reduced form is colorless. Changing the form can have a large impact on other chemical
properties. For example, FAD, the fully oxidized form is subject to nucleophilic attack,
the fully reduced form, FADH2 has high polarizability, while the half reduced form is
unstable in aqueous solution. FAD is an aromatic ring system, whereas FADH2 is not.
This means that FADH2 is significantly higher in energy, without the stabilization
through resonance that the aromatic structure provides. FADH2 is an energy-carrying
molecule, because, once oxidized it regains aromaticity and releases the energy represented by this stabilization.
https://en.wikipedia.org/wiki/Flavin_adenine_dinucleotide
FADH2
In biochemistry, flavin adenine dinucleotide (FAD) is a redox cofactor, more specifically a prosthetic group, involved in several important reactions in metabolism. FAD
can exist in three (or four: flavin-N(5)-oxide) different redox states, which are the quinone, semiquinone, and hydroquinone. FAD is converted between these states by accepting or donating electrons.
FAD, in its fully oxidized form, or quinone form, accepts two electrons and two protons
to become FADH2 (hydroquinone form). The semiquinone (FADH) can be formed by
either reduction of FAD or oxidation of FADH2 by accepting or donating one electron
and one proton, respectively. See the mechanism section below for details.
A flavoprotein is a protein that contains a flavin moiety, this may be in the form of FAD
or flavin mononucleotide (FMN). There are many flavoproteins besides components of
the succinate dehydrogenase complex, including -ketoglutarate dehydrogenase and a
component of the pyruvate dehydrogenase complex.
Flavin adenine dinucleotide consists of two main portions: an adenine nucleotide
(adenosine monophosphate) and a flavin mononucleotide bridged together through
their phosphate groups. Adenine is bound to a cyclic ribose at the 1' carbon, while phosphate is bound to the ribose at the 5' carbon to form the adenine nucledotide. Riboflavin is formed by a carbon-nitrogen (C-N) bond between a isoalloxazine and a ribitol.
The phosphate group is then bound to the on the terminal ribose carbon to form a
FMN. Because the bond between the isoalloxazine and the ribitol is not considered to
be a glycosidic bond, the flavin mononucleotide is not truly a nucleotide. This makes
the dinucleotide name misleading. However, the flavin mononucleotide group is still
very close to a nucleotide in its structure and chemical properties.
FAD can be reduced to FADH2 through by the addition of two H+ and two e-. FADH2
can also be oxidized by the loss of one H+ and one e- to form FADH. The FAD form
can be recreated from another loss on one H+ and one e-. FAD formation can also occur through the reduction and dehydration of flavin-N(5)-oxide. Based on the oxidation state, flavins take specific colors when in aqueous solution. FAD (fully oxidized) is
yellow, FADH(half reduced) is either blue or red based on the pH, and the fully reduced FADH2 form is colorless. Changing the form can have a large impact on other
chemical properties. For example, FAD, the fully oxidized form is subject to nucleophilic attack, the fully reduced form, FADH2 has high polarizability, while the half reduced form is unstable in aqueous solution. FAD is an aromatic ring system, whereas
FADH2 is not. This means that FADH2 is significantly higher in energy, without the stabilization through resonance that the aromatic structure provides. FADH2 is an
energy-carrying molecule, because, once oxidized it regains aromaticity and releases
the energy represented by this stabilization.
https://en.wikipedia.org/wiki/Flavin_adenine_dinucleotide
Index
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FAICAR
https://en.wikipedia.org/wiki/5-Formamidoimidazole-4-carboxamide_ribotid
Index
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Familial Hypercholesterolemia
Familial hypercholesterolemia (abbreviated FH) is a genetic disorder characterized by
high cholesterol levels, specifically very high levels of low-density lipoprotein (LDL,
"bad cholesterol"), in the blood and early cardiovascular disease. Since individuals
with FH underlying body biochemistry is slightly different, their high cholesterol levels
are less responsive to the kinds of cholesterol control methods which are usually more
effective in people without FH (such as dietary modification and statin tablets). Nevertheless, treatment (including higher statin doses) is usually effective.
Many people have mutations in the LDLR gene that encodes the LDL receptor protein,
which normally removes LDL from the circulation, or apolipoprotein B (ApoB), which
is the part of LDL that binds with the receptor. Mutations in other genes are rare. People who have one abnormal copy (are heterozygous) of the LDLR gene may have premature cardiovascular disease at the age of 30 to 40. Having two abnormal copies (being
homozygous) may cause severe cardiovascular disease in childhood. Heterozygous FH
is a common genetic disorder, inherited in an autosomal dominant pattern, occurring
in 1:500 people in most countries. Homozygous FH is much rarer, occurring in 1 in a
million births.
Heterozygous FH is normally treated with statins, bile acid sequestrants, or other lipid
lowering agents that lower cholesterol levels. New cases are generally offered genetic
counseling. Homozygous FH often does not respond to medical therapy and may require other treatments, including LDL apheresis (removal of LDL in a method similar
to dialysis) and occasionally liver transplantation.
https://en.wikipedia.org/wiki/Familial_hypercholesterolemia
Farnesyl Groups
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Farnesyl Pyrophosphate
Farnesyl pyrophosphate (FPP), also known as farnesyl diphosphate (FDP), is an intermediate in both the mevalonate and non-mevalonate pathways used by organisms in
the biosynthesis of terpenes, terpenoids, and sterols.
It is used in the synthesis of CoQ (part of the electron transport chain), as well as being
the immediate precursor of squalene (via the enzyme squalene synthase), dehydrodolichol diphosphate (a precursor of dolichol, which transports proteins to the ER lumen
for N-glycosylation), and geranylgeranyl pyrophosphate (GGPP).
Farnesyl pyrophosphate synthase (a prenyl transferase) catalyzes sequential condensation reactions of dimethylallyl pyrophosphate with 2 units of 3-isopentenyl pyrophosphate to form farnesyl pyrophosphate in the following two steps:
Dimethylallyl pyrophosphate reacts with 3-isopentenyl pyrophosphate to form geranyl pyrophosphate:
Geranyl pyrophosphate then reacts with another molecule of 3-isopentenyl pyrophosphate to form farnesyl pyrophosphate
https://en.wikipedia.org/wiki/Farnesyl_pyrophosphate
Fat
Fat is one of the three main macronutrients: fat, carbohydrate, and protein. Fats, also
known as triglycerides or triacylglycerols, are esters of three fatty acid chains and the
alcohol glycerol.
The terms "oil", "fat", and "lipid" are often confused. "Oil" normally refers to a fat with
short or unsaturated fatty acid chains that is liquid at room temperature, while "fat"
may specifically refer to fats that are solids at room temperature. "Lipid" is the general
term, as a lipid is not necessarily a triglyceride. Fats, like other lipids, are generally hydrophobic, and are soluble in organic solvents and insoluble in water.
Fat is an important foodstuff for many forms of life, and fats serve both structural and
metabolic functions. They are necessary part of the diet of most heterotrophs (including humans). Some fatty acids that are set free by the digestion of fats are called essential because they cannot be synthesized in the body from simpler constituents. There
are two essential fatty acids (EFAs) in human nutrition: -linolenic acid (an -3 fatty
acid) and linoleic acid (an -6 fatty acid). Other lipids needed by the body can be synthesized from these and other fats. Fats and other lipids are broken down in the body
by enzymes called lipases produced in the pancreas.
Fats and oils are categorized according to the number and bonding of the carbon atoms in the aliphatic chain. Fats that are saturated fats have no double bonds between
the carbons in the chain. Unsaturated fats have one or more double bonded carbons in
the chain. The nomenclature is based on the non-acid (non-carbonyl) end of the chain.
This end is called the omega end or the n-end. Thus -linolenic acid is called an -3
fatty acid because the 3rd carbon from that end is the first double bonded carbon in
the chain counting from that end.
Some oils and fats have multiple double bonds and are therefore called polyunsaturated fats. Unsaturated fats can be further divided into cis fats, which are the most common in nature, and trans fats, which are rare in nature. Unsaturated fats can be altered
by reaction with hydrogen effected by a catalyst. This action, called hydrogenation,
tends to break all the double bonds and makes a fully saturated fat. To make vegetable
shortening, then, liquid cis-unsaturated fats such as vegetable oils are hydrogenated to
produce saturated fats, which have more desirable physical properties e.g., they melt at
a desirable temperature (3040C), and store well, whereas polyunsaturated oils go
rancid when they react with oxygen in the air. However, trans fats are generated during hydrogenation as contaminants created by an unwanted side reaction on the catalyst during partial hydrogenation. Consumption of such trans fats has shown to increase the risk of coronary heart disease.
Saturated fats can stack themselves in a closely packed arrangement, so they can solidify easily and are typically solid at room temperature. For example, animal fats tallow
and lard are high in saturated fatty acid content and are solids. Olive and linseed oils
on the other hand are unsaturated and liquid.
Fats serve both as energy sources for the body, and as stores for energy in excess of
what the body needs immediately. Each gram of fat when burned or metabolized releases about 9 food calories (37 kJ = 8.8 kcal). Fats are broken down in the healthy
body to release their constituents, glycerol and fatty acids. Glycerol itself can be converted to glucose by the liver and so become a source of energy.
https://en.wikipedia.org/wiki/Fat
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Fat Catabolism
Fatty acids are released, between meals, from the fat depots in adipose tissue, where
they are stored as triglycerides, as follows:
Lipolysis, the removal of the fatty acid chains from the glycerol to which they are
bound in their storage form as triglycerides (or fats), is carried out by lipases.
Once freed from glycerol, the free fatty acids enter the blood, which transports them,
attached to plasma albumin, throughout the body.
Long chain free fatty acids enter the metabolizing cells (i.e. most living cells in the
body except red blood cells and neurons in the central nervous system) through specific transport proteins, such as the SLC27 family fatty acid transport protein.
Once inside the cell long-chain-fatty-acidCoA ligase catalyzes the reaction between a
fatty acid molecule with ATP (which is broken down to AMP and inorganic pyrophosphate) to give a fatty acyl-adenylate, which then reacts with free coenzyme A to give a
fatty acyl-CoA molecule.
In order for the acyl-CoA to enter the mitochondrion the carnitine shuttle is used:
1 Acyl-CoA is transferred to the hydroxyl group of carnitine by carnitine palmitoyltransferase I, located on the cytosolic faces of the outer and inner mitochondrial membranes.
2 Acyl-carnitine is shuttled inside by a carnitine-acylcarnitine translocase, as a carnitine is shuttled outside.
3 Acyl-carnitine is converted back to acyl-CoA by carnitine palmitoyltransferase II, located on the interior face of the inner mitochondrial membrane. The liberated carnitine is shuttled back to the cytosol, as an acyl-CoA is shuttled into the matrix.
oxidation, in the mitochondrial matrix, then cuts the long carbon chains of the fatty
acids (in the form of acyl-CoA molecules) into a series of two-carbon (acetate) units,
which, combined with co-enzyme A, form molecules of acetyl CoA, which condense
with oxaloacetate to form citrate at the "beginning" of the citric acid cycle. It is convenient to think of this reaction as marking the "starting point" of the cycle, as this is when
fuel - acetyl-CoA - is added to the cycle, which will be dissipated as CO2 and H2O with
the release of a substantial quantity of energy captured in the form of ATP, during the
course of each turn of the cycle.
Briefly, the steps in -oxidation (the initial breakdown of free fatty acids into acetylCoA) are as follows:
1 Dehydrogenation by acyl-CoA dehydrogenase, yielding 1 FADH2
2 Hydration by enoyl-CoA hydratase
3 Dehydrogenation by 3-hydroxyacyl-CoA dehydrogenase, yielding 1 NADH + H+
4 Cleavage by thiolase, yielding 1 acetyl-CoA and a fatty acid that has now been shortened by 2 carbons (forming a new, shortened acyl-CoA)
This -oxidation reaction is repeated until the fatty acid has been completely reduced
to acetyl-CoA or, in, the case of fatty acids with odd numbers of carbon atoms, acetylCoA and 1molecule of propionyl-CoA per molecule of fatty acid. Each -oxidative cut
of the acyl-CoA molecule yields 5 ATP molecules. Additional ATPs come from oxidation of the acetyl-CoA molecules in the mitochondrion.
https://en.wikipedia.org/wiki/Fatty_acid_metabolism#Fatty_acid_catabolism
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called sporadic fatal insomnia (sFI). FFI has no known cure and involves pr
like that of dementia. The average survival span for patients diagnosed with
the onset of symptoms is 18 months.
The mutated protein, called PrPSc, has been found in just 40 families world
ing about 100 people. If only one parent has the gene, the offspring have a
inheriting it and developing the disease.
https://en.wikipedia.org/wiki/Fatal_familial_insomnia
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Fatty Acid
In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with a long
aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty
acids have an unbranched chain of an even number of carbon atoms, from 4 to 28.
Fatty acids are usually derived from triglycerides or phospholipids. Fatty acids are important sources of fuel because, when metabolized, they yield large quantities of ATP.
Many cell types can use either glucose or fatty acids for this purpose. Long-chain fatty
acids cannot cross the bloodbrain barrier and so cannot be used as fuel by the cells of
the central nervous system, but medium-chain fatty acids octanoic acid and heptanoic
acid can be used, in addition to glucose and ketone bodies.
Saturated fatty acids have no double bonds. Thus, saturated fatty acids are saturated
with hydrogen (since double bonds reduce the number of hydrogens on each carbon).
Because saturated fatty acids have only single bonds, each carbon atom within the
chain has 2 hydrogen atoms (except for the carbon at the end that has 3 hydrogens).
Unsaturated fatty acids have one or more double bonds between carbon atoms.
The two carbon atoms in the chain that are bound next to either side of the double
bond can occur in a cis or trans configuration.
A cis configuration means that the two hydrogen atoms adjacent to the double bond
stick out on the same side of the chain. The rigidity of the double bond freezes its conformation and, in the case of the cis isomer, causes the chain to bend and restricts the
conformational freedom of the fatty acid. The more double bonds the chain has in the
cis configuration, the less flexibility it has. When a chain has many cis bonds, it becomes quite curved in its most accessible conformations. For example, oleic acid, with
one double bond, has a "kink" in it, whereas linoleic acid, with two double bonds, has a
more pronounced bend. -linolenic acid, with three double bonds, favors a hooked
shape. The effect of this is that, in restricted environments, such as when fatty acids
are part of a phospholipid in a lipid bilayer, or triglycerides in lipid droplets, cis bonds
limit the ability of fatty acids to be closely packed, and therefore can affect the melting
temperature of the membrane or of the fat.
A trans configuration, by contrast, means that the adjacent two hydrogen atoms lie on
opposite sides of the chain. As a result, they do not cause the chain to bend much, and
their shape is similar to straight saturated fatty acids. In most naturally occurring unsaturated fatty acids, each double bond has three n carbon atoms after it, for some n,
and all are cis bonds. Most fatty acids in the trans configuration are not found in nature and are the result of human processing (e.g., hydrogenation).
The differences in geometry between the various types of unsaturated fatty acids, as
well as between saturated and unsaturated fatty acids, play an important role in biological processes, and in the construction of biological structures (such as cell membranes).
Fatty acids that are required by the human body but cannot be made in sufficient quantity from other substrates, and therefore must be obtained from food, are called essential fatty acids. There are two series of essential fatty acids: one has a double bond
three carbon atoms removed from the methyl end. The other has a double bond six carbon atoms removed from the methyl end. Humans lack the ability to introduce double
bonds in fatty acids beyond carbons 9 and 10, as counted from the carboxylic acid side.
Two essential fatty acids are linoleic acid (LA) and -linolenic acid (ALA). They are
widely distributed in plant oils. The human body has a limited ability to convert ALA
into the longer-chain -3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which can also be obtained from fish.
https://en.wikipedia.org/wiki/Fatty_acid
Index
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Index
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https://en.wikipedia.org/wiki/Fatty_acid_synthase
Index
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https://en.wikipedia.org/wiki/Fatty_acid_synthesis
Index
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Feedback Inhibition
Enzyme inhibitors also occur naturally and are involved in the regulation of
tion line when products begin to build up and is an important way to maint
stasis in a cell.
https://en.wikipedia.org/wiki/Enzyme_inhibitor
Index
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Feedforward Activation
Feedforward activation occurs when a metabolite activates an enzyme that
reaction further ahead in the metabolic pathway in which the metabolite is
vates pyruvate kinase, the enzyme catalyzing the tenth reaction of the the p
This has the effect of pulling the entire pathway forwards by reducing the
tion of metabolites after F1,6BP.
Fermentation
Fermentation is a metabolic process that converts sugar to acids, gases, or alcohol
when oxygen is not available. It occurs in yeast and bacteria, and also in oxygenstarved muscle cells, as in the case of lactic acid fermentation.
Fermentation takes place when the electron transport chain is unusable (often due to
lack of a final electron receptor, such as oxygen), and becomes the cells primary means
of ATP (energy) production. It turns NADH and pyruvate produced in glycolysis into
NAD+ and an organic molecule.
Humans have used fermentation to produce food and beverages since the Neolithic
age. For example, fermentation is used for preservation in a process that produces lactic acid as found in such sour foods as pickled cucumbers, kimchi and yogurt (see fermentation in food processing), as well as for producing alcoholic beverages such as
wine (see fermentation in winemaking) and beer. Fermentation can even occur within
the stomachs of animals, such as humans.
https://en.wikipedia.org/wiki/Fermentation
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Ferredoxin
Ferredoxins are iron-sulfur proteins that mediate electron transfer in a range of meta
bolic reactions.
Ferredoxins are small proteins containing iron and sulfur atoms organized as iron-
sulfur clusters. These biological "capacitors" can accept or discharge electrons, with th
effect of a change in the oxidation state of the iron atoms between +2 and +3. In this
way, ferredoxin acts as an electron transfer agent in biological redox reactions.
https://en.wikipedia.org/wiki/Ferredoxin
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Ferritin
Ferritin is a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including algae,
bacteria, higher plants, and animals. In humans, it acts as a buffer against iron deficiency and iron overload. Ferritin is found in most tissues as a cytosolic protein, but
small amounts are secreted into the serum where it functions as an iron carrier.
Plasma ferritin is also an indirect marker of the total amount of iron stored in the
body, hence serum ferritin is used as a diagnostic test for iron deficiency anemia.
Ferritin is a globular protein complex consisting of 24 protein subunits and is the primary intracellular iron-storage protein in both prokaryotes and eukaryotes, keeping
iron in a soluble and non-toxic form. Ferritin that is not combined with iron is called
apoferritin.
https://en.wikipedia.org/wiki/Ferritin
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Fetal Hemoglobin
Fetal hemoglobin (also hemoglobin F, HbF, or 22) is the main oxygen transport protein in the human fetus during the last seven months of development in the uterus and
persists in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity
than the adult form, giving the developing fetus better access to oxygen from the
mother's bloodstream.
In newborns, fetal hemoglobin is nearly completely replaced by adult hemoglobin by
approximately 6 months postnatally, except in a few thalassemia cases in which there
may be a delay in cessation of HbF production until 35 years of age. In adults, fetal hemoglobin production can be reactivated pharmacologically, which is useful in the treatment of diseases such as sickle-cell disease.
When fetal hemoglobin production is switched off after birth, normal children begin
producing adult hemoglobin (HbA). Children with sickle-cell disease instead begin producing a defective form of hemoglobin called hemoglobin S which aggregates together
and forms filaments that cause red blood cells to change their shape from round to
sickle-shaped. These defective red blood cells have a greater tendency to stack on top
of one another and block blood vessels. These invariably lead to so-called painful vasoocclusive episodes, which are a hallmark of the disease.
If fetal hemoglobin remains the predominant form of hemoglobin after birth, the number of painful episodes decreases in patients with sickle-cell disease. Hydroxyurea promotes the production of fetal hemoglobin and can thus be used to treat sickle-cell disease. The fetal hemoglobin's reduction in the severity of the disease comes from its ability to inhibit the formation of hemoglobin aggregates within red blood cells which also
contain hemoglobin S. Combination therapy with hydroxyurea and recombinant
erythropoietinrather than treatment with hydroxyurea alonehas been shown to further elevate hemoglobin F levels and to promote the development of HbF-containing
F-cells.
https://en.wikipedia.org/wiki/Fetal_hemoglobin
Index
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fGAM
https://en.wikipedia.org/wiki/5%27-Phosphoribosylformylglycinamidine
Index
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Fibrin
Fibrin (also called Factor Ia) is a fibrous, non-globular protein involved in the clotting
of blood. It is formed by the action of the protease thrombin on fibrinogen which
causes it to polymerize. The polymerized fibrin together with platelets forms a hemostatic plug or clot over a wound site.
When the lining of a blood vessel is broken, platelets are attracted forming a platelet
plug. These platelets have thrombin receptors on their surfaces that bind serum thrombin molecules which in turn convert soluble fibrinogen in the serum into fibrin at the
wound site. Fibrin forms long strands of tough insoluble protein that are bound to the
platelets. Factor XIII completes the cross-linking of fibrin so that it hardens and contracts. The cross-linked fibrin forms a mesh atop the platelet plug that completes the
clot.
https://en.wikipedia.org/wiki/Fibrin
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Fibrinogen
Fibrinogen (factor I) is a glycoprotein in vertebrates that helps in the formation of
blood clots. The fibrinogen molecule is a soluble, large, and complex 340kDa plasma
glycoprotein, that is converted by thrombin into fibrin during blood clot formation. It
has a rod-like shape with dimensions of 9 47.5 6nm and it shows a negative net
charge at physiological pH (IP at pH 5.2). Fibrinogen is synthesized in the liver by the
hepatocytes. The concentration of fibrinogen in the blood plasma is 200400mg/dL
(normally measured using the Clauss method).
During normal blood coagulation, a coagulation cascade activates the zymogen
prothrombin by converting it into the serine protease thrombin. Thrombin then converts the soluble fibrinogen into insoluble fibrin strands. These strands are then crosslinked by factor XIII to form a blood clot. FXIIIa stabilizes fibrin further by incorporation of the fibrinolysis inhibitors -2-antiplasmin and TAFI (thrombin activatable fibrinolysis inhibitor, procarboxypeptidase B), and binding to several adhesive proteins of
various cells. Both the activation of factor XIII by thrombin and plasminogen activator
(t-PA) are catalyzed by fibrin. Fibrin specifically binds the activated coagulation factors
factor Xa and thrombin and entraps them in the network of fibers, thus functioning as
a temporary inhibitor of these enzymes, which stay active and can be released during
fibrinolysis. Research from 2011 has shown that fibrin plays a key role in the inflammatory response and development of rheumatoid arthritis.
https://en.wikipedia.org/wiki/Fibrinogen
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Fibroblasts
A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the
structural framework (stroma) for animal tissues, and plays a critical role in wound
healing. Fibroblasts are the most common cells of connective tissue in animals.
The main function of fibroblasts is to maintain the structural integrity of connective tissues by continuously secreting precursors of the extracellular matrix. Fibroblasts secrete the precursors of all the components of the extracellular matrix, primarily the
ground substance and a variety of fibers. The composition of the extracellular matrix
determines the physical properties of connective tissues.
Like other cells of connective tissue, fibroblasts are derived from primitive mesenchyme. Thus they express the intermediate filament protein vimentin, a feature used
as a marker to distinguish their mesodermal origin. However, this test is not specific as
epithelial cells cultured in vitro on adherent substratum may also express vimentin after some time.
In certain situations epithelial cells can give rise to fibroblasts, a process called
epithelial-mesenchymal transition (EMT). Conversely, fibroblasts in some situations
may give rise to epithelia by undergoing a mesenchymal to epithelial transition (MET)
and organizing into a condensed, polarized, laterally connected true epithelial sheet.
This process is seen in many developmental situations (e.g. nephron and notocord development), as well as in wound healing and tumorigenesis.
https://en.wikipedia.org/wiki/Fibroblast
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Fibroin
Fibroin is an insoluble protein present in silk created by spiders, the larvae of Bombyx
mori, other moth genera such as Antheraea, Cricula, Samia and Gonometa, and numerous other insects. Silk in its raw state consists of two main proteins, sericin and fibroin, with a glue-like layer of sericin coating two singular filaments of fibroin called
brins.
The fibroin protein consists of layers of antiparallel sheets. Its primary structure
mainly consists of the recurrent amino acid sequence (Gly-Ser-Gly-Ala-Gly-Ala)n. The
high glycine (and, to a lesser extent, alanine) content allows for tight packing of the
sheets, which contributes to silk's rigid structure and tensile strength. A combination
of stiffness and toughness make it a material with applications in several areas, including biomedicine and textile manufacture.
Fibroin is known to arrange itself in three structures, called silk I, II, and III. Silk I is
the natural form of fibroin, as emitted from the Bombyx mori silk glands. Silk II refers
to the arrangement of fibroin molecules in spun silk, which has greater strength and is
often used in various commercial applications. Silk III is a newly discovered structure
of fibroin. Silk III is formed principally in solutions of fibroin at an interface (i.e. airwater interface, water-oil interface, etc.).
Below, the repeating sequence structure of fibroin is shown.
https://en.wikipedia.org/wiki/Fibroin
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Fibronectin
Fibronectin is a high-molecular weight (~440kDa) glycoprotein of the extracellular matrix that binds to membrane-spanning receptor proteins called integrins. Similar to integrins, fibronectin binds extracellular matrix components such as collagen, fibrin, and
heparan sulfate proteoglycans (e.g. syndecans).
Fibronectin exists as a protein dimer, consisting of two nearly identical monomers
linked by a pair of disulfide bonds. The fibronectin protein is produced from a single
gene, but alternative splicing of its pre-mRNA leads to the creation of several isoforms.
Fibronectin plays a major role in cell adhesion, growth, migration, and differentiation,
and it is important for processes such as wound healing and embryonic development.
Altered fibronectin expression, degradation, and organization has been associated with
a number of pathologies, including cancer and fibrosis.
https://en.wikipedia.org/wiki/Fibronectin
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Fibrous Protein
Scleroproteins or fibrous proteins constitute one of the three main types of proteins
(alongside globular and membrane proteins). There are many scleroprotein superfamilies including keratin, collagen, elastin, and fibroin. The roles of such proteins include
protection and support, forming connective tissue, tendons, bone matrices, and muscle
fiber.
A scleroprotein forms long protein filaments, which are shaped like rods or wires. Scleroproteins are structural proteins or storage proteins that are typically inert and waterinsoluble. A scleroprotein occurs as an aggregate due to hydrophobic side chains that
protrude from the molecule.
A scleroprotein's peptide sequence often has limited residues with repeats. These can
form unusual secondary structures, such as a collagen helix. The structures often feature cross-links between chains (e.g., cys-cys disulfide bonds between keratin chains).
Scleroproteins tend not to denature as easily as globular proteins.
https://en.wikipedia.org/wiki/Scleroprotein
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Flagella
A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The primary role of the flagellum is locomotion but it
also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure. There are large differences between different types of flagella. The prokaryotic
and eukaryotic flagella differ greatly in protein composition, structure, and mechanism
of propulsion. However, both can be used for swimming.
https://en.wikipedia.org/wiki/Flagellum
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Flavin Mononucleotide
Flavin mononucleotide (FMN), or riboflavin-5-phosphate, is a biomolecule produced
from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as prosthetic group of various oxidoreductases including NADH dehydrogenase as well as cofactor in biological blue-light photo receptors. During the catalytic cycle, a reversible
interconversion of the oxidized (FMN), semiquinone (FMNH) and reduced (FMNH2)
forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than
NAD and is particularly useful because it can take part in both one- and two-electron
transfers.
https://en.wikipedia.org/wiki/Flavin_mononucleotide
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Flavonoids
Flavonoids (or bioflavonoids) are a class of plant and fungus secondary metabolites.
Chemically, they have the general structure of a 15-carbon skeleton, which consists of
two phenyl rings (A and B) and heterocyclic ring (C). This carbon structure can be abbreviated C6-C3-C6. According to the IUPAC nomenclature, they can be classified into:
flavonoids or bioflavonoids (flavon backbone shown below)
isoflavonoids, derived from 3-phenylchromen-4-one (3-phenyl-1,4-benzopyrone)
structure
neoflavonoids, derived from 4-phenylcoumarine (4-phenyl-1,2-benzopyrone) structure
The three flavonoid classes above are all ketone-containing compounds, and as such,
are anthoxanthins (flavones and flavonols). This class was the first to be termed bioflavonoids.
https://en.wikipedia.org/wiki/Flavonoid
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Flavoproteins
Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin: the flavin
adenine dinucleotide (FAD) or flavin mononucleotide (FMN).
Flavoproteins are involved in a wide array of biological processes, including, but by no
means limited to, bioluminescence, removal of radicals contributing to oxidative
stress, photosynthesis, DNA repair, and apoptosis. The spectroscopic properties of the
flavin cofactor make it a natural reporter for changes occurring within the active site.
This makes flavoproteins one of the most-studied enzyme families.
The flavoprotein family contains a diverse range of enzymes, including:
Epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein
that binds FMN. This enzyme catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a
--C==C-- double bond.
The B chain of dipicolinate synthase, an enzyme which catalyzes the formation of dipicolinic acid from dihydroxydipicolinic acid.
Phenylacrylic acid decarboxylase EC 4.1.1.-, and enzyme which confers resistance to
cinnamic acid in yeast
https://en.wikipedia.org/wiki/Flavoprotein
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Flippase
Flippases are transmembrane lipid transporter proteins located in the membrane responsible for aiding the movement of phospholipid molecules between the two leaflets
that compose a cell's membrane (transverse diffusion, also known as a "flip-flop" transition). The possibility of active maintenance of an asymmetric distribution of molecules
in the phospholipid bilayer was predicted in the early 1970s by Mark Bretscher. Although phospholipids diffuse rapidly in the plane of the membrane, their polar head
groups cannot pass easily through the hydrophobic center of the bilayer, limiting their
diffusion in this dimension. Some flippases are energy-independent and bidirectional,
causing reversible equilibration of phospholipid between the two sides of the membrane, whereas others are energy-dependent and unidirectional, using energy from
ATP hydrolysis to pump the phospholipid in a preferred direction. Flippases are described as transporters that move lipids from the exoplasmic to the cytosolic face,
while floppases transport in the reverse direction.
https://en.wikipedia.org/wiki/Flippase
Floppase
Flippases are transmembrane lipid transporter proteins located in the membrane responsible for aiding the movement of phospholipid molecules between the two leaflets
that compose a cell's membrane (transverse diffusion, also known as a "flip-flop" transition). The possibility of active maintenance of an asymmetric distribution of molecules
in the phospholipid bilayer was predicted in the early 1970s by Mark Bretscher. Although phospholipids diffuse rapidly in the plane of the membrane, their polar head
groups cannot pass easily through the hydrophobic center of the bilayer, limiting their
diffusion in this dimension. Some flippases are energy-independent and bidirectional,
causing reversible equilibration of phospholipid between the two sides of the membrane, whereas others are energy-dependent and unidirectional, using energy from
ATP hydrolysis to pump the phospholipid in a preferred direction. Flippases are described as transporters that move lipids from the exoplasmic to the cytosolic face,
while floppases transport in the reverse direction.
https://en.wikipedia.org/wiki/Flippase
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Fluorescence
has a longer wavelength, and therefore lower energy, than the absorbed rad
traviolet region of the spectrum, and thus invisible to the human eye, while
light is in the visible region, which gives the fluorescent substance a distinct
can only be seen when exposed to UV light.
https://en.wikipedia.org/wiki/Fluorescence
Index
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https://en.wikipedia.org/wiki/Fluorescence_recovery_after_photobleachi
phore, initially in its electronic excited state, may transfer energy to an acce
Fluoroquinolone
The quinolones are a family of synthetic broad-spectrum antibiotic drugs. Quinolones,
and derivatives, have also been isolated from natural sources (such as plants, animals
and bacteria) and can act as natural antimicrobials and/or signaling molecules.
Quinolones exert their antibacterial effect by preventing bacterial DNA from unwinding and duplicating. The majority of quinolones in clinical use are fluoroquinolones,
which have a fluorine atom attached to the central ring system, typically at the 6position or C-7 position. Most of them are named with the -oxacin suffix.
Shown below is ciprofloxacin, a fluoroquinolone.
https://en.wikipedia.org/wiki/Quinolone
Foam Cells
Foam cells are fat-laden macrophages seen in atherosclerosis. They are an indication
of plaque build-up, or atherosclerosis, which is commonly associated with increased
risk of heart attack and stroke.
Foam cells are formed when the body sends macrophages to the location of a fatty deposit on the blood vessel walls. The macrophage surrounds the fatty material in an attempt to destroy it. The cell becomes filled with lipids (fats). The lipids surrounded by
the macrophage give it a foamy appearance.
In chronic hyperlipidemia, lipoproteins aggregate within the intima of blood vessels
and become oxidized by the action of oxygen free radicals generated either by macrophages or endothelial cells. The macrophages engulf oxidized low-density lipoproteins
(LDLs) by endocytosis via scavenger receptors, which are distinct from LDL receptors.
The oxidized LDL accumulates in the macrophages and other phagocytes, which are
then known as foam cells. Foam cells form the fatty streaks of the plaques of atheroma
in the tunica intima of arteries.
Low-density lipoprotein (LDL) cholesterol is contained by a foam cell. LDL is also
known as bad cholesterol. It becomes a marker for atherosclerosis. Foam cells are the
bodys way of trying to get rid of bad cholesterol from the blood vessels. Foam cells do
not give off any explicit signs or symptoms, but they are part of the origin of atherosclerosis. Foam cells are very small in size and can only be truly detected by examining a
fatty plaque under a microscope after it is removed from the body. HDL cholesterol is
good cholesterol and it removes harmful bad cholesterol from where it does not belong.
Foam cells are not dangerous as such, but can become a problem when they accumulate at particular foci thus creating a necrotic center of atherosclerosis. If the fibrous
cap that prevents the necrotic center from spilling into the lumen of a vessel ruptures,
a thrombus can form which can lead to emboli occluding smaller vessels. The occlusion
of small vessels results in ischemia, and contributes to stroke and myocardial infarction, two of the leading causes of cardiovascular-related death.
https://en.wikipedia.org/wiki/Foam_cell
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Index
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Focal Adhesions
In cell biology, focal adhesions are large macromolecular assemblies through which mechanical force and regulatory signals are transmitted between the extracellular matrix
(ECM) and an interacting cell. More precisely, focal adhesions are the sub-cellular
structures that mediate the regulatory effects (i.e., signaling events) of a cell in response to ECM adhesion.
Focal adhesions are integrin-containing, multi-protein structures that form mechanical links between intracellular actin bundles and the extracellular substrate in many
cell types. Focal adhesions are large, dynamic protein complexes through which the cytoskeleton of a cell connects to the ECM. They are limited to clearly defined ranges of
the cell, at which the plasma membrane closes to within 15nm of the ECM substrate.
Focal adhesions are in a state of constant flux. Proteins associate and disassociate with
it continually as signals are transmitted to other parts of the cell, relating to anything
from cell motility to cell cycle. Focal adhesions can contain over 100 different proteins,
which suggests a considerable functional diversity. More than anchoring the cell, they
function as signal carriers (sensors), which inform the cell about the condition of the
ECM and thus affect their behavior. In sessile cells, focal adhesions are quite stable under normal conditions, while in moving cells their stability is diminished: this is because in motile cells, focal adhesions are being constantly assembled and disassembled
as the cell establishes new contacts at the leading edge, and breaks old contacts at the
trailing edge of the cell. One example of their important role is in the immune system,
in which white blood cells migrate along the connective endothelium following cellular
signals to damaged biological tissue.
https://en.wikipedia.org/wiki/Focal_adhesion
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Folate
Folic acid (conjugate base folate) is a B vitamin. It is also referred to as vitamin M, vitamin B9, vitamin Bc (or folacin), pteroyl-L-glutamic acid, and pteroyl-L-glutamate.
Food supplement manufacturers often use the term folate for something different from
"pure" folic acid. In chemistry, folate refers to the deprotonated ion, and folic acid to
the neutral moleculewhich both coexist in water.
Folate indicates a collection of "folates" that is not chemically well-characterized, including other members of the family of pteroylglutamates, or mixtures of them, having
various levels of reduction of the pteridine ring, one-carbon substitutions and different
numbers of glutamate residues.
Folic acid is synthetically produced, and used in fortified foods and supplements on the
theory that it is converted into folate. However, folic acid is a synthetic oxidized form,
not significantly found in fresh natural foods. To be used it must be converted to tetrahydrofolate (tetrahydrofolic acid) by dihydrofolate reductase (DHFR). Increasing evidence suggests that this process may be slow in humans.
A lack of dietary folates can lead to folate deficiency. A complete lack of dietary folate
takes months before deficiency develops as normal individuals have about 500
20,000micrograms (g) of folate in body stores. This deficiency can result in many
health problems, the most notable one being neural tube defects in developing embryosa relatively rare birth defect affecting 300,000 (0.2%) births globally each year
and 3,000 pregnancies in the United States each year.
The structure of folic acid is shown below.
https://en.wikipedia.org/wiki/Folic_acid
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Folded Protein
Protein folding is the physical process by which a protein chain acquires its native
folds into its characteristic and functional three-dimensional structure from rando
coil.
Failure to fold into native structure generally produces inactive proteins, but in so
erative and other diseases are believed to result from the accumulation of amyloid
brils formed by misfolded proteins. Many allergies are caused by incorrect folding
some proteins, because the immune system does not produce antibodies for certai
protein structures.
https://en.wikipedia.org/wiki/Protein_folding
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Folding
Protein folding is the physical process by which a protein chain acquires its native 3dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. It is the physical process by which a polypeptide
folds into its characteristic and functional three-dimensional structure from random
coil.
The correct three-dimensional structure is essential to function, although some parts
of functional proteins may remain unfolded, so that protein dynamics is important.
Failure to fold into native structure generally produces inactive proteins, but in some
instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by incorrect folding of
some proteins, because the immune system does not produce antibodies for certain
protein structures.
https://en.wikipedia.org/wiki/Protein_folding
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Folding funnel
The folding funnel hypothesis is a specific version of the energy landscape theory of
protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells. Although energy landscapes may be "rough", with many non-native local minima in which partially
folded proteins can become trapped, the folding funnel hypothesis assumes that the native state is a deep free energy minimum with steep walls, corresponding to a single
well-defined tertiary structure.
https://en.wikipedia.org/wiki/Folding_funnel
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Follicle-stimulating Hormone
mone. FSH is synthesized and secreted by the gonadotropic cells of the ante
tive processes of the body. FSH and luteinizing hormone (LH) work togethe
productive system.
https://en.wikipedia.org/wiki/Follicle-stimulating_hormone
Index
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Formyl
https://en.wikipedia.org/wiki/Formylation
Formylated
Formylation has been identified in several critical biological processes. Two form
tion reactions occur in the de novo biosynthesis of purines. These reactions are c
lyzed by the enzymes glycinamide ribonucleotide (GAR) transformylase and 5aminoimidazole-4-carboxyamide ribotide (AICAR) transformylase.
The methionine initiator tRNA is also formylated.
Francis Crick
Francis Harry Compton Crick (8 June 1916 28 July 2004) was a British molecular biologist, biophysicist, and neuroscientist, most noted for being a co-discoverer of the
structure of the DNA molecule in 1953 with James Watson. Together with Watson and
Maurice Wilkins, he was jointly awarded the 1962 Nobel Prize in Physiology or Medicine "for their discoveries concerning the molecular structure of nucleic acids and its
significance for information transfer in living material".
https://en.wikipedia.org/wiki/Francis_Crick
FRAP
https://en.wikipedia.org/wiki/Fluorescence_recovery_after_photobleachi
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Free Radical
A radical (more precisely, a free radical) is an atom, molecule, or ion that has unpaired
valence electrons. With some exceptions, these unpaired electrons make free radicals
highly chemically reactive towards other substances, or even towards themselves: their
molecules will often spontaneously dimerize or polymerize if they come in contact with
each other. Most radicals are reasonably stable only at very low concentrations in inert
media or in a vacuum.
A notable example of a free radical is the hydroxyl radical (shown below), a molecule
that has one unpaired electron on the oxygen atom. Two other examples are triplet oxygen and triplet carbene (:CH2) which have two unpaired electrons. In contrast, the hydroxyl anion (HO) is not a radical, since the unpaired electron is resolved by the addition of an electron. Singlet oxygen and singlet carbene are not radicals as the two electrons are paired.
Free radicals may be created in a number of ways, including synthesis with very dilute
or rarefied reagents, reactions at very low temperatures, or breakup of larger molecules. The latter can be affected by any process that puts enough energy into the parent
molecule, such as ionizing radiation, heat, electrical discharges, electrolysis, and chemical reactions. Indeed, radicals are intermediate stages in many chemical reactions.
Free radicals play an important role in combustion, atmospheric chemistry, polymerization, plasma chemistry, biochemistry, and many other chemical processes. In living
organisms, the free radicals superoxide and nitric oxide and their reaction products
regulate many processes, such as control of vascular tone and thus blood pressure.
They also play a key role in the intermediary metabolism of various biological compounds. Such radicals can even be messengers in a process dubbed redox signaling. A
radical may be trapped within a solvent cage or be otherwise bound.
https://en.wikipedia.org/wiki/Radical_(chemistry)
Fructokinase
Fructokinase also known as D-fructokinase or D-fructose (D-mannose) kinase,
zyme of the liver, intestine, and kidney cortex. Fructokinase is in a family of enz
group from ATP (the substrate) to fructose as the initial step in its utilization. T
Index
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Fructose
Fructose, or fruit sugar, is a simple ketonic monosaccharide found in many plants,
where it is often bonded to glucose to form the disaccharide sucrose. It is one of the
three dietary monosaccharides, along with glucose and galactose, that are absorbed directly into the bloodstream during digestion. Fructose was discovered by French chemist Augustin-Pierre Dubrunfaut in 1847. The name "fructose" was coined in 1857 by the
English chemist William Miller. Pure, dry fructose is a very sweet, white, odorless, crystalline solid and is the most water-soluble of all the sugars. Fructose is found in honey,
tree and vine fruits, flowers, berries, and most root vegetables.
Fructose exists in foods either as a monosaccharide (free fructose) or as a unit of a disaccharide (sucrose). Free fructose is absorbed directly by the intestine. When fructose
is consumed in the form of sucrose, it is digested (broken down) and then absorbed as
free fructose. As sucrose comes into contact with the membrane of the small intestine,
the enzyme sucrase catalyzes the cleavage of sucrose to yield one glucose unit and one
fructose unit, which are then each absorbed. After absorption, it enters the hepatic portal vein and is directed toward the liver.
There are speculations that excessive fructose consumption is a cause of insulin resistance, obesity, elevated LDL cholesterol and triglycerides, leading to metabolic syndrome, type 2 diabetes, and cardiovascular disease. However, the UK's Scientific Advisory Committee on Nutrition in 2015 disputed the claims, demonstrating that "there is
insufficient evidence to demonstrate that fructose intake... leads to adverse health outcomes independent of any effects related to its presence as a component of total and
free sugars.
https://en.wikipedia.org/wiki/Fructose
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Fructose 1,6-bisphosphatase
lyze the reaction in one direction each, and are regulated by metabolites suc
tose 2,6-bisphosphate so that high activity of one of the two enzymes is acco
most organisms. FBPase requires metal ions for catalysis (Mg++ and Mn++ b
ferred) and the enzyme is potently inhibited by Li+.
https://en.wikipedia.org/wiki/Fructose_1,6-bisphosphatase
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Fructose-1-phosphate
Fructose-1-phosphate is a derivative of fructose. It is generated mainly by hepatic fructokinase but is also generated in smaller amounts in the small intestinal mucosa and
proximal epithelium of the renal tubule. It is an important intermediate of glucose metabolism. Because fructokinase has a high Vmax fructose entering cells is quickly phosphorylated to fructose 1-phosphate. In this form it is usually accumulated in the liver
until it undergoes further conversion by aldolase B (the rate limiting enzyme of fructose metabolism).
Aldolase B converts it into glyceraldehyde and dihydroxyacetone phosphate (DHAP).
Glyceraldehyde is then phosphorylated by triose kinase to glyceraldehyde 3-phosphate.
https://en.wikipedia.org/wiki/Fructose_1-phosphate
Fructose-1-phosphate Aldolase
Fructose-1-phosphate aldolase catalyzes the reaction below. It is notable in allowing
metabolism of fructose to bypass PFK and Hexokinase regulation of glycolysis.
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Fructose-6-phosphate
Fructose 6-phosphate (F6P) is fructose sugar phosphorylated on carbon 6 (i.e., is a
fructosephosphate). The -D-form of this compound is very common in cells. The vast
majority of glucose and fructose entering a cell will become converted to this at some
point.
Fructose 6-phosphate lies within the glycolysis metabolic pathway and is produced by
isomerization of glucose 6-phosphate. It is in turn further phosphorylated to fructose1,6-bisphosphate.
F6P can be produced from mannose-6-phosphate action of mannose isomerase.
https://en.wikipedia.org/wiki/Fructose_6-phosphate
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G-G
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Fucose
Fucose is a hexose deoxy sugar with the chemical formula C6H12O5. It is found on Nlinked glycans on the mammalian, insect and plant cell surface, and is the fundamental
sub-unit of the fucoidan polysaccharide. (13) linked core fucose is a suspected carbohydrate antigen for IgE-mediated allergy.
Two structural features distinguish fucose from other six-carbon sugars present in
mammals: the lack of a hydroxyl group on the carbon at the 6-position (C-6) (thereby
making it a deoxy sugar) and the L-configuration. It is equivalent to 6-deoxy-Lgalactose.
In the fucose-containing glycan structures, fucosylated glycans, fucose can exist as a
terminal modification or serve as an attachment point for adding other sugars. In human N-linked glycans, fucose is most commonly linked -1,6 to the reducing terminal
-N-acetylglucosamine. However, fucose at the non-reducing termini linked -1,2 to
galactose forms the H antigen, the substructure of the A and B blood group antigens.
Fucose is released from fucose-containing polymers by an enzyme called -fucosidase.
L-Fucose is claimed to have application in cosmetics, pharmaceuticals, and dietary supplements. However, these claims are often not supported by peer-reviewed scientific
studies.
https://en.wikipedia.org/wiki/Fucose
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Fucoxanthin
ment in the chloroplasts of brown algae and most other heterokonts, giving
https://en.wikipedia.org/wiki/Fucoxanthin
Index
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Fumarase
Fumarase (or fumarate hydratase) is an enzyme that catalyzes the reversible
hydration/dehydration of fumarate to malate. Fumarase comes in two forms: mitochondrial and cytosolic. The mitochondrial isoenzyme is involved in the citric acid cycle and the cytosolic isoenzyme is involved in the metabolism of amino acids and fumarate. Subcellular localization is established by the presence of a signal sequence on
the amino terminus in the mitochondrial form, while subcellular localization in the cytosolic form is established by the absence of the signal sequence found in the mitochondrial variety.
This enzyme participates in two metabolic pathways: citric acid cycle, reductive citric
acid cycle (CO2 fixation), and is also important in renal cell carcinoma. Mutations in
this gene have been associated with the development of leiomyomas in the skin and
uterus in combination with renal cell carcinoma.
https://en.wikipedia.org/wiki/Fumarase
Fumarate
Fumaric acid or trans-butenedioic acid is the chemical compound with the formula
HO2CCH=CHCO2H. This white crystalline compound is one of two isomeric unsaturated dicarboxylic acids, the other being maleic acid. In fumaric acid the carboxylic
acid groups are trans (E) and in maleic acid they are cis (Z). Fumaric acid has a fruitlike taste. The salts and esters are known as fumarates.
https://en.wikipedia.org/wiki/Fumaric_acid
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G-G
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Fungal
A fungus is any member of the group of eukaryotic organisms that includes unicellular
microorganisms such as yeasts and molds, as well as multicellular fungi that produce
familiar fruiting forms known as mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants and
animals.
One difference that places fungi in a different kingdom is that its cell walls contain chitin, unlike the cell walls of plants, bacteria and some protists. Similar to animals, fungi
are heterotrophs, that is, they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Growth is their means of
mobility, except for spores, which may travel through the air or water (a few of which
are flagellated). Fungi are the principal decomposers in ecological systems. These and
other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (is a monophyletic
group), an interpretation that is also strongly supported by molecular phylogenetics.
This fungal group is distinct from the structurally similar myxomycetes (slime molds)
and oomycetes (water molds). The discipline of biology devoted to the study of fungi is
known as mycology (from the Greek , muks, meaning "fungus"). In the past, mycology was regarded as a branch of botany; today it is a separate kingdom in biological
taxonomy. Fungi are genetically more closely related to animals than to plants.
https://en.wikipedia.org/wiki/Fungus
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Furan
Furan is a heterocyclic organic compound, consisting of a five-membered aromatic
ring with four carbon atoms and one oxygen. The class of compounds containing suc
rings are also referred to as furans.
Furan is a colorless, flammable, highly volatile liquid with a boiling point close to roo
temperature. It is soluble in common organic solvents, including alcohol, ether, and
acetone, but is slightly soluble in water. It is toxic and may be carcinogenic in human
Furan is used as a starting point to other specialty chemicals.
https://en.wikipedia.org/wiki/Furan
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Furanoses
A furanose is a collective term for carbohydrates that have a chemical structure that includes a five-membered ring system consisting of four carbon atoms and one oxygen
atom. The name derives from its similarity to the oxygen heterocycle furan, but the furanose ring does not have double bonds.
The chemical structure of fructose in its furanose form is shown below.
A furanose ring is a cyclic hemiacetal of an aldopentose or a cyclic hemiketal of a ketohexose. A furanose ring structure consists of four carbon and one oxygen atom with
the anomeric carbon to the right of the oxygen. The highest numbered chiral carbon
(typically to the left of the oxygen in a Haworth projection) determines whether or not
the structure has a d-configuration or L-configuration. In an l-configuration furanose,
the substituent on the highest numbered chiral carbon is pointed downwards out of
the plane, and in a D-configuration furanose, the highest numbered chiral carbon is facing upwards.
The furanose ring will have either or configuration, depending on which direction
the anomeric hydroxy group is pointing. In a d-configuration furanose, configuration
has the hydroxy pointing down, and has the hydroxy pointing up. It is the opposite in
an l-configuration furanose. Typically, the anomeric carbon undergoes mutarotation in
solution, and the result is an equilibrium mixture of - configurations.
https://en.wikipedia.org/wiki/Furanose
Futile Cycle
A futile cycle, also known as a substrate cycle, occurs when two metabolic pathways
run simultaneously in opposite directions and have no overall effect other than to dissipate energy in the form of heat. For example, if glycolysis and gluconeogenesis were to
be active at the same time, glucose would be converted to pyruvate by glycolysis and
then converted back to glucose by gluconeogenesis, with an overall consumption of
ATP. Futile cycles may have a role in metabolic regulation, where a futile cycle would
be a system oscillating between two states and very sensitive to small changes in the activity of any of the enzymes involved. The cycle does generate heat, and may be used to
maintain thermal homeostasis, for example in the brown adipose tissue of young mammals, or to generate heat rapidly, for example in insect flight muscles and in hibernating animals during periodical arousal from torpor. It has been reported that the glucose metabolism substrate cycle is not a futile cycle but a regulatory process. For example, when energy is suddenly needed, ATP is replaced by AMP, a much more reactive
adenine.
https://en.wikipedia.org/wiki/Futile_cycle
Index
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Futile Cycles
A futile cycle, also known as a substrate cycle, occurs when two metabolic pathw
run simultaneously in opposite directions and have no overall effect other than
pate energy in the form of heat. For example, if glycolysis and gluconeogenesis
ATP. Futile cycles may have a role in metabolic regulation, where a futile cycle w
be a system oscillating between two states and very sensitive to small changes in
tivity of any of the enzymes involved. The cycle does generate heat, and may be
maintain thermal homeostasis, for example in the brown adipose tissue of youn
mals, or to generate heat rapidly, for example in insect flight muscles and in hib
ing animals during periodical arousal from torpor. It has been reported that the
cose metabolism substrate cycle is not a futile cycle but a regulatory process. Fo
ple, when energy is suddenly needed, ATP is replaced by AMP, a much more rea
adenine.
https://en.wikipedia.org/wiki/Futile_cycle
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inlinked receptors (GPLR), constitute a large protein family of receptors, that sense
molecules outside the cell and activate inside signal transduction pathways and, ulti
mately, cellular responses. Coupling with G proteins, they are called seven-
transmembrane receptors because they pass through the cell membrane seven times
There are two principal signal transduction pathways involving the G proteincoupl
receptors:
https://en.wikipedia.org/wiki/G_proteincoupled_receptor
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G-actin
sent as either a free monomer called G-actin (globular) or as part of a linear polym
microfilament called F-actin (filamentous), both of which are essential for such im
tant cellular functions as the mobility and contraction of cells during cell division.
Scanning electron microscope images indicate that G-actin has a globular structur
However, X-ray crystallography shows that each of these globules consists of two l
separated by a cleft. This structure represents the ATPase fold, which is a center
enzymatic catalysis that binds ATP and Mg2+ and hydrolyzes the former to ADP pl
phosphate. This fold is a conserved structural motif that is also found in other pro
that interact with triphosphate nucleotides such as hexokinase (an enzyme used in
cleft but the form that is bound to ATP predominates in cells when actin is present
its free state.
https://en.wikipedia.org/wiki/Actin
G-protein
G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins
that act as molecular switches inside cells, and are involved in transmitting signals
from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to
guanosine diphosphate (GDP). When they are bound to GTP, they are 'on', and, when
they are bound to GDP, they are 'off'. G proteins belong to the larger group of enzymes
called GTPases.
There are two classes of G proteins. The first function as monomeric small GTPases,
while the second form and function as heterotrimeric G protein complexes. The latter
class of complexes is made up of alpha (), beta () and gamma () subunits. In addition, the and subunits can form a stable dimeric complex referred to as the - complex.
G proteins located within the cell are activated by G protein-coupled receptors
(GPCRs) that span the cell membrane. Signaling molecules bind to a domain of the
GPCR located outside the cell, and an intracellular GPCR domain then in turn activates
a particular G protein. Some inactive-state GPCRs have also been shown to be "precoupled" with G proteins. The G protein activates a cascade of further signaling events
that finally results in a change in cell function. G protein-coupled receptor and G proteins working together transmit signals from many hormones, neurotransmitters, and
other signaling factors. G proteins regulate metabolic enzymes, ion channels, transporter proteins, and other parts of the cell machinery, controlling transcription, motility, contractility, and secretion, which in turn regulate diverse systemic functions such
as embryonic development, learning and memory, and homeostasis.
https://en.wikipedia.org/wiki/G_protein
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their intracellular domains after their associated G proteins have been releas
tivated.
The phosphorylated serine and threonine residues act as binding sites for arr
teins that prevent the reassociation of the G proteins with their receptors, the
venting reactivation of the signaling pathway.
Index
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https://en.wikipedia.org/wiki/G_proteincoupled_receptor
Index
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G6P Dehydrogenase
turn maintains the level of glutathione in these cells that helps protect the red bloo
cells against oxidative damage from compounds like hydrogen peroxide. Of greate
synthesis of fatty acids and/or isoprenoids, such as the liver, mammary glands, ad
tissue, and the adrenal glands. G6PD reduces NADP+ to NADPH while oxidizing
glucose-6-phosphate.
https://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase
Index
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G6Pase
resulting in the creation of a phosphate group and free glucose. Glucose is then e
ported from the cell via glucose transporter membrane proteins. This catalysis c
pletes the final step in gluconeogenesis and glycogenolysis and therefore plays a
role in the homeostatic regulation of blood glucose levels.
mic reticulum (ER) by nine transmembrane helices. Its N-terminal and active si
found on the lumen side of the ER and its C-terminus projects into the cytoplasm
Index
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Galactitol
Galactitol (dulcitol) is a sugar alcohol, the reduction product of galactose. In people
with galactokinase deficiency, a form of galactosemia, excess dulcitol forms in the lens
of the eye leading to cataracts.
Galactitol is produced from galactose in a reaction catalyzed by aldose reductase. Galactose itself comes from the metabolism of the disaccharide lactose into glucose and galactose.
The other common galactose metabolism defect is a defect in galactose-1-phosphate
uridylyltransferase, an autosomal recessive disorder, which also causes a buildup of galactitol as a result of increased concentrations of galactose-1-phosphate and galactose.
The toxicity associated with galactose-1-phosphate uridylyltransferase deficiency is associated with symptoms of hepatosplenomegaly and mental retardation in addition to
the cataracts caused by galactitol buildup.
https://en.wikipedia.org/wiki/Galactitol
Galactokinase
tokinase catalyzes the second step of the Leloir pathway, a metabolic pathw
Index
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Galactose
Galactose (galacto- + -ose, "milk sugar"), sometimes abbreviated Gal, is a monosaccharide sugar that is less sweet than glucose and fructose. It is a C-4 epimer of glucose.
Galactose is a monosaccharide. When combined with glucose (monosaccharide),
through a condensation reaction, the result is the disaccharide lactose. The hydrolysis
of lactose to glucose and galactose is catalyzed by the enzymes lactase and galactosidase. The latter is produced by the lac operon in Escherichia coli.
In nature, lactose is found primarily in milk and milk products. Consequently, various
food products made with dairy-derived ingredients, e.g. breads and cereals, can contain lactose. Galactose metabolism, which converts galactose into glucose, is carried
out by the three principal enzymes in a mechanism known as the Leloir pathway. The
enzymes are listed in the order of the metabolic pathway: galactokinase (GALK),
galactose-1-phosphate uridyltransferase (GALT), and UDP-galactose-4-epimerase
(GALE).
In the human body, glucose is changed into galactose via hexoneogenesis to enable the
mammary glands to secrete lactose. However, most lactose in breast milk is synthesized from galactose taken up from the blood, and only 356% is made from galactose
from de novo synthesis. Glycerol also contributes some to the mammary galactose production.
https://en.wikipedia.org/wiki/Galactose
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Galactose-1-phosphate
https://en.wikipedia.org/wiki/Galactose_1-phosphate
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Galacturonic Acid
ponent of pectin, in which it exists as the polymer polygalacturonic acid. In its ope
form, it has an aldehyde group at C1 and a carboxylic acid group at C6. Other oxidiz
forms of D-galactose are D-galactonic acid (carboxylic group at C1) and meso-
galactaric acid (mucic acid) (carboxylic groups at C1 and C6). It is also a uronic acid
hexuronic acid. Naturally occurring uronic acids are D-glucuronic acid, D-galactur
acid, L-iduronic acid and D-mannuronic acid.
https://en.wikipedia.org/wiki/D-Galacturonic_acid
Gamma-aminobutyric Acid
the mammalian central nervous system. It plays the principal role in reducing
GABA is also found in plants. It is the most abundant amino acid in the apopl
matoes. It has also a role in cell signaling in plants.
https://en.wikipedia.org/wiki/Gamma-Aminobutyric_acid
Gamma-glutamylcysteine Synthetase
Glutamate Cysteine Ligase (GCL), previously known as -glutamylcysteine
(GCS), is the first enzyme of the cellular glutathione (GSH) biosynthetic pat
catalyzes the chemical reaction:
L-glutamate + L-cysteine + ATP <---> -glutamyl cysteine + ADP + Pi
GSH, and by extension GCL, is critical to cell survival. Nearly every eukaryo
from plants to yeast to humans, expresses a form of the GCL protein for the
synthesizing GSH.
https://en.wikipedia.org/wiki/Glutamatecysteine_ligase
Gamma-secretase
brane protein that, when cleaved by both and secretase, produces a shor
acid peptide called amyloid whose abnormally folded fibrillar form is the
secretase is also critical in the related processing of several other type I inte
brane proteins, such as Notch, ErbB4, E-cadherin, N-cadherin, ephrin-B2,
https://en.wikipedia.org/wiki/Gamma_secretase
Gamma-turns
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
Turns are classified according to the separation between the two end residues:
In an -turn the end residues are separated by four peptide bonds
(i --> i +/- 4).
In a -turn, by two bonds
(i --> i +/- 2).
Shown below is a turn
https://en.wikipedia.org/wiki/Turn_(biochemistry)
Ganglioside
A ganglioside is a molecule composed of a glycosphingolipid (ceramide and oligosaccharide) with one or more sialic acids (e.g. n-acetylneuraminic acid, NANA) linked on
the sugar chain. NeuNAc, an acetylated derivative of the carbohydrate sialic acid,
makes the head groups of gangliosides anionic at pH 7, which distinguishes them from
globosides.
The oligosaccharide groups on gangliosides extend well beyond the surfaces of the cell
membranes, and act as distinguishing surface markers that can serve as specific determinants in cellular recognition and cell-to-cell communication. These carbohydrate
head groups also act as specific receptors for certain pituitary glycoprotein hormones
and certain bacterial protein toxins such as cholera toxin.
The functions of gangliosides as specific determinants suggest its important role in the
growth and differentiation of tissues as well as in carcinogenesis. It has been found
that tumor formation can induce the synthesis of a new complement of ganglioside,
and very low concentrations of a specific ganglioside can induce differentiation of cultured neuronal tumor cells. Gangliosides GM1, GM2, and GM3 are shown below.
https://en.wikipedia.org/wiki/Ganglioside
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Gap Junctions
A gap junction may also be called a nexus or macula communicans. When found in
nerves it may also be called an electrical synapse. While an ephapse has some similarities to a gap junction, by modern definition the two are different.
Gap junctions are a specialized intercellular connection between a multitude of animal
cell-types. They directly connect the cytoplasm of two cells, which allows various molecules, ions and electrical impulses to directly pass through a regulated gate between
cells.
https://en.wikipedia.org/wiki/Gap_junction
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GAR Synthetase
Phosphoribosylamine-glycine ligase, also known as glycinamide ribonucleotide synthetase (GARS), is an enzyme that catalyzes the chemical reaction:
ATP + 5-phospho-D-ribosylamine + glycine <---> ADP + phosphate + N1-(5-phosphoD-ribosyl)glycinamide
which is the second step in purine biosynthesis. This enzyme belongs to the family of
ligases, specifically those forming generic carbon-nitrogen bonds.
In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). The purD
genes often contain PurD RNA motif in their 5' UTR. In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS). In higher eukaryotes,including humans,
GARS is part of a trifunctional enzyme in conjunction with AIRS and with phosphoribosylglycinamide formyltransferase (GART), forming GARS-AIRS-GART.
In humans, the gene that codes for GARS-AIRS-GART is on chromosome 21, and individuals with Down Syndrome have higher purine levels, which has been correlated
with mental retardation. Thus, studies have been conducted to investigate its involvement in Down Syndrome. It has been found that GARS is expressed for longer in individuals with Down Syndrome than in unaffected individuals. In unaffected individuals,
GARS is highly expressed in the cerebellum before birth but is barely expressed by
three weeks after birth. In individuals with Down Syndrome, GARS expression continues until at least seven weeks after birth. This suggests that GARS may be a main contributor to the development of Down Syndrome. However, so far no mutations to
GARS have been identified that could change its function and cause Down Syndrome
related mental retardation
https://en.wikipedia.org/wiki/Phosphoribosylamineglycine_ligase
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https://en.wikipedia.org/wiki/Ion_channel
Index
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GC Box
In molecular biology, a GC box is a distinct pattern of nucleotides found in
moter region of some eukaryotic genes upstream of the TATA box and appr
110 bases upstream from the transcription initiation site. It has a consensus
Index
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GDP
Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of
pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine.
GDP is the product of GTP dephosphorylation by GTPases, e.g., the G-proteins that are
involved in signal transduction. GDP is converted into GTP with the help of pyruvate
kinase and phosphoenolpyruvate.
https://en.wikipedia.org/wiki/Guanosine_diphosphate
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GDP-glucose
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GDP-mannose
Guanosine diphosphate mannose or GDP-mannose is a nucleotide sugar that is a substrate for glycosyltransferase reactions in metabolism. This compound is a substrate
for enzymes called mannosyltransferases.
GDP-mannose is produced from GTP and mannose-6-phosphate by the enzyme
mannose-1-phosphate guanylyltransferase.
https://en.wikipedia.org/wiki/Guanosine_diphosphate_mannose
Gene
A gene is a locus (or region) of DNA that encodes a functional RNA or protein product,
and is the molecular unit of heredity. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. Most biological traits are under the influence of polygenes (many different genes) as well as the geneenvironment
interactions. Some genetic traits are instantly visible, such as eye color or number of
limbs, and some are not, such as blood type, risk for specific diseases, or the thousands
of basic biochemical processes that comprise life.
Genes can acquire mutations in their sequence, leading to different variants, known as
alleles, in the population. These alleles encode slightly different versions of a protein,
which cause different phenotype traits. Colloquial usage of the term "having a gene"
(e.g., "good genes," "hair color gene") typically refers to having a different allele of the
gene. Genes evolve due to natural selection or survival of the fittest of the alleles.
The concept of a gene continues to be refined as new phenomena are discovered.
For example, regulatory regions of a gene can be far removed from its coding regions,
and coding regions can be split into several exons. Some viruses store their genome in
RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional
product or by regulation of gene expression.
https://en.wikipedia.org/wiki/Gene
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Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein
coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the
product is a functional RNA. The process of gene expression is used by all known life
eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea),
and utilized by virusesto generate the macromolecular machinery for life.
https://en.wikipedia.org/wiki/Gene_expression
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Gene Silencing
Gene silencing is a general term used to describe the regulation of gene expression. In
particular, this term refers to the ability of a cell to prevent the expression of a certain
gene. Gene silencing can occur during either transcription or translation and is often
used in research. In particular, methods used to silence genes are being increasingly
used to produce therapeutics to combat cancer and diseases, such as infectious diseases and neurodegenerative disorders.
Gene silencing is often considered the same as gene knockout. When genes are silenced, their expression is reduced. In contrast, when genes are knocked out, they are
completely erased from the organism's genome and, thus, have no expression. Gene silencing is considered a gene knockdown mechanism since the methods used to silence
genes, such as RNAi, CRISPR, or siRNA, generally reduce the expression of a gene by
at least 70% but do not completely eliminate it. Methods using gene silencing are often
considered better than gene knockouts since they allow researchers to study essential
genes that are required for the animal models to survive and cannot be removed. In addition, they provide a more complete view on the development of diseases since diseases are generally associated with genes that have a reduced expression.
https://en.wikipedia.org/wiki/Gene_silencing
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TFIIA
TFIIB
TFIID
TFIIE
TFIIF
TFIIH
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Genes
A gene is a locus (or region) of DNA that encodes a functional RNA or protein product,
and is the molecular unit of heredity. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. Most biological traits are under the influence of polygenes (many different genes) as well as the geneenvironment
interactions. Some genetic traits are instantly visible, such as eye color or number of
limbs, and some are not, such as blood type, risk for specific diseases, or the thousands
of basic biochemical processes that comprise life.
Genes can acquire mutations in their sequence, leading to different variants, known as
alleles, in the population. These alleles encode slightly different versions of a protein,
which cause different phenotype traits. Colloquial usage of the term "having a gene"
(e.g., "good genes," "hair color gene") typically refers to having a different allele of the
gene. Genes evolve due to natural selection or survival of the fittest of the alleles.
The concept of a gene continues to be refined as new phenomena are discovered.
For example, regulatory regions of a gene can be far removed from its coding regions,
and coding regions can be split into several exons. Some viruses store their genome in
RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional
product or by regulation of gene expression.
https://en.wikipedia.org/wiki/Gene
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Genetic Code
The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) can be both translated into proteins by living cells or
transcribed into non-coding RNAs that serve as regulatory tools in gene regulation. Biological decoding is accomplished by the ribosome, which links amino acids in an order
specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to
read the mRNA three nucleotides at a time. The genetic code is highly similar among
all organisms and can be expressed in a simple table with 64 entries.
https://en.wikipedia.org/wiki/Genetic_code
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Genome
In modern molecular biology and genetics, the genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the
genes, (the coding regions), the noncoding DNA and the genomes of the mitochondria
and chloroplasts.
Some organisms have multiple copies of chromosomes: diploid, triploid, tetraploid
and so on. In classical genetics, in a sexually reproducing organism (typically eukarya)
the gamete has half the number of chromosomes of the somatic cell and the genome is
a full set of chromosomes in a diploid cell. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis.
In haploid organisms, including cells of bacteria, archaea, and in organelles including
mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or
set of circular or linear chains of DNA (or RNA for some viruses), likewise constitute
the genome. The term genome can be applied specifically to mean what is stored on a
complete set of nuclearDNA (i.e.,the "nuclear genome") but can also be applied to
what is stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise
non-chromosomal genetic elements such as viruses, plasmids, and transposable elements.
Typically, when it is said that the genome of a sexually reproducing species has been
"sequenced", it refers to a determination of the sequences of one set of autosomes and
one of each type of sex chromosome, which together represent both of the possible
sexes. Even in species that exist in only one sex, what is described as a "genome sequence" may be a composite read from the chromosomes of various individuals. Colloquially, the phrase "genetic makeup" is sometimes used to signify the genome of a particular individual or organism. The study of the global properties of genomes of related
organisms is usually referred to as genomics, which distinguishes it from genetics
which generally studies the properties of single genes or groups of genes.
Both the number of base pairs and the number of genes vary widely from one species
to another, and there is only a rough correlation between the two (an observation
known as the C-value paradox). At present, the highest known number of genes is
around 60,000, for the protozoan causing trichomoniasis (see List of sequenced
eukaryotic genomes), almost three times as many as in the human genome.
https://en.wikipedia.org/wiki/Genome
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Genomics
structure of genomes (the complete set of DNA within a single cell of an org
stand even the most complex biological systems such as the brain. The field
tasis, pleiotropy and other interactions between loci and alleles within the g
contrast, the investigation of the roles and functions of single genes is a prim
of molecular biology or genetics and is a common topic of modern medical
cal research.
https://en.wikipedia.org/wiki/Genomics
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Geranyl Pyrophosphate
https://en.wikipedia.org/wiki/Geranyl_pyrophosphate
Geranylgeranyl Pyrophosphate
https://en.wikipedia.org/wiki/Geranylgeranyl_pyrophosphate
Ghrelin
Ghrelin (pronounced GREL-in), the "hunger hormone", also known as lenomorelin
petite, ghrelin also plays a significant role in regulating the distribution and rate of use
of energy.
When the stomach is empty, ghrelin is secreted. When the stomach is stretched, secre
tion stops.a It acts on hypothalamic brain cells both to increase hunger, and to increas
gastric acid secretion and gastrointestinal motility to prepare the body for food intake
https://en.wikipedia.org/wiki/Ghrelin
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Index
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Gleevec
Imatinib (INN), marketed by Novartis as Gleevec (Canada, South Africa and the USA)
or Glivec (Australia, Europe and Latin America), investigational name STI-571, is a
tyrosine-kinase inhibitor used in the treatment of multiple cancers, most notably Philadelphia chromosome-positive (Ph+) chronic myelogenous leukemia (CML).
Imatinib kills cancer cells by turning off tyrosine kinase. In order to survive, cells need
signaling through proteins (signal cascade) to keep them alive. Some of the proteins in
this cascade use a phosphate group as an "on" switch. This phosphate group is added
by a tyrosine kinase enzyme. In healthy cells, these tyrosine kinase enzymes are turned
on and off as needed. In Ph-positive CML cells, one tyrosine kinase enzyme, BCR-Abl,
is stuck on the "on" position, and keeps adding phosphate groups. Imatinib blocks this
BCR-Abl enzyme, and stops it from adding phosphate groups. As a result, these cells
stop growing, and even die by a process of cell death (apoptosis). Because the BCR-Abl
tyrosine kinase enzyme exists only in cancer cells and not in healthy cells, imatinib
works as a form of targeted therapyonly cancer cells are killed through the drug's action. In this regard, imatinib was one of the first cancer therapies to show the potential
for such targeted action, and is often cited as a paradigm for research in cancer therapeutics.
Due in large part to the development of Gleevec and related drugs having a similar
mechanism of action, the five year survival rate for people with chronic myeloid leukemia nearly doubled from 31% in 1993 (before Gleevec's 2001 FDA approval) to 59% for
those diagnosed between 2003 and 2009. Compared to older drugs imatinib has a relatively benign side effect profile, allowing many patients to live a normal lifestyle. Median survival for imatinib-treated people with gastrointestinal stromal tumors (GIST)
is nearly 5 years compared to 9 to 20 months in the pre-imatinib-era.
https://en.wikipedia.org/wiki/Imatinib
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Glia
Glial cells, sometimes called neuroglia or simply glia, are non-neuronal cell
tain homeostasis, form myelin, and provide support and protection for neu
central and peripheral nervous systems. In the central nervous system, glia
https://en.wikipedia.org/wiki/Neuroglia
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Globin
The globins are a family of globular proteins, which are thought to share a common ancestor. These proteins all incorporate the globin fold, a series of eight helical segments. Two prominent members of this family include myoglobin and hemoglobin,
which both bind the heme prosthetic group. Both of these proteins are reversible oxygen binders.
Globins are heme-containing proteins involved in binding and/or transporting oxygen.
They belong to a very large and well studied family that is widely distributed in many
organisms.
Globins evolved from a common ancestor and can be divided into three groups: singledomain globins, and two types of chimeric globins, flavohaemoglobins and globincoupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors. Several functionally different
haemoglobins can coexist in the same species. Eight globins are known to occur in vertebrates: androglobin, cytoglobin, globin E, globin X, globin Y, haemoglobin, myoglobin and neuroglobin.
https://en.wikipedia.org/wiki/Globin
Globular
Globular proteins or spheroproteins are spherical ("globe-like") proteins and are one
of the common protein types (the others being fibrous, disordered and membrane proteins). Globular proteins are somewhat water-soluble (forming colloids in water), unlike the fibrous or membrane proteins. There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical
shape.
The spherical structure is induced by the protein's tertiary structure. The molecule's
apolar (hydrophobic) amino acids are bounded towards the molecule's interior
whereas polar (hydrophilic) amino acids are bound outwards, allowing dipole-dipole
interactions with the solvent, which explains the molecule's solubility.
Globular proteins are only marginally stable because the free energy released when the
protein folded into its native conformation is relatively small. This is because protein
folding requires entropic cost. As a primary sequence of a polypeptide chain can form
numerous conformations, native globular structure restricts its conformation to a few
only. It results in a decrease in randomness, although non-covalent interactions such
as hydrophobic interactions stabilize the structure.
https://en.wikipedia.org/wiki/Globular_protein
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Globular Protein
Globular proteins or spheroproteins are spherical ("globe-like") proteins and are one
of the common protein types (the others being fibrous, disordered and membrane proteins). Globular proteins are somewhat water-soluble (forming colloids in water), unlike the fibrous or membrane proteins. There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical
shape.
The spherical structure is induced by the protein's tertiary structure. The molecule's
apolar (hydrophobic) amino acids are bounded towards the molecule's interior
whereas polar (hydrophilic) amino acids are bound outwards, allowing dipole-dipole
interactions with the solvent, which explains the molecule's solubility.
Globular proteins are only marginally stable because the free energy released when the
protein folded into its native conformation is relatively small. This is because protein
folding requires entropic cost. As a primary sequence of a polypeptide chain can form
numerous conformations, native globular structure restricts its conformation to a few
only. It results in a decrease in randomness, although non-covalent interactions such
as hydrophobic interactions stabilize the structure.
https://en.wikipedia.org/wiki/Globular_protein
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Glucagon
Glucagon is a peptide hormone, produced by cells of the pancreas. It works to raise
the concentration of glucose in the bloodstream. Its effect is opposite that of insulin,
which lowers the glucose.
The pancreas releases glucagon when the concentration of glucose in the bloodstream
falls too low. Glucagon causes the liver to convert stored glycogen into glucose, which
is released into the bloodstream. High blood-glucose levels stimulate the release of insulin. Insulin allows glucose to be taken up and used by insulin-dependent tissues.
Thus, glucagon and insulin are part of a feedback system that keeps blood glucose levels at a stable level. It increases energy expenditure and is elevated under conditions of
stress. Glucagon belongs to a family of several other related hormones.
Glucagon generally elevates the concentration of glucose in the blood by promoting gluconeogenesis and glycogenolysis. Glucose is stored in the liver in the form of the polysaccharide glycogen, which is a glucan (a polymer made up of glucose molecules).
Liver cells (hepatocytes) have glucagon receptors. When glucagon binds to the glucagon receptors, the liver cells convert the glycogen into individual glucose molecules
and release them into the bloodstream, in a process known as glycogenolysis. As these
stores become depleted, glucagon then encourages the liver and kidney to synthesize
additional glucose by gluconeogenesis. Glucagon turns off glycolysis in the liver, causing glycolytic intermediates to be shuttled to gluconeogenesis.
Glucagon also regulates the rate of glucose production through lipolysis. Glucagon induces lipolysis in humans under conditions of insulin suppression (such as diabetes
mellitus type 1).
https://en.wikipedia.org/wiki/Glucagon
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Glucocorticoid Hormones
Glucocorticoids (GCs) are a class of corticosteroids, which are a class of steroid hormones. Glucocorticoids are corticosteroids that bind to the glucocorticoid receptor
(GR), that is present in almost every vertebrate animal cell. The name glucocorticoid
(glucose + cortex + steroid) is composed from its role in regulation of glucose metabolism, synthesis in the adrenal cortex, and its steroidal structure. A less common synonym is glucocorticosteroid. GCs are part of the feedback mechanism in the immune
system which reduces certain aspects of immune function, such as reduction of inflammation.
https://en.wikipedia.org/wiki/Glucocorticoid
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Glucocorticoid Receptor
The glucocorticoid receptor (GR, or GCR) also known as NR3C1 (nuclear receptor sub
family 3, group C, member 1) is the receptor to which cortisol and other glucocorticoids bind.
The GR is expressed in almost every cell in the body and regulates genes controlling
the development, metabolism, and immune response. Because the receptor gene is ex
pressed in several forms, it has many different (pleiotropic) effects in different parts o
the body.
When the GR binds to glucocorticoids, its primary mechanism of action is the regula-
tion of gene transcription. The unbound receptor resides in the cytosol of the cell. Aft
Index
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Glucogenic
(although not ketogenic amino acids); from breakdown of lipids (such as tri
they include glycerol (although not fatty acids); and from other steps in met
they include pyruvate and lactate.
https://en.wikipedia.org/wiki/Gluconeogenesis
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Glucokinase
Glucokinase is an enzyme that facilitates phosphorylation of glucose to glucose-6phosphate. Glucokinase occurs in cells in the liver, pancreas, gut, and brain of humans
and most other vertebrates. In each of these organs it plays an important role in the
regulation of carbohydrate metabolism by acting as a glucose sensor, triggering shifts
in metabolism or cell function in response to rising or falling levels of glucose, such as
occur after a meal or when fasting. Mutations of the gene for this enzyme can cause unusual forms of diabetes or hypoglycemia.
Glucokinase (GK) is a hexokinase isozyme, related homologously to at least three other
hexokinases. All of the hexokinases can mediate phosphorylation of glucose to glucose6-phosphate (G6P), which is the first step of both glycogen synthesis and glycolysis.
However, glucokinase is coded by a separate gene and its distinctive kinetic properties
allow it to serve a different set of functions. Glucokinase has a lower affinity for glucose
than the other hexokinases do, and its activity is localized to a few cell types, leaving
the other three hexokinases as more important preparers of glucose for glycolysis and
glycogen synthesis for most tissues and organs. Because of this reduced affinity, the activity of glucokinase, under usual physiological conditions, varies substantially according to the concentration of glucose.
https://en.wikipedia.org/wiki/Glucokinase
Gluconeogenesis
Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. From breakdown of proteins,
these substrates include glucogenic amino acids (although not ketogenic amino acids).
From breakdown of lipids (such as triglycerides), they include glycerol (although not
fatty acids). From other steps in metabolism they include pyruvate and lactate.
Gluconeogenesis is one of several main mechanisms used by humans and many other
animals to maintain blood glucose levels, avoiding low levels (hypoglycemia). Other
means include the degradation of glycogen (glycogenolysis), fatty acid breakdown.
Gluconeogenesis is a ubiquitous process, present in plants, animals, fungi, bacteria,
and other microorganisms. In vertebrates, gluconeogenesis takes place mainly in the
liver and, to a lesser extent, in the cortex of the kidneys. In ruminants, this tends to be
a continuous process. In many other animals, the process occurs during periods of fasting, starvation, low-carbohydrate diets, or intense exercise. The process is highly endergonic until it is coupled to the hydrolysis of ATP or GTP, effectively making the process
exergonic. For example, the pathway leading from pyruvate to glucose-6-phosphate requires 4 molecules of ATP and 2 molecules of GTP to proceed spontaneously. Gluconeogenesis is often associated with ketosis. Gluconeogenesis is also a target of therapy for
type 2 diabetes, such as the antidiabetic drug, metformin, which inhibits glucose formation and stimulates glucose uptake by cells. In ruminants, because metabolizable dietary carbohydrates tend to be metabolized by rumen organisms, gluconeogenesis occurs regardless of fasting, low-carbohydrate diets, exercise, etc.
https://en.wikipedia.org/wiki/Gluconeogenesis
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Glucosamine-6-phosphate
Glucosamine-6-phosphate is a precursor of N-acetylglucosamine and is an
ate in synthesis of the peptidoglycan cell wall layer of bacteria.
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Glucose
Glucose is a sugar with the molecular formula C6H12O6. The suffix "-ose" is a chemical classifier, denoting a carbohydrate. It is also known as grape sugar. With 6 carbon
atoms, it is classed as a hexose, a sub-category of monosaccharides. -D-glucose is one
of the 16 aldose stereoisomers. The D-isomer (D-glucose), also known as dextrose, occurs widely in nature, but the L-isomer (L-glucose) does not. Glucose is made during
photosynthesis from water and carbon dioxide, using energy from sunlight. The reverse of the photosynthesis reaction, which releases this energy, is a very important
source of power for cellular respiration. Glucose is stored as a polymer, in plants as
starch and in animals as glycogen, for times when the organism will need it. Glucose
circulates in the blood of animals as blood sugar. Glucose can be obtained by hydrolysis of carbohydrates such as milk, cane sugar, maltose, cellulose, glycogen etc. It is however, manufactured by hydrolysis of cornstarch by steaming and diluting acid.
Glucose is the most widely used aldohexose in living organisms. One possible explanation for this is that glucose has a lower tendency than other aldohexoses to react nonspecifically with the amine groups of proteins. This reaction glycation impairs or
destroys the function of many proteins. Glucose's low rate of glycation can be attributed to it having a more stable cyclic form compared to other aldohexoses, which
means it spends less time than they do in its reactive open-chain form. The reason for
glucose having the most stable cyclic form of all the aldohexoses is that its hydroxy
groups (with the exception of the hydroxy group on the anomeric carbon of D-glucose)
are in the equatorial position. Many of the long-term complications of diabetes (e.g.,
blindness, renal failure, and peripheral neuropathy) are probably due to the glycation
of proteins or lipids. In contrast, enzyme-regulated addition of sugars to protein is
called glycosylation and is essential for the function of many proteins.
https://en.wikipedia.org/wiki/Glucose
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https://en.wikipedia.org/wiki/Cahill_cycle
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Glucose Metabolism
from carbon dioxide and water by photosynthesis storing the absorbed energy i
nally, often in the form of starch or lipids. Plant components are consumed by a
and fungi, and used as fuel for cellular respiration. Oxidation of one gram of car
drate yields approximately 4 kcal of energy, while the oxidation of one gram of l
yields about 9 kcal. Energy obtained from metabolism (e.g., oxidation of glucos
usually stored temporarily within cells in the form of ATP. Organisms capable o
bic respiration metabolize glucose and oxygen to release energy with carbon dio
and water as byproducts.
https://en.wikipedia.org/wiki/Carbohydrate_metabolism
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Glucose-1-phosphate
Glucose 1-phosphate (also called Cori ester or G1P) is a glucose molecule with a phosphate group on the 1'-carbon. It can exist in either the - or -anomeric form.
Catabolically, G1P is the direct product of the reaction in which glycogen phosphorylase cleaves off a molecule of glucose from a greater glycogen structure.
To be utilized in cellular catabolism it must first be converted to glucose 6-phosphate
by the enzyme phosphoglucomutase. One reason that cells form glucose 1-phosphate
instead of glucose during glycogen breakdown is that the very polar phosphorylated
glucose cannot leave the cell membrane and so is marked for intracellular catabolism.
In glycogen synthesis, free glucose 1-phosphate can react with UTP to form UDPglucose, by using the enzyme UDP-glucose pyrophosphorylase. It can then return to
the greater glycogen structure via glycogen synthase.
https://en.wikipedia.org/wiki/Glucose_1-phosphate
Index
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Glucose-6-phosphate
Glucose 6-phosphate (also known as Robison ester) is glucose sugar phosphorylated
on carbon 6. This compound is very common in cells as the vast majority of glucose entering a cell will become phosphorylated in this way.
Because of its prominent position in cellular chemistry, glucose 6-phosphate has many
possible fates within the cell. It lies at the start of two major metabolic pathways: glycolysis and the pentose phosphate pathway. In addition to these metabolic pathways, glucose 6-phosphate may also be converted to glycogen or starch for storage. This storage
is in the liver and muscles in the form of glycogen for most multicellular animals, and
in intracellular starch or glycogen granules for most other organisms.
Glycolysis
If the cell needs energy or carbon skeletons for synthesis then glucose 6-phosphate is
targeted for glycolysis. Glucose 6-phosphate is first isomerized to fructose 6-phosphate
by phosphoglucose isomerase.
Pentose Phosphate Pathway
When the ratio of NADP+: NADPH increases, the body realizes it needs to produce
more NADPH (a reducing agent for several reactions like fatty acid synthesis and glutathione reduction in erythrocytes). This will cause the G6P to be dehydrogenated by
glucose 6-phosphate dehydrogenase. This irreversible reaction is the initial step of the
pentose phosphate pathway, which generates the useful cofactor NADPH as well as
ribulose-5-phosphate, a carbon source for the synthesis of other molecules. Also, if the
body needs nucleotide precursors of DNA for growth and synthesis, G6P will also be dehydrogenated and enter the pentose phosphate pathway.
Glycogen Synthesis
If blood glucose levels are high, the body needs a way to store the excess glucose. After
being converted to G6P, the molecule can be turned into glucose-1-phosphate by phosphoglucomutase. Glucose-1-phosphate can then be combined with uridine triphosphate (UTP) to form UDP-glucose, driven by the hydrolysis of UTP, releasing phosphate. Now, the activated UDP-glucose can add to a growing glycogen molecule with
the help of glycogen synthase. This is a very efficient storage mechanism for glucose
since it costs the body only 1 ATP to store the 1 glucose molecule and virtually no energy to remove it from storage. It is important to note that glucose-6-phosphate is an
allosteric activator of glycogen synthase, which makes sense because when the level of
glucose is high the body should store the excess glucose as glycogen. On the other
hand, glycogen synthase is inhibited when it is phosphorylated by protein kinase during times of high stress or low levels of blood glucose, via hormone induction by glucagon or adrenaline.
When the body needs glucose for energy, glycogen phosphorylase, with the help of an
orthophosphate, can cleave away a molecule from the glycogen chain. The cleaved
molecule is in the form of glucose-1-phosphate, which can be converted into G6P by
phosphoglucomutase. Next, the phosphoryl group on G6P can be cleaved by glucose-6phosphatase so that a free glucose can be formed. This free glucose can pass through
membranes and can enter the bloodstream to travel to other places in the body.
https://en.wikipedia.org/wiki/Glucose_6-phosphate
Index
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Glucuronic Acid
Glucuronic acid is a uronic acid that was first isolated from urine (hence the name). It
is found in many gums such as Gum arabic (ca. 18%) and Xanthan, and is important
for the metabolism of microorganisms, plants and animals.
Glucuronic acid is a sugar acid derived from glucose, with its sixth carbon atom oxidized to a carboxylic acid. In living beings, this primary oxidation occurs with UDP-D-glucose (UDPG), not with the free sugar.
Glucuronic acid is a common building block of proteoglycans and glycoglycerolipids
such as:
Heparin is an inhibitor of blood coagulation, and occurs in mast cells, lung and liver.
Chondroitin sulfate is found in large quantities in cartilage, aorta, connective tissue,
bone, and skin.
Dermatan sulfate is a proteoglycan in skin, heart, and blood vessels.
Keratan sulfate being found in the cornea, cartilage, and bone.
Hyaluronic acid occurs in large quantities in connective tissues, skin, cartilage, and
synovial fluid.
Glycoglycerolipids of glucuronic or galacturonic acids form the cell walls of bacteria.
https://en.wikipedia.org/wiki/Glucuronic_acid
Index
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Glutamate Dehydrogenase
Glutamate dehydrogenase (GLDH) is an enzyme, present in most microbes and the mitochondria of eukaryotes, as are some of the other enzymes required for urea synthesis, that converts glutamate to -ketoglutarate, and vice versa. In animals, the produced ammonia is usually used as a substrate in the urea cycle. Typically, the ketoglutarate to glutamate reaction does not occur in mammals, as glutamate dehydrogenase equilibrium favors the production of ammonia and -ketoglutarate.
Glutamate dehydrogenase also has a very low affinity for ammonia (high Michaelis constant of about 1 mM), and therefore toxic levels of ammonia would have to be present
in the body for the reverse reaction to proceed (that is, -ketoglutarate and ammonia
to glutamate and NAD(P)+). In bacteria, the ammonia is assimilated to amino acids via
glutamate and aminotransferases. In plants, the enzyme can work in either direction
depending on environment and stress. Transgenic plants expressing microbial GLDHs
are improved in tolerance to herbicide, water deficit, and pathogen infections. They are
more nutritionally valuable.
https://en.wikipedia.org/wiki/Glutamate_dehydrogenase
Index
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Glutamate-5-kinase
Index
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Glutamate-5-semialdehyde
https://en.wikipedia.org/wiki/Glutamate-5-semialdehyde
Glutamate-5-semialdehydy Dehydrogenase
https://en.wikipedia.org/wiki/Glutamate-5-semialdehyde_dehydrogenase
Glutamic Acid
Glutamic acid (abbreviated as Glu or E - encoded by the codons GAA or GAG) is an amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain carboxylic acid, classifying it as a polar negatively charged (at physiological pH), aliphatic amino acid. It is non-essential in humans, meaning the body can
synthesize it.
Glutamate is a key compound in cellular metabolism. In humans, dietary proteins are
broken down by digestion into amino acids, which serve as metabolic fuel for other
functional roles in the body. A key process in amino acid degradation is transamination, in which the amino group of an amino acid is transferred to an -ketoacid, typically catalyzed by a transaminase. The reaction can be generalized as such:
R1-amino acid + R2--ketoacid R1--ketoacid + R2-amino acid
A very common -keto acid is -ketoglutarate, an intermediate in the citric acid cycle.
Transamination of -ketoglutarate gives glutamate. The resulting -ketoacid product
is often a useful one as well, which can contribute as fuel or as a substrate for further
metabolism processes. Examples are as follows:
Alanine + -ketoglutarate Pyruvate + Glutamate
Aspartate + -ketoglutarate Oxaloacetate + Glutamate
Both pyruvate and oxaloacetate are key components of cellular metabolism, contributing as substrates or intermediates in fundamental processes such as glycolysis, gluconeogenesis, and the citric acid cycle.
Glutamate also plays an important role in the body's disposal of excess or waste nitrogen. Glutamate undergoes deamination, an oxidative reaction catalyzed by glutamate
dehydrogenase, as follows:
Glutamate + H2O + NADP+ -ketoglutarate + NADPH + NH3 + H+
Ammonia (as ammonium) is then excreted predominantly as urea, synthesized in the
liver. Transamination can thus be linked to deamination, effectively allowing nitrogen
from the amine groups of amino acids to be removed, via glutamate as an intermediate, and finally excreted from the body in the form of urea.
Glutamate is also a neurotransmitter, which makes it one of the most abundant molecules in the brain. Malignant brain tumors known as glioma or glioblastoma exploit
this phenomenon by using glutamate as an energy source, especially when these mutations become more dependent on glutamate due to mutations in the gene IDH1.
https://en.wikipedia.org/wiki/Glutamic_acid
Index
Find Term
G-G
G-G
G-G
G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure and Function: Proteins
Chapter 2 - Structure & Function: Lipids
Chapter 3 - Membranes: Transport
Chapter 3 - Membranes: Other Considerations
Chapter 4 - Catalysis: Mechanism
Chapter 4 - Catalysis: Mechanism
Chapter 4 - Catalysis: Blood Clotting
Chapter 4 - Catalysis: Blood Clotting
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Glutamine
Glutamine (abbreviated as Gln or Q; encoded by the codons CAA and CAG) is an amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a side chain amide which replaces the side chain hydroxyl of glutamic acid with an
amine functional group, classifying it as a charge neutral, polar (at physiological pH)
amino acid. It is non-essential and conditionally essential in humans, meaning the
body can usually synthesize sufficient amounts of it, but in some instances of stress,
the body's demand for glutamine increases and glutamine must be obtained from the
diet.
Glutamine plays a role in a variety of biochemical functions:
Protein synthesis, as any other of the 20 proteinogenic amino acids
Lipid synthesis, especially by cancer cells.
Regulation of acid-base balance in the kidney by producing ammonium
Cellular energy, as a source, next to glucose
Nitrogen donation for many anabolic processes, including the synthesis of purines
Carbon donation, as a source, refilling the citric acid cycle
Nontoxic transporter of ammonia in the blood circulation
https://en.wikipedia.org/wiki/Glutamine
Index
Find Term
G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Proteins I
Chapter 2 - Structure & Function: Lipids
Chapter 4 - Catalysis: Blood Clotting
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 7 - Information Processing: RNA Processing
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Catalysis
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Information Processing
Glutamine Synthetase
Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism
of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:
Glutamate + ATP + NH3 Glutamine + ADP + Pi
Glutamine Synthetase uses ammonia produced by nitrate reduction, amino acid degradation, and photorespiration. The amide group of glutamate is a nitrogen source for
the synthesis of glutamine pathway metabolites.
Other reactions may take place via GS. Competition between ammonium ion and water, their binding affinities, and the concentration of ammonium ion, influences glutamine synthesis and glutamine hydrolysis. Glutamine is formed if an ammonium ion attacks the acyl-phosphate intermediate, while glutamate is remade if water attacks the
intermediate. Ammonium ion binds more strongly than water to GS due to electrostatic forces between a cation and a negatively charged pocket. Another possible reaction is upon NH2OH binding to GS, rather than NH4+, yields -glutamylhydroxamate.
GS is present predominantly in the brain, kidneys, and liver. GS in the brain participates in the metabolic regulation of glutamate, the detoxification of brain ammonia,
the assimilation of ammonia, recyclization of neurotransmitters, and termination of
neurotransmitter signals. GS, in the brain, is found primarily in astrocytes. Astrocytes
protect neurons against excitotoxicity by taking up excess ammonia and glutamate. In
hyperammonemic environments (high levels of ammonia), astroglial swelling occurs.
Different perspectives have approached the problem of astroglial swelling. One study
shows that morphological changes occur that increase GS expression in glutamatergic
areas or other adaptations that alleviates high levels of glutamate and ammonia. Another perspective is that astrocyte swelling is due to glutamine accumulation. To prevent increased levels of cortical glutamate and cortical water content, a study has been
conducted to prevent GS activity in rats by the use of MSO.
https://en.wikipedia.org/wiki/Glutamine_synthetase
Index
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Glutaredoxin
Glutaredoxins are small redox enzymes of approximately one hundred amino-acid residues that use glutathione as a cofactor. Glutaredoxins are oxidized by substrates, and
reduced non-enzymatically by glutathione. In contrast to thioredoxins, which are reduced by thioredoxin reductase, no oxidoreductase exists that specifically reduces glutaredoxins. Instead, glutaredoxins are reduced by the oxidation of glutathione. Oxidized glutathione is then regenerated by glutathione reductase. Together these components compose the glutathione system.
Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active
center disulfide bond. It exists in either a reduced or an oxidized form where the two
cysteine residues are linked in an intramolecular disulfide bond. Glutaredoxins function as electron carriers in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Moreover, GRX act in antioxidant defence by reducing dehydroascorbate, peroxiredoxins, and methionine sulfoxide reductase. Beside their function in antioxidant defence, bacterial and plant GRX were shown
to bind iron-sulfur clusters and to deliver the cluster to enzymes on demand.
https://en.wikipedia.org/wiki/Glutaredoxin
Index
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Glutathione
Glutathione (GSH) is an important antioxidant in plants, animals, fungi, and some bacteria and archaea, preventing damage to important cellular components caused by reactive oxygen species such as free radicals, peroxides, lipid peroxides and heavy metals.
It is a tripeptide with a peptide linkage between the carboxyl group of the glutamate
side-chain and the amine group of cysteine (which is attached by normal peptide linkage to a glycine).
Thiol groups are reducing agents, existing at a concentration around 5 mM in animal
cells. Glutathione reduces disulfide bonds formed within cytoplasmic proteins to cysteines by serving as an electron donor. In the process, glutathione is converted to its
oxidized form, glutathione disulfide (GSSG), also called L-()-glutathione.
Once oxidized, glutathione can be reduced back by glutathione reductase, using
NADPH as an electron donor. The ratio of reduced glutathione to oxidized glutathione
within cells is often used as a measure of cellular toxicity.
Glutathione exists in both reduced (GSH) and oxidized (GSSG) states. In the reduced
state, the thiol group of cysteine is able to donate a reducing equivalent (H+ + e) to
other unstable molecules, such as reactive oxygen species. In donating an electron, glutathione itself becomes reactive, but readily reacts with another reactive glutathione to
form glutathione disulfide (GSSG). Such a reaction is probable due to the relatively
high concentration of glutathione in cells (up to 5 mM in the liver).
Generally, interactions between GSH and other molecules with higher relative electrophilicity deplete GSH levels within the cell. An exception to this case involves the sensitivity of GSH to the electrophilic compound's relative concentration. In high concentrations, the organic molecule Diethyl maleate fully depleted GSH levels in cells. However, in low concentrations, a minor decease in cellular GSH levels was followed by a
two-fold increase.
GSH can be regenerated from GSSG by the enzyme glutathione reductase (GSR):
NADPH reduces FAD present in GSR to produce a transient FADH-anion. This anion
then quickly breaks a disulfide bond (Cys58 - Cys63) and leads to Cys63's nucleophilically attacking the nearest sulfide unit in the GSSG molecule (promoted by His467),
which creates a mixed disulfide bond (GS-Cys58) and a GS-anion. His467 of GSR then
protonates the GS-anion to form the first GSH. Next, Cys63 nucleophilically attacks
the sulfide of Cys58, releasing a GS-anion, which, in turn, picks up a solvent proton
and is released from the enzyme, thereby creating the second GSH. So, for every GSSG
and NADPH, two reduced GSH molecules are gained, which can again act as antioxidants scavenging reactive oxygen species in the cell.
In healthy cells and tissue, more than 90% of the total glutathione pool is in the reduced form (GSH) and less than 10% exists in the disulfide form (GSSG). An increased
GSSG-to-GSH ratio is considered indicative of oxidative stress.
Glutathione has multiple functions:
It is the major endogenous antioxidant produced by the cells, participating directly in
the neutralization of free radicals and reactive oxygen compounds, as well as maintaining exogenous antioxidants such as vitamins C and E in their reduced (active) forms.
Regulation of the nitric oxide cycle is critical for life, but can be problematic if unregulated.
It is used in metabolic and biochemical reactions such as DNA synthesis and repair,
protein synthesis, prostaglandin synthesis, amino acid transport, and enzyme activation. Thus, every system in the body can be affected by the state of the glutathione system, especially the immune system, the nervous system, the gastrointestinal system,
and the lungs.
It has a vital function in iron metabolism. Yeast cells depleted of or containing toxic
levels of GSH show an intense iron starvation-like response and impairment of the activity of extramitochondrial ISC enzymes, followed by death.
https://en.wikipedia.org/wiki/Glutathione
Index
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Glutathione Peroxidase
Glutathione peroxidase (GPx) is the general name of an enzyme family with peroxidase
activity whose main biological role is to protect the organism from oxidative damage.
The biochemical function of glutathione peroxidase is to reduce lipid hydroperoxides
to their corresponding alcohols and to reduce free hydrogen peroxide to water.
The main reaction that glutathione peroxidase catalyzes is:
2GSH + H2O2 GSSG + 2H2O
where GSH represents reduced monomeric glutathione, and GSSG represents glutathione disulfide. The mechanism involves oxidation of the selenol of a selenocysteine
residue by hydrogen peroxide. This process gives the derivative with a selenenic acid
(RSeOH) group. The selenenic acid is then converted back to the selenol by a two step
process that begins with reaction with GSH to form the GS-SeR and water. A second
GSH molecule reduces the GS-SeR intermediate back to the selenol, releasing GS-SG
as the by-product. A simplified representation is shown below:
RSeH + H2O2 RSeOH + H2O
RSeOH + GSH GS-SeR + H2O
GS-SeR + GSH GS-SG + RSeH
Glutathione reductase then reduces the oxidized glutathione to complete the cycle:
GSSG + NADPH + H+ 2 GSH + NADP+.
It has been shown that low levels of glutathione peroxidase as measured in the serum
may be a contributing factor to vitiligo. Lower plasma glutathione peroxide levels were
also observed in patients with type 2 diabetes with macroalbuminuria and this was correlated to the stage of diabetic nephropathy. In one study, the activity of glutathione
peroxidase along with other antioxidant enzymes such as superoxide dismutase and
catalase was not associated with coronary heart disease risk in women. Glutathione peroxidase activity was found to be much lower in patients with relapsing-remitting multiple sclerosis. One study has suggested that glutathione peroxidase and superoxide dismutase polymorphisms play a role in the development of celiac disease.
https://en.wikipedia.org/wiki/Glutathione_peroxidase
Index
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Glutathione Reductase
Glutathione reductase (GR) also known as glutathione-disulfide reductase (GSR) is an
enzyme that in humans is encoded by the GSR gene. Glutathione reductase catalyzes
the reduction of glutathione disulfide (GSSG) to the sulfhydryl form glutathione
(GSH), which is a critical molecule in resisting oxidative stress and maintaining the reducing environment of the cell. Glutathione reductase functions as dimeric disulfide
oxidoreductase and utilizes an FAD prosthetic group and NADPH to reduce one molar
equivalent of GSSG to two molar equivalents of GSH.
Glutathione plays a key role in maintaining proper function and preventing oxidative
stress in human cells. It can act as a scavenger for hydroxyl radicals, singlet oxygen,
and various electrophiles. Reduced glutathione reduces the oxidized form of the enzyme glutathione peroxidase, which in turn reduces hydrogen peroxide (H2O2), a dangerously reactive species within the cell. In addition, it plays a key role in the metabolism and clearance of xenobiotics, acts as a cofactor in certain detoxifying enzymes, participates in transport, and regenerates antioxidants such and Vitamins E and C to their
reactive forms. The ratio of GSSG/GSH present in the cell is a key factor in properly
maintaining the oxidative balance of the cell, that is, it is critical that the cell maintains
high levels of the reduced glutathione and a low level of the oxidized Glutathione disulfide. This narrow balance is maintained by glutathione reductase, which catalyzes the
reduction of GSSG to GSH.
https://en.wikipedia.org/wiki/Glutathione_reductase
Index
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Glutathione Synthetase
Glutathione synthetase (GSS) is the second enzyme in the glutathione (GSH) biosynthesis pathway. It catalyzes the condensation of -glutamylcysteine and glycine, to form
glutathione. Glutathione synthetase is also a potent antioxidant. It is found in a large
number of species including bacteria, yeast, mammals, and plants.
Glutathione synthetase is important for a variety of biological functions in multiple organisms. In Arabidopsis thaliana, low levels of glutathione synthetase have resulted in
increased vulnerability to stressors such as heavy metals, toxic organic chemicals, and
oxidative stress. The presence of a thiol functional group allows its product GSH to
serve both as an effective oxidizing and reducing agent in numerous biological scenarios. Thiols can easily accept a pair of electrons and become oxidized to disulfides, and
the disulfides can be readily reduced to regenerate thiols. Additionally, the thiol side
chain of cysteines serve as potent nucleophiles and react with oxidants and electrophilic species that would otherwise cause damage to the cell. Interactions with certain
metals also stabilize thiolate intermediates.
In humans, glutathione synthetase functions in a similar manner. Its product GSH participates in cellular pathways involved in homeostasis and cellular maintenance. For
instance, glutathione peroxidases catalyze the oxidation of GSH to glutathione disulfide (GSSG) by reducing free radicals and reactive oxygen species such as hydrogen peroxide. Glutathione S-transferases uses GSH to clean up various metabolites, xenobiotics, and electrophiles to mercapturates for excretion. Because of its antioxidant role,
GSS mostly produce GSH inside the cytoplasm of liver cells and imported to mitochondria where detoxification occurs. GSH is also essential for the activation of the immune
system to generate robust defense mechanisms against invading pathogens. GSH is capable of preventing infection from the influenza virus.
https://en.wikipedia.org/wiki/Glutathione_synthetase
Index
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GLUTs
Glucose transporters are a wide group of membrane proteins that facilitate the transport of glucose over a plasma membrane. Because glucose is a vital source of energy for
all life, these transporters are present in all phyla. The GLUT or SLC2A family are a protein family that is found in most mammalian cells. 12 GLUTS are encoded by human
genome. GLUT is a type of uniporter transporter protein.
GLUTs are integral membrane proteins that contain 12 membrane-spanning helices
with both the amino and carboxyl termini exposed on the cytoplasmic side of the
plasma membrane. GLUT proteins transport glucose and related hexoses according to
a model of alternate conformation, which predicts that the transporter exposes a single
substrate binding site toward either the outside or the inside of the cell. Binding of glucose to one site provokes a conformational change associated with transport, and releases glucose to the other side of the membrane. The inner and outer glucose-binding
sites are, it seems, located in transmembrane segments 9, 10, 11. Also, the QLS motif
located in the seventh transmembrane segment could be involved in the selection and
affinity of transported substrate.
https://en.wikipedia.org/wiki/Glucose_transporter
Index
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Glycans
The terms glycan and polysaccharide are defined by IUPAC as synonyms mea
However, in practice the term glycan may also be used to refer to the carbohy
general, they are found on the exterior surface of cells. O- and N-linked glyca
very common in eukaryotes but may also be found, although less commonly,
karyotes.
https://en.wikipedia.org/wiki/Glycan
Index
Find Term
Glycation
Glycation (sometimes called non-enzymatic glycosylation) is the result of the
or glucose, without the controlling action of an enzyme. All blood sugars are r
molecules. Glycation may occur either inside the body (endogenous glycation
side the body (exogenous glycation).
Enzyme-controlled addition of sugars to protein or lipid molecules is termed
whereas glycosylation occurs at defined sites on the target molecule and is req
order for the molecule to function. Much of the early laboratory research work
tose glycations used inaccurate assay techniques that led to drastic underestim
the importance of fructose in glycation.
https://en.wikipedia.org/wiki/Glycation
Glyceraldehyde
https://en.wikipedia.org/wiki/Glyceraldehyde
Index
Find Term
Glyceraldehyde-3-phosphate
Glyceraldehyde 3-phosphate, also known as triose phosphate or 3phosphoglyceraldehyde and abbreviated as GLYAL3P, G3P, GA3P, GADP, GAP, TP,
GALP or PGAL, is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms. It is a phosphate ester of the 3-carbon sugar
glyceraldehyde and has chemical formula C3H7O6P.
During plant photosynthesis, 2 molecules of glycerate 3-phosphate (GP - also known as
3-phosphoglycerate) are produced by the first step of the light-independent reactions
when ribulose 1,5-bisphosphate (RuBP) and carbon dioxide are catalyzed by the
rubisco enzyme. The GP is converted to D-glyceraldehyde 3-phosphate (G3P) using the
energy in ATP and the reducing power of NADPH as part of the Calvin cycle. This returns ADP, phosphate ions Pi, and NADP+ to the light-dependent reactions of photosynthesis for their continued function. RuBP is regenerated for the Calvin cycle to continue.
G3P is generally considered the prime end-product of photosynthesis and it can be
used as an immediate food nutrient, combined and rearranged to form monosaccharide sugars, such as glucose, which can be transported to other cells, or packaged for
storage as insoluble polysaccharides such as starch.
Balance sheet
6 CO2 + 6 RuBP (+ energy from 12 ATP and 12 NADPH) 12 G3P (3-carbon)
10 G3P (+ energy from 6 ATP) 6 RuBP (i.e. starting material regenerated)
2 G3P glucose (6-carbon).
https://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate
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G-G
G-G
Chapter 3 - Membranes: Other Considerations
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Glyceraldehyde-3-phosphate Dehydrogenase
Glyceraldehyde 3-phosphate dehydrogenase (abbreviated as GAPDH or less commonly
as G3PDH) is an enzyme of ~37kDa that catalyzes the sixth step of glycolysis and thus
serves to break down glucose for energy and carbon molecules. In addition to this long
established metabolic function, GAPDH has recently been implicated in several nonmetabolic processes, including transcription activation, initiation of apoptosis, ER to
Golgi vesicle shuttling, and fast axonal, or axoplasmic transport. In sperm, a testisspecific isoenzyme GAPDHS is expressed.
As its name indicates, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes
the conversion of glyceraldehyde 3-phosphate to D-glycerate 1,3-bisphosphate. This is
the 6th step in the glycolytic breakdown of glucose, an important pathway of energy
and carbon molecule supply which takes place in the cytosol of eukaryotic cells. The
conversion occurs in two coupled steps. The first is favorable and allows the second unfavorable step to occur.
GAPDH can itself activate transcription. The OCA-S transcriptional coactivator complex contains GAPDH and lactate dehydrogenase, two proteins previously only thought
to be involved in metabolism. GAPDH moves between the cytosol and the nucleus and
may thus link the metabolic state to gene transcription.
In 2005, Hara et al. showed that GAPDH initiates apoptosis. This is not a third function, but can be seen as an activity mediated by GAPDH binding to DNA like in transcription activation, discussed above. The study demonstrated that GAPDH is Snitrosylated by NO in response to cell stress, which causes it to bind to the protein SIAH1, a ubiquitin ligase. The complex moves into the nucleus where Siah1 targets nuclear proteins for degradation, thus initiating controlled cell shutdown. In subsequent
study the group demonstrated that deprenyl, which has been used clinically to treat
Parkinson's disease, strongly reduces the apoptotic action of GAPDH by preventing its
S-nitrosylation and might thus be used as a drug.
GAPDH acts as reversible metabolic switch under oxidative stress. When cells are exposed to oxidants, they need excessive amounts of the antioxidant cofactor NADPH. In
the cytosol, NADPH is reduced from NADP+ by several enzymes, three of them catalyze
the first steps of the Pentose phosphate pathway. Oxidant-treatments cause an inactivation of GAPDH. This inactivation re-routes temporally the metabolic flux from glycolysis to the Pentose Phosphate Pathway, allowing the cell to generate more NADPH. Under stress conditions, NADPH is needed by some antioxidant-systems including glutaredoxin and thioredoxin as well as being essential for the recycling of gluthathione.
GAPDH also appears to be involved in the vesicle transport from the endoplasmic reticulum (ER) to the Golgi apparatus which is part of shipping route for secreted proteins. It was found that GAPDH is recruited by rab2 to the vesicular-tubular clusters of
the ER where it helps to form COP 1 vesicles. GAPDH is activated via tyrosine phosphorylation by Src.
GAPDH, like many other enzymes, has multiple functions. In addition to catalyzing the
6th step of glycolysis, recent evidence implicates GAPDH in other cellular
processes.GAPDH has been described to exhibit higher order multifunctionality in the
context of maintaining cellular iron homeostasis. This came as a surprise to researchers but it makes evolutionary sense to re-use and adapt existing proteins instead of
evolving a novel protein from scratch.
https://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase
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Glycerol
Glycerol (also called glycerine) is a simple polyol (sugar alcohol) compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. It is widely used in
the food industry as a sweetener and humectant and in pharmaceutical formulations.
Glycerol has three hydroxyl groups that are responsible for its solubility in water and
its hygroscopic nature. The glycerol backbone is central to all lipids known as triglycerides.
Glycerol is a precursor for synthesis of triacylglycerols and of phospholipids in the liver
and adipose tissue. When the body uses stored fat as a source of energy, glycerol and
fatty acids are released into the bloodstream. Circulating glycerol does not glycate proteins as do glucose or fructose, and does not lead to the formation of advanced glycation endproducts (AGEs). In some organisms, the glycerol component can enter the glycolysis pathway directly and, thus, provide energy for cellular metabolism (or, potentially, be converted to glucose through gluconeogenesis).
Before glycerol can enter the pathway of glycolysis or gluconeogenesis (depending on
physiological conditions), it must be converted to the intermediate glyceraldehyde 3phosphate.
https://en.wikipedia.org/wiki/Glycerol
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https://en.wikipedia.org/wiki/Glycerol_phosphate_shuttle
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Glycerol-3-phosphate
sn-Glycerol 3-phosphate is a phosphoric ester of glycerol, which is a component of glycerophospholipids.
Glycerol 3-phosphate is synthesized by reducing dihydroxyacetone phosphate (DHAP),
a glycolysis intermediate, with glycerol-3-phosphate dehydrogenase. DHAP and thus
glycerol 3-phosphate is also possible to be synthesized from amino acids and citric acid
cycle intermediates via glyceroneogenesis pathway.
Glycerol 3-phosphate is a starting material for de novo synthesis of glycerolipids.
Glycerol 3-phosphate is synthesized by reducing dihydroxyacetone phosphate (DHAP),
a glycolysis intermediate, with glycerol-3-phosphate dehydrogenase. DHAP and thus
glycerol 3-phosphate is also possible to be synthesized from amino acids and citric acid
cycle intermediates via glyceroneogenesis pathway.
It is also synthesized by phosphorylating glycerol generated upon hydrolyzing fats with
glycerol kinase, and can feed into glycolysis or glyconeogenesis pathways.
Glycerol 3-phosphate is a starting material for de novo synthesis of glycerolipids. In
eukaryotes, it is first acylated on its sn-1 position by an ER- or mitochondrial membrane enzyme, glycerol-3-phosphate O-acyltransferase, and another acyl group is then
added on the sn-2 position making phosphatidic acids.
Some fungi have glycerol-1-phosphatase, which removes the phosphate group of glycerol 3-phosphate to generate glycerol. They can perform glycerol fermentation producing glycerol from glucose through glycolysis pathway.
https://en.wikipedia.org/wiki/Glycerol_3-phosphate
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Glycerol-3-phosphate Dehydrogenase
GPDH plays a major role in lipid biosynthesis. Through the reduction of dih
tone phosphate into glycerol 3-phosphate, GPDH allows the prompt dephos
taining the redox potential across the inner mitochondrial membrane in gly
https://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase
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Glycerophospholipid
Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids. They
are the main components of biological membranes.
The term glycerophospholipid signifies any derivative of glycerophosphoric acid that
contains at least one O-acyl, or O-alkyl, or O-alk-1'- enyl residue attached to the glycerol moiety.
Plasmalogens are a type of phosphoglyceride. The first carbon of glycerol has a hydrocarbon chain attached via an ether, not ester, linkage. The linkages are more resistant
to chemical attack than ester linkages are. The second (central) carbon atom has a fatty
acid linked by an ester. The third carbon links to an ethanolamine or choline by means
of a phosphate ester. These compounds are key components of the membranes of muscles and nerves.
Phosphatidates are lipids in which the first two carbon atoms of the glycerol are fatty
acid esters, and the third is a phosphate ester. The phosphate serves as a link to another alcohol-usually ethanolamine, choline, serine, or a carbohydrate. The identity of
the alcohol determines the subcategory of the phosphatidate. There is a negative
charge on the phosphate and, in the case of choline or serine, a positive quaternary ammonium ion. (Serine also has a negative carboxylate group.) The presence of charges
give a "head" with an overall charge. The phosphate ester portion ("head") is hydrophilic, whereas the remainder of the molecule, the fatty acid "tail", is hydrophobic.
These are important components for the formation of lipid bilayers. Phosphatidylethanoamines, phosphatidylcholines, and other phospholipids are examples of phosphatidates.
Phosphatidylcholines are lecithins. Choline is the alcohol, with a positively charged
quaternary ammonium, bound to the phosphate, with a negative charge. Lecithins are
present in all living organisms. An egg yolk has a high concentration of lecthins- which
are commercially important as an emulsifying agent in products such as mayonnaise.
Lecithins are also present in brain and nerve tissue.
There are many other phospholipids, some of which are glycolipids. The glycolipids include phosphatidyl sugars where the alcohol functional group is part of a carbohydrate.
Phosphatidyl sugars are present in plants and certain microorganisms. A carbohydrate
is very hydrophilic due to the large number of hydroxyl groups present.
https://en.wikipedia.org/wiki/Glycerophospholipid
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Glycerophospholipids
Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids. They
are the main components of biological membranes.
The term glycerophospholipid signifies any derivative of glycerophosphoric acid that
contains at least one O-acyl, or O-alkyl, or O-alk-1'- enyl residue attached to the glycerol moiety.
Plasmalogens are a type of phosphoglyceride. The first carbon of glycerol has a hydrocarbon chain attached via an ether, not ester, linkage. The linkages are more resistant
to chemical attack than ester linkages are. The second (central) carbon atom has a fatty
acid linked by an ester. The third carbon links to an ethanolamine or choline by means
of a phosphate ester. These compounds are key components of the membranes of muscles and nerves.
Phosphatidates are lipids in which the first two carbon atoms of the glycerol are fatty
acid esters, and the third is a phosphate ester. The phosphate serves as a link to another alcohol-usually ethanolamine, choline, serine, or a carbohydrate. The identity of
the alcohol determines the subcategory of the phosphatidate. There is a negative
charge on the phosphate and, in the case of choline or serine, a positive quaternary ammonium ion. (Serine also has a negative carboxylate group.) The presence of charges
give a "head" with an overall charge. The phosphate ester portion ("head") is hydrophilic, whereas the remainder of the molecule, the fatty acid "tail", is hydrophobic.
These are important components for the formation of lipid bilayers. Phosphatidylethanoamines, phosphatidylcholines, and other phospholipids are examples of phosphatidates.
Phosphatidylcholines are lecithins. Choline is the alcohol, with a positively charged
quaternary ammonium, bound to the phosphate, with a negative charge. Lecithins are
present in all living organisms. An egg yolk has a high concentration of lecthins- which
are commercially important as an emulsifying agent in products such as mayonnaise.
Lecithins are also present in brain and nerve tissue.
There are many other phospholipids, some of which are glycolipids. The glycolipids include phosphatidyl sugars where the alcohol functional group is part of a carbohydrate.
Phosphatidyl sugars are present in plants and certain microorganisms. A carbohydrate
is very hydrophilic due to the large number of hydroxyl groups present.
https://en.wikipedia.org/wiki/Glycerophospholipid
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Glycine
Glycine (abbreviated as Gly or G) is the smallest of the 20 amino acids commonly
found in proteins, and indeed is the smallest possible (having a hydrogen substituent
as its side-chain). Most proteins incorporate only small quantities of glycine. A notable
exception is collagen, which contains about 35% glycine. The formula is
NH2CH2COOH. Its codons are GGU, GGC, GGA, GGG of the genetic code.
Glycine is a colorless, sweet-tasting crystalline solid. It is unique among the proteinogenic amino acids in that it is achiral. It can fit into hydrophilic or hydrophobic environments, due to its minimal side chain of only one hydrogen atom. The acyl radical is
glycyl.
Synthesis
Glycine is not essential to the human diet, as it is biosynthesized in the body from the
amino acid serine, which is in turn derived from 3-phosphoglycerate, but the metabolic
capacity for glycine biosynthesis does not satisfy the need for collagen synthesis. In
most organisms, the enzyme serine hydroxymethyltransferase catalyzes this transformation via the cofactor pyridoxal phosphate:
Serine + Tetrahydrofolate Glycine + N5,N10-Methylene tetrahydrofolate + H2O
In the liver of vertebrates, glycine synthesis is catalyzed by glycine synthase. This conversion is readily reversible:
CO2 + NH4+ + N5,N10-Methylene tetrahydrofolate + NADH + H+ Glycine + Tetrahydrofolate + NAD+
Degradation
Glycine is degraded via three pathways. The predominant pathway in animals and
plants involves the glycine cleavage enzyme:
Glycine + Tetrahydrofolate + NAD+ CO2 + NH4+ + N5,N10-Methylene Tetrahydrofolate + NADH + H+
In the second pathway, glycine is degraded in two steps. The first step is the reverse of
glycine biosynthesis from serine with serine hydroxymethyl transferase. Serine is then
converted to pyruvate by serine dehydratase.
In the third pathway of glycine degradation, glycine is converted to glyoxylate by Damino acid oxidase. Glyoxylate is then oxidized by hepatic lactate dehydrogenase to oxalate in an NAD+-dependent reaction.
The half-life of glycine and its elimination from the body varies significantly based on
dose. In one study, the half-life was between 0.5 and 4.0 hours.
https://en.wikipedia.org/wiki/Glycine
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Glycine Betaine
Trimethylglycine (TMG) is an amino acid derivative that occurs in plants. Trimethylglycine was the first betaine discovered. Originally it was simply called betaine because, in the 19th century, it was discovered in sugar beets. Since then, many other betaines have been discovered, and the more specific name glycine betaine distinguishes
this one.
TMG is an important cofactor in methylation, a process that occurs in every cell of
mammals to synthesize and donate methyl groups (CH3) for other processes in the
body. These processes include the synthesis of neurotransmitters such as dopamine
and serotonin. Methylation is also required for the biosynthesis of melatonin and the
electron transport chain constituent coenzyme Q10.
https://en.wikipedia.org/wiki/Trimethylglycine
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Glycine Synthase
The glycine cleavage system (GCS) is also known as the glycine decarboxyla
or GDC. The system is a series of enzymes that are triggered in response to
trations of the amino acid glycine. The same set of enzymes is sometimes re
other proteins and acts as a shuttle for some of the intermediate products in
carboxylation. In both animals and plants the glycine cleavage system is loo
tached to the inner membrane of the mitochondria.
https://en.wikipedia.org/wiki/Glycine_cleavage_system
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Glycineamide Ribonucleotide
Glycineamide ribonucleotide (or GAR) is an intermediate in de novo purine biosynthesis.
It is formed from phosphoribosylamine by the enzyme phosphoribosylamineglycine
ligase. In the next step of purine biosynthesis the enzyme phosphoribosylglycinamide
formyltransferase acts on GAR to form FGAR.
GAR formation is stimulated by luteinizing hormone (LH) and chorionic gonadotropin
(HCG) via activation of Glc-6-P-dehydrogenase.
https://en.wikipedia.org/wiki/Glycineamide_ribonucleotide
Glycocalyx
The glycocalyx is a glycoprotein-polysaccharide covering that surrounds the cell membranes of some bacteria, epithelia and other cells.
Most animal epithelial cells have a fuzz-like coat on the external surface of their
plasma membranes. This coating consists of several carbohydrate moieties of membrane glycolipids and glycoproteins, which serve as backbone molecules for support.
Generally, the carbohydrate portion of the glycolipids found on the surface of plasma
membranes helps these molecules contribute to cell-cell recognition, communication,
and intercellular adhesion.
The glycocalyx is a type of identifier that the body uses to distinguish between its own
healthy cells and transplanted tissues, diseased cells, or invading organisms. Included
in the glycocalyx are cell-adhesion molecules that enable cells to adhere to each other
and guide the movement of cells during embryonic development. The glycocalyx plays
a major role in regulation of endothelial vascular tissue, including the modulation of
red blood cell volume in capillaries.
The slime on the outside of a fish is an example of glycocalyx. The term was initially applied to the polysaccharide matrix coating epithelial cells, but its functions have been
discovered to go well beyond that. The glycocalyx surrounding a Bacillus subtilis bacterium is shown below.
https://en.wikipedia.org/wiki/Glycocalyx
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Glycocholic Acid
https://en.wikipedia.org/wiki/Glycocholic_acid
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Glycogen
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy
storage in animals and fungi. The polysaccharide structure represents the main storage
form of glucose in the body.
In humans, glycogen is made and stored primarily in the cells of the liver and the muscles hydrated with three or four parts of water. Glycogen functions as the secondary
long-term energy storage, with the primary energy stores being fats held in adipose tissue. Muscle glycogen is converted into glucose by muscle cells, and liver glycogen converts to glucose for use throughout the body including the central nervous system.
Glycogen is the analogue of starch, a glucose polymer that functions as energy storage
in plants. It has a structure similar to amylopectin (a component of starch), but is more
extensively branched and compact than starch. Both are white powders in their dry
state. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell
types, and plays an important role in the glucose cycle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is
less compact than the energy reserves of triglycerides (lipids).
In the liver, glycogen can comprise from 5 to 6% of its fresh weight (100120g in an
adult). Only the glycogen stored in the liver can be made accessible to other organs. In
the muscles, glycogen is found in a low concentration (1-2% of the muscle mass). The
amount of glycogen stored in the bodyespecially within the muscles, liver, and red
blood cellsmostly depends on physical training, basal metabolic rate, and eating habits. Small amounts of glycogen are found in the kidneys, and even smaller amounts in
certain glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy to nourish the embryo.
https://en.wikipedia.org/wiki/Glycogen
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Glycogen Metabolism
Glycogen is cleaved from the nonreducing ends of the chain by the enzyme glycogen
phosphorylase to produce monomers of glucose-1-phosphate:
Glucose-1-phosphate is then converted to glucose 6-phosphate (G6P) by phosphoglucomutase. A special debranching enzyme is needed to remove the (1-6) branches in
branched glycogen and reshape the chain into a linear polymer. The G6P monomers
produced have three possible fates:
G6P can enter the pentose phosphate pathway via the enzyme glucose-6-
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Glycogen Phosphorylase
Glycogen phosphorylase is one of the phosphorylase enzymes. Glycogen phosphorylase
catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1phosphate from the terminal -1,4-glycosidic bond. Glycogen phosphorylase is also
studied as a model protein regulated by both reversible phosphorylation and allosteric
effects.
https://en.wikipedia.org/wiki/Glycogen_phosphorylase
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Glycogen Synthase
Glycogen synthase (UDP-glucose-glycogen glucosyltransferase) is a glycosyltransferase
enzyme (EC 2.4.1.11) that catalyzes the reaction of UDP-glucose and (1,4--Dglucosyl)n to yield UDP and (1,4--D-glucosyl)n+1.
In other words, this enzyme converts excess glucose residues one by one into a polymeric chain for storage as glycogen. Glycogen synthase concentration is highest in the
bloodstream 30 to 60 minutes following intense exercise. It is a key enzyme in glycogenesis.
The reaction is highly regulated by allosteric effectors such as glucose-6-phosphate
(which allows glycogen synthase to operate as a glucose-6-phosphate sensor), by phosphorylation reactions (catalyzed by GSK3, see below), and indirectly triggered by the
hormone insulin, which is secreted by the pancreas in response to elevated blood glucose levels. Phosphorylation of glycogen synthase decreases its activity. The enzyme
also cleaves the ester bond between the C1 position of glucose and the pyrophosphate
of UDP itself.
The control of glycogen synthase is a key step in regulating glycogen metabolism and
glucose storage. Glycogen synthase is directly regulated by glycogen synthase kinase 3
(GSK-3), AMPK, protein kinase A (PKA), and casein kinase 2 (CK2). Each of these protein kinases lead to phosphorylated and catalytically inactive glycogen synthase.
For enzymes in the GT3 family, these regulatory kinases inactivate glycogen synthase
by phosphorylating it at the N-terminal of the 25th residue and the C-terminal of the
120th residue. Glycogen synthase is also regulated by protein phosphatase 1 (PP1),
which activates glycogen synthase via dephosphorylation. PP1 is targeted to the glycogen pellet by four targeting subunits, GM, GL, PTG and R6. These regulatory enzymes
are regulated by insulin and glucagon signaling pathways.
https://en.wikipedia.org/wiki/Glycogen_synthase
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tion of phosphate molecules onto serine and threonine amino acid residues
since been identified as a kinase for over forty different proteins in a variety
and GSK-3 (GSK3B). GSK-3 has recently been the subject of much resear
mellitus type 2), Alzheimer's Disease, inflammation, cancer, and bipolar dis
https://en.wikipedia.org/wiki/GSK-3
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Glycogenin
Glycogenin is an enzyme involved in converting glucose to glycogen. It acts as a
primer, by polymerizing the first few glucose molecules, after which other enzymes
take over. It is a homodimer of 37-kDa subunits and is classified as a glycosyltransferase.
It catalyzes the chemical reaction:
UDP--D-glucose + Glycogenin <---> UDP + -D-glucosylglycogenin
The main enzyme involved in glycogen polymerization, glycogen synthase, can only
add to an existing chain of at least 4 glucose residues. Glycogenin acts as the primer, to
which further glucose monomers may be added. It achieves this by catalyzing the addition of glucose to itself (autocatalysis) by first binding glucose from UDP-glucose to the
hydroxyl group of Tyr-194. Seven more glucoses can be added, each derived from
UDP-glucose, by glycogenin's glucosyltransferase activity. Once sufficient residues
have been added, glycogen synthase takes over extending the chain. Glycogenin remains covalently attached to the reducing end of the glycogen molecule.
https://en.wikipedia.org/wiki/Glycogenin
Glycolipids
Glycolipids are lipids with a carbohydrate attached by a glycosidic bond. Their role is
to serve as markers for cellular recognition and also to provide energy. The carbohydrates are found on the outer surface of all eukaryotic cell membranes. They extend
from the phospholipid bilayer into the aqueous environment outside the cell where it
acts as a recognition site for specific chemicals as well as helping to maintain the stability of the membrane and attaching cells to one another to form tissues.
https://en.wikipedia.org/wiki/Glycolipid
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Glycolysis
Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate,
CH3COCOO + H+. The free energy released in this process is used to form the highenergy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide
adenine dinucleotide).
Glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as
fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.
Glycolysis is an oxygen independent metabolic pathway, meaning that it does not use
molecular oxygen (i.e. atmospheric oxygen) for any of its reactions. However the products of glycolysis (pyruvate and NADH + H+) are sometimes disposed of using atmospheric oxygen. When molecular oxygen is used in the disposal of the products of glycolysis the process is usually referred to as aerobic, whereas if the disposal uses no oxygen the process is said to be anaerobic.
Thus, glycolysis occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient
metabolic pathways. Indeed, the reactions that constitute glycolysis and its parallel
pathway, the pentose phosphate pathway, occur metal-catalyzed under the oxygen-free
conditions of the Archean oceans, also in the absence of enzymes. Glycolysis could thus
have originated from chemical constraints of the prebiotic world.
Glycolysis occurs in most organisms in the cytosol of the cell. The most common type
of glycolysis is the EmbdenMeyerhofParnas (EMP pathway), which was discovered
by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to
other pathways, such as the EntnerDoudoroff pathway and various heterofermentative and homofermentative pathways. However, the discussion here will be limited to
the EmbdenMeyerhofParnas pathway.
https://en.wikipedia.org/wiki/Glycolysis
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Glycophorin
(60%). Glycophorins are rich in sialic acid, which gives the red blood cells a
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Glycoprotein
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or post-translational modification. This process is known as glycosylation. Secreted extracellular proteins are often glycosylated.
In proteins that have segments extending extracellularly, the extracellular segments
are also often glycosylated. Glycoproteins are also often important integral membrane
proteins, where they play a role in cellcell interactions. It is important to distinguish
endoplasmic reticulum-based glycosylation of the secretory system without of reversible cytosolic/nuclear glycosylation. Glycoprotein of the cytosol and nucleus can be
modified through the reversible addition of a single GlcNAc residues that is consider
reciprocal to phosphorylation and the functions of these are likely to be additional regulatory mechanism that controls phosphorylation-based signaling. In contrast, classical
secretory glycosylation can be structurally essential. For example, inhibition of
asparagine-linked, i.e. N-linked, glycosylation can prevent glycoprotein folding and full
inhibition can be toxic to an individual cell. In contrast, perturbations of terminal processing, which occurs in the Golgi apparatus, is dispensable for isolated cells(as evidence by survival with glycosides inhibitors) but can lead to human disease (Congenital disorders of glycosylation) and can be lethal in animal models. It is therefore likely
that the fine processing of glycans is important for endogeneous functionality, such as
cell trafficking, but that this is likely to have been secondary to its role in hostpathogen interactions. A famous example of this latter effect is the ABO blood system.
An N-linked glycoprotein is depicted below.
https://en.wikipedia.org/wiki/Glycoprotein
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Glycoproteins
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or post-translational modification. This process is known as glycosylation. Secreted extracellular proteins are often glycosylated.
In proteins that have segments extending extracellularly, the extracellular segments
are also often glycosylated. Glycoproteins are also often important integral membrane
proteins, where they play a role in cellcell interactions. It is important to distinguish
endoplasmic reticulum-based glycosylation of the secretory system without of reversible cytosolic/nuclear glycosylation. Glycoprotein of the cytosol and nucleus can be
modified through the reversible addition of a single GlcNAc residues that is consider
reciprocal to phosphorylation and the functions of these are likely to be additional regulatory mechanism that controls phosphorylation-based signaling. In contrast, classical
secretory glycosylation can be structurally essential. For example, inhibition of
asparagine-linked, i.e. N-linked, glycosylation can prevent glycoprotein folding and full
inhibition can be toxic to an individual cell. In contrast, perturbations of terminal processing, which occurs in the Golgi apparatus, is dispensable for isolated cells(as evidence by survival with glycosides inhibitors) but can lead to human disease (Congenital disorders of glycosylation) and can be lethal in animal models. It is therefore likely
that the fine processing of glycans is important for endogeneous functionality, such as
cell trafficking, but that this is likely to have been secondary to its role in hostpathogen interactions. A famous example of this latter effect is the ABO blood system.
An N-linked glycoprotein is depicted below.
https://en.wikipedia.org/wiki/Glycoprotein
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Glycosaminoglycan
Glycosaminoglycans (GAGs) or mucopolysaccharides are long unbranched polysaccharides consisting of a repeating disaccharide unit. The repeating unit (except for keratan) consists of an amino sugar (N-acetylglucosamine or N-acetylgalactosamine)
along with a uronic sugar (glucuronic acid or iduronic acid) or galactose. Glycosaminoglycans are highly polar and attract water. They are therefore useful to the body as a lubricant or as a shock absorber.
Glycosaminoglycans have high degrees of heterogeneity with regards to molecular
mass, disaccharide construction, and sulfation due to the fact that GAG synthesis, unlike proteins or nucleic acids, is not template driven, and dynamically modulated by
processing enzymes.
Based on core disaccharide structures, GAGs are classified into four groups. Heparin/
heparan sulfate (HSGAGs) and chondroitin sulfate/dermatan sulfate (CSGAGs) are
synthesized in the Golgi apparatus, where protein cores made in the rough endoplasmic reticulum are posttranslationally modified with O-linked glycosylations by glycosyltransferases forming proteoglycans. Keratan sulfate may modify core proteins through
N-linked glycosylation or O-linked glycosylation of the proteoglycan. The fourth class
of GAG, hyaluronic acid, is not synthesized by the Golgi, but rather by integral membrane synthases which immediately secrete the dynamically elongated disaccharide
chain.
HSGAG and CSGAG modified proteoglycans first begin with a consensus Ser-Gly/AlaX-Gly motif in the core protein. Construction of a tetrasaccharide linker that consists
of -GlcA13Gal13Gal14Xyl1-O-(Ser)-, where xylosyltransferase, 4-galactosyl
transferase (GalTI),3-galactosyl transferase (GalT-II), and 3-GlcA transferase
(GlcAT-I) transfer the four monosaccharides, begins synthesis of the GAG modified
protein. The first modification of the tetrasaccharide linker determines whether the
HSGAGs or CSGAGs will be added. Addition of a GlcNAc promotes the addition of
HSGAGs while addition of GalNAc to the tetrasaccharide linker promotoes CSGAG development. GlcNAcT-I transfers GlcNAc to the tetrasaccahride linker, which is distinct
from glycosyltransferase GlcNAcT-II, the enzyme that is utilized to build HSGAGs. Interestingly, EXTL2 and EXTL3, two genes in the EXT tumor suppressor family, have
been shown to have GlcNAcT-I activity. Conversely, GalNAc is transferred to the linker
by the enzyme GalNAcT to initiate synthesis of CSGAGs, an enzyme which may or may
not have distinct activity compared to the GalNAc transferase activity of chondroitin
synthase.
https://en.wikipedia.org/wiki/Glycosaminoglycan
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Glycoside
In chemistry, a glycoside is a molecule in which a sugar is bound to another functional
group via a glycosidic bond. Glycosides play numerous important roles in living organisms. Many plants store chemicals in the form of inactive glycosides. These can be activated by enzyme hydrolysis, which causes the sugar part to be broken off, making the
chemical available for use. Many such plant glycosides are used as medications. In animals and humans, poisons are often bound to sugar molecules as part of their elimination from the body.
In formal terms, a glycoside is any molecule in which a sugar group is bonded through
its anomeric carbon to another group via a glycosidic bond. Glycosides can be linked
by an O- (an O-glycoside), N- (a glycosylamine), S-(a thioglycoside), or C- (a Cglycoside) glycosidic bond.
Salicin, an aspirin-like glycoside, is depicted below.
https://en.wikipedia.org/wiki/Glycoside
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Glycosidic
In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that
joins a carbohydrate (sugar) molecule to another group, which may or may not be a
other carbohydrate.
(or a molecule derived from a saccharide) and the hydroxyl group of some compoun
such as an alcohol. A substance containing a glycosidic bond is a glycoside.
https://en.wikipedia.org/wiki/Glycosidic_bond
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Glycosidic Bond
joins a carbohydrate (sugar) molecule to another group, which may or may not be
other carbohydrate.
(or a molecule derived from a saccharide) and the hydroxyl group of some compo
such as an alcohol. A substance containing a glycosidic bond is a glycoside.
https://en.wikipedia.org/wiki/Glycosidic_bond
Glycosyl
ing the hemiacetal hydroxyl group from the cyclic form of a monosaccharide an
In the image below, the -D-glucopyranosyl group was obtained by the remova
hemiacetal hydroxyl group from -D-glucopyranose.
https://en.wikipedia.org/wiki/Glycosyl
Glycosylation
Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached
to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches
glycans to proteins, lipids, or other organic molecules. This enzymatic process produces one of the fundamental biopolymers found in cells (along with DNA, RNA, and
proteins). Glycosylation is a form of co-translational and post-translational modification. Glycans serve a variety of structural and functional roles in membrane and secreted proteins. The majority of proteins synthesized in the rough ER undergo glycosylation. It is an enzyme-directed site-specific process, as opposed to the non-enzymatic
chemical reaction of glycation. Glycosylation is also present in the cytoplasm and nucleus as the O-GlcNAc modification. Aglycosylation is a feature of engineered antibodies to bypass glycosylation.
Five classes of glycans are produced:
N-linked glycans attached to a nitrogen of asparagine or arginine side-chains. Nlinked glycosylation requires participation of a special lipid called dolichol phosphate.
O-linked glycans attached to the hydroxyl oxygen of serine, threonine, tyrosine, hydroxylysine, or hydroxyproline side-chains, or to oxygens on lipids such as ceramide
Phospho-glycans linked through the phosphate of a phospho-serine
C-linked glycans, a rare form of glycosylation where a sugar is added to a carbon on a
tryptophan side-chain
Glypiation, which is the addition of a GPI anchor that links proteins to lipids through
glycan linkages.
https://en.wikipedia.org/wiki/Glycosylation
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Glycosylphosphatidylinositol
Glycosylphosphatidylinositol (GPI anchor) is a glycolipid that can be attached to the Cterminus of a protein during posttranslational modification. Proteins containing a GPI
anchor (called glypiated) play key roles in a wide variety of biological processes. It is
composed of a phosphatidylinositol group linked through a carbohydrate-containing
linker (glucosamine and mannose glycosidically bound to the inositol residue) and via
an ethanolamine phosphate (EtNP) bridge to the C-terminal amino acid of a mature
protein. The two fatty acids within the hydrophobic phosphatidyl-inositol group anchor the protein to the cell membrane.
Glypiated (GPI-linked) proteins contain a signal sequence, thus directing them to the
endoplasmic reticulum (ER). The protein is co-translationally inserted in the ER membrane and is attached to the ER membrane by its hydrophobic C terminus. The majority of the protein extends into the ER lumen. The hydrophobic C-terminal sequence is
then cleaved off and replaced by the GPI-anchor. As the protein processes through the
secretory pathway, it is transferred via vesicles to the Golgi apparatus and finally to the
plasma membrane where it remains attached to the exterior leaflet of the cell membrane. Since the glypiation is the sole means of attachment of such proteins to the
membrane, cleavage of the group by phospholipases will result in controlled release of
the protein from the membrane. The latter mechanism is used in vitro, i.e., the membrane proteins released from the membranes in the enzymatic assay are glypiated proteins.
Phospholipase C (PLC) is an enzyme that is known to cleave the phospho-glycerol
bond found in GPI-anchored proteins. Treatment with PLC will cause release of GPIlinked proteins from the outer cell membrane. The T-cell marker Thy-1 and acetylcholinesterase, as well as both intestinal and placental alkaline phosphatases, are known
to be GPI-linked and are released by treatment with PLC. GPI-linked proteins are
thought to be preferentially located in lipid rafts, suggesting a high level of organization within plasma membrane microdomains.
https://en.wikipedia.org/wiki/Glycophosphatidylinositol
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Glyoxylate
Glyoxylic acid or oxoacetic acid is an organic compound. Together with acetic acid, glycolic acid, and oxalic acid, glyoxylic acid is one of the C2 carboxylic acids. It is a colorless solid that occurs naturally and is useful industrially.
The conjugate base of gloxylic acid is known as glyoxylate and is the form that the compound exists in solution at neutral pH. Glyoxylate is an intermediate of the glyoxylate
cycle, which enables organisms, such as bacteria, fungi, and plants to convert fatty acids into carbohydrates. Glyoxylate is the byproduct of the amidation process in biosynthesis of several amidated peptides.
https://en.wikipedia.org/wiki/Glyoxylic_acid
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Glyoxylate Cycle
The glyoxylate cycle, a variation of the tricarboxylic acid cycle, is an anabolic pathway
occurring in plants, bacteria, protists, and fungi. The glyoxylate cycle centers on the
conversion of acetyl-CoA to succinate for the synthesis of carbohydrates. In microorganisms, the glyoxylate cycle allows cells to utilize simple carbon compounds as a carbon source when complex sources such as glucose are not available. The cycle is generally assumed to be absent in animals, with the exception of nematodes at the early
stages of embryogenesis. In recent years, however, the detection of malate synthase
(MS) and isocitrate lyase (ICL), key enzymes involved in the glyoxylate cycle, in some
animal tissue has raised questions regarding the evolutionary relationship of enzymes
in bacteria and animals and suggests that animals encode alternative enzymes of the
cycle that differ in function from known MS and ICL in non-metazoan species.
The glyoxylate cycle utilizes five of the eight enzymes associated with the tricarboxylic
acid cycle: citrate synthase, aconitase, succinate dehydrogenase, fumarase, and malate
dehydrogenase. The two cycles differ in that in the glyoxylate cycle, isocitrate is converted into glyoxylate and succinate by ICL instead of into -ketoglutarate. This bypasses the decarboxylation steps that take place in the TCA cycle, allowing simple carbon compounds to be used in the later synthesis of macromolecules, including glucose.
Glyoxylate is subsequently combined with acetyl-CoA to produce malate, catalyzed by
MS. Malate is also formed in parallel from succinate by the action of succinate dehydrogenase and fumarase.
https://en.wikipedia.org/wiki/Glyoxylate_cycle
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Glyoxysome
age tissues of germinating seeds) and also in filamentous fungi. As in all per
the key enzymes of glyoxylate cycle (isocitrate lyase and malate synthase) w
plish the glyoxylate cycle bypass.
Thus, glyoxysomes (as all peroxisomes) contain enzymes that initiate the br
Index
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Glyoxysomes
age tissues of germinating seeds) and also in filamentous fungi. As in all per
the key enzymes of glyoxylate cycle (isocitrate lyase and malate synthase) w
plish the glyoxylate cycle bypass.
Thus, glyoxysomes (as all peroxisomes) contain enzymes that initiate the br
Glypiation
Glypiation is the covalent bond of a glycosylphosphatidylinositol (GPI) anchor and is a
common post-translational modification that localizes proteins to cell membranes.
This special kind of glycosylation is widely detected on surface glycoproteins in
eukaryotes and some Archaea.
GPI anchors consist of a phosphoethanolamine linker that binds to the C-terminus of
target proteins. Glycan's core structure has a phospholipid tail that anchors the structure to the membrane.
Both the lipid moiety of the tail and the sugar residues in the glycan core has considerable variation, demonstrating vast functional diversity that includes signal transduction, cell adhesion and immune recognition. GPI anchors can also be cleaved by enzymes such as phospholipase C to regulate the localization of proteins that are anchored at the plasma membrane.
https://en.wikipedia.org/wiki/Glypiation
GMP
Guanosine monophosphate (GMP), also known as 5'-guanidylic acid or guanylic acid
(conjugate base guanylate), is a nucleotide that is used as a monomer in RNA. It is an
ester of phosphoric acid with the nucleoside guanosine. GMP consists of the phosphate
group, the pentose sugar ribose, and the nucleobase guanine. Hence it is a ribonucleoside monophosphate. Guanosine monophosphate is commercially produced by microbial fermentation.
Guanosine monophosphate in the form of its salts, such as disodium guanylate (E627),
dipotassium guanylate (E628) and calcium guanylate (E629), are food additives used
as flavor enhancers to provide the umami taste. It is often used in synergy with disodium inosinate. The combination is known as disodium 5'-ribonucleotides. Disodium
guanylate is often found in instant noodles, potato chips and snacks, savoury rice,
tinned vegetables, cured meats, and packet soup.
As it is a fairly expensive additive, it is usually not used independently of glutamic acid
or monosodium glutamate (MSG), which also contribute umami. If inosinate and
guanylate salts are present in a list of ingredients but MSG does not appear to be, the
glutamic acid is likely provided as part of another ingredient, such as a processed soy
protein complex (hydrolyzed soy protein), autolyzed yeast or soy sauce.
https://en.wikipedia.org/wiki/Guanosine_monophosphate
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G-G
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 7 - Information Processing: RNA Processing
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
GMP Reductase
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GMP Synthase
Guanosine monophosphate synthetase, also known as GMPS is an enzyme
sis of purine nucleotides, IMP is the branch point metabolite at which point
Golden Rice
Golden rice is a variety of rice (Oryza sativa) produced through genetic engineering to
biosynthesize -carotene, a precursor of vitamin A, in the edible parts of rice. It is intended to produce a fortified food to be grown and consumed in areas with a shortage
of dietary vitamin A, a deficiency which is estimated to kill 670,000 children under the
age of 5 each year.
Golden rice differs from its parental strain by the addition of three -carotene biosynthesis genes. The rice plant can naturally produce -carotene in its leaves, where it is
involved in photosynthesis. However, the plant does not normally produce the pigment
in the endosperm, where photosynthesis does not occur.
https://en.wikipedia.org/wiki/Golden_rice
Golgi
The Golgi apparatus, also known as the Golgi complex, Golgi body, or simply the Golgi,
is an organelle found in most eukaryotic cells. It was identified in 1897 by the Italian
physician Camillo Golgi and named after him in 1898.
Part of the cellular endomembrane system, the Golgi apparatus packages proteins into
membrane-bound vesicles inside the cell before the vesicles are sent to their destination. The Golgi apparatus resides at the intersection of the secretory, lysosomal, and endocytic pathways. It is of particular importance in processing proteins for secretion,
containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus.
The image below shows the Golgi as a set of flattened disks near the bottom.
https://commons.wikimedia.org/wiki/File:Human_leukocyte,_showing_golgi_-_TE
M.jpg
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Golgi Apparatus
The Golgi apparatus, also known as the Golgi complex, Golgi body, or simply the Golgi,
is an organelle found in most eukaryotic cells. It was identified in 1897 by the Italian
physician Camillo Golgi and named after him in 1898.
Part of the cellular endomembrane system, the Golgi apparatus packages proteins into
membrane-bound vesicles inside the cell before the vesicles are sent to their destination. The Golgi apparatus resides at the intersection of the secretory, lysosomal, and endocytic pathways. It is of particular importance in processing proteins for secretion,
containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus.
The image below shows the Golgi as a set of flattened disks near the bottom.
https://commons.wikimedia.org/wiki/File:Human_leukocyte,_showing_golgi_-_TE
M.jpg
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Gopalasamudram Ramachandran
Gopalasamudram Narayana Ramachandran, or G.N. Ramachandran, FRS (8 October
1922 7 April 2001) was an Indian physicist who was known for his work that led to
his creation of the Ramachandran plot for understanding peptide structure. He was
the first to propose a triple-helical model for the structure of collagen and subsequently went on to make other major contributions in biology and physics. Leading scientists including Professor Linus Pauling and Professor Francis Crick regarded Professor Ramchandran as a Nobel Prize caliber scientist of great reputation.
https://en.wikipedia.org/wiki/G._N._Ramachandran
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Gp41
protein that contains several sites within its ectodomain that are required for infectio
of host cells.
The interaction of gp41 fusion peptides with the target cell causes a formation of an i
termediate, pre-hairpin structure which bridges and fuses the viral and host mem-
branes together. The pre-hairpin structure has a relatively long half-life which makes
a target for therapeutic intervention and inhibitory peptides.
Enfuvirtide (also known as T-20) is a fusion inhibitor drug that binds to the pre-
hairpin structure and prevents membrane fusion and HIV-1 entry to the cell. The vul
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Gp120
the HIV envelope. The 120 in its name comes from its molecular weight of 1
Gp120 is essential for virus entry into cells as it plays a vital role in attachm
cific cell surface receptors.
Index
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GPa
Glycogen phosphorylase a (GPa) is a phosphroylated form of glycogen phoshorylase,
the primary enzyme in glycogen breakdown. It catalyzes the phosphorolysis of glycogen (uses a phosphate for cleavage) to yield glucose-1-phosphate and a glycogen molecule shortened by one residue.
GPb
Glycogen phosphorylase b (GPb) is a phosphroylated form of glycogen phoshorylase,
the primary enzyme in glycogen breakdown. It catalyzes the phosphorolysis of glycogen (uses a phosphate for cleavage) to yield glucose-1-phosphate and a glycogen molecule shortened by one residue.
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GPI Anchor
Glycosylphosphatidylinositol (GPI anchor) is a glycolipid that can be attached to the Cterminus of a protein during posttranslational modification. Proteins containing a GPI
anchor play key roles in a wide variety of biological processes. It is composed of a phosphatidylinositol group linked through a carbohydrate-containing linker (glucosamine
and mannose glycosidically bound to the inositol residue) and via an ethanolamine
phosphate (EtNP) bridge to the C-terminal amino acid of a mature protein. The two
fatty acids within the hydrophobic phosphatidyl-inositol group anchor the protein to
the cell membrane.
Glypiated (GPI-linked) proteins contain a signal sequence, thus directing them to the
endoplasmic reticulum (ER). The protein is co-translationally inserted in the ER membrane and is attached to the ER membrane by its hydrophobic C terminus. The majority of the protein extends into the ER lumen. The hydrophobic C-terminal sequence is
then cleaved off and replaced by the GPI-anchor. As the protein processes through the
secretory pathway, it is transferred via vesicles to the Golgi apparatus and finally to the
plasma membrane where it remains attached to the exterior leaflet of the cell membrane. Since the glypiation is the sole means of attachment of such proteins to the
membrane, cleavage of the group by phospholipases will result in controlled release of
the protein from the membrane. The latter mechanism is used in vitro. That is, the
membrane proteins released from the membranes in the enzymatic assay are glypiated
protein.
Phospholipase C (PLC) is an enzyme that is known to cleave the phospho-glycerol
bond found in GPI-anchored proteins. Treatment with PLC will cause release of GPIlinked proteins from the outer cell membrane. The T-cell marker Thy-1 and acetylcholinesterase, as well as both intestinal and placental alkaline phosphatases, are known
to be GPI-linked and are released by treatment with PLC. GPI-linked proteins are
thought to be preferentially located in lipid rafts, suggesting a high level of organization within plasma membrane microdomains.
https://en.wikipedia.org/wiki/Glycophosphatidylinositol
Index
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https://en.wikipedia.org/wiki/Gram-negative_bacteria
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https://en.wikipedia.org/wiki/Gram-positive_bacteria
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Gramicidins
Gramicidin is a heterogeneous mixture of three antibiotic compounds, gramicidins A,
B and C, making up 80%, 6%, and 14%, respectively, all of which are obtained from the
soil bacterial species Bacillus brevis and called collectively gramicidin D. Gramicidin D
contains linear pentadecapeptides, that is chains made up of 15 amino acids.
Gramicidin is active against Gram-positive bacteria, except for the Gram-positive bacilli, and against select Gram-negative organisms, such as Neisseria bacteria. Its therapeutic use is limited to topical application, as it induces hemolysis in lower concentrations than bacteria cell death, so it cannot be administered internally. Since the exterior epidermis is composed of dead cells, applying it to the surface of the skin will not
cause harm.
https://en.wikipedia.org/wiki/Gramicidin
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Granzyme B
Granzyme B is a serine protease most commonly found in the granules of cytotoxic lymphocytes (CTLs), natural killer cells (NK cells) and cytotoxic T cells. It is secreted by
these cells along with the pore forming protein perforin to mediate apoptosis in target
cells.
Granzyme B has also more recently found to be produced by a wide range of noncytotoxic cells ranging from basophils and mast cells to smooth muscle cells. The secondary functions of granzyme B are also numerous. Granzyme B has shown to be involved in inducing inflammation by stimulating cytokine release and is also involved in
extracellular matrix remodeling.
Granzyme B is released with perforin which inserts into a target cell's plasma membrane forming a pore. Perforin has a radius of 5.5nm and granzyme B has a stokes radius of 2.5nm and can therefore pass through the perforin pore into the target to be destroyed.
Alternatively, once released, granzyme B can bind to negatively charged heparan sulphate containing receptors on a target cell and become endocytosed. The vesicles that
carry the enzyme inside then burst, exposing granzyme b to the cytoplasm and its substrates. Hsp-70 has also been linked to aiding granzyme B entry.
Granzyme B has also been proposed to enter a target by first exchanging its bound serglycin for negative phospholipids in a target's plasma membrane. Entry then occurs by
the less selective process of absorptive pinocytosis.
Once inside the target cell granzyme B can cleave and activate initiator caspases 8 and
10, and executioner caspases 3 and 7 which trigger apoptosis. Caspase 7 is the most sensitive to granzyme B and caspases 3, 8, and 10 are only cleaved to intermediate fragments and need further cleavage for full activation.
https://en.wikipedia.org/wiki/Granzyme_B
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GroEL
GroEL belongs to the chaperonin family of molecular chaperones, and is found in a
large number of bacteria. It is required for the proper folding of many proteins. To
function properly, GroEL requires the lid-like cochaperonin protein complex GroES. In
eukaryotes the proteins Hsp60 and Hsp10 are structurally and functionally nearly identical to GroEL and GroES, respectively.
Within the cell, the process of GroEL/ES mediated protein folding involves multiple
rounds of binding, encapsulation, and release of substrate protein. Unfolded substrate
proteins bind to a hydrophobic binding patch on the interior rim of the open cavity of
GroEL, forming a binary complex with the chaperonin. Binding of substrate protein in
this manner, in addition to binding of ATP, induces a conformational change that allows association of the binary complex with a separate lid structure, GroES. Binding of
GroES to the open cavity of the chaperonin induces the individual subunits of the chaperonin to rotate such that the hydrophobic substrate binding site is removed from the
interior of the cavity, causing the substrate protein to be ejected from the rim into the
now largely hydrophilic chamber.
The hydrophilic environment of the chamber favors the burying of hydrophobic residues of the substrate, inducing substrate folding. Hydrolysis of ATP and binding of a
new substrate protein to the opposite cavity sends an allosteric signal causing GroES
and the encapsulated protein to be released into the cytosol. A given protein will undergo multiple rounds of folding, returning each time to its original unfolded state, until the native conformation or an intermediate structure committed to reaching the native state is achieved. Alternatively, the substrate may succumb to a competing reaction, such as misfolding and aggregation with other misfolded proteins.
https://en.wikipedia.org/wiki/GroEL
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GroES
Heat shock 10 kDa protein 1 (Hsp10) also known as chaperonin 10 (cpn10) or earlypregnancy factor (EPF) is a protein that in humans is encoded by the HSPE1 gene. The
homolog in E. coli is GroES that is a chaperonin which usually works in conjunction
with GroEL.
GroES exists as a ring-shaped oligomer of between six to eight identical subunits, while
the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2
stacked rings, each ring containing 7 identical subunits. These ring structures assemble
by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical
cpn60 tetradecamer provides an isolated environment for protein folding whilst cpn10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg++-ATP
dependent manner. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of
cpn60.
Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate.
The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers
allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organized in two heptameric rings stacked back to back. Each
GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an
isolated environment for protein folding. The identical 10 kDa subunits of GroES form
a dome-like heptameric oligomer in solution. ATP binding to GroES may be important
in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.
https://en.wikipedia.org/wiki/GroES
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Growth Factor
A growth factor is a naturally occurring substance capable of stimulating cellular
growth, proliferation, healing, and cellular differentiation. Usually it is a protein or a
steroid hormone. Growth factors are important for regulating a variety of cellular processes.
Growth factors typically act as signaling molecules between cells. Examples are cytokines and hormones that bind to specific receptors on the surface of their target cells.
Growth factor is sometimes used interchangeably among scientists with the term cytokine. Historically, cytokines were associated with hematopoietic (blood forming) cells
and immune system cells (e.g., lymphocytes and tissue cells from spleen, thymus, and
lymph nodes). For the circulatory system and bone marrow in which cells can occur in
a liquid suspension and not bound up in solid tissue, it makes sense for them to communicate by soluble, circulating protein molecules. However, as different lines of research converged, it became clear that some of the same signaling proteins the hematopoietic and immune systems used were also being used by all sorts of other cells and
tissues, during development and in the mature organism.
While growth factor implies a positive effect on cell division, cytokine is a neutral term
with respect to whether a molecule affects proliferation. While some cytokines can be
growth factors, such as G-CSF and GM-CSF, others have an inhibitory effect on cell
growth or proliferation. Some cytokines, such as Fas ligand, are used as "death" signals. They cause target cells to undergo programmed cell death or apoptosis.
https://en.wikipedia.org/wiki/Growth_factor
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GTP
Guanosine-5'-triphosphate (GTP) is a purine nucleoside triphosphate. It can act as a
substrate for the synthesis of RNA during the transcription process of DNA during
DNA replication. Its structure is similar to that of the guanine nucleobase, the only difference being that nucleotides like GTP have a ribose sugar and three phosphates, with
the nucleobase attached to the 1' and the triphosphate moiety attached to the 5' carbons of the ribose.
It also has the role of a source of energy or an activator of substrates in metabolic reactions, like that of ATP, but more specific. It is used as a source of energy for protein synthesis and gluconeogenesis.
GTP is essential to signal transduction, in particular with G-proteins, in secondmessenger mechanisms where it is converted to guanosine diphosphate (GDP) through
the action of GTPases.
GTP is involved in energy transfer within the cell. For instance, a GTP molecule is generated by one of the enzymes in the citric acid cycle. This is tantamount to the generation of one molecule of ATP, since GTP is readily converted to ATP with nucleosidediphosphate kinase (NDK).
During the elongation stage of translation, GTP is used as an energy source for the
binding of a new amino-bound tRNA to the A site of the ribosome. GTP is also used as
an energy source for the translocation of the ribosome towards the 3' end of the
mRNA.
During microtubule polymerization, each heterodimer formed by an and a tubulin
molecule carries two GTP molecules, and the GTP is hydrolyzed to GDP when the tubulin dimers are added to the plus end of the growing microtubule. Such GTP hydrolysis
is not mandatory for microtubule formation, but it appears that only GDP-bound tubulin molecules are able to depolymerize. Thus, a GTP-bound tubulin serves as a cap at
the tip of microtubule to protect from depolymerization. Once the GTP is hydrolyzed,
the microtubule begins to depolymerize and shrink rapidly.
https://en.wikipedia.org/wiki/Guanosine_triphosphate
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GTPase
GTPases (singular GTPase) are a large family of hydrolase enzymes that can bind and
hydrolyze guanosine triphosphate (GTP). The GTP binding and hydrolysis takes place
in the highly conserved G domain common to all GTPases.
GTPases play an important role in:
Signal transduction at the intracellular domain of transmembrane receptors, including recognition of taste, smell and light.
Protein biosynthesis (a.k.a. translation) at the ribosome.
Control and differentiation during cell division.
Translocation of proteins through membranes.
Transport of vesicles within the cell. (GTPases control assembly of vesicle coats.)
All regulatory GTPases have a common mechanism that enables them to switch a signal transduction chain on and off. Toggling the switch is performed by the unidirectional change of the GTPase from the active, GTP-bound form to the inactive, GDPbound form by hydrolysis of the GTP through intrinsic GTPase-activity, effectively
switching the GTPase off. This reaction is initiated by GTPase-activating proteins
(GAPs), coming from another signal transduction pathway. It can be reversed (switching the GTPase on again) by Guanine nucleotide exchange factors (GEFs), which cause
the GDP to dissociate from the GTPase, leading to its association with a new GTP. This
closes the cycle to the active state of the GTPase. The irreversible hydrolysis of the
GTP to GDP forces the cycle to run only in one direction. Only the active state of the
GTPase can transduce a signal to a reaction chain.
https://en.wikipedia.org/wiki/GTPase
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Guanidinium
Guanidine is protonated in physiological conditions. This conjugate acid is called the
guanidinium cation, [CH6N3]+. It is a highly stable +1 cation in aqueous solution due
to the efficient resonance stabilization of the charge and efficient solvation by water
molecules. As a result, its pKa is 13.6 meaning that guanidine is a very strong base in
water.
Guanidinium chloride has chaotropic properties and is used to denature proteins. Guanidine hydrochloride is known to denature proteins with a linear relationship between
concentration and free energy of unfolding. In aqueous solutions containing 6M guanidinium chloride, almost all proteins lose their entire secondary structure and become randomly coiled peptide chains. Guanidinium thiocyanate is also used for its denaturing effect on various biological samples. Guanidine hydrochloride is used as an
adjuvant in treatment of botulism, introduced in 1968, but now its role is considered
controversial - because in some patients there was no improvement after this drug administration.
https://en.wikipedia.org/wiki/Guanidine#Guanidinium_salts
Index
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Guanine
Guanine (G, Gua) is one of the four main nucleobases found in the nucleic acids DNA
and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA,
guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of
purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double
bonds. Being unsaturated, the bicyclic molecule is planar. The guanine nucleoside is
called guanosine.
Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas
thymine is usually seen only in DNA, and uracil only in RNA. Guanine has two tautomeric forms, the major keto form (see figures) and rare enol form. It binds to cytosine
through three hydrogen bonds. In cytosine, the amino group acts as the hydrogen bond
donor and the C-2 carbonyl and the N-3 amine as the hydrogen-bond acceptors. Guanine has the C-6 carbonyl group that acts as the hydrogen bond acceptor, while a group
at N-1 and the amino group at C-2 act as the hydrogen bond donors.
https://en.wikipedia.org/wiki/Guanine
Index
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G-G
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure and Function: Nucleic Acids
Chapter 2 - Structure & Function: Lipids
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 7 - Information Processing: DNA Replication
Chapter 7 - DNA Repair
Chapter 7 - DNA Repair
Chapter 7 - DNA Repair
Chapter 7 - Information Processing: RNA Processing
Chapter 7 - Information Processing: Gene Expression
Chapter 7 - Information Processing: Gene Expression
Chapter 7 - Information Processing: Gene Expression
Chapter 7 - Information Processing: Signaling
Chapter 7 - Information Processing: Signaling
Chapter 7 - Information Processing: Signaling
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Chapter 9 - Point by Point: Information Processing
Guanine Deaminase
Guanine deaminase also known as cypin, guanase, guanine aminase, GAH,
thine. Cypin is a major cytosolic protein that interacts with PSD-95. It prom
ized microtubule assembly in neuronal dendrites.
https://en.wikipedia.org/wiki/Guanine_deaminase
Index
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Guanosine
Guanosine is a purine nucleoside comprising guanine attached to a ribose (ribofuranose) ring via a -N9-glycosidic bond. Guanosine can be phosphorylated to become
guanosine monophosphate (GMP), cyclic guanosine monophosphate (cGMP), guanosine diphosphate (GDP), and guanosine triphosphate (GTP). These forms play important roles in various biochemical processes such as synthesis of nucleic acids and proteins, photosynthesis, muscle contraction, and intracellular signal transduction
(cGMP). When guanine is attached by its N9 nitrogen to the C1 carbon of a deoxyribose
ring it is known as deoxyguanosine.
The antiviral drug aciclovir, often used in herpes treatment, and the anti-HIV drug abacavir, are structurally similar to guanosine.
Guanosine is required for an RNA splicing reaction in mRNA, when a "self-splicing" intron removes itself from the mRNA message by cutting at both ends, re-ligating, and
leaving just the exons on either side to be translated into protein.
https://en.wikipedia.org/wiki/Guanosine
Guide RNA
The term guide RNA is used to refer to three things in molecular biology.
First, guide RNAs (aka gRNA) are the RNAs that guide the insertion or deletion of
uridine residues into mitochondrial mRNAs in kinetoplastid protists in the process
known as RNA editing.
Second in the process of RNA silencing, the term guide RNA refers to the strand of
RNA in the RISC complex that is retained (the other strand is the passenger and it is
released) and used to base pair with a target RNA.
Third, in the CRISPR/Cas9 technique, a guide RNA is the molecule used to target a location in a DNA for cutting by Cas9.
Index
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Gyrase
DNA gyrase, also known as topoisomerase II or simply as gyrase, is an enzyme that relieves strain while double-stranded DNA is being unwound by helicase. This causes
negative supercoiling of the DNA. The gyrase supercoils (or relaxes positive supercoils)
into DNA by looping the template so as to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break, changing the
linking number by two in each enzymatic step.
This process occurs in prokaryotes (in particular, in bacteria), whose single circular
DNA is cut by DNA gyrase and the two ends are then twisted around each other to
form supercoils. Gyrase has been found in the apicoplast of the malarial parasite Plasmodium falciparum, a unicellular eukaryote. Bacterial DNA gyrase is the target of
many antibiotics, including nalidixic acid, novobiocin, and ciprofloxacin.
The unique ability of gyrase to introduce negative supercoils into DNA is what allows
bacterial DNA to have free negative supercoils. The ability of gyrase to relax positive supercoils comes into play during DNA replication and prokaryotic transcription. The
right-handed nature of the DNA double helix causes positive supercoils to accumulate
ahead of a translocating enzyme, in the case of DNA replication, a DNA polymerase.
The ability of gyrase (and topoisomerase IV) to relax positive supercoils allows superhelical tension ahead of the polymerase to be released so that replication can continue.
https://en.wikipedia.org/wiki/DNA_gyrase
Index
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H1
Histone H1 is one of the five main histone protein families which are components of
chromatin in eukaryotic cells. Though highly conserved, it is nevertheless the most variable histone in sequence across species.
Unlike the other histones, H1 does not make up the nucleosome "bead". Instead, it sits
on top of the structure, keeping in place the DNA that has wrapped around the nucleosome. H1 is present in half the amount of the other four histones, which contribute two
molecules to each nucleosome bead. In addition to binding to the nucleosome, the H1
protein binds to the "linker DNA" (approximately 20-80 nucleotides in length) region
between nucleosomes, helping stabilize the zig-zagged 30nm chromatin fiber.
It is uncertain whether H1 promotes a solenoid (DNA)-like chromatin fiber, in which
exposed linker DNA is shortened, or whether it merely promotes a change in the angle
of adjacent nucleosomes, without affecting linker length. Nuclease digestion and DNA
footprinting experiments suggest that the globular domain of histone H1 localizes near
the nucleosome dyad, where it protects approximately 15-30 base pairs of additional
DNA.
https://en.wikipedia.org/wiki/Histone_H1
Index
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H2A
Histone H2A is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells.
H2A consists of a main globular domain and a long N-terminal tail or C-terminal on
one end of the molecule. The N-terminal tail or C-terminal tail is the location of posttranslational modification. Thus far, researchers have not identified any secondary
structures that arise in the tail. H2A utilizes a protein fold known as the histone fold.
The histone fold is a three-helix core domain that is connected by two loops. This connection forms a handshake arrangement. Most notably, this is termed the helix-turnhelix motif, which allows for dimerization with H2B. The histone fold is conserved
among H2A at the structural level. However the genetic sequence that encodes for this
structure differs between variants.
Histone H2A is composed of non-allelic variants. The term "Histone H2A" is intentionally non-specific and refers to a variety of closely related proteins that vary often by
only a few amino acids. Notable variants include H2A.1, H2A.2, H2A.X, and H2A.Z.
Changes in variant composition occur in differentiating cells. This was observed in differentiating neurons during synthesis and turnover. Changes in variant composition
were seen among the H2A.1 histone. The only variant that remained constant in the neural differentiation was variant H2AZ. H2AZ is a variant that exchanges with conventional
H2A core protein. This variant is important for gene silencing.
https://en.wikipedia.org/wiki/Histone_H2A
Index
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H2B
Histone H2B is one of the 5 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and long N-terminal and Cterminal tails, H2B is involved with the structure of the nucleosomes.
Histone H2B is a lightweight structural protein made of 126 amino acids. Many of these
amino acids have a basic pH, which allows them to interact with the negatively charged
phosphate groups in DNA. Along with a central globular domain, histone H2B has two
flexible histone tails that extend outwards one at the N-terminal end and one at Cterminal end. These are highly involved in condensing chromatin from the beads-on-astring conformation to a 30-nm fiber. Similar to other histone proteins, histone H2B
has a distinct histone fold that is optimized for histone-histone as well as histone-DNA
interactions.
Two copies of histone H2B come together with two copies each of histone H2A, histone
H3, and histone H4 to form the octamer core of the nucleosome to give structure to
DNA. To facilitate this formation, histone H2B first binds to histone H2A to form a heterodimer. Two of these heterodimers then bind together with a heterotetramer made
of histone H3 and histone H4, giving the nucleosome its characteristic disk shape. Chromatin is then wrapped around the entire nucleosome in groups of approximately 160
base pairs of DNA. The wrapping continues until all chromatin has been packaged with
the nucleosomes.
https://en.wikipedia.org/wiki/Histone_H2B
Index
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H2O2
Hydrogen peroxide is a chemical compound with the formula H2O2. In its pure form, it
is a colorless liquid, slightly more viscous than water. However, for safety reasons it is
normally used as an aqueous solution. Hydrogen peroxide is the simplest peroxide (a
compound with an oxygenoxygen single bond) and finds use as a strong oxidizer,
bleaching agent and disinfectant. Concentrated hydrogen peroxide, or "high-test peroxide", is a reactive oxygen species and has been used as a propellant in rocketry.
Hydrogen peroxide is often described as being "water but with one more oxygen
atom", a description that can give the incorrect impression of significant chemical similarity between the two compounds. While they have a similar melting point and appearance, pure hydrogen peroxide will explode if heated to boiling, will cause serious contact burns to the skin and can set materials alight on contact. For these reasons it is
usually handled as a dilute solution (household grades are typically 36% in the U.S.
and somewhat higher in Europe). Its chemistry is dominated by the nature of its unstable peroxide bond.
https://en.wikipedia.org/wiki/Hydrogen_peroxide
Index
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H2S
Hydrogen sulfide is the chemical compound with the formula H2S. It is a colorless gas
with the characteristic foul odor of rotten eggs. It is heavier than air, very poisonous,
corrosive, flammable, and explosive.
Hydrogen sulfide often results from the prokaryotic breakdown of organic matter in
the absence of oxygen gas, such as in swamps and sewers. This process is commonly
known as anaerobic digestion. H2S also occurs in volcanic gases, natural gas, and in
some sources of well water. The human body produces small amounts of H2S and uses
it as a signaling molecule.
https://en.wikipedia.org/wiki/Hydrogen_sulfide
Index
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G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
H2Se
0.05 ppm over an 8-hour period. Even at extremely low concentrations, thi
https://en.wikipedia.org/wiki/Hydrogen_selenide
Index
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H3
Histone H3 is one of the five main histone proteins involved in the structure of chr
tin in eukaryotic cells. Featuring a main globular domain and a long N-terminal ta
H3 is involved with the structure of the nucleosomes of the 'beads on a string' struc
the most extensively modified of the five histones. The term "Histone H3" alone is
The N-terminal meme of histone H3 protrudes from the globular nucleosome core
tyl groups to lysine and arginine amino acids and the phosphorylation of serine or
threonine.
https://en.wikipedia.org/wiki/Histone_H3
H4
Histone H4 is one of the five main histone proteins involved in the structure
tin in eukaryotic cells. Featuring a main globular domain and a long N-term
fications may alter expression of genes located on DNA associated with its p
matin, where its sequence variants and variable modification states are thou
a role in the dynamic and long term regulation of genes.
https://en.wikipedia.org/wiki/Histone_H4
H5
The histone H1 family in animals includes multiple H1 isoforms that can be
The reason for these multiple isoforms remains unclear, but both their evol
amino acid sequences suggest that they are not functionally equivalent. One
histone H5, which is only found in avian erythrocytes, which are unlike mam
erythrocytes in that they have nuclei.
https://en.wikipedia.org/wiki/Histone_H1
Hair
Hair is a protein filament that grows from follicles found in the dermis, or skin. Hair is
one of the defining characteristics of mammals. The human body, apart from areas of
glabrous skin, is covered in follicles which produce thick terminal and fine vellus hair.
Most common interest in hair is focused on hair growth, hair types and hair care, but
hair is also an important biomaterial primarily composed of protein, notably keratin.
Shown below is a cross-section of a human hair.
https://en.wikipedia.org/wiki/Hair
Handedness
Helices can be either right-handed or left-handed. With the line of sight alo
lix's axis, if a clockwise screwing motion moves the helix away from the obs
handed helix cannot be turned to look like a left-handed one unless it is view
mirror, and vice versa.
Index
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HbA
Hemoglobin A (HbA), also known as adult hemoglobin or 22, is the most
man hemoglobin tetramer, comprising over 97% of the total red blood cell h
It consists of two chains and two chains.
https://en.wikipedia.org/wiki/Hemoglobin_A
HbS
distort the shape of the red blood cell from a smooth doughnut-like shape t
and full of spikes, making it fragile and susceptible to breaking within capil
ers have symptoms only if they are deprived of oxygen (for example, while c
When enough hemoglobin collapses on itself the red blood cells become sic
https://en.wikipedia.org/wiki/Sickle-cell_disease
HCl
The compound hydrogen chloride has the chemical formula HCl. At room tem
ture, it is a colorless gas, which forms white fumes of hydrochloric acid upon
with atmospheric humidity. Hydrogen chloride gas and hydrochloric acid are
more electronegative than the hydrogen atom, the covalent bond between th
oms is quite polar. Consequently, the molecule has a large dipole moment wi
tive partial charge () at the chlorine atom and a positive partial charge (+
drogen atom. In part because of its high polarity, HCl is very soluble in water
other polar solvents).
https://en.wikipedia.org/wiki/Hydrogen_chloride
HDL
High-density lipoproteins (HDL) are one of the five major groups of lipoproteins. Lipoproteins are complex particles composed of multiple proteins which transport all fat
molecules (lipids) around the body within the water outside cells. They are typically
composed of 80-100 proteins per particle (organized by one, two or three ApoA, more
as the particles enlarge picking up and carrying more fat molecules) and transporting
up to hundreds of fat molecules per particle. Unlike the larger lipoprotein particles
which deliver fat molecules to cells, HDL particles remove fat molecules from cells
which need to export molecules. The molecules carried include cholesterol, phospholipids, and triglycerides. Amounts of each are quite variable.
Increasing concentrations of HDL particles are strongly associated with decreasing accumulation of atherosclerosis within the walls of arteries. This is important because
atherosclerosis eventually results in sudden plaque ruptures, cardiovascular disease,
stroke and other vascular diseases. HDL particles are sometimes referred to as "good
cholesterol" because they can transport fat molecules out of artery walls, reduce macrophage accumulation, and thus help prevent or even regress atherosclerosis. However,
studies have shown that HDL-lacking mice still have the ability to transport cholesterol
to bile, suggesting that there are alternative mechanisms for cholesterol removal.
https://en.wikipedia.org/wiki/High-density_lipoprotein
Index
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HDLs
High-density lipoproteins (HDL) are one of the five major groups of lipoproteins. Lipoproteins are complex particles composed of multiple proteins which transport all fat
molecules (lipids) around the body within the water outside cells. They are typically
composed of 80-100 proteins per particle (organized by one, two or three ApoA, more
as the particles enlarge picking up and carrying more fat molecules) and transporting
up to hundreds of fat molecules per particle. Unlike the larger lipoprotein particles
which deliver fat molecules to cells, HDL particles remove fat molecules from cells
which need to export molecules. The molecules carried include cholesterol, phospholipids, and triglycerides. Amounts of each are quite variable.
Increasing concentrations of HDL particles are strongly associated with decreasing accumulation of atherosclerosis within the walls of arteries. This is important because
atherosclerosis eventually results in sudden plaque ruptures, cardiovascular disease,
stroke and other vascular diseases. HDL particles are sometimes referred to as "good
cholesterol" because they can transport fat molecules out of artery walls, reduce macrophage accumulation, and thus help prevent or even regress atherosclerosis. However,
studies have shown that HDL-lacking mice still have the ability to transport cholesterol
to bile, suggesting that there are alternative mechanisms for cholesterol removal.
https://en.wikipedia.org/wiki/High-density_lipoprotein
Index
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Heat Shock
Heat shock is the effect of subjecting a cell to a higher temperature than that of the
ideal body temperature of the organism from which the cell line was derived.
encoding heat shock proteins (HSPs) as part of the cell's internal repair mechanism
They are also called stress-proteins. and respond to heat, cold and oxygen depriva
by activating several cascade pathways. HSPs are also present in cells under perfec
normal conditions. Some HSPs, called chaperones, ensure that the cells proteins a
the right shape and in the right place at the right time. For example, HSPs help ne
essential for their function. They also shuttle proteins from one compartment to a
other inside the cell, and target old or terminally misfolded proteins to proteases f
degradation. Heat shock proteins are also believed to play a role in the presentatio
pieces of proteins (or peptides) on the cell surface to help the immune system reco
nize diseased cells.
https://en.wikipedia.org/wiki/Heat_shock
Index
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Hedgehog Protein
the adult. Diseases associated with the malfunction of this pathway include
carcinoma.
The Hedgehog signaling pathway is one of the key regulators of animal deve
and is present in all bilaterians. The pathway takes its name from its polype
volved in establishing the basis of the fly body plan. The molecule remains i
during later stages of embryogenesis and metamorphosis.
https://en.wikipedia.org/wiki/Hedgehog_signaling_pathway
Helicase
Helicases are a class of enzymes vital to all living organisms. Their main function is to
unpackage an organism's genes. They are motor proteins that move directionally along
a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands
(i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis.
There are many helicases resulting from the great variety of processes in which strand
separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases.
The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31
DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of
nucleic acid strands that necessitates the use of helicases.
Helicases are often used to separate strands of a DNA double helix or a self-annealed
RNA molecule using the energy from ATP hydrolysis, a process characterized by the
breaking of hydrogen bonds between annealed nucleotide bases. They also function to
remove nucleic acid-associated proteins and catalyze homologous DNA recombination.
Metabolic processes of RNA such as translation, transcription, ribosome biogenesis,
RNA splicing, RNA transport, RNA editing, and RNA degradation are all facilitated by
helicases. Helicases move incrementally along one nucleic acid strand of the duplex
with a directionality and processivity specific to each particular enzyme.
Helicases adopt different structures and oligomerization states. Whereas DnaB-like
helicases unwind DNA as donut-shaped hexamers, other enzymes have been shown to
be active as monomers or dimers. Studies have shown that helicases may act passively,
waiting for uncatalyzed unwinding to take place and then translocating between displaced strands, or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis. In the latter case, the helicase acts comparably to an
active motor, unwinding and translocating along its substrate as a direct result of its
ATPase activity. Helicases may process much faster in vivo than in vitro due to the
presence of accessory proteins that aid in the destabilization of the fork junction.
https://en.wikipedia.org/wiki/Helicase
Helix
A helix is a type of smooth space curve, i.e. a curve in three-dimensional space. It has
the property that the tangent line at any point makes a constant angle with a fixed line
called the axis. Examples of helices are coil springs and the handrails of spiral staircases. Helices are important in biology, as the DNA molecule is formed as two intertwined helices, and many proteins have helical substructures, known as -helices. A
right-handed helix is shown below.
https://en.wikipedia.org/wiki/Helix
Index
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Helix-turn-helix
Index
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Heme
Heme is a cofactor consisting of an Fe++ (ferrous or iron) ion contained in the center of
a large heterocyclic organic ring called a porphyrin, made up of four pyrrolic groups
joined together by methine bridges. Not all porphyrins contain iron, but a substantial
fraction of porphyrin-containing metalloproteins have heme as their prosthetic group.
These are known as hemoproteins. Hemes are most commonly recognized as components of hemoglobin, the red pigment in blood, but are also found in a number of other
biologically important hemoproteins such as myoglobin, cytochrome, catalase, heme
peroxidase, and endothelial nitric oxide synthase. Shown below is heme b.
https://en.wikipedia.org/wiki/Heme
Index
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Heme Oxygenase
duces biliverdin, ferrous iron, and carbon monoxide. Heme oxygenase clea
heme ring at the -methene bridge to form either biliverdin or, if the heme
Index
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Hemicellulose
A hemicellulose (also known as polyose) is any of several heteropolymers (matrix polysaccharides), such as arabinoxylans, present along with cellulose in almost all plant
cell walls. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicellulose has a random, amorphous structure with little strength. It is easily hydrolyzed by
dilute acid or base as well as myriad hemicellulase enzymes.
https://en.wikipedia.org/wiki/Hemicellulose
Hemiterpenes
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Hemocyanin
Hemocyanins (also spelled haemocyanins and abbreviated Hc) are proteins that transport oxygen throughout the bodies of some invertebrate animals. These metalloproteins contain two copper atoms that reversibly bind a single oxygen molecule (O2).
They are second only to hemoglobin in frequency of use as an oxygen transport molecule. Unlike the hemoglobin in red blood cells found in vertebrates, hemocyanins are
not bound to blood cells but are instead suspended directly in the hemolymph. Oxygenation causes a color change between the colorless Cu(I) deoxygenated form and the
blue Cu(II) oxygenated form.
Hemocyanins are found only in the Mollusca and Arthropoda: the earliest hemocyanins were found in the snail Helix pomatia (a mollusc) and in the horseshoe crab
(an arthropod). They were subsequently found to be common among crustaceans and
are utilized by some land arthropods such as the tarantula Eurypelma californicum,
the emperor scorpion, and the centipede Scutigera coleoptrata. Also, larval storage
proteins in many insects appear to be derived from hemocyanins.
Although the respiratory function of hemocyanin is similar to that of hemoglobin,
there are a significant number of differences in its molecular structure and mechanism. Whereas hemoglobin carries its iron atoms in porphyrin rings (heme groups),
the copper atoms of hemocyanin are bound as prosthetic groups coordinated by histidine residues. The active site of hemocyanin is composed of a pair of copper(I) cations
which are directly coordinated to the protein through the driving force of imidazolic
rings of six histidine residues. It has been noted that species using hemocyanin for oxygen transportation include crustaceans living in cold environments with low oxygen
pressure. Under these circumstances hemoglobin oxygen transportation is less efficient than hemocyanin oxygen transportation. Nevertheless there are also terrestrial
arthropods using hemocyanin, notably spiders and scorpions, that live in warm climates.
Most hemocyanins bind with oxygen non-cooperatively and are roughly one-fourth as
efficient as hemoglobin at transporting oxygen per amount of blood. Hemoglobin
binds oxygen cooperatively due to steric conformation changes in the protein complex,
which increases hemoglobin's affinity for oxygen when partially oxygenated. In some
hemocyanins of horseshoe crabs and some other species of arthropods, cooperative
binding is observed, with Hill coefficients of 1.6 - 3.0. Hill coefficients vary depending
on species and laboratory measurement settings. Hemoglobin, for comparison, has a
Hill coefficient of usually 2.8 - 3.0. In these cases of cooperative binding hemocyanin
was arranged in protein sub-complexes of 6 subunits (hexamer) each with one oxygen
binding site. Binding of oxygen on one unit in the complex would increase the affinity
of the neighboring units. Each hexamer complex was arranged together to form a
larger complex of dozens of hexamers. In one study, cooperative binding was found to
be dependent on hexamers being arranged together in the larger complex, suggesting
cooperative binding between hexamers. Hemocyanin oxygen-binding profile is also affected by dissolved salt ion levels and pH.
https://en.wikipedia.org/wiki/Hemocyanin
Hemoglobin
Hemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood
cells of all vertebrates (with the exception of the fish family Channichthyidae) as well
as the tissues of some invertebrates. Hemoglobin in the blood carries oxygen from the
respiratory organs (lungs or gills) to the rest of the body (i.e. the tissues). There it releases the oxygen to permit aerobic respiration to provide energy to power the functions of the organism in the process called metabolism.
In mammals, the protein makes up about 96% of the red blood cells' dry content (by
weight), and around 35% of the total content (including water). Hemoglobin has an
oxygen-binding capacity of 1.34 mL O2 per gram, which increases the total blood oxygen capacity seventy-fold compared to dissolved oxygen in blood. The mammalian hemoglobin molecule can bind (carry) up to four oxygen molecules.
Hemoglobin is involved in the transport of other gases: It carries some of the body's
respiratory carbon dioxide (about 2025% of the total) as carbaminohemoglobin, in
which CO2 is bound to the globin protein. The molecule also carries the important regulatory molecule nitric oxide bound to a globin protein thiol group, releasing it at the
same time as oxygen.
Hemoglobin is also found outside red blood cells and their progenitor lines. Other cells
that contain hemoglobin include the A9 dopaminergic neurons in the substantia nigra,
macrophages, alveolar cells, and mesangial cells in the kidney. In these tissues, hemoglobin has a non-oxygen-carrying function as an antioxidant and a regulator of iron metabolism.
Hemoglobin and hemoglobin-like molecules are also found in many invertebrates,
fungi, and plants. In these organisms, hemoglobins may carry oxygen, or they may act
to transport and regulate other small molecules and ions such as carbon dioxide, nitric
oxide, hydrogen sulfide and sulfide. A variant of the molecule, called leghemoglobin, is
used to scavenge oxygen away from anaerobic systems, such as the nitrogen-fixing nodules of leguminous plants, before the oxygen can poison (deactivate) the system.
https://en.wikipedia.org/wiki/Hemoglobin
Index
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Hemophilia
impairs the body's ability to control blood clotting, which is used to stop ble
Index
Find Term
Here, [HA] is the molar concentration of the undissociated weak acid, [A] is the molar
concentration (molarity, M) of this acid's conjugate base and pKa is log10 Ka where
Ka is the acid dissociation constant, that is:
In these equations, A denotes the ionic form of the relevant acid. Bracketed quantities
such as [base] and [acid] denote the molar concentration of the quantity enclosed.
https://en.wikipedia.org/wiki/HendersonHasselbalch_equation
Henderson-Hasselbalch
The HendersonHasselbalch equation describes the derivation of pH as a measure of
acidity (using pKa, the negative log of the acid dissociation constant) in biological and
chemical systems. The equation is also useful for estimating the pH of a buffer solution
and finding the equilibrium pH in acid-base reactions (it is widely used to calculate the
isoelectric point of proteins).
The equation is given by:
Here, [HA] is the molar concentration of the undissociated weak acid, [A] is the molar
concentration (molarity, M) of this acid's conjugate base and pKa is log10 Ka where
Ka is the acid dissociation constant, that is:
In these equations, A denotes the ionic form of the relevant acid. Bracketed quantities
such as [base] and [acid] denote the molar concentration of the quantity enclosed.
https://en.wikipedia.org/wiki/HendersonHasselbalch_equation
Index
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Heparan Sulfate
Heparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It occurs as
a proteoglycan (HSPG) in which two or three HS chains are attached in close proximity
to cell surface or extracellular matrix proteins. It is in this form that HS binds to a variety of protein ligands and regulates a wide variety of biological activities, including developmental processes, angiogenesis, blood coagulation, abolishing detachment activity by GrB (Granzyme B), and tumor metastasis. HS has been shown to serve as cellular receptor for a number of viruses including the respiratory syncytial virus (Hallak et
al. 2000). The structure of a heparan sulfate subunit is shown below.
https://en.wikipedia.org/wiki/Heparan_sulfate
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Heparin
Heparin is a widely used injectable blood thinner. It is used to treat and prevent deep
vein thrombosis and pulmonary embolism (collectively known as venous thromboembolism) and is also used as part of the treatment of myocardial infarction and unstable
angina. Heparin is used on the inside surfaces of various devices such as test tubes and
kidney dialysis machines.
Heparin's normal role in the body is unclear. Heparin is usually stored within the secretory granules of mast cells and released only into the vasculature at sites of tissue injury. It has been proposed that, rather than anticoagulation, the main purpose of heparin is defense at such sites against invading bacteria and other foreign materials. The
repeating unit of a heparin polymer is shown below.
https://en.wikipedia.org/wiki/Heparin
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Herceptin
Trastuzumab, sold under the brandname Herceptin among others, is a monoclonal antibody that interferes with the HER2/neu receptor. Its main use is to treat certain
breast cancers.
The HER receptors are proteins that are embedded in the cell membrane and communicate molecular signals from outside the cell (molecules called EGFs) to inside the
cell, and turn genes on and off. The HER protein, Human Epidermal Growth Factor Receptor, binds to Human Epidermal Growth Factor, and stimulates cell proliferation. In
some cancers, notably certain types of breast cancer, HER2 is over-expressed, and
causes cancer cells to reproduce uncontrollably.
The HER2 gene (also known as HER2/neu and ErbB2 gene) is amplified in 20-30% of
early-stage breast cancers. The HER2 pathway promotes cell growth and division
when it is functioning normally. However, when it is overexpressed, cell growth accelerates beyond its normal limits. In some types of cancer the pathway is exploited to promote rapid cell growth and proliferation and hence tumor formation. The EGF pathway includes the receptors HER1 (EGFR), HER2, HER3, and HER4. The binding of
EGF to HER is required to activate the pathway. The pathway initiates the MAP Kinase
pathway as well as the PI3 Kinase/AKT pathway, which in turn activates the NF-B
pathway. In cancer cells the HER2 protein can be expressed up to 100 times more than
in normal cells (2 million versus 20,000 per cell). This overexpression leads to strong
and constant proliferative signaling and hence tumor formation. Overexpression of
HER2 also causes deactivation of checkpoints, allowing for even greater increases in
proliferation.
Trastuzumab binds to domain IV of the extracellular segment of the HER2/neu receptor. Cells treated with trastuzumab undergo arrest during the G1 phase of the cell cycle
so there is reduced proliferation. It has been suggested that trastuzumab does not alter
HER-2 expression, but downregulates activation of AKT. In addition, trastuzumab suppresses angiogenesis both by induction of antiangiogenic factors and repression of proangiogenic factors. It is thought that a contribution to the unregulated growth observed in cancer could be due to proteolytic cleavage of HER2/neu that results in the
release of the extracellular domain.
Experiments in laboratory animals indicate that antibodies, including trastuzumab,
when bound to a cell, induce immune cells to kill that cell, and that such antibodydependent cell-mediated cytotoxicity is another important mechanism of action.
https://en.wikipedia.org/wiki/Trastuzumab
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Heterochromatin
Heterochromatin is a tightly packed form of DNA, which comes in multiple varieties.
Because it is tightly packed, it is inaccessible to polymerases and is therefore not transcribed, (or so we thought. According to Volpe et al, and many other papers since, we
see that much of this DNA is in fact transcribed, however it is continuously turned over
via a RITS pathway) . These varieties lie on a continuum between the two extremes of
constitutive and facultative heterochromatin. Both play a role in the expression of
genes.
Chromatin is found in two varieties: euchromatin and heterochromatin. Originally, the
two forms were distinguished cytologically by how intensely they stained the euchromatin is less intense, while heterochromatin stains intensely, indicating tighter packing. Heterochromatin is usually localized to the periphery of the nucleus. Despite this
early dichotomy, recent evidence in both animals and plants has suggested that there
are more than two distinct heterochromatin states, and it may in fact exist in four or
five 'states', each marked by different combinations of epigenetic marks.
Heterochromatin mainly consists of genetically inactive satellite sequences, and many
genes are repressed to various extents, although some cannot be expressed in euchromatin at all. Both centromeres and telomeres are heterochromatic, as is the Barr body
of the second, inactivated X-chromosome in a female.
https://en.wikipedia.org/wiki/Heterochromatin
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Heterocyclic
https://en.wikipedia.org/wiki/Heterocyclic_compound
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Heterotrophic
A heterotroph is an organism that cannot fix carbon and uses organic carbo
growth. Heterotrophs can be further divided based on how they obtain ener
Heterotrophs
A heterotroph is an organism that cannot fix carbon and uses organic carbo
growth. Heterotrophs can be further divided based on how they obtain ener
Heterotropic
https://en.wikipedia.org/wiki/Allosteric_regulation#Types_of_allosteric_
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Heterotropic Effectors
https://en.wikipedia.org/wiki/Allosteric_regulation#Types_of_allosteric_
Heterozygous
case letter (representing the recessive allele), such as "Rr" or "Ss". Alternati
erozygote for gene "R" is assumed to be "Rr". The capital letter is usually wr
sive allele will not be present. In more complex dominance schemes the res
erozygosity can be more complex.
https://en.wikipedia.org/wiki/Zygosity#Heterozygous
Hexokinase
A hexokinase is an enzyme that phosphorylates hexoses (six-carbon sugars), forming
hexose phosphate. In most organisms, glucose is the most important substrate of
hexokinases, and glucose-6-phosphate is the most important product. Hexokinase can
transfer an inorganic phosphate group from ATP to a substrate.
Genes that encode hexokinase have been discovered in every domain of life, and exist
among a variety of species that range from bacteria, yeast, and plants to humans and
other vertebrates. They are categorized as actin fold proteins, sharing a common ATP
binding site core that is surrounded by more variable sequences which determine substrate affinities and other properties.
Several hexokinase isoforms or isozymes that provide different functions can occur in a
single species.
https://en.wikipedia.org/wiki/Hexokinase
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Hexoses
In bio-organic chemistry, a hexose is a monosaccharide with six carbon atoms, having
the chemical formula C6H12O6. Hexoses are classified by functional group, with aldohexoses having an aldehyde at position 1, and ketohexoses having a ketone at position
2.
Hexoses play a key role in several different biochemical pathways, including cellular energy release, signaling, carbohydrate synthesis, and the regulation of gene expression.
The most common hexoses in biological systems are D-galactose, D-glucose and Dmannose.
Researchers have used computational algorithms to model protein-galactose, proteinglucose and protein-mannose binding-sites. Individual hexoses share multiple physiochemical similarities leading to the development of a general protein-hexose bindingsite model.
https://en.wikipedia.org/wiki/Hexose
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Hind III
HindIII (pronounced "Hin Dee Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg++ via hydrolysis.
HindIII restrictions process results in formation of overhanging palindromic sticky
ends. The cleavage of this sequence between the AA's results in 5' overhangs on the
DNA called sticky ends:
5'-A |A G C T T-3'
3'-T T C G A| A-5'
Restriction endonucleases are used as defense mechanisms in prokaryotic organisms
in the restriction modification system. Their primary function is to protect the host genome against invasion by foreign DNA, primarily bacteriophage DNA. There is also evidence that suggests the restriction enzymes may act alongside modification enzymes as
selfish elements, or may be involved in genetic recombination and transposition.
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Histamine
duced by basophils and by mast cells found in nearby connective tissues. Hist
creases the permeability of the capillaries to white blood cells and some prote
low them to engage pathogens in the infected tissues.
https://en.wikipedia.org/wiki/Histamine
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Histidine
Histidine (abbreviated as His or H; encoded by the codons CAU and CAC) is an amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), a carboxylic acid
group (which is in the deprotonated COO form under biological conditions), and a
side chain imidazole, which can be positively charged.
The conjugate acid (protonated form) of the imidazole side chain in histidine has a pKa
of approximately 6.0. This means that, at physiologically relevant pH values, relatively
small shifts in pH will change its average charge. Below a pH of 6, the imidazole ring is
mostly protonated as described by the HendersonHasselbalch equation. When protonated, the imidazole ring bears two NH bonds and has a positive charge. The positive
charge is equally distributed between both nitrogens and can be represented with two
equally important resonance structures. As the pH increases past approximately 6, one
of the protons is lost. The remaining proton of the now-neutral imidazole ring can reside on either nitrogen, giving rise to what are known as the N1-H or N3-H tautomers.
The N3-H tautomer is protonated on the #3 nitrogen, farther from the amino acid backbone bearing the amino and carboxyl groups, whereas the N1-H tautomer is protonated
on the nitrogen nearer the backbone.
https://en.wikipedia.org/wiki/Histidine
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Histidine Tagging
A polyhistidine-tag is an amino acid motif in proteins that consists of at least six histidine (His) residues, often at the N- or C-terminus of the protein. It is also known as
hexa histidine-tag, 6xHis-tag, His6 tag and by the trademarked name His-tag (registered by EMD Biosciences).
Polyhistidine-tags are often used for affinity purification of polyhistidine-tagged recombinant proteins expressed in Escherichia coli and other prokaryotic expression systems. Bacterial cells are harvested via centrifugation and the resulting cell pellet lysed
either by physical means or by means of detergents and enzymes such as lysozyme or
any combination of these. At this stage raw lysate contains the recombinant protein
among many other proteins originating from the bacterial host. This mixture is incubated with an affinity resin containing bound bivalent nickel or cobalt ions, which are
available commercially in different varieties. Nickel and cobalt have similar properties
and as they are adjacent period 4 transition metals ((v. iron triad)). These resins are
generally sepharose/agarose functionalized with a chelator, such as iminodiacetic acid
(Ni-IDA) and nitrilotriacetic acid (Ni-NTA) for nickel and carboxylmethylaspartate
(Co-CMA) for cobalt, which the polyhistidine-tag binds with micromolar affinity. The
resin is then washed with phosphate buffer to remove proteins that do not specifically
interact with the cobalt or nickel ion. With Ni-based methods, washing efficiency can
be improved by the addition of 20 mM imidazole (proteins are usually eluted with 150300 mM imidazole). Generally nickel-based resins have higher binding capacity, while
cobalt-based resins offer the highest purity. The purity and amount of protein can be
assessed by SDS-PAGE and Western blotting.
Affinity purification using a polyhistidine-tag usually results in relatively pure protein
when the recombinant protein is expressed in prokaryotic organisms. Depending on
downstream applications, including the purification of protein complexes to study protein interactions, purification from higher organisms such as yeasts or other eukaryotes may require a tandem affinity purification using two tags to yield higher purity. Alternatively, single-step purification using immobilized cobalt ions rather than nickel
ions generally yields a substantial increase in purity and requires lower imidazole concentrations for elution of the his-tagged protein.
Polyhistidine-tagging is the option of choice for purifying recombinant proteins in denaturing conditions because its mode of action is dependent only on the primary structure of proteins. Generally for this sort of a technique, histidine binding is titrated using pH instead of imidazole bindingat a high pH, histidine binds to nickel or cobalt,
but at low pH (~6 for cobalt and ~4 for nickel), histidine becomes protonated and is
competed off of the metal ion. Compare this to antibody purification and GST purification, a prerequisite to which is the proper (native) folding of proteins involved.
https://en.wikipedia.org/wiki/Polyhistidine-tag
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Histidinol
Histidinol is an intermediate in the biosynthesis of the amino acid histidine. It is the
immediate precursor of histidine.
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Histidinol Dehydrogenase
The two substrates of this enzyme are L-histidinol and NAD+, and its 3 prod
histidine, NADH, and H+.
Histidinol dehydrogenase catalyzes the terminal step in the biosynthesis of
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Histidinol-phosphate
Histidinol-phosphate is an intermediate in the biosynthesis of the amino acid histidine.
Histidinol-phosphate Aminotransferase
Histidinol-phosphate transaminase (EC 2.6.1.9) is an enzyme that catalyzes the chemical reaction
L-histidinol phosphate + 2-oxoglutarate <---> 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate
The two substrates of this enzyme are L-histidinol phosphate and 2-oxoglutarate and
its two products are 3-(imidazol-4-yl)-2-oxopropyl phosphate and L-glutamate.
This enzyme belongs to the family of transferases, specifically the transaminases,
which transfer nitrogenous groups. The systematic name of this enzyme class is
L-histidinol-phosphate:2-oxoglutarate aminotransferase. Other names in common use
include imidazolylacetolphosphate transaminase, glutamic-imidazoleacetol phosphate
transaminase, histidinol phosphate aminotransferase, imidazoleacetol phosphate transaminase, L-histidinol phosphate aminotransferase, histidine:imidazoleacetol phosphate transaminase, IAP transaminase, and imidazolylacetolphosphate aminotransferase. This enzyme participates in 5 metabolic pathways: histidine metabolism, tyrosine
metabolism, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and novobiocin biosynthesis. It employs one cofactor, pyridoxal phosphate.
https://en.wikipedia.org/wiki/Histidinol-phosphate_transaminase
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Histidinol-phosphate Phosphatase
phoric monoester bonds. The systematic name of this enzyme class is L-his
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Histone
Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and
order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in
gene regulation. Without histones, the unwound DNA in chromosomes would be very
long (a length to width ratio of more than 10 million to 1 in human DNA). For example,
each human cell has about 1.8 meters of DNA, (~6ft) but wound on the histones it has
about 90 micrometers (0.09mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.
Five major families of histones exist: H1/H5, H2A, H2B, H3 and H4. Histones H2A,
H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known
as the linker histones.
The core histones all exist as dimers, which are similar in that they all possess the histone fold domain - three helices linked by two loops. It is this helical structure that
allows for interaction between distinct dimers, particularly in a head-tail fashion (also
called the handshake motif). The resulting four distinct dimers then come together to
form one octameric nucleosome core, approximately 63 Angstroms in diameter (a solenoid (DNA)-like particle). 147 base pairs of DNA wrap around this core particle 1.65
times in a left-handed super-helical turn to give a particle of around 100 Angstroms
across. The linker histone H1 binds the nucleosome at the entry and exit sites of the
DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50
base pairs of DNA separating each pair of nucleosomes (also referred to as linker
DNA). Higher-order structures include the 30nm fiber (forming an irregular zigzag)
and 100nm fiber, these being the structures found in normal cells. During mitosis and
meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.
https://en.wikipedia.org/wiki/Histone
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Histone Deacetylases
Histone deacetylases (EC 3.5.1.98, HDAC) are a class of enzymes that remove acetyl
groups (O=C-CH3) from an -N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped
around histones, and DNA expression is regulated by acetylation and de-acetylation.
Its action is opposite to that of histone acetyltransferase. HDAC proteins are now also
called lysine deacetylases (KDAC), to describe their function rather than their target,
which also includes non-histone proteins.
Histone tails are normally positively charged due to amine groups present on their lysine and arginine amino acids. These positive charges help the histone tails to interact
with and bind to the negatively charged phosphate groups on the DNA backbone. Acetylation, which occurs normally in a cell, neutralizes the positive charges on the histone
by changing amines into amides and decreases the ability of the histones to bind to
DNA. This decreased binding allows chromatin expansion, permitting genetic transcription to take place. Histone deacetylases remove those acetyl groups, increasing
the positive charge of histone tails and encouraging high-affinity binding between the
histones and DNA backbone. The increased DNA binding condenses DNA structure,
preventing transcription.
Histone acetylation plays an important role in the regulation of gene expression. Hyperacetylated chromatin is transcriptionally active, and hypoacetylated chromatin is silent. A study on mice found that a specific subset of mouse genes (7%) was deregulated
in the absence of HDAC1. Their study also found a regulatory crosstalk between
HDAC1 and HDAC2 and suggest a novel function for HDAC1 as a transcriptional coactivator. HDAC1 expression was found to be increased in the prefrontal cortex of schizophrenia subjects, negatively correlating with the expression of GAD67 mRNA.
https://en.wikipedia.org/wiki/Histone_deacetylase
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Histone Demethylases
Demethylases are enzymes that remove methyl (CH3-) groups from nucleic acids,
teins (in particular histones), and other molecules. Demethylase enzymes are impo
tional regulation of the genome by controlling the methylation levels that occur on
DNA and histones and, in turn, regulate the chromatin state at specific gene loci w
organisms.
For many years histone methylation was thought to be irreversible, due to the fact
the half-life of the histone methylation was approximately equal to the half-life of
tones themselves. In 2004, Shi et al. published their discovery of the histone deme
lase LSD1 (later classified as KDM1A), a nuclear amine oxidase homolog. With the
flavin adenine dinucleotide (FAD)-dependent amine oxidase, and an Fe(II) and ketoglutarate-dependent dioxygenase.
https://en.wikipedia.org/wiki/Demethylase
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Histone Methyltransferases
Histone methyltransferases (HMT) are histone-modifying enzymes (e.g., histonelysine N-methyltransferases and histone-arginine N-methyltransferases), that catalyze
the transfer of one, two, or three methyl groups to lysine and arginine residues of histone proteins. The attachment of methyl groups occurs predominantly at specific lysine or arginine residues on histones H3 and H4. Two major types of histone methyltranferases exist, lysine-specific (which can be SET (Su(var)3-9, Enhancer of Zeste,
Trithorax) domain containing or non-SET domain containing) and arginine-specific.
In both types of histone methyltransferases, cofactor S-Adenosyl methionine (SAM)
serves as a cofactor and methyl donor group. In eukaryotic cells, the genome is tightly
condensed into chromatin (composed of DNA and histone proteins), so enzymes, such
as histone methyltransferases, must overcome this inaccessibility. Histone methyltransferase does so by modifying histones at certain sites through methylation. Methylation
of histones is important biologically because it is the principal epigenetic modification
of chromatin that determines gene expression, genomic stability, stem cell maturation,
cell lineage development, genetic imprinting, DNA methylation, and cell mitosis.
There are two different types of protein arginine methyltransferases (PRMTs) and
three types of methylation that can occur at arginine residues on histone tails.
Histone methylation plays an important role in epigenetic gene regulation. Methylated
histones can either repress or activate transcription as different experimental findings
suggest. For example, it is likely that the methylation of lysine 9 on histone H3
(H3K9me3) in the promoter region of genes prevents excessive expression of these
genes and, therefore, delays cell cycle transition and/or proliferation.
https://en.wikipedia.org/wiki/Histone_methyltransferase
HIV-1 Protease
life-cycle of HIV, the retrovirus that causes AIDS. HIV protease cleaves new
of an infectious HIV virion. Without effective HIV protease, HIV virions rem
fectious. Thus, mutation of HIV protease's active site or inhibition of its act
rupts HIVs ability to replicate and infect additional cells, making HIV prote
tion the subject of considerable pharmaceutical research.
https://en.wikipedia.org/wiki/HIV-1_protease
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HMG-CoA
HMG-CoA (or 3-hydroxy-3-methylglutaryl-coenzyme A) is an intermediate in the mevalonate and ketogenesis pathways. It is formed from acetyl CoA and acetoacetyl CoA
by HMG-CoA synthase.
It is also an intermediate in the metabolism of leucine. Its immediate precursor is 3methylglutaconyl CoA.
https://en.wikipedia.org/wiki/HMG-CoA
HMG-CoA Reductase
HMG-CoA reductase (3-hydroxy-3-methyl-glutaryl-coenzyme A reductase, officially abbreviated HMGCR) is the rate-controlling enzyme (NADH-dependent) of the mevalonate pathway, the metabolic pathway that produces cholesterol and other isoprenoids.
Normally in mammalian cells this enzyme is suppressed by cholesterol derived from
the internalization and degradation of low density lipoprotein (LDL) via the LDL receptor as well as oxidized species of cholesterol. Competitive inhibitors of the reductase induce the expression of LDL receptors in the liver, which in turn increases the catabolism of plasma LDL and lowers the plasma concentration of cholesterol, an important
determinant of atherosclerosis. This enzyme is thus the target of the widely available
cholesterol-lowering drugs known collectively as the statins.
HMG-CoA reductase is anchored in the membrane of the endoplasmic reticulum, and
was long regarded as having seven transmembrane domains, with the active site located in a long carboxyl terminal domain in the cytosol. More recent evidence shows it
to contain eight transmembrane domains.
https://en.wikipedia.org/wiki/HMG-CoA_reductase
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HMG-CoA Synthase
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Holliday Junction
A Holliday junction is a branched nucleic acid structure that contains four doublestranded arms joined together. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the
junction. The structure is named after the molecular biologist Robin Holliday, who proposed its existence in 1964.
In biology, Holliday junctions are a key intermediate in many types of genetic recombination, as well as in double-strand break repair. These junctions usually have a symmetrical sequence and are thus mobile, meaning that the four individual arms may
slide though the junction in a specific pattern that largely preserves base pairing. Additionally, four-arm junctions similar to Holliday junctions appear in some functional
RNA molecules.
The Holliday junction is a key intermediate in homologous recombination, a biological
process that increases genetic diversity by shifting genes between two chromosomes,
as well as site-specific recombination events involving integrases. They are additionally
involved in repair of double-strand breaks. In addition, cruciform structures involving
Holliday junctions can arise to relieve helical strain in symmetrical sequences in DNA
supercoils. While four-arm junctions also appear in functional RNA molecules, such
as U1 spliceosomal RNA and the hairpin ribozyme of the tobacco ringspot virus, these
usually contain unpaired nucleotides in between the paired double-helical domains,
and thus do not strictly adopt the Holliday structure.
The Holliday junctions in homologous recombination are between identical or nearly
identical sequences, leading to a symmetric arrangement of sequences around the central junction. This allows a branch migration process to occur where the strands move
through the junction point. Cleavage, or resolution, of the Holliday junction can occur
in two ways. Cleavage of the original set of strands leads to two molecules that may
show gene conversion but not chromosomal crossover, while cleavage of the other set
of two strands causes the resulting recombinant molecules to show crossover. All products, regardless of cleavage, are heteroduplexes in the region of Holliday junction migration.
https://en.wikipedia.org/wiki/Holliday_junction
Holoenzymes
Enzymes that require a cofactor but do not have one bound are called apoen
that contain multiple protein subunits, such as the DNA polymerases. Here
zyme is the complete complex containing all the subunits needed for activit
https://en.wikipedia.org/wiki/Enzyme
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Homeostasis
lated so that internal conditions remain stable and relatively constant. Exam
alkalinity (pH). Human homeostasis is the process that maintains the stabi
trol center, and an effector mechanism that can vary that condition, and a n
feedback connection between the two.
https://en.wikipedia.org/wiki/Homeostasis
Homocysteine
Homocysteine is a non-protein -amino acid. It is a homologue of the amino acid cysteine, differing by an additional methylene bridge (-CH2-). It is biosynthesized from
methionine by the removal of its terminal C methyl group. Homocysteine can be recycled into methionine or converted into cysteine with the aid of certain B-vitamins.
https://en.wikipedia.org/wiki/Homocysteine
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Homologous Recombination
Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most
widely used by cells to accurately repair harmful breaks that occur on both strands of
DNA, known as double-strand breaks. Homologous recombination also produces new
combinations of DNA sequences during meiosis, the process by which eukaryotes
make gamete cells, like sperm and egg cells in animals. These new combinations of
DNA represent genetic variation in offspring, which in turn enables populations to
adapt during the course of evolution. Homologous recombination is also used in horizontal gene transfer to exchange genetic material between different strains and species
of bacteria and viruses.
Although homologous recombination varies widely among different organisms and cell
types, most forms involve the same basic steps. After a double-strand break occurs, sections of DNA around the 5' ends of the break are cut away in a process called resection.
In the strand invasion step that follows, an overhanging 3' end of the broken DNA
molecule then "invades" a similar or identical DNA molecule that is not broken. After
strand invasion, the further sequence of events may follow either of two main pathways discussed below (see Models) - the DSBR (double-strand break repair) pathway
or the SDSA (synthesis-dependent strand annealing) pathway. Homologous recombination that occurs during DNA repair tends to result in non-crossover products, in effect
restoring the damaged DNA molecule as it existed before the double-strand break.
Homologous recombination is conserved across all three domains of life as well as viruses, suggesting that it is a nearly universal biological mechanism. The discovery of
genes for homologous recombination in protistsa diverse group of eukaryotic microorganismshas been interpreted as evidence that meiosis emerged early in the evolution of eukaryotes. Since their dysfunction has been strongly associated with increased
susceptibility to several types of cancer, the proteins that facilitate homologous recombination are topics of active research.
https://en.wikipedia.org/wiki/Homologous_recombination
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Homoserine Dehydrogenase
The 2 substrates of this enzyme are L-homoserine and NAD+ (or NADP+), a
products are L-aspartate 4-semialdehyde, NADH (or NADPH), and H+.
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Homoserine Kinase
Homoserine kinase is an enzyme that catalyzes the chemical reaction
ATP + L-homoserine <---> ADP + O-phospho-L-homoserine
The two substrates of this enzyme are ATP and L-homoserine, and its two pr
ADP and O-phospho-L-homoserine.
phorylating), and HSK. This enzyme participates in glycine, serine and threo
tabolism.
https://en.wikipedia.org/wiki/Homoserine_kinase
Homoserine O-transsuccinylase
Homotropic
https://en.wikipedia.org/wiki/Allosteric_regulation#Types_of_allosteric_
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Homotropic Effectors
https://en.wikipedia.org/wiki/Allosteric_regulation#Types_of_allosteric_
Homozygotes
Hormone
A hormone is any member of a class of signaling molecules produced by glands in multicellular organisms that are transported by the circulatory system to target distant organs to regulate physiology and behavior. Hormones have diverse chemical structures,
mainly of 3 classes: eicosanoids, steroids, and amino acid derivatives (amines, peptides, and proteins). The glands that secrete hormones comprise the endocrine signaling system. The term hormone is sometimes extended to include chemicals produced
by cells that affect the same cell (autocrine or intracrine signaling) or nearby cells (paracrine signaling).
https://en.wikipedia.org/wiki/Hormone
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Hormone-response Elements
A hormone response element (HRE) is a short sequence of DNA within the
of a gene that is able to bind a specific hormone receptor complex and there
by three nucleotides, which also indicates that the receptor binds as a dime
cally, HRE responds to steroid hormones, as the activated steroid receptor
scription factor binding HRE. This regulates the transcription of genes sign
steroid hormone.
A gene may have many different response elements, allowing complex cont
erted over the level and rate of transcription.
HRE are used in transgenic animal cells as inducers of gene expression.
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The enzyme has a long and a short form. The long form is expressed in steroido
tissues such as testis, where it converts cholesteryl esters to free cholesterol for
hormone production. The short form is expressed in adipose tissue, among oth
where it hydrolyzes stored triglycerides to free fatty acids.
https://en.wikipedia.org/wiki/Hormone-sensitive_lipase
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Hormones
tides, and proteins). The glands that secrete hormones comprise the endocr
by cells that affect the same cell (autocrine or intracrine signaling) or nearb
acrine signaling).
https://en.wikipedia.org/wiki/Hormone
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Hox
Hox genes (a subset of homeotic genes) are a group of related genes that contro
body plan of an embryo along the cranio-caudal (head-tail) axis. After the embr
segments have formed, the Hox proteins determine the type of segment structu
legs, antennae, and wings in fruit flies or the different types of vertebrae in hum
that will form on a given segment. Hox proteins thus confer segmental identity,
not form the actual segments themselves.
Hox genes are defined as having the following properties:
In many animals, the organization of the Hox genes in the chromosome is the s
the order of their expression along the anterior-posterior axis of the developing
mal, and are thus said to display colinearity.
https://en.wikipedia.org/wiki/Hox_gene
HPLC
with the adsorbent material, causing different flow rates for the different co
and leading to the separation of the components as they flow out the colum
https://en.wikipedia.org/wiki/High-performance_liquid_chromatography
Hsp40
In molecular biology, chaperone DnaJ, also known as Hsp40 (heat shock protein 40
kD), is a molecular chaperone protein. Molecular chaperones are a diverse family of
proteins that function to protect proteins from irreversible aggregation during synthesis and in times of cellular stress.
Molecular chaperones are a diverse family of proteins that function to protect proteins
from irreversible aggregation during synthesis and in times of cellular stress. The bacte
rial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange
factor, stimulating the rate of ADP release 5000-fold. DnaK is itself a weak ATPase.
ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone,
DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the
nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for
the normal housekeeping functions and stress-related functions of the DnaK molecular
chaperone cycle.
https://en.wikipedia.org/wiki/Chaperone_DnaJ
Hsp70
The 70 kilodalton heat shock proteins (Hsp70s) are a family of conserved ubiquitously
expressed heat shock proteins. Proteins with similar structure exist in virtually all living organisms. The Hsp70s are an important part of the cell's machinery for protein
folding, and help to protect cells from stress.
Members of the Hsp70 family are very strongly upregulated by heat stress and toxic
chemicals, particularly heavy metals such as arsenic, cadmium, copper, mercury, etc.
When not interacting with a substrate peptide, Hsp70 is usually in an ATP bound state.
Hsp70 by itself is characterized by a very weak ATPase activity, such that spontaneous
hydrolysis will not occur for many minutes. As newly synthesized proteins emerge
from the ribosomes, the substrate binding domain of Hsp70 recognizes sequences of
hydrophobic amino acid residues, and interacts with them. This spontaneous interaction is reversible, and in the ATP bound state Hsp70 may relatively freely bind and release peptides. However, the presence of a peptide in the binding domain stimulates
the ATPase activity of Hsp70, increasing its normally slow rate of ATP hydrolysis.
When ATP is hydrolyzed to ADP the binding pocket of Hsp70 closes, tightly binding
the now-trapped peptide chain. Further speeding ATP hydrolysis are the so-called Jdomain cochaperones: primarily Hsp40 in eukaryotes, and DnaJ in prokaryotes. These
cochaperones dramatically increase the ATPase activity of Hsp70 in the presence of interacting peptides.
By binding tightly to partially synthesized peptide sequences (incomplete proteins),
Hsp70 prevents them from aggregating and being rendered nonfunctional. Once the
entire protein is synthesized, a nucleotide exchange factor (BAG-1 and HspBP1 are
among those which have been identified) stimulates the release of ADP and binding of
fresh ATP, opening the binding pocket. The protein is then free to fold on its own, or to
be transferred to other chaperones for further processing. HOP (the Hsp70/Hsp90 Organizing Protein) can bind to both Hsp70 and Hsp90 at the same time, and mediates
the transfer of peptides from Hsp70 to Hsp90.
Hsp70 also aids in transmembrane transport of proteins, by stabilizing them in a partially folded state. Hsp70 proteins can act to protect cells from thermal or oxidative
stress. These stresses normally act to damage proteins, causing partial unfolding and
possible aggregation. By temporarily binding to hydrophobic residues exposed by
stress, Hsp70 prevents these partially denatured proteins from aggregating, and allows
them to refold. Low ATP is characteristic of heat shock and sustained binding is seen
as aggregation suppression, while recovery from heat shock involves substrate binding
and nucleotide cycling. In a thermophile anaerobe (Thermotoga maritima) the Hsp70
demonstrates redox sensitive binding to model peptides, suggesting a second mode of
binding regulation based on oxidative stress.
https://en.wikipedia.org/wiki/Hsp70
Hsp90
Hsp90 (heat shock protein 90) is a chaperone protein that assists other proteins to fold
properly, stabilizes proteins against heat stress, and aids in protein degradation. It also
stabilizes a number of proteins required for tumor growth, which is why Hsp90 inhibitors are investigated as anti-cancer drugs.
Heat shock proteins, as a class, are among the most highly expressed cellular proteins
across all species. As their name implies, heat shock proteins protect cells when
stressed by elevated temperatures. They account for 12% of total protein in unstressed cells. However, when cells are heated, the fraction of heat shock proteins increases to 46% of cellular proteins.
Heat shock protein 90 (Hsp90) is one of the most common of the heat-related proteins. The "90" comes from the fact that it weighs roughly 90 kiloDaltons. A 90kDa
protein is considered fairly large for a non-fibrous protein. Hsp90 is found in bacteria
and all branches of eukarya, but it is apparently absent in archaea. Whereas cytoplasmic Hsp90 is essential for viability under all conditions in eukaryotes, the bacterial
homologue HtpG is dispensable under non-heat stress conditions.
The glucocorticoid receptor (GR) is the most thoroughly studied example of a steroid
receptor whose function is crucially dependent on interactions with Hsp90. In the absence of the steroid hormone cortisol, GR resides in the cytosol complexed with several
chaperone proteins including Hsp90. These chaperones maintain the GR in a state capable of binding hormone.
https://en.wikipedia.org/wiki/Hsp90
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mors produce this hormone. Therefore, elevated levels measured when the
not pregnant can lead to a cancer diagnosis. However, it is not known wheth
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Human Genome
The human genome is the complete set of nucleic acid sequence for humans
piens), encoded as DNA within the 23 chromosome pairs in cell nuclei and
contained in germ cells (the egg and sperm gamete cells created in the meio
base pairs, while diploid genomes (found in somatic cells) have twice the D
While there are significant differences among the genomes of human indivi
the order of 0.1%), these are considerably smaller than the differences betw
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Humans
Modern humans (Homo sapiens, primarily ssp. Homo sapiens sapiens) are
tant members of Hominina clade (or human clade), a branch of the taxonom
and bipedal locomotion; manual dexterity and increased tool use, compared
animals; and a general trend toward larger, more complex brains and socie
https://en.wikipedia.org/wiki/Human
Huntingtin
The huntingtin gene, also called the HTT or HD (Huntington disease) gene, is
("interesting transcript 15") gene, which codes for a protein called the hunting
tein. The gene and its product are under heavy investigation as part of Huntin
disease clinical research and the suggested role for huntingtin in long-term m
storage.
It is variable in its structure, as the many polymorphisms of the gene can lead
ton's disease (an autosomal dominant genetic disorder), it contains more than
mine residues (highest reported repeat length is about 250). Its commonly us
is derived from this disease. Previously, the IT15 label was commonly used.
https://en.wikipedia.org/wiki/Huntingtin
Hyaluronic Acid
Hyaluronic acid (HA/conjugate base hyaluronate), also called hyaluronan, is an anionic, nonsulfated glycosaminoglycan distributed widely throughout connective, epithelial, and neural tissues. It is unique among glycosaminoglycans in that it is nonsulfated, forms in the plasma membrane instead of the Golgi, and can be very large, with
its molecular weight often reaching the millions. One of the chief components of the extracellular matrix, hyaluronan contributes significantly to cell proliferation and migration, and may also be involved in the progression of some malignant tumors.
Hyaluronic acid is an important component of articular cartilage, where it is present as
a coat around each cell (chondrocyte). When aggrecan monomers bind to hyaluronan
in the presence of HAPLN1 (Hyaluronanic acid and proteoglycan link protein 1), large,
highly negatively charged aggregates form. These aggregates imbibe water and are responsible for the resilience of cartilage (its resistance to compression). The molecular
weight (size) of hyaluronan in cartilage decreases with age, but the amount increases.
Hyaluronanic acid is also a major component of skin, where it is involved in tissue repair. When skin is exposed to excessive UVB rays, it becomes inflamed (sunburn) and
the cells in the dermis stop producing as much hyaluronan, and increase the rate of its
degradation. Hyaluronan degradation products then accumulate in the skin after UV
exposure.
While it is abundant in extracellular matrices, hyaluronan also contributes to tissue hydrodynamics, movement and proliferation of cells, and participates in a number of cell
surface receptor interactions, notably those including its primary receptors, CD44 and
RHAMM. Upregulation of CD44 itself is widely accepted as a marker of cell activation
in lymphocytes. Hyaluronan's contribution to tumor growth may be due to its interaction with CD44. Receptor CD44 participates in cell adhesion interactions required by
tumor cells.
Although hyaluronan binds to receptor CD44, there is evidence hyaluronan degradation products transduce their inflammatory signal through toll-like receptor 2 (TLR2),
TLR4 or both TLR2, and TLR4 in macrophages and dendritic cells. TLR and hyaluronan play a role in innate immunity.
There are limitations including the in vivo loss of this compound limiting the duration
of effect.
The repeating unit of hyaluronic acid is shown below.
https://en.wikipedia.org/wiki/Hyaluronic_acid
Hyaluronidases
The hyaluronidases (EC 3.2.1.35) are a family of enzymes that degrade hyaluronic acid.
Karl Meyer classified these enzymes in 1971 into three distinct groups, a scheme based
on the enzyme reaction products. The three main types of hyaluronidases are two
classes of eukaryotic endoglycosidase hydrolases and a prokaryotic lyase-type of glycosidase.
In most mammalian fertilization, hyaluronidase is released by the acrosome of the
sperm cell after it has reached the oocyte, by digesting hyaluronan in the corona radiata, thus enabling conception. Gene-targeting studies show that hyaluronidases such
as PH20 are not essential for fertilization, although exogenous hyaluronidases can disrupt the cumulus matrix.
The majority of mammalian ova are covered in a layer of granulosa cells intertwined in
an ECM that contains a high concentration of hyaluronan. When a capacitated sperm
reaches the ovum, it is able to penetrate this layer with the assistance of hyaluronidase
enzymes present on the surface of the sperm. Once this occurs, the sperm is capable of
binding with the zona pellucida, and the acrosome reaction can occur.
https://en.wikipedia.org/wiki/Hyaluronidase
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Hybridization
In molecular biology, hybridization (or hybridisation) is a phenomenon in which
single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA. Though a double-stranded DNA sequence is generally stable under physiological conditions, changing these conditions in the laboratory (generally by raising the surrounding temperature) will cause the molecules to
separate into single strands. These strands are complementary to each other but may
also be complementary to other sequences present in their surroundings. Lowering the
surrounding temperature allows the single-stranded molecules to anneal or hybridize to each other.
DNA replication and transcription of DNA into RNA both rely upon nucleotide hybridization, as do molecular biology techniques including Southern blots and Northern
blots, the polymerase chain reaction (PCR), and most approaches to DNA sequencing.
Hybridization is a basic property of nucleotide sequences and is taken advantage of in
numerous molecular biology techniques. Overall genetic relatedness of two species can
be determined by hybridizing segments of their DNA (DNA-DNA hybridization). Due
to sequence similarity between closely related organisms, higher temperatures are required to melt such DNA hybrids when compared to more distantly related organisms.
A variety of different methods use hybridization to pinpoint the origin of a DNA sample, including the polymerase chain reaction (PCR). In another technique, short DNA
sequences are hybridized to cellular mRNAs to identify expressed genes. Pharmaceutical drug companies are exploring the use of antisense RNA to bind to undesired
mRNA, preventing the ribosome from translating the mRNA into protein.
https://en.wikipedia.org/wiki/Nucleic_acid_hybridization
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Hydration
clude the citric acid cycle (hydration of fumarate) and fatty acid oxidation (
of the trans intermediate).
https://en.wikipedia.org/wiki/Hydration_reaction
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Hydration Shell
A solvation shell is a shell of any chemical species that acts as a solvent and
to the positive charge on the metal ion. The result is a solvation shell of wat
cules that surround the ion. This shell can be several molecules thick, depen
the charge of the ion.
The hydration shell is a factor in the exclusion of sodium ions from potassiu
nels.
https://en.wikipedia.org/wiki/Solvation_shell
Hydrogen Bonding
A hydrogen bond is the electrostatic attraction between polar groups that occurs when
a hydrogen (H) atom bound to a highly electronegative atom such as nitrogen (N), oxygen (O) or fluorine (F) experiences attraction to some other nearby highly electronegative atom.
These hydrogen-bond attractions can occur between molecules (intermolecular) or
within different parts of a single molecule (intramolecular). Depending on geometry
and environmental conditions, the hydrogen bond may be worth between 5 and 30 kJ/
mole in thermodynamic terms. This makes it stronger than a van der Waals interaction, but weaker than covalent or ionic bonds. This type of bond can occur in inorganic
molecules such as water and in organic molecules like DNA and proteins.
Intermolecular hydrogen bonding is responsible for the high boiling point of water
(100C) compared to the other group 16 hydrides that have no hydrogen bonds. Hydrogen bonding also plays an important role in determining the three-dimensional
structures adopted by proteins and nucleic bases. In these macromolecules, bonding
between parts of the same macromolecule cause it to fold into a specific shape, which
helps determine the molecule's physiological or biochemical role. For example, the double helical structure of DNA is due largely to hydrogen bonding between its base pairs
(as well as Pi stacking interactions), which link one complementary strand to the other
and enable replication.
In the secondary structure of proteins, hydrogen bonds form between the backbone
oxygens and amide hydrogens. When the spacing of the amino acid residues participating in a hydrogen bond occurs regularly between positions i and i+4, an helix is
formed. When the spacing is less, between positions i and i+3, then a 310 helix is
formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a sheet is formed. Hydrogen bonds also play a part
in forming the tertiary structure of protein through interaction of R-groups.
The role of hydrogen bonds in protein folding has also been linked to osmolyteinduced protein stabilization. Protective osmolytes, such as trehalose and sorbitol,
shift the protein folding equilibrium toward the folded state, in a concentration dependent manner. While the prevalent explanation for osmolyte action relies on excluded volume effects, that are entropic in nature, recent Circular dichroism (CD) experiments
have shown osmolyte to act through an enthalpic effect. The molecular mechanism for
their role in protein stabilization is still not well established, though several mechanism have been proposed. Recently, computer molecular dynamics simulations suggested that osmolytes stabilize proteins by modifying the hydrogen bonds in the protein hydration layer.
https://en.wikipedia.org/wiki/Hydrogen_bond
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Hydrogen Bonds
A hydrogen bond is the electrostatic attraction between polar groups that occurs when
a hydrogen (H) atom bound to a highly electronegative atom such as nitrogen (N), oxygen (O) or fluorine (F) experiences attraction to some other nearby highly electronegative atom.
These hydrogen-bond attractions can occur between molecules (intermolecular) or
within different parts of a single molecule (intramolecular). Depending on geometry
and environmental conditions, the hydrogen bond may be worth between 5 and 30 kJ/
mole in thermodynamic terms. This makes it stronger than a van der Waals interaction, but weaker than covalent or ionic bonds. This type of bond can occur in inorganic
molecules such as water and in organic molecules like DNA and proteins.
Intermolecular hydrogen bonding is responsible for the high boiling point of water
(100C) compared to the other group 16 hydrides that have no hydrogen bonds. Hydrogen bonding also plays an important role in determining the three-dimensional
structures adopted by proteins and nucleic bases. In these macromolecules, bonding
between parts of the same macromolecule cause it to fold into a specific shape, which
helps determine the molecule's physiological or biochemical role. For example, the double helical structure of DNA is due largely to hydrogen bonding between its base pairs
(as well as Pi stacking interactions), which link one complementary strand to the other
and enable replication.
In the secondary structure of proteins, hydrogen bonds form between the backbone
oxygens and amide hydrogens. When the spacing of the amino acid residues participating in a hydrogen bond occurs regularly between positions i and i+4, an helix is
formed. When the spacing is less, between positions i and i+3, then a 310 helix is
formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a sheet is formed. Hydrogen bonds also play a part
in forming the tertiary structure of protein through interaction of R-groups.
The role of hydrogen bonds in protein folding has also been linked to osmolyteinduced protein stabilization. Protective osmolytes, such as trehalose and sorbitol,
shift the protein folding equilibrium toward the folded state, in a concentration dependent manner. While the prevalent explanation for osmolyte action relies on excluded volume effects, that are entropic in nature, recent Circular dichroism (CD) experiments
have shown osmolyte to act through an enthalpic effect. The molecular mechanism for
their role in protein stabilization is still not well established, though several mechanism have been proposed. Recently, computer molecular dynamics simulations suggested that osmolytes stabilize proteins by modifying the hydrogen bonds in the protein hydration layer.
https://en.wikipedia.org/wiki/Hydrogen_bond
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Hydrogen Sulfide
with the characteristic foul odor of rotten eggs. It is heavier than air, very p
corrosive, flammable, and explosive.
the absence of oxygen gas, such as in swamps and sewers. This process is c
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Hydrolysis
The term hydrolysis refers to using a molecule of water to break a bond. Hydrolysis
can break bonds in proteins, nucleic acids, carbohydrates and fats. When a carbohydrate is broken into its component sugar molecules by hydrolysis (e.g. sucrose being
broken down into glucose and fructose), this is termed saccharification. Generally, hydrolysis or saccharification is a step in the degradation of a substance.
Hydrolysis can be the reverse of a condensation reaction in which two molecules join
together into a larger one and eject a water molecule. Thus hydrolysis adds water to
break down, whereas condensation builds up by removing water.
https://en.wikipedia.org/wiki/Hydrolysis
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Hydrolysis of Fat
The term hydrolysis refers to using a molecule of water to break a bond. Hydrolysis
can break bonds in proteins, nucleic acids, carbohydrates and fats. When a carbohydrate is broken into its component sugar molecules by hydrolysis (e.g. sucrose being
broken down into glucose and fructose), this is termed saccharification. Generally, hy
drolysis or saccharification is a step in the degradation of a substance.
Hydrolysis can be the reverse of a condensation reaction in which two molecules join
together into a larger one and eject a water molecule. Thus hydrolysis adds water to
break down, whereas condensation builds up by removing water.
Perhaps the oldest commercially practiced example of ester hydrolysis is saponifica-
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Hydrophilic
A hydrophile is a molecule or other molecular entity that is attracted to, and tends to
be dissolved by water.
A hydrophilic molecule or portion of a molecule is one whose interactions with water
and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents. They are typically charge-polarized and
capable of hydrogen bonding. This makes these molecules soluble not only in water but
also in other polar solvents.
Hydrophilic molecules (and portions of molecules) can be contrasted with hydrophobic molecules (and portions of molecules). In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiphilic molecules is the lipids that comprise the cell membrane. Another example is soap, which
has a hydrophilic head and a hydrophobic tail, allowing it to dissolve in both water and
oil.
Hydrophilic and hydrophobic molecules are also known as polar molecules and nonpolar molecules, respectively. Some hydrophilic substances do not dissolve. This type of
mixture is called a colloid.
An approximate rule of thumb for hydrophilicity of organic compounds is that solubility of a molecule in water is more than 1 mass % if there is at least one neutral hydrophile group per 5 carbons, or at least one electrically charged hydrophile group per 7
carbons.
Hydrophilic substances (ex: salts) can seem to attract water out of the air. Sugar is also
hydrophilic, and like salt is sometimes used to draw water out of foods. Sugar sprinkled on cut fruit will "draw out the water" through hydrophilia, making the fruit mushy
and wet, as in a common strawberry compote recipe.
https://en.wikipedia.org/wiki/Hydrophile
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Hydrophilicity
Hydrophilicity refers to the hydrophilic nature of a substance.
A hydrophilic molecule or portion of a molecule is one whose interactions with water
and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents. They are typically charge-polarized and
capable of hydrogen bonding. This makes these molecules soluble not only in water but
also in other polar solvents.
Hydrophilic molecules (and portions of molecules) can be contrasted with hydrophobic molecules (and portions of molecules). In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiphilic molecules is the lipids that comprise the cell membrane. Another example is soap, which
has a hydrophilic head and a hydrophobic tail, allowing it to dissolve in both water and
oil.
Hydrophilic and hydrophobic molecules are also known as polar molecules and nonpolar molecules, respectively. Some hydrophilic substances do not dissolve. This type of
mixture is called a colloid.
An approximate rule of thumb for hydrophilicity of organic compounds is that solubility of a molecule in water is more than 1 mass % if there is at least one neutral hydrophile group per 5 carbons, or at least one electrically charged hydrophile group per 7
carbons.
Hydrophilic substances (ex: salts) can seem to attract water out of the air. Sugar is also
hydrophilic, and like salt is sometimes used to draw water out of foods. Sugar sprinkled on cut fruit will "draw out the water" through hydrophilia, making the fruit mushy
and wet, as in a common strawberry compote recipe.
https://en.wikipedia.org/wiki/Hydrophile
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Hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule (known as a hydrophobe) that is seemingly repelled from a mass of water. (Strictly speaking, there is no
repulsive force involved. It is an absence of attraction.)
Hydrophobic molecules tend to be non-polar and, thus, prefer other neutral molecules
and non-polar solvents. Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle.
Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the
management of oil spills, and chemical separation processes to remove non-polar substances from polar compounds.
https://en.wikipedia.org/wiki/Hydrophobe
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Hydrophobic Effect
The hydrophobic effect is the observed tendency of nonpolar substances to
in aqueous solution and exclude water molecules. This occurs because inter
gen bonds more freely with each other and increase the number of hydroge
they are involved with, thereby decreasing the overall free energy. The word
bic literally means "water-fearing," and it describes the segregation and app
sion between water and nonpolar substances.
https://en.wikipedia.org/wiki/Hydrophobic_effect
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Hydrophobicity
Hydrophobicity refers to the hydrophobic nature of a substance.
phobe) that is seemingly repelled from a mass of water. (Strictly speaking, there is no
repulsive force involved. It is an absence of attraction.)
Hydrophobic molecules tend to be non-polar and, thus, prefer other neutral molecule
and non-polar solvents. Hydrophobic molecules in water often cluster together, form
ing micelles. Water on hydrophobic surfaces will exhibit a high contact angle.
Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the
management of oil spills, and chemical separation processes to remove non-polar sub
stances from polar compounds.
https://en.wikipedia.org/wiki/Hydrophobe
Hydroxide
hydrogen atom held together by a covalent bond, and carries a negative elec
ligand, a nucleophile and a catalyst. The hydroxide ion forms salts, some of
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Hydroxyethyl
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Hydroxyethyl-TPP
Hydroxyl
A hydroxyl or hydroxy group is a chemical functional group containing one oxygen
atom connected by a covalent bonding to one hydrogen atom (OH). It is sometimes
called the alcohol functional group because when bonded to carbon in a molecule that
otherwise contains only hydrogen and carbon the hydroxy (not hydroxyl) group defines the molecule as an alcohol, resulting in a name ending in -ol. A hydroxyl group
bonded covalently to the carbon of a carbonyl group (C=O) produces a carboxyl group
(C(O)OH) that is the defining group of a carboxylic acid. When the OH group participates in an ionic bond, the [OH] anion is called the hydroxide ion. As a free radical, it
is the hydroxyl radical.
https://en.wikipedia.org/wiki/Hydroxyl
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Hydroxyl Radical
The hydroxyl radical, OH, is the neutral form of the hydroxide ion (OH). H
radicals are highly reactive (easily becoming hydroxyl groups) and consequ
lived. However, they form an important part of radical chemistry. Most not
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Hydroxylation
Hydroxylation is a chemical process that introduces a hydroxyl group (-OH) into an organic compound. In biochemistry, hydroxylation reactions are often facilitated by enzymes called hydroxylases. Hydroxylation is the first step in the oxidative degradation
of organic compounds in air. It is extremely important in detoxification since hydroxylation converts lipophilic compounds into water-soluble (hydrophilic) products that
are more readily excreted. Some drugs (e.g. steroids) are activated or deactivated by hydroxylation.
https://en.wikipedia.org/wiki/Hydroxylation
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Hydroxylmethylbilane
volved in the metabolism of porphyrin. In the third step, it is generated by the enzym
porphobilinogen deaminase, and in the next step the enzyme uroporphyrinogen III
https://en.wikipedia.org/wiki/Hydroxymethylbilane
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Hydroxylysine
https://en.wikipedia.org/wiki/Hydroxylysine
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Hydroxyproline
(2S,4R)-4-Hydroxyproline, or L-hydroxyproline (C5H9O3N), is a common nonproteinogenic amino acid, abbreviated as Hyp, e.g., in Protein Data Bank.
Hydroxyproline is produced by hydroxylation of the amino acid proline by the enzyme
prolyl hydroxylase following protein synthesis (as a post-translational modification).
The enzyme catalyzed reaction takes place in the lumen of the endoplasmic reticulum.
Although it is not directly incorporated into proteins, hydroxyproline comprises
roughly 4% of all amino acids found in animal tissue, an amount greater than seven
other amino acids that are translationally incorporated.
https://en.wikipedia.org/wiki/Hydroxyproline
Hydroxyurea
Hydroxycarbamide (INN, BAN) or hydroxyurea (USAN, AAN) is an antineoplastic
drug used in myeloproliferative disorders, specifically polycythemia vera and essential
thrombocythemia. It is also used to reduce the rate of painful attacks in sickle-cell disease and has antiretroviral properties in diseases such as HIV/AIDS.
Hydroxycarbamide decreases the production of deoxyribonucleotides via inhibition of
the enzyme ribonucleotide reductase by scavenging tyrosyl free radicals as they are involved in the reduction NDPs.
In the treatment of sickle-cell disease, hydroxycarbamide increases the concentration
of fetal hemoglobin. The precise mechanism of action is not yet clear, but it appears
that hydroxycarbamide increases nitric oxide levels, causing soluble guanylyl cyclase
activation with a resultant rise in cyclic GMP, and the activation of globin chain synthesis necessary for fetal hemoglobin production (which inhibits the formation of
sickle hemoglobin aggregates). A few red cell clones called F cells are progeny of a
small pool of immature committed erythroid precursors (BFU-e) that retain the ability
to produce HbF.
Hydroxyurea is on the World Health Organization's List of Essential Medicines, a list
of the most important medication needed in a basic health system.
https://en.wikipedia.org/wiki/Hydroxycarbamide
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Hyperbolic
two pieces, called connected components or branches, that are mirror imag
other and resemble two infinite bows. The hyperbola is one of the three kin
section, formed by the intersection of a plane and a double cone.
Index
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Hypercalcemia
Hyperchromic Effect
Hyperchromicity is the increase of absorbance (optical density) of a material. The most
famous example is the hyperchromicity of DNA that occurs when the DNA duplex is denatured. The UV absorption is increased when the two single DNA strands are being
separated, either by heat or by addition of denaturant or by increasing the pH level.
The opposite, a decrease of absorbance is called hypochromicity.
https://en.wikipedia.org/wiki/Hyperchromicity
Hyperforin
Hyperforin is a phytochemical produced by some of the members of the plant genus
Hypericum, notably Hypericum perforatum (St John's wort).
Hyperforin is a prenylated phloroglucinol derivative that is unstable in the presence of
light and oxygen.
Hyperforin is believed to be the primary active constituent responsible for the antidepressant and anxiolytic properties of the extracts of St. John's wort. It acts as a reuptake inhibitor of monoamines, including serotonin, norepinephrine, dopamine, and of
GABA and glutamate, with IC50 values of 0.05-0.10 g/mL for all compounds, with
the exception of glutamate, which is in the 0.5 g/mL range. Hyperforin also inhibits
the reuptake of glycine and choline (IC50=8.5M). It also modulates acetylcholine release in rat hippocampus and facilitates acetylcholine release in the striatum. It appears to exert these effects by activating the transient receptor potential ion channel
TRPC6. Activation of TRPC6 induces the entry of sodium and calcium into the cell
which causes inhibition of monoamine reuptake. It also antagonizes the NMDA receptor, AMPA receptor and GABA receptors.
https://en.wikipedia.org/wiki/Hyperforin
Hypertonic
Hypertonic refers to a greater concentration. In biology, a hypertonic solution is one
with a higher concentration of solutes outside the cell than inside the cell. When a cell
is immersed into a hypertonic solution, the tendency is for water to flow out of the cell
in order to balance the concentration of the solutes. Likewise, the cytosol of the cell is
conversely categorized as hypotonic, opposite of the outer solution.
When plant cells are in a hypertonic solution, the flexible cell membrane pulls away
from the rigid cell wall, but remains joined to the cell wall at points called plasmodesmata. The cell takes on the appearance of a pincushion, and the plasmodesmata almost
cease to function because they become constricted: a condition known as plasmolysis.
In plant cells the terms isotonic, hypotonic and hypertonic cannot strictly be used accurately because the pressure exerted by the cell wall significantly affects the osmotic
equilibrium point.
https://en.wikipedia.org/wiki/Tonicity#Hypertonicity
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Hypothalamus
The hypothalamus (from Greek , "under" and , thalamus) is a portion of
the brain that contains a number of small nuclei with a variety of functions. One of the
most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).
The hypothalamus is located below the thalamus and is part of the limbic system. In
the terminology of neuroanatomy, it forms the ventral part of the diencephalon. All vertebrate brains contain a hypothalamus. In humans, it is the size of an almond.
The hypothalamus is responsible for certain metabolic processes and other activities of
the autonomic nervous system. It synthesizes and secretes certain neurohormones,
called releasing hormones or hypothalamic hormones, and these in turn stimulate or
inhibit the secretion of pituitary hormones. The hypothalamus controls body temperature, hunger, important aspects of parenting and attachment behaviors, thirst, fatigue,
sleep, and circadian rhythms.
The hypothalamus has a central neuroendocrine function, most notably by its control
of the anterior pituitary, which in turn regulates various endocrine glands and organs.
Releasing hormones (also called releasing factors) are produced in hypothalamic nuclei then transported along axons to either the median eminence or the posterior pituitary, where they are stored and released as needed.
https://en.wikipedia.org/wiki/Hypothalamus
Index
Find Term
Hypotonic
concentration of solutes outside the cell than inside the cell. In an attempt to b
the concentrations of solutes inside and outside the cell, water will rush into th
and can cause it to burst.
https://en.wikipedia.org/wiki/Tonicity#Hypotonicity
Index
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Hypoxanthine
Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a
constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of
its nucleoside inosine. It has a tautomer known as 6-hydroxypurine. Hypoxanthine is a
necessary additive in certain cell, bacteria, and parasite cultures as a substrate and nitrogen source.
https://en.wikipedia.org/wiki/Hypoxanthine
Index
Find Term
G-G
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Hypoxanthine/guanine Phosphoribosyltransferase
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is an enzyme encoded in
humans by the HPRT1 gene.
HGPRT is a transferase that catalyzes conversion of hypoxanthine to inosine monophosphate and guanine to guanosine monophosphate. This reaction transfers the 5phosphoribosyl group from 5-phosphoribosyl 1-pyrophosphate (PRPP) to the purine.
HGPRT plays a central role in the generation of purine nucleotides through the purine
salvage pathway.
Hypoxanthine + PRPP
Guanine + PRPP
IMP + PPi
GMP + PPi
Index
Find Term
Hypoxia
Hypoxia (also known as hypoxiation) is a condition in which the body or a region of
the body is deprived of adequate oxygen supply. Hypoxia may be classified as either
generalized, affecting the whole body, or local, affecting a region of the body. Although
hypoxia is often a pathological condition, variations in arterial oxygen concentrations
can be part of the normal physiology, for example, during hypoventilation training or
strenuous physical exercise.
Hypoxia differs from hypoxemia and anoxemia in that hypoxia refers to a state in
which oxygen supply is insufficient, whereas hypoxemia and anoxemia refer specifically to states that have low or zero arterial oxygen supply. Hypoxia in which there is
complete deprivation of oxygen supply is referred to as anoxia.
Generalized hypoxia occurs in healthy people when they ascend to high altitude, where
it causes altitude sickness leading to potentially fatal complications: high altitude pulmonary edema (HAPE) and high altitude cerebral edema (HACE). Hypoxia also occurs
in healthy individuals when breathing mixtures of gasses with a low oxygen content,
e.g. while diving underwater especially when using closed-circuit rebreather systems
that control the amount of oxygen in the supplied air. A mild and non-damaging intermittent hypoxia is used intentionally during altitude trainings to develop an athletic
performance adaptation at both the systemic and cellular level.
Hypoxia is also a serious consequence of preterm birth in the neonate. The main cause
for this is that the lungs of the human fetus are among the last organs to develop during pregnancy. To assist the lungs to distribute oxygenated blood throughout the body,
infants at risk of hypoxia are often placed inside an incubator capable of providing continuous positive airway pressure (also known as a humidicrib).
https://en.wikipedia.org/wiki/Hypoxia_(medical)
Index
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Hypoxia-inducible Factor
The HIF signaling cascade mediates the effects of hypoxia, the state of low o
centration, on the cell. Hypoxia often keeps cells from differentiating. Howe
poxia promotes the formation of blood vessels, and is important for the form
vascular system in embryos, and cancer tumors. The hypoxia in wounds als
the migration of keratinocytes and the restoration of the epithelium.
https://en.wikipedia.org/wiki/Hypoxia-inducible_factors
Index
Find Term
Hypoxia-Inducible Factors
The HIF signaling cascade mediates the effects of hypoxia, the state of low o
centration, on the cell. Hypoxia often keeps cells from differentiating. Howe
poxia promotes the formation of blood vessels, and is important for the form
vascular system in embryos, and cancer tumors. The hypoxia in wounds als
the migration of keratinocytes and the restoration of the epithelium.
https://en.wikipedia.org/wiki/Hypoxia-inducible_factors
I-cell Disease
Inclusion-cell (I-cell) disease, also referred to as mucolipidosis II (ML II), is
within the cell. Without this marker, the proteins are instead excreted outsid
cellthe default pathway for proteins moving through the Golgi apparatus. L
IAP
Imidazole acetol phosphate (IAP) is an intermediate in the biosynthesis of histidine. It
is formed from imidazole glycerol phosphate (IGP) in the following reaction
IGP
IAP
and then converted to histidinol phosphate in the following reaction
IAP + Glutamate
Histidinol-phosphate + -KG
Ibuprofen
Ibuprofen, from isobutylphenylpropanoic acid, is a nonsteroidal anti-inflammatory
drug (NSAID) used for treating pain, fever, and inflammation. This includes painful
menstrual periods, migraines, and rheumatoid arthritis. About 60% of people improve
with any given NSAID, and it is recommended that if one does not work, then another
should be tried. It may also be used to close a patent ductus arteriosus in a premature
baby. It can be used by mouth or intravenously. It typically begins working within an
hour.
Nonsteroidal anti-inflammatory drugs such as ibuprofen work by inhibiting the COX
enzymes, which convert arachidonic acid to prostaglandin H2 (PGH2). PGH2, in turn, is
converted by other enzymes to several other prostaglandins (which are mediators of
pain, inflammation, and fever) and to thromboxane A2 (which stimulates platelet aggregation, leading to the formation of blood clots).
https://en.wikipedia.org/wiki/Ibuprofen
Index
Find Term
IDLs
Intermediate-density lipoproteins (IDLs) belong to the lipoprotein particle family and
are formed from the degradation of very low-density lipoproteins. IDL is one of the five
major groups of lipoproteins (chylomicrons, VLDL, IDL, LDL, HDL) that enable fats
and cholesterol to move within the water-based solution of the bloodstream. Each native IDL particle consists of protein that encircles various fatty acids, enabling, as a
water-soluble particle, these fatty acids to travel in the aqueous blood environment as
part of the fat transport system within the body. Their size is, in general, 25 to 35nm
in diameter, and they contain primarily a range of triacylglycerols and cholesterol esters. They are cleared from the plasma into the liver by receptor-mediated endocytosis,
or further degraded to form LDL particles.
Although one might intuitively assume that "intermediate-density" refers to a density
between that of high-density and low-density lipoproteins, it in fact refers to a density
between that of low-density and very-low-density lipoproteins. Lipoproteins are classified as less dense when the fat to protein ratio is increased.
In general, IDL, somewhat similar to low-density lipoprotein (LDL), transports a variety of triglyceride fats and cholesterol and, like LDL, can also promote the growth of
atheroma.
https://en.wikipedia.org/wiki/Intermediate-density_lipoprotein
Index
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Iduronic Acid
L-Iduronic acid (IdoA) is the major uronic acid component of the glycosaminoglycans
(GAGs) dermatan sulfate, and heparin. It is also present in heparan sulfate although
here in a minor amount relative to its carbon-5 epimer glucuronic acid.
IdoA is a hexapyranose sugar. Most hexapyranoses are stable in one of two chair conformations 1C4 or 4C1. L-iduronate is different and adopts more than one solution conformation, with an equilibrium existing between three low-energy conformers. These
are the 1C4 and 4C1 chair forms and an additional 2S0 skew-boat conformation.
IdoA may be modified by the addition of an O-sulfate group at carbon position 2 to
form 2-O-sulfo-L-iduronic acid (IdoA2S).
https://en.wikipedia.org/wiki/Iduronic_acid
Index
Find Term
IF1
Prokaryotes require the use of three initiation factors: IF1, IF2, and IF3, for translation.
IF1 associates with the 30S ribosomal subunit in the A site and prevents an aminoacyltRNA from entering. It modulates IF2 binding to the ribosome by increasing its affinity. It may also prevent the 50S subunit from binding, stopping the formation of the
70S subunit. It also contains a -domain fold common for nucleic acid binding proteins.
IF2 binds to an initiator tRNA and controls the entry of that tRNA into the ribosome.
IF2, bound to GTP, binds to the 30S P site. After associating with the 30S subunit,
fMet-tRNAf binds to the IF2 then IF2 transfers the tRNA into the partial P site. When
the 50S subunit joins, it hydrolyzes GTP to GDP and Pi, causing a conformational
change in the IF2 that causes IF2 to release and allow the 70S subunit to form.
IF3 is not universally found in all bacterial species but in E. coli it is required for the
30S subunit to bind to the initiation site in mRNA. In addition, it has several other jobs
including stabilization of free 30S subunits, facilitation of 30S subunits binding to
mRNA and checking for accuracy against the first aminoacyl-tRNA. It also allows for
rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required
by the small subunit to form initiation complexes, but has to be released to allow the
50S subunit to bind.
https://en.wikipedia.org/wiki/Prokaryotic_initiation_factor
Index
Find Term
IF2
Prokaryotes require the use of three initiation factors: IF1, IF2, and IF3, for translation.
IF1 associates with the 30S ribosomal subunit in the A site and prevents an aminoacyltRNA from entering. It modulates IF2 binding to the ribosome by increasing its affinity. It may also prevent the 50S subunit from binding, stopping the formation of the
70S subunit. It also contains a -domain fold common for nucleic acid binding proteins.
IF2 binds to an initiator tRNA and controls the entry of that tRNA into the ribosome.
IF2, bound to GTP, binds to the 30S P site. After associating with the 30S subunit,
fMet-tRNAf binds to the IF2 then IF2 transfers the tRNA into the partial P site. When
the 50S subunit joins, it hydrolyzes GTP to GDP and Pi, causing a conformational
change in the IF2 that causes IF2 to release and allow the 70S subunit to form.
IF3 is not universally found in all bacterial species but in E. coli it is required for the
30S subunit to bind to the initiation site in mRNA. In addition, it has several other jobs
including stabilization of free 30S subunits, facilitation of 30S subunits binding to
mRNA and checking for accuracy against the first aminoacyl-tRNA. It also allows for
rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required
by the small subunit to form initiation complexes, but has to be released to allow the
50S subunit to bind.
https://en.wikipedia.org/wiki/Prokaryotic_initiation_factor
Index
Find Term
IF3
Prokaryotes require the use of three initiation factors: IF1, IF2, and IF3, for translation.
IF1 associates with the 30S ribosomal subunit in the A site and prevents an aminoacyltRNA from entering. It modulates IF2 binding to the ribosome by increasing its affinity. It may also prevent the 50S subunit from binding, stopping the formation of the
70S subunit. It also contains a -domain fold common for nucleic acid binding proteins.
IF2 binds to an initiator tRNA and controls the entry of that tRNA into the ribosome.
IF2, bound to GTP, binds to the 30S P site. After associating with the 30S subunit,
fMet-tRNAf binds to the IF2 then IF2 transfers the tRNA into the partial P site. When
the 50S subunit joins, it hydrolyzes GTP to GDP and Pi, causing a conformational
change in the IF2 that causes IF2 to release and allow the 70S subunit to form.
IF3 is not universally found in all bacterial species but in E. coli it is required for the
30S subunit to bind to the initiation site in mRNA. In addition, it has several other jobs
including stabilization of free 30S subunits, facilitation of 30S subunits binding to
mRNA and checking for accuracy against the first aminoacyl-tRNA. It also allows for
rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required
by the small subunit to form initiation complexes, but has to be released to allow the
50S subunit to bind.
https://en.wikipedia.org/wiki/Prokaryotic_initiation_factor
Index
Find Term
IgA
Immunoglobulin A (IgA, also referred to as sIgA) is an antibody that plays a critical
role in immune function in the mucous membranes. More IgA is produced in mucosa
linings than all other types of antibody combined. Between three and five grams are
secreted into the intestinal lumen each day. This accumulates up to 15% of the total i
munoglobulin produced in the entire body.
IgA has two subclasses (IgA1 and IgA2) and can exist in a dimeric form called secreto
IgA (sIgA). In its secretory form, IgA is the main immunoglobulin found in mucous s
cretions, including tears, saliva, sweat, colostrum and secretions from the genitouri-
nary tract, gastrointestinal tract, prostate and respiratory epithelium. It is also found
in small amounts in blood. The secretory component of sIgA protects the immunoglobulin from being degraded by proteolytic enzymes, thus sIgA can survive in the
multiply in body secretions. sIgA can also inhibit inflammatory effects of other immu
noglobulins. IgA is a poor activator of the complement system, and opsonises only
weakly. Its heavy chains are of the type .
https://en.wikipedia.org/wiki/Immunoglobulin_A
Index
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IgD
Immunoglobulin D (IgD) is an antibody isotype that makes up about 1% of proteins in
the plasma membranes of mature B-lymphocytes where it is usually coexpressed with
another cell surface antibody called IgM. IgD is also produced in a secreted form that is
found in very small amounts in blood serum, representing 0.25% of immunoglobulins
in serum. Relative molecular mass and half-life of sIgD is 185 kDa and 2.8 days, respectively. Secreted IgD is produced as a monomeric antibody with two heavy chains of the
delta () class, and two Ig light chains.
In B cells, IgD's function is to signal the B cells to be activated. By being activated, they
are ready to take part in the defense of the body in the immune system. During B-cell
differentiation, IgM is the exclusive isotype expressed by immature B cells. IgD starts
to be expressed when the B-cell exits the bone marrow to populate peripheral lymphoid tissues. When a B-cell reaches its mature state, it co-expresses both IgM and
IgD. It is not well understood whether IgM and IgD antibodies are functionally different on B cells. C knockout mice (mice that have been genetically altered so that they
do not produce IgD) have no major B-cell intrinsic defects. IgD may have some role in
allergic reactions.
https://en.wikipedia.org/wiki/Immunoglobulin_D
IgE
has only been found in mammals. Monomers of IgE consist of two heavy ch
chain) and two light chains, with the chain containing 4 Ig-like constant d
IgE also has an essential role in type I hypersensitivity, which manifests var
gic diseases, such as allergic asthma, most types of sinusitis, allergic rhinitis
gies, and specific types of chronic urticaria and atopic dermatitis. IgE also p
otal role in responses to allergens, such as: anaphylactic drugs, bee stings, a
preparations used in desensitization immunotherapy.
https://en.wikipedia.org/wiki/Immunoglobulin_E
Index
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IgG
Immunoglobulin G (IgG) is a type of antibody. It is a protein complex composed of
four peptide chainstwo identical heavy chains and two identical light chains arranged
in a Y-shape typical of antibody monomers. Each IgG has two antigen binding sites.
Representing approximately 75% of serum antibodies in humans, IgG is the most common type of antibody found in the circulation. IgG molecules are created and released
by plasma B cells.
Antibodies are major components of humoral immunity. IgG is the main type of antibody found in blood and extracellular fluid allowing it to control infection of body tissues. By binding many kinds of pathogens such as viruses, bacteria, and fungi, IgG protects the body from infection. It does this through several mechanisms: IgG-mediated
binding of pathogens causes their immobilization and binding together via agglutination. IgG coating of pathogen surfaces (known as opsonization) allows their recognition and ingestion by phagocytic immune cells. IgG activates the classical pathway of
the complement system, a cascade of immune protein production that results in pathogen elimination. IgG also binds and neutralizes toxins. IgG also plays an important
role in antibody-dependent cell-mediated cytotoxicity (ADCC) and intracellular
antibody-mediated proteolysis, in which it binds to TRIM21 (the receptor with greatest
affinity to IgG in humans) in order to direct marked virions to the proteasome in the
cytosol. IgG is also associated with type II and type III hypersensitivity reactions.
https://en.wikipedia.org/wiki/Immunoglobulin_G
IgM
IgM is by far the physically largest antibody in the human circulatory system
mass of approximately 970 kDa (in its pentamer form). Because each mono
two antigen binding sites, a pentameric IgM has 10 binding sites. Typically,
IgM cannot bind 10 antigens at the same time because the large size of mos
hinders binding to nearby sites.
https://en.wikipedia.org/wiki/Immunoglobulin_M
Index
Find Term
IGP
PRFAR = (N-[(5-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide
ribonucleotide
IGP = Imidazole glycerol-phosphate
AICAR = 5-phosphoribosyl-4-carboximide-5-aminoimidazole
Imidazole
Imidazole is an organic compound with the formula (CH)2N(NH)CH. It is a white or
colorless solid that is soluble in water, producing a mildly alkaline solution. In chemistry, it is an aromatic heterocycle, classified as a diazole, and having non-adjacent nitrogen atoms.
Many natural products, especially alkaloids, contain the imidazole ring. These imidazoles, share the 1,3-C3N2 ring but feature varied substituents. This ring system is present in important biological building-blocks, such as histidine, and the related hormone histamine. Many drugs contain an imidazole ring, such as certain antifungal
drugs, the nitroimidazole series of antibiotics, and the sedative midazolam.
https://en.wikipedia.org/wiki/Imidazole
Index
Find Term
This reaction is the sixth step in the biosynthesis of histidine in bacteria, fun
plants.
https://en.wikipedia.org/wiki/Imidazoleglycerol-phosphate_dehydratase
Index
Find Term
Immune system
The immune system is a system of many biological structures and processes
and distinguish them from the organism's own healthy tissue. In many speci
mune system can be classified into subsystems, such as the innate immune s
lar fluidbrain barriers separate the peripheral immune system from the neu
mune system which protects the brain.
https://en.wikipedia.org/wiki/Immune_system
Index
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Immunity
In biology, immunity is the balanced state of having adequate biological defenses to
fight infection, disease, or other unwanted biological invasion, while having adequate
tolerance to avoid allergy, and autoimmune diseases.
The basic premise for the division of the immune system into innate and adaptive co
ponents comes down to the innate system being composed of primitive bone marrow
cells that are programmed to recognise foreign substances and react, versus the adap
tive system being composed of more advanced lymphatic cells that are programmed
recognize self substances and don't react. The reaction to foreign substances is etymo
ogically described as inflammation, meaning to set on fire, while the non-reaction to
action of these two components of the immune system creates a dynamic biological e
vironment where "Health" can be seen as an active physical state where what is self i
immunologically spared, and what is foreign is inflammatorily and immunologically
eliminated. Extending this concept, "Disease" then can arise when what is foreign ca
not be eliminated, or what is self is not spared.
https://en.wikipedia.org/wiki/Immunity_(medical)
Immunoglobulin
produced mainly by plasma cells that is used by the immune system to identify and
neutralize pathogens such as bacteria and viruses. The antibody recognizes a uniqu
molecule of the harmful agent, called an antigen, via the variable region. Each tip o
the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for o
particular epitope (similarly analogous to a key) on an antigen, allowing these two
structures to bind together with precision. Using this binding mechanism, an antibo
can tag a microbe or an infected cell for attack by other parts of the immune system
can neutralize its target directly (for example, by blocking a part of a microbe that is
sential for its invasion and survival). Depending on the antigen, the binding may im
pede the biological process causing the disease or may recruit macrophages to destr
the foreign substance. The ability of an antibody to communicate with the other com
nents of the immune system is mediated via its Fc region (located at the base of the
Index
Find Term
IMP
Inosinic acid or inosine monophosphate (IMP) is a nucleoside monophosphate.
Inosinic acid is important in metabolism. It is the ribonucleotide of hypoxanthine and
the first nucleotide formed during the synthesis of purine. IMP is formed by the deamination of adenosine monophosphate, and is hydrolyzed from inosine. IMP is an intermediate ribonucleoside monophosphate in purine metabolism.
https://en.wikipedia.org/wiki/Inosinic_acid
Index
Find Term
G-G
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
IMP Dehydrogenase
IMP dehydrogenase EC 1.1.1.205 (Inosine-5'-monophosphate dehydrogenase)
(Inosinic acid dehydrogenaseis) (IMPDH) an enzyme that converts inosine monophosphate to xanthosine monophosphate:
Inosine 5'-phosphate + NAD+ + H2O <=> Xanthosine 5'-phosphate + NADH + H+
It catalyzes the rate-limiting reaction of de novo GTP biosynthesis.
IMP dehydrogenase is associated with cell proliferation and is a possible target for cancer chemotherapy. Mammalian and bacterial IMPDHs are tetramers of identical
chains. There are two IMP dehydrogenase isozymes in humans. IMP dehydrogenase
nearly always contains a long insertion that has two CBS domains within it.
The structure of this enzyme is composed of a TIM barrel domain with two CBS domains inserted within a loop.
https://en.wikipedia.org/wiki/IMP_dehydrogenase
Index
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In situ
Index
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Indole
pyrrole ring. Indole is widely distributed in the natural environment and can
https://en.wikipedia.org/wiki/Indole
Indole-3-acetic Acid
Indole-3-acetic acid (IAA) is the most common, naturally-occurring, plant hormone of
the auxin class. It is the best known of the auxins, and has been the subject of extensive
studies by plant physiologists. Chemically, IAA is a carboxylic acid in which the carboxyl group is attached through a methylene group to the C-3 position of an indole
ring. In appearance, IAA is a colorless solid.
As all auxins, IAA has many different effects, such as inducing cell elongation and cell
division with all subsequent results for plant growth and development. On a larger
scale, IAA serves as signaling molecule necessary for development of plant organs and
coordination of growth.
https://en.wikipedia.org/wiki/Indole-3-acetic_acid
Induced Fit
The favored model for the enzyme-substrate interaction is the induced fit model.This
model proposes that the initial interaction between enzyme and substrate is relatively
weak, but that these weak interactions rapidly induce conformational changes in the
enzyme that strengthen binding. The scheme below depicts conformational changes in
the enzyme hexokinase upon binding of substrate.
https://en.wikipedia.org/wiki/Enzyme_catalysis#Induced_fit
Index
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Inducer
The gene is expressed because an inducer binds to the repressor. The bindin
ducer to the repressor prevents the repressor from binding to the operator.
lymerase can then begin to transcribe operon genes.
the complex binds to the activation sequence and activates target gene. Rem
inducer stops transcription.
https://en.wikipedia.org/wiki/Inducer
Index
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Inflammation
Inflammation (Latin, inflammatio) is part of the complex biological response of body
tissues to harmful stimuli, such as pathogens, damaged cells, or irritants.
Inflammation is a protective response that involves immune cells, blood vessels, and
molecular mediators. The purpose of inflammation is to eliminate the initial cause of
cell injury, clear out necrotic cells and tissues damaged from the original insult and the
inflammatory process, and to initiate tissue repair.
https://en.wikipedia.org/wiki/Inflammation
Index
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Electron transport inhibitors are molecules that bind to and prevent the mo
electrons through electron transport complexes in the inner mitochondrial
A few are listed below
Complex I - rotenone, amytal
Complex II - malonate
Complex III - Antimycin A
Complex IV - carbon monoxide, azide, cyanide
Index
Find Term
Initiator tRNA
An initiator tRNA is the tRNA that binds to the P site of the ribosome durin
Index
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Inner Leaflet
The lipid bilayer consists of two layers- an outer leaflet and an inner leaflet. Th
ponents of bilayers are distributed unequally between the two surfaces to create
metry between the outer and inner surfaces. This asymmetric organization is im
tant for cell functions such as cell signaling. The asymmetry of the biological me
brane reflects the different functions of the two leaflets of the membrane. As see
the fluid membrane model of the phospholipid bilayer, the outer leaflet and inn
In human red blood cells, the inner (cytoplasmic) leaflet is composed mostly of
Index
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Inner Membrane
Inner membrane, as used in this book, refers to the inner mitochondrial membrane
(IMM) which separates the mitochondrial matrix from the intermembrane space.
The structure of the inner mitochondrial membrane is extensively folded and compartmentalized. The numerous invaginations of the membrane are called cristae, separated
by crista junctions from the inner boundary membrane juxtaposed to the outer membrane. Cristae significantly increase the total membrane surface area compared to a
smooth inner membrane and thereby the available working space.
The inner membrane creates two compartments. The region between the inner and
outer membrane, called the intermembrane space which is largely continuous with the
cytosol, and the more sequestered space inside the inner membrane, called matrix.
https://en.wikipedia.org/wiki/Inner_mitochondrial_membrane
https://en.wikipedia.org/wiki/Inner_mitochondrial_membrane
Index
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https://en.wikipedia.org/wiki/Inner_mitochondrial_membrane
Index
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Inosine
Inosine is a nucleoside that is formed when hypoxanthine is attached to a ribose ring
(also known as a ribofuranose) via a -N9-glycosidic bond.
Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs. Phosphorylation of inosine creates the nucleotide inosine monophosphate (IMP).
https://en.wikipedia.org/wiki/Inosine
Index
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Index
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Inositol
Inositol or cyclohexane-1,2,3,4,5,6-hexol is a chemical compound with formula
C6H12O6 or (-CHOH-)6, a six-fold alcohol (polyol) of cyclohexane. It exists in nine possible stereoisomers, of which the most prominent form, widely occurring in nature, is
cis-1,2,3,5-trans-4,6-cyclohexanehexol, or myo-inositol (former names meso-inositol
or i-inositol). Inositol is a sugar alcohol. Its taste has been assayed at half the sweetness of table sugar (sucrose).
https://en.wikipedia.org/wiki/Inositol
Index
Find Term
Inositol-1,4,5-trisphosphate
logical cells. While DAG stays inside the membrane, IP3 is soluble and diffu
https://en.wikipedia.org/wiki/Inositol_trisphosphate
Index
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Insulin
Insulin (from the Latin, insula meaning island) is a peptide hormone produced by
cells in the pancreas, and by Brockmann body in some teleost fish. It regulates the metabolism of carbohydrates and fats by promoting the absorption of glucose from the
blood to skeletal muscles and fat tissue and by causing fat to be stored rather than used
for energy. Insulin also inhibits the production of glucose by the liver. Insulin counters
the effects of glucagon or epinephrine by stimulating dephosphorylation of proteins in
the kinase cascade.
https://en.wikipedia.org/wiki/Insulin
Index
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Insulin Receptor
IGF-I, IGF-II and belongs to the large class of tyrosine kinase receptors. Meta
the insulin receptor plays a key role in the regulation of glucose homeostasis,
tional process that under degenerate conditions may result in a range of clinic
festations including diabetes and cancer.
nate splicing during transcription results in either IR-A or IR-B isoforms. Dow
Index
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domain binds the NPXY sequence. Thus, the insulin receptor binds IRS. IR
pathways: mice deficient of IRS1 have only a mild diabetic phenotype, but a
nounced growth impairment, i.e., IRS-1 knockout mice only reach 50% of th
normal mice.
https://en.wikipedia.org/wiki/Insulin_receptor_substrate
domain binds the NPXY sequence. Thus, the insulin receptor binds IRS. IR
pathways: mice deficient of IRS1 have only a mild diabetic phenotype, but a
nounced growth impairment, i.e., IRS-1 knockout mice only reach 50% of th
normal mice.
https://en.wikipedia.org/wiki/Insulin_receptor_substrate
Insulin Resistance
Insulin resistance (IR) is generally regarded as a pathological condition in which cells
fail to respond to the normal actions of the hormone insulin. The body produces insulin when glucose starts to be released into the bloodstream from the digestion of the
carbohydrates we have eaten. Normally this insulin response triggers glucose being
taken into body cells, to be used for energy, and inhibits the body from using fat as energy. The level of glucose in the blood decreases as a result, staying within the normal
range even when a large amount of carbohydrates is consumed. When the body produces insulin under conditions of insulin resistance, the cells in the body are resistant
to the insulin and are unable to use it as effectively, leading to high blood sugar. Beta
cells in the pancreas subsequently increase their production of insulin, further contributing to a high blood insulin level. This often remains undetected and can contribute to
a diagnosis of Type 2 diabetes or latent autoimmune diabetes of adults. Although this
type of chronic insulin resistance is harmful, during acute illness it is actually a wellevolved protective mechanism. Recent investigations have revealed that insulin resistance helps to conserve the brain's glucose supply by preventing muscles from taking
up excessive glucose. Insulin resistance should even be strengthened under harsh metabolic conditions such as pregnancy, during which the expanding fetal brain demands
more glucose.
Insulin resistance implies that the body's cells (primarily muscle) lose sensitivity to insulin, a hormone secreted by the pancreas to promote glucose utilization. At the molecular level, a cell senses insulin through insulin receptors, with the signal propagating through a cascade of molecules collectively known as PI3K/Akt/mTOR signaling
pathway. Recent studies suggested that the pathway may operate as a bistable switch
under physiologic conditions for certain types of cells, and insulin response may well
be a threshold phenomenon. The pathway's sensitivity to insulin may be blunted by
many factors such as free fatty acids, causing insulin resistance. From a broader perspective, however, sensitivity tuning (including sensitivity reduction) is a common practice for an organism to adapt to the changing environment or metabolic conditions.
Pregnancy, for example, is a prominent change of metabolic conditions, under which
the mother has to reduce her muscles' insulin sensitivity to spare more glucose for the
brains (the mother's brain and the fetal brain). This can be achieved through raising
the response threshold (i.e., postponing the onset of sensitivity) by secreting placental
growth factor to interfere with the interaction between insulin receptor substrate (IRS)
and PI3K, which is the essence of the so-called adjustable threshold hypothesis of insulin resistance.
https://en.wikipedia.org/wiki/Insulin_resistance
Insulin Signaling
Activation of insulin receptors leads to internal cellular mechanisms that directly affect
glucose uptake by regulating the number and operation of protein molecules in the cell
membrane that transport glucose into the cell.
Insulin binds to the extracellular portion of the subunits of the insulin receptor. This,
in turn, causes a conformational change in the insulin receptor that activates the kinase domain residing on the intracellular portion of the subunits. The activated kinase domain autophosphorylates tyrosine residues on the C-terminus of the receptor
as well as tyrosine residues in the IRS-1 protein.
1 Phosphorylated IRS-1, in turn, binds to and activates phosphoinositol 3 kinase (PI3K)
2 PI3K catalyzes the reaction PIP2 + ATP PIP3 + ADP
3 PIP3 activates protein kinase B (PKB)
4 PKB phosphorylates glycogen synthase kinase (GSK) and thereby inactivates GSK
5 GSK can no longer phosphorylate glycogen synthase (GS)
6 Unphosphorylated GS makes more glycogen
7 PKB also facilitates vesicle fusion, resulting in an increase in GLUT4 transporters in
the plasma membrane
https://en.wikipedia.org/wiki/Insulin#Signal_transduction
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https://en.wikipedia.org/wiki/Integral_membrane_protein
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Integrin
Integrins are transmembrane receptors that are the bridges for cell-cell and cell-
chemical pathways to the interior (signal transduction), such as the chemical com
tion and mechanical status of the ECM, which results in a response (activation of
scription) such as regulation of the cell cycle, cell shape, and/or motility or new r
tors being added to the cell membrane. This allows rapid and flexible responses t
events at the cell surface, for example to signal platelets to initiate an interaction
coagulation factors.
https://en.wikipedia.org/wiki/Integrin
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Integrins
Integrins are transmembrane receptors that are the bridges for cell-cell and
tion and mechanical status of the ECM, which results in a response (activatio
scription) such as regulation of the cell cycle, cell shape, and/or motility or n
tors being added to the cell membrane. This allows rapid and flexible respon
events at the cell surface, for example to signal platelets to initiate an interac
coagulation factors.
https://en.wikipedia.org/wiki/Integrin
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Intermediate Filaments
Intermediate filaments (IFs) are cytoskeletal components found in the cells of many
animal species. They are composed of a family of related proteins sharing common
structural and sequence features. Intermediate filaments have an average diameter of
10 nanometers, which is between that of 7nm actin (microfilaments), and that of
25nm microtubules, and they were initially designated 'intermediate' because their average diameter is between those of narrower microfilaments (actin) and wider myosin
filaments found in muscle cells. Most types of intermediate filaments are cytoplasmic,
but one type, the lamins, are nuclear.
https://en.wikipedia.org/wiki/Intermediate_filament
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Intermembrane Space
The intermembrane space (IMS) is the region between the inner membrane and the
outer membrane of a mitochondrion or a chloroplast. The main function of mitochondrial intermembrane space is related to oxidative phosphorylation. It is to this region
that protons are pumped during electron transport and from which they re-enter the
matrix in the process of oxidative phosphorylation.
https://en.wikipedia.org/wiki/Intermembrane_space
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Intrinsic Pathway
In molecular biology, the term intrinsic pathway may refer to multiple casca
tein interactions.
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Intrinsic Terminators
Intrinsic termination (also called Rho-independent termination) is a mechanism in prokaryotes that causes RNA transcription to be stopped. In this mechanism, the mRNA
contains a sequence that can base pair with itself to form a stem-loop structure 7-20
base pairs in length that is also rich in cytosine-guanine base pairs. C-G base pairs
have significant base-stacking interactions (especially repeated G-C pairs) and can
form three hydrogen bonds between each other, resulting in a stable RNA duplex. Following the stem-loop structure is a chain of uracil residues. The bonds between uracil
and adenine are very weak. A protein bound to RNA polymerase (nusA) binds to the
stem-loop structure tightly enough to cause the polymerase to temporarily stall. This
pausing of the polymerase coincides with transcription of the poly-uracil sequence.
The weak Adenine-Uracil bonds lower the energy of destabilization for the RNA-DNA
duplex, allowing it to unwind and dissociate from the RNA polymerase.
Stem-loop structures that are not followed by a poly-Uracil sequence cause the RNA polymerase to pause, but it will typically continue transcription after a brief time because
the duplex is too stable to unwind far enough to cause termination. Rho-independent
transcription termination is a frequent mechanism underlying the activity of cis-acting
RNA regulatory elements, such as riboswitches.
Shown below - predicted conserved secondary structure and sequence conservation annotation for 90 bacterial Rho-independent termination elements.
https://en.wikipedia.org/wiki/Intrinsic_termination
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Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing
during maturation of the final RNA product. The term intron refers to both the DNA
sequence within a gene and the corresponding sequence in RNA transcripts. Sequences
that are joined together in the final mature RNA after RNA splicing are exons.
Introns are found in the genes of most organisms and many viruses, and can be located
in a wide range of genes, including those that generate proteins, ribosomal RNA
(rRNA), and transfer RNA (tRNA). When proteins are generated from introncontaining genes, RNA splicing takes place as part of the RNA processing pathway that
follows transcription and precedes translation.
https://en.wikipedia.org/wiki/Intron
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Iodine
Iodine is a chemical element with symbol I and atomic number 53. The nam
which has a high fission product yield, concentrates in the thyroid, and can
died with non-radioactive potassium iodide treatment.
https://en.wikipedia.org/wiki/Iodine
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Ion
the total number of protons, giving the atom or molecule a net positive or n
trical charge. Ions can be created, by either chemical or physical means, via
https://en.wikipedia.org/wiki/Ion
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Ion Channels
Ion channels are pore-forming membrane proteins whose functions include establishing a resting membrane potential, shaping action potentials and other electrical signals
by gating the flow of ions across the cell membrane, controlling the flow of ions across
secretory and epithelial cells, and regulating cell volume. Ion channels are present in
the membranes of all cells. Ion channels are considered to be one of the two traditional
classes of ionophoric proteins, with the other class known as ion transporters (including the sodium-potassium pump, sodium-calcium exchanger, and sodium-glucose
transport proteins, amongst others).
There are two distinctive features of ion channels that differentiate them from other
types of ion transporter proteins:
1 The rate of ion transport through the channel is very high (often 106 ions per second
or greater).
2 Ions pass through channels down their electrochemical gradient, which is a function
of ion concentration and membrane potential, "downhill", without the input (or help)
of metabolic energy (e.g. ATP, co-transport mechanisms, or active transport mechanisms).
Ion channels are located within the plasma membrane of nearly all cells and many intracellular organelles. They are often described as narrow, water-filled tunnels that allow only ions of a certain size and/or charge to pass through. This characteristic is
called selective permeability. The archetypal channel pore is just one or two atoms
wide at its narrowest point and is selective for specific species of ion, such as sodium or
potassium. However, some channels may be permeable to the passage of more than
one type of ion, typically sharing a common charge: positive (cations) or negative (anions). Ions often move through the segments of the channel pore in single file nearly as
quickly as the ions move through free solution. In many ion channels, passage through
the pore is governed by a "gate", which may be opened or closed in response to chemical or electrical signals, temperature, or mechanical force.
Ion channels are integral membrane proteins, typically formed as assemblies of several
individual proteins. Such "multi-subunit" assemblies usually involve a circular arrangement of identical or homologous proteins closely packed around a water-filled pore
through the plane of the membrane or lipid bilayer. For most voltage-gated ion channels, the pore-forming subunit(s) are called the subunit, while the auxiliary subunits
are denoted , , and so on.
Because channels underlie the nerve impulse and because "transmitter-activated" channels mediate conduction across the synapses, channels are especially prominent components of the nervous system. Indeed, numerous toxins that organisms have evolved
for shutting down the nervous systems of predators and prey (e.g., the venoms produced by spiders, scorpions, snakes, fish, bees, sea snails, and others) work by modulating ion channel conductance and/or kinetics. In addition, ion channels are key components in a wide variety of biological processes that involve rapid changes in cells, such
as cardiac, skeletal, and smooth muscle contraction, epithelial transport of nutrients
and ions, T-cell activation and pancreatic -cell insulin release. In the search for new
drugs, ion channels are a frequent target.
Depicted below is a voltage gated ion channel
https://en.wikipedia.org/wiki/Ion_channel
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Ion Gradients
an ion that can move across a membrane. The gradient consists of two parts
available for work in a cell. The energy is stored in the form of chemical pot
static energy, which accounts for an ion's tendency to move under influence
transmembrane potential.
https://en.wikipedia.org/wiki/Electrochemical_gradient
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Ionic
The term ionic related to a molecule having the qualities of an ion - being charg
sists of positively charged ions called cations and negatively charged ions called
These can be simple ions such as the sodium (Na+) and chloride (Cl) in sodium
ride, or polyatomic species such as the ammonium (NH4+) and carbonate (CO3
ple nearest neighbors, so are not considered to be part of molecules, but instead
a continuous three-dimensional network, usually in a crystalline structure.
https://en.wikipedia.org/wiki/Ionic_compound
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Ionic Interactions
The term ionic interactions relates to attractive and repulsive forces arising
Ionization
tive charge by gaining or losing electrons to form ions, often in conjunction with ot
chemical changes. Ionization can result from the loss of an electron after collisions
with subatomic particles, collisions with other atoms, molecules and ions, or throu
the interaction with light.
https://en.wikipedia.org/wiki/Ionization
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Ionize
Ionizing occurs when an atom or a molecule acquires a negative or positive
gaining or losing electrons to form ions, often in conjunction with other che
changes. Ionization can result from the loss of an electron after collisions w
tomic particles, collisions with other atoms, molecules and ions, or through
tion with light.
https://en.wikipedia.org/wiki/Ionization
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Ionophores
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IP3
logical cells. While DAG stays inside the membrane, IP3 is soluble and diffu
https://en.wikipedia.org/wiki/Inositol_trisphosphate
IP3/DAG System
The two products of the Phospholipase C (PLC) catalyzed reaction, DAG and IP3, are
important second messengers that control diverse cellular processes and are substrates
for synthesis of other important signaling molecules. When PIP2 is cleaved, DAG remains bound to the membrane, and IP3 is released as a soluble structure into the cytosol. IP3 then diffuses through the cytosol to bind to IP3 receptors, particularly calcium
channels in the smooth endoplasmic reticulum (ER). This causes the cytosolic concentration of calcium to increase, causing a cascade of intracellular changes and activity.
In addition, calcium and DAG together work to activate protein kinase C, which goes
on to phosphorylate other molecules, leading to altered cellular activity. End-effects include taste, tumor promotion, as well as vesicle exocytosis, superoxide production
from NADPH oxidase, and JNK activation.
https://en.wikipedia.org/wiki/Phospholipase_C#Effects
IPTG
Isopropyl -D-1-thiogalactopyranoside (IPTG, also known as lad-y) is a molecular biology reagent. This compound is a molecular mimic of allolactose, a lactose metabolite
that triggers transcription of the lac operon, and it is therefore used to induce protein
expression where the gene is under the control of the lac operator.
IPTG is an effective inducer of protein expression in the concentration range of 100
M to 1.0 mM. Concentration used depends on the strength of induction required, as
well as the genotype of cells or plasmid used. If lacIq, a mutant that over-produces the
lac repressor, is present, then a higher concentration of IPTG may be necessary.
https://en.wikipedia.org/wiki/Isopropyl_ -D-1-thiogalactopyranoside
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Techniques
Techniques
Techniques
Techniques
IRE-binding Protein
ACO1, or IRP1, is a bifunctional protein that functions as an iron-responsive element
(IRE)-binding protein involved in the control of iron metabolism by binding mRNA to
repress translation or degradation. It functions also as the cytoplasmic isoform of aconitase. Aconitases are iron-sulfur proteins that require a 4Fe-4S cluster for their enzymatic activity, in which they catalyze conversion of citrate to isocitrate.
Cells have advanced mechanisms for sensing their own need for iron. In human cells,
the best-characterized iron-sensing mechanism is the result of post-transcriptional
regulation of mRNA (the chemical instructions derived from DNA genes to make proteins). Sequences of mRNA called iron-responsive elements (IREs) are contained
within the mRNA sequences that code for transferrin receptors and for ferritin. Ironresponsive element-binding protein (IRE-BP) binds to these mRNA sequences. On its
own, the IRE-BP binds to the IREs of ferritin and transferrin receptor mRNA. But,
when iron binds to the IRE-BP, the IRE-BP changes shape with the result that the IREBPs can no longer bind the ferritin mRNA. This liberates the mRNA to direct the cell to
make more ferritin. In other words, when there is high iron in the cell, the iron itself
causes the cell to produce more iron storage molecules.
Transferrin receptor production depends on a similar mechanism. But this one has the
opposite trigger, and the opposite ultimate effect. IRE-BPs without iron bind to the
IREs on transferrin receptor mRNA. But those IREs have a different effect: When the
IRE-BP binds to these sites, the binding not only allows for translation but also stabilizes the mRNA molecule so it can stay intact for longer.
In low-iron conditions, IRE-BPs allow the cell to keep producing transferrin receptors.
And more transferrin receptors make it easier for the cell to bring in more iron from
transferrin-iron complexes circulating outside the cell. But, as iron binds to more and
more IRE-BPs, they change shape and unbind the transferrin receptor mRNA. The
transferrin receptor mRNA is rapidly degraded without the IRE-BP attached to it. The
cell stops producing transferrin receptors.
When the cell has obtained more iron than it can bind up with ferritin or heme molecules, more and more iron will bind to the IRE-BPs. That will stop transferrin receptor
production. And iron-IRE-BP binding will also start ferritin production.
When the cell is low on iron, less and less iron will bind to IRE-BPs. The IRE-BPs without iron will bind to transferrin receptor mRNA.
https://en.wikipedia.org/wiki/Iron-responsive_element-binding_protein
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Iron
Iron is a chemical element with symbol Fe (from Latin: ferrum) and atomic
26. It is a metal in the first transition series. It is by mass the most common
on Earth, forming much of Earth's outer and inner core. It is the fourth mos
element in the Earth's crust.
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https://en.wikipedia.org/wiki/Iron_response_element
Iron-sulfur Centers
Ironsulfur proteins are proteins characterized by the presence of ironsulfur clusters
containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states.
Ironsulfur clusters are found in a variety of metalloproteins, such as the ferredoxins,
as well as NADH dehydrogenase, hydrogenases, coenzyme Q cytochrome c reductase, succinate coenzyme Q reductase and nitrogenase. Ironsulfur clusters are best
known for their role in the oxidation-reduction reactions of mitochondrial electron
transport.
Both Complex I and Complex II of oxidative phosphorylation have multiple FeS clusters. They have many other functions including catalysis as illustrated by aconitase,
generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors
in the biosynthesis of lipoic acid and biotin. Additionally, some FeS proteins regulate
gene expression. FeS proteins are vulnerable to attack by biogenic nitric oxide. In
most FeS proteins, the terminal ligands on Fe are thiolate, but exceptions exist.
https://en.wikipedia.org/wiki/Ironsulfur_protein
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Iron-sulfur Proteins
Ironsulfur proteins are proteins characterized by the presence of ironsulfur clusters
containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states.
Ironsulfur clusters are found in a variety of metalloproteins, such as the ferredoxins,
as well as NADH dehydrogenase, hydrogenases, coenzyme Q cytochrome c reductase, succinate coenzyme Q reductase and nitrogenase.
Ironsulfur clusters are best known for their role in the oxidation-reduction reactions
of mitochondrial electron transport. Both Complex I and Complex II of oxidative phosphorylation have multiple FeS clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAMdependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin.
Additionally, some FeS proteins regulate gene expression. FeS proteins are vulnerable to attack by biogenic nitric oxide. In most FeS proteins, the terminal ligands on
Fe are thiolate, but exceptions exist.
The prevalence of these proteins on the metabolic pathways of most organisms leads
some scientists to theorize that ironsulfur compounds had a significant role in the origin of life in the ironsulfur world theory.
https://en.wikipedia.org/wiki/Ironsulfur_protein
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IRS-1
coded by the IRS-1 gene. It contains a single pleckstrin homology (PH) dom
Index
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Isocitrate
Isocitric acid is an organic compound closely related to citric acid. Salts and esters of
isocitric acid are known as isocitrates. The isocitrate anion is a substrate of the citric
acid cycle. Isocitrate is formed from citrate with the help of the enzyme aconitase, and
is acted upon by isocitrate dehydrogenase.
https://en.wikipedia.org/wiki/Isocitric_acid
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Isocitrate Dehydrogenase
Isocitrate dehydrogenase (IDH) (EC 1.1.1.42) and (EC 1.1.1.41) is an enzyme that catalyzes the oxidative decarboxylation of isocitrate, producing -ketoglutarate (ketoglutarate) and CO2. This is a two-step process, which involves oxidation of
isocitrate (a secondary alcohol) to oxalosuccinate (a ketone), followed by the decarboxylation of the carboxyl group to the ketone, forming -ketoglutarate. In humans, IDH
exists in three isoforms: IDH3 catalyzes the third step of the citric acid cycle while converting NAD+ to NADH in the mitochondria. The isoforms IDH1 and IDH2 catalyze the
same reaction outside the context of the citric acid cycle and use NADP+ as a cofactor
instead of NAD+. They localize to the cytosol as well as the mitochondrion and peroxisome.
https://en.wikipedia.org/wiki/Isocitrate_dehydrogenase
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Isocitrate Lyase
Isocitrate lyase (EC 4.1.3.1), or ICL, is an enzyme in the glyoxylate cycle that catalyzes
the cleavage of isocitrate to succinate and glyoxylate. Together with malate synthase, it
bypasses the two decarboxylation steps of the citric acid cycle and is used by bacteria,
fungi, and plants.
https://en.wikipedia.org/wiki/Isocitrate_lyase
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Isoelectric Focusing
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Isoelectric Point
The isoelectric point (pI, pH(I), IEP), is the pH at which a particular molecule carries
no net electrical charge. The standard nomenclature to represent the isoelectric point
is pH(I), although pI is also commonly seen. The net charge on a molecule is affected
by pH of its surrounding environment and can become more positively or negatively
charged due to the gain or loss, respectively, of protons (H+).
The pI value can affect the solubility of a molecule at a given pH. Such molecules have
minimum solubility in water or salt solutions at the pH that corresponds to their pI
and often precipitate out of solution. Biological amphoteric molecules such as proteins
contain both acidic and basic functional groups. Amino acids that make up proteins
may be positive, negative, neutral, or polar in nature, and together give a protein its
overall charge. At a pH below their pI, proteins carry a net positive charge. Above their
pI they carry a net negative charge. Proteins can, thus, be separated by net charge in a
polyacrylamide gel using either preparative gel electrophoresis or isoelectric focusing,
which uses a pH gradient to separate proteins. Isoelectric focusing is also the first step
in 2-D gel polyacrylamide gel electrophoresis.
https://en.wikipedia.org/wiki/Isoelectric_point
Isoform
mRNAs for the same gene can have different protein-coding segments (exo
different parts of exons from RNA joined together to form different mRNA
and thus different protein forms. Each unique sequence produces a specific
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Isoforms
mRNAs for the same gene can have different protein-coding segments (exo
different parts of exons from RNA joined together to form different mRNA
and thus different protein forms. Each unique sequence produces a specific
Isoleucine
Isoleucine (abbreviated as Ile or I) encoded by the codons AUU, AUC, and AUA is an
-amino acid that is used in the biosynthesis of proteins. It contains an -amino group
(which is in the protonated NH3+ form under biological conditions), an -carboxylic
acid group (which is in the deprotonated COO form under biological conditions),
and a hydrocarbon side chain, classifying it as a non-polar, uncharged(at physiological
pH), aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it, and must be ingested in our diet. Isoleucine is synthesized from pyruvate employing leucine biosynthesis enzymes in other organisms such as bacteria.
Inability to break down isoleucine, along with other amino acids, is associated with the
disease called Maple Syrup Urine Disease, which results in discoloration and a sweet
smell in the patient's urine, which is where the name comes from. However in severe
cases, MSUD can lead to damage to the brain cells and ultimately death.
Isoleucine is both a glucogenic and a ketogenic amino acid. After transamination with
-ketoglutarate the carbon skeleton can be converted into either Succinyl CoA, and fed
into the TCA cycle for oxidation or converted into oxaloacetate for gluconeogenesis
(hence glucogenic). It can also be converted into Acetyl CoA and fed into the TCA cycle
by condensing with oxaloacetate to form citrate. In mammals Acetyl CoA cannot be
converted back to carbohydrate but can be used in the synthesis of ketone bodies or
fatty acids, hence ketogenic.
Biotin, sometimes referred to as Vitamin B7 or Vitamin H, is an absolute requirement
for the full catabolism of isoleucine (as well as leucine). Without adequate biotin, the
human body will be unable to fully break down isoleucine and leucine molecules. This
can lead to numerous physiological issues (related to muscle maintenance and protein
synthesis, lipid metabolism, and fatty acid metabolism) as well as cognitive issues resulting from general metabolic pathway failure and the irritating effects of hydroxyisovalerate, a byproduct of incomplete isoleucine catabolism. Isovaleric acidemia is an example of a disorder caused by incomplete catabolism of leucine.
https://en.wikipedia.org/wiki/Isoleucine
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Isoleucine Aminotransferase
Isoleucine aminotranferase is a transaminase that catalyzes the last step in
thesis of valine. It is shown below.
-ketoisovalerate + Glutamate
Valine + -ketoglutarate
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Isomerase
Isomerases are a general class of enzymes which convert a molecule from one is
bonds are broken and formed or they can catalyze conformational changes. The
eral form of such a reaction is as follows:
AB BA
There is only one substrate yielding one product. This product has the same mo
Isopentenyl Pyrophosphate
Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP) is an intermediate
in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway), and is used by organisms in the biosynthesis of terpenes and terpenoids. IPP is
formed from acetyl-CoA via the mevalonate pathway (the "upstream" part), and then is
isomerized to dimethylallyl pyrophosphate by the enzyme isopentenyl pyrophosphate
isomerase.
https://en.wikipedia.org/wiki/Isopentenyl_pyrophosphate
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Isoprene
The isoprene skeleton can be found in naturally occurring compounds called terpenes
(also known as isoprenoids), but these compounds do not arise from isoprene itself.
Terpenes can be viewed as multiples of isoprene subunits, and this perspective is the
cornerstone of the "isoprene rule". The precursor to isoprene units in biological systems is dimethylallyl pyrophosphate (DMAPP - bottom figure below) and its isomer
isopentenyl pyrophosphate (IPP - top figure below). The plural isoprenes is sometimes used to refer to terpenes in general. Isoprene chains are commonly found in numerous biologically active oligomers such as Vitamin A. Similarly, natural rubber is
composed of linear polyisoprene chains of very high molecular weight and other natural molecules.
https://en.wikipedia.org/wiki/Isoprene
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Isoprenoid
The terpenoids, sometimes called isoprenoids, are a large and diverse class of naturally
occurring organic chemicals similar to terpenes, derived from five-carbon isoprene
units assembled and modified in thousands of ways. Most are multicyclic structures
that differ from one another not only in functional groups but also in their basic carbon
skeletons. These lipids can be found in all classes of living things, and are the largest
group of natural products. About 60% of known natural products are terpenoids.
Plant terpenoids are used extensively for their aromatic qualities and play a role in traditional herbal remedies. Terpenoids contribute to the scent of eucalyptus, the flavors
of cinnamon, cloves, and ginger, the yellow color in sunflowers, and the red color in tomatoes. Well-known terpenoids include citral, menthol, camphor, salvinorin A in the
plant Salvia divinorum, the cannabinoids found in cannabis, ginkgolide and bilobalide
found in Ginkgo biloba, and the curcuminoids found in turmeric and mustard seed.
The steroids and sterols in animals are biologically produced from terpenoid precursors. Sometimes terpenoids are added to proteins, e.g., to enhance their attachment to
the cell membrane; this is known as isoprenylation.
A simplified isopreonid synthesis pathway is below.
https://en.wikipedia.org/wiki/Terpenoid
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Isopropylmalate Dehydratase
The enzyme is an aconitase analog and accomplishes its catalysis via dehyd
-isopropylmalate
-isopropylmalate.
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Isopropylmalate Dehydrogenase
cal reactions below. The enzyme catalyzes a reaction in the biosynthesis of vali
leucine shown in green at the bottom. It is the third reaction shown in the list.
-isopropylmalate + NAD+
-ketoisocaproate + NADH
https://en.wikipedia.org/wiki/3-Isopropylmalate_dehydrogenase
Isotonic
An isotonic solution is one in which its effective osmole concentration is the same as
the solute concentration of a cell. In this case the cell neither swells nor shrinks because there is no concentration gradient for water across the cell membrane. Water
molecules diffuse through the plasma membrane in both directions, and as the rate of
water diffusion is the same in each direction that cell will neither gain nor lose water.
An ISO-osmolar solution can be hypotonic if the solute is able to penetrate the cell
membrane. For example an ISO-osmolar urea solution is hypotonic to red blood cells
causing their lysis. This is due to urea entering the cell down its concentration gradient
followed by water. For example, the osmolarity of normal saline, 9 grams NaCl dissolved in water to a total volume of one litre, is a close approximation to the osmolarity
of NaCl in blood (about 290 mOsm/L). Thus, normal saline is almost isotonic to blood
plasma. Both sodium and chloride ions cannot freely pass through the plasma membrane as opposed to urea.
https://en.wikipedia.org/wiki/Tonicity#Isotonicity
Isozyme
zymes. In many cases, they are coded for by homologous genes that have diverg
the same gene, and isozymes represent enzymes from different genes that proce
catalyze the same reaction, the two words are usually used interchangeably.
https://en.wikipedia.org/wiki/Isozyme
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James Watson
James Dewey Watson (born April 6, 1928) is an American molecular biologist, geneticist and zoologist, best known as one of the co-discoverers of the structure of DNA in
1953 with Francis Crick. Watson, Crick, and Maurice Wilkins were awarded the 1962
Nobel Prize in Physiology or Medicine "for their discoveries concerning the molecular
structure of nucleic acids and its significance for information transfer in living material".
https://en.wikipedia.org/wiki/James_Watson
Jun-B
following the primary growth factor response. It binds to the DNA sequence
TGA[CG]TCA-3'.
https://en.wikipedia.org/wiki/JUNB
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Junk DNA
Junk DNA is term given originally to describe the large number of sequences in noncoding eukaryotic DNA for which no function was apparent.
According to T. Ryan Gregory, a genomic biologist, the first explicit discussion of the
nature of junk DNA was done by David Comings in 1972 and he applied the term to all
noncoding DNA. The term was formalized in 1972 by Susumu Ohno, who noted that
the mutational load from deleterious mutations placed an upper limit on the number
of functional loci that could be expected given a typical mutation rate. Ohno hypothesized that mammal genomes could not have more than 30,000 loci under selection before the "cost" from the mutational load would cause an inescapable decline in fitness,
and eventually extinction. This prediction remains robust, with the human genome containing approximately 20,000 genes. Another source for Ohno's theory was the observation that even closely related species can have widely (orders-of-magnitude) different genome sizes, which had been dubbed the C-value paradox in 1971.
Though the fruitfulness of the term "junk DNA" has been questioned on the grounds
that it provokes a strong a priori assumption of total non-functionality and though
some have recommended using more neutral terminology such as "noncoding DNA"
instead. "Junk DNA" remains a label for the portions of a genome sequence for which
no discernible function has been identified and that through comparative genomics
analysis appear under no functional constraint suggesting that the sequence itself has
provided no adaptive advantage.
Since the late 70s it has become apparent that the majority of non-coding DNA in large
genomes finds its origin in the selfish amplification of transposable elements, of which
W. Ford Doolittle and Carmen Sapienza in 1980 wrote in the journal Nature: "When a
given DNA, or class of DNAs, of unproven phenotypic function can be shown to have
evolved a strategy (such as transposition) which ensures its genomic survival, then no
other explanation for its existence is necessary." The amount of junk DNA can be expected to depend on the rate of amplification of these elements and the rate at which
non-functional DNA is lost. In the same issue of Nature, Leslie Orgel and Francis Crick
wrote that junk DNA has "little specificity and conveys little or no selective advantage
to the organism". The term occurs mainly in popular science and in a colloquial way in
scientific publications, and it has occasionally[quantify] been suggested that its connotations may have delayed interest in the biological functions of noncoding DNA.
Several lines of evidence indicate that some "junk DNA" sequences are likely to have
unidentified functional activity and that the process of exaptation of fragments of originally selfish or non-functional DNA has been commonplace throughout evolution. In
2012, the ENCODE project, a research program supported by the National Human Genome Research Institute, reported that 76% of the human genome's noncoding DNA
sequences were transcribed and that nearly half of the genome was in some way accessible to genetic regulatory proteins such as transcription factors.
However, the suggestion by ENCODE that over 80% of the human genome is biochemically functional has been criticized by other scientists, who argue that neither accessibility of segments of the genome to transcription factors nor their transcription guarantees that those segments have biochemical function and that their transcription is selectively advantageous. Furthermore, the much lower estimates of functionality prior to
ENCODE were based on genomic conservation estimates across mammalian lineages.
Kallikrein
lated serine proteases. These genes are localized to chromosome 19q13, form
Index
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Kcat
will execute for a given enzyme concentration. It can be calculated from the
reaction rate and catalyst site concentration as follows:
Kcat = Vmax/[Et],
where [Et] is the total enzyme concentration.
which means that each carbonic anhydrase molecule can produce up to 600
cules of product (bicarbonate ions) per enzyme molecule per second.
Index
Kcat / Km
In the field of biochemistry, Kcat/Km (also called the specificity constant or kine
an enzyme for different substrates (i.e., substrate specificity). The higher the sp
constant, the more the enzyme "prefers" that substrate.
For a kinetically perfect enzyme, every encounter between enzyme and substrat
to product and hence the reaction velocity is only limited by the rate the enzym
counters substrate in solution. Hence the upper limit for is equal to rate of sub
diffusion which is between108 and 109 s1M1
https://en.wikipedia.org/wiki/Specificity_constant
Index
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Kd
In studying proteins and ligands, it is important to understand the tightness with
which a protein (P) holds onto a ligand (L). This is measured with the dissociation
constant (Kd).
The formation of a ligand-protein complex LP occurs as
L + P <=> LP
The dissociation of the complex, therefore, is the reverse of this, or
LP <=> L + P
so the corresponding dissociation constant is defined as
Kd = [L][P]/[LP]
where [L], [P], and [LP] are the molar concentrations of the protein, ligand and the
complex when they are joined together.
Smaller values of Kd indicate tight binding, whereas larger values indicate loose binding. The dissociation constant is the inverse of the association constant.
Ka = 1/Kd
Where multiple molecules bond together, such as
JxKy <=> xJ + yK
(complex JxKy is breaking down down into x subunits of J and y subunits of K)
the dissociation constant is then defined as
Kd = [J]x[K]y/[JxKy]
where [J], [K], and [JxKy] are the concentrations of J, K, and the complex JxKy, respectively.
Keq
The equilibrium constant, Keq, of a chemical reaction is the value of the reac
Index
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Keratan Sulfate
Keratan sulfate (KS), also called keratosulfate, is any of several sulfated glyc
lage, and bone. It is also synthesized in the central nervous system where it
pates both in development and in the glial scar formation following an injur
sulfates are large, highly hydrated molecules which in joints can act as a cus
sorb mechanical shock.
https://en.wikipedia.org/wiki/Keratan_sulfate
Keratins
tects epithelial cells from damage or stress that has potential to kill the cell.
key structural material making up the outer layer of human skin. It is the ke
tural component of hair and nails, and it provides the necessary strength an
ness for masticatory organs, such as the tongue and the hard palate. Keratin
mers assemble into bundles to form intermediate filaments, which are toug
Ketogenic
ess supplies energy to certain organs (particularly the brain) under circums
Index
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Ketogenic Diet
function. However, if there is very little carbohydrate in the diet, the liver co
into fatty acids and ketone bodies. The ketone bodies pass into the brain an
Ketone Bodies
Ketone bodies are three water-soluble molecules (acetoacetate, -hydroxybutyrate, and
their spontaneous breakdown product, acetone) that are produced by the liver from
fatty acids during periods of low food intake (fasting), carbohydrate restrictive diets,
starvation, prolonged intense exercise, or in untreated (or inadequately treated) type 1
diabetes mellitus. These ketone bodies are readily picked up by the extra-hepatic tissues, and converted into acetyl-CoA which then enters the citric acid cycle and is oxidized in the mitochondria for energy.
In the brain, ketone bodies are also used to make acetyl-CoA into long-chain fatty acids. The latter cannot be obtained from the blood, because they cannot pass through
the bloodbrain barrier.
Three ketone bodies are depicted below. From top to bottom, they are acetone, acetoacetate, and -hydroxybutyrate.
https://en.wikipedia.org/wiki/Ketone_bodies
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Ketones
In chemistry, a ketone is an organic compound with the structure RC(=O)R', where R
and R' can be a variety of carbon-containing substituents. Ketones and aldehydes are
simple compounds that contain a carbonyl group (a carbon-oxygen double bond). They
are considered "simple" because they do not have reactive groups like OH or Cl attached directly to the carbon atom in the carbonyl group, as in carboxylic acids containing COOH. Many ketones are known and many are of great importance in industry
and in biology. Examples include many sugars (ketoses) and the industrial solvent acetone, which is the smallest ketone.
https://en.wikipedia.org/wiki/Ketone
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Ketose
A ketose is a monosaccharide containing one ketone group per molecule.
only one having no optical activity. Ketoses can isomerize into an aldose wh
bonyl group is located at the end of the molecule. Such ketoses are reducing
Fructose is the most common ketose.
https://en.wikipedia.org/wiki/Ketose
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Ketosis
Ketosis is a metabolic state in which most of the body's energy supply comes from ketone bodies in the blood, in contrast to a state of glycolysis in which blood glucose provides most of the energy. Ketosis is generally better known to the laypeople as acetone
breath - a common symptom of progressing diabetes mellitus type II advanced stage. It
is characterized by serum concentrations of ketone bodies over 0.5 mM, with low and
stable levels of insulin and blood glucose. The condition is almost always generalized
with hyperketonemia, that is, an elevated level of ketone bodies in the blood throughout the body.
Ketone bodies are formed by ketogenesis when liver glycogen stores are depleted (or
from metabolizing medium-chain triglycerides). The main ketone bodies used for energy are acetoacetate and -hydroxybutyrate, and the levels of ketone bodies are regulated mainly by insulin and glucagon. Most cells in the body can use both glucose and
ketone bodies for fuel, and during ketosis, free fatty acids and glucose synthesis (gluconeogenesis) fuel the remainder.
Longer-term ketosis may result from fasting or staying on a low-carbohydrate diet, and
deliberately induced ketosis serves as a medical intervention for intractable epilepsy.
In glycolysis, higher levels of insulin promote storage of body fat and block release of
fat from adipose tissues, while in ketosis, fat reserves are readily released and consumed. For this reason, ketosis is sometimes referred to as the body's "fat burning"
mode.
https://en.wikipedia.org/wiki/Ketosis
Kinase
A kinase is an enzyme that catalyzes the transfer of phosphate groups from highenergy, phosphate-donating molecules to specific substrates. This process is known as
phosphorylation, where the substrate gains a phosphate group and the high-energy
ATP molecule donates a phosphate group. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the
phosphorylated substrate donates a phosphate group and ADP gains a phosphate
group (producing a dephosphorylated substrate and the high energy molecule of ATP).
These two processes, phosphorylation and dephosphorylation, occur four times during
glycolysis.
Kinases are part of the larger family of phosphotransferases. Kinases are not to be confused with phosphorylases, which catalyze the addition of inorganic phosphate groups
to an acceptor, nor with phosphatases, which remove phosphate groups. The phosphorylation state of a molecule, whether it be a protein, lipid, or carbohydrate, can affect
its activity, reactivity, and its ability to bind other molecules. Therefore, kinases are
critical in metabolism, cell signaling, protein regulation, cellular transport, secretory
processes, and many other cellular pathways.
Kinases mediate the transfer of a phosphate moiety from a high energy molecule (such
as ATP) to their substrate molecule, as seen in the figure below. Kinases are needed to
stabilize this reaction because the phosphoanhydride bond contains a high level of energy. Kinases properly orient their substrate and the phosphoryl group within their active sites, which increases the rate of the reaction. Additionally, they commonly use
positively charged amino acid residues, which electrostatically stabilize the transition
state by interacting with the negatively charged phosphate groups. Alternatively, some
kinases utilize bound metal cofactors in their active sites to coordinate the phosphate
groups.
Kinases are used extensively to transmit signals and regulate complex processes in
cells. Phosphorylation of molecules can enhance or inhibit their activity and modulate
their ability to interact with other molecules. The addition and removal of phosphoryl
groups provides the cell with a means of control because various kinases can respond
to different conditions or signals. Mutations in kinases that lead to a loss-of-function
or gain-of-function can cause cancer and disease in humans, including certain types of
leukemia and neuroblastomas, glioblastoma, spinocerebellar ataxia (type 14), forms of
agammaglobulinaemia, and many others.
https://en.wikipedia.org/wiki/Kinase
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Kinesin
Kinesins move along microtubule (MT) filaments, and are powered by the hydroly
adenosine triphosphate (ATP) (thus kinesins are ATPases). The active movement
kinesins supports several cellular functions including mitosis, meiosis and transp
cellular cargo, such as in axonal transport. Most kinesins walk towards the positiv
membrane components from the center of the cell towards the periphery. This for
Index
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Km
The Michaelis constant Km is the substrate concentration at which the reaction rate is
half of Vmax and is an inverse measure of the substrate's affinity for the enzymeas a
small Km indicates high affinity, meaning that the rate will approach with lower than
those reactions with a larger. The value of Km is dependent on both the enzyme and the
substrate, as well as conditions such as temperature and pH.
For an enzymatic reaction obeying Michaelis-Menten kinetics,
This equation is called MichaelisMenten equation. Here, Vmax represents the maximum rate achieved by the system, at maximum saturation of the substrate concentration. The Michaelis constant KM is the substrate concentration at which the reaction
rate is half of . Biochemical reactions involving a single substrate are often assumed to
follow MichaelisMenten kinetics, without regard to the model's underlying assumptions.
https://en.wikipedia.org/wiki/MichaelisMenten_kinetics
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Kozak Sequence
The Kozak consensus sequence, Kozak consensus or Kozak sequence, is a sequence
which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG. The Kozak consensus sequence plays a major role in the initiation of the translation process.
The sequence was named after the person who brought it to prominence, Marilyn Kozak.
This sequence on an mRNA molecule is recognized by the ribosome as the translational start site, from which a protein is coded by that mRNA molecule. The ribosome
requires this sequence, or a possible variation (see below) to initiate translation. The
Kozak sequence is not to be confused with the ribosomal binding site (RBS), that being
either the 5' cap of a messenger RNA or an Internal ribosome entry site (IRES).
In vivo, this site is often not matched exactly on different mRNAs and the amount of
protein synthesized from a given mRNA is dependent on the strength of the Kozak sequence. Some nucleotides in this sequence are more important than others. The AUG
is most important because it is the actual initiation codon encoding a methionine
amino acid at the N-terminus of the protein. (Rarely, CUG is used as an initiation codon, encoding a leucine instead of the typical methionine.) The A nucleotide of the
"AUG" is referred to as number 1. For a 'strong' consensus, the nucleotides at positions
+4 (i.e. G in the consensus) and -3 (i.e. either A or G in the consensus) relative to the
number 1 nucleotide must both match the consensus (there is no number 0 position).
An 'adequate' consensus has only 1 of these sites, while a 'weak' consensus has neither.
The cc at -1 and -2 are not as conserved, but contribute to the overall strength. There is
also evidence that a G in the -6 position is important in the initiation of translation.
There are examples in vivo of each of these types of Kozak consensus, and they probably evolved as yet another mechanism of gene regulation. Lmx1b is an example of a
gene with a weak Kozak consensus sequence. For initiation of translation from such a
site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon.
https://en.wikipedia.org/wiki/Kozak_consensus_sequence
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Kuru
The term "kuru" derives from the Fore word "kuria/guria" ("to shake"), a re
the body tremors that are a classic symptom of the disease. It is also known
Fore as the "laughing sickness" due to the pathologic bursts of laughter peo
display when afflicted with the disease. It is now widely accepted that kuru
mitted among members of the Fore tribe of Papua New Guinea via funerary
ism.
https://en.wikipedia.org/wiki/Kuru_(disease)
Index
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Kyte-Doolittle
A hydrophilicity plot is a quantitative analysis of the degree of hydrophobicity or hydrophilicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein.
The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. There is a number of methods to measure the degree of interaction of polar solvents such as water with specific amino acids. For instance, the Kyte-Doolittle scale indicates hydrophobic amino acids, whereas the HoppWoods scale measures hydrophilic residues.
https://en.wikipedia.org/wiki/Hydrophilicity_plot
L=T+W
Analysis of DNA topology uses three values:
L = linking number - the number of times one DNA strand wraps around the other
is an integer for a closed loop and constant for a closed topological domain.
T = twist - total number of turns in the double stranded DNA helix. This will norm
tend to approach the number of turns that a topologically open double stranded D
helix makes free in solution: number of bases/10.5, assuming there are no intercal
ing agents (e.g., ethidium bromide) or other elements modifying the stiffness of th
DNA.
W = writhe - number of turns of the double stranded DNA helix around the superh
cal axis
L = T + W and L = T + W
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
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L-dopa
L-DOPA (alt., L-3,4-dihydroxyphenylalanine) is a chemical that is made and used as
part of the normal biology of humans, some animals and plants. Some animals and humans make it via biosynthesis from the amino acid L-tyrosine. L-DOPA is the precursor to the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline) collectively known as catecholamines. Furthermore, L-DOPA itself
mediates neurotrophic factor release by the brain and CNS. L-DOPA can be manufactured and in its pure form is sold as a psychoactive drug with the INN levodopa; trade
names include Sinemet, Pharmacopa, Atamet, Stalevo, Madopar, and Prolopa. As a
drug, it is used in the clinical treatment of Parkinson's disease and dopamineresponsive dystonia.
https://en.wikipedia.org/wiki/L-DOPA
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L-glucose
L-Glucose is an organic compound with formula C6H12O6, specifically one of the aldohexose monosaccharides. As the L-isomer of glucose, it is the enantiomer of the more
common D-glucose.
L-Glucose does not occur naturally in higher living organisms, but can be synthesized
https://en.wikipedia.org/wiki/L-Glucose
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Lac operon
The lac operon (lactose operon) is an operon required for the transport and metabolism of lactose in Escherichia coli and many other enteric bacteria. Although glucose is
the preferred carbon source for most bacteria, the lac operon allows for the effective digestion of lactose when glucose is not available.
Gene regulation of the lac operon was the first genetic regulatory mechanism to be understood clearly, so it has become a foremost example of prokaryotic gene regulation.
It is often discussed in introductory molecular and cellular biology classes at universities for this reason.
The lac operon consists of three structural genes, and a promoter, a terminator, regulator, and an operator. The three structural genes are: lacZ, lacY, and lacA.
lacZ encodes -galactosidase (LacZ), an intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose.
lacY encodes lactose permease (LacY), a transmembrane symporter that pumps galactosides into the cell using a proton gradient in the same direction.
lacA encodes galactoside O-acetyltransferase (LacA), an enzyme that transfers an acetyl group from acetyl-CoA to -galactosides.
Only lacZ and lacY appear to be necessary for lactose catabolism.
Specific control of the lac genes depends on the availability of the substrate lactose to
the bacterium. The proteins are not produced by the bacterium when lactose is unavailable as a carbon source. The lac genes are organized into an operon. That is, they are
oriented in the same direction immediately adjacent on the chromosome and are cotranscribed into a single polycistronic mRNA molecule. Transcription of all genes
starts with the binding of the enzyme RNA polymerase (RNAP), a DNA-binding protein, which binds to a specific DNA binding site, the promoter, immediately upstream
of the genes. Binding of RNA polymerase to the promoter is aided by the cAMP-bound
catabolite activator protein (CAP, also known as the cAMP receptor protein). However,
the lacI gene (regulatory gene for lac operon) produces a protein that blocks RNAP
from binding to the promoter of the operon. This protein can only be removed when
allolactose binds to it, and inactivates it. The protein that is formed by the lacI gene is
known as the lac repressor. The type of regulation that the lac operon undergoes is referred to as negative inducible, meaning that the gene is turned off by the regulatory
factor (lac repressor) unless some molecule (lactose) is added. Because of the presence
of the lac repressor protein, genetic engineers who replace the lacZ gene with another
gene will have to grow the experimental bacteria on agar with lactose available on it. If
they do not, the gene they are trying to express will not be expressed as the repressor
protein is still blocking RNAP from binding to the promoter and transcribing the gene.
Once the repressor is removed, RNAP then proceeds to transcribe all three genes (lacZYA) into mRNA. Each of the three genes on the mRNA strand has its own ShineDalgarno sequence, so the genes are independently translated.The DNA sequence of
the E. coli lac operon, the lacZYA mRNA, and the lacI genes are available from GenBank.
The first control mechanism is the regulatory response to lactose, which uses an intracellular regulatory protein called the lactose repressor to hinder production of galactosidase in the absence of lactose. The lacI gene coding for the repressor lies
nearby the lac operon and is always expressed (constitutive). If lactose is missing from
the growth medium, the repressor binds very tightly to a short DNA sequence just
downstream of the promoter near the beginning of lacZ called the lac operator. The repressor binding to the operator interferes with binding of RNAP to the promoter, and
therefore mRNA encoding LacZ and LacY is only made at very low levels. When cells
are grown in the presence of lactose, however, a lactose metabolite called allolactose,
made from lactose by the product of the lacZ gene, binds to the repressor, causing an
allosteric shift. Thus altered, the repressor is unable to bind to the operator, allowing
RNAP to transcribe the lac genes and thereby leading to higher levels of the encoded
proteins.
The second control mechanism is a response to glucose, which uses the catabolite activator protein (CAP) homodimer to greatly increase production of -galactosidase in
the absence of glucose. Cyclic adenosine monophosphate (cAMP) is a signal molecule
whose prevalence is inversely proportional to that of glucose. It binds to the CAP,
which in turn allows the CAP to bind to the CAP binding site (a 16 bp DNA sequence
upstream of the promoter on the left in the diagram below, about 60 bp upstream of
the transcription start site), which assists the RNAP in binding to the DNA. In the absence of glucose, the cAMP concentration is high and binding of CAP-cAMP to the
DNA significantly increases the production of -galactosidase, enabling the cell to hydrolyze lactose and release galactose and glucose.
https://en.wikipedia.org/wiki/Lac_operon
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Lac Repressor
The lac repressor is a DNA-binding protein which inhibits the expression of genes cod
ing for proteins involved in the metabolism of lactose in bacteria. These genes are repressed when lactose is not available to the cell, ensuring that the bacterium only in-
vests energy in the production of machinery necessary for uptake and utilization of la
tose when lactose is present. When lactose becomes available, it is converted into allo
lactose, which inhibits the lac repressor's DNA binding ability. Loss of DNA binding b
the lac repressor is required for transcriptional activation of the operon.
https://en.wikipedia.org/wiki/Lac_repressor
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Lac-Z
LacZ is a part of the lac operon, which is an operon required for the transport a
tabolism of lactose in Escherichia coli and many other enteric bacteria.
glucose and galactose. It will also cleave an artificial substrate known as X-Ga
one product of that reaction produces a blue color. X-Gal is therefore a useful
strate for easily measuring the amount of -galactosidase in a sample.
https://en.wikipedia.org/wiki/Lac_operon
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Techniques
Techniques
Techniques
Techniques
Lactase
digestion of whole milk. It breaks down lactose, a sugar which gives milk it
Lactate
During power exercises such as sprinting, when the rate of demand for energy is high,
glucose is broken down and oxidized to pyruvate, and lactate is then produced from
the pyruvate faster than the body can process it, causing lactate concentrations to rise.
The production of lactate is beneficial because it regenerates NAD+ (pyruvate is reduced to lactate while NADH is oxidized to NAD+), which is used up in oxidation of
glyceraldehyde 3-phosphate during production of pyruvate from glucose, and this ensures that energy production is maintained and exercise can continue. (During intense
exercise, the respiratory chain cannot keep up with the amount of hydrogen atoms that
join to form NADH, and cannot regenerate NAD+ quickly enough.) The resulting lactate can be used in these ways:
Oxidation back to pyruvate by well-oxygenated muscle cells, heart cells, and brain
cells
Pyruvate is then directly used to fuel the citric acid cycle
Conversion to glucose via gluconeogenesis in the liver and release back into circulation via the Cori cycle
If blood glucose concentrations are high, the glucose can be used to build up the liver's
glycogen stores.
https://en.wikipedia.org/wiki/Lactic_acid
Index
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G-G
G-G
G-G
Chapter 4 - Catalysis: Basic Principles
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Lactate Dehydrogenase
NADH + Pyruvate
Lactate + NAD+
https://en.wikipedia.org/wiki/Lactate_dehydrogenase
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Lactose
Lactose is a disaccharide sugar derived from galactose and glucose that is found in
milk. Lactose makes up around 28% of milk (by weight), although the amount varies
among species and individuals, and milk with a reduced amount of lactose also exists.
It is extracted from sweet or sour whey. The name comes from lac (gen. lactis), the
Latin word for milk, plus the -ose ending used to name sugars. It has a formula of
C12H22O11, making it an isomer of sucrose.
https://en.wikipedia.org/wiki/Lactose
Index
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Lactose Permease
Lactose permease is the lacY gene of the lac operon. In the transport performed
tose permease, sugar lies in a pocket in the center of the protein which is access
from the periplasm. On binding, a large conformational change takes place whi
makes the sugar binding site accessible from the cytoplasm.
Mechanism: hydrogen from the outside of the cell binds to a carboxyl group on
can bind lactose from outside the cell. The enzyme then everts and lactose is tra
ported inward.
https://en.wikipedia.org/wiki/Lactose_permease
Index
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Lagging Strand
The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading
strand.
The lagging strand is synthesized in short, separated segments. On the lagging strand
template, a primase "reads" the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the
fragments of DNA are joined together by DNA ligase.
DNA polymerase III (in prokaryotes) or Pol (in eukaryotes) is responsible for extension of the primers added during replication of the lagging strand. Primer removal is
performed by DNA polymerase I (in prokaryotes) and Pol (in eukaryotes). Eukaryotic
primase is intrinsic to Pol . In eukaryotes, pol helps with repair during DNA replication.
The lagging strand in the figure that follows is being synthesized from the top strand.
https://en.wikipedia.org/wiki/DNA_replication#Replication_fork
Laminin
They are a major component of the basal lamina (one of the layers of the basement
membrane), a protein network foundation for most cells and organs. The laminins
an important and biologically active part of the basal lamina, influencing cell differ
tiation, migration, and adhesion.
The laminin family of glycoproteins are an integral part of the structural scaffoldin
almost every tissue of an organism. They are secreted and incorporated into cell-
associated extracellular matrices. Laminin is vital for the maintenance and surviva
tissues. Defective laminins can cause muscles to form improperly, leading to a form
Index
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Lamins
interior of the nuclear envelope. They are involved in the disassembling and
Index
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Lanosterol
fungi steroids are derived. By contrast plant steroids are produced via cycloart
Preliminary studies in dogs and rabbits have shown that lanosterol can preven
even reverse cataract formation.
https://en.wikipedia.org/wiki/Lanosterol
Large Subunit
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S)
subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides)
bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.
The 50S subunit is primarily composed of proteins but also contains single-stranded
RNA known as ribosomal RNA (rRNA). rRNA forms secondary and tertiary structures
to maintain the structure and carry out the catalytic functions of the ribosome. 50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction),
prevents premature polypeptide hydrolysis, provides a binding site for the G-protein
factors (assists initiation, elongation, and termination), and helps protein folding after
synthesis.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S)
subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The
large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins.
Index
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Lateral Diffusion
Lateral diffusion describes the movement of lipids in the lipid bilayer of membr
tails, however the structure is quite fluid and not fixed rigidly in place. Under ph
logical conditions phospholipid molecules in the cell membrane are in the liquid
talline state. It means the lipid molecules are free to diffuse and exhibit rapid la
fusion along the layer in which they are present. However, the exchange of phos
very slow process. Lipid rafts and caveolae are examples of cholesterol-enriched
domains in the cell membrane. Also, a fraction of the lipid in direct contact with
gral membrane proteins, which is tightly bound to the protein surface is called a
lipid shell. It behaves as a part of protein complex.
https://en.wikipedia.org/wiki/Cell_membrane#Lipids
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LDL
Low-density lipoprotein (LDL) is one of the five major groups of lipoprotein. These
groups, from least dense to most dense, are chylomicrons, very low-density lipoprotein
(VLDL), intermediate-density lipoprotein (IDL), low-density lipoprotein and highdensity lipoprotein (HDL).
LDL particles pose a risk for cardiovascular disease when they invade the endothelium
and become oxidized, since the oxidized forms are more easily retained by the proteoglycans. A complex set of biochemical reactions regulates the oxidation of LDL particles, chiefly stimulated by presence of necrotic cell debris and free radicals in the endothelium. Increasing concentrations of LDL particles are strongly associated with increasing rates of accumulation of atherosclerosis within the walls of arteries over time,
eventually resulting in sudden plaque ruptures and triggering clots within the artery
opening, or a narrowing or closing of the opening, i.e. cardiovascular disease, stroke,
and other vascular disease complications.
https://en.wikipedia.org/wiki/Low-density_lipoprotein
Index
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LDL Receptor
(after removal of 21-amino acid signal peptide) that mediates the endocytosis o
which is embedded in the outer phospholipid layer of LDL particles. The recept
recognizes the apoE protein found in chylomicron remnants and VLDL remnan
(IDL). In humans, the LDL receptor protein is encoded by the LDLR gene. It be
to the Low density lipoprotein receptor gene family.
Index
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LDLs
Low-density lipoprotein (LDL) is one of the five major groups of lipoprotein. These
groups, from least dense to most dense, are chylomicrons, very low-density lipoprotein
(VLDL), intermediate-density lipoprotein (IDL), low-density lipoprotein and highdensity lipoprotein (HDL).
LDL particles pose a risk for cardiovascular disease when they invade the endothelium
and become oxidized, since the oxidized forms are more easily retained by the proteoglycans. A complex set of biochemical reactions regulates the oxidation of LDL particles, chiefly stimulated by presence of necrotic cell debris and free radicals in the endothelium. Increasing concentrations of LDL particles are strongly associated with increasing rates of accumulation of atherosclerosis within the walls of arteries over time,
eventually resulting in sudden plaque ruptures and triggering clots within the artery
opening, or a narrowing or closing of the opening, i.e. cardiovascular disease, stroke,
and other vascular disease complications.
https://en.wikipedia.org/wiki/Low-density_lipoprotein
Index
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Le Chateliers Principle
equilibrium. The principle is named after Henry Louis Le Chtelier and som
equilibrium is disturbed the system will adjust itself in such a way that the e
change will be nullified.
https://en.wikipedia.org/wiki/Le_Chatelier%27s_principle
Index
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Leader Sequence
The 5' untranslated region (5 UTR) (also known as a Leader Sequence or Leader RNA)
is the region of an mRNA that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5 UTR or
a portion of it is sometimes translated into a protein product. This product can then
regulate the translation of the main coding sequence of the mRNA. In many other organisms, however, the 5 UTR is completely untranslated, instead forming complex secondary structure to regulate translation. The 5 UTR has been found to interact with
proteins relating to metabolism and proteins translate sequences within the 5 UTR. In
addition, this region has been involved in transcription regulation, such as the sexlethal gene in Drosophila. Regulatory elements within 5' UTRs have also been linked to
mRNA export.
The 5 UTR begins at the transcription start site and ends one nucleotide (nt) before
the initiation sequence (usually AUG) of the coding region. In prokaryotes, the length
of the 5 UTR tends to be 3-10 nucleotides long, while in eukaryotes it tends to be anywhere from 100 to several thousand nucleotides long. For example, the ste11 transcript
in Schizosaccharomyces pombe has a 2273 nucleotide 5 UTR while the lac operon in
Escherichia coli only has 7 nucleotides in its 5 UTR. The differing sizes are likely due
to the complexity of the eukaryotic regulation which the 5 UTR holds, as well as the
larger preinitiation complex which must form to begin translation.
The elements of a eukaryotic and prokaryotic 5 UTR differ greatly. The prokaryotic 5
UTR contains a ribosome binding site (RBS), also known as the Shine Dalgarno sequence (AGGAGGU), which is usually 3-10 base pairs upstream from the initiation codon. In contrast, the eukaryotic 5 UTR contains the Kozak consensus sequence (ACCAUGG), which contains the initiation codon. The eukaryotic 5 UTR also contains
cis-acting regulatory elements called upstream open reading frames (uORFs) and upstream AUGs and termination codons (uAUGs), which have a great impact on the regulation of translation (see below). Unlike prokaryotes, 5' UTRs can harbor introns in
eukaryotes. In humans, ~35% of all genes harbor introns within the 5' UTR.
https://en.wikipedia.org/wiki/Five_prime_untranslated_region
Leading Strand
The leading strand is the strand of nascent DNA which is being synthesized in the
same direction as the growing replication fork. A polymerase "reads" the leading
strand template and adds complementary nucleotides to the nascent leading strand on
a continuous basis.
The polymerase involved in leading strand synthesis is DNA polymerase III (DNA Pol
III) in prokaryotes. In eukaryotes, leading strand synthesis is thought to be conducted
by Pol , however this view has been recently challenged, suggesting a role for Pol .
In the figure below, the leading strand is being synthesized from the bottom strand.
https://en.wikipedia.org/wiki/DNA_replication#Replication_fork
Index
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Leaflet
with the hydrophobic tails pointing toward the center of the sheet. This arra
results in two leaflets that are each a single molecular layer.
https://en.wikipedia.org/wiki/Lipid_bilayer
Index
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Lecithin
ing the reaction to become unidirectional since the particles are removed fr
Lectins
Lectins are carbohydrate-binding proteins, macromolecules that are highly specific for
sugar moieties. Lectins should neither be confused with glycoproteins (proteins containing sugar chains or residues), lecithins (fatty substances in animals and plants),
nor leptin (the regulator of appetite and hunger, metabolism, and behavior).
Long before a deeper understanding of their numerous biological functions, the plant
lectins, also known as phytohemagglutinins, were noted for their particular high specificity for foreign glycoconjugates (e.g. those of fungi, invertebrates, and animals). and
used in biomedicine for blood cell testing and in biochemistry for fractionation.
Lectins perform recognition on the cellular and molecular level and play numerous
roles in biological recognition phenomena involving cells, carbohydrates, and proteins.
Lectins also mediate attachment and binding of bacteria and viruses to their intended
targets. For example, it is hypothesized that some hepatitis C viral glycoproteins attach
to C-type lectins on the host cell surface (liver cells) for infection.
Lectins may be disabled by specific mono- and oligosaccharides, which bind to ingested lectins from grains, legume, nightshade plants and dairy. Binding can prevent
their attachment to the carbohydrates within the cell membrane. Some lectins may be
powerful toxins as for instance ricin, and others have been incorporated into genetically engineered crops to transfer traits, such as resistance to pests and resistance to
herbicides.
https://en.wikipedia.org/wiki/Lectin
Left-handed
Helices can be either right-handed or left-handed. With the line of sight alo
lix's axis, if a clockwise screwing motion moves the helix away from the obs
handed helix cannot be turned to look like a left-handed one unless it is view
mirror, and vice versa.
https://en.wikipedia.org/wiki/Helix
Index
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Leptin
Leptin , the "satiety hormone,"[a] is a hormone made by adipose cells that helps to
hormone ghrelin, the "hunger hormone". Both hormones act on receptors in the ar
Index
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Leucine
Leucine (abbreviated as Leu or L; encoded by the six codons UUA, UUG, CUU, CUC,
CUA, and CUG) is an -amino acid used in the biosynthesis of proteins. It contains an
-amino group (which is in the protonated NH3+ form under biological conditions),
an -carboxylic acid group (which is in the deprotonated COO form under biological
conditions), and an isobutyl side chain, classifying it as a nonpolar (at physiological
pH) amino acid. It is essential in humansmeaning the body cannot synthesize it and
thus must obtain it from the diet.
https://en.wikipedia.org/wiki/Leucine
Index
Find Term
G-G
G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure & Function: Amino Acids
Chapter 2 - Structure and Function: Proteins
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Leucine Aminotransferase
Leucine transaminase (EC 2.6.1.6) is an enzyme that catalyzes the biochemical synthesis reaction for making leucine
-ketoisocaproate + Glutamate
Leucine + -ketoglutarate
cine biosynthesis, and pantothenate and coa biosynthesis. It employs one cofactor, pyri
doxal phosphate.
https://en.wikipedia.org/wiki/Leucine_transaminase
Index
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Leucine Zipper
A leucine zipper, aka leucine scissors, is a common three-dimensional structural motif
in proteins. They were first described by Landschulz and collaborators in 1988 when
they found that an enhancer binding protein had a very characteristic 30-amino acid
segment and the display of these amino acid sequences on an idealized helix revealed
a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The polypeptide segments containing these periodic arrays of
leucine residues were proposed to exist in an -helical conformation and the leucine
side chains from one helix interdigitate with those from the helix of a second
polypeptide, facilitating dimerization.
Leucine zippers are a dimerization domain of the bZIP (Basic-region leucine zipper)
class of eukaryotic transcription factors. The bZIP domain is 60 to 80 amino acids in
length with a highly conserved DNA binding basic region and a more diversified leucine zipper dimerization region. The leucine zipper is a common three-dimensional
structural motif in proteins and it has that name because leucines occur every seven
amino acids in the dimerization domain. The localization of the leucines are critical for
the DNA binding to the proteins. Leucine zippers are present in both eukaryotic and
prokaryotic regulatory proteins, but are mainly a feature of eukaryotes. They can also
be annotated simply as ZIPs, and ZIP-like motifs have been found in proteins other
than transcription factors and are thought to be one of the general protein modules for
protein-protein interactions.
https://en.wikipedia.org/wiki/Leucine_zipper
Leucocytes
White blood cells (WBCs), also called leukocytes or leucocytes, are the cells
mune system that are involved in protecting the body against both infectiou
and foreign invaders. All white blood cells are produced and derived from a
tent cell in the bone marrow known as a hematopoietic stem cell. Leukocyte
throughout the body, including the blood and lymphatic system.
https://en.wikipedia.org/wiki/White_blood_cell
Index
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Leukocytes
White blood cells (WBCs), also called leukocytes or leucocytes, are the cells
mune system that are involved in protecting the body against both infectiou
and foreign invaders. All white blood cells are produced and derived from a
tent cell in the bone marrow known as a hematopoietic stem cell. Leukocyte
throughout the body, including the blood and lymphatic system.
https://en.wikipedia.org/wiki/White_blood_cell
Leukotrienes
Leukotrienes are a family of eicosanoid inflammatory mediators produced in leukocytes by the oxidation of the essential fatty acids arachidonic acid (AA) and eicosapentanoic acid (EPA) by the enzyme arachidonate 5-lipoxygenase. As their name implies,
leukotrienes were first discovered in leukocytes, but have since been found in other immune cells.
Leukotrienes use lipid signaling to convey information to either the cell producing
them (autocrine signaling) or neighboring cells (paracrine signaling) in order to regulate immune responses. Leukotriene production is usually accompanied by the production of histamine and prostaglandins, which also act as inflammatory mediators. Leukotriene A4 is depicted below.
https://en.wikipedia.org/wiki/Leukotriene
Index
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Leventhals Paradox
require a time longer than the age of the universe to arrive at its correct nat
or even microsecond time scale. The solution to this paradox has been estab
computational approaches to protein structure prediction.
https://en.wikipedia.org/wiki/Levinthal%27s_paradox
Index
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LexA
Repressor LexA or LexA is a transcriptional repressor (EC 3.4.21.88) that represses
SOS response genes coding primarily for error-prone DNA polymerases, DNA repair
enzymes and cell division inhibitors. LexA forms de facto a two-component regulatory
system with RecA, which senses DNA damage at stalled replication forks, forming monofilaments and acquiring an active conformation capable of binding to LexA and causing LexA to cleave itself, in a process called autoproteolysis.
DNA damage can be inflicted by the action of antibiotics, bacteriophages and UV light.
Of potential clinical interest is the induction of the SOS response by antibiotics, such as
ciprofloxacin. Bacteria require topoisomerases such as DNA gyrase or topoisomerase
IV for DNA replication. Antibiotics such as ciprofloxacin are able to prevent the action
of these molecules by attaching themselves to the gyrase - DNA complex, leading to replication fork stall and the induction of the SOS response. The expression of error-prone
polymerases under the SOS response increases the basal mutation rate of bacteria.
While mutations are often lethal to the cell, they can also enhance survival. In the specific case of topoisomerases, some bacteria have mutated one of their amino acids so
that the ciproflaxin can only create a weak bond to the topoisomerase. This is one of
the methods that bacteria use to become resistant to antibiotics. Ciprofloxacin treatment can therefore potentially lead to the generation of mutations that may render bacteria resistant to ciprofloxacin. In addition, ciprofloxacin has also been shown to induce via the SOS response dissemination of virulence factors and antibiotic resistance
determinants, as well as the activation of integron integrases, potentially increasing
the likelihood of acquisition and dissemination of antibiotic resistance by bacteria.
Impaired LexA proteolysis has been shown to interfere with ciprofloxacin resistance.
This offers potential for combination therapy that combines quinolones with strategies
aimed at interfering with the action of LexA, either directly or via RecA.
LexA contains a DNA binding domain. The winged HTH motif of LexA is a variant
form of the helix-turn-helix DNA binding motif. it is usually located at the N-terminus
of the protein.
Library
rial cells which contain the relevant nucleic acid fragments in plasmids or r
tors.
Index
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Ligand
Index
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https://en.wikipedia.org/wiki/Ligand-gated_ion_channel
Ligands
Index
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Light Cycle
In photosynthesis, the light-dependent reactions take place on the thylakoid membranes. There are four major protein complexes in the thylakoid membrane: Photosystem II (PSII), Cytochrome b6f complex, Photosystem I (PSI), and ATP synthase. These
four complexes work together to ultimately create the products ATP and NADPH.
https://en.wikipedia.org/wiki/Light-dependent_reactions
Lignin
Lignin is a class of complex organic polymers that form important structural materials
in the support tissues of vascular plants and some algae. Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity and do not rot easily. Chemically, lignins are cross-linked phenolic polymers. A
small segment of one is depicted below.
https://en.wikipedia.org/wiki/Lignin
Index
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Limonene
https://en.wikipedia.org/wiki/Limonene
Index
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Linalool
Linalool is a naturally occurring terpene alcohol chemical found in many flowers and
spice plants with many commercial applications, the majority of which are based on its
pleasant scent (floral, with a touch of spiciness). It has other names such as -linalool,
linalyl alcohol, linaloyl oxide, p-linalool, allo-ocimenol, and 3,7-dimethyl-1,6-octadien3-ol.
Over 200 species of plants produce linalool, mainly from the families Lamiaceae
(mints, scented herbs), Lauraceae (laurels, cinnamon, rosewood), and Rutaceae (citrus
fruits), but also birch trees and other plants, from tropical to boreal climate zones. It
has also been found in some fungi and cannabis.
Linalool has a stereoisomeric center at C3 and therefore there are two stereoisomers:
(R)-()-linalool is also known as licareol and (S)-(+)-linalool is also known as coriandrol. In the figure below, the S form is on the left.
Both enantiomeric forms are found in nature: (S)-linalool is found, for example, as a
major constituent of the essential oils of coriander (Coriandrum sativum L. family
Apiaceae) seed, palmarosa [Cymbopogon martinii var martinii (Roxb.) Wats., family
Poaceae], and sweet orange (Citrus sinensis Osbeck, family Rutaceae) flowers. (R)linalool is present in lavender (Lavandula officinalis Chaix, family Lamiaceae), bay
laurel (Laurus nobilis, family Lauraceae), and sweet basil (Ocimum basilicum, family
Lamiaceae), among others.
Each enantiomer evokes different neural responses in humans, and therefore are classified as possessing distinct scents. (S)-(+)-Linalool is perceived as sweet, floral,
petitgrain-like (odor threshold 7.4 ppb) and the (R)-form as more woody and lavenderlike (odor threshold 0.8 ppb).
https://en.wikipedia.org/wiki/Linalool
LINEs
ment, are the most abundant mobile elements in the human genome. Some
Index
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Lineweaver-Burk
The LineweaverBurk plot (or double reciprocal plot) is a graphical representation of
the LineweaverBurk equation of enzyme kinetics, described by Hans Lineweaver and
Dean Burk in 1934.
The LineweaverBurk plot was widely used to determine important terms in enzyme
kinetics, such as Km and Vmax, before the wide availability of powerful computers and
non-linear regression software. The y-intercept of such a graph is equivalent to the inverse of Vmax. The x-intercept of the graph represents 1/Km. It also gives a quick, visual impression of the different forms of enzyme inhibition.
https://en.wikipedia.org/wiki/LineweaverBurk_plot
Linking Number
Analysis of DNA topology uses: L = linking number - the number of times one DNA
strand wraps around the other. It is an integer for a closed loop and constant for a
closed topological domain. The two curves in the figure below have a linking number
of four.
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
Index
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Linoleate
LA is a polyunsaturated -6 fatty acid used in the biosynthesis of arachidonic acid
(AA) and thus some prostaglandins, leukotrienes (LTA, LTB, LTC), and thromboxane
(TXA). It is found in the lipids of cell membranes. It is abundant in many nuts, fatty
seeds (flax seeds, hemp seeds, poppy seeds, sesame seeds, etc.) and their derived vegetable oils, comprising over half (by weight) of poppy seed, safflower, sunflower, corn,
and soybean oils.
LA is converted by various lipoxygenases, cyclooxygenases, certain cytochrome P450
enzymes (the CYP monooxygenases), and non-enzymatic autooxidation mechanisms to
mono-hydroxyl products viz., 13-Hydroxyoctadecadienoic acid and 9Hydroxyoctadecadienoic acid. These two hydroxy metabolites are enzymatically oxidized to their keto metabolites, 13-oxo-octadecadienoic acid and 9-oxo-octadecdienoic
acid. Certain cytochrome P450 enzymes, the CYP epoxygenases, metabolize LA to epoxide products viz., its 12,13-epoxide, Vernolic acid and its 9,10-epoxide, Coronaric acid.
All of these LA products have bioactivity and are implicated in human physiology and
pathology as indicated in the cited linkages.
Linoleic acid is an essential fatty acid that must be consumed for proper health. A diet
only deficient in linoleate (the salt form of the acid) causes mild skin scaling, hair loss,
and poor wound healing in rats.
Along with oleic acid, linoleic acid is released by cockroaches upon death which has the
effect of preventing other roaches from entering the area. This is similar to the mechanism found in ants and bees, which release oleic acid upon death.
https://en.wikipedia.org/wiki/Linoleic_acid
Linoleic acid
LA is a polyunsaturated -6 fatty acid used in the biosynthesis of arachidonic acid
(AA) and thus some prostaglandins, leukotrienes (LTA, LTB, LTC), and thromboxane
(TXA). It is found in the lipids of cell membranes. It is abundant in many nuts, fatty
seeds (flax seeds, hemp seeds, poppy seeds, sesame seeds, etc.) and their derived vegetable oils, comprising over half (by weight) of poppy seed, safflower, sunflower, corn,
and soybean oils.
LA is converted by various lipoxygenases, cyclooxygenases, certain cytochrome P450
enzymes (the CYP monooxygenases), and non-enzymatic autooxidation mechanisms to
mono-hydroxyl products viz., 13-Hydroxyoctadecadienoic acid and 9Hydroxyoctadecadienoic acid. These two hydroxy metabolites are enzymatically oxidized to their keto metabolites, 13-oxo-octadecadienoic acid and 9-oxo-octadecdienoic
acid. Certain cytochrome P450 enzymes, the CYP epoxygenases, metabolize LA to epoxide products viz., its 12,13-epoxide, vernolic acid and its 9,10-epoxide, coronaric acid.
All of these LA products have bioactivity and are implicated in human physiology and
pathology as indicated in the cited linkages.
Linoleic acid is an essential fatty acid that must be consumed for proper health. A diet
only deficient in linoleate (the salt form of the acid) causes mild skin scaling, hair loss,
and poor wound healing in rats.
Along with oleic acid, linoleic acid is released by cockroaches upon death which has the
effect of preventing other roaches from entering the area. This is similar to the mechanism found in ants and bees, which release oleic acid upon death.
https://en.wikipedia.org/wiki/Linoleic_acid
Index
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Linolenate
Linolenate (in the form of esters of linolenic acid) is often found in vegetable oils.
ditionally, such fatty acylates are reported as the fatty acids:
-Linolenic acid, an omega-3 (n-3) fatty acid
-Linolenic acid, an omega-6 (n-6) fatty acid
https://en.wikipedia.org/wiki/Linolenic_acid
Index
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Linus Pauling
Linus Carl Pauling (February 28, 1901 August 19, 1994) was an American chemist,
biochemist, peace activist, author, and educator. Pauling was one of the founders of
the fields of quantum chemistry and molecular biology.
Part of Pauling's work on the nature of the chemical bond led to his introduction of the
concept of orbital hybridization. Another area which he explored was the relationship
between ionic bonding, where electrons are transferred between atoms, and covalent
bonding, where electrons are shared between atoms on an equal basis. Pauling showed
that these were merely extremes, between which most actual cases of bonding fall. It
was here especially that Pauling's electronegativity concept was particularly useful; the
electronegativity difference between a pair of atoms will be the surest predictor of the
degree of ionicity of the bond.
https://en.wikipedia.org/wiki/Linus_Pauling
Lipase
ids (e.g. triglycerides, fats, oils) in most, if not all, living organisms. Genes e
pases are even present in certain viruses.
https://en.wikipedia.org/wiki/Lipase
Index
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Lipid
Lipids are a group of naturally occurring molecules that include fats, waxes, sterols,
fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides,
triglycerides, phospholipids, and others. The main biological functions of lipids include
storing energy, signaling, and acting as structural components of cell membranes. Lipids may be broadly defined as hydrophobic or amphiphilic small molecules. The amphiphilic nature of some lipids allows them to form structures such as vesicles,
multilamellar/unilamellar liposomes, or membranes in an aqueous environment.
Common lipids are shown below.
https://en.wikipedia.org/wiki/Lipid
Index
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Lipid Bilayer
The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These
membranes are flat sheets that form a continuous barrier around all cells. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are
needed and prevents them from diffusing into areas where they should not be.
https://en.wikipedia.org/wiki/Lipid_bilayer
Index
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Lipid Metabolism
Lipid metabolism is the synthesis and degradation of lipids in cells.
The types of lipids involved include:
Bile salts
Cholesterols
Eicosanoids
Glycolipids
Ketone bodies
Phospholipids
Sphingolipids
Triacylglycerols (fats)
https://en.wikipedia.org/wiki/Lipid_metabolism
Index
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Lipid Peroxidation
Lipid peroxidation is the oxidative degradation of lipids. It is the process in which free
radicals "steal" electrons from the lipids in cell membranes, resulting in cell damage.
This process proceeds by a free radical chain reaction mechanism. It most often affects
polyunsaturated fatty acids, because they contain multiple double bonds in between
which lie methylene bridges (-CH2-) that possess especially reactive hydrogen atoms.
As with any radical reaction, the reaction consists of three major steps: initiation,
propagation, and termination. The chemical products of this oxidation are known as
lipid peroxides or lipid oxidation products (LOPs).
https://en.wikipedia.org/wiki/Lipid_peroxidation
Lipid Rafts
The plasma membranes of cells contain combinations of glycosphingolipids and protein receptors organized in glycolipoprotein microdomains termed lipid rafts.These
specialized membrane microdomains compartmentalize cellular processes by serving
as organizing centers for the assembly of signaling molecules, influencing membrane
fluidity and membrane protein trafficking, and regulating neurotransmission and receptor trafficking. Lipid rafts are more ordered and tightly packed than the surrounding bilayer, but float freely in the membrane bilayer.
The lipid raft in the figure below is under #2
https://en.wikipedia.org/wiki/Lipid_raft
Index
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Lipoamide
Lipoamide is a trivial name for 6,8-dithiooctanoic amide. It is 6,8-dithiooctanoic acid's
functional form where the carboxyl group is attached to protein (or any other amine)
by an amide linkage (containing -NH2). Sometimes lipoamide is used to refer to protein bound lipoic acid, but this can be misleading as this is technically incorrect.
Lipoyl-protein or lipoyl-domain are better terms to refer to protein bound lipoic acid.
Lipamide is shown below in oxidized and reduced forms. The lipoic acid portions are
shown in color.
https://en.wikipedia.org/wiki/Lipoamide
Index
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Lipocortin
creased expression of the gene coding for annexin-1 is one of the mechanisms by
glucocorticoids (such as cortisol) inhibit inflammation.
https://en.wikipedia.org/wiki/Annexin
Index
Find Term
Lipoic Acid
Lipoic acid (LA), also known as -lipoic acid and lipoic acid (ALA) and thioctic acid
is an organosulfur compound derived from octanoic acid. ALA is made in animals normally, and is essential for aerobic metabolism. It is also manufactured and is available
as a dietary supplement in some countries where it is marketed as an antioxidant, and
is available as a pharmaceutical drug in other countries.
The carbon atom at C6 is chiral and the molecule exists as two enantiomers (R)-(+)lipoic acid (RLA) and (S)-(-)-lipoic acid (SLA) and as a racemic mixture (R/S)-lipoic
acid (R/S-LA).
Most endogenously produced RLA is not "free" because octanoic acid, the precursor to
RLA, is bound to the enzyme complexes prior to enzymatic insertion of the sulfur atoms. As a cofactor, RLA is covalently attached by an amide bond to a terminal lysine
residue of the enzyme's lipoyl domains. One of the most studied roles of RLA is as a cofactor of the pyruvate dehydrogenase complex (PDC or PDHC), though it is a cofactor
in other enzymatic systems as well (described below).
Only the (R)-(+)-enantiomer (RLA) exists in nature and is essential for aerobic metabolism because RLA is an essential cofactor of many enzyme complexes.
https://en.wikipedia.org/wiki/Lipoic_acid
Lipopolysaccharide Layer
outer core and inner core joined by a covalent bond are found in the outer m
of Gram-negative bacteria, and elicit strong immune responses in animals.
uting greatly to the structural integrity of the bacteria, and protecting the me
from certain kinds of chemical attack. LPS also increases the negative charge
induces a strong response from normal animal immune systems. It has also b
https://en.wikipedia.org/wiki/Lipopolysaccharide#Biosynthesis_and_trans
Index
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Lipoprotein Complex
ids, bound to the proteins, which allow fats to move through the water inside a
side cells. The proteins serve to emulsify the lipid molecules. Many enzymes, tr
ers, structural proteins, antigens, adhesins, and toxins are lipoproteins. Examp
clude the plasma lipoprotein particles classified under high-density (HDL) and
density (LDL) lipoproteins, which enable fats to be carried in the blood stream
Index
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Lipoprotein Complexes
ids, bound to the proteins, which allow fats to move through the water insid
side cells. The proteins serve to emulsify the lipid molecules. Many enzyme
ers, structural proteins, antigens, adhesins, and toxins are lipoproteins. Exa
clude the plasma lipoprotein particles classified under high-density (HDL)
density (LDL) lipoproteins, which enable fats to be carried in the blood stre
Lipoprotein Lipase
Lipoprotein lipase (LPL) (EC 3.1.1.34) is a member of the lipase gene family, wh
and very low-density lipoproteins (VLDL), into three free fatty acids and one gly
cholesterol-rich lipoproteins, and free fatty acids. LPL requires ApoC-II as a cof
Index
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Liposomes
A liposome is a spherical vesicle having at least one lipid bilayer. The liposome can be
used as a vehicle for administration of nutrients and pharmaceutical drugs. Liposomes
can be prepared by disrupting biological membranes (such as by sonication).
https://en.wikipedia.org/wiki/Liposome
Lipoxins
Lipoxins are members of the family of bioactive products generated from arachidonic
acid (AA). They have a number of immunomodulatory and anti-inflammatory actions.
Lipoxins are short lived endogenously produced nonclassic eicosanoids whose appearance in inflammation signals the resolution of inflammation. They are abbreviated as
LX, an acronym for lipoxygenase (LO) interaction products. At present two lipoxins
have been identified - lipoxin A4 (LXA4) and lipoxin B4 (LXB4). LXB4 is shown at the
bottom.
Lipoxins are derived enzymatically from arachidonic acid, an -6 fatty acid. One important precursor to the lipoxins is 15-hydroxyicosatetraenoic acid (i.e. 15(S)-HETE) and
its 15-hydroperoxy precusor. Transcellular biosynthetic mechanisms play a key role in
their production. They are formed by platelets but they alone cannot synthesize them.
Platelets depend upon neutrophils for LTA4, which is converted to LXA4 and LXB4 by
the action of platelet 12-lipoxygenase. LTC4, LTD4, and LTE4 are also synthesized in
platelets from LTA4. An analogous class, the resolvins, are derived from EPA and
DHA, -3 fatty acids. Another analogous class, the epi-lipoxins, are formed by nonenzymatic peroxidation.
https://en.wikipedia.org/wiki/Lipoxin
Index
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Lnc RNAs
Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts
longer than 200 nucleotides. This somewhat arbitrary limit distinguishes long ncRNAs
from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs
(siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and
other short RNAs.
Many small RNAs, such as microRNAs or snoRNAs, exhibit strong conservation across
diverse species. In contrast, long ncRNAs (such as Air and Xist) lack strong conservation, suggesting non-functionality or the effects of different selection pressures. Unlike
mRNAs, which have to conserve the codon usage and prevent frameshift mutations in
a single long ORF, selection may conserve only short regions of long ncRNAs that are
constrained by structure or sequence-specific interactions. Therefore, we may see selection act only over small regions of the long ncRNA transcript. Thus, despite low conservation of long ncRNAs in general, it should be noted that many long ncRNAs still contain strongly conserved elements. For example, 19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions. Furthermore,
a representative set of human long ncRNAs exhibit small, yet significant, reductions in
substitution and insertion/deletion rates indicative of purifying selection that conserve
the integrity of the transcript at the levels of sequence, promoter and splicing.
Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate that long noncoding RNAs number in the
order of tens of thousands in mammals. However, despite accumulating evidence suggesting that the majority of these are likely to be functional, only a relatively small proportion has been demonstrated to be biologically relevant. As of January 2016, 294
LncRNAs have been functionally annotated in LncRNAdb (a database of literature described LncRNAs), with the majority of these (183 LncRNAs) being described in humans. A further large-scale sequencing study provides evidence that many transcripts
thought to be LncRNAs may, in fact, be translated into proteins
https://en.wikipedia.org/wiki/Long_non-coding_RNA
Index
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lncRNAs
Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts
longer than 200 nucleotides. This somewhat arbitrary limit distinguishes long ncRNAs
from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs
(siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and
other short RNAs.
Many small RNAs, such as microRNAs or snoRNAs, exhibit strong conservation across
diverse species. In contrast, long ncRNAs (such as Air and Xist) lack strong conservation, suggesting non-functionality or the effects of different selection pressures. Unlike
mRNAs, which have to conserve the codon usage and prevent frameshift mutations in
a single long ORF, selection may conserve only short regions of long ncRNAs that are
constrained by structure or sequence-specific interactions. Therefore, we may see selection act only over small regions of the long ncRNA transcript. Thus, despite low conservation of long ncRNAs in general, it should be noted that many long ncRNAs still contain strongly conserved elements. For example, 19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions. Furthermore,
a representative set of human long ncRNAs exhibit small, yet significant, reductions in
substitution and insertion/deletion rates indicative of purifying selection that conserve
the integrity of the transcript at the levels of sequence, promoter and splicing.
Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate that long noncoding RNAs number in the
order of tens of thousands in mammals. However, despite accumulating evidence suggesting that the majority of these are likely to be functional, only a relatively small proportion has been demonstrated to be biologically relevant. As of January 2016, 294
LncRNAs have been functionally annotated in LncRNAdb (a database of literature described LncRNAs), with the majority of these (183 LncRNAs) being described in humans. A further large-scale sequencing study provides evidence that many transcripts
thought to be LncRNAs may, in fact, be translated into proteins
https://en.wikipedia.org/wiki/Long_non-coding_RNA
Index
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Local Minima
are the largest and smallest value of the function, either within a given rang
Index
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both the enzyme and the substrate possess specific complementary geometr
that fit exactly into one another. This is often referred to as "the lock and ke
This early model explains enzyme specificity, but fails to explain the stabiliz
transition state that enzymes achieve.
https://en.wikipedia.org/wiki/Enzyme#.22Lock_and_key.22_model
groups, from least dense to most dense, are chylomicrons, very low-density lipo
LDL particles pose a risk for cardiovascular disease when they invade the endot
and become oxidized, since the oxidized forms are more easily retained by the p
glycans. A complex set of biochemical reactions regulates the oxidation of LDL
cles, chiefly stimulated by presence of necrotic cell debris and free radicals in th
eventually resulting in sudden plaque ruptures and triggering clots within the a
groups, from least dense to most dense, are chylomicrons, very low-density lipo
LDL particles pose a risk for cardiovascular disease when they invade the endot
and become oxidized, since the oxidized forms are more easily retained by the p
glycans. A complex set of biochemical reactions regulates the oxidation of LDL
cles, chiefly stimulated by presence of necrotic cell debris and free radicals in th
eventually resulting in sudden plaque ruptures and triggering clots within the a
Lubricin
cartilage and therefore plays an important role in joint lubrication and syno
stasis.
https://en.wikipedia.org/wiki/PRG4
Lumisterol
Lumisterol is a compound that is part of the vitamin D family of steroid compounds. It
is the (9,10) stereoisomer of ergosterol and was produced as a photochemical byproduct in the preparation of vitamin D1, which was a mixture of vitamin D2 and lumisterol. Vitamin D2 can be formed from lumisterol by an electrocyclic ring opening and
subsequent sigmatropic hydride shift.
https://en.wikipedia.org/wiki/Lumisterol
Luteinizing Hormone
acute rise of LH ("LH surge") triggers ovulation and development of the cor
teum. In males, where LH had also been called interstitial cellstimulating
Index
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Lyase
A lyase is an enzyme that catalyzes the breaking (an "elimination" reaction) of various
chemical bonds by means other than hydrolysis (a "substitution" reaction) and oxidation, often forming a new double bond or a new ring structure. The reverse reaction is
also possible (called a "Michael addition).
Isocitrate lyase is an example. It catalyzes the reaction below.
https://en.wikipedia.org/wiki/Lyase
Lycopene
Lycopene from the neo-Latin lycopersicum, the tomato species, is a bright red carotene
and carotenoid pigment and phytochemical found in tomatoes and other red fruits and
vegetables, such as red carrots, watermelons, gac, and papayas, although not in strawberries, or cherries. Although lycopene is chemically a carotene, it has no vitamin A activity.
In plants, algae, and other photosynthetic organisms, lycopene is an important intermediate in the biosynthesis of many carotenoids, including carotene, which is responsible for yellow, orange, or red pigmentation, photosynthesis, and photo-protection. Like
all carotenoids, lycopene is a polyunsaturated hydrocarbon, i.e. an unsubstituted alkene. Structurally, lycopene is a tetraterpene and assembled from eight isoprene units
that are composed entirely of carbon and hydrogen. It is insoluble in water. Lycopene's
eleven conjugated double bonds give its deep red color and its antioxidant activity. Owing to the strong color, lycopene is a useful food coloring (registered as E160d) and is
approved for usage in the USA, Australia and New Zealand (registered as 160d) and
the EU.
https://en.wikipedia.org/wiki/Lycopene
Index
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Lymph
Lymph is the fluid that circulates throughout the lymphatic system. The lym
formed when the interstitial fluid (the fluid which lies in the interstices of a
sels to lymph nodes before emptying ultimately into the right or the left sub
vein, where it mixes back with blood.
https://en.wikipedia.org/wiki/Lymph
Index
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Lymphocytes
Lymphotactin
gland and ovary. Cellular sources for XCL1 include activated thymic and pe
blood CD8+ T cells. This chemokine attracts T cells. In humans, XCL1 is clo
to another chemokine called XCL2, whose gene is found at the same locus o
Lysine
Lysine (abbreviated as Lys or K), encoded by the codons AAA and AAG) is an -amino
acid that is used in the biosynthesis of proteins. It contains an -amino group (which is
in the protonated NH3+ form under biological conditions), an -carboxylic acid
group (which is in the deprotonated COO form under biological conditions), and a
side chain lysyl ((CH2)4NH2), classifying it as a charged (at physiological pH), aliphatic
amino acid. It is essential in humans, meaning the body cannot synthesize it and thus
it must be obtained from the diet.
https://en.wikipedia.org/wiki/Lysine
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Lysosome
A lysosome (derived from the Greek words lysis, meaning "to loosen", and soma,
"body") is a membrane-bound cell organelle found in most animal cells (they are absent in red blood cells). Structurally and chemically, they are spherical vesicles containing hydrolytic enzymes capable of breaking down virtually all kinds of biomolecules,
including proteins, nucleic acids, carbohydrates, lipids, and cellular debris.
They are known to contain more than 50 different enzymes, which are all optimally active at an acidic environment of about pH 4.5 (about the pH of black coffee). Thus lysosomes act as the waste disposal system of the cell by digesting unwanted materials in
the cytoplasm, both from outside of the cell and obsolete components inside the cell.
For this function they are popularly referred to as "suicide bags" or "suicide sacs" of the
cell. Furthermore, lysosomes are responsible for cellular homeostasis for their involvements in secretion, plasma membrane repair, cell signaling and energy metabolism,
which are related to health and diseases.
The lysosome is depicted as structure #12 below
https://en.wikipedia.org/wiki/Lysosome
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Lysosomes
A lysosome (derived from the Greek words lysis, meaning "to loosen", and soma,
"body") is a membrane-bound cell organelle found in most animal cells (they are absent in red blood cells). Structurally and chemically, they are spherical vesicles containing hydrolytic enzymes capable of breaking down virtually all kinds of biomolecules,
including proteins, nucleic acids, carbohydrates, lipids, and cellular debris.
They are known to contain more than 50 different enzymes, which are all optimally active at an acidic environment of about pH 4.5 (about the pH of black coffee). Thus lysosomes act as the waste disposal system of the cell by digesting unwanted materials in
the cytoplasm, both from outside of the cell and obsolete components inside the cell.
For this function they are popularly referred to as "suicide bags" or "suicide sacs" of the
cell. Furthermore, lysosomes are responsible for cellular homeostasis for their involvements in secretion, plasma membrane repair, cell signaling and energy metabolism,
which are related to health and diseases.
The lysosome is depicted as structure #12 below
https://en.wikipedia.org/wiki/Lysosome
Index
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Lysozyme
coside hydrolases. These are enzymes (EC 3.2.1.17) that damage bacterial ce
can be found in egg white. C-type lysozymes are closely related to -lactalbu
quence and structure, making them part of the same family. In humans, the
enzyme is encoded by the LYZ gene.
https://en.wikipedia.org/wiki/Lysozyme
Index
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Lysyl-hydroxylase
zyme that is localized to the cisternae (lumen) of the rough endoplasmic ret
It requires iron and vitamin C as cofactors.
https://en.wikipedia.org/wiki/Lysyl_hydroxylase
Macrophages
Macrophages (Greek: big eaters, from Greek (makros) = large,
(phagein) = to eat) are a type of white blood cell that engulfs and digests cellular debris, foreign substances, microbes, cancer cells, and anything else that does not have
the types of proteins specific of healthy body cells on its surface in a process called
phagocytosis. These large phagocytes are found in essentially all tissues, where they patrol for potential pathogens by amoeboid movement. They take various forms (with
various names) throughout the body (e.g., histiocytes, Kupffer cells, alveolar macrophages, microglia, and others), but all are part of the mononuclear phagocyte system.
Besides phagocytosis, macrophages play a critical role in nonspecific defense (innate
immunity) and also help initiate specific defense mechanisms (adaptive immunity) by
recruiting other immune cells such as lymphocytes. For example, they are important as
antigen presenters to T cells. In humans, dysfunctional macrophages cause severe diseases such as chronic granulomatous disease that result in frequent infections.
https://en.wikipedia.org/wiki/Macrophage
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Macropinocytosis
In cellular biology, pinocytosis (pino- + cytosis), otherwise known as cell drinking,
fluid endocytosis, and bulk-phase pinocytosis, is a mode of endocytosis in which small
particles are brought into the cell, forming an invagination, and then suspended within
small vesicles. These pinocytotic vesicles subsequently fuse with lysosomes to hydrolyze (break down) the particles. This process requires a lot of energy in the form of
adenosine triphosphate (ATP), the chemical compound mostly used as energy in the
majority of animal cells.
https://en.wikipedia.org/wiki/Pinocytosis
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eration of the brain and spinal cord. BSE has a long incubation period, abou
years, usually affecting adult cattle at a peak age onset of four to five years,
being equally susceptible. BSE is caused by a misfolded proteina prion.
https://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy
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eration of the brain and spinal cord. BSE has a long incubation period, abou
years, usually affecting adult cattle at a peak age onset of four to five years,
being equally susceptible. BSE is caused by a misfolded proteina prion.
https://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy
Major Groove
The double helix structure of DNA contains a major groove and minor groove. In BDNA the major groove is wider than the minor groove. Given the difference in widths
of the major groove and minor groove, many proteins which bind to B-DNA do so
through the wider major groove.
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
to peptide fragments derived from pathogens and display them on the cell s
recognition by the appropriate T-cells.
MHC molecules mediate interactions of leukocytes, also called white blood
(WBCs), which are immune cells, with other leukocytes or with body cells. T
Index
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Malaria
modium type. Malaria causes symptoms that typically include fever, fatigue
and headaches. In severe cases it can cause yellow skin, seizures, coma, or d
toms usually begin ten to fifteen days after being bitten. If not properly trea
may have recurrences of the disease months later. In those who have recent
pears over months to years if the person has no continuing exposure to mal
https://en.wikipedia.org/wiki/Malaria
Malate
Malic acid is an organic compound with the molecular formula C4H6O5. It is a dicarboxylic acid that is made by all living organisms, contributes to the pleasantly sour taste of
fruits, and is used as a food additive. Malic acid has two stereoisomeric forms (L- and
D-enantiomers), though only the L-isomer exists biologically. The salts and esters of
malic acid are known as malates. The malate anion is an intermediate in the citric acid
cycle.
https://en.wikipedia.org/wiki/Malic_acid
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Malate Dehydrogenase
Malate dehydrogenase (EC 1.1.1.37) (MDH) is an enzyme that reversibly catalyzes the
oxidation of malate to oxaloacetate using the reduction of NAD+ to NADH. This reaction is part of many metabolic pathways, including the citric acid cycle. Other malate
dehydrogenases, which have other EC numbers and catalyze other reactions oxidizing
malate, have qualified names like malate dehydrogenase (NADP+).
Malate dehydrogenase is also involved in gluconeogenesis, the synthesis of glucose
from smaller molecules. Pyruvate in the mitochondria is acted upon by pyruvate carboxylase to form oxaloacetate, a citric acid cycle intermediate. In order to get the oxaloacetate out of the mitochondria, malate dehydrogenase reduces it to malate, and it
then traverses the inner mitochondrial membrane. Once in the cytosol, the malate is
oxidized back to oxaloacetate by cytosolic malate dehydrogenase. Finally, phosphoenolpyruvate carboxykinase (PEPCK) converts oxaloacetate to phosphoenolpyruvate
(PEP).
https://en.wikipedia.org/wiki/Malate_dehydrogenase
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Malate Synthase
Malate synthase (EC 2.3.3.9) is an enzyme that catalyzes the chemical reaction
Acetyl-CoA + H2O + Glyoxylate <---> (L)-malate + CoASH
This enzyme participates in pyruvate metabolism and glyoxylate and dicarboxylate metabolism. Malate synthase works together with isocitrate lyase in the glyoxylate cycle to
bypass two oxidative steps of citric acid cycle and permit carbon incorporation from
acetate or fatty acids in many microorganisms. As a result, the cell would not need to
lose 2 molecules of carbon dioxide when entering the glyoxylate cycle rather than the
citric acid cycle. This pathway is especially important to M. tuberculosis, allowing longterm persistence of its infection. When the M. tuberculosis becomes phagocytosed, the
bacterium upregulates genes encoding the glyoxylate shunt enzymes. Since this cycle is
not found in humans and other mammals, malate synthase is perceived as a future
drug target against tuberculosis and other microorganisms. Within germinating plants,
the glyoxylate cycle allows the conversion of reserve lipids into carbohydrates within
glyoxysomes.
https://en.wikipedia.org/wiki/Malate_synthase
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Malate-aspartate Shuttle
The malate-aspartate shuttle (sometimes also the malate shuttle) is a biochemical system for translocating electrons produced during glycolysis across the semipermeable
inner membrane of the mitochondrion for oxidative phosphorylation in eukaryotes.
These electrons enter the electron transport chain of the mitochondria via reduction
equivalents to generate ATP. The shuttle system is required because the mitochondrial
inner membrane is impermeable to NADH, the primary reducing equivalent of the electron transport chain. To circumvent this, malate carries the reducing equivalents
across the membrane.
https://en.wikipedia.org/wiki/Malate-aspartate_shuttle
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MALDI-TOF
Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique
used in mass spectrometry, allowing the analysis of biomolecules (biopolymers such as
DNA, proteins, peptides and sugars) and large organic molecules (such as polymers,
dendrimers and other macromolecules), which tend to be fragile and fragment when
ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft ways of obtaining
ions of large molecules in the gas phase, though MALDI produces far fewer multiply
charged ions.
MALDI methodology is a three-step process. First, the sample is mixed with a suitable
matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the
analyte molecules are ionized by being protonated or deprotonated in the hot plume of
ablated gases, and can then be accelerated into whichever mass spectrometer is used to
analyze them. The type of a mass spectrometer most widely used with MALDI is the
TOF (time-of-flight mass spectrometer), mainly due to its large mass range. The TOF
measurement procedure is also ideally suited to the MALDI ionization process since
the pulsed laser takes individual 'shots' rather than working in continuous operation.
In proteomics, MALDI is used for the rapid identification of proteins isolated by using
gel electrophoresis: SDS-PAGE, size exclusion chromatography, affinity chromatography, strong/weak ion exchange, isotope coded protein labelling (ICPL),and twodimensional gel electrophoresis. Peptide mass fingerprinting is the most popular analytical application of MALDI-TOF mass spectrometers. MALDI TOF/TOF mass spectrometers are used to reveal amino acid sequence of peptides using post-source decay
or high energy collision-induced dissociation (further use see mass spectrometry).
Loss of sialic acid has been identified in papers when DHB has been used as a matrix
for MALDI MS analysis of glycosylated peptides. Using sinapinic acid, 4-HCCA and
DHB as matrices, S. Martin studied loss of sialic acid in glycosylated peptides by metastable decay in MALDI/TOF in linear mode and reflector mode.
It has been reported that a reduction in loss of some post-translational modifications
can be accomplished if IR MALDI is used instead of UV MALDI
In molecular biology, a mixture of 5-methoxysalicylic acid and spermine can be used as
a matrix for oligonucleotides analysis in MALDI mass spectrometry, for instance after
oligonucleotide synthesis.
https://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization
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Malonate
The malonate or propanedioate ion is CH2(COO)2= (malonic acid minus two hydrogen
ions). Malonate compounds include salts and esters of malonic acid, such as
diethyl malonate, (C2H5)2(C3H2O4),
dimethyl malonate, (CH3)2(C3H2O4),
isodium malonate, Na2(C3H2O4).
Malonate is a competitive inhibitor of the enzyme succinate dehydrogenase: malonate
binds to the active site of the enzyme without reacting, and so competes with succinate,
the usual substrate of the enzyme. The observation that malonate is a competitive inhibitor of succinate dehydrogenase was used to deduce the structure of the active site
in that enzyme.The chemical malonate decreases cellular respiration. It resembles the
substrate succinate, without a -CH2-CH2 group required for dehydrogenation.
https://en.wikipedia.org/wiki/Malonate
Index
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Malonyl-ACP
bons in each round of synthesis of a fatty acid. The third carbon is released
dioxide in the process.
Index
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Malonyl-CoA
Malonyl-CoA is a coenzyme A thioester of malonic acid. It plays a key role in chain elongation in fatty acid biosynthesis and polyketide biosynthesis.
Malonyl-CoA is a highly-regulated molecule in fatty acid synthesis. As such, it inhibits
the rate-limiting step in -oxidation of fatty acids. Malonyl CoA inhibits fatty acids
from associating with carnitine by regulating the enzyme carnitine acyltransferase,
thereby preventing them from entering the mitochondria, where fatty acid oxidation
and degradation occur.
https://en.wikipedia.org/wiki/Malonyl-CoA
Index
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Thus, the two substrates of this enzyme are malonyl-CoA and acyl carrier p
https://en.wikipedia.org/wiki/(acyl-carrier-protein)_S-malonyltransferase
Index
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Maltose
Maltose, also known as maltobiose or malt sugar, is a disaccharide formed from two
units of glucose joined with an (14) bond, formed from a condensation reaction.
The isomer isomaltose has two glucose molecules linked through an (16) bond. Isomaltose is shown below.
Maltose is the second member of an important biochemical series of glucose chains.
Maltose is the disaccharide produced when amylase breaks down starch. It is found in
germinating seeds as they break down their starch stores to use for food, which is why
it was named after malt. It is also produced when glucose is caramelized.
https://en.wikipedia.org/wiki/Maltose
Mannases
This gene encodes a member of the glycosyl hydrolase 2 family. The encode
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Mannose
Mannose is a sugar monomer of the aldohexose series of carbohydrates. Mannose is a
C-2 epimer of glucose. Mannose is important in human metabolism, especially in the
glycosylation of certain proteins. Several congenital disorders of glycosylation are associated with mutations in enzymes involved in mannose metabolism.
Mannose commonly exists as two different sized rings, the pyranose (six-membered)
form and the furanose (five-membered) form. Each ring closure can have either an
or configuration at the anomeric position. The chemical rapidly undergoes isomerization among these four forms. The -D-mannopyranose form is shown below.
https://en.wikipedia.org/wiki/Mannose
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Mannose-6-phosphate
Mannose-6-phosphate (M6P) is a molecule bound by lectin in the immune system.
M6P is converted to fructose 6-phosphate by mannose phosphate isomerase.
M6P is a key targeting signal for acid hydrolase precursor proteins that are destined
for transport to lysosomes. The M6P tag is added to such proteins in the cis-Golgi apparatus. Specifically, in a reaction involving uridine diphosphate (UDP) and Nacetylglucosamine, the enzyme N-acetylglucosamine-1-phosphate transferase catalyzes
the N-linked glycosylation of asparagine residues with M6P.
Once appropriately marked with the M6P targeting signal, these proteins are moved to
the trans-Golgi network. There, the M6P moiety is recognized and bound by mannose
6-phosphate receptor (MPR) proteins at pH 6.5-6.7.
The M6P-tagged lysosomal enzymes are shipped to the late endosomes via vesicular
transport. Enzyme replacement therapy (ERT) for several lysosomal storage diseases
relies on this pathway to efficiently direct synthetic enzymes to the lysosome where
each can metabolize its particular substrate. The pH in the late endosome can reach
6.0, which causes dissociation of M6P from its receptor. Upon release, the enzymes are
ferried to their final destination in the lysosomes. The MPRs are packed into vesicles
that bud off the late endosome and return to the "trans"-Golgi network. In this way,
the MPRs can be recycled.
https://en.wikipedia.org/wiki/Mannose_6-phosphate
Index
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MAP Kinases
Mitogen-activated protein kinases (MAPK) are protein kinases that are specific to the
amino acids serine, threonine, and tyrosine. MAPKs belong to the CMGC (CDK/
MAPK/GSK3/CLK) kinase group.
MAPKs are involved in directing cellular responses to a diverse array of stimuli, such
as mitogens, osmotic stress, heat shock and proinflammatory cytokines. They regulate
cell functions including proliferation, gene expression, differentiation, mitosis, cell survival, and apoptosis. MAP kinases are found in eukaryotes only, but they are fairly diverse and encountered in all animals, fungi and plants, and even in an array of unicellular eukaryotes.
MAPKs typically form multi-tiered pathways, receiving input several levels above the
actual MAP kinase. In contrast to the relatively simple, phosphorylation-dependent activation mechanism of MAPKs and MAP2Ks, MAP3Ks have stunningly complex regulation. Many of the better-known MAP3Ks, such as c-Raf, MEKK4 or MLK3 require multiple steps for their activation. These are typically allosterically-controlled enzymes,
tighly locked into an inactive state by multiple mechanisms. The first step en route to
their activation consist of relieving their autoinhibition by a smaller ligand (such as
Ras for c-Raf, GADD45 for MEKK4 or Cdc42 for MLK3). This commonly (but not always) happens at the cell membrane, where most of their activators are bound (note
that small G-proteins are constitutively membrane-associated due to prenylation).
That step is followed by side-to-side homo- and heterodimerization of their now accessible kinase domains. Recently determined complex structures reveal that the dimers
are formed in an orientation that leaves both their substrate-binding regions free. Importantly, this dimerization event also forces the MAP3 kinase domains to adopt a partially active conformation. Full activity is only achieved once these dimers transphosphorylate each other on their activation loops. The latter step can also be achieved or
aided by auxiliary protein kinases (MAP4 kinases, members of the Ste20 family). Once
a MAP3 kinase is fully active, it may phosphorylate its substrate MAP2 kinases, which
in turn will phosphorylate their MAP kinase substrates.
https://en.wikipedia.org/wiki/Mitogen-activated_protein_kinase
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Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that ionizes chemical species and
sorts the ions based on their mass to charge ratio. In simpler terms, a mass spectrum
measures the masses within a sample. Mass spectrometry is used in many different
fields and is applied to pure samples as well as complex mixtures.
A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio.
These spectra are used to determine the elemental or isotopic signature of a sample,
the masses of particles and of molecules, and to elucidate the chemical structures of
molecules, such as peptides and other chemical compounds.
In a typical MS procedure, a sample, which may be solid, liquid, or gas, is ionized, for
example by bombarding it with electrons. This may cause some of the sample's molecules to break into charged fragments. These ions are then separated according to their
mass-to-charge ratio, typically by accelerating them and subjecting them to an electric
or magnetic field: ions of the same mass-to-charge ratio will undergo the same amount
of deflection.
The ions are detected by a mechanism capable of detecting charged particles, such as
an electron multiplier. Results are displayed as spectra of the relative abundance of detected ions as a function of the mass-to-charge ratio. The atoms or molecules in the
sample can be identified by correlating known masses to the identified masses or
through a characteristic fragmentation pattern. MALDI-TOF is a popular type of mass
spectrometry.
https://en.wikipedia.org/wiki/Mass_spectrometry
Index
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Mast Cells
cifically, it is a type of granulocyte derived from the myeloid stem cell that i
the immune and neuroimmune systems and contains many granules rich in
and heparin. Although best known for their role in allergy and anaphylaxis,
Index
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Mature mRNA
Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA tra
script that has been spliced and processed and is ready for translation in the course o
protein synthesis. Unlike the eukaryotic RNA immediately after transcription known
as precursor messenger RNA, it consists exclusively of exons, with all introns remove
Mature mRNA is also called "mature transcript", "mature RNA" or "mRNA".
The production of a mature mRNA molecule occurs in 3 steps:
1
end of the primary transcripts. This is otherwise known as the GTP or 5' Cap, and is
used for the stability and attachment point for ribosomes.
2
and is used for stability and guidance, so that the mRNA can exit the nucleus and fin
the ribosome.
3
RNA splicing removes the non-coding RNA introns leaving behind the ex-
ons, which are then spliced and joined together to form the final mRNA.
https://en.wikipedia.org/wiki/Mature_messenger_RNA
Meiosis
Meiosis is a specialized type of cell division that reduces the chromosome number by
half. This process occurs in all sexually reproducing single-celled and multicellular
eukaryotes, including animals, plants, and fungi. Errors in meiosis resulting in aneuploidy are the leading known cause of miscarriage and the most frequent genetic
cause of developmental disabilities.
In meiosis, DNA replication is followed by two rounds of cell division to produce four
potential daughter cells, each with half the number of chromosomes as the original parent cell. The two meiotic divisions are known as Meiosis I and Meiosis II. Before meiosis begins, during S phase of the cell cycle, the DNA of each chromosome is replicated
so that it consists of two identical sister chromatids, which remain held together
through sister chromatid cohesion. This S-phase can be referred to as "premeiotic Sphase" or "meiotic S-phase." Immediately following DNA replication, meiotic cells enter a prolonged G2-like stage known as meiotic prophase. During this time, homologous chromosomes pair with each other and undergo genetic recombination, a programmed process in which DNA is cut and then repaired, which allows them to exchange some of their genetic information. A subset of recombination events results in
crossovers, which create physical links known as chiasmata (singular:chiasma, for the
Greek letter Chi) between the homologous chromosomes. In most organisms, these
links are essential to direct each pair of homologous chromosomes to segregate away
from each other during Meiosis I, resulting in two haploid cells that half the number of
chromosomes as the parent cell. During Meiosis II, the cohesion between sister chromatids is released and they segregate from one another, as during mitosis. In some
cases all four of the meiotic products form gametes such as sperm, spores, or pollen. In
female animals, three of the four meiotic products are typically eliminated by extrusion
into polar bodies, and only one cell develops to produce an ovum.
Because the number of chromosomes is halved during meiosis, gametes can fuse (i.e.
fertilization) to form a diploid zygote that contains two copies of each chromosome,
one from each parent. Thus, alternating cycles of meiosis and fertilization enable sexual reproduction, with successive generations maintaining the same number of chromosomes. For example, diploid human cells contain 23 pairs of chromosomes (46 total), half of maternal origin and half of paternal origin. Meiosis produces haploid gametes (ova or sperm) that contain one set of 23 chromosomes. When two gametes (an
egg and a sperm) fuse, the resulting zygote is once again diploid, with the mother and
father each contributing 23 chromosomes. This same pattern, but not the same number of chromosomes, occurs in all organisms that utilize meiosis.
https://en.wikipedia.org/wiki/Meiosis
Melanin
Melanin is a broad term for a group of natural pigments found in most orga
(arachnids are one of the few groups in which it has not been detected). Me
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Melatonin
Melatonin, chemically N-acetyl-5-methoxy tryptamine, is a substance found in animals, plants, fungi, and bacteria. In animals, it is a hormone that anticipates the daily
onset of darkness. However in other organisms, it may have different functions. Likewise, the synthesis of melatonin in animals differs from that in other organisms.
In animals, melatonin is involved in the entrainment (synchronization) of the circadian rhythms of physiological functions including sleep timing, blood pressure regulation, seasonal reproduction and many others. Many of melatonin's biological effects
in animals are produced through activation of melatonin receptors, while others are
due to its role as a pervasive and powerful antioxidant, with a particular role in the protection of nuclear and mitochondrial DNA.
https://en.wikipedia.org/wiki/Melatonin
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Mellitin
Melittin is the principal active component of apitoxin (bee venom) and is a
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Membrane
A membrane is a selective barrier. It allows some things to pass through, but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes (outer coverings of cells or organelles that allow passage of certain constituents); nuclear membranes, which cover a cell nucleus; and tissue membranes, such as mucosae and serosae. Synthetic membranes are made by humans for use in laboratories and industry (such as chemical plants). The influent of an
artificial membrane is known as the feed-stream, the liquid that passes through the
membrane is known as the permeate, and the liquid containing the retained constituents is the retentate or concentrate.
https://en.wikipedia.org/wiki/Membrane
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Membrane Flexibility
In biology, membrane fluidity refers to the viscosity of the lipid bilayer of a cell membrane or a synthetic lipid membrane. Lipid packing can influence the fluidity of the
membrane. Viscosity of the membrane can affect the rotation and diffusion of proteins
and other bio-molecules within the membrane, there-by affecting the functions of
these molecules.
Membrane fluidity can be affected by a number of factors. One way to increase membrane fluidity is to heat up the membrane. Lipids acquire thermal energy when they
are heated up. Energetic lipids move around more, arranging and rearranging randomly, making the membrane more fluid. At low temperatures, the lipids are laterally
ordered and organized in the membrane, and the lipid chains are mostly in the alltrans configuration and pack well together. The composition of a membrane can also
affect its fluidity. The membrane phospholipids incorporate fatty acids of varying
length and saturation. Lipids with shorter chains are less stiff and less viscous because
they are more susceptible to changes in kinetic energy due to their smaller molecular
size and they have less surface area to undergo stabilizing van der Waals interactions
with neighboring hydrophobic chains.
Lipid chains with double bonds are more fluid than lipids that are saturated with hydrogen and thus have only single bonds. On the molecular level, unsaturated double
bonds make it harder for the lipids to pack together by putting kinks into the otherwise
straightened hydrocarbon chain. Membranes made with such lipids have lower melting points: less thermal energy is required to achieve the same level of fluidity as membranes made with lipids with saturated chains. Incorporation of particular lipids, such
as sphingomyelin, into synthetic lipid membranes is known to stiffen a membrane.
Such membranes can be described as "a glass state, i.e., rigid but without crystalline order".
Cholesterol acts as a bidirectional regulator of membrane fluidity because at high temperatures, it stabilizes the membrane and raises its melting point, whereas at low temperatures it intercalates between the phospholipids and prevents them from clustering
together and stiffening. Some drugs, e.g. Losartan, are also known to alter membrane
viscosity. Another way to change membrane fluidity is to change the pressure. In the
laboratory, supported lipid bilayers and monolayers can be made artificially. In such
cases, one can still speak of membrane fluidity. These membranes are supported by a
flat surface, e.g. the bottom of a box. The fluidity of these membranes can be controlled
by the lateral pressure applied, e.g. by the side walls of a box.
https://en.wikipedia.org/wiki/Membrane_fluidity
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Membrane Fluidity
In biology, membrane fluidity refers to the viscosity of the lipid bilayer of a
brane or a synthetic lipid membrane. Lipid packing can influence the fluidit
membrane. Viscosity of the membrane can affect the rotation and diffusion
and other bio-molecules within the membrane, there-by affecting the funct
these molecules.
https://en.wikipedia.org/wiki/Membrane_fluidity
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Membrane Fusion
formed and the internal contents of the two structures can mix. Alternative
one leaflet from each bilayer is involved in the fusion process, the bilayers a
ers can mix, but the inner leaflets remain distinct. The aqueous contents en
each bilayer also remain separated.
https://en.wikipedia.org/wiki/Lipid_bilayer_fusion
Membrane Potential
Membrane potential (also transmembrane potential or membrane voltage) is the difference in electric potential between the interior and the exterior of a biological cell. With
respect to the exterior of the cell, typical values of membrane potential range from 40
mV to 80 mV.
All animal cells are surrounded by a membrane composed of a lipid bilayer with proteins embedded in it. The membrane serves as both an insulator and a diffusion barrier
to the movement of ions. Ion transporter/pump proteins actively push ions across the
membrane and establish concentration gradients across the membrane, and ion channels allow ions to move across the membrane down those concentration gradients. Ion
pumps and ion channels are electrically equivalent to a set of batteries and resistors inserted in the membrane, and therefore create a voltage difference between the two
sides of the membrane.
Virtually all eukaryotic cells (including cells from animals, plants, and fungi) maintain
a non-zero transmembrane potential,[citation needed] usually with a negative voltage
in the cell interior as compared to the cell exterior ranging from 40 mV to 80 mV.
The membrane potential has two basic functions. First, it allows a cell to function as a
battery, providing power to operate a variety of "molecular devices" embedded in the
membrane. Second, in electrically excitable cells such as neurons and muscle cells, it is
used for transmitting signals between different parts of a cell. Signals are generated by
opening or closing of ion channels at one point in the membrane, producing a local
change in the membrane potential. This change in the electric field can be quickly affected by either adjacent or more distant ion channels in the membrane. Those ion
channels can then open or close as a result of the potential change, reproducing the signal.
In non-excitable cells, and in excitable cells in their baseline states, the membrane potential is held at a relatively stable value, called the resting potential. For neurons, typical values of the resting potential range from 70 to 80 millivolts. That is, the interior of a cell has a negative baseline voltage of a bit less than one-tenth of a volt. The
opening and closing of ion channels can induce a departure from the resting potential.
This is called a depolarization if the interior voltage becomes less negative (say from
70 mV to 60 mV), or a hyperpolarization if the interior voltage becomes more negative (say from 70 mV to 80 mV). In excitable cells, a sufficiently large depolarization
can evoke an action potential, in which the membrane potential changes rapidly and
significantly for a short time (on the order of 1 to 100 milliseconds), often reversing its
polarity. Action potentials are generated by the activation of certain voltage-gated ion
channels.
https://en.wikipedia.org/wiki/Membrane_potential
Membrane Proteins
Membrane proteins are proteins that interact with, or are part of, biological membranes. They are one of the common types of protein along with soluble globular proteins, fibrous proteins, and disordered proteins. They are targets of over 50% of all
modern medicinal drugs. It is estimated that 2030% of all genes in most genomes encode membrane proteins.
Membrane proteins perform a variety of functions vital to the survival of organisms:
Membrane receptor proteins relay signals between the cell's internal and external environments.
Transport proteins move molecules and ions across the membrane. They can be categorized according to the Transporter Classification database.
Membrane enzymes may have many activities, such as oxidoreductase, transferase or
hydrolase.
Cell adhesion molecules allow cells to identify each other and interact. For example,
proteins involved in immune response.
https://en.wikipedia.org/wiki/Membrane_protein
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Menatetrenone
Menatetrenone (INN), also known as MK4, is a vitamin K compound used as a hemostatic agent, and also as adjunctive therapy for the pain of osteoporosis. Menatetrenone is one of the nine forms of vitamin K2.
MK4 is produced via conversion of vitamin K1 in the body, in the testes, pancreas and
arterial walls. While major questions still surround the biochemical pathway for the
transformation of vitamin K1 to MK4, studies demonstrate the conversion is not dependent on gut bacteria, occurring in germ-free rats and in parenterally-administered
K1 in rats. In fact, tissues that accumulate high amounts of MK4 have a remarkable capacity to convert up to 90% of the available K1 into MK4.
https://en.wikipedia.org/wiki/Menatetrenone
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Mercaptoethanol
abbreviated, is used to reduce disulfide bonds and can act as a biological antioxid
nol is widely used because the hydroxyl group confers solubility in water and lowe
the volatility. Due to its diminished vapor pressure, its odor, while unpleasant, is
objectionable than related thiols.
https://en.wikipedia.org/wiki/2-Mercaptoethanol
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Mercury
element, mercury is the only metallic element that is liquid at standard con
temperature and pressure. The only other element that is liquid under thes
Metabolic Energy
ing organisms. The three main purposes of metabolism are the conversion o
proteins, lipids, nucleic acids, and some carbohydrates, and the elimination
lism can also refer to the sum of all chemical reactions that occur in living o
including digestion and the transport of substances into and between differ
which case the set of reactions within the cells is called intermediary metab
termediate metabolism.
https://en.wikipedia.org/wiki/Metabolism
Metabolic Pathway
In biochemistry, a metabolic pathway is a series of chemical reactions occurring within
a cell. In a pathway, the initial chemical (metabolite) is modified by a sequence of
chemical reactions. These reactions are catalyzed by enzymes, where the product of
one enzyme acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function.
Pathways are required for the maintenance of homeostasis within an organism and the
flux of metabolites through a pathway is regulated depending on the needs of the cell
and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The metabolism
of a cell consists of an elaborate network of interconnected pathways that enable the
synthesis and breakdown of molecules (anabolism and catabolism).
https://en.wikipedia.org/wiki/Metabolic_pathway
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Metabolic Pathways
In biochemistry, a metabolic pathway is a series of chemical reactions occurring within
a cell. In a pathway, the initial chemical (metabolite) is modified by a sequence of
chemical reactions. These reactions are catalyzed by enzymes, where the product of
one enzyme acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function.
Pathways are required for the maintenance of homeostasis within an organism and the
flux of metabolites through a pathway is regulated depending on the needs of the cell
and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The metabolism
of a cell consists of an elaborate network of interconnected pathways that enable the
synthesis and breakdown of molecules (anabolism and catabolism).
https://en.wikipedia.org/wiki/Metabolic_pathway
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Metabolism
Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms. The three main purposes of metabolism are the conversion of food/fuel
to energy to run cellular processes, the conversion of food/fuel to building blocks for
proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
The word metabolism can also refer to the sum of all chemical reactions that occur in
living organisms, including digestion and the transport of substances into and between
different cells, in which case the set of reactions within the cells is called intermediary
metabolism or intermediate metabolism.
Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter, for example, by cellular respiration, and anabolism, the building up of
components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which
one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms
to drive desirable reactions that require energy that will not occur by themselves, by
coupling them to spontaneous reactions that release energy. Enzymes act as catalysts
that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of
metabolic pathways in response to changes in the cell's environment or to signals from
other cells.
The metabolic system of a particular organism determines which substances it will find
nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide
as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it
is able to obtain that food.
A striking feature of metabolism is the similarity of the basic metabolic pathways and
components between even vastly different species. For example, the set of carboxylic
acids that are best known as the intermediates in the citric acid cycle are present in all
known organisms, being found in species as diverse as the unicellular bacterium
Escherichia coli and huge multicellular organisms like elephants. These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary
history, and their retention because of their efficacy.
https://en.wikipedia.org/wiki/Metabolism
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Metabolon
actions, and structural elements of the cell such as integral membrane prote
proteins of the cytoskeleton.
product from an enzyme directly as substrate into the active site of the cons
zyme of the metabolic pathway. The citric acid cycle is an example of a meta
amount of water needed to hydrate the enzymes is reduced and enzyme act
creased.
https://en.wikipedia.org/wiki/Metabolon
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Metabolons
actions, and structural elements of the cell such as integral membrane prote
proteins of the cytoskeleton.
product from an enzyme directly as substrate into the active site of the cons
zyme of the metabolic pathway. The citric acid cycle is an example of a meta
amount of water needed to hydrate the enzymes is reduced and enzyme act
creased.
https://en.wikipedia.org/wiki/Metabolon
Metalloproteases
cant role in the fusion of muscle cells during embryo development, in a proc
as myogenesis.
Most metalloproteases require zinc, but some use cobalt. The metal ion is c
to the protein via three ligands. The ligands co-ordinating the metal ion can
Metamorphic Proteins
Metaphase
Metaphase is a stage of mitosis in the eukaryotic cell cycle in which chromosomes are
at their second-most condensed and coiled stage (they are at their most condensed in
anaphase). These chromosomes, carrying genetic information, align in the equator of
the cell before being separated into each of the two daughter cells. Metaphase accounts
for approximately 4% of the cell cycle's duration. Preceded by events in prometaphase
and followed by anaphase, microtubules formed in prophase have already found and
attached themselves to kinetochores in metaphase. Human metaphase chromosomes
are shown below.
https://en.wikipedia.org/wiki/Metaphase
Metastatic
Metastasis, or metastatic disease, is the spread of a cancer or other disease from one organ or part of the body to another not directly connected with it. Cells that undergo
metastasis or that are capable of it are metastatic.
https://en.wikipedia.org/wiki/Metastasis
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Methane
Methane is a chemical compound with the chemical formula CH4 (one atom of carbon
and four atoms of hydrogen). It is the simplest alkane and the main component of natural gas. The relative abundance of methane on Earth makes it an attractive fuel, though
capturing and storing it poses challenges due to its gaseous state under normal conditions for temperature and pressure.
https://en.wikipedia.org/wiki/Methane
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Methanogenic
from the domain Archaea, a group phylogenetically distinct from both euka
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Methionine
Methionine (abbreviated as Met or M; encoded by the codon AUG) is an -amino acid
that is used in the biosynthesis of proteins. It contains an -amino group (which is in
the protonated NH3+ form under biological conditions), an -carboxylic acid group
(which is in the deprotonated COO form under biological conditions), and an Smethyl thioether side chain, classifying it as a non-polar, aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it and thus it must be obtained
from the diet.
Methionine is coded for by the initiation codon meaning it indicates the start of the coding region and is the first amino acid produced in a nascent polypeptide during mRNA
translation and is coded by the initiation codon AUG, which also indicates mRNA's coding region where translation into protein begins.
https://en.wikipedia.org/wiki/Methionine
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Methionine Adenosyltransferase
parasites which obtain AdoMet from their host. Isoenzymes are found in ba
ding yeast and even in mammalian mitochondria. Most MATs are homo-oli
the majority are tetramers. The monomers are organized into three domain
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Methionine Synthase
Methionine synthase also known as MS, MeSe, MetH is responsible for the regeneration of methionine from homocysteine. In humans it is encoded by the MTR gene (5methyltetrahydrofolate-homocysteine methyltransferase). Methionine synthase forms
part of the S-adenosylmethionine (SAMe) biosynthesis and regeneration cycle. In animals this enzyme requires Vitamin B12 (cobalamin) as a cofactor, whereas the form
found in plants is cobalamin-independent. Microorganisms express both cobalamindependent and cobalamin-independent forms.
https://en.wikipedia.org/wiki/Methionine_synthase
Methionyl-tRNA Formyltransferase
provides the fMet used for making the first amino acid in prokaryotic prote
https://en.wikipedia.org/wiki/Methionyl-tRNA_formyltransferase
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Methotrexate
Methotrexate (MTX), formerly known as amethopterin, is an anti-metabolite and antifolate drug.
It is used in treatment of cancer, autoimmune diseases, ectopic pregnancy, and for the
induction of medical abortions. It acts by inhibiting the metabolism of folic acid via dihydrofolate reductase.
https://en.wikipedia.org/wiki/Methotrexate
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Methyl
A methyl group is an alkyl derived from methane, containing one carbon atom bon
to three hydrogen atoms CH3. In formulas, the group is often abbreviated Me. S
Index
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Methyl Glyoxal
dehyde and a ketone but in the presence of water, it exists as hydrates and o
It is a reduced derivative of pyruvic acid.
https://en.wikipedia.org/wiki/Methylglyoxal
Methyl Group
Methylase
Methyltransferases (methylases) are a large group of enzymes that all methylate their
substrates but can be split into several subclasses based on their structural features.
The most common class of methyltransferases is class I, all of which contain a Rossman fold for binding S-Adenosyl methionine (SAM). Class II methyltransferases contain a SET domain, which are exemplified by SET domain Histone methyltransferases,
and class III methyltransferases, which are membrane associated. Methyltransferases
can also be grouped as different types utilizing different substrates in methyl transfer
reactions. These types include protein methyltransferases, DNA methyltransferases
(important in restriction/modification systems), natural product methyltransferases,
and non-SAM dependent methyltransferases.
SAM is the classical methyl donor for methyltransferases, however, examples of other
methyl donors are seen in nature. The general mechanism for methyl transfer is a SN2like nucleophilic attack where the methionine sulfur serves as the nucleophile that
transfers the methyl group to the enzyme substrate. SAM is converted to S-Adenosyl
homocysteine (SAH) during this process. The breaking of the SAM-methyl bond and
the formation of the substrate-methyl bond happen nearly simultaneously. These enzymatic reactions are found in many pathways and are implicated in genetic diseases,
cancer, and metabolic diseases.
https://en.wikipedia.org/wiki/Methyltransferase
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group on a substrate or the substitution of an atom or group by a methyl group. Methylation is a form
of alkylation with a methyl group, rather than a larger carbon chain, replacing a hydrogen atom.
Biomolecules implicated in addition of methyl groups (one-carbon chemistry) include
S-adenosylmethionine (SAM) and folates.
https://en.wikipedia.org/wiki/Methylation
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Methyllysine
In proteins, the amino acid residue lysine can be methylated once, twice or three times
on its terminal side chain ammonium group.
Such methylated lysines play an important role in epigenetics; the methylation of specific lysines of certain histones in a nucleosome alters the binding of the surrounding
DNA to those histones, which in turn affects the expression of genes on that DNA. The
binding is affected because the effective radius of the positive charge is increased
(methyl groups are larger than the hydrogen atoms they replace), reducing the strongest potential electrostatic attraction with the negatively charged DNA. Moreover, the
methyl groups are themselves hydrophobic, and alter the structure of water in their vicinity, similar to tetramethyl ammonium.
Trimethyllysine is shown below.
https://en.wikipedia.org/wiki/Methyllysine
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Methylmalonyl-CoA Mutase
Methylmalonyl coenzyme A mutase, also known as MCM is an enzyme that catalyzes
the isomerization of methylmalonyl-CoA to succinyl-CoA and it is involved in key metabolic pathways. It requires a vitamin B12-derived prosthetic group, adenosylcobalamin
(commonly referred to as AdoCbl), to function.
The enzyme is important in the last step of the conversion of propionyl-CoA to
succinyl-CoA and is shown in the figure below.
https://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase
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Mevalonate
els of cholesterol) stop the production of mevalonate (and the rest of the chole
biosynthetic pathway) by inhibiting HMG-CoA reductase.
https://en.wikipedia.org/wiki/Mevalonic_acid
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MHC
peptide fragments derived from pathogens and display them on the cell sur
cytes, also called white blood cells (WBCs), which are immune cells, with ot
cytes or with body cells. The MHC determines compatibility of donors for o
nization. In humans, the MHC is also called the human leukocyte antigen (H
https://en.wikipedia.org/wiki/Major_histocompatibility_complex
Micelles
A micelle is an aggregate (or supramolecular assembly) of surfactant molecules dispersed in a liquid colloid. A typical micelle in aqueous solution forms an aggregate with
the hydrophilic "head" regions in contact with surrounding solvent, sequestering the
hydrophobic single-tail regions in the micelle centre. This phase is caused by the packing behavior of single-tail lipids in a bilayer. The difficulty filling all the volume of the
interior of a bilayer, while accommodating the area per head group forced on the molecule by the hydration of the lipid head group, leads to the formation of the micelle.
This type of micelle is known as a normal-phase micelle (oil-in-water micelle). Inverse
micelles have the head groups at the center with the tails extending out (water-in-oil
micelle). Micelles are approximately spherical in shape. Other phases, including
shapes such as ellipsoids, cylinders, and bilayers, are also possible. The shape and size
of a micelle are a function of the molecular geometry of its surfactant molecules and solution conditions such as surfactant concentration, temperature, pH, and ionic
strength. The process of forming micelles is known as micellization and forms part of
the phase behavior of many lipids according to their polymorphism.
https://en.wikipedia.org/wiki/Micelle
Michaelis-Menten Kinetics
In biochemistry, MichaelisMenten kinetics is one of the best-known models of enzyme kinetics. It is named after German biochemist Leonor Michaelis and Canadian
physician Maud Menten. The model takes the form of an equation describing the rate
of enzymatic reactions, by relating reaction rate to , the concentration of a substrateS.
Its formula is given by
This equation is called MichaelisMenten equation. Here, Vmax represents the maximum rate achieved by the system, at maximum saturation of the substrate concentration. The Michaelis constant KM is the substrate concentration at which the reaction
rate is half of . Biochemical reactions involving a single substrate are often assumed to
follow MichaelisMenten kinetics, without regard to the model's underlying assumptions.
https://en.wikipedia.org/wiki/MichaelisMenten_kinetics
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Microarrays
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate (usually
a glass slide or silicon thin-film cell) that assays large amounts of biological material
using high-throughput screening miniaturized, multiplexed and parallel processing
and detection methods. The concept and methodology of microarrays was first introduced and illustrated in antibody microarrays (also referred to as antibody matrix) by
Tse Wen Chang in 1983 in a scientific publication and a series of patents.
The "gene chip" industry started to grow significantly after the 1995 Science Paper by
the Ron Davis and Pat Brown labs at Stanford University. With the establishment of
companies, such as Affymetrix, Agilent, Applied Microarrays, Arrayit, Illumina, and
others, the technology of DNA microarrays has become the most sophisticated and the
most widely used, while the use of protein, peptide and carbohydrate microarrays is expanding.
Types of microarrays include:
DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays, BAC microarrays and SNP microarrays
MMChips, for surveillance of microRNA populations
Protein microarrays
Peptide microarrays, for detailed analyses or optimization of proteinprotein interactions
Tissue microarrays
Cellular microarrays (also called transfection microarrays)
Chemical compound microarrays
Antibody microarrays
Carbohydrate arrays (glycoarrays)
Phenotype microarrays
Reverse Phase Protein Microarrays, microarrays of lysates or serum
interferometric reflectance imaging sensor (IRIS)
Pictured below is a cDNA microarray.
https://en.wikipedia.org/wiki/Microarray
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Microfilaments
Microfilaments or actin thin filaments are the thinnest filaments of the cytoskeleton, a
structure found in the cytoplasm of eukaryotic cells. These linear polymers of actin
subunits are flexible and relatively strong, resisting buckling by multi-piconewton compressive forces and filament fracture by nanonewton tensile forces. Microfilaments are
highly versatile, functioning in cytokinesis, amoeboid movement, and changes in cell
shape. In inducing this cell motility, one end of the actin filament elongates while the
other end contracts, presumably by myosin II molecular motors.
Shown below are stained actin microfilaments
https://en.wikipedia.org/wiki/Microfilament
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Microtubules
Microtubules are a component of the cytoskeleton, found throughout the cytoplasm.
These tubular polymers of tubulin can grow as long as 50micrometers and are highly
dynamic. The outer diameter of a microtubule is about 24nm while the inner diameter
is about 12nm. They are found in eukaryotic cells, as well as some bacteria, and are
formed by the polymerization of a dimer of two globular proteins, and tubulin.
https://en.wikipedia.org/wiki/Microtubule
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Mineralocorticoids
Mineralocorticoids are a class of corticosteroids, which are a class of steroid hormones.
Mineralocorticoids are corticosteroids that influence salt and water balances (electrolyte balance and fluid balance). The primary mineralocorticoid is aldosterone, notable
for a second keto group at the 18 position.
The name mineralocorticoid derives from early observations that these hormones were
involved in the retention of sodium, a mineral. The mineralocorticoid known as aldosterone is shown below.
https://en.wikipedia.org/wiki/Mineralocorticoid
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Minor Groove
The double helix structure of DNA contains a major groove and minor groove. In BDNA the major groove is wider than the minor groove. Given the difference in widths
of the major groove and minor groove, many proteins which bind to B-DNA do so
through the wider major groove.
https://en.wikipedia.org/wiki/Nucleic_acid_double_helix
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miRNAs
A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing
about 22 nucleotides) found in plants, animals and some viruses, that functions in
RNA silencing and post-transcriptional regulation of gene expression.
Encoded by eukaryotic nuclear DNA in plants and animals and by viral DNA in certain
viruses whose genome is based on DNA, miRNAs function via base-pairing with complementary sequences within mRNA molecules.As a result, these mRNA molecules are
silenced, by one or more of the following processes:
Cleavage of the mRNA strand into two pieces,
Destabilization of the mRNA through shortening of its poly(A) tail, and
Less efficient translation of the mRNA into proteins by ribosomes.
miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference
(RNAi) pathway, except miRNAs derive from regions of RNA transcripts that fold back
on themselves to form short hairpins, whereas siRNAs derive from longer regions of
double-stranded RNA. The human genome may encode over 1000 miRNAs, which are
abundant in many mammalian cell types and appear to target about 60% of the genes
of humans and other mammals.
miRNAs are well conserved in both plants and animals, and are thought to be a vital
and evolutionarily ancient component of gene regulation.While core components of
the microRNA pathway are conserved between plants and animals, miRNA repertoires
in the two kingdoms appear to have emerged independently with different primary
modes of action.
Plant miRNAs usually have near-perfect pairing with their mRNA targets, which induces gene repression through cleavage of the target transcripts. In contrast, animal
miRNAs are able to recognize their target mRNAs by using as little as 68 nucleotides
(the seed region) at the 5' end of the miRNA, which is not enough pairing to induce
cleavage of the target mRNAs. Combinatorial regulation is a feature of miRNA regulation in animals. A given miRNA may have hundreds of different mRNA targets, and a
given target might be regulated by multiple miRNAs.
https://en.wikipedia.org/wiki/MicroRNA
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Misfolding
Aggregated/misfolded proteins are associated with prion-related illnesses such as
Creutzfeldt-Jakob disease, bovine spongiform encephalopathy (mad cow disease),
amyloid-related illnesses such as Alzheimer's disease and familial amyloid cardiomyopathy or polyneuropathy, as well as intracytoplasmic aggregation diseases such as
Huntington's and Parkinson's disease. These age onset degenerative diseases are associated with the aggregation of misfolded proteins into insoluble, extracellular aggregates and/or intracellular inclusions including cross- sheet amyloid fibrils. It is not
completely clear whether the aggregates are the cause or merely a reflection of the loss
of protein homeostasis, the balance between synthesis, folding, aggregation and protein turnover.
Recently the European Medicines Agency approved the use of Tafamidis or Vyndaqel
(a kinetic stabilizer of tetrameric transthyretin) for the treatment of transthyretin amyloid diseases. This suggests that the process of amyloid fibril formation (and not the fibrils themselves) causes the degeneration of post-mitotic tissue in human amyloid diseases. Misfolding and excessive degradation instead of folding and function leads to a
number of proteopathy diseases such as antitrypsin-associated emphysema, cystic fibrosis and the lysosomal storage diseases, where loss of function is the origin of the disorder. While protein replacement therapy has historically been used to correct the latter disorders, an emerging approach is to use pharmaceutical chaperones to fold mutated proteins to render them functional.
https://en.wikipedia.org/wiki/Protein_folding#Incorrect_protein_folding_and_neur
odegenerative_disease
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Mismatch Repair
DNA mismatch repair is a system for recognizing and repairing erroneous insertion,
deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.
Mismatch repair is strand-specific. During DNA synthesis the newly synthesized
(daughter) strand will commonly include errors. In order to begin repair, the mismatch repair machinery distinguishes the newly synthesized strand from the template
(parental). In Gram-negative bacteria, transient hemimethylation distinguishes the
strands (the parental is methylated and daughter is not). However, in other prokaryotes and eukaryotes, the exact mechanism is not clear. It is suspected that, in eukaryotes, newly synthesized lagging-strand DNA transiently contains nicks (before being
sealed by DNA ligase) and provides a signal that directs mismatch proofreading systems to the appropriate strand. This implies that these nicks must be present in the
leading strand, and evidence for this has recently been found. Recent work has shown
that nicks are sites for RFC-dependent loading of the replication sliding clamp PCNA,
in an orientation-specific manner, such that one face of the donut-shape protein is juxtaposed toward the 3'-OH end at the nick. Oriented PCNA then directs the action of the
MutLalpha endonuclease to one strand in the presence of a mismatch and MutSalpha
or MutSbeta.
Any mutational event that disrupts the superhelical structure of DNA carries with it
the potential to compromise the genetic stability of a cell. The fact that the damage detection and repair systems are as complex as the replication machinery itself highlights
the importance evolution has attached to DNA fidelity.
Examples of mismatched bases include a G/T or A/C pairing (see DNA repair). Mismatches are commonly due to tautomerization of bases during G2. The damage is repaired by recognition of the deformity caused by the mismatch, determining the template and non-template strand, and excizing the wrongly incorporated base and replacing it with the correct nucleotide. The removal process involves more than just the mismatched nucleotide itself. A few or up to thousands of base pairs of the newly synthesized DNA strand can be removed.
https://en.wikipedia.org/wiki/DNA_mismatch_repair
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Information Processing
Information Processing
Information Processing
Information Processing
Information Processing
Information Processing
Mitochondria
The mitochondrion (plural mitochondria) is a double membrane-bound organelle
found in most eukaryotic cells. Mitochondria have been described as "the powerhouse
of the cell" because they generate most of the cell's supply of adenosine triphosphate
(ATP), used as a source of chemical energy.
A mitochondrion contains outer and inner membranes composed of phospholipid bilayers and proteins. The two membranes have different properties. Because of this
double-membraned organization, there are five distinct parts to a mitochondrion. They
are:
1
the intermembrane space (the space between the outer and inner mem-
branes),
3
https://en.wikipedia.org/wiki/Mitochondrion
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Mitochondrial Matrix
In the mitochondrion, the matrix contains soluble enzymes that catalyze the oxidation
of pyruvate and other small organic molecules. It is into the matrix that protons travel
during oxidative phosphorylation and where DNA is released when made in the same
process.
The mitochondrial matrix also contains the mitochondrial DNA and ribosomes. The
word "matrix" stems from the fact that this space is viscous, compared to the relatively
aqueous cytoplasm.
https://en.wikipedia.org/wiki/Mitochondrial_matrix
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Mitosis
Mitosis is a part of the cell cycle in which chromosomes in a cell nucleus are separated
into two identical sets of chromosomes, and each set ends up in its own nucleus. In general, mitosis (division of the nucleus) is often accompanied or followed by cytokinesis,
which divides the cytoplasm, organelles and cell membrane into two new cells containing roughly equal shares of these cellular components. Mitosis and cytokinesis together define the mitotic (M) phase of an animal cell cyclethe division of the mother
cell into two daughter cells, genetically identical to each other and to their parent cell.
The animal cell cycle is shown below.
https://en.wikipedia.org/wiki/Mitosis
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frog eggs. It stimulates the mitotic and meiotic phases of the cell cycle. MPF
the entrance into mitosis (the M phase) from the G2 phase by phosphorylat
The MPF is also called the M phase kinase because of its ability to phosphor
proteins at a specific point in the cell cycle and thus control their ability to f
https://en.wikipedia.org/wiki/Maturation_promoting_factor
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Mitotic Spindles
In cell biology, the spindle apparatus refers to the cytoskeletal structure of eukaryotic
cells that forms during cell division to separate sister chromatids between daughter
cells. It is referred to as the mitotic spindle during mitosis, a process that produces genetically identical daughter cells, or the meiotic spindle during meiosis, a process that
produces gametes with half the number of chromosomes of the parent cell.
https://en.wikipedia.org/wiki/Spindle_apparatus
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Molecular Response
In the process of blood clotting, the mechanism by which the process works
Index
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Molecularity
Monoacylglyceride
A monoglyceride (monoacylglyceride or monoacylglycerol) is a glyceride in which a
glycerol molecule has formed an ester bond with exactly one fatty acid molecule. The
more formally correct terms in modern convention are acylglycerol and monoacylglycerol.
In normal metabolic processes, monoacylglycerols are hydrolyzed by monoacylglycerol
lipase to produce glycerol and a free fatty acid as required.
https://en.wikipedia.org/wiki/Monoglyceride
Monoacylglyceride Lipase
Monoacylglycerol lipase, also known as MAG lipase, MAGL, MGL or MGLL is a protein
that, in humans, is encoded by the MGLL gene. MAGL is a 33-kDa, membraneassociated member of the serine hydrolase superfamily and contains the classical
GXSXG consensus sequence common to most serine hydrolases. The catalytic triad has
been identified as Ser122, His269, and Asp239.
Monoacylglycerol lipase is a key enzyme in the hydrolysis of the endocannabinoid 2arachidonoylglycerol (2-AG). It converts monoacylglycerols to the free fatty acid and
glycerol. This is shown in the reaction below.
https://en.wikipedia.org/wiki/Monoacylglycerol_lipase
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Monoacylglycerol
A monoglyceride (monoacylglyceride or monoacylglycerol) is a glyceride in which a
glycerol molecule has formed an ester bond with exactly one fatty acid molecule. The
more formally correct terms in modern convention are acylglycerol and monoacylglycerol.
In normal metabolic processes, monoacylglycerols are hydrolyzed by monoacylglycerol
lipase to produce glycerol and a free fatty acid as required.
https://en.wikipedia.org/wiki/Monoglyceride
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Monoamine Oxidases
L-Monoamine oxidases (MAO) (EC 1.4.3.4) are a family of enzymes that catalyze the
oxidation of monoamines. They are found bound to the outer membrane of mitochondria in most cell types in the body. The enzyme was originally discovered by Mary Bernheim in the liver and was named tyramine oxidase. They belong to the protein family
of flavin-containing amine oxidoreductases.
Monoamine oxidases catalyze the oxidative deamination of monoamines. Oxygen is
used to remove an amine group from a molecule, resulting in the corresponding aldehyde and ammonia.
Monoamine oxidases contain the covalently bound cofactor FAD and are, thus, classified as flavoproteins.
They are well known enzymes in pharmacology, since they are the substrate for the action of a number of monoamine oxidase inhibitor drugs. MAO-A is particularly important in the catabolism of monoamines ingested in food. Both MAOs are also vital to the
inactivation of monoaminergic neurotransmitters, for which they display different
specificities.
Serotonin, melatonin, noradrenaline, and adrenaline are mainly broken down by
MAO-A.
Phenethylamine and benzylamine are mainly broken down by MAO-B.
Both forms break down dopamine, tyramine, and tryptamine equally.
Specific reactions catalyzed by MAO include:
Adrenaline or noradrenaline to 3,4-dihydroxymandelic acid
Metanephrine or normetanephrine to vanillylmandelic acid (VMA)
Dopamine to dihydroxyphenylacetic acid
3-Methoxytyramine to homovanillic acid
https://en.wikipedia.org/wiki/Monoamine_oxidase
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Monocyte
Monocytes are a type of white blood cell, or leukocyte. They are the largest type of leukocyte, and differentiate into: macrophages, dendritic cells, and foam cells. As a part of
the vertebrate innate immune system monocytes also influence the process of adaptive
immunity.
There are at least three types of monocyte in human blood. Two monocytes below (in
blue) are shown surrounded by red blood cells.
https://en.wikipedia.org/wiki/Monocyte
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Monooxygenase
Monooxygenases are enzymes that incorporate one hydroxyl group into subst
many metabolic pathways. In this reaction, the two atoms of dioxygen are red
one hydroxyl group and one H2O molecule by the concomitant oxidation of N
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Monosaccharide
Monosaccharides (from Greek monos: single, sacchar: sugar), also called simple sugars, are the most basic units of carbohydrates. They are fundamental units of carbohydrates and cannot be further hydrolized to simpler compounds. The general formula is
C(n)H2(n)O(n). They are the simplest form of sugar and are usually colorless, watersoluble, and crystalline solids. Some monosaccharides have a sweet taste. Examples of
monosaccharides include glucose (dextrose), fructose (levulose) and galactose.
Monosaccharides are the building blocks of disaccharides (such as sucrose and lactose)
and polysaccharides (such as cellulose and starch). Further, each carbon atom that supports a hydroxyl group (so, all of the carbons except for the primary and terminal carbon) is chiral, giving rise to a number of isomeric forms, all with the same chemical formula. For instance, galactose and glucose are both aldohexoses, but have different
physical structures and chemical properties. D-glucose and L-glucose are shown below.
https://en.wikipedia.org/wiki/Monosaccharide
Monoterpenes
Monoterpenes are a class of terpenes that consist of two isoprene units and h
https://en.wikipedia.org/wiki/Monoterpene
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Morpheein Model
The morpheein model of allosteric regulation is a dissociative concerted model.
A morpheein is a homo-oligomeric structure that can exist as an ensemble of physiologically significant and functionally different alternate quaternary assemblies. Transitions between alternate morpheein assemblies involve oligomer dissociation, conformational change in the dissociated state, and reassembly to a different oligomer. The required oligomer disassembly step differentiates the morpheein model for allosteric
regulation from the classic MWC and KNF models. Porphobilinogen synthase (PBGS)
is the prototype morpheein.
The morpheein model is similar to the MWC model, but with an added step of dissociation of the subunits. The MWC model proposes that flipping between R and T states
occurs by the complex as a whole and occurs on all units simultaneously.
The morpheein model instead proposes that the multi-subunit enzyme breaks down to
individual units which can then flip in structure and re-form the complex. In the morpheein model, only identically shaped units (all R, for example) can come together in
the complex, thus explaining the all-R- or all-T- state found in the MWC model.
A large number of enzymes, including prominent ones like citrate synthase, acetyl-CoA
carboxylase, glutamate dehydrogenase, ribonucleotide reductase and lactate dehydrogenase have behavior consistent with the morpheein model.
https://en.wikipedia.org/wiki/Allosteric_regulation#Morpheein_model
Motor Neurons
A motor neuron (or motoneuron) is a nerve cell (neuron) whose cell body is located in
the spinal cord and whose fiber (axon) projects outside the spinal cord to directly or indirectly control effector organs, mainly muscles and glands. Motor neurons' axons are
efferent nerve fibers that carry signals from the spinal cord to the effectors to produce
effects. Types of motor neurons are alpha motor neurons, beta motor neurons, and
gamma motor neurons.
There are upper motor neurons and lower motor neurons, with the cell type described
above being a lower motor neuron. Upper motor neurons are cortico-spinal interneurons that arise from the motor cortex and descend to the spinal cord where they activate the lower motor neurons through synapses. The term 'motor neuron' is usually restricted to the efferent neurons that actually innervate muscles (the lower motor neurons).
A single motor neuron may innervate many muscle fibers and a muscle fiber can undergo many action potentials in the time taken for a single muscle twitch. As a result, if
an action potential arrives before a twitch has completed, the twitches can superimpose on one another, either through summation or a tetanic contraction. In summation, the muscle is stimulated repetitively such that additional action potentials coming
from the somatic nervous system arrive before the end of the twitch. The twitches thus
superimpose on one another, leading to a force greater than that of a single twitch. A
tetanic contraction is caused by constant, very high frequency stimulation - the action
potentials come at such a rapid rate that individual twitches are indistinguishable, and
tension rises smoothly eventually reaching a plateau.
https://en.wikipedia.org/wiki/Motor_neuron
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Motor Proteins
Motor proteins are a class of molecular motors that are able to move along the surface
of a suitable substrate. They convert chemical energy into mechanical work by the hydrolysis of ATP. Flagellar rotation, however, is powered by a proton pump.
The best prominent example of a motor protein is the muscle protein myosin which
"motors" the contraction of muscle fibers in animals. Motor proteins are the driving
force behind most active transport of proteins and vesicles in the cytoplasm. Kinesins
and cytoplasmic dyneins play essential roles in intracellular transport such as axonal
transport and in the formation of the spindle apparatus and the separation of the chromosomes during mitosis and meiosis. Axonemal dynein, found in cilia and flagella, is
crucial to cell motility, for example in spermatozoa, and fluid transport, for example in
trachea.
Motor proteins utilizing the cytoskeleton for movement fall into two categories based
on their substrates: Actin motors such as myosin move along microfilaments through
interaction with actin. Microtubule motors such as dynein and kinesin move along microtubules through interaction with tubulin. There are two basic types of microtubule
motors: plus-end motors and minus-end motors, depending on the direction in which
they "walk" along the microtubule cables within the cell.
https://en.wikipedia.org/wiki/Motor_protein
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mRNA
Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the
protein products of gene expression. Following transcription of primary transcript
mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of
molecular biology.
As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into codons consisting of three base pairs each. Each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. The structure of a eukaryotic mRNA is shown below.
https://en.wikipedia.org/wiki/Messenger_RNA
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mRNA cap
In molecular biology, the five-prime cap (5 cap) is a specially altered nucleotide on the
5 end of some eukaryotic primary transcripts such as precursor messenger RNA. This
process, known as mRNA capping, is highly regulated and vital in the creation of stable
and mature messenger RNA able to undergo translation during protein synthesis. Mitochondrial and chloroplast mRNA are not capped.
In eukaryotes, the 5 cap (cap-0), found on the 5 end of an mRNA molecule, consists
of a guanine nucleotide connected to mRNA via an unusual 5 to 5 triphosphate linkage. This guanosine is methylated on the 7position directly after capping in vivo by a
methyltransferase. It is referred to as a 7-methylguanylate cap, abbreviated m7G.
The 5 cap has four main functions:
1
Nuclear export of RNA is regulated by the cap binding complex (CBC), which binds exclusively to capped RNA. The CBC is then recognized by the nuclear pore complex and
exported. Once in the cytoplasm after the pioneer round of translation, the CBC is replaced by the translation factors eIF4E and eIF4G of the eIF4F complex. This complex
is then recognized by other translation initiation machinery including the ribosome.
https://en.wikipedia.org/wiki/Five-prime_cap
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mTOR
tein kinase that regulates cell growth, cell proliferation, cell motility, cell su
Index
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Mucins
Mucins are a family of high molecular weight, heavily glycosylated proteins (glycocon
jugates) produced by epithelial tissues in most organisms of Kingdom Animalia.
Mucins' key characteristic is their ability to form gels. Therefore they are a key comp
nent in most gel-like secretions, serving functions from lubrication to cell signaling to
forming chemical barriers. They often take an inhibitory role. Some mucins are assoc
of the immune system. Overexpression of the mucin proteins, especially MUC1, is ass
ciated with many types of cancer.
Although some mucins are membrane-bound due to the presence of a hydrophobic
membrane-spanning domain that favors retention in the plasma membrane, most
Muscle Tissue
Muscle is a soft tissue found in most animals. Muscle cells contain protein filaments of
actin and myosin that slide past one another, producing a contraction that changes
both the length and the shape of the cell. Muscles function to produce force and motion. They are primarily responsible for maintaining and changing posture, locomotion, as well as movement of internal organs, such as the contraction of the heart and
the movement of food through the digestive system via peristalsis.
Muscle tissues are derived from the mesodermal layer of embryonic germ cells in a
process known as myogenesis. There are three types of muscle, skeletal or striated, cardiac, and smooth. Muscle action can be classified as being either voluntary or involuntary. Cardiac and smooth muscles contract without conscious thought and are termed
involuntary, whereas the skeletal muscles contract upon command. Skeletal muscles in
turn can be divided into fast and slow twitch fibers.
Muscles are predominantly powered by the oxidation of fats and carbohydrates, but anaerobic chemical reactions are also used, particularly by fast twitch fibers. These chemical reactions produce adenosine triphosphate (ATP) molecules that are used to power
the movement of the myosin heads.
The term muscle is derived from the Latin musculus meaning "little mouse" perhaps
because of the shape of certain muscles or because contracting muscles look like mice
moving under the skin.
https://en.wikipedia.org/wiki/Muscle
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Muscular Contraction
Muscle contraction is the activation of tension-generating sites within muscle fibers. In
physiology, muscle contraction does not mean muscle shortening because muscle tension can be produced without changes in muscle length such as holding a heavy book
or a dumbbell at the same position. The termination of muscle contraction is followed
by muscle relaxation, which is a return of the muscle fibers to their low tensiongenerating state.
https://en.wikipedia.org/wiki/Muscle_contraction
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Mut Genes
Mismatch repair systems are present in essentially all cells to correct errors
tects the mismatch, and the other recruits an endonuclease that cleaves the
thesized DNA strand close to the region of damage. In E. coli , the proteins
are the Mut class proteins. This is followed by removal of damaged region b
clease, resynthesis by DNA polymerase, and nick sealing by DNA ligase.
https://en.wikipedia.org/wiki/DNA_repair
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Mutagenicity
A mutagen is a physical or chemical agent that changes the genetic material, usually
DNA, of an organism and thus increases the frequency of mutations above the natural
background level. As many mutations can cause cancer, mutagens are therefore also
likely to be carcinogens, although not always necessarily so. Not all mutations are
caused by mutagens: so-called "spontaneous mutations" occur due to spontaneous hydrolysis, errors in DNA replication, repair and recombination.
Mutagens cause changes to the DNA that can affect the transcription and replication of
the DNA, which in severe cases can lead to cell death. The mutagen produces mutations in the DNA, and deleterious mutation can result in aberrant, impaired or loss of
function for a particular gene, and accumulation of mutations may lead to cancer. Mutagens may therefore be also carcinogens. However, some mutagens exert their mutagenic effect through their metabolites, and therefore whether such mutagens actually
become carcinogenic may be dependent on the metabolic processes of an organisms,
and a compound shown to be mutagenic in one organism may not necessarily be carcinogenic in another.
Different mutagens act on the DNA differently. Powerful mutagens may result in chromosomal instability, causing chromosomal breakages and rearrangement of the chromosomes such as translocation, deletion, and inversion. Such mutagens are called clastogens.
Mutagens may also modify the DNA sequence. The changes in nucleic acid sequences
by mutations include substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences. Although some of these mutations
are lethal or cause serious disease, many have minor effects as they do not result in residue changes that have significant effect on the structure and function of the proteins.
Many mutations are silent mutations, causing no visible effects at all, either because
they occur in non-coding or non-functional sequences, or they do not change the
amino-acid sequence due to the redundancy of codons.
Some mutagens can cause aneuploidy and change the number of chromosomes in the
cell. In the Ames test, where the varying concentrations of the chemical are used in the
test, the dose response curve obtained is nearly always linear, suggesting that there is
no threshold for mutagenesis. Similar results are also obtained in studies with radiations, indicating that there may be no safe threshold for mutagens. However, some proposed that low level of some mutagens may stimulate the DNA repair processes and
therefore may not necessarily be harmful.
https://en.wikipedia.org/wiki/Mutagen
Mutase
group from one position to another within the same molecule. Examples of
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Mutation
A mutation is a permanent alteration of the nucleotide sequence of the genome of an
organism, virus, or extrachromosomal DNA or other genetic elements. Mutations result from damage to DNA which is not repaired, errors in the process of replication, or
from the insertion or deletion of segments of DNA by mobile genetic elements. Mutations may or may not produce discernible changes in the observable characteristics
(phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including evolution, cancer, and the development of the immune system, including junctional diversity.
https://en.wikipedia.org/wiki/Mutation
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Mutations
sult from damage to DNA which is not repaired, errors in the process of rep
tions may or may not produce discernible changes in the observable charac
Index
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MWC
tical subunits. The concept of two distinct symmetric states is the central po
the MWC model. The main idea of the model is that regulated proteins, suc
Myelin Sheath
Myelin is a fatty white substance that surrounds the axon of some nerve cel
Myo-inositol
https://en.wikipedia.org/wiki/Inositol
Myogenesis
Myoglobin
Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the
iron- and oxygen-binding protein in blood, specifically in the red blood cells. In humans, myoglobin is only found in the bloodstream after muscle injury. It is an abnormal finding, and can be diagnostically relevant when found in blood.
Myoglobin is the primary oxygen-carrying pigment of muscle tissues. High concentrations of myoglobin in muscle cells allow organisms to hold their breath for a longer period of time.
https://en.wikipedia.org/wiki/Myoglobin
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Myosin
Myosins comprise a family of ATP-dependent motor proteins and are best known for
their role in muscle contraction and their involvement in a wide range of other motility
processes in eukaryotes. They are responsible for actin-based motility. The term was
originally used to describe a group of similar ATPases found in the cells of both striated muscle tissue and smooth muscle tissue. Following the discovery by Pollard and
Korn (1973) of enzymes with myosin-like function in Acanthamoeba castellanii, a
large number of divergent myosin genes have been discovered throughout eukaryotes.
Thus, although myosin was originally thought to be restricted to muscle cells (hence
myo-(s) + -in), there is no single "myosin" but rather a huge superfamily of genes
whose protein products share the basic properties of actin binding, ATP hydrolysis (ATPase enzyme activity), and force transduction. Virtually all eukaryotic cells contain myosin isoforms. Some isoforms have specialized functions in certain cell types (such as
muscle), while other isoforms are ubiquitous. The structure and function of myosin is
strongly conserved across species, to the extent that rabbit muscle myosin II will bind
to actin from an amoeba.
https://en.wikipedia.org/wiki/Myosin
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Myrcene
plants including bay, cannabis, ylang-ylang, wild thyme, parsley, and hops.
duced mainly semi-synthetically from myrcia, from which it gets its name.
https://en.wikipedia.org/wiki/Myrcene
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Myristic Acid
https://en.wikipedia.org/wiki/Myristic_acid
Myxothiazol
https://en.wikipedia.org/wiki/Myxothiazol
N-acetyl-glucosamine-1-phosphate
N-acetyl-glucosamine-6-phosphate
https://en.wikipedia.org/wiki/Peptidoglycan
N-acetylgalactosamine
N-Acetylgalactosamine (GalNAc), is an amino sugar derivative of galactose.
In humans it is the terminal carbohydrate forming the antigen of blood group A.
https://en.wikipedia.org/wiki/N-Acetylgalactosamine
N-acetylglucosamine
N-acetylglucosamine (N-acetyl-D-glucosamine, or GlcNAc, or NAG) is a monosaccharide and a derivative of glucose. It is an amide between glucosamine and acetic acid. It
has a molecular formula of C8H15NO6, a molar mass of 221.21 g/mol, and it is significant in several biological systems.
It is part of a biopolymer in the bacterial cell wall, built from alternating units of
GlcNAc and N-acetylmuramic acid (MurNAc), cross-linked with oligopeptides at the
lactic acid residue of MurNAc. This layered structure is called peptidoglycan (formerly
called murein).
GlcNAc is the monomeric unit of the polymer chitin, which forms the outer coverings
of insects and crustaceans. It is the main component of the radulas of mollusks, the
beaks of cephalopods, and a major component of the cell walls of most fungi.
Polymerized with glucuronic acid, it forms hyaluronan.
GlcNAc has been reported to be an inhibitor of elastase release from human polymorphonulear leukocytes (range 8 - 17% inhibition), however this is much weaker than the
inhibition seen with N-acetyl-galactosamine (range 92 - 100%).
https://en.wikipedia.org/wiki/N-Acetylglucosamine
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N-acetylglutamate
N-acetylglutamic acid (abbreviated NAcGlu) is biosynthesized from glutamic acid and
acetyl-CoA by the enzyme N-acetylglutamate synthase. Arginine is the activator for thi
reaction.
The reverse reaction, hydrolysis of the acetyl group, is catalyzed by a specific hydrolase. NAcGlu activates carbamoyl phosphate synthetase in the urea cycle.
https://en.wikipedia.org/wiki/N-Acetylglutamic_acid
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N-acetylglutamate Dehydrogenase
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N-acetylglutamate Kinase
Acetylglutamate kinase is an enzyme that catalyzes the chemical reaction:
Thus, the two substrates of this enzyme are ATP and N-acetyl-L-glutamate,
two products are ADP and N-acetyl-L-glutamyl 5-phosphate.
tor. This enzyme participates in urea cycle and metabolism of amino groups
https://en.wikipedia.org/wiki/Acetylglutamate_kinase
N-acetylornithinase
N-acetylornithine
N-formyl-methionine
formyl group has been added to the amino group. It is specifically used for i
protein synthesis from bacterial and organellar genes, and may be removed
translationally.
https://en.wikipedia.org/wiki/N-Formylmethionine
N-glycosylation
N-linked
portant for both the structure and function of some eukaryotic proteins. Th
N-linked Glycosylation
portant for both the structure and function of some eukaryotic proteins. Th
N-terminal
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end
acid with a free amine group (-NH2). By convention, peptide sequences are written N
terminus to C-terminus, left to right in LTR languages. This correlates the translation
direction to the text direction (because when a protein is translated from messenger
RNA, it is created from N-terminus to C-terminus - amino acids are added to the carbonyl end).
https://en.wikipedia.org/wiki/N-terminus
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N,N-Methylene-bisacrylamide
https://en.wikipedia.org/wiki/N,N%27-Methylenebisacrylamide
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N5,N10-Methylene Tetrahydrofolate
N5,N10-Methylenetetrahydrofolate (5,10-CH2-THF) is the substrate used by the enzyme
methylenetetrahydrofolate reductase (MTHFR) to generate 5-methyltetrahydrofolate
(5-MTHF, or levomefolic acid).
N5,N10-CH2-THF can also be used as a coenzyme in the biosynthesis of thymidine. To
be specific, it is the C1-donor in the reactions catalyzed by thymidylate synthase and
thymidylate synthase (FAD). It also acts as a cofactor in the synthesis of serine from
glycine via the enzyme serine hydroxymethyl transferase.
https://en.wikipedia.org/wiki/5,10-Methylenetetrahydrofolate
N10-formyl-tetrahydrofolate
Index
Find Term
Na+/K+ ATPase
K+ ATPase enzyme is a solute pump that pumps sodium out of cells while p
tassium into cells, both against their concentration gradients. This pumping
(it uses energy from ATP) and is important for cell physiology. An example
is nerve conduction.
https://en.wikipedia.org/wiki/Na%2B/K%2B-ATPase
Index
Find Term
NAD+
Nicotinamide adenine dinucleotide (NAD+) is a coenzyme found in all living cells. The
compound is a dinucleotide, because it consists of two nucleotides joined through their
phosphate groups. One nucleotide contains an adenine base and the other nicotinamide. Nicotinamide adenine dinucleotide exists in two forms, an oxidized and reduced
form abbreviated as NAD+ and NADH respectively.
In metabolism, nicotinamide adenine dinucleotide is involved in redox reactions, carrying electrons from one reaction to another. The coenzyme is, therefore, found in two
forms in cells: NAD+ is an oxidizing agent it accepts electrons from other molecules
and becomes reduced. This reaction forms NADH, which can then be used as a reducing agent to donate electrons. These electron transfer reactions are the main function
of NAD+. However, it is also used in other cellular processes, the most notable one being a substrate of enzymes that add or remove chemical groups from proteins, in posttranslational modifications. Because of the importance of these functions, the enzymes
involved in NAD metabolism are targets for drug discovery.
In organisms, NAD+ can be synthesized from simple building-blocks (de novo) from
the amino acids tryptophan or aspartic acid. In an alternative fashion, more complex
components of the coenzymes are taken up from food as the vitamin called niacin. Similar compounds are released by reactions that break down the structure of NAD+. These
preformed components then pass through a salvage pathway that recycles them back
into the active form. Some NAD+ is also converted into nicotinamide adenine dinucleotide phosphate (NADP+). The chemistry of this related coenzyme is similar to that of
NAD+, but it has different roles in metabolism.
https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide
Index
Find Term
G-G
G-G
G-G
G-G
G-G
G-G
G-G
Chapter 3 - Membranes: Other Considerations
Chapter 3 - Membranes: Other Considerations
Chapter 4 - Catalysis: Basic Principles
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Membranes
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
NADH
Nicotinamide adenine dinucleotide (NAD+) is a coenzyme found in all living cells. The
compound is a dinucleotide, because it consists of two nucleotides joined through their
phosphate groups. One nucleotide contains an adenine base and the other nicotinamide. Nicotinamide adenine dinucleotide exists in two forms, an oxidized and reduced
form abbreviated as NAD+ and NADH respectively.
In metabolism, nicotinamide adenine dinucleotide is involved in redox reactions, carrying electrons from one reaction to another. The coenzyme is, therefore, found in two
forms in cells: NAD+ is an oxidizing agent it accepts electrons from other molecules
and becomes reduced. This reaction forms NADH, which can then be used as a reducing agent to donate electrons. These electron transfer reactions are the main function
of NAD+. However, it is also used in other cellular processes, the most notable one being a substrate of enzymes that add or remove chemical groups from proteins, in posttranslational modifications. Because of the importance of these functions, the enzymes
involved in NAD metabolism are targets for drug discovery.
In organisms, NAD+ can be synthesized from simple building-blocks (de novo) from
the amino acids tryptophan or aspartic acid. In an alternative fashion, more complex
components of the coenzymes are taken up from food as the vitamin called niacin. Similar compounds are released by reactions that break down the structure of NAD+. These
preformed components then pass through a salvage pathway that recycles them back
into the active form. Some NAD+ is also converted into nicotinamide adenine dinucleotide phosphate (NADP+). The chemistry of this related coenzyme is similar to that of
NAD+, but it has different roles in metabolism.
https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide
Index
Find Term
G-G
G-G
G-G
G-G
G-G
G-G
G-G
G-G
G-G
G-G
Chapter 3 - Membranes: Other Considerations
Chapter 3 - Membranes: Other Considerations
Chapter 3 - Membranes: Other Considerations
Chapter 4 - Catalysis: Basic Principles
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Fats and Fatty Acids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Point by Point: Membranes
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
NADP+
NADP+ is a cofactor used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent. NADPH is the reduced form of NADP+.
NADP+ differs from NAD+ in the presence of an additional phosphate group on the 2'
position of the ribose ring that carries the adenine moiety.
In photosynthetic organisms, NADPH is produced by ferredoxin-NADP+ reductase in
the last step of the electron chain of the light reactions of photosynthesis. It is used as
reducing power for the biosynthetic reactions in the Calvin cycle to assimilate carbon
dioxide. It is used to help turn the carbon dioxide into glucose. It is also needed in the
reduction of nitrate into ammonia for plant assimilation in nitrogen cycle.
The major source of NADPH in animals and other non-photosynthetic organisms is
the pentose phosphate pathway. However, there are several other lesser-known mechanisms of generating NADPH, all of which depend on the presence of mitochondria. The
key enzymes in these processes are: NADP-linked malic enzyme, NADP-linked
isocitrate dehydrogenase, NADP+-linked glutamate dehydrogenase and nicotinamide
nucleotide transhydrogenase. The isocitrate dehydrogenase mechanism appears to be
the major source of NADPH in fat and possibly also liver cells. Also, in mitochondria,
NADH kinase produces NADPH and ADP, using NADH and ATP as substrates.
https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate
Index
Find Term
G-G
G-G
G-G
Chapter 4 - Catalysis: Control of Activity
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 5 - Energy: Photophosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
NADPH
NADP+ is a cofactor used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent. NADPH is the reduced form of NADP+.
NADP+ differs from NAD+ in the presence of an additional phosphate group on the 2'
position of the ribose ring that carries the adenine moiety.
In photosynthetic organisms, NADPH is produced by ferredoxin-NADP+ reductase in
the last step of the electron chain of the light reactions of photosynthesis. It is used as
reducing power for the biosynthetic reactions in the Calvin cycle to assimilate carbon
dioxide. It is used to help turn the carbon dioxide into glucose. It is also needed in the
reduction of nitrate into ammonia for plant assimilation in nitrogen cycle.
The major source of NADPH in animals and other non-photosynthetic organisms is
the pentose phosphate pathway. However, there are several other lesser-known mechanisms of generating NADPH, all of which depend on the presence of mitochondria. The
key enzymes in these processes are: NADP-linked malic enzyme, NADP-linked
isocitrate dehydrogenase, NADP+-linked glutamate dehydrogenase and nicotinamide
nucleotide transhydrogenase. The isocitrate dehydrogenase mechanism appears to be
the major source of NADPH in fat and possibly also liver cells. Also, in mitochondria,
NADH kinase produces NADPH and ADP, using NADH and ATP as substrates.
https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate
Index
Find Term
NADPH Oxidase
The NADPH oxidase (nicotinamide adenine dinucleotide phosphate-oxidase) is a
membrane-bound enzyme complex that faces the extracellular space. It can be found
the cell across the membrane and coupling these to molecular oxygen to produce sup
oxide anion, a reactive free-radical.
Superoxide kills bacteria and fungi by mechanisms that are not yet fully understood,
but may inactivate critical metabolic enzymes, initiate lipid peroxidation, and liberat
redox-active iron, which allows the generation of indiscriminate oxidants such as the
hydroxyl radical. It is presumed that superoxide kills bacteria directly, as the virulenc
genes are deleted. However, downstream products of superoxide also include hydrog
peroxide and hypochlorous acid, the reactive agent in bleach.
https://en.wikipedia.org/wiki/NADPH_oxidase
Index
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NAG Synthetase
karyotes and eukaryotes, although its role and structure differ widely depen
species. NAG can be used in the production of ornithine and arginine, two i
mammals, NAGS is expressed primarily in the liver and small intestine, and
ized to the mitochondrial matrix.
https://en.wikipedia.org/wiki/N-Acetylglutamate_synthase
Index
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NaOH
Sodium hydroxide (NaOH), also known as lye and caustic soda, is an inorga
pound. It is a white solid and highly caustic metallic base and alkali salt of s
NDP Phosphatase
NDPK
Nucleoside-diphosphate kinases (NDPKs, also NDP Kinase, (poly)nucleotide kinases
and nucleoside diphosphokinases) are enzymes that catalyze the exchange of terminal
phosphate between different nucleoside diphosphates (NDP) and triphosphates (NTP)
in a reversible manner to produce nucleotide triphosphates. Many NDP serve as acceptor while NTP are donors of phosphate group. The general reaction via ping-pong
mechanism is as follows:
XDP + YTP XTP + YDP
(X and Y each represent different nitrogenous base).
NDPK activities maintain an equilibrium between the concentrations of different nucleoside triphosphates such as, for example, when guanosine triphosphate (GTP) produced in the citric acid cycle is converted to adenosine triphosphate (ATP). Other activities include cell proliferation, differentiation and development, signal transduction, G
protein-coupled receptor, endocytosis, and gene expression.
https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase
Index
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Neddylated
Index
Find Term
Neotame
Neotame is an artificial sweetener made by NutraSweet that is between 7,000 and
13,000 times sweeter than sucrose (table sugar). It is moderately heat-stable, extremely potent, rapidly metabolized, completely eliminated, and does not appear to accumulate in the body.
The major metabolic pathway is hydrolysis of the methyl ester by esterases that are present throughout the body, which yields de-esterified neotame and methanol. Because
only trace amounts of neotame are needed to sweeten foods, the amount of methanol
derived from neotame is much lower than that found in common foods.
https://en.wikipedia.org/wiki/Neotame
Nernst Equation
In electrochemistry, the Nernst equation is an equation that relates the reduction po-
tential of a half-cell (or the total voltage, i.e. the electromotive force, of the full cell) at
any point in time to the standard electrode potential, temperature, activity, and reac-
tion quotient of the underlying reactions and species used. When the reaction quotien
is equal to the equilibrium constant of the reaction for a given temperature, i.e. when
the concentration of species are at their equilibrium values, the Nernst equation gives
the equilibrium voltage of the half-cell (or the full cell), which is zero. At equilibrium,
Q = K, G = 0, and therefore, E = 0. It is named after the German physical chemist
who first formulated it, Walther Nernst.
https://en.wikipedia.org/wiki/Nernst_equation
Index
Find Term
Nerve Tissue
Nervous tissue is the main component of the two parts of the nervous system. The
brain and spinal cord of the central nervous system (CNS), and the branching peripheral nerves of the peripheral nervous system (PNS), which regulates and controls bodily functions and activity. It is composed of neurons, or nerve cells, which receive and
transmit impulses, and neuroglia, also known as glial cells or more commonly as just
glia (from the Greek, meaning glue), which assist the propagation of the nerve impulse
as well as providing nutrients to the neuron.
Nervous tissue is made up of different types of nerve cells, all of which have an axon,
the long stem-like part of the cell that sends action potential signals to the next cell.
Functions of the nervous system are sensory input, integration, control of muscles and
glands, homeostasis, and mental activity.
https://en.wikipedia.org/wiki/Nervous_tissue
Neuraminidase
dase, a drug target for the prevention of the spread of influenza infection. T
to the virus than others. Other homologs are found in mammalian cells, wh
range of functions. At least four mammalian sialidase homologs have been
the human genome.
https://en.wikipedia.org/wiki/Neuraminidase
Index
Find Term
Neurocan
Neurocan core protein is a protein that in humans is encoded by the NCAN gene. Ne
modulated by a variety of factors, but mice in which the NCAN gene has been knocke
out show no easily observable defects in brain development or behavior. However, a
firmed that association. The 2012 study examined correlations between NCAN allele
and various symptoms of bipolar disorder, and also examined the behavior of NCAN
knockout mice. In the human subjects, it was found that NCAN genotype was strongl
associated with manic symptoms but not with depressive symptoms. In the mice, the
absence of functional Neurocan resulted in a variety of manic-like behaviors, which
could be normalized by administering lithium.
https://en.wikipedia.org/wiki/Neurocan
Neurons
A neuron is an electrically excitable cell that processes and transmits information
through electrical and chemical signals. These signals between neurons occur via synapses, specialized connections with other cells. Neurons can connect to each other to
form neural networks. Neurons are the core components of the brain and spinal cord
of the central nervous system (CNS), and of the ganglia of the peripheral nervous system (PNS).
A typical neuron consists of a cell body (soma), dendrites, and an axon.
https://en.wikipedia.org/wiki/Neuron
Index
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Neuropeptide Y
in the brain and in the autonomic nervous system of humans. Slight variatio
peptide are found in many other animals. In the autonomic system it is prod
strictor and also causes growth of fat tissue. In the brain, it is produced in va
increasing food intake and storage of energy as fat, reducing anxiety and stre
ing pain perception, affecting the circadian rhythm, reducing voluntary alcoh
lowering blood pressure, and controlling epileptic seizures.
https://en.wikipedia.org/wiki/Neuropeptide_Y
Index
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Neurotoxins
affect function in both developing and mature nervous tissue. The term can
ganese glutamate, nitric oxide (NO), botulinum toxin (e.g. Botox), tetanus t
tetrodotoxin. Some substances such as nitric oxide and glutamate are in fac
for proper function of the body and only exert neurotoxic effects at excessiv
tions.
https://en.wikipedia.org/wiki/Neurotoxin
Neurotransmission
Neurotransmission, also called synaptic transmission, is the process by which signaling molecules called neurotransmitters are released by a neuron (the presynaptic neuron), and bind to and activate the receptors of another neuron (the postsynaptic neuron). Neurotransmission is essential for the process of communication between two
neurons. Synaptic transmission relies on: the availability of the neurotransmitter; the
release of the neurotransmitter by exocytosis; the binding of the postsynaptic receptor
by the neurotransmitter; the functional response of the postsynaptic cell; and the subsequent removal or deactivation of the neurotransmitter.
https://en.wikipedia.org/wiki/Neurotransmission
Index
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Neurotransmitter
Neurotransmitters are endogenous chemicals that enable neurotransmission. They
transmit signals across a chemical synapse, such as a neuromuscular junction, from
one neuron (nerve cell) to another "target" neuron, muscle cell, or gland cell. Neurotransmitters are released from synaptic vesicles in synapses into the synaptic cleft,
where they are received by receptors on the target cells. Many neurotransmitters are
synthesized from simple and plentiful precursors such as amino acids, which are readily available from the diet and only require a small number of biosynthetic steps for
conversion. Neurotransmitters play a major role in shaping everyday life and functions. Their exact numbers are unknown, but more than 100chemical messengers
have been uniquely identified.
https://en.wikipedia.org/wiki/Neurotransmitter
Index
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Neutrophils
Neutrophil (also known as neutrophils or occasionally neutrocytes) are the most abundant type of granulocytes and the most abundant (40% to 75%) type of white blood
cells in most mammals. They form an essential part of the innate immune system.
They are formed from stem cells in the bone marrow. They are short-lived and highly
motile, or mobile, as they can enter parts of tissue where other cells/molecules
wouldn't be able to enter otherwise.
Neutrophils are a type of phagocyte and are normally found in the bloodstream. During the beginning (acute) phase of inflammation, particularly as a result of bacterial infection, environmental exposure, and some cancers, neutrophils are one of the firstresponders of inflammatory cells to migrate towards the site of inflammation.
https://en.wikipedia.org/wiki/Neutrophil
Index
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NH4+
The ammonium cation is a positively charged polyatomic ion with the chem
mula NH4+. It is formed by the protonation of ammonia (NH3) in water.
ans, it is converted in the urea cycle to urea, because urea is less toxic and c
is converted into uric acid, which is solid and can therefore be excreted with
water loss.
https://en.wikipedia.org/wiki/Ammonium
Index
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Niacin
Niacin, also known as vitamin B3 and nicotinic acid, is an organic compound with the
formula C6H5NO2 and, depending on the definition used, one of the 20 to 80 essential
human nutrients. Pharmaceutical and supplemental niacin are primarily used to treat
hypercholesterolemia (high cholesterol) and pellagra (niacin deficiency). Insufficient
niacin in the diet can cause nausea, skin and mouth lesions, anemia, headaches, and
tiredness.
This colorless, water-soluble solid is a derivative of pyridine, with a carboxyl group
(COOH) at the 3-position. Other forms of vitamin B3 include the corresponding amide
and nicotinamide ("niacinamide"), where the carboxyl group has been replaced by a
carboxamide group (CONH2), as well as more complex amides and a variety of esters.
Niacin cannot be directly converted to nicotinamide, but both compounds are precursors of the coenzymes nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) in vivo.
https://en.wikipedia.org/wiki/Niacin
Nicotinamide
Nicotinamide, also known as niacinamide, NAA, and nicotinic amide, is the amide of
mide does not have the same pharmacological and toxic effects of niacin, which occur
incidental to niacin's conversion. Thus nicotinamide does not reduce cholesterol or
cause flushing, although nicotinamide may be toxic to the liver at doses exceeding 3 g
day for adults. In cells, niacin is incorporated into nicotinamide adenine dinucleotide
(NAD) and nicotinamide adenine dinucleotide phosphate (NADP), although the pathways for nicotinic acid amide and nicotinic acid are very similar.
https://en.wikipedia.org/wiki/Nicotinamide
Index
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Nitric Oxide
Nitric oxide (nitrogen oxide, nitrogen monoxide) is a molecular, chemical compound
with chemical formula of NO. One of several oxides of nitrogen, it is a colorless gas under standard conditions. Nitric oxide is a free radicali.e., its bonding structure includes an unpaired electronand it is in the class of heteronuclear diatomic molecules
that are of historic theoretical interest (for the insights they gave in formulating early
modern theories of bonding).
In mammals including humans, NO is an important cellular signaling molecule involved in many physiological and pathological processes. It is a powerful vasodilator
with a short half-life of a few seconds in the blood.
https://en.wikipedia.org/wiki/Nitric_oxide
Index
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Index
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Nitrogenous Base
gen atom that has the chemical properties of a base. The main biological fun
pyrimidine and purine. They are non-polar and due to their aromaticity, pla
pyrimidines and purines resemble pyridine and are thus weak bases and re
reactive towards electrophilic aromatic substitution.
https://en.wikipedia.org/wiki/Nitrogenous_base
Index
Find Term
Nitrosamines
Nitrosamines are chemical compounds of the chemical structure R1N(R2)N=O, that
is, a nitroso group bonded to an amine. Most nitrosamines are carcinogenic. Nitrosamines are used in the manufacture of some cosmetics, pesticides, and in most rubber
products.
Nitrosamines can cause cancers in a wide variety of animal species, a feature that suggests that they may also be carcinogenic in humans. At present, available epidemiological evidence from case-control studies on nitrite and nitrosamine intake supports a
positive association with gastric cancer risk. Regarding oesophageal cancer, available
evidence supports a positive association between nitrite and nitrosamine intake and
gastric cancer (GC), between meat and processed meat intake and GC and oesophageal
cancer, and between preserved fish, vegetable and smoked food intake and GC, but is
not conclusive.
https://en.wikipedia.org/wiki/N-acetylglucosamine-1-phosphate_transferase
Nitrous Oxide
gery and dentistry for its anaesthetic and analgesic effects. It is known as "laug
gas" due to the euphoric effects of inhaling it, a property that has led to its recr
use as a dissociative anaesthetic.
Nitrous oxide gives rise to nitric oxide (NO) on reaction with oxygen atoms, an
NO in turn reacts with ozone. As a result, it is the main naturally occurring reg
stratospheric ozone.
https://en.wikipedia.org/wiki/Nitrous_oxide
Index
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NMR
cific resonance frequency which depends on the strength of the magnetic fie
Non-competitive Inhibition
Non-competitive inhibition is a type of enzyme inhibition where the inhibitor reduces
the activity of the enzyme and binds equally well to the enzyme whether or not it has
already bound the substrate.
Non-competitive inhibition models a system where the inhibitor and the substrate may
both be bound to the enzyme at any given time. When both the substrate and the inhibitor are bound, the enzyme-substrate-inhibitor complex cannot form product and can
only be converted back to the enzyme-substrate complex or the enzyme-inhibitor complex. Non-competitive inhibition is distinguished from general mixed inhibition in that
the inhibitor has an equal affinity for the enzyme and the enzyme-substrate complex.
The most common mechanism of non-competitive inhibition involves reversible binding of the inhibitor to an allosteric site, but it is possible for the inhibitor to operate via
other means including direct binding to the active site. It differs from competitive inhibition in that the binding of the inhibitor does not prevent binding of substrate, and
vice versa, it simply prevents product formation for a limited time.
This type of inhibition reduces the maximum rate of a chemical reaction without changing the apparent binding affinity of the catalyst for the substrate (Kmapp see
Michaelis-Menten kinetics).
https://en.wikipedia.org/wiki/Non-competitive_inhibition
Non-competitive Inhibitor
A non-competitive inhibitor of an enzymatic reaction is a molecule that competes with
the substrate of an enzyme for binding the enzyme and it stops action of the active site.
Non-competitive inhibitors typically resemble the substrate they compete with.
Non-competitive inhibition models a system where the inhibitor and the substrate may
both be bound to the enzyme at any given time. When both the substrate and the inhibitor are bound, the enzyme-substrate-inhibitor complex cannot form product and can
only be converted back to the enzyme-substrate complex or the enzyme-inhibitor complex. Non-competitive inhibition is distinguished from general mixed inhibition in that
the inhibitor has an equal affinity for the enzyme and the enzyme-substrate complex.
The most common mechanism of non-competitive inhibition involves reversible binding of the inhibitor to an allosteric site, but it is possible for the inhibitor to operate via
other means including direct binding to the active site. It differs from competitive inhibition in that the binding of the inhibitor does not prevent binding of substrate, and
vice versa, it simply prevents product formation for a limited time.
This type of inhibition reduces the maximum rate of a chemical reaction without changing the apparent binding affinity of the catalyst for the substrate.
https://en.wikipedia.org/wiki/Non-competitive_inhibition
Index
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Index
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Index
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Non-polar
Index
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Nonanoic Acid
with an unpleasant, rancid odor. It is nearly insoluble in water, but very sol
roform, ether, and hexane.
https://en.wikipedia.org/wiki/Nonanoic_acid
Noradrenalin
Norepinephrine (NE), also called noradrenaline (NA) or noradrenalin, is an organic
chemical in the catecholamine family that functions in the human brain and body as a
hormone and neurotransmitter.
Norepinephrine is synthesized and released by the central nervous system, and also by
a division of the autonomic nervous system called the sympathetic nervous system. In
the brain, norepinephrine is produced in closely packed brain cell neurons or nuclei
that are small yet exert powerful effects on other brain areas.
The general function of norepinephrine is to mobilize the brain and body for action.
Norepinephrine release is lowest during sleep, rises during wakefulness, and reaches
much higher levels during situations of stress or danger, in the so-called fight-or-flight
response.
https://en.wikipedia.org/wiki/Norepinephrine
Norepinephrine
Norepinephrine (NE), also called noradrenaline (NA) or noradrenalin, is an organic
chemical in the catecholamine family that functions in the human brain and body as a
hormone and neurotransmitter.
Norepinephrine is synthesized and released by the central nervous system, and also by
a division of the autonomic nervous system called the sympathetic nervous system. In
the brain, norepinephrine is produced in closely packed brain cell neurons or nuclei
that are small yet exert powerful effects on other brain areas.
The general function of norepinephrine is to mobilize the brain and body for action.
Norepinephrine release is lowest during sleep, rises during wakefulness, and reaches
much higher levels during situations of stress or danger, in the so-called fight-or-flight
response.
https://en.wikipedia.org/wiki/Norepinephrine
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raphy, the least polar compounds elute first and the most polar compounds
with a slightly more polar solvent such as isopropanol, ethyl acetate or chlo
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Northern Blot
volves the use of electrophoresis to separate RNA samples by size, and dete
Northern blotting takes its name from its similarity to the first blotting tech
Southern blot, named for biologist Edwin Southern. The major difference is
rather than DNA, is analyzed in the northern blot.
https://en.wikipedia.org/wiki/Northern_blot
NSAIDs
The term nonsteroidal distinguishes these drugs from steroids, which, amo
The most prominent members of this group of drugs, aspirin, ibuprofen and
are all available over the counter in most countries.
https://en.wikipedia.org/wiki/Nonsteroidal_anti-inflammatory_drug
NTP Phosphatase
CDP and as such, is important also for providing substrate (CDP) for ribonu
ductase to make dCDP.
cific resonance frequency which depends on the strength of the magnetic fie
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Nuclease
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase".
Nucleases are usually further divided into endonucleases and exonucleases, although
some of the enzymes may fall in both categories. Well known nucleases are deoxyribonuclease and ribonuclease.
https://en.wikipedia.org/wiki/Nuclease
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Nucleation
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Nucleic Acid
Nucleic acids are biopolymers, or large biomolecules, essential for all known forms of
life. Nucleic acids, which include DNA (deoxyribonucleic acid) and RNA (ribonucleic
acid), are made from monomers known as nucleotides. Each nucleotide has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is
deoxyribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA. When all
three components are combined, they form a nucleic acid. Nucleotides are also known
as phosphate nucleotides.
Nucleic acids are among the most important biological macromolecules (others being
amino acids/proteins, sugars/carbohydrates, and lipids/fats). They are found in abundance in all living things, where they function in encoding, transmitting and expressing
genetic informationin other words, information is conveyed through the nucleic acid
sequence, or the order of nucleotides within a DNA or RNA molecule. Strings of nucleotides strung together in a specific sequence are the mechanism for storing and transmitting hereditary, or genetic information via protein synthesis.
Nucleic acids were discovered by Friedrich Miescher in 1869. Experimental studies of
nucleic acids constitute a major part of modern biological and medical research, and
form a foundation for genome and forensic science, as well as the biotechnology and
pharmaceutical industries.
https://en.wikipedia.org/wiki/Nucleic_acid
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Nucleoid
The nucleoid (meaning nucleus-like) is an irregularly shaped region within
prokaryote that contains all or most of the genetic material, called genopho
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looping. The most studied NAPs are HU, H-NS, Fis, CbpA, Dps that organiz
teins can form clusters (like H-NS does) in order to locally compact specific
regions, or be scattered throughout the chromosome (HU, Fis) and they see
Nucleolus
The nucleolus is the largest structure in the nucleus of eukaryotic cells, where it primarily serves as the site of ribosome synthesis and assembly. Nucleoli also have other important functions like assembly of signal recognition particles and playing a role in the
cell's response to stress. Nucleoli are made of proteins and RNA and form around specific chromosomal regions. Malfunction of nucleoli can be the cause of several human
diseases.
https://en.wikipedia.org/wiki/Nucleolus
Nucleophile
A nucleophile is a chemical species that donates an electron pair to an electrophile to
form a chemical bond in relation to a reaction. All molecules or ions with a free pair of
electrons or at least one Pi bond can act as nucleophiles. Because nucleophiles donate
electrons, they are by definition Lewis bases.
Neutral nucleophilic reactions with solvents such as alcohols and water are named sol-
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Nucleophilic
Something that is nucleophilic exhibits the traits of a nucleophile. A nucleophile is a
chemical species that donates an electron pair to an electrophile to form a chemical
bond in relation to a reaction. All molecules or ions with a free pair of electrons or at
least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they
are by definition Lewis bases.
Nucleophilic describes the affinity of a nucleophile to the nuclei. Nucleophilicity, sometimes referred to as nucleophile strength, refers to a substance's nucleophilic character
and is often used to compare the affinity of atoms.
Neutral nucleophilic reactions with solvents such as alcohols and water are named solvolysis. Nucleophiles may take part in nucleophilic substitution, whereby a nucleophile
becomes attracted to a full or partial positive charge.
https://en.wikipedia.org/wiki/Nucleophile
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Nucleoporin
The nucleoporins are a family of proteins which are the constituent building blocks of
the nuclear pore complex (NPC). The nuclear pore complex is a massive structure that
extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm. Nuclear pores in turn allow
the transport of water-soluble molecules across the nuclear envelope. Nucleoporins, a
family of around 30 proteins, are the main components of the nuclear pore complex in
eukaryotic cells. Nucleoporin 62 is the most abundant member of this family. Nucleoporins are able to transport molecules across the nuclear envelope at a very high rate.
A single NPC is able to transport 60,000 protein molecules across the nuclear envelope
every minute.
Nucleoporins mediate transport of macromolecules between the cell nucleus and cytoplasm in eukaryotes. Certain members of the nucleoporin family form the structural
scaffolding of the nuclear pore complex. However, nucleoporins primarily function by
interacting with transport molecules known as karyopherins, also known as Kaps.
These karyopherins interact with nucleoporins that contain FG peptide repeats, that is,
they contain repeating sequences of the amino acids phenylalanine (F) and glycine (G).
In doing so, karyopherins are able to shuttle their cargo across the nuclear envelope.
Nucleoporins are only required for the transport of large hydrophilic molecules above
40 kDa, as smaller molecules pass through nuclear pores via passive diffusion. Nucleoporins play an important role in the transport of mRNA from the nucleus to the cytoplasm after transcription. Depending on their function, certain nucleoporins are localized to a single side of the nuclear pore complex, either cytosolic or nucleoplasmic.
Other nucleoporins may be found on both faces. Interestingly, it has been recently
shown that FG nucleoporins have specific evolutionary conserved features encoded in
their sequences that provide insight into how they regulate the transport of molecules
through the nuclear pore complex (NPC).
https://en.wikipedia.org/wiki/Nucleoporin
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Nucleoside
Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous
base) and a 5-carbon sugar (either ribose or deoxyribose), whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the base is bound to either ribose or deoxyribose via a -glycosidic linkage. Examples of nucleosides include cytidine (shown below), uridine, adenosine, guanosine,
thymidine and inosine.
https://en.wikipedia.org/wiki/Nucleoside
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Nucleoside Diphosphokinase
and nucleoside diphosphokinases) are enzymes that catalyze the exchange of term
cleoside triphosphates such as, for example, when guanosine triphosphate (GTP) p
duced in the citric acid (Krebs) cycle is converted to adenosine triphosphate (ATP)
Other activities include cell proliferation, differentiation and development, signal
duction, G protein-coupled receptor, endocytosis, and gene expression.
https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase
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Nucleoside Monophosphates
of nucleic acids like DNA (deoxyribonucleic acid) and RNA (ribonucleic acid
Nucleotides also function to carry packets of energy within the cell in the fo
nucleoside triphosphates (ATP, GTP, CTP and UTP), playing a central role i
Nucleoside Triphosphates
A nucleoside triphosphate (NTP) is a molecule containing a nucleoside bound to three
phosphate groups. It is thus one type of nucleotide. Nucleotide derivatives are necessary for life, as they are the building blocks of nucleic acids and have thousands of
other roles in cell metabolism and regulation. NTPs generally provide energy and phosphate groups for phosphorylation.
Natural nucleoside triphosphates include adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), 5-methyluridine triphosphate
(m5UTP), and uridine triphosphate (UTP). ATP is a major source of cellular energy.
GTP is a very frequent cofactor of enzymes and proteins.
The terms ATP, GTP, CTP, and UTP refer to those nucleoside triphosphates that contain ribose. The nucleoside triphosphates containing deoxyribose are called dNTPs,
and take the prefix deoxy- in their names and small d- in their abbreviations: deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine
triphosphate (dCTP), deoxythymidine triphosphate (dTTP) and deoxyuridine triphosphate (dUTP). The dNTPs are the building blocks for DNA (they lose two of the phosphate groups in the process of incorporation).
Apart from (d)ATP, (d)GTP, (d)CTP, (d)TTP and (d)UTP, there are other less abundant NTPs, such as intermediates of nucleotide metabolism, but also "rare" natural nucleotides or even artificial nucleotides. An example of rare NTPs are the tautomeric
forms of some NTPs. They can cause mismatched base pairing during DNA replication.
For example, a tautomeric form of cytosine is capable of forming 3 hydrogen bonds
with adenine, and it will spontaneously tautomerize to its original cytosine form, causing a mismatch. By a similar token, the deamination of cytosine leads to uracil,
whereas a deamination of a commonly encountered (in eukaryotes) 5-methylcytosine
will lead to thymine. However, the 3' to 5' exonuclease activity of DNA polymerase III
ensures that mismatched bases are excised during replication.
https://en.wikipedia.org/wiki/Nucleoside_triphosphate
Nucleosome
A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment
of DNA wound in sequence around eight histone protein cores. This structure is often
compared to thread wrapped around a spool.
Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is
used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be
packed into a nucleus of roughly 10m diameter). Nucleosomes are folded through a
series of successively higher order structures to eventually form a chromosome. This
both compacts DNA and creates an added layer of regulatory control, which ensures
correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones.
https://en.wikipedia.org/wiki/Nucleosome
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Nucleotidase
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Nucleotide
Nucleotides are organic molecules that serve as the monomers, or subunits, of nucleic
acids like DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The building
blocks of nucleic acids, nucleotides are composed of a nitrogenous base, a five-carbon
sugar (ribose or deoxyribose), and at least one phosphate group. Thus a nucleoside
plus a phosphate group yields a nucleotide.
Nucleotides also function to carry packets of energy within the cell in the form of the
nucleoside triphosphates (ATP, GTP (shown below), CTP and UTP), playing a central
role in metabolism. In addition, nucleotides participate in cell signaling (cGMP and
cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).
https://en.wikipedia.org/wiki/Nucleotide
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stantly because of chemicals (e.g. intercalating agents), radiation and other mutagens
Three excision repair pathways exist to repair single stranded DNA damage: Nucleotide excision repair (NER), base excision repair (BER), and DNA mismatch repair
(MMR). While the BER pathway can recognize specific non-bulky lesions in DNA, it
can correct only damaged bases that are removed by specific glycosylases. Similarly,
the MMR pathway only targets mismatched Watson-Crick base pairs.
bulky DNA adducts - these adducts are mostly thymine dimers and 6,4-photoproduct
Recognition of the damage leads to removal of a short single-stranded DNA segment
that contains the lesion. The undamaged single-stranded DNA remains and DNA polymerase uses it as a template to synthesize a short complementary sequence.
https://en.wikipedia.org/wiki/Nucleotide_excision_repair
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Information Processing
Information Processing
Information Processing
Information Processing
Nucleus
In cell biology, the nucleus (#2 in the figure below) is a membrane-enclosed organelle
found in eukaryotic cells. Eukaryotes usually have a single nucleus, but a few cell types
have no nuclei, and a few others have many.
Cell nuclei contain most of the cell's genetic material, organized as multiple long linear
DNA molecules in complex with a large variety of proteins, such as histones, to form
chromosomes. The genes within these chromosomes are the cell's nuclear genome. The
function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expressionthe nucleus is, therefore, the control
center of the cell. The main structures making up the nucleus are the nuclear envelope,
a double membrane that encloses the entire organelle and isolates its contents from
the cellular cytoplasm, and the nucleoskeleton (which includes nuclear lamina), a network within the nucleus that adds mechanical support, much like the cytoskeleton,
which supports the cell as a whole.
https://en.wikipedia.org/wiki/Cell_nucleus
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O-acetyl-L-serine
O-Acetylserine is the -amino acid with the chemical formula HO2C-
https://en.wikipedia.org/wiki/O-Acetylserine
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O-glycosylation
O-linked glycosylation is the attachment of a sugar molecule to an oxygen atom in an
amino acid residue in a protein. O-linked glycosylation is a form of glycosylation that
occurs in the Golgi apparatus in eukaryotes. It also occurs in archaea and bacteria.
O-linked glycosylation occurs at a later stage during protein processing, probably in
the Golgi apparatus. This is the addition of N-acetyl-galactosamine to serine or threonine residues by the enzyme UDP-N-acetyl-D-galactosamine:polypeptide Nacetylgalactosaminyltransferase (EC number 2.4.1.41), followed by other carbohydrates (such as galactose and sialic acid). This process is important for certain types of
proteins such as proteoglycans, which involves the addition of glycosaminoglycan
chains to an initially unglycosylated "proteoglycan core protein." These additions are
usually serine O-linked glycoproteins, which seem to have one of two main functions.
One function involves secretion to form components of the extracellular matrix, adhering one cell to another by interactions between the large sugar complexes of proteoglycans. The other main function is to act as a component of mucosal secretions, and it is
the high concentration of carbohydrates that tends to give mucus its "slimy" feel.
GlcNAc--Ser/Thr, which are found in nuclear and cytoskeletal proteins, were the first
reported example of glycosylated proteins found in a location other than secretory
channels.
https://en.wikipedia.org/wiki/O-linked_glycosylation
O-linked
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O-linked Glycosylation
O-linked glycosylation is the attachment of a sugar molecule to an oxygen atom in an
amino acid residue in a protein. O-linked glycosylation is a form of glycosylation that
occurs in the Golgi apparatus in eukaryotes. It also occurs in archaea and bacteria.
O-linked glycosylation occurs at a later stage during protein processing, probably in
the Golgi apparatus. This is the addition of N-acetyl-galactosamine to serine or threonine residues by the enzyme UDP-N-acetyl-D-galactosamine:polypeptide Nacetylgalactosaminyltransferase (EC number 2.4.1.41), followed by other carbohydrates (such as galactose and sialic acid). This process is important for certain types of
proteins such as proteoglycans, which involves the addition of glycosaminoglycan
chains to an initially unglycosylated "proteoglycan core protein." These additions are
usually serine O-linked glycoproteins, which seem to have one of two main functions.
One function involves secretion to form components of the extracellular matrix, adhering one cell to another by interactions between the large sugar complexes of proteoglycans. The other main function is to act as a component of mucosal secretions, and it is
the high concentration of carbohydrates that tends to give mucus its "slimy" feel.
GlcNAc--Ser/Thr, which are found in nuclear and cytoskeletal proteins, were the first
reported example of glycosylated proteins found in a location other than secretory
channels.
https://en.wikipedia.org/wiki/O-linked_glycosylation
O-phosphoserine
Phosphoserine (abbreviated as SEP or J) is an ester of serine and phosphoric acid.
Phosphoserine is a component of many proteins as the result of posttranslational modifications. The phosphorylation of the alcohol functional group in serine to produce
phosphoserine is catalyzed by various types of kinases. Through the use of technologies
that utilize an expanded genetic code, phosphoserine can also be incorporated into proteins during translation.
Phosphoserine has three potential coordination sites (carboxyl, amine and phosphate
group) Determination of the mode of coordination between phosphorylated ligands
and metal ions occurring in an organism is a first step to explain the function of the
phosphoserine in bioinorganic processes.
https://en.wikipedia.org/wiki/Phosphoserine
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O6-methylguanine Methyltransferase
O6-alkylguanine DNA alkyltransferase (also known as AGT, MGMT or AGAT) is a protein that in humans is encoded by the O6-methylguanine DNA methyltransferase
(MGMT) gene. O6-methylguanine DNA methyltransferase is crucial for genome stability. It repairs the naturally occurring mutagenic DNA lesion O6-methylguanine back to
guanine and prevents mismatch and errors during DNA replication and transcription.
Accordingly, loss of MGMT increases the carcinogenic risk in mice after exposure to alkylating agents.
Shown below, O6-methylguanine
https://en.wikipedia.org/wiki/O-6-methylguanine-DNA_methyltransferase
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Obligate Anaerobes
Obligate anaerobes are microorganisms that get killed by normal atmospheric concentrations of oxygen (20.95% O2). Oxygen tolerance varies between species, some capable of surviving in up to 8% oxygen, others losing viability unless the oxygen concentration is less than 0.5%.
The oxygen sensitivity of obligate anaerobes has been attributed to a combination of
factors:
Because molecular oxygen contains two unpaired electrons in its outer orbital, it is
readily reduced to superoxide (O2-) and hydrogen peroxide (H2O2) within cells. Aerobic
organisms produce superoxide dismutase and catalase to detoxify these products, but
obligate anaerobes produce these enzymes in very small quantities, or not at all. (The
variability in oxygen tolerance of obligate anaerobes (<0.5 to 8% O2) is thought to reflect the quantity of superoxide dismutase and catalase being produced.)
Dissolved oxygen increases the redox potential of a solution, and high redox potential
inhibits the growth of some obligate anaerobes. For example, methanogens grow at a
redox potential lower than -0.3 V.
Sulfide is an essential component of some enzymes, and molecular oxygen oxidizes this
to form disulfide, thus inactivating certain enzymes (e.g. nitrogenase). Organisms may
not be able to grow with these essential enzymes deactivated. Growth may be inhibited
due to a lack of reducing equivalents for biosynthesis, because electrons are exhausted
in reducing oxygen.
https://en.wikipedia.org/wiki/Obligate_anaerobe
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Octamer
The core histones all exist as dimers, which are similar in that they all posse
tone fold domain - three helices linked by two loops. It is this helical struc
called the handshake motif). The resulting four distinct dimers then come t
noid (DNA)-like particle). 147 base pairs of DNA wrap around this core par
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Octanoic acid
Caprylic acid is the common name for the eight-carbon saturated fatty acid
the systematic name octanoic acid. Its compounds are found naturally in th
various mammals, and as a minor constituent of coconut oil and palm kern
https://en.wikipedia.org/wiki/Caprylic_acid
Oil
An oil is any neutral, nonpolar chemical substance that is a viscous liquid at ambient
temperatures and is both hydrophobic (immiscible with water, literally "water fearing") and lipophilic (miscible with other oils, literally "fat loving"). Olive oil is shown
below. Oils have a high carbon and hydrogen content and are usually flammable and
slippery.
https://en.wikipedia.org/wiki/Oil
Okazaki Fragments
Okazaki fragments are short, newly synthesized DNA fragments that are formed on the
lagging template strand during DNA replication. They are complementary to the lagging template strand, together forming short double-stranded DNA sections. Okazaki
fragments are between 1000 and 2000 nucleotides long in Escherichia coli and are approximately 150 nucleotides long in eukaryotes. They are separated by ~120nucleotide RNA primers and are unligated until RNA primers are removed, followed
by enzyme ligase connecting (ligating) the two Okazaki fragments into one continuous
newly synthesized complementary strand.
On the leading strand DNA replication proceeds continuously along the DNA molecule
as the parent double-stranded DNA is unwound, but on the lagging strand the new
DNA is made in installments, which are later joined together by a DNA ligase enzyme.
This is because the enzymes that synthesize the new DNA can only work in one direction along the parent DNA molecule. On the leading strand this route is continuous,
but on the lagging strand it is discontinuous.
DNA is synthesized from 5' to 3', so when copying the 3' to 5' strand, replication is continuous. Phosphodiester links form between the 3' to 5' and nucleotides can be added
with the aid of the enzyme DNA polymerase for the continuous leading strand. However, in order to synthesize the lagging strand (the replication fork which is traveling in
the opposite direction) synthesis occurs in small sections (100-200 nucleotides at a
time in eukaryotes). These new stretches of DNA are called Okazaki fragments and
each one requires its own RNA primer.
The image below shows Okazaki fragments being formed at a replication fork on the
bottom strand. They are labeled c.
https://en.wikipedia.org/wiki/Okazaki_fragments
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Oleate
Oleic acid (ionized form = oleate) is a fatty acid that occurs naturally in various animal
and vegetable fats and oils. It is an odorless, colorless oil, although commercial samples may be yellowish. In chemical terms, oleic acid is classified as a monounsaturated
-9 fatty acid, abbreviated with a lipid number of 18:1 cis-9. It has the formula
CH3(CH2)7CH=CH(CH2)7COOH. The term "oleic" means related to, or derived from,
oil of olive, the oil that is predominantly composed of oleic acid.
Oleic acid undergoes the reactions of carboxylic acids and alkenes. It is soluble in aqueous base to give soaps called oleates.
https://en.wikipedia.org/wiki/Oleic_acid
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Oligomerize
trimers, and tetramers are, for instance, oligomers composed of two, three a
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Oligomycin
Oligomycins are macrolides created by Streptomyces that can be poisonous to other organisms. They have use as antibiotics. Oligomycin A (shown below) is an inhibitor of
ATP synthase. In oxidative phosphorylation research, it is used to prevent state 3 (phosphorylating) respiration. Oligomycin A inhibits ATP synthase by blocking its proton
channel (Fo subunit), which is necessary for oxidative phosphorylation of ADP to ATP
(energy production).
https://en.wikipedia.org/wiki/Oligomycin
Oligosaccharide
An oligosaccharide is a saccharide polymer containing a small number (typically three
to ten) of simple sugars (monosaccharides). Oligosaccharides can have many functions
including cell recognition and cell binding. For example, glycolipids have an important
role in the immune response.
In general, oligosaccharides are found either N- or O-linked to compatible amino acid
side-chains in proteins or to lipid moieties (see glycans). N-linked oligosaccharides are
found attached to asparagine via a linkage to the amine nitrogen of the side chain. Alternately, O-linked oligosaccharides are generally attached to threonine or serine on
the alcohol group of the side chain.
https://en.wikipedia.org/wiki/Oligosaccharide
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Omega umbering
Omega-9 fatty acids (9 fatty acids or n9 fatty acids) are a family of unsaturated
fatty acids which have in common a final carboncarbon double bond in the 9 position - that is, the ninth bond from the methyl end of the fatty acid.
The position of the carbon-carbon double bonds in carboxylic acid chains in fats is designated by Greek letters. The carbon atom closest to the carboxyl group is the carbon,
the next carbon is the carbon and so on. In fatty acids the carbon atom of the methyl
group at the end of the hydrocarbon chain is called the carbon because is the last
letter of the Greek alphabet. -3 fatty acids have a double bond three carbons away
from the methyl carbon, whereas -6 fatty acids have a double bond six carbons away
from the methyl carbon.
https://en.wikipedia.org/wiki/Omega-9_fatty_acid
https://en.wikipedia.org/wiki/Polyunsaturated_fat
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https://en.wikipedia.org/wiki/Omega-3_fatty_acid
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Omega-6
-6 fatty acids (also referred to as mega-6 fatty acids or n-6 fatty acids) are a family of
pro-inflammatory and anti-inflammatory polyunsaturated fatty acids that have in common a final carbon-carbon double bond in the n-6 position, that is, the sixth bond,
counting from the methyl end.
The biological effects of the -6 fatty acids are largely produced during & after physical
activity for the purpose of promoting growth and during the inflammatory cascade to
halt cell damage and promote cell repair by their conversion to -6 eicosanoids that
bind to diverse receptors found in every tissue of the body.
Linoleic acid (18:2, n6 - pictured below), the shortest-chained -6 fatty acid, is one of
many essential fatty acids and is categorized as an essential fatty acid because the human body cannot synthesize it. Mammalian cells lack the enzyme -3 desaturase and
therefore cannot convert omega-6 fatty acids to omega-3 fatty acids. Closely related 3 and -6 fatty acids act as competing substrates for the same enzymes. This outlines
the importance of the proportion of -3 to -6 fatty acids in a diet.
https://en.wikipedia.org/wiki/Omega-6_fatty_acid
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Omega-oxidation
bon, involves the oxidation of the carbon (the carbon most distant from t
group of the fatty acid). The process is normally a minor catabolic pathway
medium-chain fatty acids (10-12 carbon atoms), but becomes more importa
oxidation is defective.
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OMP
Orotidine 5'-monophosphate (OMP), also known as orotidylic acid, is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate.
OMP is formed from orotate and phosphoribosyl pyrophosphate by the enzyme Orotate phosphoribosyltransferase. In humans, the enzyme UMP synthase converts OMP
into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result.
https://en.wikipedia.org/wiki/Orotidine_5%27-monophosphate
OMP Decarboxylase
Orotidine 5-phosphate decarboxylase (OMP decarboxylase) or orotidylate decarboxylase is an enzyme involved in pyrimidine biosynthesis. It catalyzes the decarboxylation
of orotidine monophosphate (OMP) to form uridine monophosphate (UMP). The function of this enzyme is essential to the de novo biosynthesis of the pyrimidine nucleotides uridine triphosphate, cytidine triphosphate, and thymidine triphosphate. OMP
decarboxylase has been a frequent target for scientific investigation because of its demonstrated extreme catalytic efficiency and its usefulness as a selection marker for yeast
strain engineering.
The exact mechanism by which OMP decarboxylase catalyzes its reaction has been a
subject of rigorous scientific investigation. The driving force for the loss of the carboxyl
linked to the C6 of the pyrimidine ring comes from the close proximity of an aspartate
residue carboxyl group in the enzyme's active site, which destabilizes the ground state
relative to the transition state of the uncatalyzed reaction. There have been multiple hypotheses about what form the transition state takes before protonation of the C6 carbon occurs to yield the final product. Many studies investigated the binding of a potent
inhibitor of OMP decarboxylase, 6-hydroxy uridine monophosphate (BMP, a barbituric acid derivative), within the active site, to identify which essential amino acid residues are directly involved with stabilization of the transition state. Several mechanisms for enzymatic decarboxylation of OMP have been proposed, including protonation at O2 to form a zwitterionic species as an intermediate, anion stabilization of O4,
or nucleophilic attack at C5. Current consensus suggests that the mechanism proceeds
through a stabilized carbanion at the C6 after loss of carbon dioxide. This mechanism
was suggested from studies investigating kinetic isotope effects in conjunction with
competitive inhibition and active site mutagenesis. In this mechanism the short-lived
carbanion species is stabilized by a nearby lysine residue, before it is quenched by a
proton.
https://en.wikipedia.org/wiki/Orotidine_5%27-phosphate_decarboxylase
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Oncogene
An oncogene is a gene that has the potential to cause cancer. In tumor cells
often mutated or expressed at high levels.
Most normal cells will undergo a programmed form of rapid cell death (apo
when critical functions are altered. Activated oncogenes can cause those cel
nated for apoptosis to survive and proliferate instead. Most oncogenes requ
infection, to cause cancer. Since the 1970s, dozens of oncogenes have been i
human cancer. Many cancer drugs target the proteins encoded by oncogene
https://en.wikipedia.org/wiki/Oncogene
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Open Complex
The open complex is a structure formed on a DNA during the process of transcription
in the initiation phase.
The following steps occur, in order, for transcription initiation:
RNA polymerase (RNAP) binds to one of several specificity factors, , to form a
holoenzyme. In this form, it can recognize and bind to specific promoter regions in the
DNA. The -35 region and the -10 ("Pribnow box") region comprise the core prokaryotic
promoter, and |T| stands for the terminator. The DNA on the template strand between
the +1 site and the terminator is transcribed into RNA, which is then translated into
protein. At this stage, the DNA is double-stranded ("closed"). This holoenzyme/
wound-DNA structure is referred to as the closed complex.
The DNA is unwound and becomes single-stranded ("open") in the vicinity of the initiation site (defined as +1). This holoenzyme/unwound-DNA structure is called the
open complex.
The RNA polymerase transcribes the DNA (the subunit initiates the synthesis), but
produces about 10 abortive (short, non-productive) transcripts which are unable to
leave the RNA polymerase because the exit channel is blocked by the -factor.
The -factor eventually dissociates from the core enzyme, and elongation proceeds.
https://en.wikipedia.org/wiki/Bacterial_transcription
Operator
regulate gene expression. The transcription factor is a repressor, which can bind to
operator to prevent transcription.
The main operator (O2) in the classically defined lac operon is located slightly down
stream of the promoter. Two additional operators, O1 and O3 are located at -82 and
+412, respectively.
https://en.wikipedia.org/wiki/Operator_(biology)
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Operon
An operon is a functioning unit of genomic DNA containing a cluster of genes under
the control of a single promoter. The genes are transcribed together into an mRNA
strand and either translated together in the cytoplasm, or undergo trans-splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA
that each encode a single gene product. The result of this is that the genes contained in
the operon are either expressed together or not at all. Several genes must be cotranscribed to define an operon.
https://en.wikipedia.org/wiki/Operon
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Ordered inding
Ordered binding is a consideration for enzymes that bind more than one su
Index
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Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function. Individual organelles are usually separately enclosed within their own lipid bilayers.
The name organelle comes from the idea that these structures are to cells what an organ is to the body (hence the name organelle, the suffix -elle being a diminutive). Organelles are identified by microscopy, and can also be purified by cell fractionation.
There are many types of organelles, particularly in eukaryotic cells. While prokaryotes
do not possess organelles per se, some do contain protein-based microcompartments,
which are thought to act as primitive organelles.
Eukaryotic cells are structurally complex, and by definition are organized, in part, by
interior compartments that are themselves enclosed by lipid membranes that resemble
the outermost cell membrane. The larger organelles, such as the nucleus and vacuoles,
are easily visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope.
Not all eukaryotic cells have each of the organelles listed below. Exceptional organisms
have cells that do not include some organelles that might otherwise be considered universal to eukaryotes (such as mitochondria). There are also occasional exceptions to
the number of membranes surrounding organelles, listed in the tables below (e.g.,
some that are listed as double-membrane are sometimes found with single or triple
membranes). In addition, the number of individual organelles of each type found in a
given cell varies depending upon the function of that cell.
https://en.wikipedia.org/wiki/Organelle
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Organelles
In cell biology, an organelle is a specialized subunit within a cell that has a specific function. Individual organelles are usually separately enclosed within their own lipid bilayers.
The name organelle comes from the idea that these structures are to cells what an organ is to the body (hence the name organelle, the suffix -elle being a diminutive). Organelles are identified by microscopy, and can also be purified by cell fractionation.
There are many types of organelles, particularly in eukaryotic cells. While prokaryotes
do not possess organelles per se, some do contain protein-based microcompartments,
which are thought to act as primitive organelles.
Eukaryotic cells are structurally complex, and by definition are organized, in part, by
interior compartments that are themselves enclosed by lipid membranes that resemble
the outermost cell membrane. The larger organelles, such as the nucleus and vacuoles,
are easily visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope.
Not all eukaryotic cells have each of the organelles listed below. Exceptional organisms
have cells that do not include some organelles that might otherwise be considered universal to eukaryotes (such as mitochondria). There are also occasional exceptions to
the number of membranes surrounding organelles, listed in the tables below (e.g.,
some that are listed as double-membrane are sometimes found with single or triple
membranes). In addition, the number of individual organelles of each type found in a
given cell varies depending upon the function of that cell.
https://en.wikipedia.org/wiki/Organelle
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Organic Compounds
(such as CO and CO2), and cyanides are considered inorganic. The distinctio
Index
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Origins of Replication
The origin of replication (also called the replication origin) is a particular sequence in a
genome at which replication is initiated. This can either involve the replication of DNA
in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
DNA replication may proceed from this point bidirectionally or unidirectionally.
The specific structure of the origin of replication varies somewhat from species to species, but all share some common characteristics such as high AT content (repeats of
adenine and thymine are easier to separate because their base stacking interactions are
not as strong as those of guanine and cytosine). The origin of replication binds the prereplication complex, a protein complex that recognizes, unwinds, and begins to copy
DNA.
https://en.wikipedia.org/wiki/Origin_of_replication
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Ornithine
Ornithine is a non-proteinogenic amino acid that plays a role in the urea cycle.
Ornithine is not an amino acid coded for by DNA, that is, not proteinogenic. However,
in mammalian non-hepatic tissues, the main use of the urea cycle is in arginine biosynthesis, so, as an intermediate in metabolic processes, ornithine is quite important.
L-Ornithine is one of the products of the action of the enzyme arginase on L-arginine,
creating urea. Therefore, ornithine is a central part of the urea cycle, which allows for
the disposal of excess nitrogen.
https://en.wikipedia.org/wiki/Ornithine
Index
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Ornithine Acyltransferase
Thus, the two substrates of this enzyme are benzoyl-CoA and L-ornithine, w
two products are CoASH and N2,N5-dibenzoyl-L-ornithine.
Index
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Ornithine Transcarbamoylase
Ornithine transcarbamylase (OTC) (also called ornithine carbamoyltransferase) is an
enzyme that catalyzes the reaction between carbamoyl phosphate (CP) and ornithine
(Orn) to form citrulline (Cit) and phosphate (Pi).
https://en.wikipedia.org/wiki/Ornithine_transcarbamylase
Ornithine-citrulline Antiport
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Orotate
Orotic acid is a heterocyclic compound and an acid. It is also known as pyrimidinecarboxylic acid. Historically it was believed to be part of the vitamin B complex and was
called vitamin B13, but it is now known that it is not a vitamin.
The compound is manufactured in the body via a mitochondrial enzyme, dihydroorotate dehydrogenase. or a cytoplasmic enzyme of pyrimidine synthesis pathway. It is
sometimes used as a mineral carrier in some dietary supplements (to increase their
bioavailability), most commonly for lithium orotate.
https://en.wikipedia.org/wiki/Orotic_acid
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with a unique gene coding for the protein, whereas in mammals and other m
lar organisms, the catalytic function is carried out by a domain of the bifunc
zyme UMP synthase.
https://en.wikipedia.org/wiki/Orotate_phosphoribosyltransferase
Index
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Osmotic Pressure
Osmotic pressure is the minimum pressure which needs to be applied to a solution to
prevent the inward flow of water across a semipermeable membrane. It is also defined
as the measure of the tendency of a solution to take in water by osmosis. Potential osmotic pressure is the maximum osmotic pressure that could develop in a solution if it
were separated from distilled water by a selectively permeable membrane. The phenomenon of osmosis arises from the propensity of a pure solvent to move through a
semi-permeable membrane and into a solution containing a solute to which the membrane is impermeable. This process is of vital importance in biology as the cell's membrane is semipermeable.
https://en.wikipedia.org/wiki/Osmotic_pressure
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Osteocalcin
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Outer Leaflet
The lipid bilayer consists of two layers- an outer leaflet and an inner leaflet. The co
nents of bilayers are distributed unequally between the two surfaces to create asym
try between the outer and inner surfaces. This asymmetric organization is importa
for cell functions such as cell signaling. The asymmetry of the biological membran
flects the different functions of the two leaflets of the membrane. As seen in the flu
membrane model of the phospholipid bilayer, the outer leaflet and inner leaflet of
membrane are asymmetrical in their composition. Certain proteins and lipids rest
on one surface of the membrane and not the other.
https://en.wikipedia.org/wiki/Biological_membrane
In human red blood cells, the inner (cytoplasmic) leaflet is composed mostly of ph
Oxaloacetate
Oxaloacetic acid (also known as oxalacetic acid) is a crystalline organic compound with
the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes that occur in animals. It takes part in the: gluconeogenesis, urea cycle, glyoxylate cycle, amino acid synthesis, fatty acid synthesis and citric acid cycle.
Oxaloacetate forms in several ways in nature. A principal route is upon oxidation of Lmalate, catalyzed by malate dehydrogenase, in the citric acid cycle.
https://en.wikipedia.org/wiki/Oxaloacetic_acid
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Oxidation
Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom,
or ion.
Redox reactions, or oxidation-reduction reactions, have a number of similarities to
acidbase reactions. Like acidbase reactions, redox reactions are a matched set, that
is, there cannot be an oxidation reaction without a reduction reaction happening simultaneously. The oxidation alone and the reduction alone are each called a half-reaction,
because two half-reactions always occur together to form a whole reaction. When writing half-reactions, the gained or lost electrons are typically included explicitly in order
that the half-reaction be balanced with respect to electric charge.
https://en.wikipedia.org/wiki/Redox
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Oxidative Phosphorylation
Oxidative phosphorylation (or OXPHOS in short) is the metabolic pathway in which
cells use enzymes to oxidize nutrients, thereby releasing energy which is used to reform ATP. In most eukaryotes, this takes place inside mitochondria. Almost all aerobic
organisms carry out oxidative phosphorylation. This pathway is probably so pervasive
because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis.
During oxidative phosphorylation, electrons are transferred from electron donors to
electron acceptors such as oxygen, in redox reactions. These redox reactions release energy, which is used to form ATP.
https://en.wikipedia.org/wiki/Oxidative_phosphorylation
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Oxidative Stress
Oxidative stress reflects an imbalance between the systemic manifestation of reactive
oxygen species and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage. Disturbances in the normal redox state of cells
can cause toxic effects through the production of peroxides and free radicals that damage all components of the cell, including proteins, lipids, and DNA. Oxidative stress
from oxidative metabolism causes base damage, as well as strand breaks in DNA. Base
damage is mostly indirect and caused by reactive oxygen species (ROS) generated, e.g.
O2 (superoxide radical), OH (hydroxyl radical) and H2O2 (hydrogen peroxide). Further, some reactive oxidative species act as cellular messengers in redox signaling.
Thus, oxidative stress can cause disruptions in normal mechanisms of cellular signaling.
In humans, oxidative stress is thought to be involved in the development of Asperger
syndrome, ADHD, cancer, Parkinson's disease, Lafora disease, Alzheimer's disease,
atherosclerosis, heart failure, myocardial infarction, fragile X syndrome, Sickle Cell Disease, lichen planus, vitiligo, autism, infection, Chronic fatigue syndrome, and Depression. However, reactive oxygen species can be beneficial, as they are used by the immune system as a way to attack and kill pathogens. Short-term oxidative stress may
also be important in prevention of aging by induction of a process named mitohormesis.
https://en.wikipedia.org/wiki/Oxidative_stress
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Oxidized
Redox reactions include all chemical reactions in which atoms have their oxid
chemical species. The chemical species from which the electron is stripped is
have been oxidized.
https://en.wikipedia.org/wiki/Redox
Index
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Oxygen
Oxygen is a chemical element with symbolO and atomic number8. It is a member of
the chalcogen group on the periodic table and is a highly reactive nonmetal and oxidizing agent that readily forms compounds (notably oxides) with most elements.
Many major classes of organic molecules in living organisms contain oxygen, such as
proteins, nucleic acids, carbohydrates, and fats, as do the major constituent inorganic
compounds of animal shells, teeth, and bone. Most of the mass of living organisms is
oxygen as a component of water, the major constituent of lifeforms. Oxygen is used in
cellular respiration and released by photosynthesis, which uses the energy of sunlight
to produce oxygen from water and carbon dioxide.
https://en.wikipedia.org/wiki/Oxygen
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Index
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Oxygen Transport
About 98.5% of the oxygen in a sample of arterial blood in a healthy human bre
1.5% is physically dissolved in the other blood liquids and not connected to Hgb
other species (for exceptions, see below). Hemoglobin has an oxygen binding ca
of between 1.36 and 1.40 ml O2 per gram hemoglobin, which increases the total
of 0.03ml O2 per liter blood per mmHg partial pressure of oxygen (approxima
100mmHg in arteries).
With the exception of pulmonary and umbilical arteries and their correspondin
arteries carry oxygenated blood away from the heart and deliver it to the body v
rioles and capillaries, where the oxygen is consumed. Afterwards, venules, and
carry deoxygenated blood back to the heart.
https://en.wikipedia.org/wiki/Blood#Oxygen_transport
Oxygenase
molecular oxygen O2 (as in air) to it. The oxygenases form a class of oxidore
There are two types of oxygenases:
Among the most important monooxygenases are the cytochrome P450 oxida
sible for breaking down numerous chemicals in the body.
https://en.wikipedia.org/wiki/Oxygenase
P-site
Ribosomes are the workplaces of protein biosynthesis, the process of translating
mRNA into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the mRNA as
a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it
with the appropriate amino acid provided by an aminoacyl-tRNA. Aminoacyl-tRNA
contains a complementary anticodon on one end and the appropriate amino acid on
the other. For fast and accurate recognition of the appropriate tRNA, the ribosome utilizes large conformational changes (conformational proofreading) . The small ribosomal subunit, typically bound to an aminoacyl-tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal
subunit. The ribosome contains three RNA binding sites, designated A, P and E. The A
site binds an aminoacyl-tRNA. The P site binds a peptidyl-tRNA (a tRNA bound to the
peptide being synthesized) and the E site binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA.
mRNA binds to the P site of the ribosome first. The ribosome is able to identify the
start codon by use of the Shine-Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes.
Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site adenosine in a proton shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations.
https://en.wikipedia.org/wiki/Ribosome
Index
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PAICS
https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazole_carboxylas
Index
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Palindrome
A palindromic sequence is a nucleic acid sequence on double-stranded DNA or RNA
wherein reading 5' (five-prime) to 3' (three prime) forward on one strand matches the
sequence reading backward 5' to 3' on the complementary strand with which it forms a
double helix. This definition of palindrome thus depends on complementary strands
being palindromic of each other.
The meaning of palindrome in the context of genetics is slightly different from the definition used for words and sentences. Since a double helix is formed by two paired
strands of nucleotides that run in opposite directions in the 5'-to-3' sense, and the nucleotides always pair in the same way (Adenine (A) with Thymine (T) for DNA, with
Uracil (U) for RNA, Cytosine (C) with Guanine (G)), a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example,
the DNA sequence ACCTAGGT is palindromic because its nucleotide-by-nucleotide
complement is TGGATCCA, and reversing the order of the nucleotides in the complement gives the original sequence.
A palindromic nucleotide sequence can form a hairpin. Palindromic DNA motifs are
found in most genomes or sets of genetic instructions. Palindromic motifs are made by
the order of the nucleotides that specify the complex chemicals (proteins) which, as a
result of those genetic instructions, the cell is to produce. They have been specially researched in bacterial chromosomes and in the so-called Bacterial Interspersed Mosaic
Elements (BIMEs) scattered over them. Recently, a research genome sequencing project discovered that many of the bases on the Y chromosome are arranged as palindromes. A palindrome structure allows the Y chromosome to repair itself by bending
over at the middle if one side is damaged.
Palindromes also appear to be found frequently in proteins, but their role in the protein function is not clearly known. It has recently been suggested that the existence of
palindromes in peptides might be related to the prevalence of low-complexity regions
in proteins, as palindromes are frequently associated with low-complexity sequences.
Their prevalence might be also related to an helical formation propensity of these sequences, or in formation of protein/protein complexes.
https://en.wikipedia.org/wiki/Palindromic_sequence
Palmitate
trees (palm oil), but can also be found in meats, cheeses, butter, and dairy p
Palmitate is a term for the salts and esters of palmitic acid. The palmitate an
observed form of palmitic acid at physiologic pH (7.4).
https://en.wikipedia.org/wiki/Palmitic_acid
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Palmitic Acid
Palmitic acid, or hexadecanoic acid in IUPAC nomenclature, is the most common fatty
acid (saturated) found in animals, plants and microorganisms. Its chemical formula is
CH3(CH2)14COOH. As its name indicates, it is a major component of the oil from palm
trees (palm oil), but can also be found in meats, cheeses, butter, and dairy products.
Palmitate is a term for the salts and esters of palmitic acid. The palmitate anion is the
observed form of palmitic acid at physiologic pH (7.4).
https://en.wikipedia.org/wiki/Palmitic_acid
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Palmitoyl-CoA
Palmitoyl-CoA is an acyl-CoA thioester used in the biosynthesis of sphingosine. It is
also part of the carnitine shuttle system, which transports other fatty acyl-CoA molecules into the mitochondria for -oxidation.
https://en.wikipedia.org/wiki/Palmitoyl-CoA
Index
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Pancreatic Lipase
dietary fat molecules in the human digestive system, it is one of the main digesti
sinogen), pancreatic lipase is secreted in its final form. However, it becomes effic
only in the presence of colipase in the duodenum.
In humans, pancreatic lipase is encoded by the PNLIP gene.
Triacylglycerol + 2 H2O 2-monoacylglycerol + 2 Fatty Acid Anions
https://en.wikipedia.org/wiki/Pancreatic_lipase
Index
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Pancreatitis
Pancreatitis is inflammation of the pancreas. The pancreas is a large organ
stomach that produces digestive enzymes. There are two main types, acute
abdomen, nausea and vomiting. The pain often goes into the back and is us
vere. In acute pancreatitis a fever may occur and symptoms typically resolv
days. In chronic pancreatitis weight loss, fatty stool, and diarrhea may occu
Papain
Paracrine
signaling. Cells that produce paracrine factors secrete them into the immedia
cellular environment. Factors then travel to nearby cells in which the gradien
received determines the outcome. These highly conserved receptors and path
factor (FGF) family, Hedgehog family, Wnt family, and TGF- superfamily. B
Parallel
rection, such as two strands adjacent to each other that have their amino an
ends aligned with each other. Parallel contrasts with anti-parallel, which m
entations are opposite each other. DNA strands in a double helix are arrang
anti-parallel fashion - the 3 end of one strand is aligned with the 5 end of t
Parkin
Parkin is a protein which in humans is encoded by the PARK2 gene. The precise fun
However, how loss of function of the parkin protein leads to dopaminergic cell death
this disease is unclear. The prevailing hypothesis is that parkin helps degrade one or
more proteins toxic to dopaminergic neurons. Putative substrates of parkin include
synphilin-1, CDC-rel1, cyclin E, p38 tRNA synthase, Pael-R, synaptotagmin XI, sp22
and parkin itself (see also ubiquitin ligase). Additionally, Parkin contains a C-termin
motif that binds PDZ domains. Parkin has been shown to associate in a PDZ dependent manner with the PDZ domain containing proteins CASK and PICK1.
https://en.wikipedia.org/wiki/Parkin_(ligase)
Parkinson Disease
mainly affecting the motor system. Early in the course of the disease, the m
ment and difficulty with walking and gait. Later, thinking and behavioral pr
may arise, with dementia commonly occurring in the advanced stages of the
and depression being the most common psychiatric symptom. Other sympt
clude sensory, sleep, and emotional problems. The main motor symptoms a
tively called "parkinsonism", or a "parkinsonian syndrome".
https://en.wikipedia.org/wiki/Parkinson%27s_disease
Index
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Parkinsons Disease
mainly affecting the motor system. Early in the course of the disease, the m
ment and difficulty with walking and gait. Later, thinking and behavioral pr
may arise, with dementia commonly occurring in the advanced stages of the
and depression being the most common psychiatric symptom. Other sympt
clude sensory, sleep, and emotional problems. The main motor symptoms a
tively called "parkinsonism", or a "parkinsonian syndrome".
https://en.wikipedia.org/wiki/Parkinson%27s_disease
PARP
cellular processes involving mainly DNA repair and programmed cell death. P
binding domain is composed of two zinc finger motifs. In the presence of dam
DNA (base pair-excised), the DNA-binding domain will bind the DNA and ind
conformational shift. It has been shown that this binding occurs independent
the protein from the DNA after catalysis. Also, it plays an integral role in cleav
induced inactivation.
https://en.wikipedia.org/wiki/Poly_ADP_ribose_polymerase
Partial Hydrogenation
Passenger RNA
the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molec
short double-stranded fragments of ~20 nucleotide siRNAs. Each siRNA is
into two single-stranded RNAs (ssRNAs), the passenger strand and the guid
The passenger strand is degraded and the guide strand is incorporated into
induced silencing complex (RISC).
https://en.wikipedia.org/wiki/RNA_interference
Passive Transport
Passive transport is a movement of biochemicals and other atomic or molecular substances across cell membranes without need of energy input. Unlike active transport, it
does not require an input of cellular energy because it is instead driven by the tendency
of the system to grow in entropy. The rate of passive transport depends on the permeability of the cell membrane, which, in turn, depends on the organization and characteristics of the membrane lipids and proteins. The four main kinds of passive transport
are simple diffusion, facilitated diffusion, filtration and osmosis.
Facilitated diffusion, also called carrier-mediated diffusion, is the movement of molecules across the cell membrane via special transport proteins that are embedded within
the cellular membrane. Large, insoluble molecules, such as glucose, vesicles and proteins require a carrier molecule to move through the plasma membrane. Therefore, it
will bind with its specific carrier proteins, and the complex will then be bonded to a receptor site and moved through the cellular membrane. Facilitated diffusion is a passive
process: The solutes move down the concentration gradient and don't use extra cellular
energy to move. Channel proteins are another type of facilitated diffusion that allow
the selective transport of one type of hydrophilic molecule across the cell membrane.
Aquaporins are channel proteins that allow the passage of water across the cell membrane.
Facilitated diffusion may be achieved as a consequence of charge gradients in addition
to concentration gradients. Plant cells create an unequal distribution of charge across
their plasma membrane by actively taking up or excluding ions. Active transport of protons by H+ ATPases alters membrane potential allowing for facilitated passive transport of particular ions such as potassium down their charge gradient through high affinity transporters and channels.
https://en.wikipedia.org/wiki/Passive_transport
Pathway
cules, such as a fat or protein. Pathways can also turn genes on and off, or s
move. Some of the most common biological pathways are involved in metab
Index
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PCNA
Proliferating cell nuclear antigen (PCNA) is a DNA clamp that acts as a processivity factor for DNA polymerase in eukaryotic cells and is essential for replication. PCNA is a
homotrimer and achieves its processivity by encircling the DNA, where it acts as a scaffold to recruit proteins involved in DNA replication, DNA repair, chromatin remodeling and epigenetics.
Many proteins interact with PCNA via the two known PCNA-interacting motifs PCNAinteracting peptide (PIP) box and AlkB homologue 2 PCNA interacting motif (APIM).
Proteins binding to PCNA via the PIP-box are mainly involved in DNA replication
whereas proteins binding to PCNA via APIM are mainly important in the context of
genotoxic stress.
The protein encoded by this gene is found in the nucleus and is a cofactor of DNA polymerase delta. The encoded protein acts as a homotrimer and helps increase the
processivity of leading strand synthesis during DNA replication. In response to DNA
damage, this protein is ubiquitinated and is involved in the RAD6-dependent DNA repair pathway. Two transcript variants encoding the same protein have been found for
this gene. Pseudogenes of this gene have been described on chromosome 4 and on the
X chromosome.
https://en.wikipedia.org/wiki/Proliferating_cell_nuclear_antigen
PCR
The polymerase chain reaction (PCR) is a process used in molecular biology to amplify
a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. In the first step,
the two strands of the DNA double helix are physically separated at a high temperature
in a process called DNA melting. In the second step, the temperature is lowered and
the two DNA strands become templates for DNA polymerase to selectively amplify the
target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions.
Developed in 1983 by Kary Mullis, PCR is now a common and often indispensable
technique used in medical and biological research labs for a variety of applications.
These include DNA cloning for sequencing, DNA-based phylogeny, or functional analysis of genes, the diagnosis of hereditary diseases, the identification of genetic fingerprints (used in forensic sciences and DNA paternity testing), and the detection and diagnosis of infectious diseases. In 1993, Mullis was awarded the Nobel Prize in Chemistry along with Michael Smith for his work on PCR.
The method relies on thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA. Primers
(short DNA fragments) containing sequences complementary to the target region
along with a DNA polymerase, which the method is named after, are key components
to enable selective and repeated amplification. As PCR progresses, the DNA generated
is itself used as a template for replication, setting in motion a chain reaction in which
the DNA template is exponentially amplified. PCR can be extensively modified to perform a wide array of genetic manipulations.
Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase (an enzyme originally isolated from the bacterium Thermus aquaticus). This
DNA polymerase enzymatically assembles a new DNA strand from DNA buildingblocks, the nucleotides, by using single-stranded DNA as a template and DNA oligonucleotides (also called DNA primers), which are required for initiation of DNA synthesis. The vast majority of PCR methods use thermal cycling, i.e., alternately heating and
cooling the PCR sample through a defined series of temperature steps.
https://en.wikipedia.org/wiki/Polymerase_chain_reaction
Index
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PCTP
Index
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PDK1
the complex. In humans, there have been four isozymes of Pyruvate Dehydr
nase that have been shown to phosphorylate these three sites: PDK1, PDK2
PDK4. PDK1 is the only enzyme capable of phosphorylating the 3rd serine s
the TPP coenzyme is bound, the rates of phosphorylation by all four isozym
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_lipoamide_kinas
1
PDZ domain
The PDZ domain is a common structural domain of 80-90 amino-acids found in the
signaling proteins of bacteria, yeast, plants, viruses and animals. Proteins containing
PDZ domains play a key role in anchoring receptor proteins in the membrane to cytoskeletal components. PDZ is an acronym combining the first letters of three proteins
post synaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1),
and zonula occludens-1 protein (zo-1) which were first discovered to share the domain. PDZ domains have previously been referred to as DHR (Dlg homologous region) or GLGF (glycine-leucine-glycine-phenylalanine) domains. Proteins with these
domains help hold together and organize signaling complexes at cellular membranes.
Protein domains, connected by intrinsically disordered flexible linker regions, induce
long-range allostery via protein domain dynamics. PDZ domains also play a highly significant role in the anchoring of cell surface receptors (such as CFTR[disambiguation
needed] and FZD7) to the actin cytoskeleton via mediators like NHERF and ezrin.
In general PDZ domains bind to a short region of the C-terminus of other specific proteins. These short regions bind to the PDZ domain by sheet augmentation. This
means that the sheet in the PDZ domain is extended by the addition of a further
strand from the tail of the binding partner protein.
https://en.wikipedia.org/wiki/PDZ_domain
Pectin
Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. It was first isolated and described in 1825 by Henri Braconnot. It is produced commercially as a white to light brown powder, mainly extracted from citrus
fruits, and is used in food as a gelling agent, particularly in jams and jellies. It is also
used in fillings, medicines, sweets, as a stabilizer in fruit juices and milk drinks, and as
a source of dietary fiber.
In plant biology, pectin consists of a complex set of polysaccharides that are present in
most primary cell walls and are particularly abundant in the non-woody parts of terrestrial plants. Pectin is a major component of the middle lamella, where it helps to bind
cells together, but is also found in primary cell walls.
The amount, structure and chemical composition of pectin differs among plants,
within a plant over time, and in various parts of a plant. Pectin is an important cell wall
polysaccharide that allows primary cell wall extension and plant growth. During fruit
ripening, pectin is broken down by the enzymes pectinase and pectinesterase, in which
process the fruit becomes softer as the middle lamellae break down and cells become
separated from each other. A similar process of cell separation caused by the breakdown of pectin occurs in the abscission zone of the petioles of deciduous plants at leaf
fall.
https://en.wikipedia.org/wiki/Pectin
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Pectins
Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. It was first isolated and described in 1825 by Henri Braconnot. It is produced commercially as a white to light brown powder, mainly extracted from citrus
fruits, and is used in food as a gelling agent, particularly in jams and jellies. It is also
used in fillings, medicines, sweets, as a stabilizer in fruit juices and milk drinks, and as
a source of dietary fiber.
In plant biology, pectin consists of a complex set of polysaccharides that are present in
most primary cell walls and are particularly abundant in the non-woody parts of terrestrial plants. Pectin is a major component of the middle lamella, where it helps to bind
cells together, but is also found in primary cell walls.
The amount, structure and chemical composition of pectin differs among plants,
within a plant over time, and in various parts of a plant. Pectin is an important cell wall
polysaccharide that allows primary cell wall extension and plant growth. During fruit
ripening, pectin is broken down by the enzymes pectinase and pectinesterase, in which
process the fruit becomes softer as the middle lamellae break down and cells become
separated from each other. A similar process of cell separation caused by the breakdown of pectin occurs in the abscission zone of the petioles of deciduous plants at leaf
fall.
https://en.wikipedia.org/wiki/Pectin
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Penicillin
Penicillin (PCN or pen) is a group of antibiotics which include penicillin G (intravenous use), penicillin V (oral use), procaine penicillin, and benzathine penicillin (intramuscular use). Penicillin antibiotics were among the first medications to be effective
against many bacterial infections caused by staphylococci and streptococci. Penicillins
are still widely used today, though many types of bacteria have developed resistance following extensive use.
About 10% of people report that they are allergic to penicillin, however, up to 90% of
this group may not actually be allergic. Serious allergies only occur in about 0.03%. All
penicillins are -lactam antibiotics.
Penicillin was discovered in 1928 by Scottish scientist Alexander Fleming. People began using it to treat infections in 1942. There are several enhanced penicillin families
which are effective against additional bacteria. These include the antistaphylococcal
penicillins, aminopenicillins and the antipseudomonal penicillins. They are derived
from Penicillium fungi.
https://en.wikipedia.org/wiki/Penicillin
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Pentose
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PEPCK
Phosphoenolpyruvate carboxykinase (PEPCK) is an enzyme in the lyase family used in
the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
PEPCK-C catalyzes the rate-controlling step of gluconeogenesis, the process whereby
glucose is synthesized. The enzyme has therefore been thought to be essential in glucose homeostasis, as evidenced by laboratory mice that contracted diabetes mellitus
type 2 as a result of the overexpression of PEPCK-C.
The role that PEPCK-C plays in gluconeogenesis may be mediated by the citric acid cycle, the activity of which was found to be directly related to PEPCK-C abundance.
PEPCK-C levels alone were not highly correlated with gluconeogenesis in the mouse
liver, as previous studies have suggested. While the mouse liver almost exclusively expresses PEPCK-C, humans equally present a mitochondrial isozyme (PEPCK-M).
PEPCK-M has gluconeogenic potential per se. Therefore, the role of PEPCK-C and
PEPCK-M in gluconeogenesis may be more complex and involve more factors than was
previously believed.
It is found in two forms, cytosolic and mitochondrial.
https://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase
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Pepsin
Pepsin is an enzyme that breaks down proteins into smaller peptides (that is
ase). It is produced in the stomach and is one of the main digestive enzymes
gestive systems of humans and many other animals, where it helps digest the
in food.
It is one of three principal proteases in the human digestive system, the othe
ing chymotrypsin and trypsin. During the process of digestion, these enzyme
rate to break down dietary proteins into their components, i.e., peptides and
ids, which can be readily absorbed by the small intestine. Pepsin is most effic
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Pepstatin
Pepstatin is a potent inhibitor of aspartyl proteases. It is a hexa-peptide containing the
unusual amino acid statine (Sta, (3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid),
having the sequence Isovaleryl-Val-Val-Sta-Ala-Sta (Iva-Val-Val-Sta-Ala-Sta). It was
originally isolated from cultures of various species of Actinomyces due to its ability to
inhibit pepsin at picomolar concentrations. Pepstatin A is well known to be an inhibitor of aspartic proteinases such as pepsin, cathepsins D and E. Except for its role as a
proteinase inhibitor, however, the pharmacological action of pepstatin A upon cells remain unclear.
Pepstatin A suppresses receptor activator of NF-B ligand (RANKL)induced osteoclast differentiation. Pepstatin A suppresses the formation of multinuclear osteoclasts
dose-dependently. This inhibition of the formation only affected osteoclast cells, i.e.,
not osteoblast-like cells. Furthermore, pepstatin A also suppresses differentiation from
pre-osteoclast cells to mononuclear osteoclast cells dose-dependently. This inhibition
seems to be independent of the activities of proteinases such as cathepsin D, because
the formation of osteoclasts was not suppressed with the concentration that inhibited
the activity of cathepsin D.
Cell signaling analysis indicated that the phosphorylation of ERK was inhibited in pepstatin A-treated cells, while the phosphorylation of IB and Akt showed almost no
change. Furthermore, pepstatin A decreased the expression of nuclear factor of activated T cells c1 (NFATc1). These results suggest that pepstatin A suppresses the differentiation of osteoclasts through the blockade of ERK signaling and the inhibition of
NFATc1 expression.
Pepstatin is practically insoluble in water, chloroform, ether, and benzene, however it
can be dissolved in methanol, ethanol, and DMSO with acetic acid, to between 1 and 5
mg/ml.
https://en.wikipedia.org/wiki/Pepstatin
Peptide Bond
A peptide bond (amide bond) is a covalent chemical bond formed between two amino
acid molecules.
When two amino acids form a dipeptide through a peptide bond it is called condensation. In condensation, two amino acids approach each other, with the acid moiety of
one coming near the amino moiety of the other. One loses a hydrogen and oxygen from
its carboxyl group (COOH) and the other loses a hydrogen from its amino group
(NH2). This reaction produces a molecule of water (H2O) and two amino acids joined
by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide.
The peptide bond is synthesized when the carboxyl group of one amino acid molecule
reacts with the amino group of the other amino acid molecule, causing the release of a
molecule of water (H2O), hence the process is a dehydration synthesis reaction (also
known as a condensation reaction).
The formation of the peptide bond consumes energy, which, in living systems, is derived from ATP. Polypeptides and proteins are chains of amino acids held together by
peptide bonds. Living organisms employ enzymes to produce polypeptides, and ribosomes to produce proteins. Peptides are synthesized by specific enzymes. For example,
the tripeptide glutathione is synthesized in two steps from free amino acids, by two enzymes: -glutamylcysteine synthetase and glutathione synthetase.
https://en.wikipedia.org/wiki/Peptide_bond
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Peptide Hormone
Peptide hormones and protein hormones are hormones whose molecules are peptides
or proteins, respectively. The latter have longer amino acid chain lengths than the former. These hormones have an effect on the endocrine system of animals, including humans. Most hormones can be classified as either amino acidbased hormones (amine,
peptide, or protein) or steroid hormones. The former are water-soluble and act on the
surface of target cells via second messengers - the latter, being lipid-soluble, move
through the plasma membranes of target cells (both cytoplasmic and nuclear) to act
within their nuclei.
Like all peptides and proteins, peptide hormones and protein hormones are synthesized in cells from amino acids according to mRNA transcripts, which are synthesized
from DNA templates inside the cell nucleus. Preprohormones, peptide hormone precursors, are then processed in several stages, typically in the endoplasmic reticulum, including removal of the N-terminal signal sequence and sometimes glycosylation, resulting in prohormones. The prohormones are then packaged into membrane-bound secretory vesicles, which can be secreted from the cell by exocytosis in response to specific
stimuli (e.g. --an increase in Ca2+ and cAMP concentration in cytoplasm).
https://en.wikipedia.org/wiki/Peptide_hormone
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Peptidoglycan
Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of -(1,4) linked
N-acetylglucosamine and N-acetylmuramic acid. Attached to the N-acetylmuramic
acid is a peptide chain of three to five amino acids. The peptide chain can be crosslinked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as
well as counteracting the osmotic pressure of the cytoplasm. A common misconception
is that peptidoglycan gives the cell its shape; however, whereas peptidoglycan helps
maintain the structural strength of the cell, it is actually the MreB protein that facilitates cell shape. Peptidoglycan is also involved in binary fission during bacterial cell reproduction.
The peptidoglycan layer is substantially thicker in Gram-positive bacteria (20 to 80
nanometers) than in Gram-negative bacteria (7 to 8 nanometers), with the attachment
of the S-layer. Peptidoglycan forms around 90% of the dry weight of Gram-positive bacteria but only 10% of Gram-negative strains. Thus, presence of high levels of peptidoglycan is the primary determinant of the characterization of bacteria as Gram-positive. In
Gram-positive strains, it is important in attachment roles and serotyping purposes. For
both Gram-positive and Gram-negative bacteria, particles of approximately 2 nm can
pass through the peptidoglycan.
https://en.wikipedia.org/wiki/Peptidoglycan
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cent amino acids using tRNAs during the translation process of protein biosynt
zyme. Ribozymes are the only enzymes which are not made up of proteins, but r
cleotides. All other enzymes are made up of proteins. This RNA relic is the most
cant piece of evidence supporting the RNA World hypothesis.
In prokaryotes, the 50S (23S component) ribosome subunit contains the pept
transferase component and acts as a ribozyme.
In eukaryotes, the 60S (28S component) ribosome subunit contains the peptidy
ferase component and acts as the ribozyme.
https://en.wikipedia.org/wiki/Peptidyl_transferase
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Perfect Enzymes
a reaction so efficiently that the rate limiting step is that of substrate diffusi
active site, or product diffusion out. This is also known as kinetic perfection
perfection. Since the rate of catalysis of such enzymes is set by the diffusion
mum peak height in the fitness landscape). Diffusion limited perfect enzym
than this limit. This is due to both the chemical limitations of difficult react
the evolutionary limitations that such high reaction rates do not confer any
ness.
https://en.wikipedia.org/wiki/Diffusion_limited_enzyme
Perilipins
Perilipin is a protein that coats lipid droplets in adipocytes, the fat-storing cells in adi
pose tissue. Perilipin acts as a protective coating from the bodys natural lipases, such
as hormone-sensitive lipase, which break triglycerides into glycerol and free fatty acid
for use in metabolism, a process called lipolysis. In humans, perilipin is expressed in
three different isoforms, A, B, and C, and perilipin A is the most abundant protein ass
ciated with the adipocyte lipid droplets.
Perilipin is hyperphosphorylated by PKA following -adrenergic receptor activation.
Phosphorylated perilipin changes conformation, exposing the stored lipids to
hormone-sensitive lipase-mediated lipolysis. Although PKA also phosphorylates
hormone-sensitive lipase, which can increase its activity, the more than 50-fold in-
Periostin
heart. This protein shares a homology with fasciclin I, a secreted cell adhesion m
cule found in insects. While periostin plays a wide variety of roles in tissue deve
ment along with disease, its function in tissue remodeling as a response to injur
lated during cell fate changes, whether they are related to alterations in physiol
ing, and the epithelial-mesenchymal transition, all of which can be related to tis
Index
The peripheral nervous system (PNS) is the part of the nervous system that consis
the nerves and ganglia on the outside of the brain and spinal cord. The main funct
of the PNS is to connect the central nervous system (CNS) to the limbs and organs
sentially serving as a communication relay going back and forth between the brain
spinal cord with the rest of the body. Unlike the CNS, the PNS is not protected by t
bone of spine and skull, or by the bloodbrain barrier, which leaves it exposed to t
ins and mechanical injuries. The peripheral nervous system is mainly divided into
somatic nervous system and the autonomic nervous system. In the somatic nervou
tem, the cranial nerves are part of the PNS with the exception of cranial nerve II, t
optic nerve, along with the retina. The second cranial nerve is not a true periphera
nerve but a tract of the diencephalon. Cranial nerve ganglia originate in the CNS. H
ever, the remaining ten cranial nerve axons extend beyond the brain and are there
considered part of the PNS. The Autonomic nervous system is an involuntary cont
of smooth muscle. The connection between CNS and organs allows the system to b
two different functional states: sympathetic and parasympathetic.
https://en.wikipedia.org/wiki/Peripheral_nervous_system
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Peripherin
Peripherin is a type III Intermediate filament (IF) protein expressed mainly in neu
of the peripheral nervous system (PNS). It is also found in neurons of the central n
ous system (CNS) that have projections toward peripheral structures, such as spin
motor neurons. Its size, structure, and sequence/location of protein motifs is simi
other type III IF proteins such as desmin, vimentin and glial fibrillary acidic prote
mentous networks (networks formed from peripherin protein dimers), but it can a
mans is encoded by the PRPH gene. Peripherin is thought to play a role in neurite
gation during development and axonal regeneration after injury, but its exact func
is unknown. It is also associated with some of the major neuropathologies that cha
terize amyotropic lateral sclerosis (ALS), but despite extensive research into how n
filaments and peripherin contribute to ALS, their role in this disease is still uniden
fied.
https://en.wikipedia.org/wiki/Peripherin
Periplasmic Space
The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in
gram-negative bacteria. It has been found using cryo-electron microscopy, that a much
smaller periplasmic space is present in gram-positive bacteria.
The periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, and this is a much smaller percentage in gram-positive bacteria.
Although the bacteria are conventionally divided into two main groups grampositive and gram-negative, based upon their Gram-stain retention property this
classification system is ambiguous as it can refer to three distinct aspects (staining result, cell-envelope organization, taxonomic group), which do not necessarily coalesce
for some bacterial species. However, although Gram-staining response of bacteria is an
empirical criterion, its basis lies in the marked differences in the ultrastructure and
chemical composition of the two main kinds of bacteria. These bacteria are distinguished from each other based on the presence or absence of an outer lipid membrane,
which is a more reliable and fundamental characteristic of the bacterial cells.
https://en.wikipedia.org/wiki/Periplasm
Peroxidase
For many of these enzymes the optimal substrate is hydrogen peroxide, but
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Peroxide
A peroxide is a compound containing an oxygenoxygen single bond or the peroxide
anion, O=
The OO group is called the peroxide group or peroxo group. In contrast to oxide ions,
the oxygen atoms in the peroxide ion have an oxidation state of 1.
The simplest stable peroxide is hydrogen peroxide. Superoxides, dioxygenyls, ozones
and ozonides are considered separately. Peroxide compounds can be roughly classified
into organic and inorganic. Whereas the inorganic peroxides have an ionic, salt-like
character, the organic peroxides are dominated by the covalent bonds. The oxygenoxygen chemical bond of peroxide is unstable and easily split into reactive radicals via homolytic cleavage. For this reason, peroxides are found in nature only in small quantities, in water, atmosphere, plants, and animals. Peroxide ion formation has recently
been highlighted as one of the main mechanisms by which oxides accommodate excess
oxygen in ionic crystals and may have a large impact on a range of industrial applications including solid oxide fuel cells.
Peroxides have a bleaching effect on organic substances and therefore are added to
some detergents and hair colorants. Other large-scale applications include medicine
and chemical industry, where peroxides are used in various synthesis reactions or occur as intermediate products. With an annual production of over 2 million tonnes, hydrogen peroxide is the most economically important peroxide. Many peroxides are unstable and hazardous substances. They cannot be stored and therefore are synthesized
in situ and used immediately. Different peroxide types are shown below.
https://en.wikipedia.org/wiki/Peroxide
Peroxiredoxins
ian cells. The family members in humans are PRDX1, PRDX2, PRDX3, PRD
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Peroxisomes
Peroxisomes are organelles found in virtually all eukaryotic cells. They are involved in
the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, and polyamines, reduction of reactive oxygen species - specifically hydrogen peroxide - and biosynthesis of plasmalogens, i.e. ether phospholipids critical for the normal
function of mammalian brains and lungs. They also contain approximately 10% of the
total activity of two enzymes in the pentose phosphate pathway, which is important for
energy metabolism. It is vigorously debated if peroxisomes are involved in isoprenoid
and cholesterol synthesis in animals. Other known peroxisomal functions include the
glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts.
Peroxisomes were identified as organelles by the Belgian cytologist Christian de Duve
in 1967 after they had been first described by a Swedish doctoral student, J. Rhodin in
1954.
https://en.wikipedia.org/wiki/Peroxisome
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Peroxynitrite
Peroxynitrite (sometimes called peroxonitrite) is an ion with the formula ONOO. It is
an unstable structural isomer of nitrate, NO. Although its conjugate acid is highly reactive, peroxynitrite is stable in basic solutions. It is prepared by the reaction of hydrogen peroxide with nitrite. Peroxynitrite is an oxidant and nitrating agent. Because of its
oxidizing properties, peroxynitrite can damage a wide array of molecules in cells, including DNA and proteins.
Peroxynitrite is prepared by the reaction of hydrogen peroxide with nitrite:
H2O2 + NO2= ONOO + H2O
Peroxynitrite is an oxidant and nitrating agent. Because of its oxidizing properties, peroxynitrite can damage a wide array of molecules in cells, including DNA and proteins.
Formation of peroxynitrite in vivo has been ascribed to the reaction of the free radical
superoxide with the free radical nitric oxide:
O2 + NO ONO2
The resultant pairing of these two free radicals results in peroxynitrite, a molecule that
is itself not a free radical, but that is a powerful oxidant.
In the laboratory, a solution of peroxynitrite can be prepared by treating acidified hydrogen peroxide with a solution of sodium nitrite, followed by rapid addition of NaOH.
Its concentration is indicated by the absorbance at 302 nm
https://en.wikipedia.org/wiki/Peroxynitrite
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PFK-1
Phosphofructokinase-1 (PFK-1) is one of the most important regulatory enzymes of glycolysis. It is an allosteric enzyme made of 4 subunits and controlled by many activators
and inhibitors. PFK-1 catalyzes the important "committed" step of glycolysis, the conversion of fructose 6-phosphate and ATP to fructose 1,6-bisphosphate and ADP.
F6P + ATP <=> F1,6BP + ADP
Glycolysis is the foundation for respiration, both anaerobic and aerobic. Because phosphofructokinase (PFK) catalyzes the ATP-dependent phosphorylation to convert
fructose-6-phosphate into fructose 1,6-bisphosphate and ADP, it is one of the key regulatory and rate limiting steps of glycolysis. PFK is able to regulate glycolysis through allosteric inhibition, and in this way, the cell can increase or decrease the rate of glycolysis in response to the cells energy requirements. For example, a high ratio of ATP to
ADP will inhibit PFK and glycolysis. The key difference between the regulation of PFK
in eukaryotes and prokaryotes is that in eukaryotes PFK is activated by fructose 2,6bisphosphate. The purpose of fructose 2,6-bisphosphate is to supersede ATP inhibition, thus allowing eukaryotes to have greater sensitivity to regulation by hormones
like glucagon and insulin.
https://en.wikipedia.org/wiki/Phosphofructokinase_1
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PFK-2
the conformation change of the enzyme to favor the FBPase2 activity. Othe
PFK2 activity is favored. The PFK2 domain is closely related to the superfam
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PGD2
Prostaglandin D2 (or PGD2) is a prostaglandin that binds to the receptor PTGDR
(DP1), as well as CRTH2 (DP2). It is a major prostaglandin produced by mast cells
recruits Th2 cells, eosinophils, and basophils. In mammalian organs, large amounts of
PGD2 are found only in the brain and in mast cells. It is critical to development of allergic diseases such as asthma.
Research carried out in 1989 found PGD2 is the primary mediator of vasodilation (the
"niacin flush") after ingestion of niacin (nicotinic acid).
A 2012 research paper indicates a causal link between elevated levels of localized PGD2
and hair growth inhibition. Applied topically, the researchers found PGD2 prevents
hair growth, and mice that were genetically inclined to produce higher levels of PGD2
had inhibited hair growth. The researchers also found PGD2 levels were much higher
in balding scalp tissue than nonbalding scalp tissue, through increased levels of prostaglandin D2 synthase. The paper suggested that inhibition of hair growth involved binding of PGD2 to a receptor called GPR44, and that GPR44 therefore would be a therapeutic target for androgenic alopecia in both men and women with hair loss and thinning.
Because PGD2's relation to asthma has been known for several years, several drugs that
seek to reduce the effect of PGD2 through blocking the GPR44 are already in clinical trials.
https://en.wikipedia.org/wiki/Prostaglandin_D2
PGE2
The naturally occurring prostaglandin E2 (PGE2) is known in medicine as dinopros-
tone. It has important effects in labor (softening the cervix and causing uterine contrac
tion) and also stimulates osteoblasts to release factors that stimulate bone resorption
by osteoclasts. PGE2 is also the prostaglandin that ultimately induces fever.
PGE2 also suppresses T cell receptor signaling and may play a role in resolution of inflammation.
https://en.wikipedia.org/wiki/Prostaglandin_E2
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PGF2
Prostaglandin F2 (PGF2 in prostanoid nomenclature), pharmaceutically termed dinoprost (INN), is a naturally occurring prostaglandin used in medicine to induce labor
and as an abortifacient.
In domestic mammals, it is produced by the uterus when stimulated by oxytocin, in the
event that there has been no implantation during the follicular phase. It acts on the corpus luteum to cause luteolysis, forming a corpus albicans and stopping the production
of progesterone. Action of PGF2 is dependent on the number of receptors on the corpus luteum membrane.
https://en.wikipedia.org/wiki/Prostaglandin_F2alpha
PGH2
https://en.wikipedia.org/wiki/Prostaglandin_H2
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PGI2
Prostacyclin (also called prostaglandin I2 or PGI2) is a prostaglandin member of the eicosanoid family of lipid molecules. It inhibits platelet activation and is also an effective
vasodilator.
As a drug, it is also known as "epoprostenol".
https://en.wikipedia.org/wiki/Prostacyclin
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pH
pH is a numeric scale used to specify the acidity or basicity (alkalinity) of an aqueous
solution. It is roughly the negative of the logarithm to base 10 of the molar concentration, measured in units of moles per liter, of hydrogen ions. More precisely it is the
negative of the logarithm to base 10 of the activity of the hydrogen ion. Solutions with a
pH less than 7 are acidic and solutions with a pH greater than 7 are basic. Pure water is
neutral, being neither an acid nor a base. Contrary to popular belief, the pH value can
be less than 0 or greater than 14 for very strong acids and bases respectively.
https://en.wikipedia.org/wiki/PH
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Phagocytes
Phagocytes are cells that protect the body by ingesting (phagocytosing) harmful foreign
particles, bacteria, and dead or dying cells. During an infection, chemical signals attract phagocytes to places where the pathogen has invaded the body. These chemicals
may come from bacteria or from other phagocytes already present. The phagocytes
move by a method called chemotaxis. When phagocytes come into contact with bacteria, the receptors on the phagocyte's surface will bind to them. This binding will lead to
the engulfing of the bacteria by the phagocyte. Some phagocytes kill the ingested pathogen with oxidants and nitric oxide.
After phagocytosis, macrophages and dendritic cells can also participate in antigen
presentation, a process in which a phagocyte moves parts of the ingested material back
to its surface. This material is then displayed to other cells of the immune system.
Some phagocytes then travel to the body's lymph nodes and display the material to
white blood cells called lymphocytes. This process is important in building immunity,
and many pathogens have evolved methods to evade attacks by phagocytes.
https://en.wikipedia.org/wiki/Phagocyte
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Phagocytosis
Phagocytosis is a specific form of endocytosis involving the vascular internalization of
solids such as bacteria by an organism, and is therefore distinct from other forms of endocytosis such as the vesicular internalization of various liquids (pinocytosis). Phagocytosis is involved in the acquisition of nutrients for some cells. The process is homologous to eating at the level of single-celled organisms. In multicellular animals, the
process has been adapted to eliminate debris and pathogens, as opposed to taking in
fuel for cellular processes, except in the case of the animal Trichoplax. In an organism's immune system, phagocytosis is a major mechanism used to remove pathogens
and cell debris.
For example, when a macrophage ingests a pathogenic microorganism, the pathogen
becomes trapped in a phagosome which then fuses with a lysosome to form a phagolysosome. Within the phagolysosome, enzymes and toxic peroxides digest the pathogen.
Bacteria, dead tissue cells, and small mineral particles are all examples of objects that
may be phagocytized.
https://en.wikipedia.org/wiki/Phagocytosis
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Phagolysosome
food particles or pathogens contained within the phagosome are usually dig
the hydrolytic enzymes contained within the lysosome. Products of the dige
macrophages and forms the home of several infectious agents including Lei
https://en.wikipedia.org/wiki/Phagolysosome
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Phagosome
ole is formed by the fusion of the cell membrane around the particle. A phagoso
Some bacterial pathogens that enter cells inside phagosomes either reproduce i
the formed phagolysosome (e.g. Coxiella spp.) or escape into the cytoplasm befo
phagosome fuses with the lysosome (e.g. Rickettsia spp.). Many mycobacteria, i
late the host macrophage to prevent nitrous acid-containing lysosomes from fus
Phenethylamine
Phenethylamine (PEA), also known as -phenylethylamine (-PEA) and 2phenylethylamine is an organic compound and a natural monoamine alkaloid, a trace
amine, and also the name of a class of chemicals with many members that are well
known for their psychoactive and stimulant effects.
Phenylethylamine functions as a monoaminergic neuromodulator and, to a lesser extent, a neurotransmitter in the human central nervous system. It is biosynthesized
from the amino acid L-phenylalanine by enzymatic decarboxylation via the enzyme aromatic L-amino acid decarboxylase. In addition to its presence in mammals, phenethylamine is found in many other organisms and foods, such as chocolate, especially after
microbial fermentation. It is sold as a dietary supplement for purported mood and
weight loss-related therapeutic benefits. However, orally ingested phenethylamine experiences extensive first-pass metabolism by monoamine oxidase B (MAO-B) and then
aldehyde dehydrogenase (ALDH), which metabolize it into phenylacetic acid. This prevents significant concentrations from reaching the brain when taken in low doses.
https://en.wikipedia.org/wiki/Phenethylamine
Phenotypic
A phenotype (from Greek phainein, meaning "to show", and typos, meaning "type") is
the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and
products of behavior (such as a bird's nest). A phenotype results from the expression of
an organism's genes as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the
same population of a species, the species is called polymorph.
The genotype of an organism is the inherited instructions it carries within its genome.
This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to
make clear the difference between an organism's heredity and what that heredity produces. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). The genotypephenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, which is a statement about the directionality of molecular sequential
information flowing from DNA to protein, and not the reverse.
Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype
suggested that bird nests and other built structures such as caddis fly larvae cases and
beaver dams can be considered as "extended phenotypes".
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Phenylalanine
Phenylalanine is an -amino acid with the formula C6H5CH2CH(NH2)COOH. It can
be viewed as a benzyl group substituted for the methyl group of alanine, or a phenyl
group in place of a terminal hydrogen of alanine. This essential amino acid is classified
as neutral, and nonpolar because of the inert and hydrophobic nature of the benzyl
side chain. The L-isomer is used to biochemically form proteins, coded for by DNA.
The codons for L-phenylalanine are UUU and UUC.
Phenylalanine is a precursor for tyrosine; the monoamine neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline); and the skin pigment melanin.
Phenylalanine is found naturally in the breast milk of mammals. It is used in the manufacture of food and drink products and sold as a nutritional supplement for its reputed
analgesic and antidepressant effects. It is a direct precursor to the neuromodulator phenethylamine, a commonly used dietary supplement.
https://en.wikipedia.org/wiki/Phenylalanine
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Phenylalanine Hydroxylase
ridine cofactor) and a non-heme iron for catalysis. During the reaction, mol
Index
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Phenylketonuria
Phenylketonuria (PKU) is an inborn error of metabolism involving impaired metabolism of the amino acid phenylalanine. Phenylketonuria is caused by absent or virtually
absent phenylalanine hydroxylase (PAH) enzyme activity. The condition is also known
as phenylalanine hydroxylase deficiency.
Protein-rich foods or the sweetener aspartame can act as poisons for people with phenylketonuria. The role of PAH is to break down excess phenylalanine from food. Phenylalanine is a necessary part of the human diet and is naturally present in all kinds of
dietary protein. It is also used to make aspartame, known by the trade name Nutrasweet, which is used to sweeten low-calorie and sugar free soft drinks, yogurts, and
desserts. In people without PKU, the PAH enzyme breaks down any excess phenylalanine from these sources beyond what is needed by the body. However, if there is
not enough of the PAH enzyme or its cofactor, then phenylalanine can build up in the
blood and brain to toxic levels, affecting brain development and function. PKU is rare,
but important to identify, because if caught early it is very treatable. It is not contagious, and it is lifelong, but with early diagnosis and consistent treatment, the damaging effects can be minimal or non-existent.
Untreated PKU can lead to intellectual disability, seizures, and other serious medical
problems. The best proven treatment for classical PKU patients is a strict
phenylalanine-restricted diet supplemented by a medical formula containing amino acids and other nutrients. In the United States, the current recommendation is that the
PKU diet should be maintained for life. Patients who are diagnosed early and maintain
a strict diet can have a normal life span with normal mental development.
PKU is an inherited disease. When an infant is diagnosed with PKU, it is never the result of any action of the parents or any environmental factor. Rather, for a child to inherit PKU, both of his or her parents must have at least one mutated allele of the PAH
gene. Most parents who are carriers of PKU genes are not aware that they have this mutation because being a carrier causes no medical problems. To be affected by PKU, a
child must inherit two mutated alleles, one from each parent.
https://en.wikipedia.org/wiki/Phenylketonuria
Phenylpyruvate
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Pheomelanin
Pheomelanin is a cysteine-containing red polymer of benzothiazine units largely responsible for red hair, among other pigmentation. It is one of three types of melanin.
Part of the structure of this polymer is shown below.
https://en.wikipedia.org/wiki/Melanin
Pheophytin
Pheophytin or phaeophytin (abbreviated Pheo) is a chemical compound that serves as
the first electron carrier intermediate in the electron transfer pathway of photosystem
II (PS II) in plants, and the photosynthetic reaction center (RC P870) found in purple
bacteria. In both PS II and RC P870, light drives electrons from the reaction center
through pheophytin, which then passes the electrons to a quinone (QA) in RC P870
and RC P680. The overall mechanisms, roles, and purposes of the pheophytin molecules in the two transport chains are analogous to each other. The structure of pheophytin minus the magnesium ion it normally has in the porphyrin ring, is shown below.
https://en.wikipedia.org/wiki/Pheophytin
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https://en.wikipedia.org/wiki/Ramachandran_plot
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Phosphatase PTEN
the PTEN gene. Mutations of this gene are a step in the development of many ca
PTEN orthologs have been identified in most mammals for which complete gen
data are available.
This gene was identified as a tumor suppressor that is mutated in a large numb
lytic domain similar to that of the dual specificity protein tyrosine phosphatases
like most of the protein tyrosine phosphatases, this protein preferentially depho
lates phosphoinositide substrates. It negatively regulates intracellular levels of
Index
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Phosphatases
A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolyzing phosphoric acid monoesters into a phosphate ion and a molecule with a free
hydroxyl group (see dephosphorylation). This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their substrates by using energetic molecules like ATP. A common phosphatase in many organisms is alkaline
phosphatase. Another large group of proteins present in archaea, bacteria, and eukaryotes exhibits deoxyribonucleotide and ribonucleotide phosphatase or pyrophosphatase
activities that catalyze the decomposition of dNTP/NTP into dNDP/NDP and a free
phosphate ion or dNMP/NMP and a free pyrophosphate ion. The other group of phosphatase is collectively called as protein phosphatase, which removes a phosphate group
from the phosphorylated amino acid residue of the substrate protein. Protein phosphorylation is a common post-translational modification of protein catalyzed by protein kinases, and protein phosphatases reverse the effect.
https://en.wikipedia.org/wiki/Phosphatase
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Phosphate
A phosphate (PO4-3 or abbreviated Pi) is an inorganic chemical and a salt of phosphoric
acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric
acid. Of the various phosphoric acids and phosphates, organic phosphates are important in biochemistry and biogeochemistry (ecology), and inorganic phosphates are
mined to obtain phosphorus for use in agriculture and industry. At elevated temperatures in the solid state, phosphates can condense to form pyrophosphates.
The addition and removal of phosphates from proteins in all cells is a pivotal strategy
in the regulation of metabolic processes. Phosphorylation and dephosphorylation are
important ways that energy is stored and released in living systems.
https://en.wikipedia.org/wiki/Phosphate
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Phosphate Translocase
Glucose-6-Phosphate Translocase is an enzyme that in humans is encoded
SLC37A4 gene. It consists of three subunits, each of which are vital compon
plex is located within the membrane of the endoplasmic reticulum, and cata
most abundant in liver tissue, but also present in kidney cells, small intestin
atic islets and at a lower concentration in the gallbladder. The G6Pase comp
porting the substrates and products across the endoplasmic reticulum mem
sulting in the release of free glucose into the bloodstream.
https://en.wikipedia.org/wiki/Glucose-6-phosphate_translocase
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Phosphates
A phosphate (PO4-3 or abbreviated Pi) is an inorganic chemical and a salt of
acid. In organic chemistry, a phosphate, or organophosphate, is an ester of
The addition and removal of phosphates from proteins in all cells is a pivota
Phosphatidate Cytidylyltransferase
Phosphatidate cytidylyltransferase (also known as CDP- diacylglycerol synthase) (CDS)
is the enzyme that catalyzes the synthesis of CDP-diacylglycerol from cytidine triphosphate and phosphatidate.
CTP + Phosphatidate Diphosphate + CDP-diacylglycerol
Thus, the two substrates of this enzyme are cytidine triphosphate, or CTP, and phosphatidate, whereas its two products are diphosphate and CDP-diacylglycerol.
CDP-diacylglycerol is an important branch point intermediate in both prokaryotic and
eukaryotic organisms. CDS is a membrane-bound enzyme.
This enzyme belongs to the family of transferases, specifically those transferring
phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic
name of this enzyme class is CTP:phosphatidate cytidylyltransferase. Other names in
common use include CDP diglyceride pyrophosphorylase, CDP-diacylglycerol synthase, CDP-diacylglyceride synthetase, cytidine diphosphoglyceride pyrophosphorylase, phosphatidate cytidyltransferase, phosphatidic acid cytidylyltransferase,
CTP:1,2-diacylglycerophosphate-cytidyl transferase, CTP-diacylglycerol synthetase,
DAG synthetase, and CDP-DG.
This enzyme participates in glycerophospholipid metabolism and phosphatidylinositol
signaling system.
https://en.wikipedia.org/wiki/Phosphatidate_cytidylyltransferase
Phosphatide
Phosphatidic acids (PAs) (ionized form = phosphatidate) are the acid forms of phosph
unsaturated fatty acid bonded to carbon-2, and a phosphate group bonded to carbon3.
https://en.wikipedia.org/wiki/Phosphatidic_acid
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Phosphatidic Acid
Phosphatidic acids (PAs) (ionized form = phosphatidate) are the acid forms of phosphatidates, a part of common phospholipids, major constituents of cell membranes. Phosphatidic acids are the simplest diacyl-glycerophospholipids. Phosphatidic acid consists
of a glycerol backbone, with, in general, a saturated fatty acid bonded to carbon-1, an
unsaturated fatty acid bonded to carbon-2, and a phosphate group bonded to carbon3.
https://en.wikipedia.org/wiki/Phosphatidic_acid
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Phosphatidylcholine
Phosphatidylcholines (PC) are a class of phospholipids that incorporate choline as a
headgroup. They are a major component of biological membranes and can be easily obtained from a variety of readily available sources, such as egg yolk or soybeans, from
which they are mechanically or chemically extracted using hexane. They are also a
member of the lecithin group of yellow-brownish fatty substances occurring in animal
and plant tissues. Dipalmitoyl phosphatidylcholine (aka: lecithin) is a major component of pulmonary surfactant and is often used in the L/S ratio to calculate fetal lung
maturity. While phosphatidylcholines are found in all plant and animal cells, they are
absent in the membranes of most bacteria, including Escherichia coli. Purified phosphatidylcholine is produced commercially.
Phosphatidylcholine is a major constituent of cell membranes and pulmonary surfactant, and is more commonly found in the exoplasmic or outer leaflet of a cell membrane. It is thought to be transported between membranes within the cell by phosphatidylcholine transfer protein (PCTP).
Phosphatidylcholine also plays a role in membrane-mediated cell signaling and PCTP
activation of other enzymes. One example of a phosphatidylcholine is shown below.
https://en.wikipedia.org/wiki/Phosphatidylcholine
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Phosphatidylethanolamine
Phosphatidylethanolamines (sometimes abbreviated PE) are a class of phospholipids
found in biological membranes. They are synthesized by the addition of CDPethanolamine to diglycerides, releasing CMP. S-Adenosyl methionine can subsequently
methylate the amine of phosphatidylethanolamines to yield phosphatidylcholines. It
can mainly be found in the inner (cytoplasmic) leaflet of the lipid bilayer. It is easily
made by decarboxylation of serine.
https://en.wikipedia.org/wiki/Phosphatidylethanolamine
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Phosphatidylglycerol
Phosphatidylglycerol is a glycerophospholipid found in pulmonary surfactant.
The general structure of phosphatidylglycerol consists of a L-glycerol 3-phosphate
backbone ester-bonded to either saturated or unsaturated fatty acids on carbons 1 and
2. The head group substituent glycerol is bonded through a phosphomonoester. It is
the precursor of surfactant and its presence (>0.3) in the amniotic fluid of the newborn
indicates fetal lung maturity.
Approximately 98% of alveolar wall surface area is due to the presence of type I cells,
with type II cells producing pulmonary surfactant covering around 2% of the alveolar
walls. Once surfactant is secreted by the type II cells, it must be spread over the remaining type I cellular surface area. Phosphatidylglycerol is thought to be important in
spreading of surfactant over the Type I cellular surface area. The major surfactant deficiency in premature infants relates to the lack of phosphatidylglycerol, even though it
comprises less than 5% of pulmonary surfactant phospholipids. It is synthesized by
head group exchange of a phosphatidylcholine enriched phospholipid using the enzyme phospholipase D.
https://en.wikipedia.org/wiki/Phosphatidylglycerol
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Phosphatidylinositol
Phosphatidylinositol consists of a family of lipids as illustrated on the right, a class of
the phosphatidylglycerides. In such molecules the isomer of the inositol group is assumed to be the myo- conformer unless otherwise stated. Typically phosphatidylinositols form a minor component on the cytosolic side of eukaryotic cell membranes. The
phosphate group gives the molecules a negative charge at physiological pH.
The form of phosphatidylinositol comprising the isomer muco-inositol acts as a sensory receptor in the taste function of the sensory system. In this context it is often referred to as PtdIns, but that does not imply any molecular difference from phosphatidylinositols comprising the myo- conformers of inositol.
The phosphatidylinositol can be phosphorylated to form phosphatidylinositol phosphate (PI-4-P, referred to as PIP in close context or informally), phosphatidylinositol
bisphosphate (PIP2) and phosphatidylinositol trisphosphate (PIP3). All lipids based
on phosphatidylinositol are known as inositides, or sometimes phosphoinositides.
https://en.wikipedia.org/wiki/Phosphatidylinositol
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Phosphatidylinositol (3,4,5)-trisphosphate
Phosphatidylinositol (3,4,5)-trisphosphate, abbreviated PIP3, is the product of the
class I phosphoinositide 3-kinases (PI 3-kinases) phosphorylation of phosphatidylinositol (4,5)-bisphosphate (PIP2). It is a phospholipid that resides on the plasma membrane. PIP3 functions to activate downstream signaling components, the most notable
one being the protein kinase AKT, which activates downstream anabolic signaling pathways required for cell growth and survival. Phospholipase C cleaves PIP2 to produce
inositol triphosphate IP3, and diacylglycerol.
https://en.wikipedia.org/wiki/Phosphatidylinositol_(3,4,5)-trisphosphate
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Phosphatidylinositol-4,5-bisphosphate
Phosphatidylinositol 4,5-bisphosphate or PtdIns(4,5)P2, also known simply as PIP2, is
a minor phospholipid component of cell membranes. PtdIns(4,5)P2 is enriched at the
plasma membrane where it is a substrate for a number of important signaling proteins.
PtdIns(4,5)P2 is formed primarily by the type I phosphatidylinositol 4-phosphate 5kinases from PI(4)P. In metazoans, PtdIns(4,5)P2 can also be formed by type II phosphatidylinositol 5-phosphate 4-kinases from PI(5)P.
The fatty acids of PtdIns(4,5)P2 are variable in different species and tissues, but studies
show the most common fatty acids are stearic in position 1 and arachidonic in 2.
https://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate
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Phosphatidylserine
Phosphatidylserine (abbreviated Ptd-L-Ser or PS) is an important phospholipid membrane component (i.e. component of the cell membrane) which plays a key role in cell
cycle signaling, specifically in relationship to apoptosis.
https://en.wikipedia.org/wiki/Phosphatidylserine
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Phosphocholine
Phosphocholine is an intermediate in the synthesis of phosphatidylcholine in tissues.
Phosphocholine is made in a reaction, catalyzed by choline kinase, that converts ATP
and choline into phosphocholine and ADP. Phosphocholine is a molecule found, for example, in lecithin.
It is also used by nematodes and human placentas as a posttranslational modification
to suppress an immune response by their hosts.
It is also one of the binding targets of C-reactive protein (CRP). Thus, when a cell is
damaged, CRP binds to phosphocholine, beginning the recognition and phagocytotic
immunologic response.
Phosphocholine is a natural constituent of hens' eggs (and many other eggs) often used
in biomimetic membrane studies.
https://en.wikipedia.org/wiki/Phosphocholine
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Phosphodiester
A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric
acid react with hydroxyl groups on other molecules to form two ester bonds.
Phosphodiester bonds are central to all life on Earth, as they make up the backbone of
the strands of nucleic acid. In DNA and RNA, the phosphodiester bond is the linkage
between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another,
deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.
The phosphate groups in the phosphodiester bond are negatively charged. Because the
phosphate groups have a pKa near 0, they are negatively charged at pH 7. This repulsion forces the phosphates to take opposite sides of the DNA strands and is neutralized
by proteins (histones), metal ions such as magnesium, and polyamines.
In order for the phosphodiester bond to be formed and the nucleotides to be joined,
the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken
apart to give off energy required to drive the enzyme-catalyzed reaction. When a single
phosphate or two phosphates known as pyrophosphates break away and catalyze the
reaction, the phosphodiester bond is formed.
Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterases which play an important role in repairing DNA sequences.
The phosphodiester linkage between two ribonucleotides can be broken by alkaline hydrolysis, whereas the linkage between two deoxyribonucleotides is more stable under
these conditions. The relative ease of RNA hydrolysis is an effect of the presence of the
2' hydroxyl group.
https://en.wikipedia.org/wiki/Phosphodiester_bond
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Phosphodiesterase
A phosphodiesterase (PDE) is any enzyme that breaks a phosphodiester bond. Usually,
phosphodiesterase refers to cyclic nucleotide phosphodiesterases, which have great
clinical significance and are described below. However, there are many other families
of phosphodiesterases, including phospholipases C and D, autotaxin, sphingomyelin
phosphodiesterase, DNases, RNases, and restriction endonucleases (which all break
the phosphodiester backbone of DNA or RNA), as well as numerous less-wellcharacterized small-molecule phosphodiesterases.
The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade
the phosphodiester bond in the second messenger molecules cAMP and cGMP. They
regulate the localization, duration, and amplitude of cyclic nucleotide signaling within
subcellular domains. PDEs are therefore important regulators of signal transduction
mediated by these second messenger molecules.
https://en.wikipedia.org/wiki/Phosphodiesterase
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Phosphodiesterases
clinical significance and are described below. However, there are many other
the phosphodiester bond in the second messenger molecules cAMP and cGM
Index
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Phosphoenolpyruvate
Phosphoenolpyruvic acid (PEP), or phosphoenolpyruvate (2-phosphoenolpyruvate) as
the anion, is an important chemical compound in biochemistry. It has the highestenergy phosphate bond found (-61.9 kJ/mol) in living organisms, and is involved in glycolysis and gluconeogenesis. In plants, it is also involved in the biosynthesis of various
aromatic compounds, and in carbon fixation. In bacteria, it is also used as the source
of energy for the phosphotransferase system. The acid form is shown below.
https://en.wikipedia.org/wiki/Phosphoenolpyruvic_acid
Index
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Phosphoenolpyruvate
Phosphoenolpyruvic acid (PEP), or phosphoenolpyruvate (2-phosphoenolpyruvate) as
the anion, is an important chemical compound in biochemistry. It has the highestenergy phosphate bond found (-61.9 kJ/mol) in living organisms, and is involved in glycolysis and gluconeogenesis. In plants, it is also involved in the biosynthesis of various
aromatic compounds, and in carbon fixation. In bacteria, it is also used as the source
of energy for the phosphotransferase system. The acid form is shown below.
https://en.wikipedia.org/wiki/Phosphoenolpyruvic_acid
Index
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Phosphoethanolamine
https://en.wikipedia.org/wiki/Phosphorylethanolamine
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Phosphofructokinase
Phosphofructokinase is a kinase enzyme that phosphorylates fructose 6-phosphate in
glycolysis. The reaction catalyzed is
F6P + ATP <=> F1,6BP + ADP
The enzyme-catalyzed transfer of a phosphoryl group from ATP is an important reaction in a wide variety of biological processes. One enzyme that utilizes this reaction is
phosphofructokinase (PFK), which catalyzes the phosphorylation of fructose-6phosphate to fructose-1,6- bisphosphate, a key regulatory step in the glycolytic pathway. It is allosterically inhibited by ATP and allosterically activated by AMP, thus indicating the cell's energetic needs when it undergoes the glycolytic pathway. PFK exists
as a homotetramer in bacteria and mammals (where each monomer possesses 2 similar domains) and as an octomer in yeast (where there are 4 - (PFK1) and 4 -chains
(PFK2), the latter, like the mammalian monomers, possessing 2 similar domains). This
protein may use the morpheein model of allosteric regulation.
PFK is about 300 amino acids in length, and structural studies of the bacterial enzyme
have shown it comprises two similar (/) lobes: one involved in ATP binding and the
other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme activity). The identical tetramer subunits adopt 2 different conformations: in a 'closed' state, the bound magnesium ion bridges the phosphoryl groups of the enzyme products (ADP and fructose1,6- bisphosphate). In an 'open' state, the magnesium ion binds only the ADP, as the 2
products are now further apart. These conformations are thought to be successive
stages of a reaction pathway that requires subunit closure to bring the 2 molecules sufficiently close to react.
Deficiency in PFK leads to glycogenosis type VII (Tarui's disease), an autosomal recessive disorder characterized by severe nausea, vomiting, muscle cramps and myoglobinuria in response to bursts of intense or vigorous exercise. Sufferers are usually able to
lead a reasonably ordinary life by learning to adjust activity levels.
https://en.wikipedia.org/wiki/Phosphofructokinase
Phosphoglucoisomerase
Glucose-6-phosphate isomerase (GPI), alternatively known as phosphoglucose
isomerase (PGI), phosphoglucoisomerase, or phosphohexose isomerase (PHI), is an
zyme that in humans is encoded by the GPI gene on chromosome 19. This gene en-
codes a member of the glucose phosphate isomerase protein family. The encoded pro
tein has been identified as a moonlighting protein based on its ability to perform
mechanistically distinct functions. In the cytoplasm, the gene product functions as a
glycolytic enzyme (glucose-6-phosphate isomerase) that interconverts glucose-6-
vival of skeletal motor neurons and sensory neurons, and as a lymphokine that induc
ogenic factor. Defects in this gene are the cause of nonspherocytic hemolytic anemia,
and a severe enzyme deficiency can be associated with hydrops fetalis, immediate ne
natal death and neurological impairment. Alternative splicing results in multiple tran
script variants.
https://en.wikipedia.org/wiki/Glucose-6-phosphate_isomerase
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Phosphoglucomutase
monomer from the 1' to the 6' position in the forward direction or the 6' to t
tion in the reverse direction.
Index
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Phosphoglycerate Kinase
In humans, two isozymes of PGK have been so far identified, PGK1 and PGK2. The iso
zymes have 87-88% identical amino acid sequence identity and though they are struc-
turally and functionally similar, they have different localizations: PGK2, encoded by an
autosomal gene, is unique to meiotic and postmeiotic spermatogenic cells, while PGK1
encoded on the X-chromosome, is ubiquitously expressed in all cells.
https://en.wikipedia.org/wiki/Phosphoglycerate_kinase
Phosphoglycerate Mutase
catalyzes the internal transfer of a phosphate group from C-3 to C-2 which re
These enzymes are categorized into the two distinct classes of either cofactor
as in some invertebrates, fungi, and bacteria. The iPGM (EC 5.4.2.12) class is
all plants and algae as well as in some invertebrate, fungi, and Gram-positive
This class of PGM enzyme shares the same superfamily as alkaline phosphat
https://en.wikipedia.org/wiki/Phosphoglycerate_mutase
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Phosphoglycerolipid
phosphoric acid that contains at least one O-acyl, or O-alkyl, or O-alk-1'- eny
attached to the glycerol moiety.
The alcohol here is glycerol, to which two fatty acids and a phosphoric acid a
tional group attached to the phosphate allows for many different phosphogly
cally with the phosphate attached to carbon atom number three (at the botto
malogens and phosphatidates are examples.
https://en.wikipedia.org/wiki/Glycerophospholipid
Phosphoglycolate
Phospholipase A1
Phospholipase A1 is a phospholipase enzyme which removes the 1-acyl group of a glycerolipid. It resides in a class of enzymes called phospholipase that hydrolyze phospholipids into fatty acids. There are 4 classes, which are separated by the type of reaction they catalyze. In particular, phospholipase A1 (PLA1) specifically catalyzes the
cleavage at the SN-1 position of phospholipids, forming a fatty acid and a lysophospholipid.
PLA1s are present in numerous species including humans, and have a variety of cellular functions that include regulation and facilitation of the production of lysophospholipid mediators, and acting as digestive enzymes. These enzymes are responsible
for fast turnover rates of cellular phospholipids. In addition to this, the products of the
reaction catalyzed by PLA1 which are a fatty acid and a lysophospholipid are important
in various biological functions such as platelet aggregation and smooth muscle contraction. In addition, lysophospholipids can be found as surfactants in food techniques and
cosmetics, and can be used in drug delivery. Since PLA1 is found in many species, it has
been found that there are different classes of this one specific enzyme based on the organism being studied.
https://en.wikipedia.org/wiki/Phospholipase_A1
Phospholipase A2
Phospholipases A2 (PLA2s) are enzymes that release fatty acids from the second carbon
group of glycerolipids. This particular phospholipase specifically recognizes the sn-2
acyl bond of phospholipids and catalytically hydrolyzes the bond releasing arachidonic
acid and lysophosphatidic acid. Upon downstream modification by cyclooxygenases,
arachidonic acid is modified into active compounds called eicosanoids. Eicosanoids include prostaglandins and leukotrienes, which are categorized as anti-inflammatory and
inflammatory mediators.
PLA2 enzymes are commonly found in mammalian tissues as well as arachnid, insect
and snake venom. Venom from both snakes and insects is largely composed of melittin, which is a stimulant of PLA2. Due to the increased presence and activity of PLA2 resulting from a snake or insect bite, arachidonic acid is released from the phospholipid
membrane disproportionately. As a result, inflammation and pain occur at the site.
There are also prokaryotic A2 phospholipases.
https://en.wikipedia.org/wiki/Phospholipase_A2
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Phospholipase C
Phospholipase C (PLC) is a class of membrane-associated enzymes that cleave phospholipids just before the phosphate group of a glycerophospholipid (see figure). It is
most commonly taken to be synonymous with the human forms of this enzyme, which
play an important role in eukaryotic cell physiology, in particular signal transduction
pathways. There are thirteen kinds of mammalian phospholipase C that are classified
into six isotypes (, , , , , ) according to structure. Each PLC has unique and overlapping controls over expression and subcellular distribution. Activators of each PLC
vary, but typically include heterotrimeric G protein subuntis, protein tyrosine kinases,
small G proteins, Ca2+, and phospholipids.
https://en.wikipedia.org/wiki/Phospholipase_C
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Phospholipases
A phospholipase is an enzyme that hydrolyzes glycerophospholipids into fatty acids
and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze:
Phospholipase A1 - cleaves the SN-1 acyl chain.
Phospholipase A2 - cleaves the SN-2 acyl chain, releasing arachidonic acid.
Phospholipase B - cleaves both SN-1 and SN-2 acyl chains. This enzyme is also known
as a lysophospholipase.
Phospholipase C - cleaves before the phosphate, releasing diacylglycerol and a
phosphate-containing head group. Phospholipase Cs play a central role in signal transduction, releasing the second messenger inositol triphosphate.
Phospholipase D - cleaves after the phosphate, releasing phosphatidic acid and an alcohol.
https://en.wikipedia.org/wiki/Phospholipase
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Phospholipiase D
Phospholipase D (EC 3.1.4.4, lipophosphodiesterase II, lecithinase D, choline phosphatase) (PLD) is an enzyme of the phospholipase superfamily. Phospholipases occur
widely, and can be found in a wide range of organisms, including bacteria, yeast,
plants, animals, and viruses. Phospholipase Ds principal substrate is phosphatidylcholine, which it hydrolyzes to produce the signal molecule phosphatidic acid (PA), and
soluble choline. Plants contain numerous genes that encode various PLD isoenzymes,
with molecular weights ranging from 90-125 kDa. Mammalian cells encode two isoforms of phospholipase D: PLD1 and PLD2. Phospholipase D is an important player in
many physiological processes, including membrane trafficking, cytoskeletal reorganization, receptor-mediated endocytosis, exocytosis, and cell migration. Through these
processes, it has been further implicated in the pathophysiology of multiple diseases:
in particular the progression of Parkinsons and Alzheimers, as well as various cancers.
https://en.wikipedia.org/wiki/Phospholipase_D
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Phospholipid
Phospholipids are a class of lipids that are a major component of all cell membranes.
They can form lipid bilayers because of their amphiphilic characteristic. They come in
two classes - glycerophospholipids and phosphorylated sphingolipids, such as sphingomyelin. The structure of a glycerophospholipid molecule generally consists of two hydrophobic fatty acid "tails" and a hydrophilic phosphate "head", joined together by a
glycerol molecule. The phosphate groups of glycerophospholipids can be modified with
simple organic molecules such as choline.
The 'head' of a phospholipid is hydrophilic (attracted to water), while the hydrophobic
'tails' are repelled by water and are forced to aggregate. The hydrophilic head contains
the negatively charged phosphate group and glycerol. The hydrophobic tail usually consists of 2 long fatty acid chains. When placed in water, phospholipids form a variety of
structures depending on the specific properties of the phospholipid. These specific
properties allow phospholipids to play an important role in the phospholipid bilayer.
In biological systems, the phospholipids often occur with other molecules (e.g., proteins, glycolipids, sterols) in a bilayer such as a cell membrane. Lipid bilayers occur
when hydrophobic tails line up against one another, forming a membrane of hydrophilic heads on both sides facing the water.
Such movement can be described by the fluid mosaic model, that describes the membrane as a mosaic of lipid molecules that act as a solvent for all the substances and proteins within it, so proteins and lipid molecules are then free to diffuse laterally through
the lipid matrix and migrate over the membrane. Sterols contribute to membrane fluidity by hindering the packing together of phospholipids. However, this model has now
been superseded, as through the study of lipid polymorphism it is now known that the
behavior of lipids under physiological (and other) conditions is not simple.
https://en.wikipedia.org/wiki/Phospholipid
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Phosphomannoisomerase
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Phosphopentose Epimerase
sion is required for carbon fixation in plants through the Calvin cycle an
nonoxidative phase of the pentose phosphate pathway. This enzyme has als
plicated in additional pentose and glucuronate interconversions.
https://en.wikipedia.org/wiki/Phosphopentose_epimerase
Phosphopentose Isomerase
in both the pentose phosphate pathway and the Calvin cycle. The systemati
this enzyme class is D-ribose-5-phosphate aldose-ketose-isomerase.
https://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase
Phosphoprotein Phosphatase
A protein phosphatase (phosphoprotein phosphatase) is an enzyme that removes a
phosphate group from the phosphorylated amino acid residue of its substrate protein.
Protein phosphorylation is one of the most common forms of reversible protein posttranslational modification (PTM), with up to 30% of all proteins being phosphorylated
at any given time. Protein kinases (PKs) are the effectors of phosphorylation and catalyze the transfer of a -phosphate from ATP to specific amino acids on proteins. Several hundred PKs exist in mammals and are classified into distinct super-families.
Proteins are phosphorylated predominantly on Ser, Thr and Tyr residues, which account for 86, 12 and 2% respectively of the phosphoproteome, at least in mammals. In
contrast, protein phosphatases (PPs) are the primary effectors of dephosphorylation
and can be grouped into three main classes based on sequence, structure and catalytic
function. The largest class of PPs is the phosphoprotein phosphatase (PPP) family comprising PP1, PP2A, PP2B, PP4, PP5, PP6 and PP7, and the protein phosphatase Mg2+or Mn2+-dependent (PPM) family, composed primarily of PP2C. The protein Tyr phosphatase (PTP) super-family forms the second group, and the aspartate-based protein
phosphatases the third.
https://en.wikipedia.org/wiki/Protein_phosphatase
Index
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Phosphoribosyl-AMP Cyclohydrolase
bonds other than peptide bonds, specifically in cyclic amidines. The system
Index
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Phosphoribosyl-N-formylglycineamide
https://en.wikipedia.org/wiki/Phosphoribosyl-N-formylglycineamide
Phosphoribosylaminoimidazole carboxylase
Phosphoribosylaminoimidazole carboxylase (or AIR carboxylase) is an enzyme involved in purine nucleotide biosynthesis. It catalyzes the conversion of 5'phosphoribosyl-5-aminoimidazole ("AIR") into 5'-phosphoribosyl-4-carboxy-5aminoimidazole ("CAIR") as described in the reaction below. It is the sixth reaction in
the pathway leading to synthesis of IMP.
5-aminoimidazole ribonucleotide (AIR) + HCO3- 5'-phosphoribosyl-4-carboxy-5aminoimidazole (CAIR) + 2 H+
https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazole_carboxylase
Phosphoribosylformylglycinamidine synthase
Index
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Phosphoribosylglycinamide Formyltransferase
Phosphoribosylglycinamide formyltransferase catalyzes the chemical reaction below.
10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide Tetrahydrofolate
+ N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide
This reaction plays an important role in the formation of purines through the de novo
purine biosynthesis pathway. This pathway creates inosine monophosphate (IMP), a
precursor to adenosine monophosphate (AMP) and guanosine monophosphate (GMP).
https://en.wikipedia.org/wiki/Phosphoribosylglycinamide_formyltransferase
Phosphoribulokinase
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Phosphoric Acid
Phosphoric acid (also known as orthophosphoric acid or phosphoric(V) acid) is a mineral (inorganic) acid having the chemical formula H3PO4. Orthophosphoric acid refers
to phosphoric acid, which is the IUPAC name for this compound. The prefix ortho is
used to distinguish the acid from related phosphoric acids, called polyphosphoric acids. Orthophosphoric acid is a non-toxic acid, which, when pure, is a solid at room temperature and pressure. The conjugate base of phosphoric acid is the dihydrogen phosphate ion, which in turn has a conjugate base of hydrogen phosphate, which has a conjugate base of phosphate.
https://en.wikipedia.org/wiki/Phosphoric_acid
Phosphorolysis
Phosphorolysis is the cleavage of a compound in which inorganic phosphate is the attacking group. It is analogous to hydrolysis. An example of this is glycogen breakdown
by glycogen phosphorylase, which catalyzes attack by inorganic phosphate on the terminal glycosyl residue at the nonreducing end of a glycogen molecule. If the glycogen
chain has n glucose units, the products of a single phosphorolytic event are one molecule of glucose 1-phosphate and a glycogen chain of n-1 remaining glucose units.
https://en.wikipedia.org/wiki/Phosphorolysis
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Phosphorylase Kinase
Phosphorylase kinase (PhK) is a serine/threonine-specific protein kinase which activates glycogen phosphorylase to release glucose-1-phosphate from glycogen. PhK phosphorylates glycogen phosphorylase at two serine residues, triggering a conformational
shift which favors the more active glycogen phosphorylase a form over the less active
glycogen phosphorylase b.
The protein is a hexadecameric holoenzyme--that is, a homotetramer in which each
subunit is itself a tetramer--arranged in an approximate butterfly shape. Each of the
subunits is composed of an , , and subunit. The subunit is the site of the enzyme's catalytic activity while the other three subunits serve regulatory functions.
When unmodified, the and subunits inhibit the enzyme's catalysis, but phosphorylation of both these subunits by protein kinase A (PKA, or cAMP-dependent protein kinase) reduces their respective inhibitory activities. The subunit is the ubiquitous
eukaryotic protein calmodulin which itself has 4 calcium ion binding sites. When cytosolic Ca++ levels rise-to as low as 10-7 M the subunit undergoes a large conformational change that activates the kinase's activity by binding to a complementary hydrophobic patch on the catalytic subunit.
https://en.wikipedia.org/wiki/Phosphorylase_kinase
Index
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Phosphorylated Tyrosine
Tyrosine phosphorylation is the addition of a phosphate group to the amino acid tyro
sine on the protein. This transfer of phosphate group from ATP to the amino acid tyr
sine on the protein is made possible through enzymes called tyrosine kinases. Tyrosi
phosphorylation is considered to be one of the key steps in signal transduction and
regulation of enzymatic activity.
Two important classes of tyrosine kinase in tyrosine phosphorylation are receptor tyr
sine kinase and nonreceptor tyrosine kinase. Receptor tyrosine kinases are type I tra
membrane domain. Most are soluble intracellular proteins, but a subset associate wi
membranes via a membrane-targeting posttranslational modification, such as an Nterminal myristoyl group, and can act as the catalytic subunit for receptors that lack
their own catalytic domain.
https://en.wikipedia.org/wiki/Tyrosine_phosphorylation
Index
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Phosphorylation
Phosphorylation is the addition of a phosphoryl group (PO4=) to a molecule. Phosphorylation and its counterpart, dephosphorylation, turn many protein enzymes on and off,
thereby altering their function and activity. Protein phosphorylation is one type of
post-translational modification.
Protein phosphorylation in particular plays a significant role in a wide range of cellular
processes. Its prominent role in biochemistry is the subject of a very large body of research.
Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms. Kinases phosphorylate proteins
and phosphatases dephosphorylate proteins. Many enzymes and receptors are
switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. Phosphorylation usually occurs on serine, threonine, tyrosine and histidine residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than
tyrosine phosphorylation. In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or arginine or lysine residues. The addition of a phosphate molecule to a polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of molecule. In this
way protein dynamics can induce a conformational change in the structure of the protein via long-range allostery with other hydrophobic and hydrophilic residues in the
protein.
One such example of the regulatory role that phosphorylation plays is the p53 tumor
suppressor protein. The p53 protein is heavily regulated and contains more than 18 different phosphorylation sites. Activation of p53 can lead to cell cycle arrest, which can
be reversed under some circumstances, or apoptotic cell death. This activity occurs
only in situations wherein the cell is damaged or physiology is disturbed in normal
healthy individuals.
Upon the deactivating signal, the protein becomes dephosphorylated again and stops
working. This is the mechanism in many forms of signal transduction, for example the
way in which incoming light is processed in the light-sensitive cells of the retina.
https://en.wikipedia.org/wiki/Phosphorylation
Index
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Phosphorylation of Tyrosine
sine on the protein is made possible through enzymes called tyrosine kinases. Tyro
sine kinase and nonreceptor tyrosine kinase. Receptor tyrosine kinases are type I t
main that includes the catalytic domain. Nonreceptor tyrosine kinases lack a trans
membrane domain. Most are soluble intracellular proteins, but a subset associate
terminal myristoyl group, and can act as the catalytic subunit for receptors that lac
their own catalytic domain.
https://en.wikipedia.org/wiki/Tyrosine_phosphorylation
Index
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Phosphoserine
Phosphoserine is an ester of serine and phosphoric acid. Phosphoserine is a component of many proteins as the result of posttranslational modifications. The phosphorylation of the alcohol functional group in serine to produce phosphoserine is catalyzed
by various types of kinases. Through the use of technologies that utilize an expanded
genetic code, phosphoserine can also be incorporated into proteins during translation.
Phosphoserine is a normal metabolite found in human biofluids. Phosphoserine has
three potential coordination sites (carboxyl, amine and phosphate group) Determination of the mode of coordination between phosphorylated ligands and metal ions occurring in an organism is a first step to explain the function of the phosphoserine in bioinorganic processes.
https://en.wikipedia.org/wiki/Phosphoserine
Phosphoserine Aminotransferase
Index
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Phosphoserine Phosphatase
ric monoester bonds. This enzyme participates in glycine, serine and threon
lism.
https://en.wikipedia.org/wiki/Phosphoserine_phosphatase
Phosphotyrosine
Aside from being a proteinogenic amino acid, tyrosine has a special role by virtu
the phenol functionality. It occurs in proteins that are part of signal transductio
https://en.wikipedia.org/wiki/Tyrosine
Photolyases
Photolyases (EC 4.1.99.3) are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. This enzyme mechanism requires visible light, preferentially
from the violet/blue end of the spectrum, and is known as photoreactivation.
Photolyase is a phylogenetically old enzyme which is present and functional in many
species, from the bacteria to the fungi to plants and to the animals. Photolyase is particularly important in repairing UV induced damage in plants. The photolyase mechanism is no longer working in humans and other placental mammals who instead rely
on the less efficient nucleotide excision repair mechanism.
Photolyases bind complementary DNA strands and break certain types of pyrimidine
dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA
become covalently linked. These dimers result in a 'bulge' of the DNA structure, referred to as a lesion. The more common covalent linkage involves the formation of a cyclobutane bridge. Photolyases have a high affinity for these lesions and reversibly bind
and convert them back to the original bases.
https://en.wikipedia.org/wiki/Photolyase
Photophosphorylation
In the process of photosynthesis, the phosphorylation of ADP to form ATP using the energy of sunlight is called photophosphorylation. Only two sources of energy are available to living organisms: sunlight and reduction-oxidation (redox) reactions. All organisms produce ATP, which is the universal energy currency of life. This involves photolysis of water and a continuous unidirectional flow of electron from water to PSII.
In photophosphorylation, light energy is used to create a high-energy electron donor
and a lower-energy electron acceptor. Electrons then move spontaneously from donor
to acceptor through an electron transport chain.
https://en.wikipedia.org/wiki/Photophosphorylation
Index
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Photorespiration
Photorespiration (also known as the oxidative photosynthetic carbon cycle, or C2 photosynthesis) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, causing some of the energy produced by photosynthesis to be wasted. The
desired reaction is the addition of carbon dioxide to RuBP (carboxylation), a key step
in the CalvinBenson cycle, however approximately 25% of reactions by RuBisCO instead add oxygen to RuBP (oxygenation), creating a product that cannot be used
within the CalvinBenson cycle. This process reduces the efficiency of photosynthesis,
potentially reducing photosynthetic output by 25% in C3 plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria.
The oxygenation reaction of RuBisCO is a wasteful process because 3phosphoglycerate is created at a reduced rate and higher metabolic cost compared with
RuBP carboxylase activity. While photorespiratory carbon cycling results in the formation of G3P eventually, there is still a net loss of carbon (around 25% of carbon fixed by
photosynthesis is re-released as CO2) and nitrogen, as ammonia. Ammonia must be detoxified at a substantial cost to the cell. Photorespiration also incurs a direct cost of one
ATP and one NAD(P)H.
While it is common to refer to the entire process as photorespiration, technically the
term refers only to the metabolic network which acts to rescue the products of the oxygenation reaction (phosphoglycolate).
https://en.wikipedia.org/wiki/Photorespiration
Index
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Photosynthesis
Photosynthesis is a process used by plants and other organisms to convert light energy,
normally from the Sun, into chemical energy that can be later released to fuel the organisms' activities (energy transformation). This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water
hence the name photosynthesis, from the Greek , phs, "light", and ,
synthesis, "putting together". In most cases, oxygen is also released as a waste product.
Most plants, most algae, and cyanobacteria perform photosynthesis. Such organisms
are called photoautotrophs. Photosynthesis maintains atmospheric oxygen levels and
supplies all of the organic compounds and most of the energy necessary for life on
Earth.
Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centres
that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria
they are embedded in the plasma membrane. In these light-dependent reactions, some
energy is used to strip electrons from suitable substances, such as water, producing oxygen gas.
The hydrogen freed by water splitting is used in the creation of two further compounds: reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the "energy currency" of cells. In plants, algae and cyanobacteria, sugars are produced by a subsequent sequence of light-independent reactions
called the Calvin cycle, but some bacteria use different mechanisms, such as the reverse citric acid (Krebs) cycle. In the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate (RuBP). Using the ATP and NADPH produced by the light-dependent reactions,
the resulting compounds are then reduced and removed to form further carbohydrates,
such as glucose.
https://en.wikipedia.org/wiki/Photosynthesis
Index
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Photosynthetic
Index
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Photosystem I
Photosystem I (PSI) is an integral membrane protein complex that uses light energy to
mediate electron transfer from plastocyanin to ferredoxin. Linear electron transport in
PSI produces both ATP and NADPH, while cyclic electron transport drives the production of ATP but not the production NADPH. The PS I system comprises more than 110
co-factors, significantly more than photosystem II. These various components have a
wide range of functions. The electron transfer components of the reaction center of PSI
are a primary electron donor P-700 (chlorophyll dimer) and five electron acceptors: A0
(chlorophyll), A1 (a phylloquinone) and three Fe4-S4 iron-sulphur centres: Fx, Fa, and
F b.
Molecular data show that PS I likely evolved from the photosystems of green-sulfur bacteria. The photosystems of green sulfur bacteria and those of cyanobacteria, algae, and
higher plants are not the same, however there are many analogous functions and similar structures. Three main features are similar between the different photosystems.
First, redox potential is negative enough to reduce ferredoxin. Next, the electronaccepting reaction centers include iron-sulfur proteins. Last, redox centrers in complexes of both photosystems are constructed upon a protein subunit dimer. The photosystem of green sulfur bacteria even contains all of the same co-factors of the electron
transport chain in PS I. The number and degree of similarities between the two photosystems strongly indicates that PS I is derived from the analogous photosystem of
green-sulfur bacteria.
https://en.wikipedia.org/wiki/Photosystem_I
Photosystem II
Photosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in
the light-dependent reactions of oxygenic photosynthesis. It is located in the thylakoid
membrane of plants, algae, and cyanobacteria. Within the photosystem, enzymes capture photons of light to energize electrons that are then transferred through a variety of
coenzymes and cofactors to reduce plastoquinone to plastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen.
By replenishing lost electrons with electrons from the splitting of water, photosystem
II provides the electrons for all of photosynthesis to occur. The hydrogen ions (protons) generated by the oxidation of water help to create a proton gradient that is used
by ATP synthase to generate ATP. The energized electrons transferred to plastoquinone are ultimately used to reduce NADP+ to NADPH or are used in cyclic photophosphorylation.
Photosynthetic water splitting (or oxygen evolution) is one of the most important reactions on the planet, since it is the source of nearly all the atmosphere's oxygen. Moreover, artificial photosynthetic water-splitting may contribute to the effective use of sunlight as an alternative energy-source.
The mechanism of water oxidation is still not fully elucidated, but we know many details about this process. The oxidation of water to molecular oxygen requires extraction
of four electrons and four protons from two molecules of water. The experimental evidence that oxygen is released through cyclic reaction of oxygen evolving complex
(OEC) within one PSII was provided by Pierre Joliot et al. They have shown that, if
dark-adapted photosynthetic material (higher plants, algae, and cyanobacteria) is exposed to a series of single turnover flashes, oxygen evolution is detected with typical
period-four damped oscillation with maxima on the third and the seventh flash and
with minima on the first and the fifth flash . Based on this experiment, Bessel Kok and
co-workers introduced a cycle of five flash-induced transitions of the so-called S-states,
describing the four redox states of OEC: When four oxidizing equivalents have been
stored (at the S4-state), OEC returns to its basic and in the dark stable S0-state. Finally,
the intermediate S-states were proposed by Jablonsky and Lazar as a regulatory mechanism and link between S-states and tyrosine Z.
https://en.wikipedia.org/wiki/Photosystem_II
Index
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Photosystems
Photosystems are functional and structural units of protein complexes involved in photosynthesis that together carry out the primary photochemistry of photosynthesis: the
absorption of light and the transfer of energy and electrons. Photosystems are found in
the thylakoid membranes of plants, algae and cyanobacteria (in plants and algae these
are located in the chloroplasts), or in the cytoplasmic membrane of photosynthetic bacteria. There are two kinds of photosystems: II and I, respectively.
At the heart of a photosystem lies the reaction center, which is an enzyme that uses
light to reduce molecules (provide with electrons). This reaction center is surrounded
by light-harvesting complexes that enhance the absorption of light.
Two families of reaction centers in photosystems exist: type I reaction centers (such as
photosystem I (P700) in chloroplasts and in green-sulphur bacteria) and type II reaction centers (such as photosystem II (P680) in chloroplasts and in non-sulphur purple
bacteria).
Each photosystem can be identified by the wavelength of light to which it is most reactive (700 and 680 nanometers, respectively for PSI and PSII in chloroplasts), the
amount and type of light-harvesting complexes present and the type of terminal electron acceptor used.
Type I photosystems use ferredoxin-like iron-sulfur cluster proteins as terminal electron acceptors, while type II photosystems ultimately shuttle electrons to a quinone terminal electron acceptor. Both reaction center types are present in chloroplasts and cyanobacteria, and work together to form a unique photosynthetic chain able to extract
electrons from water, creating oxygen as a byproduct.
https://en.wikipedia.org/wiki/Photosystem
Index
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Phototrophs
Phototrophs are organisms that carry out photon capture to acquire energy. They use
the energy from light to carry out various cellular metabolic processes. It is a common
misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic
material to be utilized structurally, functionally, or as a source for later catabolic processes (e.g. in the form of starches, sugars and fats). All phototrophs either use electron
transport chains or direct proton pumping to establish an electro-chemical gradient
which is utilized by ATP synthase, to provide the molecular energy currency for the
cell. Phototrophs can be either autotrophs or heterotrophs.
Most of the well-recognized phototrophs are autotrophic, also known as photoautotrophs, and can fix carbon. They can be contrasted with chemotrophs that obtain their
energy by the oxidation of electron donors in their environments. Photoautotrophs are
capable of synthesizing their own food from inorganic substances using light as an energy source. Green plants and photosynthetic bacteria are photoautotrophs. Photoautotrophic organisms are sometimes referred to as holophytic. Such organisms derive
their energy for food synthesis from light and are capable of using carbon dioxide as
their principal source of carbon.
Oxygenic photosynthetic organisms use chlorophyll for light-energy capture and oxidize water, "splitting" it into molecular oxygen. In contrast, anoxygenic photosynthetic
bacteria have a substance called bacteriochlorophyll - which absorbs predominantly at
non-optical wavelengths - for light-energy capture, live in aquatic environments, and
will, using light, oxidize chemical substances such as hydrogen sulfide rather than water.
https://en.wikipedia.org/wiki/Phototroph
Index
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Phycoerythrin
phores called phycobilins. In the phycoerythrin family, the most known phy
ized in a disk-shaped trimer ()3 or hexamer ()6 (second one is the func
of the antenna rods). These typical complexes contain also third type of sub
chain.
https://en.wikipedia.org/wiki/Phycoerythrin
Index
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Phylloquinone
Phylloquinone, also Vitamin K1, is a polycyclic aromatic ketone, based on 2-methyl-1,4naphthoquinone, with a 3-phytyl substituent.
It is a fat-soluble vitamin that is stable to air and moisture but decomposes in sunlight.
It is found naturally in a wide variety of green plants, particularly leaves, since it functions as an electron acceptor during photosynthesis, forming part of the electron transport chain of Photosystem I.
Phylloquinone is an electron acceptor during photosynthesis, forming part of the electron transport chain of Photosystem I.
Its best-known function in animals is as a cofactor in the formation of coagulation factors II (prothrombin), VII, IX, and X by the liver. It is also required for the formation
of anticoagulant factors protein C and S. It is commonly used to treat warfarin toxicity,
and as an antidote for coumatetralyl.
Vitamin K is required for bone protein formation.
https://en.wikipedia.org/wiki/Phylloquinone
Physiological pH
The pH of blood is usually slightly basic with a value of pH 7.365. This value is often referred to as physiological pH in biology and medicine. Plaque can create a local acidic
environment that can result in tooth decay by demineralization. Enzymes and other
proteins have an optimum pH range and can become inactivated or denatured outside
this range.
https://en.wikipedia.org/wiki/PH#pH_in_nature
Index
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Phytanic Acid
acid that humans can obtain through the consumption of dairy products, rum
mal fats, and certain fish. Western diets are estimated to provide 50100 mg o
tanic acid per day. Unlike most fatty acids, phytanic acid cannot be metabolize
into pristanic acid by the removal of one carbon. Pristanic acid can undergo se
rounds of -oxidation in the peroxisome to form medium chain fatty acids tha
converted to carbon dioxide and water in mitochondria.
https://en.wikipedia.org/wiki/Phytanic_acid
Index
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Phytic Acid
Phytic acid (known as inositol hexakisphosphate (IP6), inositol polyphosphate, or phytate when in salt form), discovered in 1903, a saturated cyclic acid, is the principal storage form of phosphorus in many plant tissues, especially bran and seeds.
Phosphorus and inositol in phytate form are not, in general, bioavailable to nonruminant animals because these animals lack the digestive enzyme phytase required to remove phosphate from the inositol in the phytate molecule. Ruminants are readily able
to digest phytate because of the phytase produced by rumen microorganisms.
In most commercial agriculture, nonruminant livestock, such as swine, fowl, and fish,
are fed mainly grains, such as maize, legumes, and soybeans. Because phytate from
these grains and beans is unavailable for absorption, the unabsorbed phytate passes
through the gastrointestinal tract, elevating the amount of phosphorus in the manure.
Excess phosphorus excretion can lead to environmental problems, such as eutrophication.
The bioavailability of phytate phosphorus can be increased by supplementation of the
diet with the enzyme phytase.
Also, viable low-phytic acid mutant lines have been developed in several crop species
in which the seeds have drastically reduced levels of phytic acid and concomitant increases in inorganic phosphorus. However, reported germination problems have hindered the use of these cultivars thus far. Probability due to its critical role in both phosphorus and metal ion storage.
The use of sprouted grains will reduce the quantity of phytic acids in feed, with no significant reduction of nutritional value.
Phytate variants also have the potential to be used in soil remediation, to immobilize
uranium, nickel and other inorganic contaminants.
https://en.wikipedia.org/wiki/Phytic_acid
Phytocannabinoids
The classical cannabinoids are concentrated in a viscous resin produced in structures
known as glandular trichomes. At least 113 different cannabinoids have been isolated
from the Cannabis plant. To the right, the main classes of cannabinoids from Cannabis are shown. The best studied cannabinoids include tetrahydrocannabinol (THC shown below), cannabidiol (CBD) and cannabinol (CBN).
Endocannabinoids serve as intercellular 'lipid messengers', signaling molecules that
are released from one cell and activating the cannabinoid receptors present on other
nearby cells. Although in this intercellular signaling role they are similar to the wellknown monoamine neurotransmitters, such as acetylcholine and dopamine, endocannabinoids differ in numerous ways from them. For instance, they are used in retrograde signaling between neurons. Furthermore, endocannabinoids are lipophilic molecules that are not very soluble in water. They are not stored in vesicles, and exist as integral constituents of the membrane bilayers that make up cells. They are believed to
be synthesized 'on-demand' rather than made and stored for later use. The mechanisms and enzymes underlying the biosynthesis of endocannabinoids remain elusive
and continue to be an area of active research.
https://en.wikipedia.org/wiki/Cannabinoid
Index
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Phytohormone
Plant hormones (also known as phytohormones) are chemicals that regulate plant
growth. Plant hormones are signal molecules produced within the plant, and occur in
extremely low concentrations. Hormones regulate cellular processes in targeted cells
locally and, moved to other locations, in other functional parts of the plant. Hormones
also determine the formation of flowers, stems, leaves, the shedding of leaves, and the
development and ripening of fruit. Plants, unlike animals, lack glands that produce
and secrete hormones. Instead, each cell is capable of producing hormones.
Plant hormones shape the plant, affecting seed growth, time of flowering, the sex of
flowers, senescence of leaves, and fruits. They affect which tissues grow upward and
which grow downward, leaf formation and stem growth, fruit development and ripening, plant longevity, and even plant death. Hormones are vital to plant growth, and,
lacking them, plants would be mostly a mass of undifferentiated cells. So they are also
known as growth factors or growth hormones. Phytohormones are found not only in
higher plants, but in algae too, showing similar functions, and in microorganisms, like
fungi and bacteria, but, in this case, they play no hormonal or other immediate physiological role in the producing organism and can, thus, be regarded as secondary metabolites. Shown below is indole acetic acid, an auxin hormone.
https://en.wikipedia.org/wiki/Plant_hormone
Index
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Phytol
Phytol is an acyclic diterpene alcohol that can be used as a precursor for the
ture of synthetic forms of vitamin E and vitamin K1. In ruminants, the gut fe
then converted to phytanic acid and stored in fats. In shark liver it yields pr
https://en.wikipedia.org/wiki/Phytol
Index
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Phytosterols
Phytosterols, which encompass plant sterols and stanols, are steroid compounds similar to cholesterol which occur in plants and vary only in carbon side chains and/or presence or absence of a double bond. Stanols are saturated sterols, having no double
bonds in the sterol ring structure. More than 200 sterols and related compounds have
been identified. Free phytosterols extracted from oils are insoluble in water, relatively
insoluble in oil, and soluble in alcohols. The most commonly occurring phytosterols in
the human diet are -sitosterol (shown below), campesterol and stigmasterol, which
account for about 65%, 30% and 3% of diet contents, respectively.
https://en.wikipedia.org/wiki/Phytosterol
Pi
Pi is a shortcut abbreviation for inorganic phosphate, such as released in dephosphorylation reactions catalyzed by phosphatases or released by hydrolytic cleavages (such as
hydrolysis of ATP).
Index
Find Term
G-G
Chapter 2 - Structure and Function: Protein Function
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Structure and Function
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Techniques
Chapter 9 - Point by Point: Techniques
Pi -turns
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
Turns are classified according to the separation between the two end residues:
In an -turn the end residues are separated by four peptide bonds
(i --> i +/- 4).
In a -turn, by five bonds
(i --> i +/- 5)
Shown below is a turn
https://en.wikipedia.org/wiki/Turn_(biochemistry)
Index
Find Term
PI-1
nases are active, PI-1 gets phosphorylated and actively inhibits phosphopro
Index
Find Term
Pi-helix
A Pi helix (or -helix) is a type of secondary structure found in proteins. Although once
thought to be rare, short -helices are found in 15% of known protein structures and
are believed to be an evolutionary adaptation derived by the insertion of a single amino
acid into an -helix.
The amino acids in a standard -helix are arranged in a right-handed helical structure.
Each amino acid corresponds to an 87 turn in the helix (i.e., the helix has 4.1 residues
per turn), and a translation of 1.15 (=0.115nm) along the helical axis. Most importantly, the N-H group of an amino acid forms a hydrogen bond with the C=O group of
the amino acid five residues earlier. This repeated i+5i hydrogen bonding defines a
-helix.
https://en.wikipedia.org/wiki/Pi_helix
PI3-kinase
Phosphatidylinositol-4,5-bisphosphate 3-kinase (also called phosphatidylinositide 3kinases, phosphatidylinositol-3-kinases, PI 3-kinases, PI(3)Ks, PI-3Ks or by the HUGO
official stem symbol for the gene family, PI3K(s)) are a family of enzymes involved in
cellular functions such as cell growth, proliferation, differentiation, motility, survival
and intracellular trafficking, which in turn are involved in cancer.
PI3Ks are a family of related intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of phosphatidylinositol
(PtdIns). The pathway, with oncogene PIK3CA and tumor suppressor PTEN, is implicated in insensitivity of cancer tumors to insulin and IGF1, and in calorie restriction.
PI 3-kinases have been linked to an extraordinarily diverse group of cellular functions,
including cell growth, proliferation, differentiation, motility, survival and intracellular
trafficking. Many of these functions relate to the ability of class I PI 3-kinases to activate protein kinase B (PKB, aka Akt) as in the PI3K/AKT/mTOR pathway. The p110
and p110 isoforms regulate different aspects of immune responses. PI 3-kinases are
also a key component of the insulin signaling pathway. Hence there is great interest in
the role of PI 3-kinase signaling in diabetes mellitus.
https://en.wikipedia.org/wiki/Phosphoinositide_3-kinase
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Pili
A pilus (Latin for 'hair'; plural : pili) is a hairlike appendage found on the su
many bacteria. The terms pilus and fimbria (Latin for 'fringe'; plural: fimbr
used interchangeably, although some researchers reserve the term pilus for
age required for bacterial conjugation. All pili are primarily composed of oli
pilin proteins.
Dozens of these structures can exist on the bacteria. Some bacterial viruses
phages attach to receptors on pili at the start of their reproductive cycle.
https://en.wikipedia.org/wiki/Pilus
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Pinene
Pinene (C10H16) is a bicyclic monoterpene chemical compound. There are two structural isomers of pinene found in nature: -pinene and -pinene. As the name suggests,
both forms are important constituents of pine resin. They are also found in the resins
of many other conifers, as well as in non-coniferous plants such as camphorweed (Heterotheca) and big sagebrush (Artemisia tridentata). Both isomers are used by many
insects in their chemical communication system. The two isomers of pinene constitute
the major component of turpentine.
https://en.wikipedia.org/wiki/Pinene
Ping-pong
Ping-pong is a term used to describe an enzymatic reaction in which the enzyme can
exist in two different states that it switches between. These are called E and a chemically modified form of the enzyme called E*. This modified enzyme is known as an intermediate. In such mechanisms, substrate A binds, changes the enzyme to E* by, for
example, transferring a chemical group to the active site, and is then released. Only after the first substrate is released can substrate B bind and react with the modified enzyme, regenerating the unmodified E form. When a set of v by [S] curves (fixed A, varying B) from an enzyme with a pingpong mechanism are plotted in a LineweaverBurk plot, a set of parallel lines will be produced. This is called a secondary plot.
Enzymes with pingpong mechanisms include some oxidoreductases such as thioredoxin peroxidase, transferases such as acylneuraminate cytidylyltransferase and serine
proteases such as trypsin and chymotrypsin. Serine proteases are a very common and
diverse family of enzymes, including digestive enzymes (trypsin, chymotrypsin, and
elastase), several enzymes of the blood clotting cascade and many others. In these serine proteases, the E* intermediate is an acyl-enzyme species formed by the attack of an
active site serine residue on a peptide bond in a protein substrate.
https://en.wikipedia.org/wiki/Enzyme_kinetics#Ping.E2.80.93pong_mechanisms
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PIP2
Phosphatidylinositol 4,5-bisphosphate or PtdIns(4,5)P2, also known simply as PIP2, is
a minor phospholipid component of cell membranes. PtdIns(4,5)P2 is enriched at the
plasma membrane where it is a substrate for a number of important signaling proteins.
PtdIns(4,5)P2 is formed primarily by the type I phosphatidylinositol 4-phosphate 5kinases from PI(4)P. In metazoans, PtdIns(4,5)P2 can also be formed by type II phosphatidylinositol 5-phosphate 4-kinases from PI(5)P.
The fatty acids of PtdIns(4,5)P2 are variable in different species and tissues, but studies
show the most common fatty acids are stearic in position 1 and arachidonic in 2.
https://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate
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PIP3
Phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), abbreviated PIP3, is the
product of the class I phosphoinositide 3-kinases (PI 3-kinases) phosphorylation of
phosphatidylinositol (4,5)-bisphosphate (PIP2). It is a phospholipid that resides on the
plasma membrane.
PIP3 functions to activate downstream signaling components, the most notable one being the protein kinase AKT, which activates downstream anabolic signaling pathways
required for cell growth and survival. Phospholipase C cleaves PIP2 to produce inositol
triphosphate IP3, and diacylglycerol.
PtdIns(3,4,5)P3 is dephosphorylated by the phosphatase PTEN on the 3 position, generating PI(4,5)P2, and by SHIPs (SH2-containing inositol phosphatase) on the 5' position
of the inositol ring, producing PI(3,4)P2.
The PH domain in a number of proteins binds to PtdIns(3,4,5)P3. Such proteins include Akt/PKB, PDK1, Btk1, and ARNO. The generation of PtdIns(3,4,5)P3 at the
plasma membrane upon the activation of class I PI 3-kinases causes these proteins to
translocate to the plasma membrane and affects their activity accordingly.
The PH domain allows binding between PtdIns(3,4,5)P3 and G protein-coupled receptor kinases (GRKs). This enhances the binding of the GRK to the plasma membrane.
https://en.wikipedia.org/wiki/Phosphatidylinositol_(3,4,5)-trisphosphate
Index
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Pitch
In a helix, the pitch is the height of one complete helix turn, measured para
axis of the helix.
https://en.wikipedia.org/wiki/Helix#Types
Index
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pKa
The negative base 10 logarithm of the acid dissociation constant, Ka. The larger the
value of pKa, the smaller the extent of dissociation at any given pH (see HendersonHasselbalch equation)that is, the weaker the acid. A weak acid has a pKa value
in the approximate range 2 to 12 in water. Acids with a pKa value of less than about
2 are said to be strong acids. The dissociation of a strong acid is effectively complete
such that concentration of the undissociated acid is too small to be measured. pKa values for strong acids can, however, be estimated by theoretical means.
https://en.wikipedia.org/wiki/Acid_dissociation_constant
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Plankton
umn of large bodies of water and that cannot swim against a current. They p
crucial source of food to many large aquatic organisms, such as fish and wh
mals that inhabit, for example, the pelagic zone of oceans, seas, or bodies of
ter. Essentially, plankton are defined by their ecological niche rather than a
netic or taxonomic classification.
Index
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Plant
Plants, also called green plants, are multicellular eukaryotes of the kingdom Pla
They form an unranked clade Viridiplantae that includes the flowering plants, c
green algae. Green plants exclude the red and brown algae, the fungi, archaea, b
and animals.
Green plants have cell walls with cellulose and obtain most of their energy from
green color. Some plants are parasitic and have lost the ability to produce norm
Plasma Membrane
The plasma membrane (also called a cell membrane) is a biological membrane that
separates the interior of all cells from the outside environment. The cell membrane is
selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. The basic function of the cell membrane is to protect the cell
from its surroundings. It consists of the phospholipid bilayer with embedded proteins.
Cell membranes are involved in a variety of cellular processes such as cell adhesion,
ion conductivity and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall, glycocalyx, and intracellular cytoskeleton.
They can also be artificially reassembled.
https://en.wikipedia.org/wiki/Cell_membrane
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Plasmalogens
Plasmalogens are a type of ether phospholipid characterized by the presence of a vinyl
ether linkage at the sn-1 position and an ester linkage at the sn-2 position. In mammals, the sn-1 position is typically derived from C16:0, C18:0, or C18:1 fatty alcohols
while the sn-2 position is most commonly occupied by polyunsaturated fatty acids. The
most common head groups present in mammalian plasmalogens are ethanolamine
(designated plasmenylethalomines) or choline (designated plasmenylcholines).
https://en.wikipedia.org/wiki/Plasmalogen
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Plasmids
A plasmid is a small DNA molecule within a cell that is physically separated from a
chromosomal DNA and can replicate independently. They are most commonly found
in bacteria as small circular, double-stranded DNA molecules. However, plasmids are
sometimes present in archaea and eukaryotic organisms. In nature, plasmids often
carry genes that may benefit the survival of the organism, for example antibiotic resistance. While the chromosomes are big and contain all the essential information for living, plasmids usually are very small and contain only additional information. Artificial
plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms.
Plasmids are considered replicons, a unit of DNA capable of replicating autonomously
within a suitable host. However, plasmids, like viruses, are not generally classified as
life.
https://en.wikipedia.org/wiki/Plasmid
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Plasmin
Plasmin is an important enzyme present in blood that degrades many blood plasma
proteins, including fibrin clots. The degradation of fibrin is termed fibrinolysis. In humans, the plasmin protein is encoded by the PLG gene.
Plasmin is a serine protease that acts to dissolve fibrin blood clots. Apart from fibrinolysis, plasmin proteolyzes proteins in various other systems: It activates collagenases,
some mediators of the complement system and weakens the wall of the Graafian follicle (leading to ovulation). It cleaves fibrin, fibronectin, thrombospondin, laminin, and
von Willebrand factor. Plasmin, like trypsin, belongs to the family of serine proteases.
Plasmin is released as a zymogen called plasminogen (PLG) from the liver into the factor IX systemic circulation and placed into the MD5+ that leads into the lungs. Two major glycoforms of plasminogen are present in humans - type I plasminogen contains
two glycosylation moieties (N-linked to N289 and O-linked to T346), whereas type II
plasminogen contains only a single O-linked sugar (O-linked to T346). Type II plasminogen is preferentially recruited to the cell surface over the type I glycoform. Conversely, type I plasminogen appears more readily recruited to blood clots.
In circulation, plasminogen adopts a closed, activation resistant conformation. Upon
binding to clots, or to the cell surface, plasminogen adopts an open form that can be
converted into active plasmin by a variety of enzymes, including tissue plasminogen activator (tPA), urokinase plasminogen activator (uPA), kallikrein, and factor XII (Hageman factor). Fibrin is a cofactor for plasminogen activation by tissue plasminogen activator. Urokinase plasminogen activator receptor (uPAR) is a cofactor for plasminogen
activation by urokinase plasminogen activator. The conversion of plasminogen to plasmin involves the cleavage of the peptide bond between Arg-561 and Val-562.
Plasmin cleavage produces angiostatin.
https://en.wikipedia.org/wiki/Plasmin
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Plasminogen
Plasminogen is a zymogen precursor to plasmin released from the liver into the factor
IX systemic circulation and placed into the MD5+ that leads into the lungs. Two majo
glycoforms of plasminogen are present in humans: type I plasminogen contains two
glycosylation moieties (N-linked to N289 and O-linked to T346), whereas type II plas
minogen contains only a single O-linked sugar (O-linked to T346). Type II plasmino-
gen is preferentially recruited to the cell surface over the type I glycoform. Conversely
type I plasminogen appears more readily recruited to blood clots.
In circulation, plasminogen adopts a closed, activation resistant conformation. Upon
binding to clots, or to the cell surface, plasminogen adopts an open form that can be
tivator (tPA), urokinase plasminogen activator (uPA), kallikrein, and factor XII (Hage
man factor). Fibrin and Urokinase plasminogen activator receptor (uPAR) are cofactors for plasminogen activation.
https://en.wikipedia.org/wiki/Plasmin
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vator inhibitor or serpin E1, is a serine protease inhibitor (serpin) that functions
PAI-1 is mainly produced by the endothelium (cells lining blood vessels), but is a
creted by other tissue types, such as adipose tissue. PAI-1 inhibits the serine pro
process that degrades blood clots. PAI-1 inhibits the activity of matrix metallopr
inases, which play a crucial role in invasion of malignant cells across the basal la
https://en.wikipedia.org/wiki/Plasminogen_activator_inhibitor-1
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Plasmodesmata
Plasmodesmata (singular: plasmodesma) are microscopic channels which traverse the
cell walls of plant cells and some algal cells, enabling transport and communication between them. Plasmodesmata evolved independently in several lineages, and species
that have these structures include members of the Charophyceae, Charales, Coleochaetales and Phaeophyceae (which are all algae), as well as all land plants. Unlike animal
cells, almost every plant cell is surrounded by a polysaccharide cell wall.
Neighboring plant cells are therefore separated by a pair of cell walls and the intervening middle lamella, forming an extracellular domain known as the apoplast. Although
cell walls are permeable to small soluble proteins and other solutes, plasmodesmata enable direct, regulated, symplastic intercellular transport of substances between cells.
There are two forms of plasmodesmata: primary plasmodesmata, which are formed
during cell division, and secondary plasmodesmata, which can form between mature
cells.
https://en.wikipedia.org/wiki/Plasmodesma
Plastocyanin
Plastocyanin is a copper-containing protein involved in electron-transfer. The protein
is a monomer, with a molecular weight around 10.5kDa. In photosynthesis, plastocyanin functions as an electron transfer agent between cytochrome f of the cytochrome
b6f complex from photosystem II and P700+ from photosystem I. Cytochrome b6f complex and P700+ are both membrane-bound proteins with exposed residues on the
lumen-side of the thylakoid membrane of chloroplasts. Cytochrome f acts as an electron donor while P700+ accepts electrons from reduced plastocyanin.
In photosynthesis, plastocyanin functions as an electron transfer agent between cytochrome f of the cytochrome b6f complex from photosystem II and P700+ from photosystem I. Cytochrome b6f complex and P700+ are both membrane-bound proteins with exposed residues on the lumen-side of the thylakoid membrane of chloroplasts. Cytochrome f acts as an electron donor while P700+ accepts electrons from reduced plastocyanin.
https://en.wikipedia.org/wiki/Plastocyanin
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Plastoquinine
Plastoquinone (PQ) is a quinone molecule involved in the electron transport chain in
the light-dependent reactions of photosynthesis. Plastoquinone is reduced when it accepts two electrons from photosystem II and two hydrogen cations (H+) from the stromal matrix of the chloroplast), thereby forming plastoquinol. It transports the protons
into the lumen of thylakoid discs, while the electrons continue further along the electron transport chain, into the cytochrome b6f protein complex.
https://en.wikipedia.org/wiki/Plastoquinone
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https://en.wikipedia.org/wiki/Platelet-activating_factor
Platelet Aggregation
Platelet aggregation begins minutes after platelet activation, and occurs as a result of
turning on the GPIIb/IIIa receptor, which allows these receptors to bind with fibrinogen. There are 50100 of these receptors per platelet. When any one or more of at least
nine different platelet surface receptors are turned on during activation, intraplatelet
signaling pathways cause existing GpIIb/IIIa receptors to change shape curled to
straight and thus become capable of binding.
Since fibrinogen is a rod-like protein with nodules on either end capable of binding
GPIIb/IIIa, activated platelets with exposed GPIIb/IIIa can bind fibrinogen to aggregate together. GPIIb/IIIa can also further anchor the platelets to subendothelial vWF
for additional clot structural stabilization.
https://en.wikipedia.org/wiki/Platelet#Aggregation
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Platelets
Platelets, also called thrombocytes, are a component of blood whose function (along
with the coagulation factors) is to stop bleeding by clumping and clotting blood vessel
injuries. Platelets have no cell nucleus: they are fragments of cytoplasm that are derived from the megakaryocytes of the bone marrow, and then enter the circulation.
These unactivated platelets are biconvex discoid (lens-shaped) structures, 23 m in
greatest diameter. Platelets are found only in mammals, whereas in other animals (e.g.
birds, amphibians) thrombocytes circulate as intact mononuclear cells.
The main function of platelets is to contribute to hemostasis: the process of stopping
bleeding at the site of interrupted endothelium. They gather at the site and unless the
interruption is physically too large, they plug the hole. First, platelets attach to substances outside the interrupted endothelium: adhesion. Second, they change shape,
turn on receptors and secrete chemical messengers: activation. Third, they connect to
each other through receptor bridges: aggregation. In the image below, platelets are the
tiny blue dots surrounded by red blood cells.
https://en.wikipedia.org/wiki/Platelet
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Pleckstrin Homology
Pleckstrin homology domain (PH domain) is a protein domain of approximately 120
amino acids that occurs in a wide range of proteins involved in intracellular signaling
or as constituents of the cytoskeleton. This domain can bind phosphatidylinositol lipids within biological membranes and proteins such as the -subunits of heterotrimeric G proteins, and protein kinase C. Through these interactions, PH domains play a
role in recruiting proteins to different membranes, thus targeting them to appropriate
cellular compartments or enabling them to interact with other components of the signal transduction pathways.
Individual PH domains possess specificities for phosphoinositides phosphorylated at
different sites within the inositol ring, e.g., some bind phosphatidylinositol (4,5)bisphosphate but not phosphatidylinositol (3,4,5)-trisphosphate or phosphatidylinositol (3,4)-bisphosphate, while others may possess the requisite affinity. This is important because it makes the recruitment of different PH domain containing proteins sensitive to the activities of enzymes that either phosphorylate or dephosphorylate these
sites on the inositol ring, such as phosphoinositide 3-kinase or PTEN, respectively.
Thus, such enzymes exert a part of their effect on cell function by modulating the localization of downstream signaling proteins that possess PH domains that are capable of
binding their phospholipid products.
https://en.wikipedia.org/wiki/Pleckstrin_homology_domain
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pOH
pOH is sometimes used as a measure of the concentration of hydroxide ions, OH,
https://en.wikipedia.org/wiki/PH#pOH
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Point Mutation
A point mutation, or single base modification, is a type of mutation that causes a single
nucleotide base substitution, insertion, or deletion of the genetic material, DNA or
RNA. The term frameshift mutation indicates the addition or deletion of a base pair.
Point mutation is a random SNP (single-nucleotide polymorphism) mutation in the deoxyribonucleic acid (DNA) that occurs at one point. Point mutations usually take place
during DNA replication. DNA replication occurs when one double-stranded DNA molecule creates two single strands of DNA, each of which is a template for the creation of
the complementary strand. A single point mutation can change the whole DNA sequence. Changing one purine or pyrimidine may change the amino acid that the nucleotides code for.
Point mutations may arise from spontaneous mutations that occur during DNA replication. The rate of mutation may be increased by mutagens. Mutagens can be physical,
such as radiation from UV rays, X-rays or extreme heat, or chemical (molecules that
misplace base pairs or disrupt the helical shape of DNA). Mutagens associated with
cancers are often studied to learn about cancer and its prevention.
There are multiple ways for point mutations to occur. First, ultraviolet (UV) light and
higher-frequency light are capable of ionizing electrons, which in turn can have an impact on DNA. Reactive oxygen molecules with free radicals, which are a byproduct of
cellular metabolism, can also be very harmful to DNA. These reactants can lead to both
single-stranded DNA breaks and double-stranded DNA breaks. Third, bonds in DNA
eventually degrade, which creates another problem to keep the integrity of DNA to a
high standard. There can also be replication errors that lead to substitution, insertion,
or deletion mutations.
It was previously believed that these mutations happened completely by chance, with
no regard for their effects on the organisms. Recently, there have been studies suggesting that these mutations occur in response to environmental challenges. That is to say,
they are more likely to occur when they are advantageous to the organism, rather than
when they are neutral or disadvantageous. When cells were deprived of a certain
amino acid, tryptophan, for prolonged periods of time, point mutations in trp operon
reverted to tryptophan, leading to an advantageous result, more frequently than under
normal conditions when the mutations were neutral. In addition, the tryptophan mutation rate was unaffected when the cells were deprived of another amino acid, cysteine,
further suggesting that the mutation rate was specific to situations in which the mutation was advantageous.
https://en.wikipedia.org/wiki/Point_mutation
Polar
Polarity is the separation of electric charge leading to a molecule or its chemical groups
having an electric dipole or multipole moment. Polar molecules interact through dipoledipole intermolecular forces and hydrogen bonds. Molecular polarity is dependent on the difference in electronegativity between atoms in a compound and the asymmetry of the compound's structure. Polarity underlies a number of physical properties
including surface tension, solubility, and melting and boiling points.
https://en.wikipedia.org/wiki/Chemical_polarity
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Polar amino acids comprise nine of the twenty naturally occurring amino ac
clude all the amino acids with polar side chains capable of participating in h
Index
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Poly(A) Polymerase
Polynucleotide adenylyltransferase (EC 2.7.7.19), also called Poly(A) polymerase or
polyadenylate polymerase (PAP) is an enzyme that catalyzes the chemical reaction
ATP + RNA-3'OH pyrophosphate + RNApA-3'OH
Thus, the two substrates of this enzyme are ATP and RNA, whereas its two products
are pyrophosphate and RNA with an extra adenosine nucleotide at its 3' end.
This enzyme is responsible for the addition of the 3' polyadenine tail to a newly synthesized pre-messenger RNA (pre-mRNA) molecule during the process of gene transcription. The protein is the final addition to a large protein complex that also contains
smaller assemblies known as the cleavage and polyadenylation specificity factor
(CPSF) and cleavage stimulatory factor (CtSF) and its binding is a necessary prerequisite to the cleavage of the 3' end of the pre-mRNA. After cleavage of the 3' signaling region that directs the assembly of the complex, polyadenylate polymerase (PAP) adds
the polyadenine tail to the new 3' end.
The rate at which PAP adds adenine nucleotides is dependent on the presence of another regulatory protein, PABPII (poly-adenine binding protein II). The first few nucleotides added by PAP are added very slowly, but the short polyadenine tail is then
bound by PABPII, which accelerates the rate of adenine addition by PAP. The final tail
is about 200-250 adenine nucleotides long.
PAP is phosphorylated by mitosis-promoting factor , a key regulator of the cell cycle.
High phosphorylation levels decrease PAP activity.
https://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase
Poly(A) Tail
Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail
consists of multiple adenosine monophosphates. In other words, it is a stretch of RNA
that has only adenine bases. In eukaryotes, polyadenylation is part of the process that
produces mature messenger RNA (mRNA) for translation. It, therefore, forms part of
the larger process of gene expression.
The process of polyadenylation begins as the transcription of a gene terminates. The
3'-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins.
These proteins then synthesize the poly(A) tail at the RNA's 3' end. In some genes
these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing.
The poly(A) tail is important for the nuclear export, translation, and stability of mRNA.
The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. However, in a few cell types, mRNAs with short poly(A) tails are stored
for later activation by re-polyadenylation in the cytosol. In contrast, when polyadenylation occurs in bacteria, it promotes RNA degradation. This is also sometimes the case
for eukaryotic non-coding RNAs.
mRNA molecules in both prokaryotes and eukaryotes have polyadenylated 3'-ends,
with the prokaryotic poly(A) tails generally shorter and fewer mRNA molecules polyadenylated.
https://en.wikipedia.org/wiki/Polyadenylation
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Polyacrylamide Gel
Polyacrylamide gel is used in one form of electrophoresis: a technique widely used in
biochemistry, forensics, genetics, molecular biology and biotechnology to separate biological macromolecules (usually proteins or nucleic acids) according to their electrophoretic mobility. Mobility is a function of the length, conformation and charge of the
molecule. As with all forms of gel electrophoresis, molecules may be run in their native
state, preserving the molecules' higher-order structure, or a chemical denaturant may
be added to remove this structure and turn the molecule into an unstructured linear
chain whose mobility depends only on its length and mass-to-charge ratio.
For nucleic acids, urea is the most commonly used denaturant. For proteins, sodium
dodecyl sulfate (SDS) is an anionic detergent applied to protein samples to linearize
proteins and to impart a negative charge to linearized proteins. This procedure is
called SDS-PAGE. In most proteins, the binding of SDS to the polypeptide chain imparts an even distribution of charge per unit mass, thereby resulting in a fractionation
by approximate size during electrophoresis. Proteins that have a greater hydrophobic
content, for instance many membrane proteins, and those that interact with surfactants in their native environment, are intrinsically harder to treat accurately using this
method, due to the greater variability in the ratio of bound SDS.
https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophoresis
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Polyadenylation signal
Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail
consists of multiple adenosine monophosphates. In other words, it is a stretch of RNA
that has only adenine bases. In eukaryotes, polyadenylation is part of the process that
produces mature messenger RNA (mRNA) for translation. It, therefore, forms part of
the larger process of gene expression.
The process of polyadenylation begins as the transcription of a gene terminates. The
3'-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins.
These proteins then synthesize the poly(A) tail at the RNA's 3' end. In some genes
these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing.
The poly(A) tail is important for the nuclear export, translation, and stability of mRNA.
The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. However, in a few cell types, mRNAs with short poly(A) tails are stored
for later activation by re-polyadenylation in the cytosol. In contrast, when polyadenylation occurs in bacteria, it promotes RNA degradation. This is also sometimes the case
for eukaryotic non-coding RNAs.
mRNA molecules in both prokaryotes and eukaryotes have polyadenylated 3'-ends,
with the prokaryotic poly(A) tails generally shorter and fewer mRNA molecules polyadenylated.
https://en.wikipedia.org/wiki/Polyadenylation
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Polyanionic
Index
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https://en.wikipedia.org/wiki/Polycyclic_aromatic_hydrocarbon
Polylinker
polylinker are typically unique, occurring only once within a given plasmid.
lecular biologist insert a piece of DNA or several pieces of DNA into the reg
polylinker. This can be used to create transgenic organisms, also known as
modified organisms (GMOs).
https://en.wikipedia.org/wiki/Multiple_cloning_site
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Polymer
subunits. Because of their broad range of properties, both synthetic and nat
mers play an essential and ubiquitous role in everyday life. Polymers range
and synthetic, are created via polymerization of many small molecules, kno
Polymerization
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Polypeptide
A polypeptide is a long, continuous, and unbranched peptide bond-linked chain of
amino acids. Peptides are biologically occurring short chains of amino acid monomers
linked by peptide (amide) bonds.
https://en.wikipedia.org/wiki/Peptide
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Polypeptide Chain
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Polysaccharide
Polysaccharides are polymeric carbohydrate molecules composed of long chains of
monosaccharide units bound together by glycosidic linkages and on hydrolysis give the
constituent monosaccharides or oligosaccharides. They range in structure from linear
to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.
Polysaccharides are often quite heterogeneous, containing slight modifications of the
repeating unit. Depending on the structure, these macromolecules can have distinct
properties from their monosaccharide building blocks. They may be amorphous or
even insoluble in water. When all the monosaccharides in a polysaccharide are the
same type, the polysaccharide is called a homopolysaccharide or homoglycan, but
when more than one type of monosaccharide is present they are called heteropolysaccharides or heteroglycans.
Polysaccharides contain more than ten monosaccharide units. Definitions of how large
a carbohydrate must be to fall into the categories polysaccharides or oligosaccharides
vary according to personal opinion. Polysaccharides are an important class of biological polymers. Their function in living organisms is usually either structure- or storagerelated. Starch (a polymer of glucose) is used as a storage polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the
structurally similar glucose polymer is the more densely branched glycogen, sometimes called 'animal starch'. Glycogen's properties allow it to be metabolized more
quickly, which suits the active lives of moving animals.
https://en.wikipedia.org/wiki/Polysaccharide
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Polysaccharides
Polysaccharides are polymeric carbohydrate molecules composed of long chains of
monosaccharide units bound together by glycosidic linkages and on hydrolysis give the
constituent monosaccharides or oligosaccharides. They range in structure from linear
to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.
Polysaccharides are often quite heterogeneous, containing slight modifications of the
repeating unit. Depending on the structure, these macromolecules can have distinct
properties from their monosaccharide building blocks. They may be amorphous or
even insoluble in water. When all the monosaccharides in a polysaccharide are the
same type, the polysaccharide is called a homopolysaccharide or homoglycan, but
when more than one type of monosaccharide is present they are called heteropolysaccharides or heteroglycans.
Polysaccharides contain more than ten monosaccharide units. Definitions of how large
a carbohydrate must be to fall into the categories polysaccharides or oligosaccharides
vary according to personal opinion. Polysaccharides are an important class of biological polymers. Their function in living organisms is usually either structure- or storagerelated. Starch (a polymer of glucose) is used as a storage polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the
structurally similar glucose polymer is the more densely branched glycogen, sometimes called 'animal starch'. Glycogen's properties allow it to be metabolized more
quickly, which suits the active lives of moving animals.
https://en.wikipedia.org/wiki/Polysaccharide
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Polyterpenes
Polyterpenes consist of long chains of many isoprene units. Some plants produce a
polyisoprene with trans double bonds, known as gutta-percha. Terpenes are a large
and diverse class of organic compounds, produced by a variety of plants, particularly
conifers, though also by some insects such as termites or swallowtail butterflies, which
emit terpenes from their osmeteria. They are often strong-smelling. They may protect
the plants that produce them by deterring herbivores and by attracting predators and
parasites of herbivores. Many terpenes are aromatic hydrocarbons and thus may have
had a protective function. The building blocks of terpenes are isoprenoids known as dimethylallylpyrophosphate (shown on top below) and isopentenylpyrophosphate (bottom).
https://en.wikipedia.org/wiki/Terpene
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Polyubiquitin
Polyubiquitin is a chain of four or more ubiquitin proteins. Ubiquitin is a small protein
that exists in all eukaryotic cells. It performs its myriad functions through conjugation
to a large range of target proteins.
The addition of ubiquitin to a substrate protein is called ubiquitination or ubiquitylation. Ubiquitination can affect proteins in many ways: it can signal for their degradation via the proteasome, alter their cellular location, affect their activity, and promote
or prevent protein interactions. Ubiquitination is carried out in three main steps: activation, conjugation, and ligation, performed by ubiquitin-activating enzymes (E1s),
ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively. The result of this sequential cascade binds ubiquitin to lysine residues on the protein substrate via an isopeptide bond, cysteine residues through a thioester bond, serine and
threonine residues through an ester bond, or the amino group of the protein's Nterminus via a peptide bond.
The protein modifications can be either a single ubiquitin protein (monoubiquitination) or a chain of ubiquitin (polyubiquitination). The ubiquitination bonds are always
formed with one of the seven lysine residues as well as the very N-terminal methionine
from the ubiquitin molecule. These 'linking' residues are represented by a "K" or "M"
(which is the one-letter amino acid notation of lysine and methionine, respectively)
and a number, referring to its position in the ubiquitin molecule. First, a ubiquitin
molecule is bonded by its C-terminus to a specific lysine residue on the target protein.
Poly-ubiquitination occurs when the C-terminus of another ubiquitin, will be linked to
one of the seven lysine residues or the first methionine on the previously added ubiquitin molecule itself (for example on K48, K29 or M1), forming a chain. This process repeats several times, leading to the addition of several ubiquitins. Only polyubiquitination on defined lysines, mostly on K48 and K29, is related to degradation by
the proteasome (referred to as the "molecular kiss of death"), while other polyubiquitinations (e.g. on K63, K11, K6 and M1) and monoubiquitinations may regulate processes such as endocytic trafficking, inflammation, translation and DNA repair.
The discovery that ubiquitin chains target proteins to the proteasome, which degrades
and recycles proteins, was honored with the Nobel Prize in chemistry in 2004.
https://en.wikipedia.org/wiki/Ubiquitin#The_protein
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Polyubiquitination
strate, further ubiquitin molecules can be added to the first, yielding a polyu
Index
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Polyunsaturated
The term polyunsatured refers to a molecule with multiple double bonded carbons.
Specifically, the term is used to describe fatty acids or fats with this property. Polyunsaturated fats are lipids in which the constituent hydrocarbon chain possesses two or
more carboncarbon double bonds. Polyunsaturated fat can be found mostly in nuts,
seeds, fish, algae, leafy greens, and krill. "Unsaturated" refers to the fact that the mole-
cules contain less than the maximum amount of hydrogen. These materials exist as cis
or trans isomers depending on the geometry of the double bond.
Linoleic acid, shown below, is polyunsaturated and a fat containing it would also be
polyunsaturated.
https://en.wikipedia.org/wiki/Polyunsaturated_fat
Porins
Porins are barrel proteins that cross a cellular membrane and act as a pore through
which molecules can diffuse. Unlike other membrane transport proteins, porins are
large enough to allow passive diffusion, i.e., they act as channels that are specific to different types of molecules. They are present in the outer membrane of Gram-negative
bacteria and some Gram-positive bacteria of the group Mycolata (mycolic acidcontaining actinomycetes), the mitochondria, and the chloroplast.
Porins typically control the diffusion of small metabolites like sugars, ions, and amino
acids. In gram-negative bacteria, the inner membrane is the major permeability barrier, whereas the outer membrane contains porins, which render it largely permeable
to molecules less than about 1500 daltons.
The term "nucleoporin" refers to porins facilitating transport through nuclear pores in
the nuclear envelope. However, they are often considered distinct from other porins
(they are not classified as porins in MeSH.)
Porins are chemically selective transporting only one group of molecules or may be
specific for one molecule. -lactam and fluoroquinolone antibiotics must pass through
porins to reach their targets in gram negative bacteria. Bacteria can develop resistance
to these antibiotics by mutating the gene that encodes the porin the antibiotics are
then excluded from passing through the outer membrane
https://en.wikipedia.org/wiki/Porin_(protein)
Porphobilinogen
Porphobilinogen (PBG) is a pyrrole involved in porphyrin metabolism.
It is generated from aminolevulinate (ALA) by the enzyme ALA dehydratase. PBG is
https://en.wikipedia.org/wiki/Porphobilinogen
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Porphyrias
The porphyrias are a group of rare diseases in which chemical substances called porphyrins accumulate with high metabolism. The body requires porphyrins to produce
heme, which carries oxygen in the blood. But in the porphyrias, there is a deficiency (i
herited or acquired) of the enzymes that transform the various porphyrins into others
leading to abnormally high levels of one or more of these substances. This manifests
with neurological symptoms or skin problems, or occasionally both.
matically, acute porphyrias primarily cause brain and nerve involvement, often with s
vere abdominal pain, vomiting, neuropathy, and mental disturbances. Cutaneous por-
phyrias cause skin problems, often after exposure to sunlight, because porphyrins rea
on the sites of accumulation of heme precursors, either in the liver or in the bone mar
row and red blood cells.
https://en.wikipedia.org/wiki/Porphyria
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Porphyrin Ring
Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of
four modified pyrrole subunits interconnected at their carbon atoms via methine
bridges (=CH). The parent porphyrin is porphin, and substituted porphines are called
porphyrins. The porphyrin ring structure is aromatic, with a total of 26 atoms in the
conjugated system. The main role of porphyrins is their support of aerobic life. Porphin, the simplest porphyrin, is shown below.
https://en.wikipedia.org/wiki/Porphyrin
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Porphyrins
Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of
four modified pyrrole subunits interconnected at their carbon atoms via methine
bridges (=CH). The parent porphyrin is porphin, and substituted porphines are called
porphyrins. The porphyrin ring structure is aromatic, with a total of 26 atoms in the
conjugated system. The main role of porphyrins is their support of aerobic life. Porphin, the simplest porphyrin, is shown below.
https://en.wikipedia.org/wiki/Porphyrin
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Post-translational Modification
Post-translational modification (PTM) refers to the covalent and generally enzymatic
modification of proteins during or after protein biosynthesis. Proteins are synthesized
by ribosomes translating mRNA into polypeptide chains, which may then undergo
PTM to form the mature protein product. PTMs are important components in cell signaling.
Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini. They can extend the chemical repertoire of the 20 standard
amino acids by introducing new functional groups such as phosphate, acetate, amide
groups, or methyl groups. Phosphorylation is a very common mechanism for regulating the activity of enzymes and is the most common post-translational modification.
Many eukaryotic proteins also have carbohydrate molecules attached to them in a process called glycosylation, which can promote protein folding and improve stability as
well as serving regulatory functions. Attachment of lipid molecules, known as lipidation, often targets a protein or part of a protein to the cell membrane.
Other forms of post-translational modification consist of cleaving peptide bonds, as in
processing a propeptide to a mature form or removing the initiator methionine residue. The formation of disulfide bonds from cysteine residues may also be referred to as
a post-translational modification. For instance, the peptide hormone insulin is cut
twice after disulfide bonds are formed, and a propeptide is removed from the middle of
the chain. The resulting protein consists of two polypeptide chains connected by disulfide bonds.
https://en.wikipedia.org/wiki/Post-translational_modification
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Potassium Channel
Potassium channels are the most widely distributed type of ion channel and are found
in virtually all living organisms. They form potassium-selective pores that span cell
membranes. Furthermore potassium channels are found in most cell types and control
a wide variety of cell functions.
Potassium channels function to conduct potassium ions down their electrochemical
gradient, doing so both rapidly (up to the diffusion rate of K+ ions in bulk water) and
selectively (excluding, most notably, sodium despite the sub-angstrom difference in
ionic radius). Biologically, these channels act to set or reset the resting potential in
many cells. In excitable cells, such as neurons, the delayed counterflow of potassium
ions shapes the action potential.
By contributing to the regulation of the action potential duration in cardiac muscle,
malfunction of potassium channels may cause life-threatening arrhythmias. Potassium
channels may also be involved in maintaining vascular tone. They also regulate cellular
processes such as the secretion of hormones (e.g., insulin release from -cells in the
pancreas) so their malfunction can lead to diseases (such as diabetes).
There are four major classes of potassium channels:
Calcium-activated potassium channel - open in response to the presence of calcium
ions or other signaling molecules.
Inwardly rectifying potassium channel - passes current (positive charge) more easily
in the inward direction (into the cell).
Tandem pore domain potassium channel - are constitutively open or possess high basal activation, such as the "resting potassium channels" or "leak channels" that set the
negative membrane potential of neurons.
Voltage-gated potassium channel - are voltage-gated ion channels that open or close
in response to changes in the transmembrane voltage.
https://en.wikipedia.org/wiki/Potassium_channel
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PQA
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PRAMP
Phosphoribosyl AMP (PRAMP) is an intermediate in biosynthesis of histidine. It
product of the third reaction and the substrate of the fourth reaction.
PRATP
Phosphoribosyl ATP (PRATP) is the product of reaction 2 in the biosynthesis of histidine from ribose-5-phosphate and is the substrate of the third reaction. PRAMP is
made from PRATP.
Pre-miRNAs
(miRNA) derived from small nucleolar RNA (snoRNA). MicroRNAs are usu
which bypasses Pasha and Drosha. Some microRNAs are also known to be d
from small nucleolar RNA.
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Pre-mRNA
Precursor mRNA (pre-mRNA) is an immature single strand of messenger ribonucleic
acid (mRNA). Pre-mRNA is synthesized from a DNA template in the cell nucleus by
transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA).
The term hnRNA is often used as a synonym for pre-mRNA, although, in the strict
sense, hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic
mRNA.
Once pre-mRNA has been completely processed, it is termed "mature messenger
RNA", "mature mRNA", or simply "mRNA".
Eukaryotic pre-mRNA exists only briefly before it is fully processed into mRNA. PremRNAs include two different types of segments, exons and introns. Exons are segments that are retained in the final mRNA, whereas introns are removed in a process
called splicing, which is performed by the spliceosome (except for self-splicing introns).
Additional processing steps attach modifications to the 5' and 3' ends of Eukaryotic
pre-mRNA. These include a 5' cap of 7-methylguanosine and a poly-A tail. In addition,
eukaryotic pre-mRNAs have their introns spliced out by spliceosomes made up of
small nuclear ribonucleoproteins.
When a pre-mRNA strand has been properly processed to an mRNA sequence, it is exported out of the nucleus and eventually translated into a protein a process accomplished in conjunction with ribosomes.
https://en.wikipedia.org/wiki/Precursor_mRNA
Pre-steady State
In the first moment after an enzyme is mixed with substrate, no product has been
formed and no intermediates exist. The study of the next few milliseconds of the reaction is called Pre-steady-state kinetics also referred to as Burst kinetics. Pre-steadystate kinetics is therefore concerned with the formation and consumption of enzymesubstrate intermediates (such as ES or E*) until their steady-state concentrations are reached.
https://en.wikipedia.org/wiki/Enzyme_kinetics#Pre-steady-state_kinetics
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Pre-tRNA
tRNAs are synthesized by RNA polymerase III, which makes precursor molecules
called pre-tRNA that then undergo processing to generate mature tRNAs. The initi
transcripts contain additional RNA sequences at both the 5 and 3 ends. Some pre-
tRNAs also contain introns. These additional sequences are removed from the tran
script during processing.
The 5 leader sequence of the pre-tRNA (the additional nucleotides at the 5-end) is
trailer sequence (extra nucleotides at the 3 end of the pre-tRNA) is later removed b
different nucleases. All tRNAs must have a 3 CCA sequence that is necessary for th
charging of the tRNAs with amino acids. In bacteria, this CCA sequence is encoded
the tRNA gene, but in eukaryotes, the CCA sequence is added post-transcriptionall
an enzyme called tRNA nucleotidyl transferase (tRNT).
https://en.wikipedia.org/wiki/Transfer_RNA
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Pregnenolone
Pregnenolone, also known as P5, is an endogenous steroid hormone. It is the precursor
of the progestogens, mineralocorticoids, glucocorticoids, androgens, and estrogens, as
well as the neuroactive steroids. In addition, pregnenolone is biologically active in its
own right, acting as a neurosteroid.
Pregnenolone is synthesized from cholesterol. This conversion involves hydroxylation
at the side-chain at C20 and C22 positions, with cleavage of the side-chain. The enzyme
performing this task is cytochrome P450scc, located in the mitochondria, and controlled
by anterior pituitary tropic hormones, such as ACTH, FSH, LH.
https://en.wikipedia.org/wiki/Pregnenolone
Prenylated
Prenylation (also known as isoprenylation or lipidation) is the addition of hydrophobic
molecules to a protein or chemical compound. It is usually assumed that prenyl groups
(3-methyl-but-2-en-1-yl) facilitate attachment to cell membranes, similar to lipid anchors like the GPI anchor, though direct evidence is missing. Prenyl groups have been
shown to be important for proteinprotein binding through specialized prenyl-binding
domains.
Protein prenylation involves the transfer of either a farnesyl or a geranyl-geranyl moiety to C-terminal cysteine(s) of the target protein. There are three enzymes that carry
out prenylation in the cell, farnesyl transferase, Caax protease and geranylgeranyl
transferase I.
Farnesylation is a type of prenylation, a post-translational modification of proteins by
which an isoprenyl group is added to a cysteine residue. It is an important process to
mediate proteinprotein interactions and proteinmembrane interactions.
https://en.wikipedia.org/wiki/Prenylation
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Prephenate
Prephenic acid, commonly also known by its anionic form prephenate, is an intermediate in the biosynthesis of the aromatic amino acids phenylalanine and tyrosine. It is
synthesized by a [3,3]-sigmatropic Claisen rearrangement of chorismate.
https://en.wikipedia.org/wiki/Prephenic_acid
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Pri-miRNA
miR-30 microRNA precursor is a small non-coding RNA that regulates gene
sion. Animal microRNAs are transcribed as pri-miRNA (primary miRNA) of
length which in turns are processed in the nucleus by Drosha into ~70 nucleo
essed by the Dicer enzyme to give a mature ~22 nucleotide product. In this c
ture sequence comes from both the 3' (miR-30) and 5' (mir-97-6) arms of the
sor. The products are thought to have regulatory roles through complementa
mRNA.
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Primary Structure
The primary structure of a peptide or protein is the linear sequence of its amino acid
structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal
(N) end to the carboxyl-terminal (C) end.
In general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. However, proteins can become cross-linked, most commonly by disulfide bonds, and the primary
structure also requires specifying the cross-linking atoms, e.g., specifying the cysteines
involved in the protein's disulfide bonds. Other crosslinks include desmosine.
The chiral centers of a polypeptide chain can undergo racemization. In particular, the
L-amino acids normally found in proteins can spontaneously isomerize at the atom to
form D-amino acids, which cannot be cleaved by most proteases. Finally, the protein
can undergo a variety of post-translational modifications.
https://en.wikipedia.org/wiki/Protein_primary_structure
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Primary Transcript
A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized
by transcription of DNA, and processed to yield various mature RNA products such as
mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are
modified in preparation for translation. For example, a precursor messenger RNA
(pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA)
after processing.
There are several steps contributing to the production of primary transcripts. All these
steps involve a series of interactions to initiate and complete the transcription of DNA
in the nucleus of eukaryotes. Certain factors play key roles in the activation and inhibition of transcription, where they regulate primary transcript production. Transcription
produces primary transcripts that are further modified by several processes. These
processes include the 5' cap, 3'-polyadenylation, and alternative splicing. In particular,
alternative splicing directly contributes to the diversity of mRNA found in cells. The
modifications of primary transcripts have been further studied in research seeking
greater knowledge of the role and significance of these transcripts. Experimental studies based on molecular changes to primary transcripts the processes before and after
transcription have led to greater understanding of diseases involving primary transcripts.
https://en.wikipedia.org/wiki/Primary_transcript
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Primase
DNA primase, also called as DNA primerase, is an enzyme involved in the replication
of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short
RNA (or DNA in some organisms) segment called a primer complementary to a ssDNA
template. Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA
primer (for temporary DNA elongation). After this elongation the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
In bacteria, primase binds to the DNA helicase forming a complex called the primosome. Primase is activated by DNA helicase where it then synthesizes a short RNA
primer approximately 11 1 nucleotides long, to which new nucleotides can be added
by DNA polymerase.
The RNA segments are first synthesized by primase and then elongated by DNA polymerase. Then the DNA polymerase forms a protein complex with two primase
subunits to form the alpha DNA Polymerase primase complex. Primase is one of the
most error prone and slow polymerases. Primases in organisms such as E. coli, synthesize around 2000 to 3000 primers at the rate of one primer per second. Primase also
acts as a halting mechanism to prevent the leading strand from outpacing the lagging
strand by halting the progression of the replication fork. The rate determining step in
primase is when the first phosphodiester bond is formed between two molecules of
RNA.
The replication mechanisms differ between different bacteria and viruses where the primase covalently link to helicase in viruses such as the T7 bacteriophage. In viruses
such as herpes simplex virus (HSV-1), primase can form complexes with helicase. The
primase-helicase complex is used to unwind dsDNA and synthesizes the lagging strand
using RNA primers[ The majority of primers synthesized by primase are two to three
nucleotides long.
https://en.wikipedia.org/wiki/Primase
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Primer
A primer is a strand of short nucleic acid sequences (generally about 10 base pairs)
that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end
of the primer, and copies the opposite strand.
In most cases of natural DNA replication, the primer for DNA synthesis and replication
is a short strand of RNA (which can be made de novo). Many of the laboratory techniques of biochemistry and molecular biology that involve DNA polymerase, such as
DNA sequencing and the polymerase chain reaction (PCR), require DNA primers.
These primers are usually short, chemically synthesized oligonucleotides, with a length
of about twenty bases. They are hybridized to a target DNA, which is then copied by
the polymerase.
https://en.wikipedia.org/wiki/Primer_(molecular_biology)
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Prions
A prion is an infectious agent thought to be the cause of the transmissible spongiform
encephalopathies (TSEs). It is composed entirely of protein material, called PrP (short
for prion protein), that can fold in multiple, structurally distinct ways, at least one of
which is transmissible to other prion proteins, leading to disease that is similar to viral
infection. The word prion, coined in 1982 by Stanley B. Prusiner, is a portmanteau derived from protein and infection, hence prion, and is short for "proteinaceous infectious particle" in reference to its ability to self-propagate and transmit its conformation
to other proteins.
A protein as a standalone infectious agent stands in contrast to all other known infectious agents such as viruses, bacteria, fungi, and parasites, all of which contain nucleic
acids (DNA, RNA, or both). For this reason, a minority of researchers still consider the
prion/TSE hypothesis unproven. All known prion diseases in mammals affect the structure of the brain or other neural tissue. All are currently untreatable and universally
fatal.
Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the
misfolded prion form. In this way, the prion acts as a template to guide the misfolding
of more proteins into prion form. In yeast, this refolding is assisted by chaperone proteins such as Hsp104p. These refolded prions can then go on to convert more proteins
themselves, leading to a chain reaction resulting in large amounts of the prion form.
All known prions induce the formation of an amyloid fold, in which the protein polymerizes into an aggregate consisting of tightly packed sheets. Amyloid aggregates are
fibrils, growing at their ends, and replicate when breakage causes two growing ends to
become four growing ends. The incubation period of prion diseases is determined by
the exponential growth rate associated with prion replication, which is a balance between the linear growth and the breakage of aggregates. The propagation of the prion
depends on the presence of normally folded protein in which the prion can induce misfolding. Animals that do not express the normal form of the prion protein can neither
develop nor transmit the disease.
Prion aggregates are extremely stable and accumulate in infected tissue, causing tissue
damage and cell death. This structural stability means that prions are resistant to denaturation by chemical and physical agents, making disposal and containment of these
particles difficult. Prion structure varies slightly between species, but nonetheless
prion replication is subject to occasional epimutation and natural selection just like
other forms of replication.
https://en.wikipedia.org/wiki/Prion
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Processivity
enzyme, such as DNA polymerase, per association event with the template strand
DNA polymerases associated with DNA replication tend to be highly processive,
those associated with DNA repair tend to have low processivity. Because the bind
the polymerase to the template is the rate-limiting step in DNA synthesis, the ov
rate of DNA replication during S phase of the cell cycle is dependent on the proce
ity of the DNA polymerases performing the replication. DNA clamp proteins are
gral components of the DNA replication machinery and serve to increase the pro
ity of their associated polymerases. Some polymerases add over 50,000 nucleoti
a growing DNA strand before dissociating from the template strand, giving a rep
tion rate of up to 1,000 nucleotides per second.
https://en.wikipedia.org/wiki/Processivity
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Product
Products are the species formed from chemical reactions. In biochemistry, enzymes act
as biological catalysts to convert substrate to product. For example, the products of the
enzyme lactase are galactose and glucose, which are produced from the substrate lactose.
https://en.wikipedia.org/wiki/Product_(chemistry)#Biochemistry
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Products
Products are the species formed from chemical reactions. In biochemistry,
enzyme lactase are galactose and glucose, which are produced from the sub
tose.
https://en.wikipedia.org/wiki/Product_(chemistry)#Biochemistry
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ProFAR
ProFAR-I (N-[(5-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide) ribonucleotide) is an intermediate in the biosynthesis of histidine. It is the product of
the fourth reaction from ribose-5-phosphate and the substrate for the fifth reaction.
ProFAR-I
PROFAR-I N-[(5phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ri
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Profilin
ment, wound healing, and the hunting down of infectious intruders by cells o
mune system.
Profilin also binds sequences rich in the amino acid proline in diverse protein
most profilin in the cell is bound to actin, profilins have over 50 different bin
ners. Many of those are related to actin regulation, but profilin also seems to
volved in activities in the nucleus such as mRNA splicing.
https://en.wikipedia.org/wiki/Profilin
Progestagens
Progestogens (also sometimes spelled progestagens or gestagens) are a class of steroid
hormones that bind to and activate the progesterone receptor (PR). The most important progestogen in the body is progesterone (P4 - shown below). Other endogenous
progestogens include 17-hydroxyprogesterone, 20-dihydroprogesterone, 5dihydroprogesterone, 11-deoxycorticosterone, and 5-dihydrodeoxycorticosterone. Synthetic progestogens are generally referred to as progestins. However, the terms progesterone, progestogen, and progestin are frequently used interchangeably both in the scientific literature and in clinical settings.
https://en.wikipedia.org/wiki/Progestogen
Progesterone
Progesterone (abbreviated as P4), also known as pregn-4-ene-3,20-dione, is an endogenous steroid and progestogen sex hormone involved in the menstrual cycle, pregnancy,
and embryogenesis of humans and other species. It belongs to a group of steroid hormones called the progestogens, and is the major progestogen in the body. Progesterone
is also a crucial metabolic intermediate in the production of other endogenous steroids, including the sex hormones and the corticosteroids, and plays an important role
in brain function as a neurosteroid.
Progesterone is a potent agonist of the nuclear progesterone receptor (nPR) (with an
affinity of KD = 1 nM). In addition, progesterone is an agonist of the more recently discovered membrane progesterone receptors (mPRs), as well as a ligand of the PGRMC1
(progesterone receptor membrane component 1 - formerly known as the 2 receptor).
Moreover, progesterone is also known to be an antagonist of the 1 receptor, a negative
allosteric modulator of the nACh receptors, and a potent antagonist of the mineralocorticoid receptor (MR). Progesterone prevents MR activation by binding to this receptor
with an affinity exceeding even those of aldosterone and glucocorticoids such as cortisol and corticosterone, and produces antimineralocorticoid effects, such as natriuresis,
at physiological concentrations. In addition, progesterone binds to and behaves as a
partial agonist of the glucocorticoid receptor (GR), albeit with very low potency (EC50
>100-fold less relative to cortisol).
https://en.wikipedia.org/wiki/Progesterone
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Progesterone Receptor
The progesterone receptor (PR, also known as NR3C3 or nuclear receptor subfamily
group C, member 3), is a protein found inside cells. It is activated by the steroid hormone progesterone.
two main forms, A and B, that differ in their molecular weight. Progesterone is neces
sary to induce the progesterone receptors. When no binding hormone is present the
carboxyl terminal inhibits transcription. Binding to a hormone induces a structural
change that removes the inhibitory action. Progesterone antagonists prevent the stru
tural reconfiguration.
After progesterone binds to the receptor, restructuring with dimerization follows and
the complex enters the nucleus and binds to DNA. There transcription takes place, re
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Prokaryotes
A prokaryote is a single-celled organism that lacks a membrane-bound nucleus (karyon), mitochondria, or any other membrane-bound organelle. In the prokaryotes all
the intracellular water-soluble components (proteins, DNA and metabolites) are located together in the cytoplasm enclosed by the cell membrane, rather than in separate
cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein
shells. Some prokaryotes, such as cyanobacteria may form large colonies. Others, such
as myxobacteria, have multicellular stages in their life cycles.
https://en.wikipedia.org/wiki/Prokaryote
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Prokaryotic
A prokaryote is a single-celled organism that lacks a membrane-bound nucleus (karyon), mitochondria, or any other membrane-bound organelle. In the prokaryotes all
the intracellular water-soluble components (proteins, DNA and metabolites) are located together in the cytoplasm enclosed by the cell membrane, rather than in separate
cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein
shells. Some prokaryotes, such as cyanobacteria may form large colonies. Others, such
as myxobacteria, have multicellular stages in their life cycles.
https://en.wikipedia.org/wiki/Prokaryote
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Proline
Proline (abbreviated as Pro or P; encoded by the codons CCU, CCC, CCA, and CCG) is
an -amino acid that is used in the biosynthesis of proteins. It contains an -amino
group (which is in the protonated -NH2+ form under biological conditions), an carboxylic acid group (which is in the deprotonated COO form under biological conditions), and a side chain pyrrolidine, classifying it as a nonpolar(at physiological pH),
aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it
from the non-essential amino acid L-glutamate.
Proline is the only amino acid with a secondary amine. Furthermore, it is unique in
that the -amino group is attached directly to the side chain, making the carbon a direct substituent of the side chain.
https://en.wikipedia.org/wiki/Proline
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Prolyl Hydroxylase
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Prolyl-4-hydroxylase
Promoter
For transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA
polymerase and for proteins called transcription factors that recruit RNA polymerase.
These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression.
Promoters are located near the transcription start sites of genes, on the same strand
and upstream on the DNA (towards the 5' region of the sense strand). Promoters can
be about 1001000 base pairs long.
In bacteria:
The promoter is recognized by RNA polymerase and an associated sigma factor, which
in turn are often brought to the promoter DNA by an activator protein's binding to its
own DNA binding site nearby.
In eukaryotes:
The process is more complicated, and at least seven different factors are necessary for
the binding of an RNA polymerase II to the promoter. Promoters represent critical elements that can work in concert with other regulatory regions (enhancers, silencers,
boundary elements/insulators) to direct the level of transcription of a given gene.
https://en.wikipedia.org/wiki/Promoter_(genetics)
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Proofreading
The term proofreading is used in genetics to refer to the error-correcting processes,
first proposed by John Hopfield and Jacques Ninio, involved in DNA replication, immune system specificity, enzyme-substrate recognition among many other processes
that require enhanced specificity. The proofreading mechanisms of Hopfield and Ninio
are non-equilibrium active processes that consume ATP to enhance specificity of various biochemical reactions.
In bacteria, all three DNA polymerases (I, II and III) have the ability to proofread, using 3 5 exonuclease activity. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched
base. Following base excision, the polymerase can re-insert the correct base and replication can continue.
In eukaryotes only the polymerase that deal with the elongation (delta, and epsilon)
have proofreading ability (3 5 exonuclease activity).
Proofreading also occurs in mRNA translation for protein synthesis. In this case, one
mechanism is release of any incorrect aminoacyl-tRNA prior to peptide bond formation.
The extent of proofreading in DNA replication determines the mutation rate, and is different in different species. For example, loss of proof-reading due to mutations in the
DNA polymerase epsilon gene results in a hyper-mutated genotype with >100 mutations per Mbase of DNA in human colorectal cancers.
https://en.wikipedia.org/wiki/Proofreading_(biology)
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Propionic Acid
Propionic acid,also known as propanoic acid, is a naturally occurring carboxylic acid
with chemical formula CH3CH2COOH. It is a clear liquid with a pungent and unpleasant smell somewhat resembling body odor. The anion CH3CH2COO- as well as the salts
and esters of propionic acid are known as propionates (or propanoates).
Propionyl-CoA is a metabolic product of metabolism of amino acids with odd numbers
of carbons. The metabolism of propionic acid begins with its conversion to propionyl
coenzyme A (propionyl-CoA), the usual first step in the metabolism of carboxylic acids.
Since propionic acid has three carbons, propionyl-CoA cannot directly enter either
oxidation or the citric acid cycle. In most vertebrates, propionyl-CoA is carboxylated to
D-methylmalonyl-CoA, which is isomerized to L-methylmalonyl-CoA. A vitamin B12dependent enzyme catalyzes rearrangement of L-methylmalonyl-CoA to succinyl-CoA,
which is an intermediate of the citric acid cycle and can be readily incorporated there.
In propionic acidemia, a rare inherited genetic disorder, propionate acts as a metabolic
toxin in liver cells by accumulating in mitochondria as propionyl-CoA and its derivative, methylcitrate, two tricarboxylic acid cycle inhibitors. Propanoate is metabolized
oxidatively by glia, which suggests astrocytic vulnerability in propionic acidemia when
intramitochondrial propionyl-CoA may accumulate. Propionic acidemia may alter both
neuronal and glial gene expression by affecting histone acetylation. When propionic
acid is infused directly into rodents' brains, it produces reversible behavior (e.g., hyperactivity, dystonia, social impairment, perseveration) and brain changes (e.g., innate
neuroinflammation, glutathione depletion) that may be used as a means to model
autism in rats.
It also, being a three-carbon molecule, feeds into hepatic gluconeogenesis (that is, the
creation of glucose molecules from simpler molecules in the liver).
https://en.wikipedia.org/wiki/Propionic_acid
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Propionyl-CoA
Propionyl-CoA is a coenzyme A derivative of propionic acid. There are several different
ways in which it is formed: It is formed as a product of -oxidation of odd-chain fatty
acids. It is also a product of metabolism of isoleucine and valine. It is a product of ketobutyric acid, which in turn is a product of catabolism of threonine and methionine.
It can also be formed as a by-product during the conversion of cholesterol to bile acids.
https://en.wikipedia.org/wiki/Propionyl-CoA
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Prostacyclin
Prostacyclin (also called prostaglandin I2 or PGI2) chiefly prevents formation of the
platelet plug involved in primary hemostasis (a part of blood clot formation). It does
this by inhibiting platelet activation. It is also an effective vasodilator. Prostacyclin's interactions in contrast to thromboxane (TXA2), another eicosanoid, strongly suggest a
mechanism of cardiovascular homeostasis between the two hormones in relation to vascular damage.
As a drug, it is also known as "epoprostenol".
https://en.wikipedia.org/wiki/Prostacyclin
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Prostacyclin Synthase
is encoded by the PTGIS gene. This gene encodes a member of the cytochrome P450 su
perfamily of enzymes. The cytochrome P450 proteins are monooxygenases which cata-
lyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids
and other lipids. However, this protein is considered a member of the cytochrome P450
superfamily on the basis of sequence similarity rather than functional similarity. This
endoplasmic reticulum membrane protein catalyzes the conversion of prostaglandin
Index
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Prostaglandin G2
https://en.wikipedia.org/wiki/Prostaglandin_G2
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Prostaglandin H2
https://en.wikipedia.org/wiki/Prostaglandin_H2
Prostaglandins
The prostaglandins (PG) are a group of physiologically active lipid compounds having
diverse hormone-like effects in animals. Prostaglandins have been found in almost
every tissue in humans and other animals. They are derived enzymatically from fatty
acids. Every prostaglandin contains 20 carbon atoms, including a 5-carbon ring. They
are a subclass of eicosanoids and of the prostanoid class of fatty acid derivatives.
The structural differences between prostaglandins account for their different biological
activities. A given prostaglandin may have different and even opposite effects in different tissues. The ability of the same prostaglandin to stimulate a reaction in one tissue
and inhibit the same reaction in another tissue is determined by the type of receptor to
which the prostaglandin binds. They act as autocrine or paracrine factors with their target cells present in the immediate vicinity of the site of their secretion. Prostaglandins
differ from endocrine hormones in that they are not produced at a specific site but in
many places throughout the human body.
https://en.wikipedia.org/wiki/Prostaglandin
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Prosthetic Group
A cofactor that is tightly or even covalently bound to a protein is termed a prosthetic
group. A cofactor is a non-protein chemical compound that is required for the protein's
biological activity to happen. These proteins are commonly enzymes, and cofactors can
be considered "helper molecules" that assist in biochemical transformations.
Cofactors can be subdivided into either one or more inorganic ions, or a complex organic or metalloorganic molecule called a coenzyme, most of which are derived from
vitamins and from required organic nutrients in small amounts. A cofactor that is
tightly or even covalently bound is termed a prosthetic group. Additionally, some
sources also limit the use of the term "cofactor" to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at the junction of glycolysis and the citric
acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide
(FAD), and the co-substrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg++).
Organic cofactors are often vitamins or are made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the
AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.
https://en.wikipedia.org/wiki/Cofactor_(biochemistry)
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Protease
A protease (also called a peptidase or proteinase) is any enzyme that performs proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link
amino acids together in a polypeptide chain. Proteases have evolved multiple times,
and different classes of protease can perform the same reaction by completely different
catalytic mechanisms. Proteases can be found in animals, plants, bacteria, archaea and
viruses.
Proteases are involved in digesting long protein chains into shorter fragments by splitting the peptide bonds that link amino acid residues. Some detach the terminal amino
acids from the protein chain (exopeptidases, such as aminopeptidases, carboxypeptidase A). Others attack internal peptide bonds of a protein (endopeptidases, such as
trypsin, chymotrypsin, pepsin, papain, elastase).
Catalysis is achieved by one of two mechanisms:
Aspartic, glutamic and metallo- proteases activate a water molecule which performs a
nucleophilic attack on the peptide bond to hydrolyze it.
Serine, threonine and cysteine proteases use a nucleophilic residue in a (usually in a
catalytic triad). That residue performs a nucleophilic attack to covalently link the protease to the substrate protein, releasing the first half of the product. This covalent acylenzyme intermediate is then hydrolyzed by activated water to complete catalysis by releasing the second half of the product and regenerating the free enzyme.
https://en.wikipedia.org/wiki/Protease
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Protease Inhibitors
In biology and biochemistry, protease inhibitors are molecules that inhibit the function
of proteases. Many naturally occurring protease inhibitors are proteins. Protease inhibitors may be classified either by the type of protease they inhibit, or by their mechanism
of action.
Protease inhibitors may be classified either by the type of protease they inhibit, or by
their mechanism of action. In 2004 Rawlings and colleagues introduced a classification of protease inhibitors based on similarities detectable at the level of amino acid sequence. This classification initially identified 48 families of inhibitors that could be
grouped into 26 related superfamily (or clans) by their structure. According to the
MEROPS database there are now 85 families of inhibitors. These families are named
with an I followed by a number, for example, I14 contains hirudin-like inhibitors.
https://en.wikipedia.org/wiki/Protease_inhibitor_(biology)
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Proteases
A protease (also called a peptidase or proteinase) is any enzyme that performs proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link
amino acids together in a polypeptide chain. Proteases have evolved multiple times,
and different classes of protease can perform the same reaction by completely different
catalytic mechanisms. Proteases can be found in animals, plants, bacteria, archaea and
viruses.
Proteases are involved in digesting long protein chains into shorter fragments by splitting the peptide bonds that link amino acid residues. Some detach the terminal amino
acids from the protein chain (exopeptidases, such as aminopeptidases, carboxypeptidase A). Others attack internal peptide bonds of a protein (endopeptidases, such as
trypsin, chymotrypsin, pepsin, papain, elastase).
Catalysis is achieved by one of two mechanisms:
Aspartic, glutamic and metallo- proteases activate a water molecule which performs a
nucleophilic attack on the peptide bond to hydrolyze it.
Serine, threonine and cysteine proteases use a nucleophilic residue in a (usually in a
catalytic triad). That residue performs a nucleophilic attack to covalently link the protease to the substrate protein, releasing the first half of the product. This covalent acylenzyme intermediate is then hydrolyzed by activated water to complete catalysis by releasing the second half of the product and regenerating the free enzyme.
https://en.wikipedia.org/wiki/Protease
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Proteasome
Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.
In eukaryotes, proteasomes are located in the nucleus and the cytoplasm. The main
function of the proteasome is to degrade unneeded or damaged proteins by proteolysis,
a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are
called proteases. Proteasomes are part of a major mechanism by which cells regulate
the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then
be further degraded into shorter amino acid sequences and used in synthesizing new
proteins. Proteins are tagged for degradation with a small protein called ubiquitin. The
tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is
tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein. The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of
gene expression, and responses to oxidative stress.
https://en.wikipedia.org/wiki/Proteasome
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Proteasomes
Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.
In eukaryotes, proteasomes are located in the nucleus and the cytoplasm. The main
function of the proteasome is to degrade unneeded or damaged proteins by proteolysis,
a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are
called proteases. Proteasomes are part of a major mechanism by which cells regulate
the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then
be further degraded into shorter amino acid sequences and used in synthesizing new
proteins. Proteins are tagged for degradation with a small protein called ubiquitin. The
tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is
tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein. The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of
gene expression, and responses to oxidative stress.
https://en.wikipedia.org/wiki/Proteasome
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Protein
Proteins are large biomolecules, or macromolecules, consisting of one or more long
chains of amino acid residues. Proteins perform a vast array of functions within living
organisms, including catalyzing metabolic reactions, DNA replication, responding to
stimuli, and transporting molecules from one location to another. Proteins differ from
one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific
three-dimensional structure that determines its activity.
A linear chain of amino acid residues is called a polypeptide. A protein contains at least
one long polypeptide. Short polypeptides, containing less than 20-30 residues, are
rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds
and adjacent amino acid residues. The sequence of amino acid residues in a protein is
defined by the sequence of a gene, which is encoded in the genetic code. In general, the
genetic code specifies 20 standard amino acids. However, in certain organisms the genetic code can include selenocysteine andin certain archaeapyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by
posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins
have non-peptide groups attached, which can be called prosthetic groups or cofactors.
Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.
Once formed, proteins only exist for a certain period of time and are then degraded
and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 12 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within
cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to
metabolism. Proteins also have structural or mechanical functions, such as actin and
myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune
responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down
ingested protein into free amino acids that are then used in metabolism.
Proteins may be purified from other cellular components using a variety of techniques
such as ultracentrifugation, precipitation, electrophoresis, and chromatography. The
advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry.
https://en.wikipedia.org/wiki/Protein
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Protein Folding
Protein folding is the physical process by which a protein chain acquires its native 3dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. It is the physical process by which a polypeptide
folds into its characteristic and functional three-dimensional structure from random
coil. Each protein exists as an unfolded polypeptide or random coil when translated
from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any
stable (long-lasting) three-dimensional structure (the left hand side of the first figure).
Amino acids interact with each other to produce a well-defined three-dimensional
structure, the folded protein (the right hand side of the figure), known as the native
state. The resulting three-dimensional structure is determined by the amino acid sequence (Anfinsen's dogma). Experiments beginning in the 1980s indicate the codon for
an amino acid can also influence protein structure.
The correct three-dimensional structure is essential to function, although some parts
of functional proteins may remain unfolded, so that protein dynamics is important.
Failure to fold into native structure generally produces inactive proteins, but in some
instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by incorrect folding of
some proteins, because the immune system does not produce antibodies for certain
protein structures.
https://en.wikipedia.org/wiki/Protein_folding
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Protein Kinase A
In cell biology, protein kinase A (PKA) is a family of enzymes whose activity is dependent on cellular levels of cyclic AMP (cAMP). PKA is also known as cAMP-dependent
protein kinase .Protein kinase A has several functions in the cell, including regulation
of glycogen, sugar, and lipid metabolism. PKA phosphorylates proteins that have the
motif Arginine-Arginine-X-Serine exposed, in turn (de)activating the proteins.
The PKA enzyme is also known as cAMP-dependent enzyme because it is activated
only when cAMP is present. Hormones such as glucagon and epinephrine begin the activation cascade (that triggers protein kinase A) by binding to a G proteincoupled receptor (GPCR) on the target cell. When a GPCR is activated by its extracellular ligand,
a conformational change is induced in the receptor that is transmitted to an attached
intracellular heterotrimeric G protein complex by protein domain dynamics. The Gs
subunit of the stimulated G protein complex exchanges GDP for GTP and is released
from the complex. The activated Gs subunit binds to and activates an enzyme called
adenylyl cyclase, which, in turn, catalyzes the conversion of ATP into cyclic adenosine
monophosphate (cAMP) increasing cAMP levels. Four cAMP molecules are required
to activate a single PKA enzyme. This is done by two cAMP molecules binding to each
of the two regulatory subunits on a PKA enzyme causing the subunits to detach exposing the two (now activated) catalytic subunits. Next the catalytic subunits can go on to
phosphorylate other proteins.
Below is a list of the steps involved in PKA activation:
1 Cytosolic cAMP increases
2 Two cAMP molecules bind to each PKA regulatory subunit
3 The regulatory subunits move out of the active sites of the catalytic subunits and the
R2C2 complex dissociates
4 The free catalytic subunits interact with proteins to phosphorylate Ser or Thr residues.
https://en.wikipedia.org/wiki/Protein_kinase_A
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Protein Kinase C
Protein kinase C also known as PKC (EC 2.7.11.13) is a family of protein kinase enzymes that are involved in controlling the function of other proteins through the phosphorylation of hydroxyl groups of serine and threonine amino acid residues on these
proteins. PKC enzymes in turn are activated by signals such as increases in the concentration of diacylglycerol (DAG) or calcium ions (Ca2+). Hence PKC enzymes play important roles in several signal transduction cascades.
The PKC family consists of fifteen isozymes in humans. They are divided into three subfamilies, based on their second messenger requirements: conventional (or classical),
novel, and atypical. Conventional (c)PKCs contain the isoforms , I, II, and . These
require Ca++, DAG, and a phospholipid such as phosphatidylserine for activation.
Novel (n)PKCs include the , , , and isoforms, and require DAG, but do not require
Ca++ for activation. Thus, conventional and novel PKCs are activated through the same
signal transduction pathway as phospholipase C. On the other hand, atypical (a)PKCs
(including protein kinase M and / isoforms) require neither Ca++ nor diacylglycerol
for activation. The term "protein kinase C" usually refers to the entire family of isoforms. PKC is involved in receptor desensitization, in modulating membrane structure
events, in regulating transcription, in mediating immune responses, in regulating cell
growth, and in learning and memory. These functions are achieved by PKC-mediated
phosphorylation of other proteins.
https://en.wikipedia.org/wiki/Protein_kinase_C
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Protein Kinases
A protein kinase is a kinase enzyme that modifies other proteins by chemically adding
phosphate groups to them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes. Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate
the majority of cellular pathways, especially those involved in signal transduction. Protein kinases are also found in bacteria and plants.
Serine/threonine protein kinases (EC 2.7.11.1) phosphorylate the OH group of serine
or threonine (which have similar side-chains). Activity of these protein kinases can be
regulated by specific events (e.g., DNA damage), as well as numerous chemical signals,
including cAMP/cGMP, diacylglycerol, and Ca++/calmodulin. One very important
group of protein kinases are the MAP kinases (acronym from: "mitogen-activated protein kinases"). Important subgroups are the kinases of the ERK subfamily, typically activated by mitogenic signals, and the stress-activated protein kinases JNK and p38.
While MAP kinases are serine/threonine-specific, they are activated by combined phosphorylation on serine/threonine and tyrosine residues. Activity of MAP kinases is restricted by a number of protein phosphatases, which remove the phosphate groups
that are added to specific serine or threonine residues of the kinase and are required to
maintain the kinase in an active conformation. Two major factors influence activity of
MAP kinases: a) signals that activate transmembrane receptors (either natural ligands
or crosslinking agents) and proteins associated with them (mutations that simulate active state) b) signals that inactivate the phosphatases that restrict a given MAP kinase.
Such signals include oxidant stress.
https://en.wikipedia.org/wiki/Protein_kinase
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Protein Phosphatase 2A
Protein phosphatase 2 (PP2), also known as PP2A, is an enzyme that consists of a dimeric core enzyme composed of the structural A and catalytic C subunits, and a regulatory B subunit. The PP2A heterotrimeric protein phosphatase is a ubiquitous and conserved serine/threonine phosphatase with broad substrate specificity and diverse cellular functions. Among the targets of PP2A are proteins of oncogenic signaling cascades,
such as Raf, MEK, and AKT.
PP2A consists of a dimeric core enzyme composed of the structural A and catalytic C
subunits, and a regulatory B subunit. When the PP2A catalytic C subunit associates
with the A and B subunits several species of holoenzymes are produced with distinct
functions and characteristics. The A subunit, a founding member of the HEAT repeat
protein family (huntington-elongation-A subunit-TOR), is the scaffold required for the
formation of the heterotrimeric complex. When the A subunit binds it alters the enzymatic activity of the catalytic subunit, even if the B subunit is absent. While C and A
subunit sequences show remarkable sequence conservation throughout eukaryotes,
regulatory B subunits are more heterogeneous and are believed to play key roles in controlling the localization and specific activity of different holoenzymes. Multicellular
eukaryotes express four classes of variable regulatory subunits: B (PR55), B (B56 or
PR61), B (PR72), and B (PR93/PR110), with at least 16 members in these subfamilies. In addition, accessory proteins and posttranslational modifications (such as methylation) control PP2A subunit associations and activities.
https://en.wikipedia.org/wiki/Protein_phosphatase_2
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Protein Sorting
Protein targeting or protein sorting is the biological mechanism by which proteins are
transported to the appropriate destinations in the cell or outside of it. Proteins can be
targeted to the inner space of an organelle, different intracellular membranes, plasma
membrane, or to exterior of the cell via secretion. This delivery process is carried out
based on information contained in the protein itself. Correct sorting is crucial for the
cell. Errors can lead to diseases.
Targeting signals are the pieces of information that enable the cellular transport machinery to correctly position a protein inside or outside the cell. This information is contained in the polypeptide chain or in the folded protein. The continuous stretch of
amino acid residues in the chain that enables targeting are called signal peptides or targeting peptides. There are two types of targeting peptides, the presequences and the internal targeting peptides. The presequences of the targeting peptide are often found at
the N-terminal extension and is composed of between 6-136 basic and hydrophobic
amino acids. In case of peroxisomes the targeting sequence is on the C-terminal extension mostly. Other signals, known as signal patches, are composed of parts which are
separate in the primary sequence. They become functional when folding brings them
together on the protein surface. In addition, protein modifications like glycosylations
can induce targeting.
https://en.wikipedia.org/wiki/Protein_targeting
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Protein Structure
Protein structure is the three-dimensional arrangement of atoms in a protein molecule. Proteins are polymers specifically polypeptides formed from sequences of
monomer amino acids. By convention, a chain under 40 amino acids is often identified
as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van der Waals
forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is
the topic of the scientific field of structural biology, which employs techniques such as
X-ray crystallography, NMR spectroscopy, and dual polarization interferometry to determine the structure of proteins.
Protein structures range in size from tens to several thousand amino acids. By physical
size, proteins are classified as nanoparticles, between 1100 nm. Very large aggregates
can be formed from protein subunits. For example, many thousands of actin molecules
assemble into a microfilament.
A protein may undergo reversible structural changes in performing its biological function. The alternative structures of the same protein are referred to as different conformations, and transitions between them are called conformational changes.
https://en.wikipedia.org/wiki/Protein_structure
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Protein Synthesis
Protein biosynthesis is the process whereby biological cells generate new proteins. It is
balanced by the loss of cellular proteins via degradation or export. Translation, the assembly of amino acids by ribosomes, is an essential part of the biosynthetic pathway,
along with generation of messenger RNA (mRNA), aminoacylation of transfer RNA
(tRNA), co-translational transport, and post-translational modification. Protein biosynthesis is strictly regulated at multiple steps. They are principally during transcription
(phenomena of RNA synthesis from DNA template) and translation (phenomena of
amino acid assembly from RNA).
The cistron DNA is transcribed into a variety of RNA intermediates. The last version is
used as a template in synthesis of a polypeptide chain. Protein will often be synthesized
directly from genes by translating mRNA. When a protein must be available on short
notice or in large quantities, a protein precursor is produced. A proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the
inhibitory sequence is removed by proteolysis during posttranslational modification. A
preprotein is a form that contains a signal sequence (an N-terminal signal peptide)
that specifies its insertion into or through membranes, i.e., targets them for secretion.
The signal peptide is cleaved off in the endoplasmic reticulum. Preproproteins have
both sequences (inhibitory and signal) still present.
In protein synthesis, a succession of tRNA RNA molecules charged with appropriate
amino acids are brought together with an mRNA molecule and matched up by basepairing through the anti-codons of the tRNA with successive codons of the mRNA. The
amino acids are then linked together to extend the growing protein chain, and the
tRNAs, no longer carrying amino acids, are released. This whole complex of processes
is carried out by the ribosome, formed of two main chains of RNA, called ribosomal
RNA (rRNA), and more than 50 different proteins. The ribosome latches onto the end
of an mRNA molecule and moves along it, capturing loaded tRNA molecules and joining together their amino acids to form a new protein chain.
Protein biosynthesis, although very similar, is different for prokaryotes and eukaryotes.
https://en.wikipedia.org/wiki/Protein_biosynthesis
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Proteins
Proteins are large biomolecules, or macromolecules, consisting of one or more long
chains of amino acid residues. Proteins perform a vast array of functions within living
organisms, including catalyzing metabolic reactions, DNA replication, responding to
stimuli, and transporting molecules from one location to another. Proteins differ from
one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific
three-dimensional structure that determines its activity.
A linear chain of amino acid residues is called a polypeptide. A protein contains at least
one long polypeptide. Short polypeptides, containing less than 20-30 residues, are
rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds
and adjacent amino acid residues. The sequence of amino acid residues in a protein is
defined by the sequence of a gene, which is encoded in the genetic code. In general, the
genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine andin certain archaeapyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by
posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins
have non-peptide groups attached, which can be called prosthetic groups or cofactors.
Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.
Once formed, proteins only exist for a certain period of time and are then degraded
and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 12 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within
cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to
metabolism. Proteins also have structural or mechanical functions, such as actin and
myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune
responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down
ingested protein into free amino acids that are then used in metabolism.
Proteins may be purified from other cellular components using a variety of techniques
such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic
resonance and mass spectrometry.
https://en.wikipedia.org/wiki/Protein
Index
Find Term
Proteoglycans
Proteoglycans are proteins that are heavily glycosylated. The basic proteoglycan u
(GAG) chain(s). The point of attachment is a serine (Ser) residue to which the glyc
(where X can be any amino acid residue but Proline), although not every protein w
this sequence has an attached glycosaminoglycan. The chains are long, linear carb
drate polymers that are negatively charged under physiological conditions due to t
occurrence of sulfate and uronic acid groups. Proteoglycans occur in the connectiv
sue.
https://en.wikipedia.org/wiki/Proteoglycan
Index
Find Term
Proteolysis
down proteins in food to provide amino acids for the organism, while proteolyti
essing of a polypeptide chain after its synthesis may be necessary for the produc
Proteolytic Degradation
Protein degradation may take place intracellularly or extracellularly. In digestion of
food, digestive enzymes may be released into the environment for extracellular digestion whereby proteolytic cleavage breaks down proteins into smaller peptides and
amino acids so that they may be absorbed and used by an organism. In animals the
food may be processed extracellularly in specialized digestive organs or guts, but in
many bacteria the food may be internalized into the cell via phagocytosis. Microbial
degradation of protein in the environment can be regulated by nutrient availability.
For example, limitation for major elements in proteins (carbon, nitrogen, and sulfur)
has been shown to induce proteolytic activity in the fungus Neurospora crassa as well
as in whole communities of soil organisms.
Proteins in cells are also constantly being broken down into amino acids. This intracel-
lular degradation of protein serves a number of functions: It removes damaged and abnormal protein and prevent their accumulation, and it also serves to regulate cellular
processes by removing enzymes and regulatory proteins that are no longer needed. The
amino acids may then be reused for protein synthesis.
https://en.wikipedia.org/wiki/Proteolysis#Protein_degradation
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue, or
type of cell or organism, at a given time, under defined conditions. The term is a
of proteins and genome. Proteomics is the study of the proteome.
The term proteome has been applied to several different types of biological syst
cellular proteome is the collection of proteins found in a particular cell type und
tualized as the complete set of proteins from all of the various cellular proteome
is very roughly the protein equivalent of the genome. The term "proteome" has
been used to refer to the collection of proteins in certain sub-cellular biological
tems. For example, all of the proteins in a virus can be called a viral proteome.
https://en.wikipedia.org/wiki/Proteome
Index
Find Term
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. While proteomics generally refers to the large-scale experimental analysis of proteins, it is often specifically used for protein purification and mass spectrometry.
Proteomics gives a different level of understanding than genomics for many reasons:
the level of transcription of a gene gives only a rough estimate of its level of translation into a protein. An mRNA produced in abundance may be degraded rapidly or
translated inefficiently, resulting in a small amount of protein.
as mentioned above many proteins experience post-translational modifications that
profoundly affect their activities. For example some proteins are not active until they
become phosphorylated. Methods such as phosphoproteomics and glycoproteomics
are used to study post-translational modifications.
many transcripts give rise to more than one protein, through alternative splicing or
alternative post-translational modifications.
many proteins form complexes with other proteins or RNA molecules, and only function in the presence of these other molecules.
protein degradation rate plays an important role in protein content.
One major factor affecting reproducibility in proteomics experiments is the simultaneous elution of many more peptides than can be measured by mass spectrometers. This
causes stochastic differences between experiments due to data-dependant acquisition
of tryptic peptides. Although early large-scale shotgun proteomics analyses showed
considerable variability between laboratories, presumably due in part to technical and
experimental differences between labs, reproducibility has been improved in more recent mass spectrometry analysis, particularly on the protein level and using Orbitrap
mass spectrometers. Notably, targeted proteomics shows increased reproducibility and
repeatability compared with shotgun methods, although at the expense of data density
and effectiveness.
https://en.wikipedia.org/wiki/Proteomics
Proteopathy
structurally abnormal, and thereby disrupt the function of cells, tissues and
the body. Often the proteins fail to fold into their normal configuration. In
folded state, the proteins can become toxic in some way (a gain of toxic func
they can lose their normal function. The proteopathies (also known as prote
Index
Find Term
Prothrombin
Prothrombin is a coagulation factor that is proteolytically cleaved to form thrombin in
the coagulation cascade, the clotting process. Thrombin in turn acts as a serine protease that converts soluble fibrinogen into insoluble strands of fibrin, as well as catalyzing many other coagulation-related reactions.
In the blood coagulation pathway, thrombin acts to convert factor XI to XIa, VIII to
VIIIa, V to Va, fibrinogen to fibrin, and XIII to XIIIa. Factor XIIIa is a transglutaminase that catalyzes the formation of covalent bonds between lysine and glutamine residues in fibrin. The covalent bonds increase the stability of the fibrin clot. Thrombin interacts with thrombomodulin.
As part of its activity in the coagulation cascade, thrombin also promotes platelet activation and aggregation via activation of protease-activated receptors on the cell membrane of the platelet.
Negative feedback
Thrombin bound to thrombomodulin activates protein C, an inhibitor of the coagulation cascade. The activation of protein C is greatly enhanced following the binding of
thrombin to thrombomodulin, an integral membrane protein expressed by endothelial
cells. Activated protein C inactivates factors Va and VIIIa. Binding of activated protein
C to protein S leads to a modest increase in its activity. Thrombin is also inactivated by
antithrombin, a serine protease inhibitor.
https://en.wikipedia.org/wiki/Thrombin
Protists
Protists are the members of an informal grouping of diverse eukaryotic organisms that
are not animals, plants or fungi. They do not form a natural group, or clade, but are often grouped together for convenience, like algae or invertebrates. In some systems of
biological classification, such as the popular 5-kingdom scheme proposed by Robert
Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues."
Besides their relatively simple levels of organization, the protists do not have much in
common. When used, the term protists is now considered to mean similar-appearing
but diverse phyla that are not related through an exclusive common ancestor, and that
have different life cycles, trophic levels, modes of locomotion, and cellular structures.
In the classification system of Lynn Margulis, the term protist is reserved for microscopic organisms, while the more inclusive term Protoctista is applied to a biological
kingdom which includes certain large multicellular eukaryotes, such as kelp, red algae
and slime molds. Other workers use the term protist more broadly, to encompass both
microbial eukaryotes and macroscopic organisms that do not fit into the other traditional kingdoms.
In cladistic systems, there are no equivalents to the taxa Protista or Protoctista, both
terms referring to a paraphyletic group which spans the entire eukaryotic tree of life.
In cladistic classification, the contents of Protista are distributed among various supergroups (SAR, Archaeplastida, Excavata, Opisthokonta, etc. ) and "Protista", ''Protoctista'' and "Protozoa" are considered obsolete. However, there still remains some ambiguity about the position in the cladistic tree of some taxa - such as most excavata (metamonads, jakobids, Malawimonas and Collodictyon) and the term "protist" continues to
be used informally as a catch-all term for Eukaryotic microorganisms - for example
"protist pathogen" is used to denote any microbe which is not bacteria, virus, viroid or
metazoa.
https://en.wikipedia.org/wiki/Protist
Index
Find Term
Proton
A proton is a subatomic particle, symbol p, p+, or H+, with a positive electric charge of
+1e elementary charge and mass slightly less than that of a neutron. The number of
protons in the nucleus is the defining property of an element, and is referred to as the
atomic number (represented by the symbol Z). Since each element has a unique number of protons, each element has its own unique atomic number. Acids in solution are
donors of protons.
https://en.wikipedia.org/wiki/Proton
Index
Find Term
Proton Gradient
A proton gradient is a gradient of protons that can move across a membrane. The proton gradient can be used as intermediate energy storage for heat production and flagellar rotation. In addition, it is an interconvertible form of energy in active transport,
electron potential generation, NADPH synthesis, and ATP synthesis/hydrolysis.
The electrochemical potential difference between the two sides of the membrane in mitochondria, chloroplasts, bacteria, and other membranous compartments that engage
in active transport involving proton pumps, is at times called a chemiosmotic potential
or proton motive force. In this context, protons are often considered separately using
units of either concentration or pH.
https://en.wikipedia.org/wiki/Electrochemical_gradient
Index
Find Term
Protozoa
isms with animal-like behaviors, such as motility and predation. The group
Index
Find Term
PrP
The protein that prions are made of, PrP, is found throughout the body, eve
healthy people and animals. However, PrP found in infectious material has
structure and is resistant to proteases, the enzymes in the body that can nor
break down proteins. The normal form of the protein is called PrPC, while t
tious form is called PrPSc the C refers to 'cellular' PrP, while the Sc refers
pie', the prototypic prion disease, occurring in sheep. While PrPC is structu
PrPc
PrPc is a normal protein found on the membranes of cells. It has 209 amino a
humans), one disulfide bond, a molecular mass of 3536 kDa and a mainly
structure. Several topological forms exist - one cell surface form anchored via
colipid and two transmembrane forms. The normal protein is not sedimenta
sue that continues to be investigated. PrPc binds copper (II) ions with high af
significance of this finding is not clear, but it is presumed to relate to PrP stru
PRPP
Phosphoribosyl pyrophosphate (PRPP) is a pentosephosphate.It is formed from ribose
5-phosphate by the enzyme ribose-phosphate diphosphokinase. It plays a role in transferring phospho-ribose groups in several reactions. In de novo generation of purines,
the enzyme amidophosphoribosyltransferase acts upon PRPP to create phosphoribosylamine.
Increased levels of PRPP is characterized by the overproduction and accumulation of
uric acid leading to hyperuricemia and hyperuricosuria. It is one of the causes of gout.
Increased levels of PRPP are present in Lesch-Nyhan Syndrome. Decreased levels of hypoxanthine guanine phosphoribosyl transferase (HGPRT) causes this accumulation, as
PRPP is a substrate used by HGPRT during purine salvage. Shown below is the form
of PRPP.
https://en.wikipedia.org/wiki/Phosphoribosyl_pyrophosphate
Index
Find Term
G-G
G-G
Chapter 5 - Energy: Basics
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
PRPP Amidotransferase
Amidophosphoribosyltransferase (ATase), also known as glutamine phosphoribosylpyrophosphate amidotransferase (GPAT) or PRPP amidotransferase, is an enzyme responsible for catalyzing the conversion of 5-phosphoribosyl-1-pyrophosphate (PRPP)
into 5-phosphoribosyl-1-amine (PRA), using the ammonia group from a glutamine
side-chain. This is the committing step in de novo purine synthesis. In humans it is encoded by the PPAT (phosphoribosyl pyrophosphate amidotransferase) gene. ATase is
a member of the purine/pyrimidine phosphoribosyltransferase family.
In an example of feedback inhibition, ATase is inhibited mainly by the end-products of
the purine synthesis pathway, AMP, GMP, ADP, and GDP. Each enzyme subunit from
the homotetramer has two binding sites for these inhibitors. The allosteric (A) site overlaps with the site for the ribose-5-phosphate of PRPP, while the catalytic (C) site overlaps with the site for the pyrophosphate of PRPP. The binding of specific nucleotide
pairs to the two sites results in synergistic inhibition stronger than additive inhibition.
Inhibition occurs via a structural change in the enzyme where the flexible glutamine
loop gets locked in an open position, preventing the binding of PRPP.
https://en.wikipedia.org/wiki/Amidophosphoribosyltransferase
Index
Find Term
PRPP Synthetase
duced by the HMP Shunt Pathway from Glucose-6-Phosphate. The product pho
the de novo synthesis of purines. Dysfunction of the enzyme would thereby und
purine metabolism.
Index
Find Term
PrPres
"PrPres" has been made to distinguish between PrPSc, which is isolated from
PrPsc
The infectious isoform of PrP, known as PrPSc, is able to convert normal PrPc pr
ters the way the proteins interconnect. PrPSc always causes prion disease. Altho
of cell damage or are simply a side-effect of the underlying disease process. The
each fiber acts as a template onto which free protein molecules may attach, allo
the fiber to grow. Under most circumstances, only PrP molecules with an identi
amino acid sequence to the infectious PrPSc are incorporated into the growing f
However, rare cross-species transmission is also possible.
https://en.wikipedia.org/wiki/Prion#PrPSc
PrPSc
The infectious isoform of PrP, known as PrPSc, is able to convert normal PrPc
ters the way the proteins interconnect. PrPSc always causes prion disease. Alt
each fiber acts as a template onto which free protein molecules may attach, a
the fiber to grow. Under most circumstances, only PrP molecules with an ide
amino acid sequence to the infectious PrPSc are incorporated into the growin
However, rare cross-species transmission is also possible.
https://en.wikipedia.org/wiki/Prion#PrPSc
Pseudouridine
Pseudouridine (abbreviated by the Greek letter psi- ) is an isomer of the nucleoside
uridine in which the uracil is attached via a carbon-carbon instead of a nitrogencarbon glycosidic bond. It is the most prevalent of the over one hundred different modified nucleosides found in RNA. is found in all species and in many classes of RNA.
is formed by enzymes called synthases, which post-transcriptionally isomerize specific uridine residues in RNA in a process termed pseudouridylation.
It is commonly found in tRNA, associated with thymidine and cytosine in the TC arm
and is one of the invariant regions of tRNA. The function of it is not very clear, but it is
expected to play a role in association with aminoacyl transferases during their interaction with tRNA, and hence in the initiation of translation. Recent studies suggest it
may offer protection from radiation.
Shown below is pseudouridine (right) synthesis from uridine (left)
https://en.wikipedia.org/wiki/Pseudouridine
Pst I
https://en.wikipedia.org/wiki/PstI
Index
Find Term
Pulling a Reaction
which the amount of substrate is increased. Both have the effect of increasi
amount of forward reaction.
Index
Find Term
Pupylated
then delivers the Pup-substrate to the 20S proteasome by coupling of ATP hyd
for proteasomal degradation. The discovery of Pup indicates that like eukaryo
teria may use a small-protein modifier to control protein stability.
https://en.wikipedia.org/wiki/Prokaryotic_ubiquitin-like_protein
Adenosine uses the enzyme adenosine kinase, which is a very important enzyme in the
cell. Attempts are being made to develop an inhibitor for the enzyme for use in cancer
chemotherapy.
https://en.wikipedia.org/wiki/Purine_nucleoside_phosphorylase
Purines
A purine is a heterocyclic aromatic organic compound. It consists of a pyrimidine ring
fused to an imidazole ring. Purines, which include substituted purines and their
tautomers, are the most widely occurring nitrogen-containing heterocycle in nature.
Purines and pyrimidines make up the two groups of nitrogenous bases, including the
two groups of nucleotide bases. Two of the four deoxyribonucleotides and two of the
four ribonucleotides, the respective building-blocks of DNA and RNA, are purines. In
order to form DNA and RNA, both purines and pyrimidines are needed by the cell in
approximately equal quantities. Both purine and pyrimidine are self-inhibiting and activating. When purines are formed, they inhibit the enzymes required for more purine
formation. This self-inhibiting occurs as they also activate the enzymes needed for pyrimidine formation. Pyrimidine simultaneously self-inhibits and activates purine in
similar manner. Because of this, there is nearly an equal amount of both substances in
the cell at all times.
https://en.wikipedia.org/wiki/Purine
Index
Find Term
Pushing a Reaction
which the amount of product is reduced. Both have the effect of increasing
of forward reaction.
Index
Find Term
Pyran
sisting of five carbon atoms and one oxygen atom and containing two double bonds
The molecular formula is C5H6O. There are two isomers of pyran that differ by the l
tion of the double bonds. In 2H-pyran (shown below), the saturated carbon is at po
tion 2, whereas, in 4H-pyran, the saturated carbon is at position 4.
Pyranoses are sugars in a ring structure with a six-membered ring, of which one of t
members is an oxygen. They are named for pyran.
https://en.wikipedia.org/wiki/Pyran
Pyranoses
Pyranose is a collective term for carbohydrates that have a chemical structure that includes a six-membered ring consisting of five carbon atoms and one oxygen atom.
There may be other carbons external to the ring. The name derives from its similarity
to the oxygen heterocycle pyran, but the pyranose ring does not have double bonds. A
pyranose in which the anomeric OH at C(l) has been converted into an OR group is
called a pyranoside.
Illustrations of pyranoses are said to be in the Haworth structures. The Haworth structure of glucose is shown below.
https://en.wikipedia.org/wiki/Pyranose
Pyridine
Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It
is structurally related to benzene, with one methine group (=CH-) replaced by a nitrogen atom. The pyridine ring occurs in many important compounds, including azines
and the vitamins niacin and pyridoxal.
Pyridine is used as a precursor to agrochemicals and pharmaceuticals and is also an important solvent and reagent. Pyridine is added to ethanol to make it unsuitable for
drinking (see denatured alcohol). It is used in the in vitro synthesis of DNA, in the synthesis of sulfapyridine (a drug against bacterial and viral infections), antihistaminic
drugs tripelennamine and mepyramine, as well as water repellents, bactericides, and
herbicides. Some chemical compounds, although not synthesized from pyridine, contain its ring structure. They include B vitamins niacin and pyridoxal, the antituberculosis drug isoniazid, nicotine and other nitrogen-containing plant products. Historically, pyridine was produced from coal tar and as a by-product of coal gasification.
However, increased demand for pyridine resulted in the development of more economical methods of synthesis from acetaldehyde and ammonia, and more than 20,000 tons
per year are manufactured worldwide.
https://en.wikipedia.org/wiki/Pyridine
Index
Find Term
Pyrimidine
Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of
the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it
has the nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine
(nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2
positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).
The pyrimidine ring system has wide occurrence in nature as substituted and ring
fused compounds and derivatives, including the nucleotides, thiamine (vitamin B1) and
alloxan. It is also found in many synthetic compounds such as barbiturates and the
HIV drug, zidovudine.
https://en.wikipedia.org/wiki/Pyrimidine
Index
Find Term
Pyrimidine Dimers
Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in
DNA via photochemical reactions. Ultraviolet light induces the formation of covalent
linkages by reactions localized on the C=C double bonds. In dsRNA (double-stranded
RNA), uracil dimers may also accumulate as a result of UV radiation. Two common UV
products are cyclobutane pyrimidine dimers (CPDs, including thymine dimers) and
6,4 photoproducts. These premutagenic lesions alter the structure of DNA and consequently inhibit polymerases and arrest replication. Dimers may be repaired by photoreactivation or nucleotide excision repair, but unrepaired dimers are mutagenic. Pyrimidine dimers are the primary cause of melanomas in humans.
Pyrimidine dimers introduce local conformational changes in the DNA structure,
which allow recognition of the lesion by repair enzymes. In most organisms (excluding
placental mammals such as humans) they can be repaired by photoreactivation. Photoreactivation is a repair process in which photolyase enzymes directly reverse CPDs via
photochemical reactions. Lesions on the DNA strand are recognized by these enzymes,
followed by the absorption of light wavelengths >300nm (i.e. fluorescent and sunlight). This absorption enables the photochemical reactions to occur, which results in
the elimination of the pyrimidine dimer, returning it to its original state.
Nucleotide excision repair is a more general mechanism for repair of lesions. This process excises the CPD and synthesizes new DNA to replace the surrounding region in the
molecule. Xeroderma pigmentosum is a genetic disease in humans in which the nucleotide excision repair process is lacking, resulting in skin discoloration and multiple tumors on exposure to UV light. Unrepaired pyrimidine dimers in humans may lead to
melanoma.
https://en.wikipedia.org/wiki/Pyrimidine_dimer
Index
Find Term
Pyrimidine-specific 5 Nucleotidase
ways. It catalyzes removal of phosphate from CMP and UMP to form cytosi
cil, respectively.
Index
Find Term
Pyrophosphate
Pyrophosphate is a phosphorus oxyanion. Compounds such as salts and esters are also
called pyrophosphates. The group is also called diphosphate or dipolyphosphate, although this should not be confused with two phosphates.
Pyrophosphates are very important in biochemistry. The anion P2O74 is abbreviated
PPi and is formed by the hydrolysis of ATP into AMP in cells.
ATP AMP + PPi
For example, when a nucleotide is incorporated into a growing DNA or RNA strand by
a polymerase, pyrophosphate (PPi) is released. Pyrophosphorolysis is the reverse of the
polymerization reaction in which pyrophosphate reacts with the 3'nucleosidemonophosphate (NMP or dNMP), which is removed from the oligonucleotide to release the corresponding triphosphate (dNTP from DNA, or NTP from RNA).
The pyrophosphate anion has the structure P2O74, and is an acid anhydride of phosphate. It is unstable in aqueous solution and hydrolyzes into inorganic phosphate:
P2O74 + H2O 2 HPO42
or in biologists' shorthand notation:
PPi + H2O 2 Pi
In the absence of enzymic catalysis, hydrolysis reactions of simple polyphosphates
such as pyrophosphate, linear triphosphate, ADP, and ATP normally proceed extremely slowly in all but highly acidic media.
(The reverse of this reaction is a method of preparing pyrophosphates by heating phosphates.)
This hydrolysis to inorganic phosphate effectively renders the cleavage of ATP to AMP
and PPi irreversible, and biochemical reactions coupled to this hydrolysis are irreversible as well.
PPi occurs in synovial fluid, blood plasma, and urine at levels sufficient to block calcification and may be a natural inhibitor of hydroxyapatite formation in extracellular fluid
(ECF). Cells may channel intracellular PPi into ECF. ANK is a nonenzymatic plasmamembrane PPi channel that supports extracellular PPi levels. Defective function of the
membrane PPi channel ANK is associated with low extracellular PPi and elevated intracellular PPi. Ectonucleotide pyrophosphatase/phosphodiesterase (ENPP) may function
to raise extracellular PPi.
From the standpoint of high energy phosphate accounting, the hydrolysis of ATP to
AMP and PPi requires two high-energy phosphates, as to reconstitute AMP into ATP
requires two phosphorylation reactions.
AMP + ATP 2 ADP
2 ADP + 2 Pi 2 ATP
https://en.wikipedia.org/wiki/Pyrophosphate
Index
Find Term
G-G
G-G
G-G
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Basics
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Other Lipids
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 6 - Metabolism: Nucleotides
Chapter 7 - Information Processing: DNA Replication
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Short & Sweet: Energy
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Information Processing
Pyrroline-5-carboxylate Reductase
Pyrroline-5-carboxylate reductase is an enzyme that catalyzes the chemical
L-proline + NAD(P)+ 1-pyrroline-5-carboxylate + NAD(P)H + H+
Index
Find Term
Pyrrolysine
amino acid that is used in the biosynthesis of proteins in some methanogenic archa
group (which is in the deprotonated COO- form under biological conditions). Its p
roline side-chain is similar to that of lysine in being basic and positively charged at
neutral pH.
https://en.wikipedia.org/wiki/Pyrrolysine
Index
Find Term
Pyruvate
Pyruvic acid (CH3COCOOH) is the simplest of the -keto acids, with a carboxylic acid
and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is a key intermediate in several metabolic pathways.
In glycolysis, one molecule of glucose breaks down into two molecules of pyruvate,
which are then used to provide further energy, in one of two ways. Pyruvate is converted into acetyl-coenzyme A, which is the main input for a series of reactions known
as the citric acid cycle. Pyruvate is also converted to oxaloacetate by an anaplerotic reaction, which replenishes citric acid cycle intermediates. Also, the oxaloacetate is used
for gluconeogenesis.
If insufficient oxygen is available, the acid is broken down anaerobically, creating lactate in animals and ethanol in plants and microorganisms. Pyruvate from glycolysis is
converted by fermentation to lactate using the enzyme lactate dehydrogenase and the
coenzyme NADH in lactate fermentation, or to acetaldehyde and then to ethanol in alcoholic fermentation.
Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be
converted into carbohydrates via gluconeogenesis, to fatty acids or energy through
acetyl-CoA, to the amino acid alanine, and to ethanol. Therefore, it unites several key
metabolic processes.
Pyruvic acid supplies energy to cells through the citric acid cycle (also known as the
Krebs or TCA cycle) when oxygen is present (aerobic respiration), and alternatively ferments to produce lactate (in mammals) when oxygen is lacking (fermentation).
https://en.wikipedia.org/wiki/Pyruvic_acid
Index
Find Term
G-G
G-G
G-G
G-G
G-G
Chapter 2 - Structure & Function: Amino Acids
Chapter 4 - Catalysis: Basic Principles
Chapter 5 - Energy: Basics
Chapter 5 - Energy: Electron Transport & Oxidative Phosphorylation
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Citric Acid Cycle & Related Pathways
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Pyruvate Carboxylase
Pyruvate carboxylase (PC) is an enzyme of the ligase class that catalyzes the (depending on the species) irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
The enzyme is a mitochondrial protein containing a biotin prosthetic group, requiring
magnesium or manganese and acetyl CoA. It catalyzes the reaction that follows:
Pyruvate + Bicarbonate + ATP <=> Oxaloacetate + ADP
During gluconeogenesis, pyruvate carboxylase is involved in the synthesis of phosphoenolpyruvate (PEP) from pyruvate. Pyruvate is first converted by pyruvate carboxylase
to oxaloacetate (OAA) in the mitochondrion requiring hydrolysis of one molecule of
ATP. The OAA is then decarboxylated and simultaneously phosphorylated, which is
catalyzed by one of two isoforms of phosphoenolpyruvate carboxykinase (PEPCK) either in the cytosol or in the mitochondria to produce PEP. Under ordinary gluconeogenic conditions, OAA is converted into PEP by mitochondrial PEPCK. The resultant
PEP is then transported out of the mitochondrial matrix by an anion transporter carrier system, and converted into glucose by cytosolic gluconeogenic enzymes. However,
during starvation when cytosolic NADH concentration is low and mitochrondrial
NADH levels are high oxaloacetate can be used as a shuttle of reducing equivalents. As
such OAA is converted into malate by mitochondrial Malate dehydrogenase (MDH). After export into the cytosol, malate is converted back into OAA, with concomitant reduction of NAD+. OAA is subsequently converted to PEP which is available for gluconeogenesis in the cytosol along with the transported reducing equivalent NADH.
Very high levels of PC activity, together with high activities of other gluconeogenic enzymes including PEPCK, fructose-1,6-bisphosphatase and glucose-6-phosphatase in
liver and kidney cortex, suggest that a primary role of PC is to participate in gluconeogenesis in these organs. During fasting or starvation when endogenous glucose is required for certain tissues (brain, white blood cells and kidney medulla), expression of
PC and other gluconeogenic enzymes is elevated. Fasting promotes hepatic glucose production sustained by an increased pyruvate flux, and increases in PC activity and protein concentration. Diabetes similarly increases gluconeogenesis through enhanced uptake of substrate and increased flux through liver PC in mice and rats. Similarly to
other gluconeogenic enzymes, PC is positively regulated by glucagon and glucocorticoids while negatively regulated by insulin. Further supporting the key role of PC in gluconeogenesis, in dairy cattle, which have hexose absorption ability at adequate nutrition levels, PC and the associated gluconeogenic enzyme PEPCK are markedly elevated
during the transition to lactation in proposed support of lactose synthesis for milk production.
Aside from the role of PC in gluconeogenesis, PC serves an anaplerotic role (an enzyme
catalyzed reaction that can replenish the supply of intermediates in the citric acid cycle) for the tricarboxylic acid cycle (essential to provide oxaloacetate), when intermediates are removed for different biosynthetic purposes.
Pyruvate carboxylase uses a covalently attached biotin cofactor which is used to catalyze the ATP dependent carboxylation of pyruvate to oxaloacetate in two steps. Biotin
is initially carboxylated by ATP and bicarbonate. The carboxyl group is subsequently
transferred by carboxybiotin to a second active site where pyruvate is carboxylated to
generate oxaloacetate. The BCCP domain transfers the tethered cofactor between the
two remote active sites. The allosteric binding site in PC offers a target for modifiers of
activity that may be useful in the treatment of obesity or type II diabetes, and the
mechanistic insights gained from the complete structural description of RePC (R. etli)
permit detailed investigations into the individual catalytic and regulatory sites of the
enzyme.
https://en.wikipedia.org/wiki/Pyruvate_carboxylase
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Pyruvate Dehydrogenase
Pyruvate dehydrogenase is the first component enzyme of pyruvate dehydrogenase
complex (PDC) that catalyzes the decarboxylation of pyruvate to produce acetyl-CoA
and NADH. The pyruvate dehydrogenase complex contributes by a process called pyruvate decarboxylation . Acetyl-CoA may then be used in the citric acid cycle to carry out
cellular respiration, so pyruvate dehydrogenase contributes to linking the glycolysis
metabolic pathway to the citric acid cycle and releasing energy via NADH.
Pyruvate dehydrogenase (E1) performs the first two reactions within the pyruvate dehydrogenase complex (PDC): a decarboxylation of substrate 1 (pyruvate) and a reductive
acetylation of substrate 2 (lipoic acid). Lipoic acid is covalently bound to dihydrolipoamide acetyltransferase (E2), which is the second catalytic component enzyme of
PDC. The reaction catalyzed by pyruvate dehydrogenase (E1) is considered to be the
rate-limiting step for the pyruvate dehydrogenase complex (PDHc).
Phosphorylation of E1 by pyruvate dehydrogenase kinase (PDK) inactivates E1 and subsequently the entire complex. PDK is inhibited by dichloroacetic acid and pyruvate, resulting in a higher quantity of active, unphosphorylated PDH. Phosphorylaton is reversed by pyruvate dehydrogenase phosphatase, which is stimulated by insulin, PEP,
and AMP, but competitively inhibited by ATP, NADH, and Acetyl-CoA.
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase
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nase, or PDK; EC 2.7.11.2) is a kinase enzyme which acts to inactivate the enzy
vate dehydrogenase by phosphorylating it using ATP.
which pyruvate dehydrogenase is the first component. Both PDK and the pyru
which is then oxidized in the mitochondria to produce energy, in the citric acid
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phorylation of serine residues of E1 to inactivate the E1 component and inhibit the com
plex. Pyruvate dehydrogenase phosphatases catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases. Pyruvate dehydrogenase phosphatase is a heterodimer consisting of catalytic and regulatory subunits. Two catalytic subunits have been reported. One is predominantly expressed in skeletal muscle and another one is much more abundant in the liver. The
catalytic subunit, encoded by this gene, is the former, and belongs to the protein phosphatase 2C (PP2C) superfamily. Along with the pyruvate dehydrogenase complex and
pyruvate dehydrogenase kinases, this enzyme is located in the mitochondrial matrix.
https://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_phosphatase
Pyruvate Kinase
Pyruvate kinase is an enzyme involved in glycolysis. It catalyzes the transfer of a phosphate group from phosphoenolpyruvate (PEP) to ADP, yielding one molecule of pyruvate and one molecule of ATP.
Pyruvate kinase activity is regulated by
Its own substrate PEP and fructose 1,6-bisphosphate, an intermediate in glycolysis,
both of which enhance enzymatic activity. Thus, glycolysis is driven to operate faster
when more substrate is present.
ATP is a negative allosteric inhibitor. This accounts for parallel regulation with PFK 1.
It is not known whether citrate plays a role in negative allosteric inhibition, however
it is believed that acetyl-CoA does.
Alanine, a negative allosteric modulator
This protein may use the morpheein model of allosteric regulation.
Like PFK, pyruvate kinase is regulated both by allosteric effectors and by covalent
modification (phosphorylation). Pyruvate kinase is activated by F-1,6-BP in the liver, a
second example of feedforward stimulation. ATP and alanine (a biosynthetic product
of pyruvate) act as allosteric inhibitors of pyruvate kinase.
Liver pyruvate kinase is also regulated indirectly by epinephrine and glucagon,
through protein kinase A. This protein kinase phosphorylates liver pyruvate kinase to
deactivate it. Muscle pyruvate kinase is not inhibited by epinephrine activation of protein kinase A. Glucagon signals fasting (no glucose available). Thus, glycolysis is inhibited in the liver but unaffected in muscle when fasting. An increase in blood sugar
leads to secretion of insulin, which activates phosphoprotein phosphatase I, leading to
dephosphorylation and activation of pyruvate kinase. These controls prevent pyruvate
kinase from being active at the same time as the enzymes that catalyze the reverse reaction (pyruvate carboxylase and phosphoenolpyruvate carboxykinase), preventing a futile cycle.
https://en.wikipedia.org/wiki/Pyruvate_kinase
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Q-cycle
TheQ cycle(named for CoQ10) describes a series of reactions that describe how the sequential oxidation and reduction of the lipophilic electron carrier,Coenzyme
Q10(CoQ10), between theubiquinoland ubiquinoneforms, can result in the net pumping ofprotonsacross alipidbilayer (in the case of the mitochondria, the innermitochondrial membrane).
To summarize, the first reaction of Q cycle is:
CoQH2+ Cytochromec1(Fe3+) CoQ+ Cytochromec1(Fe2+) + 2 H+(intermembrane)
Then the second reaction of the cycle involves the reduction of the transient semiquinone by another electron to give CoQH2:
CoQH2+ CoQ+ cytochromec1(Fe3+) + 2 H+(matrix) CoQ + CoQH2+ cytochromec1(Fe2+) + 2 H+(intermembrane)
Combining the two equations, we have the overall reaction of Q cycle:
CoQH2+ 2 cytochromec1(Fe3+) + 2 H+(matrix) CoQ + 2 cytochromec1(Fe2+) + 4
H+(intermembrane).
https://en.wikipedia.org/wiki/Q_cycle
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Quaternary Structure
Inbiochemistry,quaternary structureis the number and arrangement of multiplefoldedprotein subunitsin amulti-subunit complex. It includes organizations from simpledimersto large homooligomers andcomplexeswith defined or variable numbers of
subunits.
The quaternary structure refers to the number and arrangement of the protein
subunits with respect to one another. Examples of proteins with quaternary structure
include hemoglobin, DNA polymerase, and ion channels.
Enzymes composed of subunits with diverse functions are sometimes called holoenzymes, in which some parts may be known as regulatory subunits and the functional
core is known as the catalytic subunit. Other assemblies referred to instead as multiprotein complexes also possess quaternary structure. Examples include nucleosomes and
microtubules. Changes in quaternary structure can occur through conformational
changes within individual subunits or through reorientation of the subunits relative to
each other. It is through such changes, which underlie cooperativity and allostery in
"multimeric" enzymes, that many proteins undergo regulation and perform their
physiological function.
The above definition follows a classical approach to biochemistry, established at times
when the distinction between a protein and a functional, proteinaceous unit was difficult to elucidate. More recently, people refer to protein-protein interaction when discussing quaternary structure of proteins and consider all assemblies of proteins as protein complexes.
https://en.wikipedia.org/wiki/Protein_quaternary_structure
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Quorum Sensing
Quorum sensingis a system of stimuli and response correlated topopulation density.
Many species ofbacteriause quorum sensing to coordinategene expressionaccording
to the density of their local population. In similar fashion, somesocial insectsuse quorum sensing to determine where to nest. In addition to its function in biological systems, quorum sensing has several useful applications for computing and robotics.
Quorum sensing can function as a decision-making process in anydecentralized system, as long as individual components have: (a) a means of assessing the number of
other components they interact with and (b) a standard response once a threshold
number of components is detected.
Bacteria use quorum sensing to coordinate certain behaviors such asbiofilm formation,virulence, andantibiotic resistance, based on the local density of the bacterial
population.
Bacteria that use quorum sensing constitutively produce and secrete certainsignaling
molecules(calledautoinducersorpheromones). These bacteria also have areceptorthat can specifically detect the signaling molecule (inducer). When the inducer
binds the receptor, it activatestranscriptionof certaingenes, including those for inducer synthesis. There is a low likelihood of a bacterium detecting its own secreted inducer. Thus, in order for gene transcription to be activated, the cell must encounter signaling molecules secreted by other cells in its environment.
https://en.wikipedia.org/wiki/Quorum_sensing
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R-group
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R-state
Most allosteric effects can be explained by the concerted MWC model put forth by
Monod, Wyman, and Changeux, or by the sequential model described by Koshland, Nemethy, and Filmer. Both postulate that enzyme subunits exist in one of two conformations, tensed (T) or relaxed (R), and that relaxed subunits bind substrate more readily
than those in the tense state. The two models differ most in their assumptions about
subunit interaction and the preexistence of both states.
https://en.wikipedia.org/wiki/Allosteric_regulation
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Ramachandran Plot
A Ramachandran plot (also known as a Ramachandran diagram or a [,] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles
against of amino acid residues in protein structure. The angle at the peptide bond
is 180, since the partial-double-bond character keeps the peptide planar. The figure at
below shows the allowed , backbone conformational regions. Because dihedral angle values are circular and 0 is the same as 360, the edges of the Ramachandran plot
"wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values
along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.
https://en.wikipedia.org/wiki/Ramachandran_plot
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Random Binding
One of the mechanisms enzymes that bind multiple substrates use is called
displacement. There are two types of sequential displacement. The first is
dom binding. In it, the order of binding of the substrates to the enzyme has
on the ability of the enzyme to function. The other mechanism is called ord
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Random Coils
RAS
RASis afamily of related proteinswhich is ubiquitously expressed in all cell lineages
and organs. All RAS protein family members belong to a class of protein calledsmall
GTPase, and are involved in transmitting signals within cells (cellularsignal transduction). RAS is the prototypical member of theRAS superfamilyof proteins, which are all
related in 3D structure and regulate diverse cell behaviors.
When RAS is 'switched on' by incoming signals, it subsequently switches on other proteins, which ultimately turn on genes involved incell growth,differentiationandsurvival. As a result, mutations inRASgenes can lead to the production of permanently
activated RAS proteins. This can cause unintended and overactive signaling inside the
cell, even in the absence of incoming signals.
Because these signals result in cell growth and division, overactive RAS signaling can
ultimately lead tocancer.The 3 RAS genes in humans (HRas,KRas, andNRas) are the
most commononcogenesin humancancer. Mutations that permanently activate RAS
are found in 20% to 25% of all human tumors and up to 90% in certain types of cancer
(e.g.,pancreatic cancer).For this reason, RAS inhibitors are being studied as a treatment for cancer, and other diseases with RAS overexpression.
https://en.wikipedia.org/wiki/Ras_subfamily
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Reactants
tants react with each other and form the reaction products. For example, hy
oxygen are reactants and react with each other and form the final product of
Reactants are part of the stoichiometric equation in contrast to, for example
A catalyst participates in the reaction but does not occur in the stoichiometr
tion.
https://en.wikipedia.org/wiki/Reagent
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Reaction Center
co-factors that together execute the primary energy conversion reactions ofphot
ated is then used to reduce a chain of nearbyelectron acceptors, which have subs
ergy of photons to the storage of that energy by the production of chemical bond
https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre
Reaction Centers
co-factors that together execute the primary energy conversion reactions ofpho
ated is then used to reduce a chain of nearbyelectron acceptors, which have sub
ergy of photons to the storage of that energy by the production of chemical bond
https://en.wikipedia.org/wiki/Photosynthetic_reaction_centre
damage of DNA
https://en.wikipedia.org/wiki/Reactive_oxygen_species
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RecA
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A
RecA structural and functional homolog has been found in every species in which one
has been seriously sought and serves as an archetype for this class of homologous DNA
repair proteins. The homologous protein is called RAD51 in eukaryotes and RadA in archaea.
RecA has multiple activities, all related to DNA repair. In the bacterial SOS response, it
has a co-protease function in the autocatalytic cleavage of the LexA repressor and the
repressor.
RecA's association with DNA major is based on its central role in homologous recombination. The RecA protein binds strongly and in long clusters to ssDNA to form a nucleoprotein filament. The protein has more than one DNA binding site, and thus can hold a
single strand and double strand together. This feature makes it possible to catalyze a
DNA synapsis reaction between a DNA double helix and a complementary region of single stranded DNA. The RecA-ssDNA filament searches for sequence similarity along
the dsDNA. The search process induces stretching of the DNA duplex, which enhances
sequence complimentarity recognition (a mechanism termed conformational proofreading). The reaction initiates the exchange of strands between two recombining DNA
double helices. After the synapsis event, in the heteroduplex region a process called
branch migration begins. In branch migration an unpaired region of one of the single
strands displaces a paired region of the other single strand, moving the branch point
without changing the total number of base pairs. Spontaneous branch migration can
occur, however as it generally proceeds equally in both directions it is unlikely to complete recombination efficiently. The RecA protein catalyzes unidirectional branch migration and by doing so makes it possible to complete recombination, producing a region of heteroduplex DNA that is thousands of base pairs long.
Since it is a DNA-dependent ATPase, RecA contains an additional site for binding and
hydrolyzing ATP. RecA associates more tightly with DNA when it has ATP bound than
when it has ADP bound.
https://en.wikipedia.org/wiki/RecA
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Receptor Protein
In biochemistry and pharmacology, a receptor is a protein-molecule that receives
chemical-signals from outside a cell. When such chemical-signals bind to a receptor,
they cause some form of cellular/tissue-response, e.g. a change in the electrical-activity
of a cell. In this sense, a receptor is a protein-molecule that recognizes and responds to
endogenous-chemical signals, e.g. an acetylcholine-receptor recognizes and responds
to its endogenous-ligand, acetylcholine. However, sometimes in pharmacology, the
term is also used to include other proteins that are drug-targets, such as enzymes,
transporters and ion-channels.
Receptor-proteins are embedded in all cells' plasmatic-membranes, facing
extracellular-(cell surface receptors), cytoplasmic (cytoplasmic-receptors), or in the nucleus (nuclear receptors). A molecule that binds to a receptor is called a ligand, and can
be a peptide (short-protein) or another small molecule such as a neurotransmitter, hormone, pharmaceutical-drug, toxin, or parts of the outside of a virus or microbe. The
endogenously designated-molecule for a particular receptor is referred to as its
endogenous-ligand. For example, the endogenous-ligand for the nicotinicacetylcholine receptor is acetylcholine but the receptor can also be activated by nicotine and blocked by curare.
Each receptor is linked to a specific cellular-biochemical pathway. While numerous receptors are found in most cells, each receptor will only bind with ligands of a particular
structure, much like how locks will only accept specifically shaped-keys. When a ligand
binds to its corresponding receptor, it activates or inhibits the receptor's associatedbiochemical pathway.
https://en.wikipedia.org/wiki/Receptor_(biochemistry)
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https://en.wikipedia.org/wiki/Receptor_tyrosine_kinase
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Receptor-mediated Endocytosis
Receptor-mediated endocytosis(RME), also calledclathrin-mediated endocytosis, is a
process by which cells absorb metabolites, hormones, other proteins - and in some
cases viruses - (endocytosis) by the inward budding ofplasma membranevesicles containing proteins with receptor sites specific to the molecules being absorbed.
Clathrin-mediated endocytosis of many receptor types begins with ligand binding and
receptor activation. The ligand and receptor (often bound to an adaptor protein) then
diffuse through the plasma membrane until captured by a preformed or forming
clathrin-coated pit.A mature pit will pinch off from the plasma membrane forming a
clathrin-coated vesicle that then uncoats and typically fuses to an earlyendosome.
Once fused the endocytosed cargo (receptor and/or ligand) can then be sorted tolysosomal, recycling, or other trafficking pathways.
The functions of receptor-mediated endocytosis are diverse. The process is widely used
for the specific uptake of certain substances required by the cell (examples include
LDL via the LDL receptor or iron via transferrin). The role of receptor-mediated endocytosis is also well recognized in the downregulation of transmembrane signal transduction. The activated receptor becomes internalized and is transported to late endosomes and lysosomes for degradation. However, receptor-mediated endocytosis is also
actively implicated in transducing signals from the cell periphery to the nucleus. This
became apparent when it was found that the association and formation of specific signaling complexes is required for the effective signaling of hormones (e.g. EGF). Additionally it has been proposed that the directed transport of active signaling complexes
to the nucleus might be required to enable signaling as random diffusion is too slow
and mechanisms permanently down-regulating incoming signals are strong enough to
shut down signaling completely without additional signal-transducing mechanisms.
https://en.wikipedia.org/wiki/Receptor-mediated_endocytosis
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Recessive Trait
Dominance in genetics is a relationship between alleles of one gene, in which the effect
on phenotype of one allele masks the contribution of a second allele at the same locus.
The first allele is dominant and the second allele is recessive. For genes on an autosome (any chromosome other than a sex chromosome), the alleles and their associated
traits are autosomal dominant or autosomal recessive. Dominance is a key concept in
Mendelian inheritance and classical genetics. Often the dominant allele codes for a
functional protein whereas the recessive allele does not.
A classic example of dominance is the inheritance of seed shape in peas. Peas may be
round, associated with allele R or wrinkled, associated with allele r. In this case, three
combinations of alleles (genotypes) are possible: RR, Rr, and rr. The RR individuals
have round peas and the rr individuals have wrinkled peas. In Rr individuals the R allele masks the presence of the r allele, so these individuals also have round peas. Thus,
allele R is dominant to allele r, and allele r is recessive to allele R. This use of upper
case letters for dominant alleles and lower case ones for recessive alleles is a widely followed convention.
More generally, where a gene exists in two allelic versions (designated A and a), three
combinations of alleles are possible: AA, Aa, and aa. If AA and aa individuals (homozygotes) show different forms of some trait (phenotypes), and Aa individuals (heterozygotes) show the same phenotype as AA individuals, then allele A is said to dominate or
be dominant to or show dominance to allele a, and a is said to be recessive to A.
Dominance is not inherent to an allele. It is a relationship between alleles; one allele
can be dominant over a second allele, recessive to a third allele, and codominant to a
fourth. Also, an allele may be dominant for a particular aspect of phenotype but not for
other aspects influenced by the same gene. Dominance differs from epistasis, a relationship in which an allele of one gene affects the expression of another allele at a different
gene.
https://en.wikipedia.org/wiki/Dominance_(genetics)
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Reciprocal Regulation
Reciprocal regulation is a coordinated means of simultaneously controlling metabolic
pathways that do opposite things. In reciprocal regulation, a single molecule (allosteric regulation) or a single covalent modification (phosphorylation/
dephosphorylation, for example) has opposite effects on the different pathways.
For example, in glycolysis, the enzyme known as phosphofructokinase (PFK-1) is allosterically activated by AMP and a molecule known as F2,6BP. The corresponding enzyme from gluconeogenesis catalyzing a reversal of the glycolysis reaction is known as
F1,6BPase. F1,6BPase is inhibited by both AMP and F2,6BP.
In glycogen metabolism, the enzymes phosphorylase kinase and glycogen phosphorylase catalyze reactions important for the breakdown of glycogen. The enzyme glycogen
synthase catalyzes the synthesis of glycogen. Each of these enzymes is at least partly
regulated by attachment and removal of phosphate.
Phosphorylation of phosphorylase kinase and glycogen phosphorylase has the effect of
making them more active, whereas phosphorylation of glycogen synthase makes it less
active. Conversely, dephosphorylation has the reverse effects on these enzymes - phosphorylase kinase and glycogen phosphorylase become less active and glycogen synthase becomes more active.
The advantage of reciprocal regulation schemes is that they are very efficient. It
doesnt require separate molecules or separate treatments to control two pathways simultaneously. Further, its simplicity ensures that when one pathway is turned on, the
other is turned off.
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Recombinant DNA
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in
the genome. Recombinant DNA is possible because DNA molecules from all organisms
share the same chemical structure. They differ only in the nucleotide sequence within
that identical overall structure.
Recombinant DNA is the general name for a piece of DNA that has been created by the
combination of at least two strands. Recombinant DNA molecules are sometimes
called chimeric DNA, because they can be made of material from two different species,
like the mythical chimera. R-DNA technology uses palindromic sequences and leads to
the production of sticky and blunt ends.
The DNA sequences used in the construction of recombinant DNA molecules can originate from any species. For example, plant DNA may be joined to bacterial DNA, or human DNA may be joined with fungal DNA. In addition, DNA sequences that do not occur anywhere in nature may be created by the chemical synthesis of DNA, and incorporated into recombinant molecules. Using recombinant DNA technology and synthetic
DNA, literally any DNA sequence may be created and introduced into any of a very
wide range of living organisms.
Proteins that can result from the expression of recombinant DNA within living cells are
termed recombinant proteins. When recombinant DNA encoding a protein is introduced into a host organism, the recombinant protein is not necessarily produced. Expression of foreign proteins requires the use of specialized expression vectors and often necessitates significant restructuring by foreign coding sequences.
Recombinant DNA differs from genetic recombination in that the former results from
artificial methods in the test tube, while the latter is a normal biological process that
results in the remixing of existing DNA sequences in essentially all organisms.
https://en.wikipedia.org/wiki/Recombinant_DNA
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Recombinant Protein
A protein that can result from the expression of recombinant DNA within living
Following transplantation into the host organism, a foreign DNA contained wit
combinant DNA construct may or may not be expressed. That is, the DNA may
structuring the gene to include sequences that are required for producing an mR
molecule that can be used by the host's translational apparatus (e.g. promoter,
tein soluble, direct the recombinant protein to the proper cellular or extracellul
tion, and stabilize the protein from degradation.
https://en.wikipedia.org/wiki/Recombinant_DNA
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Recombination
Genetic recombination is the production of offspring with combinations of traits that
differ from those found in either parent. In eukaryotes, genetic recombination during
meiosis can lead to a novel set of genetic information that can be passed on from the
parents to the offspring. Most recombination is naturally occurring. During meiosis in
eukaryotes, genetic recombination involves the pairing of homologous chromosomes.
This may be followed by information exchange between the chromosomes.
Recombination may also occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case,
new combinations of alleles are not produced since the sister chromosomes are usually
identical. In meiosis and mitosis, recombination occurs between similar molecules of
DNA (homologs). In meiosis, non-sister homologous chromosomes pair with each
other so that recombination characteristically occurs between non-sister homologues.
In both meiotic and mitotic cells, recombination between homologous chromosomes is
a common mechanism used in DNA repair.
Genetic recombination and recombinational DNA repair also occurs in bacteria and archaea, which use asexual reproduction.
https://en.wikipedia.org/wiki/Genetic_recombination
Reduced
A term that refers to a chemical species that has gained electrons in a redox reaction.
Reduction is the part of a chemical reaction that involves the gaining of electrons. It refers to the side that accepts electrons. When iron reacts with oxygen it forms a chemical called rust. In that example, the iron is oxidized and the oxygen is reduced.
Biochemistry oxidation - reduction (redox) reactions usually involve electron carriers.
For example, in the reaction catalyzed by lactate dehydrogenase,
NADH + Pyruvate
Lactate + NAD+
pyruvate gets reduced by electrons and protons from NADH and NADH gets oxidized
as it give up its electrons and proton. Reduction is the opposite of oxidation. A reduction reaction always comes together with an oxidation reaction.
https://simple.wikipedia.org/wiki/Reduction_(chemistry)
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Reduction
Reduction is the part of a chemical reaction that involves the gaining of electrons. It refers to the side that accepts electrons. When iron reacts with oxygen it forms a chemical called rust. In that example, the iron is oxidized and the oxygen is reduced.
Biochemistry oxidation - reduction (redox) reactions usually involve electron carriers.
For example, in the reaction catalyzed by lactate dehydrogenase,
NADH + Pyruvate
Lactate + NAD+
pyruvate gets reduced by electrons and protons from NADH and NADH gets oxidized
as it give up its electrons and proton. Reduction is the opposite of oxidation. A reduction reaction always comes together with an oxidation reaction.
https://simple.wikipedia.org/wiki/Reduction_(chemistry)
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Reduction Potential
A measure of the tendency of a chemical species to acquire electrons and thereby be reduced. Reduction potential is measured in volts (V), or millivolts (mV). Each species
has its own intrinsic reduction potential. The more positive the potential, the greater
the species' affinity for electrons and tendency to be reduced.
In aqueous solutions, reduction potential is a measure of the tendency of the solution
to either gain or lose electrons when it is subject to change by introduction of a new species. A solution with a higher (more positive) reduction potential than the new species
will have a tendency to gain electrons from the new species (i.e. to be reduced by oxidizing the new species) and a solution with a lower (more negative) reduction potential
will have a tendency to lose electrons to the new species (i.e. to be oxidized by reducing
the new species). Because the absolute potentials are difficult to accurately measure,
reduction potentials are defined relative to a reference electrode. Reduction potentials
of aqueous solutions are determined by measuring the potential difference between an
inert sensing electrode in contact with the solution and a stable reference electrode connected to the solution by a salt bridge.
The sensing electrode acts as a platform for electron transfer to or from the reference
half cell. It is typically platinum, although gold and graphite can be used either. The reference half cell consists of a redox standard of known potential. The standard hydrogen electrode (SHE) is the reference from which all standard redox potentials are determined and has been assigned an arbitrary half cell potential of 0.0 mV. However, it is
fragile and impractical for routine laboratory use. Therefore, other more stable reference electrodes such as silver chloride and saturated calomel (SCE) are commonly
used because of their more reliable performance.
Although measurement of the reduction potential in aqueous solutions is relatively
straightforward, many factors limit its interpretation, such as effects of solution temperature and pH, irreversible reactions, slow electrode kinetics, non-equilibrium, presence of multiple redox couples, electrode poisoning, small exchange currents and inert
redox couples. Consequently, practical measurements seldom correlate with calculated
values. Nevertheless, reduction potential measurement has proven useful as an analytical tool in monitoring changes in a system rather than determining their absolute value
(e.g. process control and titrations).
https://en.wikipedia.org/wiki/Reduction_potential
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Regulatory Sequences
A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation
of gene expression is an essential feature of all living organisms and viruses.
In DNA, regulation of gene expression normally happens at the level of RNA biosynthesis (transcription), and is accomplished through the sequence-specific binding of proteins (transcription factors) that activate or inhibit transcription. Transcription factors
may act as activators, repressors, or both. Repressors often act by preventing RNA polymerase from forming a productive complex with the transcriptional initiation region
(promoter), while activators facilitate formation of a productive complex. Furthermore, DNA motifs have been shown to be predictive of epigenomic modifications, suggesting that transcription factors play a role in regulating the epigenome.
In RNA, regulation may occur at the level of protein biosynthesis (translation), RNA
cleavage, RNA splicing, or transcriptional termination. Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to
control mRNA biogenesis or translation. A variety of biological molecules may bind to
the RNA to accomplish this regulation, including proteins (e.g. translational repressors
and splicing factors), other RNA molecules (e.g. miRNA) and small molecules, in the
case of riboswitches.
https://en.wikipedia.org/wiki/Regulatory_sequence
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Regulatory Subunits
A single protein molecule that assembles (or "coassembles") with other pro
cules to facilitate or inhibit their activity. The enzyme ATCase, for example
six catalytic subunits and six regulatory subunits. The regulatory subunits c
ATP or CTP. If they bind ATP, the regulatory subunits convert the enzyme
state, activating it. If they bind CTP, the regulatory subunits convert the en
the T-state, inactivating it.
https://en.wikipedia.org/wiki/Protein_subunit
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Release Factor
A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence.
During translation of mRNA, most codons are recognized by "charged" tRNA molecules, called aminoacyl-tRNAs because they are adhered to specific amino acids corresponding to each tRNA's anticodon.
In the standard genetic code, there are three mRNA stop codons: UAG ("amber"), UAA
("ochre"), and UGA ("opal" or "umber").
Although these stop codons are triplets just like ordinary codons, they are not decoded
by tRNAs. It was discovered by Mario Capecchi in 1967 that, instead, tRNAs do not ordinarily recognize stop codons at all, and that what he named "release factor" was not a
tRNA molecule but a protein. Later, it was demonstrated that different release factors
recognize different stop codons.
Prokaryotic translation termination is mediated by three prokaryotic release factors:
RF1, RF2, and RF3.
RF1 recognizes the termination codons UAA and UAG
RF2 recognizes UAA and UGA
RF3 is a GTP-binding protein that leads to the dissociation of RF1/RF2 after peptide
release
Likewise, eukaryotic translation termination involves two eukaryotic release factors:
eRF1 and eRF3.
eRF1 recognizes all three termination codons
eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed
polypeptide
https://en.wikipedia.org/wiki/Release_factor
Release factors
A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence.
During translation of mRNA, most codons are recognized by "charged" tRNA molecules, called aminoacyl-tRNAs because they are adhered to specific amino acids corresponding to each tRNA's anticodon.
In the standard genetic code, there are three mRNA stop codons: UAG ("amber"), UAA
("ochre"), and UGA ("opal" or "umber").
Although these stop codons are triplets just like ordinary codons, they are not decoded
by tRNAs. It was discovered by Mario Capecchi in 1967 that, instead, tRNAs do not ordinarily recognize stop codons at all, and that what he named "release factor" was not a
tRNA molecule but a protein. Later, it was demonstrated that different release factors
recognize different stop codons.
Prokaryotic translation termination is mediated by three prokaryotic release factors:
RF1, RF2, and RF3.
RF1 recognizes the termination codons UAA and UAG
RF2 recognizes UAA and UGA
RF3 is a GTP-binding protein that leads to the dissociation of RF1/RF2 after peptide
release
Likewise, eukaryotic translation termination involves two eukaryotic release factors:
eRF1 and eRF3.
eRF1 recognizes all three termination codons
eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed
polypeptide
https://en.wikipedia.org/wiki/Release_factor
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Renaturation
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Repetitive Sequences
Repeated sequences (aka. repetitive elements, or repeats) are patterns of nucleic acids
(DNA or RNA) that occur in multiple copies throughout the genome. Repetitive DNA
was first detected because of its rapid reassociation kinetics.
In many organisms, a significant fraction of the genomic DNA is highly repetitive, with
over two-thirds of the sequence consisting of repetitive elements in human.
Debates regarding the potential in vivo functions of these elements have been long
standing. Controversial references to junk or selfish DNA were put forward early on,
implying that repetitive DNA segments are remainders from past evolution or autonomous self-replicating sequences hacking the cell machinery to proliferate. Repetitive
elements found in eukaryotic genomes fall into different classes, depending on their
mode of multiplication and/or structure. The disposition of repetitive elements consists either in arrays of tandemly repeated sequences, or in repeats dispersed throughout the genome. Originally discovered by Barbara McClintock, dispersed repeats have
been increasingly recognized as a potential source of genetic variation and regulation.
Together with these regulatory roles, a structural role of repeated DNA in shaping the
3D folding of genomes has also been proposed. This hypothesis is only supported by a
limited set of experimental evidence. For instance in human, mouse and fly, several
classes of repetitive elements present a high tendency for co-localization within the nuclear space, suggesting that DNA repeats positions can be used by the cell as a genome
folding map.
https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)
Replication Fork
The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA
strands together. The resulting structure has two branching "prongs", each one made
up of a single strand of DNA. These two strands serve as the template for the leading
and lagging strands, which will be created as DNA polymerase matches complementary nucleotides to the templates. The templates may be properly referred to as the
leading strand template and the lagging strand template.
DNA is always synthesized in the 5' to 3' direction. Since the leading and lagging strand
templates are oriented in opposite directions at the replication fork, a major issue is
how to achieve synthesis of nascent (new) lagging strand DNA, whose direction of synthesis is opposite to the direction of the growing replication fork.
Leading Strand
The leading strand is the strand of nascent DNA which is being synthesized in the
same direction as the growing replication fork. A polymerase "reads" the leading
strand template and adds complementary nucleotides to the nascent leading strand on
a continuous basis. The polymerase involved in leading strand synthesis is DNA polymerase III (DNA Pol III) in prokaryotes. In eukaryotes, leading strand synthesis is
thought to be conducted by Pol , however this view has been recently challenged, suggesting a role for Pol .
Lagging Strand
The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading
strand.The lagging strand is synthesized in short, separated segments. On the lagging
strand template, a primase "reads" the template DNA and initiates synthesis of a short
complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA,
and the fragments of DNA are joined together by DNA ligase.
Dynamics at the Replication Fork
As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate.
This process results in a build-up of twists in the DNA ahead. This build-up forms a torsional resistance that would eventually halt the progress of the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix. Topoisomerases (including DNA gyrase) achieve this by adding negative supercoils to the DNA helix. Bare
single-stranded DNA tends to fold back on itself forming secondary structures. These
structures can interfere with the movement of DNA polymerase. To prevent this,
single-strand binding proteins bind to the DNA until a second strand is synthesized,
preventing secondary structure formation.
https://en.wikipedia.org/wiki/DNA_replication#Replication_fork
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Repolarization
Repolarization refers to a cells response after its ion gradient has been altered - a process called depolarizatio. Depolarization, in biology, refers to a sudden change within a
cell, during which the cell undergoes a dramatic electrical change. Most cells, especially those that compose the tissues of highly organized animals, typically maintain an
internal environment that is negatively charged compared to the cell's surrounding environment. This difference in charge is called the cell's membrane potential. In the
process of depolarization, the negative internal charge of the cell becomes positive for
a very brief time. This shift from a negative to a positive internal cellular environment
allows for the transmission of electrical impulses both within a cell and, in certain instances, between cells. This communicative function of depolarization is essential to
the function of many cells, communication between cells, and the overall function of
an organism.
After a cell has been depolarized, it undergoes one final change in internal charge. Following depolarization, the voltage gated sodium ion channels that had been open while
the cell was undergoing depolarization close again. The increased positive charge
within the cell now causes the potassium channels to open. Potassium ions (K+) begin
to move down the electrochemical gradient (in favor of the concentration gradient and
the newly established electrical gradient). As potassium moves out of the cell the potential within the cell plummets and approaches its resting potential once more. The sodium potassium pump works continuously throughout this process.
https://en.wikipedia.org/wiki/Depolarization
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Repressors
In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the
expression of one or more genes by binding to the operator or associated silencers. A
DNA-binding repressor blocks the attachment of RNA polymerase to the promoter,
thus preventing transcription of the genes into messenger RNA. An RNA-binding repressor binds to the mRNA and prevents translation of the mRNA into protein. This
blocking of expression is called repression.
If an inducer, a molecule that initiates the gene expression, is present, then it can interact with the repressor protein and detach it from the operator. RNA polymerase then
can transcribe the message (expressing the gene). A corepressor is a molecule that can
bind to repressor and make it bind to the operator tightly, which decreases transcription. A repressor that binds with a corepressor is termed an aporepressor or inactive
repressor. One type of aporepressor is the trp repressor, an important metabolic protein in bacteria.
The above mechanism of repression is a type of a feedback mechanism because it only
allows transcription to occur if a certain condition is present: the presence of specific
inducer(s). Within the Eukaryotic genome are regions of DNA known as silencers.
These DNA sequences bind to repressors to partially or fully repress the expression of
a gene. Silencers can be located several bases upstream or downstream from the actual
promoter of the gene. Repressors can also have two binding sites: one for the silencer
region and one for the promoter. This causes chromosome looping, allowing the promoter region and the silencer region to come to close proximity.
https://en.wikipedia.org/wiki/Repressor
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Resistin
Resistin also known as adipose tissue-specific secretory factor (ADSF) or C/EBPepsilon-regulated myeloid-specific secreted cysteine-rich protein (XCP1) is a cysteinerich adipose-derived peptide hormone that in humans is encoded by the RETN gene.
Resistin is an adipose-derived hormone (similar to a cytokine) whose physiologic role
has been the subject of much controversy regarding its involvement with obesity and
type II diabetes mellitus (T2DM). Resistin has been shown to cause "high levels of
'bad' cholesterol (low-density lipoprotein or LDL), increasing the risk of heart disease
[...] resistin increases the production of LDL in human liver cells and also degrades
LDL receptors in the liver. As a result, the liver is less able to clear 'bad' cholesterol
from the body. Resistin accelerates the accumulation of LDL in arteries, increasing the
risk of heart disease. [...] resistin adversely impacts the effects of statins, the main
cholesterol-reducing drug used in the treatment and prevention of cardiovascular disease."
https://en.wikipedia.org/wiki/Resistin
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Resonant Structure
within certain molecules or polyatomic ions where the bonding cannot be exp
one single Lewis structure. A molecule or ion with such delocalized electrons
sented by several contributing structures (also called resonance structures or
structures).
https://en.wikipedia.org/wiki/Resonance_(chemistry)
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Resonant Structures
one single Lewis structure. A molecule or ion with such delocalized electron
https://en.wikipedia.org/wiki/Resonance_(chemistry)
Respirasome
Modern biological research has revealed strong evidence that the enzymes of the mitochondrial respiratory chain assemble into larger, supramolecular structures called respirasomes or supercomplexes, instead of the traditional fluid model of discrete enzymes dispersed in the inner mitochondrial membrane. These supercomplexes are
functionally active and necessary for forming stable respiratory complexes.
The most common supercomplexes observed are Complex I/III, Complex I/III/IV, and
Complex III/IV. Most of Complex II is found in a free-floating form in both plant and
animal mitochondria. Complex V can be found co-migrating as a dimer with other supercomplexes, but scarcely as part of the supercomplex unit.
Supercomplex assembly appears to be dynamic and respiratory enzymes are able to alternate between participating in large respirasomes and existing in a free state. It is
not known what triggers changes in complex assembly, but research has revealed that
the formation of supercomplexes is heavily dependent upon the lipid composition of
the mitochondrial membrane, and in particular requires the presence of cardiolipin, a
unique mitochondrial lipid. In yeast mitochondria lacking cardiolipin, the number of
enzymes forming respiratory supercomplexes was significantly reduced.
Another hypothesis for respirasome formation is that membrane potential may initiate
changes in the electrostatic/hydrophobic interactions mediating the assembly/
disassembly of supercomplexes.
https://en.wikipedia.org/wiki/Respirasome
Respiration
concerns the bulk flow and transport of metabolites between the organism a
ternal environment.
https://en.wikipedia.org/wiki/Respiration_(physiology)
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Respiratory Control
Control of ventilation refers to the physiological mechanisms involved in the control of
physiologic ventilation, which refers to the movement of air into and out of the lungs.
Ventilation facilitates respiration. Respiration refers to the uptake of oxygen and the
removal of carbon dioxide. Under most conditions, the partial pressure of carbon dioxide controls the rate of respiration.
At the molecular level, respiratory control relates to the interlinks between the electron
transport system and oxidative phosphorylation. Normally these systems are tightly
coupled, meaning that each depends on the other and stopping one stops both. Because of this interdependence, when ATP is not being used, oxidative phosphorylation
slows, causing electron transport to slow. Since electron transport is linked to oxygen
consumption, the breathing rate slows. When exercise begins, ATP is used, speeding
up oxidative phosphorylation and electron transport. This causes oxygen consumption
to increase and you start to breath more rapidly and deeply.
https://en.wikipedia.org/wiki/Control_of_ventilation
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Resting Potential
The relatively static membrane potential of quiescent cells is called the resting membrane potential (or resting voltage), as opposed to the specific dynamic electrochemical
phenomena called action potential and graded membrane potential.
Apart from the latter two, which occur in excitable cells (neurons, muscles, and some
secretory cells in glands), membrane voltage in the majority of non-excitable cells can
also undergo changes in response to environmental or intracellular stimuli. In principle, there is no difference between resting membrane potential and dynamic voltage
changes like action potential from a biophysical point of view: all these phenomena are
caused by specific changes in membrane permeabilities for potassium, sodium, calcium, and chloride ions, which in turn result from concerted changes in functional activity of various ion channels, ion transporters, and exchangers. Conventionally, resting membrane potential can be defined as a relatively stable, ground value of transmembrane voltage in animal and plant cells.
Any voltage is a difference in electric potential between two pointsfor example, the
separation of positive and negative electric charges on opposite sides of a resistive barrier. The typical resting membrane potential of a cell arises from the separation of potassium ions from intracellular, relatively immobile anions across the membrane of the
cell. Because the membrane permeability for potassium is much higher than that for
other ions (disregarding voltage-gated channels at this stage), and because of the
strong chemical gradient for potassium, potassium ions flow from the cytosol into the
extracellular space carrying out positive charge, until their movement is balanced by
build-up of negative charge on the inner surface of the membrane. Again, because of
the high relative permeability for potassium, the resulting membrane potential is almost always close to the potassium reversal potential. But in order for this process to
occur, a concentration gradient of potassium ions must first be set up. This work is
done by the ion pumps/transporters and/or exchangers and generally is powered by
ATP.
In the case of the resting membrane potential across an animal cell's plasma membrane, potassium (and sodium) gradients are established by the Na+/K+-ATPase
(sodium-potassium pump) which transports 2 potassium ions inside and 3 sodium
ions outside at the cost of 1 ATP molecule.
https://en.wikipedia.org/wiki/Resting_potential
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Restriction Enzyme
A restriction enzyme or restriction endonuclease is an enzyme that cuts DNA at or near
specific recognition nucleotide sequences known as restriction sites. Restriction enzymes are commonly classified into three types, which differ in their structure and
whether they cut their DNA substrate at their recognition site, or if the recognition and
cleavage sites are separate from one another. To cut DNA, all restriction enzymes make
two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the
DNA double helix.
These enzymes are found in bacteria and archaea and provide a defense mechanism
against invading viruses. Inside a prokaryote, the restriction enzymes selectively cut up
foreign DNA in a process called restriction. Meanwhile, host DNA is protected by a
modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and
blocks cleavage. Together, these two processes form the restriction modification system.
Restriction enzymes recognize a specific sequence of nucleotides and produce a
double-stranded cut in the DNA. The recognition sequences can also be classified by
the number of bases in its recognition site, usually between 4 and 8 bases, and the
amount of bases in the sequence will determine how often the site will appear by
chance in any given genome, e.g., a 4-base pair sequence would theoretically occur
once every 44 or 256bp, 6 bases, 46 or 4,096bp, and 8 bases would be 48 or 65,536bp.
https://en.wikipedia.org/wiki/Restriction_enzyme
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Techniques
Techniques
Techniques
Techniques
Techniques
Techniques
Techniques
Techniques
Resveratrol
Resveratrol (3,5,4-trihydroxy-trans-stilbene) is a stilbenoid, a type of natural phenol,
and a phytoalexin produced naturally by several plants in response to injury or when
the plant is under attack by pathogens such as bacteria or fungi. Food sources of resveratrol include the skin of grapes, blueberries, raspberries, and mulberries.
Although in vitro studies indicate resveratrol activates sirtuin 1 and PGC-1, and affects functioning of mitochondria, other research disputes this effect. In cells treated
with resveratrol, an increase is observed in the action of MnSOD (SOD2) which reduces superoxide, implying resistance to mitochondrial dysfunction, permeability transition, and apoptotic death in various diseases. Resveratrol has also been found to act
as an agonist of the GPER (GPR30).
https://en.wikipedia.org/wiki/Resveratrol
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Retinal
Retinal is also known as retinaldehyde. It was originally called retinene, and renamed
afterwards it was discovered to be vitamin A aldehyde. Retinal is one of the many
forms of vitamin A (the number of which varies from species to species). Retinal is a
polyene chromophore, bound to proteins called opsins, and is the chemical basis of animal vision. Retinal allows certain microorganisms to convert light into metabolic energy.
Structurally, all retinoids also possess a -ionone ring and a polyunsaturated side
chain, with either an alcohol, aldehyde, a carboxylic acid group or an ester group. The
side chain is composed of four isoprenoid units, with a series of conjugated double
bonds which may exist in trans- or cis-configuration.
Vision begins with the photoisomerization of retinal. When the 11-cis-retinal chromophore absorbs a photon it isomerizes from the 11-cis state to the all-trans state. The absorbance spectrum of the chromophore depends on its interactions with the opsin protein to which it is bound. Different opsins produce different absorbance spectra.
Vertebrate animals ingest retinal directly from meat, or they produce retinal from carotenoids, either from one of two carotenes (-carotene, -carotene) or from cryptoxanthin, a type of xanthophyll. These carotenoids must be obtained from plants
or other photosynthetic organisms. No other carotenoids can be converted by animals
to retinal, and some carnivores cannot convert any carotenoids at all. The other main
forms of vitamin A, retinol, and a partially active form, retinoic acid, may both be produced from retinal.
Living organisms produce retinal (RAL) by irreversible oxidative cleavage of carotenoids. For example
-carotene + O2 2 Retinal
catalyzed by a -carotene 15,15'-monooxygenase or a -carotene 15,15'-dioxygenase.
Just as carotenoids are the precursors of retinal, retinal is the precursor of the other
forms of vitamin A. Retinal is interconvertible with retinol (ROL), the transport and
storage form of vitamin A
Retinal + NADPH + H+ Retinol + NADP+
Retinol + NAD+ Retinal + NADH + H+
catalyzed by retinol dehydrogenases (RDHs) and alcohol dehydrogenases (ADHs). Retinol is called vitamin A alcohol, or more often, simply vitamin A. Retinal can also be oxidized to retinoic acid (RA)
retinal + NAD+ + H2O Retinoic acid + NADH + H+ (catalyzed by RALDH)
retinal + O2 + H2O Retinoic acid + H2O2 (catalyzed by retinal oxidase)
Retinoic acid, sometimes called vitamin A acid, is an important signaling molecule and
hormone in vertebrate animals.
https://en.wikipedia.org/wiki/Retinal
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Retinoic Acid
Retinoic acid is a metabolite of vitamin A (retinol) that mediates the functions of vitamin A required for growth and development. Retinoic acid is required in chordate animals, which includes all higher animals from fish to humans. During early embryonic
development, retinoic acid generated in a specific region of the embryo helps determine position along the embryonic anterior/posterior axis by serving as an intercellular signaling molecule that guides development of the posterior portion of the embryo.
It acts through Hox genes, which ultimately control anterior/posterior patterning in
early developmental stages.
The key role of retinoic acid in embryonic development mediates the high teratogenicity of retinoid pharmaceuticals, such as isotretinoin used for treatment of cancer and
acne. Oral megadoses of pre-formed vitamin A (retinyl palmitate), and retinoic acid itself, also have teratogenic potential by this same mechanism.
Retinoic acid acts by binding to the retinoic acid receptor (RAR), which is bound to
DNA as a heterodimer with the retinoid X receptor (RXR) in regions called retinoic
acid response elements (RAREs). Binding of the retinoic acid ligand to RAR alters the
conformation of the RAR, which affects the binding of other proteins that either induce
or repress transcription of a nearby gene (including Hox genes and several other target
genes). Retinoic acid receptors mediate transcription of different sets of genes controlling differentiation of a variety of cell types, thus the target genes regulated depend
upon the target cells. In some cells, one of the target genes is the gene for the retinoic
acid receptor itself (RAR-beta in mammals), which amplifies the response. Control of
retinoic acid levels is maintained by a suite of proteins that control synthesis and degradation of retinoic acid.
The molecular basis for the interaction between retinoic acid and the Hox genes has
been studied by using deletion analysis in transgenic mice carrying constructs of GFP
reporter genes. Such studies have identified functional RAREs within flanking sequences of some of the most 3' Hox genes (including Hoxa1, Hoxb1, Hoxb4, Hoxd4),
suggesting a direct interaction between the genes and retinoic acid. These types of studies strongly support the normal roles of retinoids in patterning vertebrate embryogenesis through the Hox genes.
https://en.wikipedia.org/wiki/Retinoic_acid
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The retinoic acid receptor (RAR) is a type of nuclear receptor which can also a
transcription factor that is activated by both all-trans retinoic acid and 9-cis r
acid. There are three retinoic acid receptors (RAR), RAR-, RAR-, and RARcoded by the RARA, RARB, RARG genes, respectively. Each receptor isoform
eral splice variants: four- for , four- for , and two- for .
As with other type II nuclear receptors, RAR heterodimerizes with RXR and in
Index
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Retinol
Retinol is one of the animal forms of vitamin A. It is a diterpenoid and an alcohol and
is convertible to other forms of vitamin A. The retinyl ester derivative of the alcohol
serves as the storage form of the vitamin in animals.
When converted to the retinal (retinaldehyde) form, vitamin A is essential for vision,
and when converted to retinoic acid is essential for skin health, teeth remineralization
and bone growth. These chemical compounds are collectively known as retinoids, and
possess the structural motif of all-trans retinol as a common feature in their structure.
Structurally, all retinoids also possess a -ionone ring and a polyunsaturated side
chain, with either an alcohol, aldehyde, a carboxylic acid group or an ester group. The
side chain is composed of four isoprenoid units, with a series of conjugated double
bonds which may exist in trans- or cis-configuration.
Retinol is produced in the body from the hydrolysis of retinyl esters, and from the reduction of retinal. Retinol in turn is ingested in a precursor form. Animal sources
(liver and eggs) contain retinyl esters, whereas plants (carrots, spinach) contain provitamin A carotenoids (these may also be considered simply vitamin A). Hydrolysis of
retinyl esters results in retinol, while provitamin A carotenoids can be cleaved to produce retinal by carotene dioxygenase in the intestinal mucosa. Retinal, also known as
retinaldehyde, can be reversibly reduced to produce retinol or it can be irreversibly oxidized to produce retinoic acid, which then cannot function as the vitamin in the eye.
https://en.wikipedia.org/wiki/Retinol
Retinol Dehydrogenase
Retinol Dehydrogenase is an enzyme that catalyzes the chemical reaction
Retinol + NAD+ Retinal + NADH + H+
Sometimes, in addition to or along with NAD+ , NADP+ can act as a cofactor in the reaction as well. The substrate of the enzyme can be all-trans- or -cis- retinol. There are at
least over 20 different isolated enzymes with RDH activity to date.
Retinoid dehydrogenases/reductases (oxidoreductases), including retinol dehydrogenase, catalyze the key oxidation-reduction reactions in the visual cycle, converting vitamin A to 11-cis retinal, which is the chromophore of the rod and cone photoreceptors.
It is believed that RDHs at rod and cone are different, but related and can catalyze the
same reaction. RDH12 is the primary enzyme that reduces all-trans retinal released
from bleached photopigments during recovery phase in the visual cycle. The RDH12 enzyme can use either cis or trans retinoid isomers as substrates and can also function as
both dehydrogenase (i.e. retinol to retinal) and reductase (i.e. retinal to retinol).
The conversion of retinol to retinal is the rate-limiting step in the retinoic acid biosynthesis. In vertebrates, the retinoic acid is the ligand that controls nuclear receptor signaling pathway, which is responsible for growth and development as well as epithelial
maintenance, therefore can be used for cancer and acne treatment. In human, ADH4
can exhibit at least 10 fold higher Vmax/Km than other ADH.
https://en.wikipedia.org/wiki/Retinol_dehydrogenase
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Retrotransposition
Transposable elements represent one of several types of mobile genetic elements. TEs
are assigned to one of two classes according to their mechanism of transposition,
which can be described as either copy and paste (Class I TEs) or cut and paste (Class II
TEs).
Class I (retrotransposons)
Class I TEs are copied in two stages: first, they are transcribed from DNA to RNA, and
the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted back into the genome at a new position. The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar to retroviruses, such as HIV.
Retrotransposons are commonly grouped into three main orders:
TEs with long terminal repeats (LTRs), which encode reverse transcriptase, similar to
retroviruses
Long interspersed nuclear elements (LINEs, LINE-1s, or L1s), which encode reverse
transcriptase but lack LTRs, and are transcribed by RNA polymerase II
Short interspersed nuclear elements do not encode reverse transcriptase and are transcribed by RNA polymerase III
Retroviruses can also be considered TEs. For example, after conversion of retroviral
RNA into DNA inside a host cell, the newly produced retroviral DNA is integrated into
the genome of the host cell. These integrated DNAs are termed proviruses. The provirus is a specialized form of eukaryotic retrotransposon, which can produce RNA intermediates that may leave the host cell and infect other cells. The transposition cycle of
retroviruses has similarities to that of prokaryotic TEs, suggesting a distant relationship between the two.
Class II (DNA transposons)
The cut-and-paste transposition mechanism of class II TEs does not involve an RNA
intermediate. The transpositions are catalyzed by several transposase enzymes. Some
transposases non-specifically bind to any target site in DNA, whereas others bind to
specific target sequences. The transposase makes a staggered cut at the target site resulting in single-strand 5' or 3' DNA overhangs, so-called "sticky ends". This step cuts
out the DNA transposon, which is then ligated into a new target site. The process involves activity of a DNA polymerase that fills in gaps and of a DNA ligase that closes
the sugar-phosphate backbone. This results in duplication of the target site. The insertion sites of DNA transposons may be identified by short direct repeats (created by the
staggered cut in the target DNA and filling in by DNA polymerase) followed by a series
of inverted repeats important for the TE excision by transposase. Cut-and-paste TEs
may be duplicated if their transposition takes place during S phase of the cell cycle,
when a donor site has already been replicated but a target site has not yet been replicated. Such duplications at the target site can result in gene duplication, which plays
an important role in genomic evolution. Not all DNA transposons transpose through
the cut-and-paste mechanism. In some cases, a replicative transposition is observed in
which a transposon replicates itself to a new target site (e.g. helitron (biology)). Class
II TEs comprise less than 2% of the human genome, making the rest Class I.
https://en.wikipedia.org/wiki/Transposable_element
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Retrotransposons
Transposable elements represent one of several types of mobile genetic elements. TEs
are assigned to one of two classes according to their mechanism of transposition,
which can be described as either copy and paste (Class I TEs) or cut and paste (Class II
TEs).
Class I (retrotransposons)
Class I TEs are copied in two stages: first, they are transcribed from DNA to RNA, and
the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted back into the genome at a new position. The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar to retroviruses, such as HIV.
Retrotransposons are commonly grouped into three main orders:
TEs with long terminal repeats (LTRs), which encode reverse transcriptase, similar to
retroviruses
Long interspersed nuclear elements (LINEs, LINE-1s, or L1s), which encode reverse
transcriptase but lack LTRs, and are transcribed by RNA polymerase II
Short interspersed nuclear elements do not encode reverse transcriptase and are transcribed by RNA polymerase III
Retroviruses can also be considered TEs. For example, after conversion of retroviral
RNA into DNA inside a host cell, the newly produced retroviral DNA is integrated into
the genome of the host cell. These integrated DNAs are termed proviruses. The provirus is a specialized form of eukaryotic retrotransposon, which can produce RNA intermediates that may leave the host cell and infect other cells. The transposition cycle of
retroviruses has similarities to that of prokaryotic TEs, suggesting a distant relationship between the two.
Class II (DNA transposons)
The cut-and-paste transposition mechanism of class II TEs does not involve an RNA
intermediate. The transpositions are catalyzed by several transposase enzymes. Some
transposases non-specifically bind to any target site in DNA, whereas others bind to
specific target sequences. The transposase makes a staggered cut at the target site resulting in single-strand 5' or 3' DNA overhangs, so-called "sticky ends". This step cuts
out the DNA transposon, which is then ligated into a new target site. The process involves activity of a DNA polymerase that fills in gaps and of a DNA ligase that closes
the sugar-phosphate backbone. This results in duplication of the target site. The insertion sites of DNA transposons may be identified by short direct repeats (created by the
staggered cut in the target DNA and filling in by DNA polymerase) followed by a series
of inverted repeats important for the TE excision by transposase. Cut-and-paste TEs
may be duplicated if their transposition takes place during S phase of the cell cycle,
when a donor site has already been replicated but a target site has not yet been replicated. Such duplications at the target site can result in gene duplication, which plays
an important role in genomic evolution. Not all DNA transposons transpose through
the cut-and-paste mechanism. In some cases, a replicative transposition is observed in
which a transposon replicates itself to a new target site (e.g. helitron (biology)). Class
II TEs comprise less than 2% of the human genome, making the rest Class I.
https://en.wikipedia.org/wiki/Transposable_element
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Retroviruses
Retroviridae is a family of enveloped viruses that replicate in a host cell through the
process of reverse transcription. A retrovirus is a single-stranded positive-sense RNA
virus with a DNA intermediate and, as an obligate parasite, targets a host cell. Once inside the host cell cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome the reverse of the usual pattern, thus retro (backwards). This new DNA is then incorporated into the host cell genome by an integrase
enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell
then treats the viral DNA as part of its own genome, translating and transcribing the
viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus.
In most systems, DNA is transcribed into RNA, and then RNA is translated into protein. However, retroviruses function differently their RNA is reverse-transcribed into
DNA, which is integrated into the host cell's genome (when it becomes a provirus), and
then undergoes the usual transcription and translational processes to express the
genes carried by the virus. So, the information contained in a retroviral gene is used to
generate the corresponding protein via the sequence: RNA DNA RNA polypeptide. This extends the fundamental process identified by Francis Crick (one gene-one
peptide) in which the sequence is: DNA RNA peptide (proteins are made of one
or more polypeptide chain, e.g. hemoglobin is a four-chain peptide).
Retroviruses are valuable research tools in molecular biology, and have been used successfully in gene delivery systems.
https://en.wikipedia.org/wiki/Retrovirus
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Reverse Transcriptase
A reverse transcriptase (RT) is an enzyme used to generate complementary DNA
(cDNA) from an RNA template, a process termed reverse transcription. It is mainly associated with retroviruses. However, non-retroviruses also use RT (for example, the
hepatitis B virus, a member of the Hepadnaviridae, which are dsDNA-RT viruses,
while retroviruses are ssRNA viruses). RT inhibitors are widely used as antiretroviral
drugs. RT activities are also associated with the replication of chromosome ends (telomerase) and some mobile genetic elements (retrotransposons).
Retroviral RT has three sequential biochemical activities:
These activities are used by the retrovirus to convert single-stranded genomic RNA
into double-stranded cDNA which can integrate into the host genome, potentially generating a long-term infection that can be very difficult to eradicate. The same sequence
of reactions is widely used in the laboratory to convert RNA to DNA for use in molecular cloning, RNA sequencing, polymerase chain reaction (PCR), or genome analysis.
https://en.wikipedia.org/wiki/Reverse_transcriptase
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Reverse Transcription
tary DNA (cDNA) from an RNA template, a process termed reverse transcri
ple, the hepatitis B virus, a member of the Hepadnaviridae, which are dsDN
ruses, while retroviruses are ssRNA viruses). RT inhibitors are widely used
viral drugs. RT activities are also associated with the replication of chromos
(telomerase) and some mobile genetic elements (retrotransposons).
https://en.wikipedia.org/wiki/Reverse_transcriptase
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Rhamnose
Rhamnose (Rha, Rham) is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose occurs in nature in its L-form
as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Exceptions are the methyl pentoses L-fucose and Lrhamnose and the pentose L-arabinose.
Rhamnose can be isolated from Buckthorn (Rhamnus), poison sumac, and plants in
the genus Uncaria. Rhamnose is also produced by microalgae belonging to class Bacillariophyceae (diatoms).
Rhamnose is commonly bound to other sugars in nature. It is a common glycone component of glycosides from many plants. Rhamnose is also a component of the outer cell
membrane of acid-fast bacteria in the Mycobacterium genus, which includes the organism that causes tuberculosis.
https://en.wikipedia.org/wiki/Rhamnose
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Rho Factor
A factor (Rho factor) is a prokaryotic protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of
single stranded RNA (a stretch of 72 nucleotides) after the open reading frame at Crich, G-poor sequences that lack obvious secondary structure.
Rho factor is an essential transcription protein in prokaryotes. In Escherichia coli, it is
a ~274.6 kD hexamer of identical subunits. Each subunit has an RNA-binding domain
and an ATP-hydrolysis domain. Rho is a member of the family of ATP-dependent hexameric helicases that function by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for RNA polymerase.
There are two types of transcriptional termination in prokaryotes, rho-dependent termination and intrinsic termination (also called Rho-independent termination). Rhodependent terminators account for about half of the E. coli factor-dependent terminators. Other termination factors discovered in E. coli include Tau and nusA. Rhodependent terminators were first discovered in bacteriophage genomes.
A Rho factor acts on an RNA substrate. Rho's key function is its helicase activity, for
which energy is provided by an RNA-dependent ATP hydrolysis. The initial binding
site for Rho is an extended (~70 nucleotides, sometimes 80100 nucleotides) singlestranded region, rich in cytosine and poor in guanine, called the rho utilization site
(rut), in the RNA being synthesized, upstream of the actual terminator sequence. Several rho binding sequences have been discovered. No consensus is found among these,
but the different sequences each seem specific, as small mutations in the sequence disrupts its function. Rho binds to RNA and then uses its ATPase activity to provide the
energy to translocate along the RNA until it reaches the RNADNA helical region,
where it unwinds the hybrid duplex structure. RNA polymerase pauses at the termination sequence, which is because there is a specific site around 100 nt away from the
Rho binding site called the Rho-sensitive pause site. So, even though the RNA polymerase is about 40 nt per second faster than Rho, it does not pose a problem for the
Rho termination mechanism as the RNA polymerase allows Rho factor to catch up.
In short, Rho factor acts as an ATP-dependent unwinding enzyme, moving along the
newly forming RNA molecule towards its 3 end and unwinding it from the DNA template as it proceeds.
https://en.wikipedia.org/wiki/Rho_factor
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Rho-dependent terminators
Termination is part of the process of transcribing RNA. In eukaryotes, a termination
factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat
followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop
structure which destabilizes binding by the RNA polymerase and causes Rhoindependent transcription termination.
The most extensively studied transcriptional termination factor is the Rho protein of E.
coli. The Rho protein recognizes a cytosine-rich region of the elongating mRNA, but
the exact features of the recognized sequences remain unknown. Rho forms a ringshaped hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5' to 3' with respect to the mRNA). When the Rho protein reaches the RNA
polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA. The structure, as well as the activity, of the Rho protein is similar to that of the F1 subunit of ATP synthase, supporting the theory that the two share
an evolutionary link. The antibiotic bicyclomycin works by inhibiting Rho.
https://en.wikipedia.org/wiki/Termination_factor
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Rhodopsin
Rhodopsin (also known as visual purple) is a light-sensitive receptor protein involved
in visual phototransduction. Rhodopsin is a biological pigment found in the rods of the
retina and is an essential G-protein-coupled receptor (GPCR) in phototransduction.
Rhodopsin is extremely sensitive to light, and thus enables vision in low-light conditions. When rhodopsin is exposed to light, it immediately photobleaches. In humans, it
is regenerated fully in about 45 minutes.
In rhodopsin, the aldehyde group of retinal is covalently linked to the amino group of a
lysine residue on the protein in a protonated Schiff base (-NH+=CH-). When rhodopsin
absorbs light, its retinal cofactor isomerizes from the 11-cis to the all-trans configuration, and the protein subsequently undergoes a series of relaxations to accommodate
the altered shape of the isomerized cofactor. The intermediates formed during this
process were first investigated in the laboratory of George Wald, who received the Nobel prize for this research in 1967.
In subsequent intermediates lumirhodopsin and metarhodopsin I, the Schiff's base
linkage to all-trans retinal remains protonated, and the protein retains its reddish
color. The critical change that initiates the neuronal excitation involves the conversion
of metarhodopsin I to metarhodopsin II, which is associated with deprotonation of the
Schiff's base and change in color from red to yellow. Metarhodopsin II activates the G
protein transducin (Gt) to activate the visual phototransduction pathway. When transducin's subunit is bound to GTP, it activates cGMP phosphodiesterase. cGMP phosphodiesterase hydrolyzes cGMP (breaks it down). cGMP can no longer activate cation
channels. This leads to the hyperpolarization of photoreceptor cells and a change in the
rate of transmitter release by these photoreceptor cells.
https://en.wikipedia.org/wiki/Rhodopsin
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Ribitol
Ribitol or adonitol is a crystalline pentose alcohol (C5H12O5) formed by the
ribose. It occurs naturally in the plant Adonis vernalis, as well as in the cell
https://en.wikipedia.org/wiki/Ribitol
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Ribonuclease
Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the
degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC
2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.
All organisms studied contain many RNases of many different classes, showing that
RNA degradation is a very ancient and important process. As well as cleaning of cellular RNA that is no longer required, RNases play key roles in the maturation of all RNA
molecules, both messenger RNAs that carry genetic material for making proteins, and
non-coding RNAs that function in varied cellular processes. In addition, active RNA
degradation systems are a first defense against RNA viruses, and provide the underlying machinery for more advanced cellular immune strategies such as RNAi.
Some cells also secrete copious quantities of non-specific RNases such as A and T1.
RNases are, therefore, extremely common, resulting in very short lifespans for any
RNA that is not in a protected environment. Intracellular RNAs may be protected from
RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).
Another mechanism of protection is ribonuclease inhibitor (RI), which comprises a
relatively large fraction of cellular protein (~0.1%) in some cell types, and which binds
to certain ribonucleases with the highest affinity of any protein-protein interaction; the
dissociation constant for the RI-RNase A complex is ~20 fM under physiological conditions. RI is used in most laboratories that study RNA to protect their samples against
degradation from environmental RNases.
Similar to restriction enzymes, which cleave highly specific sequences of doublestranded DNA, a variety of endoribonucleases that recognize and cleave specific sequences of single-stranded RNA have been recently classified.
RNases play a critical role in many biological processes, including angiogenesis and
self-incompatibility in flowering plants (angiosperms). Many stress-response toxins of
prokaryotic toxin-antitoxin systems have been shown to have RNase activity and homology.
https://en.wikipedia.org/wiki/Ribonuclease
Ribonuclease P
Ribonuclease P (EC 3.1.26.5, RNase P) is a type of ribonuclease which cleaves RNA.
RNase P is unique from other RNases in that it is a ribozyme a ribonucleic acid that
acts as a catalyst in the same way that a protein based enzyme would. Its function is to
cleave off an extra, or precursor, sequence of RNA on tRNA molecules.
Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in archaea, bacteria
and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is
the generation of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of
precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins (RNP). RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is
a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein
content than the bacterial ones, the RNA cores from all the three lineages are homologoushelices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular
RNase P RNAs. Yet, there is considerable sequence variation, particularly among the
eukaryotic RNAs.
https://en.wikipedia.org/wiki/Ribonuclease_P
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Ribonucleoside Diphosphates
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Ribonucleoside Triphosphates
A nucleoside triphosphate (NTP) is a molecule containing a nucleoside bound to three
phosphate groups. It is thus one type of nucleotide. Nucleotide derivatives are necessary for life, as they are the building blocks of nucleic acids and have thousands of
other roles in cell metabolism and regulation. NTPs generally provide energy and phosphate groups for phosphorylation.
Natural nucleoside triphosphates include adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), 5-methyluridine triphosphate
(m5UTP), and uridine triphosphate (UTP). ATP is a major source of cellular energy.
GTP is a very frequent cofactor of enzymes and proteins.
The terms ATP, GTP, CTP, and UTP refer to those nucleoside triphosphates that contain ribose. The nucleoside triphosphates containing deoxyribose are called dNTPs,
and take the prefix deoxy- in their names and small d- in their abbreviations: deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine
triphosphate (dCTP), deoxythymidine triphosphate (dTTP) and deoxyuridine triphosphate (dUTP). The dNTPs are the building blocks for DNA (they lose two of the phosphate groups in the process of incorporation).
Apart from (d)ATP, (d)GTP, (d)CTP, (d)TTP and (d)UTP, there are other less abundant NTPs, such as intermediates of nucleotide metabolism, but also "rare" natural nucleotides or even artificial nucleotides. An example of rare NTPs are the tautomeric
forms of some NTPs. They can cause mismatched base pairing during DNA replication.
For example, a tautomeric form of cytosine is capable of forming 3 hydrogen bonds
with adenine, and it will spontaneously tautomerize to its original cytosine form, causing a mismatch. By a similar token, the deamination of cytosine leads to uracil,
whereas a deamination of a commonly encountered (in eukaryotes) 5-methylcytosine
will lead to thymine. However, the 3' to 5' exonuclease activity of DNA polymerase III
ensures that mismatched bases are excised during replication.
Generally nucleotides are nucleosides (a ribose/deoxyribose sugar covalently bonded
to a nitrogenous base, such as adenine) that have 5' phosphate(s). However, for the
sake of technical terminology, nucleotides are given classifications as nucleosides with
a suffix describing the number of phosphates present in a specific unit. For example, if
a nucleotide has one phosphate, it is a nucleoside monophosphate (NMP). If the nucleotide has two phosphates, then it is called a nucleoside diphosphate (NDP), and for
three, it is a nucleoside triphosphate (NTP). The nucleotides that contain a ribose
sugar are the monomers of RNA and those that contain a deoxyribose sugar compose
DNA.
NTPs, NDPs and NMPs are ubiquitous in the cell cytoplasm, nucleus and organelles.
Given their multifarious functions, their levels are under fairly tight metabolic control.
Shifts in the ratio of available nucleotides can cause shifts in their incorporation,
which, if not corrected, can lead to mutations. Most of the discussion on mutual ratios
of nucleotides should belong under entry nucleotide, but concentrating strictly on the
abundance of the triphosphorylated versions, we find that ATP spending is replenished
by oxidative phosphorylation, while phosphorylation status of other nucleotides is regulated by NDP kinases (EC 2.7.4.6) and NMP kinases (EC 2.7.4.4) that use ATP pool as
their cross-phosphorylation source.
Shown below - UTP
https://en.wikipedia.org/wiki/Nucleoside_triphosphate
Ribonucleotide Reductase
Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase,
is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a
critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is
maintained at a constant ratio during cell division and DNA repair.
A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP,
CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme
(thymidylate kinase) from dTMP (deoxythymidine monophosphate).
The enzyme ribonucleotide reductase (RNR) catalyzes the de novo synthesis of dNDPs.
Catalysis of ribonucleoside 5-diphosphates (NDPs) involves a reduction at the 2carbon of ribose 5-phosphate to form the 2-deoxy derivative-reduced 2deoxyribonucleoside 5-diphosphates (dNDPs). This reduction is initiated with the generation of a free radical. Following a single reduction, RNR requires electrons donated
from the dithiol groups of the protein thioredoxin. Regeneration of thioredoxin occurs
when nicotinamide adenine dinucleotide phosphate (NADPH) provides two hydrogen
atoms that are used to reduce the disulfide groups of thioredoxin.
Regulation of RNR is designed to maintain balanced quantities of dNTPs. Binding of
effector molecules either increases or decreases RNR activity. When ATP binds to the
allosteric activity site, it activates RNR. In contrast, when dATP binds to this site, it deactivates RNR. In addition to controlling activity, the allosteric mechanism also regulates the substrate specificity and ensures the enzyme produces an equal amount of
each dNTP for DNA synthesis. In all classes, binding of ATP or dATP to the allosteric
site induces reduction of cytidine 5-diphosphate (CDP) and uridine 5-diphosphate
(UDP); 2-deoxyguanosine 5-triphosphate (dGTP) induces reduction of adenosine 5diphosphate (ADP); and 2-deoxythymidine 5-triphosphate (dTTP) induces reduction
of guanosine 5-diphosphate (GDP).
https://en.wikipedia.org/wiki/Ribonucleotide_reductase
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Ribonucleotides
In biochemistry, a ribonucleotide or ribotide is a nucleotide containing ribose as its
pentose component. It is a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms
the basic building blocks for RNA. However, the reduction of ribonucleotides, by enzyme ribonucleotide reductase (RNR), forms deoxyribonucleotides, which are the essential building block for DNA. Successive nucleotides are linked together via phosphodiester bonds by 3'-5'.
Ribonucleotides are also utilized in other cellular functions. These special monomers
are utilized in both cell regulation and cell signaling as seen in adenosinemonophosphate (AMP). Furthermore, ribonucleotides can be converted to adenosine
triphosphate (ATP), the energy currency in organisms. Ribonucleotides can be converted to cyclic adenosine monophosphate (cyclic AMP) to regulate hormones in organisms as well. In living organisms, the most common bases for ribonucleotides are adenine (A), guanine (G), cytosine (C), or uracil (U). The nitrogenous bases are classified
into two parent compounds, purine and pyrimidine.
https://en.wikipedia.org/wiki/Ribonucleotide
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Ribose
Ribose is a carbohydrate with the formula C5H10O5; specifically, it is a pentose monosaccharide (simple sugar) with linear form H(C=O)(CHOH)4H, which has all the
hydroxyl groups on the same side in the Fischer projection.
The term may refer to either of two enantiomers. The term usually indicates D-ribose,
which occurs widely in nature and is discussed here. Its synthetic mirror image, Lribose, is not found in nature.
The ribose -D-ribofuranose (shown below) forms part of the backbone of RNA. It is
related to deoxyribose, which is found in DNA. Phosphorylated derivatives of ribose
such as ATP and NADH play central roles in metabolism. cAMP and cGMP, formed
from ATP and GTP, serve as secondary messengers in some signalling pathways.
Ribose is an aldopentose (a monosaccharide containing five carbon atoms) that, in its
open chain form, has an aldehyde functional group at one end. In the conventional
numbering scheme for monosaccharides, the carbon atoms are numbered from C1' (in
the aldehyde group) to C5'. The deoxyribose derivative found in DNA differs from ribose by having a hydrogen atom in place of the hydroxyl group at C2'. This hydroxyl
group performs a function in RNA splicing.
https://en.wikipedia.org/wiki/Ribose
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Ribose-1-phosphate
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Ribose-5-phosphate
Ribose 5-phosphate is both a product and an intermediate of the pentose phosphate
pathway. The last step of the oxidative reactions in the pentose phosphate pathway is
the production of ribulose 5-phosphate. Depending on the body's state, ribulose 5phosphate can reversibly isomerize to ribose 5-phosphate. Ribulose 5-phosphate can
alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates as well as fructose
6-phosphate and glyceraldehyde 3-phosphate (both intermediates in glycolysis).
Ribose-5-phosphate can also be used to make nucleotides. The first step in the process
is formation of phosphoribosyl pyrophosphate, catalyzed by ribose-phosphate diphosphokinase.
https://en.wikipedia.org/wiki/Ribose_5-phosphate
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Ribose-5-phosphate Isomerase
phosphate pathway and the Calvin cycle. This gene is highly conserved in m
isms. The enzyme plays an essential role in the carbohydrate metabolism.
https://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase
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Ribose-phosphate Diphosphokinase
Ribose-phosphate diphosphokinase (or phosphoribosyl pyrophosphate synthetase or
ribose-phosphate pyrophosphokinase) is an enzyme that converts ribose 5-phosphate
into phosphoribosyl pyrophosphate (PRPP).
Ribose-5-P + ATP <=> AMP + PRPP
The enzyme is involved in the synthesis of nucleotides (purines and pyrimidines), cofactors NAD+ and NADP+, and amino acids histidine and tryptophan, linking these biosynthetic processes to the pentose phosphate pathway, from which the substrate ribose 5phosphate is derived.
The product of this reaction, phosphoribosyl pyrophosphate (PRPP), is used in numerous biosynthesis (de novo and salvage) pathways. PRPP provides the ribose sugar in de
novo synthesis of purines and pyrimidines, used in the nucleotide bases that form RNA
and DNA. PRPP reacts with orotate to form orotidylate, which can be converted to uridylate (UMP). UMP can then be converted to the nucleotide cytidine triphosphate
(CTP).
The reaction of PRPP, glutamine, and ammonia forms 5-phosphoribosyl-1-amine, a
precursor to inosinate (IMP), which can ultimately be converted to adenosine triphosphate (ATP) or guanosine triphosphate (GTP). PRPP plays a role in purine salvage
pathways by reacting with free purine bases to form adenylate, guanylate, and inosinate. PRPP is also used in the synthesis of NAD. The reaction of PRPP with nicotinic
acid yields the intermediate nicotinic acid mononucleotide.
https://en.wikipedia.org/wiki/Ribose-phosphate_diphosphokinase
Ribosomal RNAs
In molecular biology, ribosomal ribonucleic acid (rRNA) is the RNA component of the
ribosome, and is essential for protein synthesis in all living organisms. It constitutes
the predominant material within the ribosome, which is approximately 60% rRNA and
40% protein by weight. Ribosomes contain two major rRNAs and 50 or more proteins.
The ribosomal RNAs form two subunits, the large subunit (LSU) and small subunit
(SSU). The LSU rRNA acts as a ribozyme, catalyzing peptide bond formation.
Ribosomal RNA characteristics are important in evolution, thus taxonomy, and medicine.
rRNA is one of only a few gene products present in all cells. For this reason, genes
that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic
group, calculate related groups, and estimate rates of species divergence. As a result,
many thousands of rRNA sequences are known and stored in specialized databases
such as RDP-II and SILVA.
rRNA is the target of numerous clinically relevant antibiotics: chloramphenicol, erythromycin, kasugamycin, micrococcin, paromomycin, ricin, sarcin, spectinomycin, streptomycin, and thiostrepton.
rRNA have been shown to be the origin of species-specific microRNAs, like miR-663
in humans and miR-712 in mouse. These miRNAs originate from the Internal Transcribed Spacers of the rRNA.
In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The
large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal
RNAs). Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. The 3' end of the 16S ribosomal RNA (in a
ribosome) binds to a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.
Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of
cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 18S rRNA in most
eukaryotes is in the small ribosomal subunit, and the large subunit contains three
rRNA species (the 5S, 5.8S and 28S in mammals, 25S in plants, rRNAs).
https://en.wikipedia.org/wiki/Ribosomal_RNA
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Ribosome
The ribosome is a complex molecular machine found within all living cells, that serves
as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and
the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is
composed of one or more ribosomal RNA (rRNA) molecule and a variety of proteins.
The ribosomes and associated molecules are also known as the translational apparatus.
The sequence of DNA, which encodes the sequence of the amino acids in a protein, is
copied into a messenger RNA chain. It may be copied many times into RNA chains. Ribosomes can bind to a messenger RNA chain and use its sequence for determining the
correct sequence of amino acids. Amino acids are selected, collected, and carried to the
ribosome by transfer RNA (tRNA) molecules, which enter one part of the ribosome and
bind to the messenger RNA chain. It is during this binding that the correct translation
of nucleic acid sequence to amino acid sequence occurs. For each coding triplet in the
messenger RNA there is a distinct transfer RNA that matches and which carries the correct amino acid for that coding triplet. The attached amino acids are then linked together by another part of the ribosome. Once the protein is produced, it can then fold
to produce a specific functional three-dimensional structure although during synthesis
some proteins start folding into their correct form.
A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein. Each ribosome is divided into two subunits: 1. a smaller subunit which
binds to a larger subunit and the mRNA pattern, and 2. a larger subunit which binds to
the tRNA, the amino acids, and the smaller subunit. When a ribosome finishes reading
an mRNA molecule, these two subunits split apart. Ribosomes are ribozymes, because
the catalytic peptidyl transferase activity that links amino acids together is performed
by the ribosomal RNA. Ribosomes are often embedded in the intracellular membranes
that make up the rough endoplasmic reticulum.
Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth)
resemble each other to a remarkable degree, evidence of a common origin. They differ
in their size, sequence, structure, and the ratio of protein to RNA. The differences in
structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while
leaving human ribosomes unaffected. In bacteria and archaea, more than one ribosome may move along a single mRNA chain at one time, each "reading" its sequence
and producing a corresponding protein molecule.
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S)
subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides)
bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S)
subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The
large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins.
https://en.wikipedia.org/wiki/Ribosome
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Ribosomes
The ribosome is a complex molecular machine found within all living cells, that serves
as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and
the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is
composed of one or more ribosomal RNA (rRNA) molecule and a variety of proteins.
The ribosomes and associated molecules are also known as the translational apparatus.
The sequence of DNA, which encodes the sequence of the amino acids in a protein, is
copied into a messenger RNA chain. It may be copied many times into RNA chains. Ribosomes can bind to a messenger RNA chain and use its sequence for determining the
correct sequence of amino acids. Amino acids are selected, collected, and carried to the
ribosome by transfer RNA (tRNA) molecules, which enter one part of the ribosome and
bind to the messenger RNA chain. It is during this binding that the correct translation
of nucleic acid sequence to amino acid sequence occurs. For each coding triplet in the
messenger RNA there is a distinct transfer RNA that matches and which carries the correct amino acid for that coding triplet. The attached amino acids are then linked together by another part of the ribosome. Once the protein is produced, it can then fold
to produce a specific functional three-dimensional structure although during synthesis
some proteins start folding into their correct form.
A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein. Each ribosome is divided into two subunits: 1. a smaller subunit which
binds to a larger subunit and the mRNA pattern, and 2. a larger subunit which binds to
the tRNA, the amino acids, and the smaller subunit. When a ribosome finishes reading
an mRNA molecule, these two subunits split apart. Ribosomes are ribozymes, because
the catalytic peptidyl transferase activity that links amino acids together is performed
by the ribosomal RNA. Ribosomes are often embedded in the intracellular membranes
that make up the rough endoplasmic reticulum.
Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth)
resemble each other to a remarkable degree, evidence of a common origin. They differ
in their size, sequence, structure, and the ratio of protein to RNA. The differences in
structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while
leaving human ribosomes unaffected. In bacteria and archaea, more than one ribosome may move along a single mRNA chain at one time, each "reading" its sequence
and producing a corresponding protein molecule.
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S)
subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides)
bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S)
subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The
large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins.
https://en.wikipedia.org/wiki/Ribosome
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Riboswitch
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, a mRNA that contains a riboswitch is directly involved in
regulating its own activity, in response to the concentrations of its effector molecule.
The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA
beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.
The original definition of the term "riboswitch" specified that they directly sense smallmolecule metabolite concentrations. Although this definition remains in common use,
some biologists have used a broader definition that includes other cis-regulatory
RNAs. However, this article will discuss only metabolite-binding riboswitches.
Most known riboswitches occur in bacteria, but functional riboswitches of one type
(the TPP riboswitch) have been discovered in plants and certain fungi. TPP riboswitches have also been predicted in archaea, but have not been experimentally
tested.
Below - an FMN riboswitch
https://en.wikipedia.org/wiki/Riboswitch
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Ribosylpyrimidine Nucleosidase
Index
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Ribothymidine
which lacks a hydroxyl group at the 2' position. 5-Methyluridine contains a thy
base joined to a ribose pentose sugar.
https://en.wikipedia.org/wiki/5-Methyluridine
Ribozymes
Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. The most
common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation
of RNA and DNA and peptide bond formation.
Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to
link amino acids during protein synthesis. They also participate in a variety of RNA
processing reactions, including RNA splicing, viral replication, and transfer RNA biosynthesis. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme, Leadzyme and the hairpin ribozyme.
Although most ribozymes are quite rare in the cell, their roles are sometimes essential
to life. For example, the functional part of the ribosome, the molecular machine that
translates RNA into proteins, is fundamentally a ribozyme, composed of RNA tertiary
structural motifs that are often coordinated to metal ions such as Mg++ as cofactors. In
a model system, there is no requirement for divalent cations in a five-nucleotide RNA
catalyzing trans-phenylalanation of a four-nucleotide substrate with 3 base pairs complementary with the catalyst, where the catalyst/substrate were devised by truncation
of the C3 ribozyme. RNA may catalyze folding of the pathological protein conformation
of a prion in a manner similar to that of a chaperonin, and may be involved in the viral
concatemer cleavage that precedes the packing of viral genetic material into some virons.
RNA can also act as a hereditary molecule, which encouraged Walter Gilbert to propose that in the distant past, the cell used RNA as both the genetic material and the
structural and catalytic molecule rather than dividing these functions between DNA
and protein as they are today; this hypothesis is known as the "RNA world hypothesis"
of the origin of life. Evidence that ribozymes were the first molecular machines used by
early life suggests that they are in effect "molecular fossils".
https://en.wikipedia.org/wiki/Ribozyme
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Ribulose 1,5-bisphosphate
Ribulose-1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis. The enzyme ribulose bisphosphate carboxylase oxygenase (RuBisCO) catalyzes
the reaction between RuBP and carbon dioxide. The product is the highly unstable 6carbon intermediate known as 3-keto-2-carboxyarabinitol 1,5-bisphosphate. This sixcarbon intermediate decays virtually instantaneously into two molecules of 3phosphoglycerate (3-PG). RuBisCO also catalyzes RuBP with oxygen (O2) in a process
called photorespiration, a process that is more prevalent at high temperatures. During
photorespiration RuBP combines with O2 to become 3-PG + phosphoglycolic acid. In
the Calvin Cycle, RuBP is a product of the phosphorylation of ribulose-5-phosphate by
ATP.
https://en.wikipedia.org/wiki/Ribulose-1,5-bisphosphate
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Index
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Ribulose-1,5-bisphosphate Carboxylase
Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviation RuBisCO, is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate (also known as RuBP). It is probably the most abundant enzyme on Earth.
Ribulose-1,5-bisphosphate + CO2 + H2O <=> 2 3-PG
RuBisCO is important biologically because it catalyzes the primary chemical reaction
by which inorganic carbon enters the biosphere. While many autotrophic bacteria and
archaea fix carbon via the reductive acetyl CoA pathway, the 3-hydroxypropionate cycle, or the reverse citric acid cycle, these pathways are relatively smaller contributors to
global carbon fixation than that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only temporarily fixes carbon. Reflecting its importance,
RuBisCO is the most abundant protein in leaves, accounting for 50% of soluble leaf protein in C3 plants (2030% of total leaf nitrogen) and 30% of soluble leaf protein in C4
plants (59% of total leaf nitrogen).
When carbon dioxide is the substrate, the product of the carboxylase reaction is a
highly unstable six-carbon phosphorylated intermediate known as 3-keto-2carboxyarabinitol-1,5-bisphosphate, which decays virtually instantaneously into two
molecules of glycerate-3-phosphate. The extremely unstable molecule created by the
initial carboxylation was unknown until 1988, when it was isolated. The 3phosphoglycerate can be used to produce larger molecules such as glucose. Also,
Rubisco side activities can lead to useless or inhibitory by-products. One such product
is xylulose-1,5-bisphosphate, which inhibits Rubisco activity. When molecular oxygen
is the substrate, the products of the oxygenase reaction are phosphoglycolate and 3phosphoglycerate. Phosphoglycolate is recycled through a sequence of reactions called
photorespiration, which involves enzymes and cytochromes located in the mitochondria and peroxisomes (this is a case of metabolite repair). In this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one
molecule of 3-phosphoglycerate, which can reenter the Calvin cycle.
Some of the phosphoglycolate entering this pathway can be retained by plants to produce other molecules such as glycine. At ambient levels of carbon dioxide and oxygen,
the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation
of only 3.5. Thus, the inability of the enzyme to prevent the reaction with oxygen
greatly reduces the photosynthetic capacity of many plants. Some plants, many algae,
and photosynthetic bacteria have overcome this limitation by devising means to increase the concentration of carbon dioxide around the enzyme, including C4 carbon
fixation, crassulacean acid metabolism, and the use of pyrenoid.
https://en.wikipedia.org/wiki/RuBisCO
Ribulose-5-phosphate
Ribulose 5-phosphate is one of the end-products of the pentose phosphate pathway. It
is also an intermediate in the Calvin cycle. The molecule is formed by phosphogluconate dehydrogenase, and it can be acted upon by phosphopentose isomerase and phosphopentose epimerase. It is a metabolic precursor of ribulose-1,5-bisphosphate.
https://en.wikipedia.org/wiki/Ribulose_5-phosphate
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G-G
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Right Handed
When describing a helix, if when looking down the line of sight along the he
clockwise screwing motion moves the helix away from the observer, then it
right-handed helix. Otherwise, it is a left-handed helix.
https://en.wikipedia.org/wiki/Helix
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Right-handed
When describing a helix, if when looking down the line of sight along the he
clockwise screwing motion moves the helix away from the observer, then it
right-handed helix. Otherwise, it is a left-handed helix.
https://en.wikipedia.org/wiki/Helix
RISC
The RNA-induced silencing complex, or RISC, is a multiprotein complex, specifically a
ribonucleoprotein, which incorporates one strand of a single-stranded RNA (ssRNA)
fragment, such as microRNA (miRNA), or double stranded small interfering RNA
(siRNA). The single strand acts as a template for RISC to recognize complementary
messenger RNA (mRNA) transcript. Once found, one of the proteins in RISC, called Argonaute, activates and cleaves the mRNA. This process is called RNA interference
(RNAi) and it is found in many eukaryotes. It is a key process in gene silencing and defense against viral infections.
The RNase III Dicer aids RISC in RNA interference by cleaving dsRNA into 21-23 nucleotide long fragments with a two-nucleotide 3' overhang. These dsRNA fragments are
loaded into RISC and each strand has a different fate based on the asymmetry rule phenomenon.
The strand with the less stable 5' end is selected by the RNase Argonaute and integrated into RISC. This strand is known as the guide strand.
The other strand, known as the passenger strand, is degraded by RISC
RISC uses the bound guide strand to target complementary 3'-untranslated regions
(3'UTR) of mRNA transcripts via Watson-Crick base pairing. RISC can now regulate
gene expression of the mRNA transcript in a number of ways.
The most understood function of RISC is degrading target mRNA which reduces the
levels of transcript available to be translated by ribosomes. There are two main requirements for mRNA degradation to take place:
a near-perfect complementary match between the guide strand and target mRNA sequence, and,
a catalytically active Argonaute protein, called a 'slicer', to cleave the target mRNA.
mRNA degradation is localized in cytoplasmic bodies called P-bodies.
https://en.wikipedia.org/wiki/RNA-induced_silencing_complex
Rise
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RNA
Ribonucleic acid (RNA) is a polymeric molecule implicated in various biological roles
in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, constitute the three major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of
nucleotides, but unlike DNA it is more often found in nature as a single-strand folded
onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA
(mRNA) to convey genetic information (using the letters G, U, A, and C to denote the
nitrogenous bases guanine, uracil, adenine, and cytosine) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.
Some RNA molecules play an active role within cells by catalyzing biological reactions,
controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function wherein
mRNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA (tRNA) molecules to deliver amino acids to the ribosome, where ribosomal
RNA (rRNA) then links amino acids together to form proteins.
Some RNA molecules play an active role within cells by catalyzing biological reactions,
controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function wherein
mRNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA (tRNA) molecules to deliver amino acids to the ribosome, where ribosomal
RNA (rRNA) then links amino acids together to form proteins.
Synthesis of RNA is usually catalyzed by an enzymeRNA polymeraseusing DNA as
a template, a process known as transcription. Initiation of transcription begins with
the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses reading the template strand in the 3 to 5 direction,
synthesizing a complementary RNA in the 5 to 3 direction. The DNA sequence also
dictates where termination of RNA synthesis will occur.
Messenger RNA (mRNA) carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon) correspond to one amino acid. In eukaryotic cells, once precursor
mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA.
This removes its intronsnon-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells,
which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases.
Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region
for codon recognition that binds to a specific sequence on the messenger RNA chain
through hydrogen bonding.
Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of
the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein
called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time. Nearly all the RNA
found in a typical eukaryotic cell is rRNA.
Several types of RNA can down-regulate gene expression by being complementary to a
part of an mRNA or a gene's DNA. MicroRNAs (miRNA; 21-22nt) are found in
eukaryotes and act through RNA interference (RNAi), where an effector complex of
miRNA and enzymes can cleave complementary mRNA, block the mRNA from being
translated, or accelerate its degradation.
While small interfering RNAs (siRNA; 20-25nt) are often produced by breakdown of
viral RNA, there are also endogenous sources of siRNAs. siRNAs act through RNA interference in a fashion similar to miRNAs. Some miRNAs and siRNAs can cause genes
they target to be methylated, thereby decreasing or increasing transcription of those
genes. Animals have Piwi-interacting RNAs (piRNA; 29-30nt) that are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.
Many RNAs are involved in modifying other RNAs. Introns are spliced out of premRNA by spliceosomes, which contain several small nuclear RNAs (snRNA), or the introns can be ribozymes that are spliced by themselves. RNA can also be altered by having its nucleotides modified to other nucleotides than A, C, G and U. In eukaryotes,
modifications of RNA nucleotides are in general directed by small nucleolar RNAs
(snoRNA; 60-300nt), found in the nucleolus and cajal bodies. snoRNAs associate with
enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively
modified, but snRNAs and mRNAs can also be the target of base modification. RNA
can also be methylated.
https://en.wikipedia.org/wiki/RNA
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RNA Editing
RNA editing is a molecular process through which some cells can make discrete
changes to specific nucleotide sequences within a RNA molecule after it has been generated by RNA polymerase. RNA editing is relatively rare, and common forms of RNA
processing (e.g. splicing, 5'-capping and 3'-polyadenylation) are not usually included
as editing. Editing events may include the insertion, deletion, and base substitution of
nucleotides within the edited RNA molecule.
RNA editing has been observed in some tRNA, rRNA, mRNA or miRNA molecules of
eukaryotes and their viruses, archaea and prokaryotes. RNA editing occurs in the cell
nucleus and cytosol, as well as within mitochondria and plastids. In vertebrates, editing is rare and usually consists of a small number of changes to the sequence of affected molecules. In other organisms, extensive editing (pan-editing) can occur. In
some cases the majority of nucleotides in a mRNA sequence may result from editing.
RNA-editing processes show great molecular diversity, and some appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing
phenomena includes nucleobase modifications such as cytidine (C) to uridine (U) and
adenosine (A) to inosine (I) deaminations, as well as non-templated nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence
of the encoded protein so that it differs from that predicted by the genomic DNA sequence.
https://en.wikipedia.org/wiki/RNA_editing
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RNA Polymerase
RNA polymerase (RNAP or RNApol) (Ribonucleic acid), also known as DNAdependent RNA polymerase, is an enzyme that produces primary transcript RNA. In
cells, RNAP is necessary for constructing RNA chains using DNA genes as templates, a
process called transcription. RNA polymerase enzymes are essential to life and are
found in all organisms and many viruses. In chemical terms, RNAP is a nucleotidyl
transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript.
RNAP can initiate transcription at specific DNA sequences known as promoters. It
then produces an RNA chain, which is complementary to the template DNA strand.
The process of adding nucleotides to the RNA strand is known as elongation. In
eukaryotes, RNAP can build chains as long as 2.4 million nucleotides (the full length of
the dystrophin gene). RNAP will preferentially release its RNA transcript at specific
DNA sequences encoded at the end of genes, which are known as terminators.
Products of RNAP include:
Messenger RNA (mRNA)template for the synthesis of proteins by ribosomes.
Non-coding RNA or "RNA genes"a broad class of genes that encode RNA that is not
translated into protein. The most prominent examples of RNA genes are transfer RNA
(tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus
RNA genes may play a much more significant role than previously thought.
Transfer RNA (tRNA)transfers specific amino acids to growing polypeptide chains
at the ribosomal site of protein synthesis during translation
Ribosomal RNA (rRNA)a component of ribosomes
Micro RNAregulates gene activity
Catalytic RNA (Ribozyme)enzymatically active RNA molecules
RNAP accomplishes de novo synthesis. It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers
to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to
DNA polymerase, RNAP includes helicase activity, therefore no separate enzyme is
needed to unwind DNA.
https://en.wikipedia.org/wiki/RNA_polymerase
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RNA Polymerase I
RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes, the polymerase that
only transcribes ribosomal RNA (but not 5S rRNA, which is synthesized by RNA polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in
a cell.
Pol I is a 590 kDa enzyme that consists of 14 protein subunits (polypeptides), and its
crystal structure in the yeast Saccharomyces cerevisiae was solved at 2.8 resolution
in 2013. Twelve of its subunits have identical or related counterparts in RNA polymerase II (Pol II) and RNA polymerase III (Pol III). The other two subunits are related to Pol II initiation factors and have structural homologues in Pol III.
Ribosomal DNA transcription is confined to the nucleolus, where about 400 copies of
the 32-kb rDNA gene are present, arranged as tandem repeats in nucleolus organizer
regions. Each copy contains a ~13.3 kb sequence encoding the 18S, the 5.8S, and the
28S RNA molecules, interlaced with two internal transcribed spacers, ITS1 and ITS2,
and flanked upstream by a 5' external transcribed spacer and a downstream 3' external
transcribed spacer. These components are transcribed together to form the 45S prerRNA. The 45S pre-rRNA is then post-transcriptionally cleaved by C/D box and H/
ACA box snoRNAs, removing the two spacers and resulting in the three rRNAs by a
complex series of steps. The 5S ribosomal RNA is transcribed by Pol III. Because of the
simplicity of Pol I transcription, it is the fastest-acting polymerase and contributes up
to 60% of cellular transcription levels in exponentially growing cells.
https://en.wikipedia.org/wiki/RNA_polymerase_I
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RNA polymerase II
RNA polymerase II (RNAP II and Pol II) is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and
microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of
RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.
The eukaryotic core RNA polymerase II was first purified using transcription assays.
The purified enzyme has typically 10-12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition. Many subunit-subunit interactions are known.
DNA-directed RNA polymerase II subunit RPB1 - an enzyme that in humans is encoded by the POLR2A gene and in yeast is encoded by RPO21. RPB1 is the largest
subunit of RNA polymerase II. It contains a carboxy terminal domain (CTD) composed of up to 52 heptapeptide repeats (YSPTSPS) that are essential for polymerase
activity. The CTD was first discovered in the laboratory of C.J. Ingles at the University of Toronto and by JL Corden at Johns Hopkins University. In combination with
several other polymerase subunits, the RPB1 subunit forms the DNA binding domain
of the polymerase, a groove in which the DNA template is transcribed into RNA. It
strongly interacts with RPB8.
RPB2 (POLR2B) - the second-largest subunit that in combination with at least two
other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA.
RPB3 (POLR2C) - the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 strongly interacts with
RPB1-5, 7, 10-12.
RNA polymerase II subunit B4 (RPB4) - encoded by the POLR2D gene is the fourthlargest subunit and may have a stress protective role.
RPB5 - In humans is encoded by the POLR2E gene. Two molecules of this subunit are
present in each RNA polymerase II. RPB5 strongly interacts with RPB1, RPB3, and
RPB6.
RPB6 (POLR2F) - forms a structure with at least two other subunits that stabilizes
the transcribing polymerase on the DNA template.
RPB7 - encoded by POLR2G and may play a role in regulating polymerase function.
RPB7 interacts strongly with RPB1 and RPB5.
RPB8 (POLR2H) - interacts with subunits RPB1-3, 5, and 7.
RPB9 - The groove in which the DNA template is transcribed into RNA is composed
of RPB9 (POLR2I) and RPB1.
RPB10 - the product of gene POLR2L. It interacts with RPB1-3 and 5, and strongly
with RPB3.
RPB11 - the RPB11 subunit is itself composed of three subunits in humans: POLR2J
(RPB11-a), POLR2J2 (RPB11-b), and POLR2J3 (RPB11-c).
RPB12 - Also interacting with RPB3 is RPB12 (POLR2K)
https://en.wikipedia.org/wiki/RNA_polymerase_II
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Transfer RNAs
5S ribosomal RNA
U6 spliceosomal RNA
Vault RNAs
Y RNA
7SK RNA
Several microRNAs
https://en.wikipedia.org/wiki/RNA_polymerase_III
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RNA Processing
Post-transcriptional modification or co-transcriptional modification is a process in cell
biology by which, in eukaryotic cells, primary transcript RNA is converted into mature
RNA. A notable example is the conversion of precursor messenger RNA into mature
messenger RNA (mRNA), which includes splicing and occurs prior to protein synthesis. This process is vital for the correct translation of the genomes of eukaryotes, including humans, because the primary RNA transcript that is produced, as a result of transcription, contains both exons, which are either coding sections of the transcript or are
important sequences involved in translation, and introns, which are the non-coding
sections of the primary RNA transcript.
The pre-mRNA molecule undergoes three main modifications. These modifications are
5' capping, 3' polyadenylation, and RNA splicing, which occur in the cell nucleus before
the RNA is translated.
https://en.wikipedia.org/wiki/RNA_polymerase_III
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RNase
Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the
degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC
2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.
All organisms studied contain many RNases of many different classes, showing that
RNA degradation is a very ancient and important process. As well as cleaning of cellular RNA that is no longer required, RNases play key roles in the maturation of all RNA
molecules, both messenger RNAs that carry genetic material for making proteins, and
non-coding RNAs that function in varied cellular processes. In addition, active RNA
degradation systems are a first defense against RNA viruses, and provide the underlying machinery for more advanced cellular immune strategies such as RNAi.
Some cells also secrete copious quantities of non-specific RNases such as A and T1.
RNases are, therefore, extremely common, resulting in very short lifespans for any
RNA that is not in a protected environment. Intracellular RNAs may be protected from
RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).
Another mechanism of protection is ribonuclease inhibitor (RI), which comprises a
relatively large fraction of cellular protein (~0.1%) in some cell types, and which binds
to certain ribonucleases with the highest affinity of any protein-protein interaction; the
dissociation constant for the RI-RNase A complex is ~20 fM under physiological conditions. RI is used in most laboratories that study RNA to protect their samples against
degradation from environmental RNases.
Similar to restriction enzymes, which cleave highly specific sequences of doublestranded DNA, a variety of endoribonucleases that recognize and cleave specific sequences of single-stranded RNA have been recently classified.
RNases play a critical role in many biological processes, including angiogenesis and
self-incompatibility in flowering plants (angiosperms). Many stress-response toxins of
prokaryotic toxin-antitoxin systems have been shown to have RNase activity and homology.
https://en.wikipedia.org/wiki/Ribonuclease
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RNR
Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase,
is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a
critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is
maintained at a constant ratio during cell division and DNA repair.
A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP,
CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme
(thymidylate kinase) from dTMP (deoxythymidine monophosphate).
The enzyme ribonucleotide reductase (RNR) catalyzes the de novo synthesis of dNDPs.
Catalysis of ribonucleoside 5-diphosphates (NDPs) involves a reduction at the 2carbon of ribose 5-phosphate to form the 2-deoxy derivative-reduced 2deoxyribonucleoside 5-diphosphates (dNDPs). This reduction is initiated with the generation of a free radical. Following a single reduction, RNR requires electrons donated
from the dithiol groups of the protein thioredoxin. Regeneration of thioredoxin occurs
when nicotinamide adenine dinucleotide phosphate (NADPH) provides two hydrogen
atoms that are used to reduce the disulfide groups of thioredoxin.
Regulation of RNR is designed to maintain balanced quantities of dNTPs. Binding of
effector molecules either increases or decreases RNR activity. When ATP binds to the
allosteric activity site, it activates RNR. In contrast, when dATP binds to this site, it deactivates RNR. In addition to controlling activity, the allosteric mechanism also regulates the substrate specificity and ensures the enzyme produces an equal amount of
each dNTP for DNA synthesis. In all classes, binding of ATP or dATP to the allosteric
site induces reduction of cytidine 5-diphosphate (CDP) and uridine 5-diphosphate
(UDP); 2-deoxyguanosine 5-triphosphate (dGTP) induces reduction of adenosine 5diphosphate (ADP); and 2-deoxythymidine 5-triphosphate (dTTP) induces reduction
of guanosine 5-diphosphate (GDP).
https://en.wikipedia.org/wiki/Ribonucleotide_reductase
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Rosalind Franklin
Rosalind Elsie Franklin (25 July 1920 16 April 1958) was an English chemist and Xray crystallographer who made contributions to the understanding of the molecular
structures of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), viruses, coal, and
graphite.
Franklin is best known for her work on the X-ray diffraction images of DNA while at
King's College, London, which led to the discovery of the DNA double helix for which
James Watson, Francis Crick and Maurice Wilkins shared the Nobel Prize in Physiology or Medicine in 1962.
https://en.wikipedia.org/wiki/Rosalind_Franklin
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Rotenone
Rotenone is an odorless, colorless, crystalline isoflavone used as a broad-spectrum insecticide, piscicide, and pesticide. It occurs naturally in the seeds and stems of several
plants, such as the jicama vine plant, and the roots of several members of Fabaceae. It
was the first described member of the family of chemical compounds known as rotenoids.
Rotenone is used as a pesticide, insecticide, and as a nonselective piscicide (fish killer).
It works by interfering with the electron transport chain in mitochondria. To be specific, it inhibits the transfer of electrons from iron-sulfur centers in complex I to ubiquinone. This interferes with NADH during the creation of usable cellular energy (ATP).
Complex I is unable to pass off its electron to CoQ, creating a back-up of electrons
within the mitochondrial matrix. Cellular oxygen is reduced to the radical, creating a
reactive oxygen species, which can damage DNA and other components of the mitochondria.
https://en.wikipedia.org/wiki/Rotenone
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rRNAs
In molecular biology, ribosomal ribonucleic acid (rRNA) is the RNA component of the
ribosome, and is essential for protein synthesis in all living organisms. It constitutes
the predominant material within the ribosome, which is approximately 60% rRNA and
40% protein by weight. Ribosomes contain two major rRNAs and 50 or more proteins.
The ribosomal RNAs form two subunits, the large subunit (LSU) and small subunit
(SSU). The LSU rRNA acts as a ribozyme, catalyzing peptide bond formation.
Ribosomal RNA characteristics are important in evolution, thus taxonomy, and medicine.
rRNA is one of only a few gene products present in all cells. For this reason, genes
that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic
group, calculate related groups, and estimate rates of species divergence. As a result,
many thousands of rRNA sequences are known and stored in specialized databases
such as RDP-II and SILVA.
rRNA is the target of numerous clinically relevant antibiotics: chloramphenicol, erythromycin, kasugamycin, micrococcin, paromomycin, ricin, sarcin, spectinomycin, streptomycin, and thiostrepton.
rRNA have been shown to be the origin of species-specific microRNAs, like miR-663
in humans and miR-712 in mouse. These miRNAs originate from the Internal Transcribed Spacers of the rRNA.
In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The
large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal
RNAs). Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. The 3' end of the 16S ribosomal RNA (in a
ribosome) binds to a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.
Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of
cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 18S rRNA in most
eukaryotes is in the small ribosomal subunit, and the large subunit contains three
rRNA species (the 5S, 5.8S and 28S in mammals, 25S in plants, rRNAs).
https://en.wikipedia.org/wiki/Ribosomal_RNA
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Rubber
Natural rubber, also called India rubber or caoutchouc, as initially produced, cons
of polymers of the organic compound isoprene, with minor impurities of other org
compounds plus water. Malaysia is one of the leading producers of rubber. Forms
polyisoprene that are used as natural rubbers are classified as elastomers.
Currently, rubber is harvested mainly in the form of the latex from the para rubbe
or others. Latex is the polymer cis-1,4-polyisoprene with a molecular weight of
other materials, such as proteins, fatty acids, resins, and inorganic materials (salts
ral routes are completely different. Some natural rubber sources, such as gutta-pe
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Rumen
The rumen, also known as a paunch, forms the larger part of the reticulorum
mary site for microbial fermentation of ingested feed. The smaller part of th
rumen is the reticulum, which is fully continuous with the rumen, but differ
with regard to the texture of its lining.
https://en.wikipedia.org/wiki/Rumen
S-Adenosyl Homocysteine
https://en.wikipedia.org/wiki/S-Adenosyl-L-homocysteine
S-Adenosyl Methioinine
S-Adenosyl methionine (SAM-e) is a common co-substrate involved in methyl group
transfers, transsulfuration, and aminopropylation. Although these anabolic reactions
occur throughout the body, most SAM-e is produced and consumed in the liver. More
than 40 methyl transfers from SAM-e are known, to various substrates such as nucleic
acids, proteins, lipids and secondary metabolites. It is made from ATP and methionine
by methionine adenosyltransferase.
The reactions that produce, consume, and regenerate SAM-e are called the SAM-e cycle. In the first step of this cycle, the SAM-dependent methylases (EC 2.1.1) that use
SAM-e as a substrate produce S-adenosyl homocysteine as a product. This is hydrolyzed to homocysteine and adenosine by S-adenosylhomocysteine hydrolase EC 3.3.1.1
and the homocysteine recycled back to methionine through transfer of a methyl group
from 5-methyltetrahydrofolate, by one of the two classes of methionine synthases (i.e.
cobalamin-dependent (EC 2.1.1.13) or cobalamin-independent (EC 2.1.1.14)). This methionine can then be converted back to SAM-e, completing the cycle. In the ratelimiting step of the SAM cycle, MTHFR (methylenetetrahydrofolate reductase) irreversibly reduces 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate.
High levels of homocysteine have been associated with atherosclerosis (hardening and
narrowing of the arteries), as well as an increased risk of heart attacks, strokes, liver
damage, and possibly Alzheimer's disease. Therefore, vitamin B supplements are often
taken along with SAM. These vitamins help metabolize the homocysteine into other
useful compounds.
https://en.wikipedia.org/wiki/S-Adenosyl_methionine
S-adenosylhomocysteine Hydrolase
cyase is a highly conserved protein of about 430 to 470 amino acids. The fam
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S1 Pocket
The S1 pocket is the part of a serine protease where the substrate recognition and bin
ing occurs. The S1 pocket determines a serine protease's specificity. Show below are
schematic reprsesentations of the S1 pockets of three serine proteases.
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Saccharide
A carbohydrate/saccharide is a biological molecule consisting of carbon (C), hydrogen
(H) and oxygen (O) atoms, usually with a hydrogenoxygen atom ratio of 2:1 (as in water). In other words, it has the empirical formula Cn(H2O)n. Carbohydrates are technically hydrates of carbon. Some exceptions exist. For example, deoxyribose, a sugar
component of DNA, has the empirical formula C5H10O4. Structurally it is more accurate to view them as polyhydroxy aldehydes and ketones.
The term is most common in biochemistry, where it is a synonym of saccharide, a
group that includes sugars, starch, and cellulose. The saccharides are divided into four
chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars. The word saccharide comes from the Greek word (skkharon), meaning "sugar." While the
scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, grape sugar is
the monosaccharide glucose, cane sugar is the disaccharide sucrose, and milk sugar is
the disaccharide lactose.
Carbohydrates perform numerous roles in living organisms. Polysaccharides serve for
the storage of energy (e.g. starch and glycogen) and as structural components (e.g. cellulose in plants and chitin in arthropods). The 5-carbon monosaccharide ribose is an
important component of coenzymes (e.g. ATP, FAD and NAD+) and the backbone of
the genetic molecule known as RNA. The related deoxyribose is a component of DNA.
Saccharides and their derivatives include many other important biomolecules that play
key roles in the immune system, fertilization, preventing pathogenesis, blood clotting,
and development.
https://en.wikipedia.org/wiki/Carbohydrate
Saccharin
Saccharin is an artificial sweetener with effectively no food energy which is
400 times as sweet as sucrose or table sugar, but has a bitter or metallic afte
https://en.wikipedia.org/wiki/Saccharin
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SAICAR
SAICAR (or phosphoribosylaminoimidazolesuccinocarboxamide) is an intermediate in
the formation of purines. The conversion of ATP, L-aspartate, and 5-aminoimidazole4-carboxyribonucleotide (CAIR) to 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide, ADP, and phosphate by
phosphoribosylaminoimidazolesuccinocarboxamide synthetase (SAICAR synthetase)
represents the eighth step (bottom image below) of de novo purine nucleotide biosynthesis.
https://en.wikipedia.org/wiki/Phosphoribosylaminoimidazolesuccinocarboxamide
Salvage Pathways
Salvage pathways are used to recover bases and nucleosides that are formed
The salvaged bases and nucleosides can then be converted back into nucleo
https://en.wikipedia.org/wiki/Nucleotide_salvage
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Sarcolemma
The sarcolemma also called the myolemma, is the cell membrane of a striated muscle
fiber cell. It consists of a plasma membrane, which is a lipid bilayer, and an outer coat
consisting of a thin layer of polysaccharide material (glycocalyx) that contacts the basement membrane, which contains numerous thin collagen fibrils and specialized proteins such as laminin that provide a scaffold for the muscle fiber to adhere to. Through
transmembrane proteins residing in the plasma membrane, the actin skeleton inside
the cell is connected to the basement membrane and the cell's exterior. At each end of
the muscle fiber, the surface layer of the sarcolemma fuses with a tendon fiber, and the
tendon fibers in turn collect into bundles to form the muscle tendons that then adhere
onto bones.
The sarcolemma generally maintains the same function in muscle cells as the plasma
membrane does in other eukaryote cells. It acts as a barrier between the extracellular
and intracellular compartments, defining the individual muscle fiber from its surroundings. The lipid nature of the membrane allows it to separate the fluids of the intra- and
extracellular compartments, since it is only selectively permeable to water through aquaporin channels. As in other cells this allows for the compositions of the compartments to be controlled by selective transport through the membrane. Membrane proteins, such as ion pumps, may create ion gradients with the consumption of ATP, that
may later be used to drive transport of other substances through the membrane (Cotransport) or generate electrical impulses such as Action potentials.
A special feature of the sarcolemma is that it invaginates into the cytoplasm of the muscle cell, forming membranous tubules radially and longitudinally within the fiber
called transverse tubules (T-tubules). On either side of the transverse tubules are terminal cisterna enlargements of smooth endoplasmic reticulum termed sarcoplasmatic reticulum (SR) in muscle. A transverse tubule surrounded by two SR cisterna are known
as triads, and the contact between these structures is located at the junction of the A
and I bands.
https://en.wikipedia.org/wiki/Sarcolemma
Sarcomeres
A sarcomere (Greek sarx "flesh", meros "part") is the basic unit of striated muscle tissue. Skeletal muscles are composed of tubular muscle cells (myocytes called muscle fibers) which are formed in a process known as myogenesis. Muscle fibers are composed
of tubular myofibrils. Myofibrils are composed of repeating sections of sarcomeres,
which appear under the microscope as dark and light bands. Sarcomeres are composed
of long, fibrous proteins as filaments that slide past each other when a muscle contracts or relaxes.
Two of the important proteins are myosin, which forms the thick filament, and actin,
which forms the thin filament. Myosin has a long, fibrous tail and a globular head,
which binds to actin. The myosin head also binds to ATP, which is the source of energy
for muscle movement. Myosin can only bind to actin when the binding sites on actin
are exposed by calcium ions.
The sarcomeres are what give skeletal and cardiac muscles their striated appearance.
A sarcomere is defined as the segment between two neighboring Z-lines (or Z-discs,
or Z bodies). In electron micrographs of cross-striated muscle, the Z-line (from the German "Zwischenscheibe", the disc in between the I bands) appears as a series of dark
lines.
Surrounding the Z-line is the region of the I-band (for isotropic). I-band is the zone of
thin filaments that is not superimposed by thick filaments.
Following the I-band is the A-band (for anisotropic). Named for their properties under a polarizing microscope. An A-band contains the entire length of a single thick filament.
Within the A-band is a paler region called the H-zone (from the German "heller",
brighter). Named for their lighter appearance under a polarization microscope. Hband is the zone of the thick filaments that is not superimposed by the thin filaments.
Within the H-zone is a thin M-line (from the German "Mittelscheibe", the disc in the
middle of the sarcomere) formed of cross-connecting elements of the cytoskeleton.
The relationship between the proteins and the regions of the sarcomere are as follows:
Actin filaments, the thin filaments, are the major component of the I-band and extend into the A-band.
Myosin filaments, the thick filaments, are bipolar and extend throughout the A-band.
They are cross-linked at the center by the M-band.
The giant protein titin (connectin) extends from the Z-line of the sarcomere, where it
binds to the thick filament (myosin) system, to the M-band, where it is thought to interact with the thick filaments. Titin (and its splice isoforms) is the biggest single highly
elasticated protein found in nature. It provides binding sites for numerous proteins
and is thought to play an important role as sarcomeric ruler and as blueprint for the assembly of the sarcomere.
Another giant protein, nebulin, is hypothesized to extend along the thin filaments
and the entire I-Band. Similar to titin, it is thought to act as a molecular ruler along for
thin filament assembly.
Several proteins important for the stability of the sarcomeric structure are found in
the Z-line as well as in the M-band of the sarcomere.
Actin filaments and titin molecules are cross-linked in the Z-disc via the Z-line protein -actinin.
The M-band proteins myomesin as well as C-protein crosslink the thick filament system (myosins) and the M-band part of titin (the elastic filaments).
The interaction between actin and myosin filaments in the A-band of the sarcomere is
responsible for the muscle contraction (sliding filament model).
https://en.wikipedia.org/wiki/Sarcomere
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Sarcoplasmic Reticulum
The sarcoplasmic reticulum (SR) is smooth ER found in myocytes. The only structural
difference between this organelle and the smooth endoplasmic reticulum is the medley
of proteins they have, both bound to their membranes and drifting within the confines
of their lumens. This fundamental difference is indicative of their functions: The endoplasmic reticulum synthesizes molecules, while the sarcoplasmic reticulum stores calcium ions and pumps them out into the sarcoplasm when the muscle fiber is stimulated. After their release from the sarcoplasmic reticulum, calcium ions interact with
contractile proteins that utilize ATP to shorten the muscle fiber. The sarcoplasmic reticulum plays a major role in excitation-contraction coupling.
https://en.wikipedia.org/wiki/Endoplasmic_reticulum#Sarcoplasmic_reticulum
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Saturated
each carbon centre has four single bonds as is characteristic of other satura
single and one double bond. The term is often used to describe fats or the f
them that lack double bonds.
https://en.wikipedia.org/wiki/Saturation_(chemistry)
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Saturated Fat
A saturated fat is a fat in which the fatty acids all have single bonds. Fats are made of
two kinds of smaller molecules: monoglyceride and fatty acids. Fats are made of long
chains of carbon (C) atoms. Some carbon atoms are linked by single bonds (-C-C-) and
others are linked by double bonds (-C=C-). Double bonds can react with hydrogen to
form single bonds. They are called saturated, because the second bond is broken up
and each half of the bond is attached to (saturated with) a hydrogen atom. Most animal
fats are saturated. The fats of plants and fish are generally unsaturated. Saturated fats
tend to have higher melting points than their corresponding unsaturated fats, leading
to the popular understanding that saturated fats tend to be solids at body temperatures, while unsaturated fats tend to be liquid oils.
Various fats contain different proportions of saturated and unsaturated fat. Examples
of foods containing a high proportion of saturated fat include animal fat products such
as cream, cheese, butter, other whole milk dairy products and fatty meats which also
contain dietary cholesterol. Certain vegetable products have high saturated fat content,
such as coconut oil and palm kernel oil. Many prepared foods are high in saturated fat
content, such as pizza, dairy desserts, and sausage.
The effect of saturated fat on risk of disease is controversial. Many reviews recommend
a diet low in saturated fat and argue it will lower risks of cardiovascular diseases, diabetes, or death. However, other reviews have rejected those arguments.
https://en.wikipedia.org/wiki/Saturated_fat
(containing no double bonds) or unsaturated (having at least one double bond). Most
naturally occurring fatty acids have an unbranched chain of an even number of carbon
atoms, from 4 to 28. Fatty acids are usually derived from triglycerides or phospholipids. Fatty acids are important sources of fuel because, when metabolized, they yield
large quantities of ATP. Many cell types can use either glucose or fatty acids for this
purpose. Long-chain fatty acids cannot cross the bloodbrain barrier and so cannot b
used as fuel by the cells of the central nervous system. However, medium-chain fatty
acids octanoic acid and heptanoic acid can be used, in addition to glucose and ketone
bodies.
Pictured below is a saturated fatty acid, stearic acid
https://en.wikipedia.org/wiki/Fatty_acid
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Saturation
The term saturation is used to refer to the relative amount of single bonds i
cule. Something that is highly saturated has relatively few double bonds, w
compound that is highly unsaturated has many double bonds.
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or substrate. The common enzyme cofactor PLP forms a Schiff base with a l
Scramblase
https://en.wikipedia.org/wiki/Phospholipid_scramblase
Scrapie
Scrapie is a fatal, degenerative disease that affects the nervous systems of sheep and
goats. It is one of several transmissible spongiform encephalopathies (TSEs), which are
related to bovine spongiform encephalopathy (BSE or "mad cow disease") and chronic
wasting disease of deer. Like other spongiform encephalopathies, scrapie is caused by
a prion.
The name scrapie is derived from one of the clinical signs of the condition, wherein affected animals will compulsively scrape off their fleeces against rocks, trees, or fences.
The disease apparently causes an itching sensation in the animals. Other clinical signs
include excessive lip smacking, altered gaits, and convulsive collapse.
Scrapie is infectious and transmissible among conspecifics, so one of the most common ways to contain it (since it is incurable) is to quarantine and destroy those affected. However, scrapie tends to persist in flocks and can also arise apparently spontaneously in flocks that have not previously had cases of the disease. The mechanism of
transmission between animals and other aspects of the biology of the disease are only
poorly understood, and these are active areas of research. Recent studies suggest prions may be spread through urine and persist in the environment for decades.
Scrapie usually affects sheep around three to five years of age. The potential for transmission at birth and from contact with placental tissues is apparent. No evidence indicates scrapie is infectious to humans.
https://en.wikipedia.org/wiki/Scrapie
Scurvy
scurvy are initially fatigue, followed by formation of spots on the skin, spon
and bleeding from the mucous membranes. Spots are most abundant on th
legs, and a person may look pale, feel depressed, and be partially immobiliz
scurvy advances, there can be open, suppurating wounds, loss of teeth, yello
ver, neuropathy and finally death from bleeding.
https://en.wikipedia.org/wiki/Scurvy
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SDS
Sodium dodecyl sulfate, synonymously sodium lauryl sulfate (or laurilsulfate - SDS or
SLS, respectively), is a synthetic organic compound with the formula
CH3(CH2)11SO4Na. The compound is commonly used in to aid lysing cells during DNA
extraction, and for denaturing proteins in preparation for electrophoresis in the SDSPAGE technique.
It is an anionic surfactant used in many cleaning and hygiene products. The sodium
salt is of an organosulfate class of organics. It consists of a 12-carbon tail attached to a
sulfate group, i.e., it is the sodium salt of dodecyl hydrogen sulfate, the ester of dodecyl
alcohol and sulfuric acid. Its hydrocarbon tail combined with a polar "headgroup" give
the compound amphiphilic properties and so make it useful as a detergent. Also derived as a component of mixtures produced from inexpensive coconut and palm oils,
SDS is a common component of many domestic cleaning, personal hygiene and cosmetic, pharmaceutical, and food products, as well as of industrial and commercial
cleaning and product formulations.
https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate#Laboratory_applications
SDS-PAGE
A gel electrophoresis technique that uses SDS to linearize proteins and to impart a
negative charge to linearized proteins in order to determine their molecular weight irrespective of their shape.
When a protein mixture is heated to 100C in presence of SDS, the detergent wraps
around the polypeptide backbone. It binds to polypeptides in a constant weight ratio of
1.4 g SDS/g of polypeptide. In this process, the intrinsic charges of polypeptides become negligible when compared to the negative charges contributed by SDS. Thus
polypeptides after treatment become rod-like structures possessing a uniform charge
density, that is same net negative charge per unit weight. The electrophoretic mobilities of these proteins is a linear function of the logarithms of their molecular weights.
Without SDS, different proteins with similar molecular weights would migrate differently due to differences in mass-charge ratio, as each protein has an isoelectric point
and molecular weight particular to its primary structure. This is known as native
PAGE. Adding SDS solves this problem, as it binds to and unfolds the protein, giving a
near uniform negative charge along the length of the polypeptide.
https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophoresis
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Se-methylselenocysteine
Se-methylselenocysteine (also known as methylselenocysteine), is an analog of Smethylcysteine in which the sulfur atom is replaced with a selenium atom. It is an inhibitor of DMBA-induced mammary tumors and a chemopreventive agent that blocks
cell cycle progression and proliferation of premalignant mammary lesions and induces
apoptosis of cancer cell lines in culture.
Apoptosis has been proposed as the most plausible mechanism for the chemopreventive activities of selenocompounds. Se-Methylselenocysteine was more efficient at inducing apoptosis than selenite, but was less toxic." The "selenite-induced cell death
could be derived from necrosis rather than apoptosis, since selenite did not significantly induce several apoptotic phenomena, including the activation of caspase-3."
In the Nutritional Prevention of Cancer Trial, selenized yeast resulted in "a reduction
in the incidence of prostate cancer and in total cancer incidence. Subsequent anticancer studies using selenomethionine did not show any benefit against cancer, but selenized yeast contains both selenomethionine and methylselenocysteine.
https://en.wikipedia.org/wiki/Methylselenocysteine
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SECIS
The SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element
around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the cell to translate UGA codons as selenocysteines.
(UGA is normally a stop codon.) SECIS elements are thus a fundamental aspect of messenger RNAs encoding selenoproteins, proteins that include one or more selenocysteine residues.
In bacteria the SECIS element appears soon after the UGA codon it affects. In archaea
and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine. One archaeal SECIS element, in
Methanococcus, is located in the 5' UTR.
The SECIS element appears defined by sequence characteristics, i.e. particular nucleotides tend to be at particular positions in it, and a characteristic secondary structure.
The secondary structure is the result of base-pairing of complementary RNA nucleotides, and causes a hairpin-like structure. The eukaryotic SECIS element includes noncanonical A-G base pairs, which are uncommon in nature, but are critically important
for correct SECIS element function. Although the eukaryotic, archaeal and bacterial SECIS elements each share a general hairpin structure, they are not alignable, e.g. an
alignment-based scheme to recognize eukaryotic SECIS elements will not be able to recognize archaeal SECIS elements.
https://en.wikipedia.org/wiki/SECIS_element
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The second law of thermodynamics states that the total entropy of an isolat
always increases over time, or remains constant in ideal cases where the sys
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Second Messengers
Second messengers are intracellular signaling molecules released by the cell to trigger
physiological changes such as proliferation, differentiation, migration, survival, and
apoptosis. Secondary messengers are therefore one of the initiating components of intracellular signal transduction cascades. Examples of second messenger molecules include cyclic AMP, cyclic GMP, inositol trisphosphate, diacylglycerol, and calcium. The
cell releases second messenger molecules in response to exposure to extracellular signaling moleculesthe first messengers.
First messengers are extracellular factors, often hormones or neurotransmitters, such
as epinephrine, growth hormone, and serotonin. Because peptide hormones and neurotransmitters typically are biochemically hydrophilic molecules, these first messengers
may not physically cross the phospholipid bilayer cell membrane to initiate changes
within the cell directlyunlike steroid hormones, which usually do. This functional
limitation necessitates the cell to devise signal transduction mechanisms to transduce
first messenger into second messengers, so that the extracellular signal may be propagated intracellularly.
An important feature of the second messenger signaling system is that second messengers may be coupled downstream to multi-cyclic kinase cascades to greatly amplify the
strength of the original first messenger signal. For example, Ras.GTP signals link with
the Mitogen Activated Protein Kinase (MAPK) cascade to amplify the allosteric activation of proliferative transcription factors such as Myc and CREB.
https://en.wikipedia.org/wiki/Second_messenger_system
https://en.wikipedia.org/wiki/Active_transport#Secondary_active_transport
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Secondary Amine
An aliphatic amine has no aromatic ring attached directly to the nitrogen atom. Aromatic amines have the nitrogen atom connected to an aromatic ring as in the various
anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents. The presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect.
Amines are organized into four subcategories:
Primary amines Primary amines arise when one of three hydrogen atoms in
ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include
methylamine, ethanolamine (2-aminoethanol), and the buffering agent tris, while primary aromatic amines include aniline.
Secondary amines Secondary amines have two organic substituents (alkyl,
aryl or both) bound to N together with one hydrogen (or no hydrogen if one of the substituent bonds is double). Important representatives include dimethylamine and methylethanolamine, while an example of an aromatic amine would be diphenylamine.
Tertiary amines In tertiary amines, all three hydrogen atoms are replaced by
organic substituents. Examples include trimethylamine, which has a distinctively fishy
smell, or triphenylamine.
Cyclic amines Cyclic amines are either secondary or tertiary amines. Examples of cyclic amines include the 3-membered ring aziridine and the six-membered
ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of cyclic tertiary amines.
It is also possible to have four organic substituents on the nitrogen. These species are
not amines but are quaternary ammonium cations and have a charged nitrogen center.
Quaternary ammonium salts exist with many kinds of anions.
https://en.wikipedia.org/wiki/Amine
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Secondary Structure
Protein secondary structure is the general three-dimensional form of local segments of
proteins. Secondary structure can be formally defined by the pattern of hydrogen
bonds of the protein (such as alpha helices and beta sheets) that are observed in an
atomic-resolution structure. More specifically, the secondary structure is defined by
the patterns of hydrogen bonds formed between amine hydrogen and carbonyl oxygen
atoms contained in the backbone peptide bonds of the protein. The secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot; thus, a segment of residues with
such dihedral angles may be called a helix, regardless of whether it has the correct hydrogen bonds. The secondary structure may be provided by crystallographers in the
corresponding PDB file.
Secondary structure does not describe the specific identity of amino acids in the protein which are defined as the primary structure, nor the global atomic positions in
three-dimensional space, which are considered to be tertiary structure. Other types of
biopolymers such as nucleic acids also possess characteristic secondary structures.
The most common secondary structures are helices and sheets. Other helices, such
as the 310 helix and helix, are calculated to have energetically favorable hydrogenbonding patterns but are rarely observed in natural proteins except at the ends of
helices due to unfavorable backbone packing in the center of the helix. Other extended
structures such as the polyproline helix and sheet are rare in native state proteins but
are often hypothesized as important protein folding intermediates. Tight turns and
loose, flexible loops link the more "regular" secondary structure elements. The random
coil is not a true secondary structure, but is the class of conformations that indicate an
absence of regular secondary structure.
Amino acids vary in their ability to form the various secondary structure elements. Proline and glycine are sometimes known as "helix breakers" because they disrupt the
regularity of the helical backbone conformation. However, both have unusual conformational abilities and are commonly found in turns. Amino acids that prefer to adopt
helical conformations in proteins include methionine, alanine, leucine, glutamate and
lysine ("MALEK" in amino-acid 1-letter codes). By contrast, the large aromatic residues (tryptophan, tyrosine and phenylalanine) and C-branched amino acids (isoleucine, valine, and threonine) prefer to adopt -strand conformations. However, these
preferences are not strong enough to produce a reliable method of predicting secondary structure from sequence alone.
Show below - an a-helix stabilized by H-bonds (yellow)
https://en.wikipedia.org/wiki/Protein_secondary_structure
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Secretory Vesicles
Secretory vesicles contain materials that are to be excreted from the cell. Cells have
many reasons to excrete materials. One reason is to dispose of wastes. Another reason
is tied to the function of the cell. Within a larger organism, some cells are specialized to
produce certain chemicals. These chemicals are stored in secretory vesicles and released when needed.
Types of secretory vesicles
Synaptic vesicles are located at presynaptic terminals in neurons and store neurotransmitters. When a signal comes down an axon, the synaptic vesicles fuse with the
cell membrane releasing the neurotransmitter so that it can be detected by receptor
molecules on the next nerve cell.
In animals endocrine tissues release hormones into the bloodstream. These hormones are stored within secretory vesicles. A good example is the endocrine tissue
found in the islets of Langerhans in the pancreas. This tissue contains many cell types
that are defined by which hormones they produce.
Secretory vesicles hold the enzymes that are used to make the cell walls of
plants, protists, fungi, bacteria, and Archaea cells as well as the extracellular matrix of
animal cells.
Bacteria, Archaea, fungi, and parasites release membrane vesicles (MVs) containing varied but specialized toxic compounds and biochemical signal molecules,
which are transported to target cells to initiate processes in favor of the microbe, which
include invasion of host cells and killing of competing microbes in the same niche.
Shown below - lipid vesicles
https://en.wikipedia.org/wiki/Vesicle_(biology_and_chemistry)#Secretory_vesicles
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Sedoheptulose 1,7-bisphosphatase
https://en.wikipedia.org/wiki/Sedoheptulose-bisphosphatase
Index
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Sedoheptulose-1,7 bisphosphatase
https://en.wikipedia.org/wiki/Sedoheptulose-bisphosphatase
Sedoheptulose-1,7 bisphosphate
Sedoheptulose-7-phosphate
Sedoheptulose 7-phosphate is an intermediate in the pentose phosphate pathway.
It is formed by transketolase and acted upon by transaldolase.
Sedoheptulokinase is an enzyme that uses sedoheptulose and ATP to produce ADP and
sedoheptulose 7-phosphate.
Sedoheptulose-bisphosphatase is an enzyme that uses sedoheptulose 1,7-bisphosphate
and H2O to produce sedoheptulose 7-phosphate and phosphate.
https://en.wikipedia.org/wiki/Sedoheptulose_7-phosphate
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G-G
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 6 - Metabolism: Sugars
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Chapter 9 - Point by Point: Metabolism
Selectins
The selectins (cluster of differentiation 62 or CD62) are a family of cell adhesion molecules (or CAMs). All selectins are single-chain transmembrane glycoproteins that share
similar properties to C-type lectins due to a related amino terminus and calciumdependent binding. Selectins bind to sugar moieties and so are considered to be a type
of lectin, cell adhesion proteins that bind sugar polymers.
Selectins are involved in constitutive lymphocyte homing, and in chronic and acute inflammation processes, including post-ischemic inflammation in muscle, kidney and
heart, skin inflammation, atherosclerosis, glomerulonephritis and lupus erythematosus and cancer metastasis.
During an inflammatory response, stimuli such as histamine and thrombin cause endothelial cells to mobilize P-selectin from stores inside the cell to the cell surface. In addition, cytokines such as TNF-alpha stimulate the expression of E-selectin and additional
P-selectin a few hours later.
As the leukocyte rolls along the blood vessel wall, the distal lectin-like domain of the selectin binds to certain carbohydrate groups presented on proteins (such as PSGL-1) on
the leukocyte, which slows the cell and allows it to leave the blood vessel and enter the
site of infection. The low-affinity nature of selectins is what allows the characteristic
"rolling" action attributed to leukocytes during the leukocyte adhesion cascade.
Each selectin has a carbohydrate recognition domain that mediates binding to specific
glycans on apposing cells. They have remarkably similar protein folds and carbohydrate binding residues, leading to overlap in the glycans to which they bind.
Selectins bind to the sialyl Lewis X (SLex) determinant NeuAc2-3Gal1-4(Fuc13)GlcNAc. However, SLex, per se, does not constitute an effective selectin receptor. Instead, SLex and related sialylated, fucosylated glycans are components of more extensive binding determinants.
The best-characterized ligand for the three selectins is P-selectin glycoprotein ligand-1
(PSGL-1), which is a mucin-type glycoprotein expressed on all white blood cells.
https://en.wikipedia.org/wiki/Selectin
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Selection
Selection generally refers to the pressures on crops and organisms to evolve. These
pressures include natural selection, and, in eukaryotic cells that reproduce sexually,
sexual selection. Certain phenotypic traits (characteristics of an organism)or, on a genetic level, alleles of genessegregate within a population, where individuals with
adaptive advantages or traits tend to succeeded more than their peers when they reproduce, and so contribute more offspring to the succeeding generation.
Whether or not selection takes place depends on the conditions in which the individuals of a species find themselves. Adults, juveniles, embryos, and gamete eggs and
sperm all undergo selection. Factors fostering natural selection include sexual selection, primarily caused by mate choice in the mating phase of sexual reproduction, limits on resources (nourishment, habitat space, mates) and the existence of threats
(predators, disease, adverse weather). Biologists often refer to such factors as selective
or evolutionary pressures.
Natural selection has, since the 1930s, included sexual selection because biologists at
the time did not think it was of great importance though it has become to be seen as
more important in the 21st Century. Other subcategories of natural selection include
ecological selection, stabilizing selection, disruptive selection and directional selection.
Selective breeding can be seen in the breeding of dogs, and the domestication of farm
animals and crops, now commonly known as selective breeding.
https://en.wikipedia.org/wiki/Selection_(biology)
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Selenium
Selenium is a chemical element with symbol Se and atomic number 34. Sele
are toxic in large amounts, but trace amounts are necessary for cellular func
Index
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Selenocysteine
Selenocysteine (abbreviated as Sec or U, in older publications also as Se-Cys) is the
21st proteinogenic amino acid.
Selenocysteine exists naturally in three domains of life, but not in every lineage, as a
building block of selenoproteins. Selenocysteine is a cysteine analogue with a
selenium-containing selenol group in place of the sulfur-containing thiol group.
Unlike other amino acids present in biological proteins, selenocysteine is not coded for
directly in the genetic code. Instead, it is encoded in a special way by a UGA codon,
which is normally a stop codon. Such a mechanism is called translational recoding and
its efficiency depends on the selenoprotein being synthesized and on translation initiation factors. When cells are grown in the absence of selenium, translation of selenoproteins terminates at the UGA codon, resulting in a truncated, nonfunctional enzyme.
The UGA codon is made to encode selenocysteine by the presence of a selenocysteine
insertion sequence (SECIS) in the mRNA. The SECIS element is defined by characteristic nucleotide sequences and secondary structure base-pairing patterns. In bacteria,
the SECIS element is typically located immediately following the UGA codon within
the reading frame for the selenoprotein. In Archaea and in eukaryotes, the SECIS element is in the 3' untranslated region (3' UTR) of the mRNA, and can direct multiple
UGA codons to encode selenocysteine residues.
No free pool of selenocysteine exists in the cell. Its high reactivity would cause damage
to cells. Instead, cells store selenium in the less reactive selenide form (H2Se). Selenocysteine synthesis occurs on a specialized tRNA, which also functions to incorporate it
into nascent polypeptides.
Selenocysteine is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases,
glycine reductases, selenophosphate synthetase 2, methionine-R-sulfoxide reductase
B1 (SEPX1), and some hydrogenases).
https://en.wikipedia.org/wiki/Selenocysteine
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Selenomethionine
Selenomethionine is a naturally occurring amino acid. The L-selenomethionine enantiomer is the main form of selenium found in Brazil nuts, cereal grains, soybeans, and
grassland legumes. In vivo, selenomethionine is randomly incorporated instead of methionine. Selenomethionine is readily oxidized.
Selenomethionine's antioxidant activity arises from its ability to deplete reactive oxygen species. Selenium and sulfur are chalcogens that share many chemical properties
so the substitution of methionine with selenomethionine may have only a limited effect
on protein structure and function. However, the incorporation of selenomethionine
into tissue proteins and keratin in horses causes alkali disease.
Alkali disease is characterized by emaciation, loss of hair, deformation and shedding of
hooves, loss of vitality, and erosion of the joints of long bones.
https://en.wikipedia.org/wiki/Selenomethionine
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Selenoprotein P
In molecular biology, the protein domain SelP stands for selenoprotein P which
dues. It is a secreted glycoprotein, often found in the plasma. It's precise functio
SelP may have antioxidant properties. It can attach to epithelial cells, and may p
vascular endothelial cells against peroxynitrite toxicity. The high selenium cont
The promoter structure of bovine SelP suggests that it may be involved in count
heavy metal intoxication, and may also have a developmental function.
https://en.wikipedia.org/wiki/Selenoprotein_P
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Selenoproteins
A selenoprotein is any protein that includes a selenocysteine (Sec, U, Se-Cys) amino
acid residue. Selenoproteins exist in all major forms of life, eukaryotes, bacteria and archaea. Among eukaryotes, selenoproteins appear to be common in animals, but rare or
absent in other phyla (one has been identified in the green alga Chlamydomonas, but
almost none in other plants or in fungi). Selenium occurs in proteins as unspecifically
incorporated selenomethionine, which replaces methionine residues. Proteins containing such unspecifically incorporated selenomethionine residues are not regarded as
selenoproteins.
Human selenoproteins include:
Iodothyronine deiodinases: DIO1, DIO2, DIO3
Glutathione peroxidases: GPX1, GPX2, GPX3, GPX4, GPX6
Selenoproteins: SelH (C11orf31), SelI (EPT1), SelK, SelM, SelN (SEPN1), SelO, SelP
(SEPP1), SelR (MSRB1), SelS, SelT, SelV, SelW (SEPW1), Sel15
Selenophosphate synthetase: (SEPHS2, SPS2)
Thioredoxin reductases: TXNRD1, TXNRD2, TXNRD3
https://en.wikipedia.org/wiki/Selenoprotein
Self-splicing RNA
Self-splicing occurs for rare introns that form a ribozyme, performing the fu
the spliceosome by RNA alone. There are three kinds of self-splicing intron
Group II and Group III. Group I and II introns perform splicing similar to t
some without requiring any protein. This similarity suggests that Group I a
ancient, and may have existed in an RNA world present before protein. Abo
all bacterial genomes sequenced to date contain at least one Group II intron
https://en.wikipedia.org/wiki/RNA_splicing#Self-splicing
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https://en.wikipedia.org/wiki/Semiconservative_replication
Sensory Neurons
Sensory neurons are nerve cells that transmit sensory information (sight, so
ing, etc.). They are activated by sensory input, and send projections to other
travels down the nerve fiber to the central nervous system, where it may act
less complex organisms, such as the hydra, sensory neurons transmit data t
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Sequential Model
losterism of enzymes. This model for allosteric regulation suggests that the su
the binding of the ligand causes conformational change, whereas in the Conce
(MWC) model, it does not. Although the subunits go through conformational
independently the switch of one subunit makes the other subunits more likely
Serine
Serine (abbreviated as Ser or S) encoded by the codons UCU, UCC, UCA, UCG, AGU
and AGC is an -amino acid that is used in the biosynthesis of proteins. It contains an
-amino group (which is in the protonated form under biological conditions), a carboxyl group (which is in the deprotonated form in physiological conditions), and a side
chain consisting of a hydroxymethyl group, classifying it as a polar amino acid. It can
be synthesized in the human body under normal physiological circumstances, making
it a nonessential amino acid.
Serine plays an important role in the catalytic function of many enzymes. It has been
shown to occur in the active sites of chymotrypsin, trypsin, and many other enzymes.
The so-called nerve gases and many substances used in insecticides have been shown
to act by combining with a residue of serine in the active site of acetylcholine esterase,
inhibiting the enzyme completely.
Serine sidechains are often hydrogen bonded; the commonest small motifs formed are
ST turns, ST motifs (often at the beginning of alpha helices) and ST staples (usually at
the middle of alpha helices).
As a constituent (residue) of proteins, its side chain can undergo O-linked glycosylation, which may be functionally related to diabetes. It is one of three amino acid residues that are commonly phosphorylated by kinases during cell signaling in eukaryotes.
Phosphorylated serine residues are often referred to as phosphoserine.
Serine proteases are a common type of protease.
https://en.wikipedia.org/wiki/Serine
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Serine Hydroxymethyltransferase
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Serine Protease
Serine proteases (or serine endopeptidases) are enzymes that cleave peptide bonds in
proteins, in which serine serves as the nucleophilic amino acid at the (enzyme's) active
site. They are found ubiquitously in both eukaryotes and prokaryotes. Serine proteases
fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like)
or subtilisin-like. In humans, they are responsible for co-ordinating various physiological functions, including digestion, immune response, blood coagulation and reproduction.
The main player in the catalytic mechanism in the chymotrypsin and subtillisin-related
enzymes mentioned above is the catalytic triad. The triad is located in the active site of
the enzyme, where catalysis occurs, and is preserved in all serine protease enzymes.
The triad is a coordinated structure consisting of three amino acids: His 57, Ser 195
(hence the name "serine protease") and Asp 102. These three key amino acids each
play an essential role in the cleaving ability of the proteases. While the amino acid
members of the triad are located far from one another on the sequence of the protein,
due to folding, they will be very close to one another in the heart of the enzyme. The
particular geometry of the triad members are highly characteristic to their specific function: it was shown that the position of just four points of the triad characterize the function of the containing enzyme.
In the event of catalysis, an ordered mechanism occurs in which several intermediates
are generated. The catalysis of the peptide cleavage can be seen as a ping-pong catalysis, in which a substrate binds (in this case, the polypeptide being cleaved), a product is
released (the N-terminus "half" of the peptide), another substrate binds (in this case,
water), and another product is released (the C-terminus "half" of the peptide).
Each amino acid in the triad performs a specific task in this process:
The serine has an -OH group that is able to act as a nucleophile, attacking the carbonyl carbon of the scissile peptide bond of the substrate.
A pair of electrons on the histidine nitrogen has the ability to accept the hydrogen
from the serine -OH group, thus coordinating the attack of the peptide bond.
The carboxyl group on the aspartic acid in turn hydrogen bonds with the histidine,
making the nitrogen atom mentioned above much more electronegative.
Additional amino acids of the protease, Gly 193 and Ser 195, are involved in creating
what is called an oxyanion hole. Both Gly 193 and Ser 195 can donate backbone hydrogens for hydrogen bonding. When the tetrahedral intermediate of step 1 and step 3 are
generated, the negative oxygen ion, having accepted the electrons from the carbonyl
double bond fits perfectly into the oxyanion hole. In effect, serine proteases preferentially bind the transition state and the overall structure is favored, lowering the activation energy of the reaction. This "preferential binding" is responsible for much of the
catalytic efficiency of the enzyme.
https://en.wikipedia.org/wiki/Serine_protease
Serine Proteases
Serine proteases (or serine endopeptidases) are enzymes that cleave peptide bonds in
proteins, in which serine serves as the nucleophilic amino acid at the (enzyme's) active
site. They are found ubiquitously in both eukaryotes and prokaryotes. Serine proteases
fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like)
or subtilisin-like. In humans, they are responsible for co-ordinating various physiological functions, including digestion, immune response, blood coagulation and reproduction.
The main player in the catalytic mechanism in the chymotrypsin and subtillisin-related
enzymes mentioned above is the catalytic triad. The triad is located in the active site of
the enzyme, where catalysis occurs, and is preserved in all serine protease enzymes.
The triad is a coordinated structure consisting of three amino acids: His 57, Ser 195
(hence the name "serine protease") and Asp 102. These three key amino acids each
play an essential role in the cleaving ability of the proteases. While the amino acid
members of the triad are located far from one another on the sequence of the protein,
due to folding, they will be very close to one another in the heart of the enzyme. The
particular geometry of the triad members are highly characteristic to their specific function: it was shown that the position of just four points of the triad characterize the function of the containing enzyme.
In the event of catalysis, an ordered mechanism occurs in which several intermediates
are generated. The catalysis of the peptide cleavage can be seen as a ping-pong catalysis, in which a substrate binds (in this case, the polypeptide being cleaved), a product is
released (the N-terminus "half" of the peptide), another substrate binds (in this case,
water), and another product is released (the C-terminus "half" of the peptide).
Each amino acid in the triad performs a specific task in this process:
The serine has an -OH group that is able to act as a nucleophile, attacking the carbonyl carbon of the scissile peptide bond of the substrate.
A pair of electrons on the histidine nitrogen has the ability to accept the hydrogen
from the serine -OH group, thus coordinating the attack of the peptide bond.
The carboxyl group on the aspartic acid in turn hydrogen bonds with the histidine,
making the nitrogen atom mentioned above much more electronegative.
Additional amino acids of the protease, Gly 193 and Ser 195, are involved in creating
what is called an oxyanion hole. Both Gly 193 and Ser 195 can donate backbone hydrogens for hydrogen bonding. When the tetrahedral intermediate of step 1 and step 3 are
generated, the negative oxygen ion, having accepted the electrons from the carbonyl
double bond fits perfectly into the oxyanion hole. In effect, serine proteases preferentially bind the transition state and the overall structure is favored, lowering the activation energy of the reaction. This "preferential binding" is responsible for much of the
catalytic efficiency of the enzyme.
https://en.wikipedia.org/wiki/Serine_protease
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Serotonin
Serotonin is a monoamine neurotransmitter. Biochemically derived from tryptophan,
serotonin is primarily found in the gastrointestinal tract (GI tract), blood platelets, and
the central nervous system (CNS) of animals, including humans. It is popularly
thought to be a contributor to feelings of well-being and happiness.
Approximately 90% of the human body's total serotonin is located in the enterochromaffin cells in the GI tract, where it is used to regulate intestinal movements. The serotonin is secreted luminally and basolaterally which leads to increased serotonin uptake
by circulating platelets and activation after stimulation, which gives increased stimulation of myenteric neurons and gastrointestinal motility. The remainder is synthesized
in serotonergic neurons of the CNS, where it has various functions. These include the
regulation of mood, appetite, and sleep. Serotonin also has some cognitive functions,
including memory and learning. Modulation of serotonin at synapses is thought to be a
major action of several classes of pharmacological antidepressants.
Serotonin secreted from the enterochromaffin cells eventually finds its way out of tissues into the blood. There, it is actively taken up by blood platelets, which store it.
When the platelets bind to a clot, they release serotonin, where it serves as a vasoconstrictor and helps to regulate hemostasis and blood clotting. Serotonin also is a growth
factor for some types of cells, which may give it a role in wound healing. There are various serotonin receptors.
Serotonin is metabolized mainly to 5-HIAA, chiefly by the liver. Metabolism involves
first oxidation by monoamine oxidase to the corresponding aldehyde. This is followed
by oxidation by aldehyde dehydrogenase to 5-HIAA, the indole acetic acid derivative.
The latter is then excreted by the kidneys.
https://en.wikipedia.org/wiki/Serotonin
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Serpins
Serpins are a superfamily of proteins with similar structures that were first identified
for their protease inhibition activity and are found in all kingdoms of life. The acronym
serpin was originally coined because the first serpins to be identified act on
chymotrypsin-like serine proteases (serine protease inhibitors). They are notable for
their unusual mechanism of action, in which they irreversibly inhibit their target protease by undergoing a large conformational change to disrupt its active site. This contrasts with the more common competitive mechanism for protease inhibitors that bind
to and block access to the protease active site.
Protease inhibition by serpins controls an array of biological processes, including coagulation and inflammation, and consequently these proteins are the target of medical
research. Their unique conformational change also makes them of interest to the structural biology and protein folding research communities. The conformational-change
mechanism confers certain advantages, but it also has drawbacks: serpins are vulnerable to mutations that can result in serpinopathies such as protein misfolding and the
formation of inactive long-chain polymers. Serpin polymerization not only reduces the
amount of active inhibitor, but also leads to accumulation of the polymers, causing cell
death and organ failure.
Although most serpins control proteolytic cascades, some proteins with a serpin structure are not enzyme inhibitors, but instead perform diverse functions such as storage
(as in egg whiteovalbumin), transport as in hormone carriage proteins (thyroxinebinding globulin, cortisol-binding globulin) and molecular chaperoning (HSP47). The
term serpin is used to describe these members as well, despite their non-inhibitory
function, since they are evolutionarily related.
https://en.wikipedia.org/wiki/Serpin
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Serum Albumin
Serum albumin, often referred to simply as blood albumin, is an albumin (a type of
globular protein) found in vertebrate blood. Human serum albumin is encoded by the
ALB gene. Other mammalian forms, such as bovine serum albumin, are chemically
similar.
Serum albumin is produced by the liver, occurs dissolved in blood plasma and is the
most abundant blood protein in mammals. Albumin is essential for maintaining the oncotic pressure needed for proper distribution of body fluids between blood vessels and
body tissues. Without albumin, the high pressure in the blood vessels would force
more fluids out into the tissues. It also acts as a plasma carrier by non-specifically binding several hydrophobic steroid hormones and as a transport protein for hemin and
fatty acids. Too much or too little circulating serum albumin may be harmful. Albumin
in the urine usually denotes the presence of kidney disease. Occasionally albumin appears in the urine of normal persons following long standing (postural albuminuria).
Albumin functions primarily as a carrier protein for steroids, fatty acids, and thyroid
hormones in the blood and plays a major role in stabilizing extracellular fluid volume
by contributing to oncotic pressure (known also as colloid osmotic pressure) of plasma.
Because smaller animals (for example rats) function at a lower blood pressure, they
need less oncotic pressure to balance this, and thus need less albumin to maintain
proper fluid distribution.
https://en.wikipedia.org/wiki/Serum_albumin
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Serum Amyloid A
Serum amyloid A (SAA) proteins are a family of apolipoproteins associated with highdensity lipoprotein (HDL) in plasma. Different isoforms of SAA are expressed constitutively (constitutive SAAs) at different levels or in response to inflammatory stimuli
(acute phase SAAs). These proteins are produced predominantly by the liver. The conservation of these proteins throughout invertebrates and vertebrates suggests that
SAAs play a highly essential role in all animals.
Acute-phase serum amyloid A proteins (A-SAAs) are secreted during the acute phase
of inflammation. These proteins have several roles, including the transport of cholesterol to the liver for secretion into the bile, the recruitment of immune cells to inflammatory sites, and the induction of enzymes that degrade extracellular matrix. A-SAAs
are implicated in several chronic inflammatory diseases, such as amyloidosis, atherosclerosis, and rheumatoid arthritis.
Three acute-phase SAA isoforms have been reported in mice, called SAA1, SAA2, and
SAA3. During inflammation, SAA1 and SAA2 are expressed and induced principally in
the liver, whereas SAA3 is induced in many distinct tissues. SAA1 and SAA2 genes are
regulated in liver cells by the proinflammatory cytokines IL-1, IL-6, and TNF-. Both
SAA1 and SAA2 are induced up to a 1000-fold in mice under acute inflammatory conditions following exposure to bacterial lipopolysaccharide (LPS). Three A-SAA genes
have also been identified in humans, although the third gene, SAA3, is believed to represent a pseudogene that does not generate messenger RNA or protein. Molecular
weights of the human proteins are estimated at 11.7 kDa for SAA1 and 12.8 kDa for
SAA4.
https://en.wikipedia.org/wiki/Serum_amyloid_A
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Sesquarterpenes
Terpenes are lipid molecules that may be classified by the number of isopre
they contain. A prefix in the name indicates the number of terpene units ne
semble the molecule.
Sesquarterpenes are composed of seven isoprene units and have the molecu
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Sesquiterpenes
Sesterterpenes
Terpenes are lipid molecules that may be classified by the number of isopre
they contain. A prefix in the name indicates the number of terpene units ne
semble the molecule.
Sesterterpenes, having 25 carbons and five isoprene units, are rare relative
sizes. (The sester- prefix means half to three, i.e. two and a half.) An examp
terterpenoid is geranylfarnesol.
https://en.wikipedia.org/wiki/Terpene
SH2 domain
The SH2 (Src Homology 2) domain is a structurally conserved protein domain contained within the Src oncoprotein and in many other intracellular signal-transducing
proteins. SH2 domains allow proteins containing those domains to dock to phosphorylated tyrosine residues on other proteins. SH2 domains are commonly found in adapter
proteins that aid in the signal transduction of receptor tyrosine kinase pathways.
SH2 domains typically bind a phosphorylated tyrosine residue in the context of a
longer peptide motif within a target protein, and SH2 domains represent the largest
class of known pTyr-recognition domains.
Phosphorylation of tyrosine residues in a protein occurs during signal transduction
and is carried out by tyrosine kinases. In this way, phosphorylation of a substrate by tyrosine kinases acts as a switch to trigger binding to an SH2 domain-containing protein.
Many tyrosine containing short linear motifs that bind to SH2 domains are conserved
across a wide variety of higher Eukaryotes. The intimate relationship between tyrosine
kinases and SH2 domains is supported by their coordinate emergence during eukaryotic evolution.
The function of SH2 domains is to specifically recognize the phosphorylated state of tyrosine residues, thereby allowing SH2 domain-containing proteins to localize to
tyrosine-phosphorylated sites. This process constitutes the fundamental event of signal
transduction through a membrane, in which a signal in the extracellular compartment
is "sensed" by a receptor and is converted in the intracellular compartment to a different chemical form, i.e. that of a phosphorylated tyrosine. Tyrosine phosphorylation
leads to activation of a cascade of protein-protein interactions whereby SH2 domaincontaining proteins are recruited to tyrosine-phosphorylated sites. This process initiates a series of events which eventually result in altered patterns of gene expression or
other cellular responses. The SH2 domain, which was first identified in the oncoproteins Src and Fps, is about 100 amino-acid residues long. It functions as a regulatory
module of intracellular signaling cascades by interacting with high affinity to
phosphotyrosine-containing target peptides in a sequence-specific and strictly
phosphorylation-dependent manner.
https://en.wikipedia.org/wiki/SH2_domain
Sheets
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Shikimic Acid
Shikimic acid, more commonly known as its anionic form shikimate, is a cyclohexene,
a cyclitol and a cyclohexanecarboxylic acid. It is an important biochemical metabolite
in plants and microorganisms. Shikimic acid is also the glycoside part of some hydrolysable tannins.
In the pharmaceutical industry, shikimic acid from the Chinese star anise (Illicium verum) is used as a base material for production of oseltamivir (Tamiflu). Although
shikimic acid is present in most autotrophic organisms, it is a biosynthetic intermediate and in general found in very low concentrations. The low isolation yield of shikimic
acid from the Chinese star anise is blamed for the 2005 shortage of oseltamivir.
Shikimic acid can also be extracted from the seeds of the sweetgum (Liquidambar styraciflua) fruit, which is abundant in North America, in yields of around 1.5%. For example, 4kg of sweetgum seeds is needed for fourteen packages of Tamiflu. By comparison, star anise has been reported to yield 3 to 7% shikimic acid. Biosynthetic pathways
in E. coli have recently been enhanced to allow the organism to accumulate enough material to be used commercially.
https://en.wikipedia.org/wiki/Shikimic_acid
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Sialic Acid
Sialic acid is a generic term for the N- or O-substituted derivatives of neuraminic acid,
a monosaccharide with a nine-carbon backbone. It is also the name for the most common member of this group, N-acetylneuraminic acid (Neu5Ac or NANA). Sialic acids
are found widely distributed in animal tissues and to a lesser extent in other organisms, ranging from plants and fungi to yeasts and bacteria, mostly in glycoproteins and
gangliosides (they occur at the end of sugar chains connected to the surfaces of cells
and soluble proteins). That is because it seems to have appeared late in evolution. However, it has been observed in Drosophila embryos and other insects and in the capsular
polysaccharides of certain strains of bacteria.
The sialic acid family includes 43 derivatives of the nine-carbon sugar neuraminic acid,
but these acids unusually appear free in nature. Normally they can be found as components of oligosaccharide chains of mucins, glycoproteins and glycolipids occupying terminal, nonreducing positions of complex carbohydrates on both external and internal
membrane areas where they are very exposed and develop important functions.
In humans, the brain has the highest sialic acid concentration, where these acids play
an important role in neural transmission and ganglioside structure in synaptogenesis.
In general, the amino group bears either an acetyl or a glycolyl group, but other modifications have been described. These modifications along with linkages have shown to be
tissue specific and developmentally regulated expressions, so some of them are only
found on certain types of glycoconjugates in specific cells. The hydroxyl substituents
may vary considerably. Acetyl, lactyl, methyl, sulfate, and phosphate groups have been
found.
Sialic acid-rich glycoproteins (sialoglycoproteins) bind selectin in humans and other
organisms. Metastatic cancer cells often express a high density of sialic acid-rich glycoproteins. This overexpression of sialic acid on surfaces creates a negative charge on cell
membranes. This creates repulsion between cells (cell opposition) and helps these latestage cancer cells enter the blood stream.
Many bacteria also use sialic acid in their biology, although this is usually limited to
bacteria that live in association with higher animals (deuterostomes). Many of these incorporate sialic acid into cell surface features like their lipopolysaccharide and capsule,
which helps them evade the innate immune response of the host. Other bacteria simply
use sialic acid as a good nutrient source, as it contains both carbon and nitrogen and
can be converted to fructose-6-phosphate, which can then enter central metabolism.
Sialic acid-rich oligosaccharides on the glycoconjugates (glycolipids, glycoproteins, proteoglycans) found on surface membranes help keep water at the surface of cells. The
sialic acid-rich regions contribute to creating a negative charge on the cells' surfaces.
Since water is a polar molecule with partial positive charges on both hydrogen atoms,
it is attracted to cell surfaces and membranes. This also contributes to cellular fluid uptake.
Sialic acid can "hide" mannose antigens on the surface of host cellsThis prevents activation of complement. Sialic acid in the form of polysialic acid is an unusual posttranslational modification that occurs on the neural cell adhesion molecules (NCAMs). In the
synapse, the strong negative charge of the polysialic acid prevents NCAM cross-linking
of cells.
Two forms of sialic acid are shown below
https://en.wikipedia.org/wiki/Sialic_acid
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Sigma Factor
A sigma factor ( factor) is a protein needed only for initiation of RNA synthesis. It is a
bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. The specific sigma factor used to initiate transcription of a
given gene will vary, depending on the gene and on the environmental signals needed
to initiate transcription of that gene.
Every molecule of RNA polymerase holoenzyme contains exactly one factor subunit,
which in the model bacterium Escherichia coli is one of those listed below. The number of factors varies between bacterial species. E. coli has seven factors. factors
are distinguished by their characteristic molecular weights. For example, 70 refers to
the sigma factor with a molecular weight of 70 kDa.
RNA polymerase holoenzyme complex consisting of core RNA polymerase and a sigma
factor executes transcription of a DNA template strand. Once initiation of RNA transcription is complete, the factor can leave the complex.
Different sigma factors are utilized under different environmental conditions. These
specialized sigma factors bind the promoters of genes appropriate to the environmental conditions, increasing the transcription of those genes.
factors in E. coli:
70(RpoD) - A - the "housekeeping" factor or also called as primary factor, transcribes most genes in growing cells. Every cell has a housekeeping factor that keeps
essential genes and pathways operating. In the case of E. coli and other gram-negative
rod-shaped bacteria, the "housekeeping" factor is 70. Genes recognized by 70 all
contain similar promoter consensus sequences consisting of two parts. Relative to the
DNA base corresponding to the start of the RNA transcript, the consensus promoter sequences are characteristically centered at 10 and 35 nucleotides before the start of transcription (10 and 35).
19 (FecI) - the ferric citrate factor, regulates the fec gene for iron transport
24 (RpoE) - the extracytoplasmic/extreme heat stress factor
28 (RpoF) - the flagellar factor
32 (RpoH) - the heat shock factor, it is turned on when the bacteria are exposed to
heat. Due to the higher expression, the factor will bind with a high probability to the
polymerase-core-enzyme. Doing so, other heatshock proteins are expressed, which enable the cell to survive higher temperatures. Some of the enzymes that are expressed
upon activation of 32 are chaperones, proteases and DNA-repair enzymes.
38 (RpoS) - the starvation/stationary phase factor
54 (RpoN) - the nitrogen-limitation factor
There are also anti- factors that inhibit the function of factors and anti-anti- factors that restore factor function.
https://en.wikipedia.org/wiki/Sigma_factor
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Sigmoidal
Sigmoidal is a term used to describe the S-like shape of graphical plots. Sig
Index
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Signal Peptidase I
Signal peptidase I is an enzyme that catalyses the cleavage of hydrophobic,
Signal Peptidase II
and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral sidechains. Th
is present in bacterial inner membranes.
https://en.wikipedia.org/wiki/Signal_peptidase_II
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Signal Transduction
Signal transduction refers to the process of communicating information across a cellular membrane into a cell. It occurs when an extracellular signaling molecule activates
a specific receptor located on the cell surface or inside the cell. In turn, this receptor
triggers a biochemical chain of events inside the cell, eventually eliciting a response.
Depending on the cell, the response may alter the cell's metabolism, shape, gene expression, or ability to divide. The signal can be amplified at any step. Thus, one signaling molecule can generate a response involving hundreds to millions of molecules.
Signal transduction involves the binding of extracellular signaling molecules, also
called ligands, to receptors that trigger events inside the cell. The combination of a signaling molecule with a receptor causes a change in the conformation of the receptor,
known as receptor activation. This activation is always the initial step (the cause) leading to the cell's ultimate responses (effect) to the messenger. Despite the myriad of
these ultimate responses, they are all directly due to changes in particular cell proteins.
Intracellular signaling cascades can be started through cell-substratum interactions.
Examples are the integrin that binds ligands in the extracellular matrix and steroids.
Most steroid hormones have receptors within the cytoplasm and act by stimulating the
binding of their receptors to the promoter region of steroid-responsive genes. Examples of signaling molecules include the hormone melatonin, the neurotransmitter acetylcholine and the cytokine interferon .
The classifications of signaling molecules do not take into account the molecular nature of each class member. Neurotransmitters range in size from small molecules such
as dopamine to neuropeptides such as endorphins. Some molecules may fit into more
than one class. For example, epinephrine is a neurotransmitter when secreted by the
central nervous system and a hormone when secreted by the adrenal medulla.
https://en.wikipedia.org/wiki/Signal_transduction
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Signaling
Cell signaling is part of a complex system of communication that governs basic activities of cells and coordinates cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity as well as normal tissue homeostasis. Errors in cellular information processing are
responsible for diseases such as cancer, autoimmunity, and diabetes.
Cell signaling can be classified to be mechanical and biochemical based on the type of
the signal. Mechanical signals are the forces exerted on the cell and the forces produced by the cell. These forces can both be sensed and responded by the cells. Biochemical signals are the biochemical molecules such as proteins, lipids, ions and gases.
These signals can be categorized based on the distance between signaling and responder cells.
Signaling within, between, and among cells is subdivided into the following classifications:
Intracrine signals are produced by the target cell that stay within the target cell.
Autocrine signals are produced by the target cell, are secreted, and affect the target
cell itself via receptors. Sometimes autocrine cells can target cells close by if they are
the same type of cell as the emitting cell. An example of this are immune cells.
Juxtacrine signals target adjacent (touching) cells. These signals are transmitted
along cell membranes via protein or lipid components integral to the membrane and
are capable of affecting either the emitting cell or cells immediately adjacent.
Paracrine signals target cells in the vicinity of the emitting cell. Neurotransmitters
represent an example.
Endocrine signals target distant cells. Endocrine cells produce hormones that travel
through the blood to reach all parts of the body.
Cells communicate with each other via direct contact (juxtacrine signaling), over short
distances (paracrine signaling), or over large distances and/or scales (endocrine signaling). Some cellcell communication requires direct cellcell contact. Some cells can
form gap junctions that connect their cytoplasm to the cytoplasm of adjacent cells. In
cardiac muscle, gap junctions between adjacent cells allows for action potential propagation from the cardiac pacemaker region of the heart to spread and coordinately
cause contraction of the heart.
The notch signaling mechanism is an example of juxtacrine signaling (also known as
contact-dependent signaling) in which two adjacent cells must make physical contact
in order to communicate. This requirement for direct contact allows for very precise
control of cell differentiation during embryonic development. In the worm Caenorhabditis elegans, two cells of the developing gonad each have an equal chance of terminally
differentiating or becoming a uterine precursor cell that continues to divide. The
choice of which cell continues to divide is controlled by competition of cell surface signals. One cell will happen to produce more of a cell surface protein that activates the
Notch receptor on the adjacent cell. This activates a feedback loop or system that reduces Notch expression in the cell that will differentiate and that increases Notch on
the surface of the cell that continues as a stem cell.
Many cell signals are carried by molecules that are released by one cell and move to
make contact with another cell. Endocrine signals are called hormones. Hormones are
produced by endocrine cells and they travel through the blood to reach all parts of the
body. Specificity of signaling can be controlled if only some cells can respond to a particular hormone. Paracrine signals such as retinoic acid target only cells in the vicinity
of the emitting cell. Neurotransmitters represent another example of a paracrine signal. Some signaling molecules can function as both a hormone and a neurotransmitter.
For example, epinephrine and norepinephrine can function as hormones when released from the adrenal gland and are transported to the heart by way of the blood
stream. Norepinephrine can also be produced by neurons to function as a neurotransmitter within the brain. Estrogen can be released by the ovary and function as a hormone or act locally via paracrine or autocrine signaling. Active species of oxygen and
nitric oxide can also act as cellular messengers. This process is dubbed redox signaling.
https://en.wikipedia.org/wiki/Cell_signaling
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Signaling Cascade
a receptor located on the cell surface resulting in a quick and notable increa
nal. The cascade ultimately elicits a cellular response, which may alter the m
shape, gene expression, or cell life cycle.
https://en.wikipedia.org/wiki/Signal_transduction
Index
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Signaling Pathways
a receptor located on the cell surface. The cascade ultimately elicits a cellula
which may alter the metabolism, shape, gene expression, or cell life cycle.
https://en.wikipedia.org/wiki/Signal_transduction
Silencers
tion of its particular gene. There are many positions in which a silencer elem
located in DNA. The most common position is found upstream of the target
where it can help repress the transcription of the gene. This distance can va
Silencers have also been found within the 3 prime untranslated region (3' U
mRNA.
https://en.wikipedia.org/wiki/Silencer_(DNA)
Silk
Silk is a natural protein fiber, some forms of which can be woven into textil
to form cocoons. Silk emitted by silkworm larvae consists of two main prote
and fibroin, fibroin being the structural center of the silk, and serecin being
Ala and forms pleated sheets. Hydrogen bonds form between chains, and
form above and below the plane of the hydrogen bond network.
https://en.wikipedia.org/wiki/Silk#Chemical_properties
SINEs
Short Interspersed Nuclear Elements (SINEs) are short DNA sequences (<5
lymerase III into transfer RNA, 5S ribosomal RNA, and other small nuclear
and less dependent solely on the actual elements that they encode. SINEs d
code a functional reverse transcriptase protein and rely on other mobile ele
transposition. In some cases they may have their own endonuclease that wi
them to cleave their way into the genome, but the majority of SINEs integra
as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the
tion of numerous proteins involved in all of these processes.
Active E. coli SSB is composed of four identical 19 kDa subunits. Binding of sing
stranded DNA to the tetramer can occur in different "modes", with SSB occupyi
ferent numbers of DNA bases depending on a number of factors, including salt
tides of DNA wrap around the SSB tetramer and contact all four of its subunits,
vored at high salt concentrations in vitro. At lower salt concentrations, the (SSB
binding mode, in which about 35 nucleotides bind to only two of the SSB subun
tends to form.
https://en.wikipedia.org/wiki/Single-strand_DNA-binding_protein
Single-stranded DNA
Deoxyribonucleic acid (DNA) is a molecule that carries most of the genetic
ganisms and many viruses. Most DNA molecules consist of two biopolymer
coiled around each other to form a double helix. When that double helix is u
siRNAs
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 base pairs in length.
siRNA is similar to miRNA, and operates within the RNA interference (RNAi) pathway, where it interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, resulting in no translation.
The mechanism by which this occurs is as follows. Once siRNA enters the cell, it binds
to a protein complex called Dicer, which dices up siRNA into smaller fragments. One
strand of these fragments, in most cases the antisense strand, is loaded into another
protein complex called the RNA-induced Silencing Complex (RISC). The strand RISC
picks is random, which contributes to the problem of incorrect targeting in siRNA therapy, although in most cases the antisense strand is bound. The strand bound by RISC
then links the complex to the messenger RNA (mRNA) by base pairing. The mRNA is
cleaved and destroyed so no protein can be synthesized. This leads to a silenced gene,
and the disruption of translation.
siRNA can also act in RNAi-related pathways as an antiviral mechanism or play a role
in the shaping of the chromatin structure of a genome. siRNAs and their role in posttranscriptional gene silencing (PTGS) was first discovered in plants by David Baulcombe's group at the Sainsbury Laboratory in Norwich, England and reported in Science in 1999. Thomas Tuschl and colleagues soon reported in Nature that synthetic siRNAs could induce RNAi in mammalian cells. This discovery led to a surge in interest in
harnessing RNAi for biomedical research and drug development. Significant developments in siRNA therapies have been made, with both organic (carbon based) and inorganic (non-carbon based) nanoparticles, such as these which have been successful in
drug delivery to the brain, offering promising methods of delivery into human subjects.
However, significant barriers to successful siRNA therapies remain, the most significant of which is off-targeting.
https://en.wikipedia.org/wiki/Small_interfering_RNA
Sirtuin
Sirtuin or Sir2 proteins are a class of proteins that possess either mono-ADPribosyltransferase, or deacylase activity, including deacetylase, desuccinylase, demalonylase, demyristoylase and depalmitoylase activity. Sirtuins regulate important biological pathways in bacteria, archaea and eukaryotes, relevant to processes like aging, transcription, apoptosis, inflammation and stress resistance, as well as energy efficiency
and alertness during low-calorie situations. Sirtuins can also control circadian clocks
and mitochondrial biogenesis.
Yeast Sir2 and some, but not all, sirtuins are protein deacetylases. Unlike other known
protein deacetylases, which simply hydrolyze acetyl-lysine residues, the sirtuinmediated deacetylation reaction couples lysine deacetylation to NAD hydrolysis. This
hydrolysis yields O-acetyl-ADP-ribose, the deacetylated substrate and nicotinamide,
itself an inhibitor of sirtuin activity. The dependence of sirtuins on NAD links their enzymatic activity directly to the energy status of the cell via the cellular NAD:NADH ratio, the absolute levels of NAD, NADH or nicotinamide or a combination of these variables.
Preliminary studies with resveratrol, a possible SIRT1 activator, have led some scientists to speculate that resveratrol may extend lifespan. Further experiments conducted
by Rafael de Cabo et al. showed that resveratrol-mimicking drugs such as SRT1720
could extend the lifespan of obese mice by 44%. Comparable molecules are now undergoing clinical trials in humans.
Cell culture research into the behavior of the human sirtuin SIRT1 shows that it behaves like the yeast sirtuin Sir2: SIRT2 assists in the repair of DNA and regulates genes
that undergo altered expression with age. Adding resveratrol to the diet of mice inhibit
gene expression profiles associated with muscle aging and age-related cardiac dysfunction.
A study performed on transgenic mice overexpressing SIRT6, showed an increased lifespan of about 15% in males. The transgenic males displayed lower serum levels of
insulin-like growth factor 1 (IGF1) and changes in its metabolism, which may have contributed to the increased lifespan.
https://en.wikipedia.org/wiki/Sirtuin
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Sitocalciferol
https://en.wikipedia.org/wiki/Vitamin_D
https://en.wikipedia.org/wiki/Vitamin_D5
Index
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Size-exclusion chromatography (SEC), also known as molecular sieve (or gel exclusio
Typically, when an aqueous solution is used to transport the sample through the col-
umn, the technique is known as gel-filtration chromatography, versus the name gel p
meation chromatography, which is used when an organic solvent is used as a mobile
phase. SEC is a widely used polymer characterization method because of its ability to
provide good molar mass distribution (Mw) results for polymers.
nique should not be confused with gel electrophoresis, where an electric field is used
"pull" or "push" molecules through the gel depending on their electrical charges.
https://en.wikipedia.org/wiki/Size-exclusion_chromatography
Sliding Clamp
A DNA clamp, also known as a sliding clamp, is a protein fold that serves as a
processivity-promoting factor in DNA replication. As a critical component of the DNA
polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents
this enzyme from dissociating from the template DNA strand. The clamp-polymerase
proteinprotein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand. Because one of the ratelimiting steps in the DNA synthesis reaction is the association of the polymerase with
the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association
event. The presence of the DNA clamp can increase the rate of DNA synthesis up to
1,000-fold compared with a nonprocessive polymerase.
Sliding clamps are loaded onto their associated DNA template strands by specialized
proteins known as "sliding clamp loaders", which also disassemble the clamps after replication has completed. The binding sites for these initiator proteins overlap with the
binding sites for the DNA polymerase, so the clamp cannot simultaneously associate
with a clamp loader and with a polymerase. Thus the clamp will not be actively disassembled while the polymerase remains bound. DNA clamps also associate with other
factors involved in DNA and genome homeostasis, such as nucleosome assembly factors, Okazaki fragment ligases, and DNA repair proteins. All of these proteins also
share a binding site on the DNA clamp that overlaps with the clamp loader site, ensuring that the clamp will not be removed while any enzyme is still working on the DNA.
The activity of the clamp loader requires ATP hydrolysis to "close" the clamp around
the DNA.
Pictured below - human sliding clamp with DNA in center
https://en.wikipedia.org/wiki/DNA_clamp
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Small Subunit
Ribosomes contain two subunits, a large subunit and a small subunit. In bacteria, the
large subunit has a size of 50S and the small subunit has a size of 30S. It is the 30S
subunit that holds the 16S rRNA and also the one that is the first one to bind mRNA in
the initiation phase of translation. The small subunit below is shown in blue.
The 30S subunit is the site of inhibition for antibiotics such as tetracycline and aminoglycosides.
https://commons.wikimedia.org/wiki/File:Ribosome_shape.png
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Smooth Muscle
cells; as such, they allow for fine control and gradual responses, much like m
smooth muscle cells in different organs, but the inducing stimuli differ subs
order to perform individual effects in the body at individual times.
https://en.wikipedia.org/wiki/Smooth_muscle_tissue
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SNAREs
SNARE proteins (an acronym derived from "SNAP (Soluble NSF Attachment Protein)
REceptor") are a large protein superfamily consisting of more than 60 members in
yeast and mammalian cells. The primary role of SNARE proteins is to mediate vesicle
fusion, that is, the fusion of vesicles with their target membrane bound compartments
(such as a lysosome). The best studied SNAREs are those that mediate docking of synaptic vesicles with the presynaptic membrane in neurons. These SNAREs are the targets of the bacterial neurotoxins responsible for botulism and tetanus.
During membrane fusion, v-SNARE and t-SNARE proteins on separate membranes
combine to form a trans-SNARE complex, also known as a "SNAREpin". Depending on
the stage of fusion of the membranes, these complexes may be referred to differently.
During fusion of trans-SNARE complexes, the membranes merge and SNARE proteins
involved in complex formation after fusion are then referred to as a "cis"-SNARE complex, because they now reside in a single (or cis) resultant membrane. After fusion, the
cis-SNARE complex is bound and disassembled by an adaptor protein, alphaSNAP.
Then, the hexameric AAA-ATPase NSF catalyzes the ATP-dependent unfolding of the
SNARE proteins and releases them into the cytosol for recycling.
SNAREs are thought to be the core required components of the fusion machinery and
can function independently of additional cytosolic accessory proteins. This was demonstrated by engineering "flipped" SNAREs, where the SNARE domains face the extracellular space rather than the cytosol. When cells containing v-SNAREs contact cells containing t-SNAREs, trans-SNARE complexes form and cell-cell fusion ensues.
https://en.wikipedia.org/wiki/SNARE_(protein)
snoRNAs
Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily
guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs
and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are
associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs
but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.
After transcription, nascent rRNA molecules (termed pre-rRNA) undergo a series of
processing steps to generate the mature rRNA molecule. Prior to cleavage by exo- and
endonucleases, the pre-rRNA undergoes a complex pattern of nucleoside modifications. These include methylations and pseudouridylations, guided by snoRNAs.
Methylation is the attachment or substitution of a methyl group onto various substrates. The rRNA of humans contain approximately 115 methyl group modifications.
The majority of these are 2'O-ribose-methylations (where the methyl group is attached
to the ribose group).
Pseudouridylation is the conversion (isomerization) of the nucleoside uridine to a different isomeric form pseudouridine (). Mature human rRNAs contain approximately
95 modifications.
Each snoRNA molecule acts as a guide for only one (or two) individual modifications
in a target RNA. In order to carry out modification, each snoRNA associates with at
least four protein molecules in an RNA/protein complex referred to as a small nucleolar ribonucleoprotein (snoRNP). The proteins associated with each RNA depend on the
type of snoRNA molecule (see snoRNA guide families below). The snoRNA molecule
contains an antisense element (a stretch of 10-20 nucleotides), which are base complementary to the sequence surrounding the base (nucleotide) targeted for modification
in the pre-RNA molecule. This enables the snoRNP to recognize and bind to the target
RNA. Once the snoRNP has bound to the target site, the associated proteins are in the
correct physical location to catalyze the chemical modification of the target base.
Pictured below - one snoRNA secondary structure.
https://en.wikipedia.org/wiki/Small_nucleolar_RNA
Index
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snRNAs
Small nuclear ribonucleic acid (snRNA), also commonly referred to as U-RNA, is a
class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III, and studies have shown that their primary function is in the processing of
pre-messenger RNA (hnRNA) in the nucleus. They have also been shown to aid in the
regulation of transcription factors or RNA polymerase II, and maintaining the telomeres.
snRNA are always associated with a set of specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP, often pronounced "snurps").
Each snRNP particle is composed of several Sm proteins, the snRNA component, and
snRNP-specific proteins. The most common snRNA components of these complexes
are known, respectively, as: U1 spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, and U6 spliceosomal RNA. Their nomenclature derives from their high uridine content.
A large group of snRNAs is known as small nucleolar RNAs (snoRNAs). These are
small RNA molecules that play an essential role in RNA biogenesis and guide chemical
modifications of ribosomal RNAs (rRNAs) and other RNA genes (tRNA and snRNAs).
They are located in the nucleolus and the Cajal bodies of eukaryotic cells (the major
sites of RNA synthesis), where they are called scaRNAs (small Cajal body-specific
RNAs).
Shown below - U1 snRNA
https://en.wikipedia.org/wiki/Small_nuclear_RNA
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snRNPs
snRNPs (pronounced "snurps"), or small nuclear ribonucleo proteins, are RNA-protein
complexes that combine with unmodified pre-mRNA and various other proteins to
form a spliceosome, a large RNA-protein molecular complex upon which splicing of
pre-mRNA occurs. The action of snRNPs is essential to the removal of introns from
pre-mRNA, a critical aspect of post-transcriptional modification of RNA, occurring
only in the nucleus of eukaryotic cells. Additionally, U7 snRNP is not involved in splicing at all, as U7 snRNP is responsible for processing the 3 stem-loop of histone premRNA.
The two essential components of snRNPs are protein molecules and RNA. The RNA
found within each snRNP particle is known as small nuclear RNA, or snRNA, and is
usually about 150 nucleotides in length. The snRNA component of the snRNP gives
specificity to individual introns by "recognizing" the sequences of critical splicing signals at the 5' and 3' ends and branch site of introns. The snRNA in snRNPs is similar to
ribosomal RNA in that it directly incorporates both an enzymatic and a structural role.
At least five different kinds of snRNPs join the spliceosome to participate in splicing.
They can be visualized by gel electrophoresis and are known individually as: U1, U2,
U4, U5, and U6. Their snRNA components are known, respectively, as: U1 snRNA, U2
snRNA, U4 snRNA, U5 snRNA, and U6 snRNA.
https://en.wikipedia.org/wiki/SnRNP
Index
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Sodium Channels
Sodium channels are integral membrane proteins that form ion channels, conducting
sodium ions (Na+) through a cell's plasma membrane. They are classified according to
the trigger that opens the channel for such ions, i.e. either a voltage-change ("Voltagegated", "voltage-sensitive", or "voltage-dependent" sodium channel also called
"VGSCs" or "Nav channel") or a binding of a substance (a ligand) to the channel
(ligand-gated sodium channels).
In excitable cells such as neurons, myocytes, and certain types of glia, sodium channels
are responsible for the rising phase of action potentials.
Voltage-gated sodium channels play an important role in action potentials. If enough
channels open when there is a change in the cell's membrane potential, a small but significant number of Na+ ions will move into the cell down their electrochemical gradient, further depolarizing the cell. Thus, the more Na+ channels localized in a region of
a cell's membrane the faster the action potential will propagate and the more excitable
that area of the cell will be. This is an example of a positive feedback loop. The ability
of these channels to assume a closed-inactivated state causes the refractory period and
is critical for the propagation of action potentials down an axon.
Na+ channels both open and close more quickly than K+ channels, producing an influx
of positive charge (Na+) toward the beginning of the action potential and an efflux (K+)
toward the end. Ligand-gated sodium channels, on the other hand, create the change
in the membrane potential in the first place, in response to the binding of a ligand to it.
https://en.wikipedia.org/wiki/Sodium_channel
Index
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Sodium Chloride
formula NaCl, representing a 1:1 ratio of sodium and chloride ions. Sodium
the salt most responsible for the salinity of seawater and of the extracellular
many multicellular organisms.
The long held belief that a high-salt diet raises the risk of cardio-vascular di
coming under scrutiny. More recently, dietary salt was demonstrated to atte
Index
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Sodium-glucose Transporter
Sodium-dependent glucose cotransporters (or sodium-glucose linked transporter,
SGLT) are a family of glucose transporter found in the intestinal mucosa (enterocytes)
of the small intestine (SGLT1) and the proximal tubule of the nephron (SGLT2 in PCT
and SGLT1 in PST). They contribute to renal glucose reabsorption.
The SGLT proteins use the energy from the downhill sodium ion gradient created by
the ATPase pump to transport glucose across the apical membrane, against an uphill
glucose gradient. These co-transporters are an example of secondary active transport.
The Na+/K+ ATPase pump on the basolateral membrane of a cell uses ATP to move 3
sodium ions outward into the blood, while bringing in 2 potassium ions. This action
creates a downhill sodium ion gradient from the outside to the inside of the proximal
tubule cell (that is, in comparison to both the blood and the tubule itself).
The SGLT proteins use the energy from this downhill sodium ion gradient created by
the ATPase pump to transport glucose across the apical membrane, against an uphill
glucose gradient. These co-transporters are an example of secondary active transport.
Members of the GLUT family of glucose uniporters then transport the glucose across
the basolateral membrane, and into the peritubular capillaries. Because sodium and
glucose are in the same direction across the membrane, SGLT1 and SGLT2 are known
as symporters.
https://en.wikipedia.org/wiki/Sodium-glucose_transport_proteins
Solvent
The quantity of solute that can dissolve in a specific volume of solvent varie
perature.
https://en.wikipedia.org/wiki/Solvent
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Sonication
ous purposes. Ultrasonic frequencies (>20 kHz) are usually used, leading to
ess also being known as ultrasonication or ultra-sonication. Sonication can
Sorbitol
Sorbitol, also known as glucitol, is a sugar alcohol with a sweet taste which the human
body metabolizes slowly. It can be obtained by reduction of glucose, changing the aldehyde group to a hydroxyl group. Most sorbitol is made from corn syrup, but it is also
found in apples, pears, peaches, and prunes. It is converted to fructose by sorbitol-6phosphate 2-dehydrogenase. Sorbitol is an isomer of mannitol, another sugar alcohol.
The two differ only in the orientation of the hydroxyl group on carbon 2. While similar,
the two sugar alcohols have very different sources in nature, melting points, and uses.
Sorbitol is a sugar substitute. It may be listed under the inactive ingredients listed for
some foods and products. Its INS number and E number is 420. Sorbitol has approximately 60% the sweetness of sucrose (table sugar). Sorbitol is referred to as a nutritive
sweetener because it provides dietary energy: 2.6 kilocalories (11 kilojoules) per gram
versus the average 4 kilocalories (17 kilojoules) for carbohydrates. It is often used in
diet foods (including diet drinks and ice cream), mints, cough syrups, and sugar-free
chewing gum.
https://en.wikipedia.org/wiki/Sorbitol
SOS Box
SOS box is the region in the promoter of various genes to which the LexA re
of DNA damage. In the presence of DNA damage the binding of LexA is ina
the RecA activator. SOS boxes differ in DNA sequences and binding affinity
LexA from organism to organism. Furthermore, SOS boxes may be present
fashion, which indicates that more than one SOS box can be within the sam
https://en.wikipedia.org/wiki/SOS_box
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SOS Repair
The SOS response is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced. The system involves the RecA
protein (Rad51 in eukaryotes). The RecA protein, stimulated by single-stranded DNA,
is involved in the inactivation of the LexA repressor thereby inducing the response. It
is an error-prone repair system that is attributed to mutagenesis.
During normal growth, the SOS genes are negatively regulated by LexA repressor protein dimers. Under normal conditions, LexA binds to a 20-bp consensus sequence (the
SOS box) in the operator region for those genes. Some of these SOS genes are expressed at certain levels even in the repressed state, according to the affinity of LexA
for their SOS box. Activation of the SOS genes occurs after DNA damage by the accumulation of single stranded (ssDNA) regions generated at replication forks, where
DNA polymerase is blocked. RecA forms a filament around these ssDNA regions in an
ATP-dependent fashion, and becomes activated. The activated form of RecA interacts
with the LexA repressor to facilitate the LexA repressor's self-cleavage from the operator.
Once the pool of LexA decreases, repression of the SOS genes goes down according to
the level of LexA affinity for the SOS boxes. Operators that bind LexA weakly are the
first to be fully expressed. In this way LexA can sequentially activate different mechanisms of repair. Genes having a weak SOS box (such as lexA, recA, uvrA, uvrB, and
uvrD) are fully induced in response to even weak SOS-inducing treatments. Thus the
first SOS repair mechanism to be induced is nucleotide excision repair (NER), whose
aim is to fix DNA damage without commitment to a full-fledged SOS response.
If, however, NER does not suffice to fix the damage, the LexA concentration is further
reduced, so the expression of genes with stronger LexA boxes (such as sulA, umuD,
umuC - these are expressed late) is induced. SulA stops cell division by binding to FtsZ,
the initiating protein in this process. This causes filamentation, and the induction of
UmuDC-dependent mutagenic repair. As a result of these properties, some genes may
be partially induced in response to even endogenous levels of DNA damage, while
other genes appear to be induced only when high or persistent DNA damage is present
in the cell.
https://en.wikipedia.org/wiki/SOS_response
Southern Blot
A Southern blot is a method used in molecular biology for detection of a specific DNA
sequence in DNA samples. Southern blotting combines transfer of electrophoresisseparated DNA fragments to a filter membrane and subsequent fragment detection by
probe hybridization. Hybridization of the probe to a specific DNA fragment on the filter membrane indicates that this fragment contains DNA sequence that is complementary to the probe. The transfer step of the DNA from the electrophoresis gel to a membrane permits easy binding of the labeled hybridization probe to the size-fractionated
DNA. It also allows for the fixation of the target-probe hybrids, required for analysis by
autoradiography or other detection methods.
Southern blots performed with restriction enzyme-digested genomic DNA may be used
to determine the number of sequences (e.g., gene copies) in a genome. A probe that hybridizes only to a single DNA segment that has not been cut by the restriction enzyme
will produce a single band on a Southern blot, whereas multiple bands will likely be observed when the probe hybridizes to several highly similar sequences (e.g., those that
may be the result of sequence duplication). Modification of the hybridization conditions (for example, increasing the hybridization temperature or decreasing salt concentration) may be used to increase specificity and decrease hybridization of the probe to
sequences that are less than 100% similar.
The technique is performed as follows:
1 Restriction endonucleases are used to cut high-molecular-weight DNA strands into
smaller fragments.
2 The DNA fragments are then electrophoresed on an agarose gel to separate them by
size.
3 If some of the DNA fragments are larger than 15 kb, then prior to blotting, the gel
may be treated with an acid, such as dilute HCl. This depurinates the DNA fragments,
breaking the DNA into smaller pieces, thereby allowing more efficient transfer from
the gel to membrane.
4 If alkaline transfer methods are used, the DNA gel is placed into an alkaline solution
(typically containing sodium hydroxide) to denature the double-stranded DNA. The denaturation in an alkaline environment may improve binding of the negatively charged
thymine residues of DNA to a positively charged amino groups of membrane, separating it into single DNA strands for later hybridization to the probe (see below), and destroys any residual RNA that may still be present in the DNA. The choice of alkaline
over neutral transfer methods, however, is often empirical and may result in equivalent results.
5 A sheet of nitrocellulose (or, alternatively, nylon) membrane is placed on top of (or
below, depending on the direction of the transfer) the gel. Pressure is applied evenly to
the gel (either using suction, or by placing a stack of paper towels and a weight on top
of the membrane and gel), to ensure good and even contact between gel and membrane. If transferring by suction, 20X SSC buffer is used to ensure a seal and prevent
drying of the gel. Buffer transfer by capillary action from a region of high water potential to a region of low water potential (usually filter paper and paper tissues) is then
used to move the DNA from the gel onto the membrane. Ion exchange interactions
bind the DNA to the membrane due to the negative charge of the DNA and positive
charge of the membrane.
6 The membrane is then baked in a vacuum or regular oven at 80C for 2 hours (standard conditions, nitrocellulose or nylon membrane) or exposed to ultraviolet radiation
(nylon membrane) to permanently attach the transferred DNA to the membrane.
7 The membrane is then exposed to a hybridization probea single DNA fragment
with a specific sequence whose presence in the target DNA is to be determined. The
probe DNA is labelled so that it can be detected, usually by incorporating radioactivity
or tagging the molecule with a fluorescent or chromogenic dye. In some cases, the hybridization probe may be made from RNA, rather than DNA. To ensure the specificity
of the binding of the probe to the sample DNA, most common hybridization methods
use salmon or herring sperm DNA for blocking of the membrane surface and target
DNA, deionized formamide, and detergents such as SDS to reduce non-specific binding of the probe.
8 After hybridization, excess probe is washed from the membrane (typically using SSC
buffer), and the pattern of hybridization is visualized on X-ray film by autoradiography
in the case of a radioactive or fluorescent probe, or by development of color on the
membrane if a chromogenic detection method is used.
https://en.wikipedia.org/wiki/Southern_blot
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Spectrin
Spectrin is a cytoskeletal protein that lines the intracellular side of the plasma membrane in eukaryotic cells. Spectrin forms pentagonal or hexagonal arrangements, forming a scaffolding and playing an important role in maintenance of plasma membrane
integrity and cytoskeletal structure. The hexagonal arrangements are formed by tetramers of spectrin subunits associating with short actin filaments at either end of the
tetramer. These short actin filaments act as junctional complexes allowing the formation of the hexagonal mesh.
The protein is named spectrin since it was first isolated as a major protein component
of human red blood cells which had been treated with mild detergents. The detergents
lysed the cells and the hemoglobin and other cytoplasmic components were washed
out. In the light microscope the basic shape of the red blood cell could still be seen as
the spectrin containing submembranous cytoskeleton preserved the shape of the cell in
outline. This became known as a red blood cell "ghost" (spectre), and so the major protein of the ghost was named spectrin.
In certain types of brain injury such as diffuse axonal injury, spectrin is irreversibly
cleaved by the proteolytic enzyme calpain, destroying the cytoskeleton. Spectrin cleavage causes the membrane to form blebs and ultimately to be degraded, usually leading
to the death of the cell. Spectrin subunits may also be cleaved by caspase family enzymes, and calpain and caspase produce different spectrin breakdown products which
can be detected by western blotting with appropriate antibodies. Calpain cleavage may
indicate activation of necrosis, while caspase cleavage may indicate apoptosis.
https://en.wikipedia.org/wiki/Spectrin
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Spectroscopy
Spectroscopy is the study of the interaction between matter and electromagnetic radiation. Spectroscopy and spectrography are terms used to refer to the measurement of radiation intensity as a function of wavelength and are often used to describe experimental spectroscopic methods. Spectral measurement devices are referred to as spectrometers, spectrophotometers, spectrographs or spectral analyzers.
Types of spectroscopy are distinguished by the type of radiative energy involved in the
interaction. In many applications, the spectrum is determined by measuring changes
in the intensity or frequency of this energy. The types of radiative energy studied include:
Electromagnetic radiation was the first source of energy used for spectroscopic studies. Techniques that employ electromagnetic radiation are typically classified by the
wavelength region of the spectrum and include microwave, terahertz, infrared, near infrared, visible and ultraviolet, x-ray and gamma spectroscopy.
Particles, due to their de Broglie wavelength, can also be a source of radiative energy
and both electrons and neutrons are commonly used. For a particle, its kinetic energy
determines its wavelength.
Acoustic spectroscopy involves radiated pressure waves.
Mechanical methods can be employed to impart radiating energy, similar to acoustic
waves, to solid materials.
Types of spectroscopy can also be distinguished by the nature of the interaction between the energy and the material. These interactions include:
Absorption occurs when energy from the radiative source is absorbed by the material.
Absorption is often determined by measuring the fraction of energy transmitted
through the material; absorption will decrease the transmitted portion.
Emission indicates that radiative energy is released by the material. A material's
blackbody spectrum is a spontaneous emission spectrum determined by its temperature; this feature can be measured in the infrared by instruments such as the Atmospheric Emitted Radiance Interferometer (AERI). Emission can also be induced by
other sources of energy such as flames or sparks or electromagnetic radiation in the
case of fluorescence.
Elastic scattering and reflection spectroscopy determine how incident radiation is reflected or scattered by a material. Crystallography employs the scattering of high energy radiation, such as x-rays and electrons, to examine the arrangement of atoms in
proteins and solid crystals.
Impedance spectroscopy studies the ability of a medium to impede or slow the transmittance of energy. For optical applications, this is characterized by the index of refraction.
Inelastic scattering phenomena involve an exchange of energy between the radiation
and the matter that shifts the wavelength of the scattered radiation. These include Raman and Compton scattering.
Coherent or resonance spectroscopy are techniques where the radiative energy couples two quantum states of the material in a coherent interaction that is sustained by
the radiating field. The coherence can be disrupted by other interactions, such as particle collisions and energy transfer, and so often require high intensity radiation to be
sustained. Nuclear magnetic resonance (NMR) spectroscopy is a widely used resonance method and ultrafast laser methods are also now possible in the infrared and
visible spectral regions.
https://en.wikipedia.org/wiki/Spectroscopy
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Sphingolipid
Sphingolipids, or glycosylceramides, are a class of lipids containing a backbone of
sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. These
compounds play important roles in signal transmission and cell recognition. Sphingolipidoses, or disorders of sphingolipid metabolism, have particular impact on neural
tissue. A sphingolipid with an R group consisting of a hydrogen atom only is a ceramide. Other common R groups include phosphocholine, yielding a sphingomyelin, and
various sugar monomers or dimers, yielding cerebrosides and globosides, respectively.
Cerebrosides and globosides are collectively known as glycosphingolipids.
Simple sphingolipids, which include the sphingoid bases and ceramides, make up the
early products of the sphingolipid synthetic pathways.
Sphingoid bases are the fundamental building blocks of all sphingolipids. The main
mammalian sphingoid bases are dihydrosphingosine and sphingosine, while dihydrosphingosine and phytosphingosine are the principle sphingoid bases in yeast. Sphingosine, dihydrosphingosine, and phytosphingosine may be phosphorylated.
Ceramides, as a general class, are N-acylated sphingoid bases lacking additional head
groups.
Dihydroceramide is produced by N-acylation of dihydrosphingosine. Dihydroceramide is found in both yeast and mammalian systems.
Ceramide is produced in mammalian systems by desaturation of dihydroceramide by
dihydroceramide desaturase 1 (DES1). This highly bioactive molecule may also be phosphorylated to form ceramide-1-phosphate.
Phytoceramide is produced in yeast by hydroxylation of dihydroceramide at C-4.
Complex sphingolipids may be formed by addition of head groups to ceramide or phytoceramide:
Sphingomyelins have a phosphocholine or phosphoethanolamine molecule with an
ester linkage to the 1-hydroxy group of a ceramide.
Glycosphingolipids are ceramides with one or more sugar residues joined in a glycosidic linkage at the 1-hydroxyl position (see image).
Cerebrosides have a single glucose or galactose at the 1-hydroxy position.
Sulfatides are sulfated cerebrosides.
Gangliosides have at least three sugars, one of which must be sialic acid.
Inositol-containing ceramides, which are derived from phytoceramide, are produced
in yeast. These include inositol phosphorylceramide, mannose inositol phosphorylceramide, and mannose diinositol phosphorylceramide.
https://en.wikipedia.org/wiki/Sphingolipid
Index
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Sphingolipids
Sphingolipids, or glycosylceramides, are a class of lipids containing a backbone of
sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. These
compounds play important roles in signal transmission and cell recognition. Sphingolipidoses, or disorders of sphingolipid metabolism, have particular impact on neural
tissue. A sphingolipid with an R group consisting of a hydrogen atom only is a ceramide. Other common R groups include phosphocholine, yielding a sphingomyelin, and
various sugar monomers or dimers, yielding cerebrosides and globosides, respectively.
Cerebrosides and globosides are collectively known as glycosphingolipids.
Simple sphingolipids, which include the sphingoid bases and ceramides, make up the
early products of the sphingolipid synthetic pathways.
Sphingoid bases are the fundamental building blocks of all sphingolipids. The main
mammalian sphingoid bases are dihydrosphingosine and sphingosine, while dihydrosphingosine and phytosphingosine are the principle sphingoid bases in yeast. Sphingosine, dihydrosphingosine, and phytosphingosine may be phosphorylated.
Ceramides, as a general class, are N-acylated sphingoid bases lacking additional head
groups.
Dihydroceramide is produced by N-acylation of dihydrosphingosine. Dihydroceramide is found in both yeast and mammalian systems.
Ceramide is produced in mammalian systems by desaturation of dihydroceramide by
dihydroceramide desaturase 1 (DES1). This highly bioactive molecule may also be phosphorylated to form ceramide-1-phosphate.
Phytoceramide is produced in yeast by hydroxylation of dihydroceramide at C-4.
Complex sphingolipids may be formed by addition of head groups to ceramide or phytoceramide:
Sphingomyelins have a phosphocholine or phosphoethanolamine molecule with an
ester linkage to the 1-hydroxy group of a ceramide.
Glycosphingolipids are ceramides with one or more sugar residues joined in a glycosidic linkage at the 1-hydroxyl position (see image).
Cerebrosides have a single glucose or galactose at the 1-hydroxy position.
Sulfatides are sulfated cerebrosides.
Gangliosides have at least three sugars, one of which must be sialic acid.
Inositol-containing ceramides, which are derived from phytoceramide, are produced
in yeast. These include inositol phosphorylceramide, mannose inositol phosphorylceramide, and mannose diinositol phosphorylceramide.
https://en.wikipedia.org/wiki/Sphingolipid
Index
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Sphingomyelin
Sphingomyelin is a type of sphingolipid found in animal cell membranes, especially in
the membranous myelin sheath that surrounds some nerve cell axons. It usually consists of phosphocholine and ceramide, or a phosphoethanolamine head group. Therefore, sphingomyelins can also be classified as sphingophospholipids. In humans, SPH
represents ~85% of all sphingolipids, and typically make up 10-20mol% of plasma
membrane lipids.
Sphingomyelins contain phosphocholine or phosphoethanolamine as their polar head
group and are therefore classified along with glycerophospholipids as phospholipids.
Indeed, sphingomyelins resemble phosphatidylcholines in their general properties and
three-dimensional structure, and in having no net charge on their head groups . Sphingomyelins are present in the plasma membranes of animal cells and are especially
prominent in myelin, a membranous sheath that surrounds and insulates the axons of
some neuronsthus the name sphingomyelins.
Ideally, sphingomyelin molecules are shaped like a cylinder, however many molecules
of sphingomyelin have a significant chain mismatch (the lengths of the two hydrophobic chains are significantly different). The hydrophobic chains of sphingomyelin tend
to be much more saturated than other phospholipids. The main transition phase temperature of sphingomyelins is also higher compared to the phase transition temperature of similar phospholipids, near 37 C. This can introduce lateral heterogeneity in the
membrane, generating domains in the membrane bilayer (including abundance in
lipid rafts).
Sphingomyelin undergoes significant interactions with cholesterol. Cholesterol has the
ability to eliminate the liquid to solid phase transition in phospholipids. Due to sphingomyelin transition temperature being within physiological temperature ranges, cholesterol can play a significant role in the phase of sphingomyelin. Sphingomyelin are also
more prone to intermolecular hydrogen bonding than other phospholipids.
https://en.wikipedia.org/wiki/Sphingomyelin
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Sphingosine
Sphingosine (2-amino-4-octadecene-1,3-diol) is an 18-carbon amino alcohol with an
unsaturated hydrocarbon chain, which forms a primary part of sphingolipids, a class of
cell membrane lipids that include sphingomyelin, an important phospholipid.
Sphingosine can be phosphorylated in vivo via two kinases, sphingosine kinase type 1
and sphingosine kinase type 2. This leads to the formation of sphingosine-1-phosphate,
a potent signaling lipid. Sphingolipid metabolites, such as ceramides, sphingosine and
sphingosine-1-phosphate, are lipid signaling molecules involved in diverse cellular
processes.
Sphingosine is synthesized from palmitoyl CoA and serine in a condensation required
to yield dehydrosphingosine. Dehydrosphingosine is then reduced by NADPH to dihydrosphingosine (sphinganine), and finally oxidized by FAD to sphingosine.
There is no direct route of synthesis from sphinganine to sphingosine. It has to be acylated first to dihydroceramide, which is then dehydrogenated to ceramide. Sphingosine
is formed via degradation of sphingolipid in the lysosome.
https://en.wikipedia.org/wiki/Sphingosine
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Spindle
In cell biology, the spindle apparatus refers to the cytoskeletal structure of eukaryotic
cells that forms during cell division to separate sister chromatids between daughter
cells. It is referred to as the mitotic spindle during mitosis, a process that produces genetically identical daughter cells, or the meiotic spindle during meiosis, a process that
produces gametes with half the number of chromosomes of the parent cell.
Besides chromosomes, the spindle apparatus is composed of hundreds of proteins. Microtubules comprise the most abundant components of the machinery. Attachment of
microtubules to chromosomes is mediated by kinetochores, which actively monitor
spindle formation and prevent premature anaphase onset. Microtubule polymerization
and depolymerization dynamics drive chromosome congression. Depolymerization of
microtubules generates tension at kinetochores. Bipolar attachment of sister kinetochores to microtubules emanating from opposite cell poles couples opposing tension
forces, aligning chromosomes at the cell equator and poising them for segregation to
daughter cells. Once every chromosome is bi-oriented, anaphase commences and cohesin, which couples sister chromatids, is severed, permitting the transit of the sister
chromatids to opposite poles.
The cellular spindle apparatus includes the spindle microtubules, associated proteins,
which include kinesin and dynein molecular motors, condensed chromosomes, and
any centrosomes or asters that may be present at the spindle poles depending on the
cell type. The spindle apparatus is vaguely ellipsoid in cross section and tapers at the
ends. In the wide middle portion, known as the spindle midzone, antiparallel microtubules are bundled by kinesins. At the pointed ends, known as spindle poles, microtubules are nucleated by the centrosomes in most animal cells. Acentrosomal or anastral
spindles lack centrosomes or asters at the spindle poles, respectively, and occur for example during female meiosis in most animals. In this instance, a Ran GTP gradient is
the main regulator of spindle microtubule organization and assembly. In fungi, spindles form between spindle pole bodies embedded in the nuclear envelope, which does
not break down during mitosis.
https://en.wikipedia.org/wiki/Spindle_apparatus
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Spindle Formation
Spindle assembly is largely regulated by phosphorylation events catalyzed by mitotic
kinases. Cyclin dependent kinase complexes (CDKs) are activated by mitotic cyclins,
whose translation increases during mitosis. CDK1 (also called CDC2) is considered the
main mitotic kinase in mammalian cells and is activated by Cyclin B1. Aurora kinases
are required for proper spindle assembly and separation.
Aurora A associates with centrosomes and is believed to regulate mitotic entry. Aurora
B is a member of the chromosomal passenger complex and mediates chromosomemicrotubule attachment and sister chromatid cohesion. Polo-like kinase, also known
as PLK, especially PLK1 has important roles in the spindle maintenance by regulating
microtubule dynamics.
By the end of DNA replication, sister chromatids are bound together in an amorphous
mass of tangled DNA and protein that would be virtually impossible to partition into
each daughter cell. To avoid this problem, mitotic entry triggers a dramatic reorganization of the duplicated genome. Sister chromatids are disentangled and resolved from
one another. Chromosomes also shorten in length, up to 10,000 fold in animal cells, in
a process called condensation. Condensation begins in prophase and chromosomes are
maximally compacted into rod-shaped structures by the time they are aligned in the
middle of the spindle at metaphase. This gives mitotic chromosomes the classic X
shape seen in karyotypes, with each condensed sister chromatid linked along their
lengths by cohesin proteins and joined, often near the center, at the centromere.
While these dynamic rearrangements are vitally important to ensure accurate and
high-fidelity segregation of the genome, our understanding of mitotic chromosome
structure remains largely incomplete. A few specific molecular players have been identified, however: Topoisomerase II uses ATP hydrolysis to catalyze decatenation of DNA
entanglements, promoting sister chromatid resolution. Condensins are 5-subunit complexes that also use ATP-hydrolysis to promote chromosome condensation. Experiments in Xenopus egg extracts have also implicated linker Histone H1 as an important
regulator of mitotic chromosome compaction.
https://en.wikipedia.org/wiki/Spindle_apparatus#Regulation_of_spindle_assembly
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Splice Variant
Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. These multiple proteins from the same gene are
known as splice variants. In this process, particular exons of a gene may be included
within or excluded from the final, processed messenger RNA (mRNA) produced from
that gene. Consequently, the proteins translated from alternatively spliced mRNAs will
contain differences in their amino acid sequence and, often, in their biological functions. Notably, alternative splicing allows the human genome to direct the synthesis of
many more proteins than would be expected from its 20,000 protein-coding genes. Alternative splicing is sometimes termed differential splicing.
Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the biodiversity of proteins that can be encoded by the genome. In humans,
~95% of multi-exonic genes are alternatively spliced. There are numerous modes of alternative splicing observed, of which the most common is exon skipping. In this mode,
a particular exon may be included in mRNAs under some conditions or in particular tissues, and omitted from the mRNA in others.
The production of alternatively spliced mRNAs is regulated by a system of trans-acting
proteins that bind to cis-acting sites on the primary transcript itself. Such proteins include splicing activators that promote the usage of a particular splice site, and splicing
repressors that reduce the usage of a particular site. Mechanisms of alternative splicing
are highly variable, and new examples are constantly being found, particularly through
the use of high-throughput techniques. Researchers hope to fully elucidate the regulatory systems involved in splicing, so that alternative splicing products from a given
gene under particular conditions could be predicted by a "splicing code".
Abnormal variations in splicing are also implicated in disease. A large proportion of
human genetic disorders result from splicing variants. Abnormal splicing variants are
also thought to contribute to the development of cancer, and splicing factor genes are
frequently mutated in different types of cancer.
https://en.wikipedia.org/wiki/Alternative_splicing
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Spliceosome
A spliceosome is a large and complex molecular machine found primarily within the
splicing speckles of the cell nucleus of eukaryotic cells. The spliceosome is assembled
from snRNAs and protein complexes. The spliceosome removes introns from a transcribed pre-mRNA, a kind of primary transcript. This process is generally referred to
as splicing. Only eukaryotes have spliceosomes and metazoans have a second spliceosome, the minor spliceosome.
Each spliceosome is composed of five small nuclear RNAs (snRNA), and a range of associated protein factors. When these small RNA are combined with the protein factors,
they make an RNA-protein complex called snRNP.
The snRNAs that make up the major spliceosome are named U1, U2, U4, U5, and U6,
and participate in several RNA-RNA and RNA-protein interactions. The RNA component of the small nuclear ribonucleic protein or snRNP (pronounced "snurp") is rich in
uridine (the nucleoside analog of the uracil nucleotide).
The canonical assembly of the spliceosome occurs anew on each hnRNA (pre-mRNA).
The hnRNA contains specific sequence elements that are recognized and utilized during spliceosome assembly. These include the 5' end splice, the branch point sequence,
the polypyrimidine tract, and the 3' end splice site. The spliceosome catalyzes the removal of introns, and the ligation of the flanking exons.
Introns typically have a GU nucleotide sequence at the 5' end splice site, and an AG at
the 3' end splice site. The 3' splice site can be further defined by a variable length of
polypyrimidines, called the polypyrimidine tract (PPT), which serves the dual function
of recruiting factors to the 3' splice site and possibly recruiting factors to the branch
point sequence (BPS). The BPS contains the conserved adenosine required for the first
step of splicing.
https://en.wikipedia.org/wiki/Spliceosome
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Splicing
In molecular biology, splicing is the editing of the nascent pre-messenger RNA (premRNA) transcript. After splicing, introns are removed and exons are joined together
(ligated). For nuclear-encoded genes, splicing takes place within the nucleus either cotranscriptionally or immediately after transcription. For those eukaryotic genes that
contain introns, splicing is usually required in order to create an mRNA molecule that
can be translated into protein. For many eukaryotic introns, splicing is carried out in a
series of reactions which are catalyzed by the spliceosome, a complex of small nuclear
ribonucleoproteins (snRNPs). Self-splicing introns, or ribozymes capable of catalyzing
their own excision from their parent RNA molecule, also exist.
Spliceosomal introns often reside within the sequence of eukaryotic protein-coding
genes. Within the intron, a donor site (5' end of the intron), a branch site (near the 3'
end of the intron) and an acceptor site (3' end of the intron) are required for splicing.
The splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3' end
of the intron terminates the intron with an almost invariant AG sequence. Upstream
(5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide involved in lariat formation. The consensus sequence for
an intron (in IUPAC nucleic acid notation) is: G-G-[cut]-G-U-R-A-G-U (donor site) ...
intron sequence ... Y-U-R-A-C (pyrimidine-rich branch sequence 20-50 nucleotides upstream of acceptor site) ... Y-rich-N-C-A-G-[cut]-G (acceptor site).
The spliceosome is a large RNA-protein complex composed of five small nuclear ribonucleoproteins (snRNPs, pronounced 'snurps'). Assembly and activity of the spliceosome occurs during transcription of the pre-mRNA. The RNA components of snRNPs
interact with the intron and are involved in catalysis. Two types of spliceosomes have
been identified (major and minor) which contain different snRNPs.
The major spliceosome splices introns containing GU at the 5' splice site and AG at
the 3' splice site. It is composed of the U1, U2, U4, U5, and U6 snRNPs and is active
in the nucleus. In addition, a number of proteins including U2 small nuclear RNA auxiliary factor 1 (U2AF35), U2AF2 (U2AF65) and SF1 are required for the assembly of
the spliceosome. The spliceosome forms different complexes during the splicing process:
Complex E
The U1 snRNP binds to the GU sequence at the 5' splice site of an intron;
Splicing factor 1 binds to the intron branch point sequence;
U2AF1 binds at the 3' splice site of the intron;
U2AF2 binds to the polypyrimidine tract;
Complex A (pre-spliceosome)
The U2 snRNP displaces SF1 and binds to the branch point sequence and ATP is hydrolyzed;
Complex B (pre-catalytic spliceosome)
The U5/U4/U6 snRNP trimer binds, and the U5 snRNP binds exons at the 5' site,
with U6 binding to U2;
Complex B*
The U1 snRNP is released, U5 shifts from exon to intron, and the U6 binds at the 5'
splice site;
Complex C (catalytic spliceosome)
U4 is released, U6/U2 catalyzes transesterification, making the 5'-end of the intron
ligate to the A on intron and form a lariat, U5 binds exon at 3' splice site, and the 5' site
is cleaved, resulting in the formation of the lariat;
Complex C* (post-spliceosomal complex)
U2/U5/U6 remain bound to the lariat, and the 3' site is cleaved and exons are ligated
using ATP hydrolysis. The spliced RNA is released, the lariat is released and degraded, and the snRNPs are recycled.
This type of splicing is termed canonical splicing or termed the lariat pathway, which
accounts for more than 99% of splicing. By contrast, when the intronic flanking sequences do not follow the GU-AG rule, noncanonical splicing is said to occur.
https://en.wikipedia.org/wiki/RNA_splicing
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Squalene
Squalene is a natural 30-carbon organic compound originally obtained for commercial
purposes primarily from shark liver oil (hence its name), although plant sources (primarily vegetable oils) are now used as well, including amaranth seed, rice bran, wheat
germ, and olives. It is also found in high concentrations in the stomach oil of birds in
the order Procellariiformes. All plants and animals produce squalene as a biochemical
intermediate, including humans.
Squalene is a hydrocarbon and a triterpene, and is a natural and vital part of the synthesis of all plant and animal sterols, including cholesterol, steroid hormones, and vitamin D in the human body.
Squalene is used in cosmetics, and more recently as an immunologic adjuvant in vaccines. Squalene has been proposed to be an important part of the Mediterranean diet
as it may be a chemopreventive substance that protects people from cancer.
In animals, squalene is the biochemical precursor to the whole family of steroids. Oxidation (via squalene monooxygenase) of one of the terminal double bonds of squalene
yields 2,3-squalene oxide, which undergoes enzyme-catalyzed cyclization to afford lanosterol, which is then elaborated into cholesterol and other steroids.
https://commons.wikimedia.org/wiki/File:Sterol_synthesis.svg
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Src
Src (pronounced "sarc" as it is short for sarcoma) is a proto-oncogene encoding a tyrosine kinase. Proto-oncogene tyrosine-protein kinase Src, also known as protooncogene c-Src or simply c-Src , is a non-receptor tyrosine kinase protein that phosphorylates specific tyrosine residues in other proteins. An elevated level of activity of c-Src
tyrosine kinase is suggested to be linked to cancer progression by promoting other signals.
c-Src includes an SH2 domain, an SH3 domain, and a tyrosine kinase domain. c-Src
stands for "cellular Src kinase" and should not be confused with "C-terminal Src kinase" (CSK) which is an enzyme which phosphorylates c-Src at its C-terminus and provides negative regulation of Src's enzymatic activity. c-Src is a widely studied member
of non-receptor tyrosine kinases which are not associated with a cell-surface receptor.
There are 9 members part of the Src family kinases: c-Src , Yes, Fyn, Fgr, Yrk, Lyn, Blk,
Hck, and Lck. c-Src is made up of 6 functional regions: Src homology (SH) 4 domain
(SH4 domain), unique region, SH3 domain, SH2 domain, catalytic domain and short
regulatory tail. When Src is inactive, the phosphorylated tyrosine group at the 527 position interacts with the SH2 domain which helps the SH3 domain interact with the flexible linker domain and thereby keeps the inactive unit tightly bound. The activation of
c-Src causes the dephosphorylation of the tyrosine 527. This induces long-range allostery via protein domain dynamics, causing the structure to be destabilized, resulting
in the opening up of the SH3, SH2 and kinase domains and the autophosphorylation of
the residue tyrosine 416.
c-Src can be activated by many transmembrane proteins that include: adhesion receptors, receptor tyrosine kinases, G-protein coupled receptors and cytokine receptors.
Most studies have looked at the receptor tyrosine kinases and examples of these are
platelet derived growth factor receptor (PDGFR) pathway and epidermal growth factor
receptor (EGFR). When src is activated, it promotes survival, angiogenesis, proliferation and invasion pathways. It also regulates angiogenic factors and vascular permeability after focal cerebral ischemia-reperfusion.
Src contains at least three flexible protein domains, which, in conjunction with myristoylation, can mediate attachment to membranes and determine subcellular localization. The activation of the c-Src pathway has been observed in about 50% of tumors
from colon, liver, lung, breast and the pancreas. Since the activation of c-Src leads to
the promotion of survival, angiogenesis, proliferation and invasion pathways, the aberrant growth of tumors in cancers is observed. A common mechanism is that there are
genetic mutations that result in the increased activity or the overexpression of the cSrc leading to the constant activation of the c-Src.
https://en.wikipedia.org/wiki/Proto-oncogene_tyrosine-protein_kinase_Src
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SREBP
Sterol regulatory element-binding proteins (SREBPs) are transcription factors that
bind to the sterol regulatory element DNA sequence TCACNCCAC. Mammalian
SREBPs are encoded by the genes SREBF1 and SREBF2. SREBPs belong to the basichelix-loop-helix leucine zipper class of transcription factors. Unactivated SREBPs are
attached to the nuclear envelope and endoplasmic reticulum membranes. In cells with
low levels of sterols, SREBPs are cleaved to a water-soluble N-terminal domain that is
translocated to the nucleus. These activated SREBPs then bind to specific sterol regulatory element DNA sequences, thus upregulating the synthesis of enzymes involved in
sterol biosynthesis. Sterols in turn inhibit the cleavage of SREBPs and therefore synthesis of additional sterols is reduced through a negative feed back loop.
SREB proteins are indirectly required for cholesterol biosynthesis and for uptake and
fatty acid biosynthesis. These proteins work with asymmetric sterol regulatory element
(StRE). SREBPs have a structure similar to E-box-binding helix-loop-helix (HLH) proteins. However, in contrast to E-box-binding HLH proteins, an arginine residue is replaced with tyrosine making them capable of recognizing StREs and thereby regulating
membrane biosynthesis.
A feature of the SREBP pathway is the proteolytic release of a membrane-bound transcription factor, SREBP. Proteolytic cleavage frees it to move through the cytoplasm to
the nucleus. Once in the nucleus, SREBP can bind to specific DNA sequences (the
sterol regulatory elements or SREs) that are found in the control regions of the genes
that encode enzymes needed to make lipids. This binding to DNA leads to the increased transcription of the target genes.
https://en.wikipedia.org/wiki/Sterol_regulatory_element-binding_protein
Index
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Ssp I
Index
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its standard state from its constituent elements in their standard states (the
ble form of the element at 1 bar of pressure and the specified temperature, u
https://en.wikipedia.org/wiki/Standard_Gibbs_free_energy_of_formation
tivity for each ion participating in the reaction, a partial pressure of 1 bar fo
that is part of the reaction, and metals in their pure state. The standard red
https://en.wikipedia.org/wiki/Reduction_potential#Standard_reduction_
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Stanley Prusiner
Stanley Benjamin Prusiner M.D (born May 28, 1942) is an American neurologist and
https://en.wikipedia.org/wiki/Stanley_B._Prusiner
Starch
Starch or amylum is a carbohydrate consisting of a large number of glucose units
joined by glycosidic bonds. This polysaccharide is produced by most green plants as an
energy store. It is the most common carbohydrate in human diets and is contained in
large amounts in staple foods such as potatoes, wheat, maize (corn), rice, and cassava.
Pure starch is a white, tasteless and odorless powder that is insoluble in cold water or
alcohol. It consists of two types of molecules: the linear and helical amylose and the
branched amylopectin. Depending on the plant, starch generally contains 20 to 25%
amylose and 75 to 80% amylopectin by weight. Glycogen, the glucose store of animals,
is a more branched version of amylopectin.
Starch is processed to produce many of the sugars in processed foods. Dissolving
starch in warm water gives wheatpaste, which can be used as a thickening, stiffening or
gluing agent. The biggest industrial non-food use of starch is as adhesive in the papermaking process. Starch can be applied to parts of some garments before ironing, to
stiffen them.
https://en.wikipedia.org/wiki/Starch
Start Codon
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by
a ribosome. The start codon always codes for methionine in eukaryotes and a modified
Met (fMet) in prokaryotes. The most common start codon is AUG.
The start codon is often preceded by a 5' untranslated region (5' UTR). In prokaryotes
this includes the ribosome binding site.
Alternative start codons are different from the standard AUG codon and are found in
both prokaryotes (bacteria) and eukaryotes. Alternate start codons are still translated
as Met when they are at the start of a protein (even if the codon encodes a different
amino acid otherwise). This is because a separate transfer RNA (tRNA) is used for initiation.
https://en.wikipedia.org/wiki/Start_codon
Index
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Statin
Statins, also known as HMG-CoA reductase inhibitors, are a class of lipid-lowering
medications that inhibit the enzyme HMG-CoA reductase which plays a central role in
the production of cholesterol. High cholesterol levels have been associated with cardiovascular disease (CVD). Statins have been found to reduce cardiovascular disease and
mortality in those who are at high risk. The evidence is strong that statins are effective
for treating CVD in the early stages of a disease (secondary prevention) and in those at
elevated risk but without CVD (primary prevention). Side effects of statins include muscle pain, increased risk of diabetes mellitus, and abnormalities in liver enzyme tests.
Additionally, they have rare but severe adverse effects, particularly muscle damage.
As of 2010, a number of statins are on the market: atorvastatin, fluvastatin, lovastatin,
pitavastatin, pravastatin, rosuvastatin and simvastatin. Several combination preparations of a statin and another agent, such as ezetimibe/simvastatin, are also available.
Most evidence suggests that statins are effective in preventing heart disease in those
with high cholesterol, but no history of heart disease. A 2013 Cochrane review found a
decrease in risk of death and other poor outcomes without any evidence of harm. For
every 138 people treated for 5 years one fewer dies and for every 49 treated one fewer
has an episode of heart disease. A 2011 review reached similar conclusions and a 2012
review found benefits in both women and men. A 2010 review concluded that treating
people with no history of cardiovascular disease reduces cardiovascular events in men
but not women, and provides no mortality benefit in either sex. Two other meta analyses published that year, one of which used data obtained exclusively from women,
found no mortality benefit in primary prevention.
https://en.wikipedia.org/wiki/Statin
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Steady State
In Michaelis-Menten enzyme kinetics, reactions are assumed to be occurring under
steady state condition. In this state, the concentration of the ES complex (see below) is
relatively constant. This is in contrast to pre-steady state conditions in which the
amount of ES complex is rapidly varying.
https://en.wikipedia.org/wiki/MichaelisMenten_kinetics#Quasi-steadystate_approximation
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Stearate
Stearic acid (stair-ik or steer-ik) is a saturated fatty acid with an 18-carbon chain and
has the IUPAC name octadecanoic acid. It is a waxy solid and its chemical formula is
C17H35CO2H. Its name comes from the Greek word "star", which means tallow.
The salts and esters of stearic acid are called stearates. As its ester, stearic acid is one
of the most common saturated fatty acids found in nature following palmitic acid. The
triglyceride derived from three molecules of stearic acid is called stearin.
Stearic acid is mainly used in the production of detergents, soaps, and cosmetics such
as shampoos and shaving cream products. Soaps are not made directly from stearic
acid, but indirectly by saponification of triglycerides consisting of stearic acid esters.
Esters of stearic acid with ethylene glycol, glycol stearate, and glycol distearate are
used to produce a pearly effect in shampoos, soaps, and other cosmetic products. They
are added to the product in molten form and allowed to crystallize under controlled
conditions. Detergents are obtained from amides and quaternary alkylammonium derivatives of stearic acid.
https://en.wikipedia.org/wiki/Stearic_acid
Index
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Stercobilin
Stercobilin is a tetrapyrrolic bile pigment and is one end-product of heme catabolism.
It is the chemical responsible for the brown color of human feces and was originally isolated from feces in 1932. Stercobilin (and related urobilin) can be used as a marker for
biochemical identification of fecal pollution levels in rivers.
Stercobilin results from breakdown of the heme moiety of hemoglobin found in erythrocytes. Macrophages break down senescent erythrocytes and break the heme down
into biliverdin, which rapidly reduces to free bilirubin. Bilirubin binds tightly to
plasma proteins (especially albumin) in the blood stream and is transported to the
liver, where it is conjugated with one or two glucuronic acid residues into bilirubin diglucuronide, and secreted into the small intestine as bile. In the small intestine, some
bilirubin glucuronide is converted back to bilirubin via bacterial enzymes in the terminal ileum. This bilirubin is further converted to colorless urobilinogen. Urobilinogen
that remains in the colon can either be reduced to stercobilinogen and finally oxidized
to stercobilin, or it can be directly reduced to stercobilin. Stercobilin is responsible for
the brown color of human feces. Stercobilin is then excreted in the feces.
https://en.wikipedia.org/wiki/Stercobilin
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Stercobilinogen
Stercobilinogen (fecal urobilinogen) is a chemical created by bacteria in the gut. It is
made of broken-down hemoglobin. It is further processed to become the chemical that
gives feces its brown color.
Bilirubin is a pigment that results from the breakdown of the heme portion of hemoglobin. The liver conjugates bilirubin, making it water-soluble and the conjugated form is
then excreted in urine as urobilinogen, giving urine its color. In the intestine, bilirubin
is converted by bacteria to stercobilinogen. Stercobilinogen is absorbed and excreted
by either the liver or the kidney. Stercobilinogen is oxidized to stercobilin, which is responsible for the pigmentation of feces.
In early liver disease, impaired biliary excretion causes sterocobilinogen to be absorbed mostly by the kidney, and, therefore, stercobilinogen will appear in the urine in
excess as urobilinogen. This happens because "Stercobilinogen" is simply the name
given to Urobilinogen in the GI tract. In fact, its use as a separate term has fallen out
of favor due to the confusion.
https://en.wikipedia.org/wiki/Stercobilinogen
Index
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Stereochemistry
arrangement of atoms that form the structure of molecules and their manipu
Index
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Stereoisomers
Stereoisomers are isomeric molecules that have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the
same molecular formula, but the bond connections or their order differs. By definition,
molecules that are stereoisomers of each other represent the same structural isomer.
https://en.wikipedia.org/wiki/Stereoisomerism
Steric Hindrance
Steric hindrance occurs when the large size of groups within a molecule pre
chemical reactions that are observed in related molecules with smaller grou
https://en.wikipedia.org/wiki/Steric_effects#Steric_hindrance
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Steroid
A steroid is an organic compound with four rings arranged in a specific configuration.
Examples include the dietary lipid cholesterol, the sex hormones estradiol and testosterone and the anti-inflammatory drug dexamethasone. Steroids have two principal
biological functions: certain steroids (such as cholesterol) are important components
of cell membranes which alter membrane fluidity, and many steroids are signaling
molecules which activate steroid hormone receptors.
The steroid core structure is composed of seventeen carbon atoms, bonded in four
"fused" rings: three six-member cyclohexane rings (rings A, B and C in the first illustration) and one five-member cyclopentane ring (the D ring). Steroids vary by the functional groups attached to this four-ring core and by the oxidation state of the rings.
Sterols are forms of steroids with a hydroxyl group at position three and a skeleton derived from cholestane. They can also vary more markedly by changes to the ring structure (for example, ring scissions which produce secosteroids such as vitamin D3).
Hundreds of steroids are found in plants, animals and fungi. All steroids are manufactured in cells from the sterols lanosterol (animals and fungi) or cycloartenol (plants).
Lanosterol and cycloartenol are derived from the cyclization of the triterpene squalene.
https://en.wikipedia.org/wiki/Steroid
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Steroid Hormones
A steroid hormone is a steroid that acts as a hormone. Steroid hormones can be
grouped into 2 classes, corticosteroids (typically made in the adrenal cortex, hence cortico-) and sex steroids (typically made in the gonads or placenta). Within those 2
classes are 5 types according to the receptors to which they bind: glucocorticoids and
mineralocorticoids (corticosteroids) and androgens, estrogens, and progestogens (sex
steroids). Within those 2 classes are 5 types according to the receptors to which they
bind: glucocorticoids and mineralocorticoids (corticosteroids) and androgens, estrogens, and progestogens (sex steroids). Vitamin D derivatives are a sixth closely related
hormone system with homologous receptors. They have some of the characteristics of
true steroids as receptor ligands.
Steroid hormones help control metabolism, inflammation, immune functions, salt and
water balance, development of sexual characteristics, and the ability to withstand illness and injury. The term steroid describes both hormones produced by the body and
artificially produced medications that duplicate the action for the naturally occurring
steroids.
The natural steroid hormones are generally synthesized from cholesterol in the gonads
and adrenal glands. These forms of hormones are lipids. They can pass through the cell
membrane as they are fat-soluble, and then bind to steroid hormone receptors (which
may be nuclear or cytosolic depending on the steroid hormone) to bring about changes
within the cell. Steroid hormones are generally carried in the blood, bound to specific
carrier proteins such as sex hormone-binding globulin or corticosteroid-binding globulin. Further conversions and catabolism occurs in the liver, in other "peripheral" tissues, and in the target tissues.
Steroids exert a wide variety of effects, mediated by slow genomic as well as by rapid
nongenomic mechanisms. They bind to nuclear receptors in the cell nucleus for genomic actions. Membrane-associated steroid receptors activate intracellular signaling
cascades involved in nongenomic actions.
Because steroids and sterols are lipid-soluble, they can diffuse fairly freely from the
blood through the cell membrane and into the cytoplasm of target cells. This is in contrast to the actions of non-steroid hormones, which are water-soluble typically peptide
hormones, acting through membrane bound receptors and intracellular second messenger systems to exert their effects. In the cytoplasm, the steroid may or may not undergo
an enzyme-mediated alteration such as reduction, hydroxylation, or aromatization. In
the cytoplasm, the steroid binds to the specific receptor, a large metalloprotein. Upon
steroid binding, many kinds of steroid receptor dimerize: Two receptor subunits join
together to form one functional DNA-binding unit that can enter the cell nucleus. In
some of the hormone systems known, the receptor is associated with a heat shock protein, which is released on the binding of the ligand, the hormone. Once in the nucleus,
the steroid-receptor ligand complex binds to specific DNA sequences and induces transcription of its target genes.
https://en.wikipedia.org/wiki/Steroid_hormone
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Sterol
Sterols, also known as steroid alcohols, are a subgroup of the steroids and an important class of organic molecules. They occur naturally in plants, animals, and fungi, with
the most familiar type of animal sterol being cholesterol. Cholesterol is vital to animal
cell membrane structure and function as a precursor to fat-soluble vitamins and steroid hormones.
Sterols of plants are called phytosterols and sterols of animals are called zoosterols.
The most important zoosterol is cholesterol. Notable phytosterols include campesterol, sitosterol, and stigmasterol. Ergosterol is a sterol present in the cell membrane of
fungi, where it serves a role similar to cholesterol in animal cells.
Phytosterols, more commonly known as plant sterols, have been shown in clinical trials to block cholesterol absorption sites in the human intestine, thus helping to reduce
cholesterol in humans. They are currently approved by the U.S. Food and Drug Administration for use as a food additive. However, there is some concern that they may
block absorption not only of cholesterol but of other important nutrients as well. At present the American Heart Association has recommended that supplemental plant sterols be taken only by those diagnosed with elevated cholesterol, and has particularly recommended that they not be taken by pregnant women or nursing mothers.
Sterols and related compounds play essential roles in the physiology of eukaryotic organisms. For example, cholesterol forms part of the cellular membrane in animals,
where it affects the cell membrane's fluidity and serves as secondary messenger in developmental signaling. In humans and other animals, corticosteroids, such as cortisol
act as signaling compounds in cellular communication and general metabolism. Sterols are common components of human skin oils.
Shown below - general sterol structure
https://en.wikipedia.org/wiki/Sterol
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Sterols
Sterols, also known as steroid alcohols, are a subgroup of the steroids and an important class of organic molecules. They occur naturally in plants, animals, and fungi, with
the most familiar type of animal sterol being cholesterol. Cholesterol is vital to animal
cell membrane structure and function as a precursor to fat-soluble vitamins and steroid hormones.
Sterols of plants are called phytosterols and sterols of animals are called zoosterols.
The most important zoosterol is cholesterol. Notable phytosterols include campesterol, sitosterol, and stigmasterol. Ergosterol is a sterol present in the cell membrane of
fungi, where it serves a role similar to cholesterol in animal cells.
Phytosterols, more commonly known as plant sterols, have been shown in clinical trials to block cholesterol absorption sites in the human intestine, thus helping to reduce
cholesterol in humans. They are currently approved by the U.S. Food and Drug Administration for use as a food additive. However, there is some concern that they may
block absorption not only of cholesterol but of other important nutrients as well. At present the American Heart Association has recommended that supplemental plant sterols be taken only by those diagnosed with elevated cholesterol, and has particularly recommended that they not be taken by pregnant women or nursing mothers.
Sterols and related compounds play essential roles in the physiology of eukaryotic organisms. For example, cholesterol forms part of the cellular membrane in animals,
where it affects the cell membrane's fluidity and serves as secondary messenger in developmental signaling. In humans and other animals, corticosteroids, such as cortisol
act as signaling compounds in cellular communication and general metabolism. Sterols are common components of human skin oils.
Shown below - general sterol structure
https://en.wikipedia.org/wiki/Sterol
Index
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Stevia
Stevia is a sweetener and sugar substitute extracted from the leaves of the p
Stevia rebaudiana.
https://en.wikipedia.org/wiki/Stevia
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Sticky End
Sticky ends are most often created by restriction endonucleases when they c
Very often they cut the two DNA strands four to six base pairs from each ot
ing a 5' overhang in one molecule and a complementary 5' overhang in the o
ends are called cohesive since they are easily joined back together by a ligas
https://en.wikipedia.org/wiki/Sticky_and_blunt_ends#Overhangs_and_s
Stigmatellin
Stigmatellin is a potent inhibitor of the quinol oxidation (Qo) site of the cyto
https://en.wikipedia.org/wiki/Stigmatellin
Stop Codon
In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within
messenger RNA that signals a termination of translation. Proteins are based on
polypeptides, which are unique sequences of amino acids. Most codons in messenger
RNA (from DNA) correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein. Stop codons signal the termination
of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. While start codons need nearby sequences or
initiation factors to start translation, a stop codon alone is sufficient to initiate termination.
In the standard genetic code, there are three different stop codons:
in RNA:
UAG ("amber")
UAA ("ochre")
UGA ("opal")
The UGA codon has recently been identified as the codon coding for selenocysteine
(Sec). This amino acid is found in 25 selenoproteins where it is located in the active
site of the protein. Transcription of this codon is enabled by the proximity of the SECIS
element (SElenoCysteine Incorporation Sequence). The UAG codon can translate into
pyrrolysine in a similar manner.
Distribution of stop codons within the genome of an organism is non-random and can
correlate with GC-content. For example, the E. coli K-12 genome contains 2705 TAA
(63%), 1257 TGA (29%), and 326 TAG (8%) stop codons (GC content 50.8%). Also the
substrates for the stop codons release factor 1 or release factor 2 are strongly correlated
to the abundance of stop codons. Large scale study of bacteria with a broad range of
GC-contents shows that while the frequency of occurrence of TAA is negatively correlated to the GC-content and the frequency of occurrence of TGA is positively correlated
to the GC-content, the frequency of occurrence of the TAG stop codon, which is often
the minimally used stop codon in a genome, is not influenced by the GC-content.
Nonsense mutations are changes in DNA sequence that introduce a premature stop codon, causing any resulting protein to be abnormally shortened. This often causes a loss
of function in the protein, as critical parts of the amino acid chain are no longer created. Because of this terminology, stop codons have also been referred to as nonsense
codons.
https://en.wikipedia.org/wiki/Stop_codon
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Strand Invasion
Homologous recombination varies widely among different organisms and cell types,
but most forms involve the same basic steps. After a double-strand break occurs, sections of DNA around the 5' ends of the break are cut away in a process called resection.
In the strand invasion step that follows, an overhanging 3' end of the broken DNA
molecule then "invades" a similar or identical DNA molecule that is not broken. After
strand invasion, the further sequence of events may follow either of two main pathways discussed below - the DSBR (double-strand break repair) pathway or the SDSA
(synthesis-dependent strand annealing) pathway. Homologous recombination that occurs during DNA repair tends to result in non-crossover products, in effect restoring
the damaged DNA molecule as it existed before the double-strand break.
https://en.wikipedia.org/wiki/Homologous_recombination
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Stroma
Stroma, in botany, refers to the colorless fluid surrounding the grana within the chloroplast. Within the stroma are grana, stacks of thylakoids, the sub-organelles, the daughter cells, where photosynthesis is commenced before the chemical changes are completed in the stroma.
Photosynthesis occurs in two stages. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage molecules ATP and
NADPH. During the second stage, the light-independent reactions use these products
to capture and reduce carbon dioxide.
The series of biochemical redox reactions which take place in the stroma are collectively called the Calvin cycle or light-independent reactions. There are three phases:
carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.
The stroma is also the location of chloroplast DNA and chloroplast ribosomes, and
thus also the location of molecular processes including chloroplast DNA replication,
and transcription/translation of some chloroplast proteins.
https://en.wikipedia.org/wiki/Stroma_(fluid)
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Structural Domains
A protein domain is a conserved part of a given protein sequence and (tertiary) struc-
ture that can evolve, function, and exist independently of the rest of the protein chain
Each domain forms a compact three-dimensional structure and often can be indepen
ently stable and folded. Many proteins consist of several structural domains. One do-
main may appear in a variety of different proteins. Molecular evolution uses domain
as building blocks and these may be recombined in different arrangements to create
proteins with different functions. Domains vary in length from between about 25
amino acids up to 500 amino acids in length. The shortest domains such as zinc finge
are stabilized by metal ions or disulfide bridges. Domains often form functional units
such as the calcium-binding EF hand domain of calmodulin. Because they are inde-
pendently stable, domains can be "swapped" by genetic engineering between one pro
tein and another to make chimeric proteins.
https://en.wikipedia.org/wiki/Protein_domain
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Structural Motif
ments. An individual motif usually consists of only a few elements, e.g., the
helix' motif which has just three. Note that, while the spatial sequence of ele
Index
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Structural Motifs
ments. An individual motif usually consists of only a few elements, e.g., the
helix' motif which has just three. Note that, while the spatial sequence of ele
Substrate
A substrate is typically a chemical species participating in a reaction, which reacts to
generate a product. In synthetic and organic chemistry, the substrate is the chemical of
interest that is being modified. In biochemistry, the substrate is a molecule that binds
to an enzyme and is converted to product.
https://en.wikipedia.org/wiki/Substrate_(chemistry)
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https://en.wikipedia.org/wiki/Substrate-level_phosphorylation
Index
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Substrate-level Phosphorylation
Substrate-level phosphorylation is a type of metabolic reaction that results in the formation of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) by the direct
transfer and donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) or
guanosine diphosphate (GDP) from a phosphorylated reactive intermediate. Note that
the phosphate group does not have to come directly from the substrate.
An alternative way to create ATP is through oxidative phosphorylation, which takes
place during the process of cellular respiration, in addition to the substrate-level phosphorylation that occurs during glycolysis and the Krebs cycle. During oxidative phosphorylation, NADH is oxidized to NAD+, yielding 2.5 ATPs, and FADH2 (flavin adenine
dinucleotide) yields 1.5 ATPs when it is oxidized. Oxidative phosphorylation uses an
electrochemical or chemiosmotic gradient of protons (H+) across the inner mitochondrial membrane to generate ATP from ADP and a molecule of inorganic phosphate,
which is a key difference from substrate-level phosphorylation.
Unlike oxidative phosphorylation, oxidation and phosphorylation are not coupled in
the process of substrate-level phosphorylation, although both types of phosphorylation
result in the formation of ATP, and reactive intermediates are most often gained in
course of oxidation processes in catabolism. However, usually most of the ATP is generated by oxidative phosphorylation in aerobic or anaerobic respiration. Substrate-level
phosphorylation serves as fast source of ATP independent of external electron acceptors and respiration. This is the case for example in human erythrocytes, which have
no mitochondria, and in the muscle during oxygen depression.
https://en.wikipedia.org/wiki/Substrate-level_phosphorylation
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Subtilisin
Subtilisins belong to subtilases, a group of serine proteases that - like all serine proteases - initiate the nucleophilic attack on the peptide (amide) bond through a serine residue at the active site. Subtilisins typically have molecular weights of about 20,000 to
45,000 Daltons.
The active site features a charge-relay network involving Asp-32, His-64, and active
site Ser-221 arranged in a catalytic triad. The charge-relay network functions as follows: The carboxylate side-chain of Asp-32 hydrogen-bonds to a nitrogen-bonded proton on His-64's imidazole ring. This is possible because Asp is negatively charged at
physiological pH. The other nitrogen on His-64 hydrogen-bonds to the O-H proton of
Ser-221. This last interaction results in charge-separation of O-H, with the oxygen
atom being more nucleophilic. This allows the oxygen atom of Ser-221 to attack incoming substrates (i.e., peptide bonds), assisted by a neighboring carboxyamide side-chain
of Asn-155.
Even though Asp-32, His-64, and Ser-221 are sequentially far apart, they converge in
the 3D structure to form the active site.
To summarize the interactions described above, Ser-221 acts as a nucleophile and
cleaves peptide bonds with its partially negative oxygen atom. This is possible due to
the nature of the charge-relay site of subtilisin.
https://en.wikipedia.org/wiki/Subtilisin
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Succinate
Succinate is an intermediate in the citric acid cycle. It serves as an electron donor to
the electron transport chain.
It reacts in the citric acid cycle as follows:
Succinate + FAD Fumarate + FADH2
This conversion is catalyzed by the enzyme succinate dehydrogenase (or complex II of
the mitochondrial ETC). The complex is a 4 subunit membrane-bound lipoprotein
which couples the oxidation of succinate to the reduction of ubiquinone. Intermediate
electron carriers are FAD and three 2Fe-2S clusters part of subunit B.
https://en.wikipedia.org/wiki/Succinic_acid#Biochemistry
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Succinate Dehydrogenase
Succinate dehydrogenase or succinate-coenzyme Q reductase (SQR) or respiratory
Complex II is an enzyme complex, bound to the inner mitochondrial membrane of
mammalian mitochondria and many bacterial cells. It is the only enzyme that partici
pates in both the citric acid cycle and the electron transport chain.
The reaction it catalyzes is as follows:
Succinate + FAD Fumarate + FADH2
https://en.wikipedia.org/wiki/Succinate_dehydrogenase
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Succinyl-CoA
Succinyl-Coenzyme A, abbreviated as Succinyl-CoA is a combination of succinic acid
and coenzyme A. It is an important intermediate in the citric acid cycle, where it is synthesized from -Ketoglutarate by -ketoglutarate dehydrogenase through decarboxylation. During the process, coenzyme A is added.
Succinyl CoA can also be formed from methylmalonyl CoA through the utilization of
deoxyadenosyl-B12 (deoxyadenosylcobalamin) by the enzyme methylmalonyl-CoA mutase. This reaction, which requires vitamin B12 as a cofactor, is important in the catabolism of some branched-chain amino acids as well as odd-chain fatty acids.
https://en.wikipedia.org/wiki/Succinyl-CoA
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Succinyl-CoA Synthetase
CoA to succinate. The enzyme facilitates the coupling of this reaction to the form
key role as one of the catalysts involved in the citric acid cycle, a central pathwa
lular metabolism, and it is located within the mitochondrial matrix of a cell.
Succinyl CoA synthetase catalyzes the following reversible reaction:
Succinyl CoA + Pi + NDP Succinate + CoA + NTP
Index
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Succinyl-diaminopimelate Desuccinylase
bonds other than peptide bonds, specifically in linear amides. The systemat
Succinyl-diaminopimelate Transaminase
which transfer nitrogenous groups. The systematic name of this enzyme clas
N-succinyl-L-2,6-diaminoheptanedioate:2-oxoglutarate aminotransferase. O
Sucralose
Sucralose is a non-nutritive sweetener. The majority of ingested sucralose is not broken down by the body, so it is noncaloric. Sucralose is about 320 to 1,000 times
sweeter than sucrose, three times as sweet as aspartame and twice as sweet as saccharin. It is stable under heat and over a broad range of pH conditions. Therefore, it can
be used in baking or in products that require a longer shelf life. The commercial success of sucralose-based products stems from its favorable comparison to other lowcalorie sweeteners in terms of taste, stability, and safety. Common brand names of
sucralose-based sweeteners are Splenda, Zerocal, Sukrana, SucraPlus, Candys, Cukren,
and Nevella.
Sucralose is manufactured by the selective chlorination of sucrose in a multistep synthesis, which substitutes three of the hydroxyl groups of sucrose with chlorine atoms.
This chlorination is achieved by selective protection of a primary alcohol group, followed by chlorination of the partially acetylated sugar with excess chlorinating agent,
and then by removal of the acetyl groups to give the desired sucralose product.
https://en.wikipedia.org/wiki/Sucralose
Sucrose
Sucrose is a common, naturally occurring carbohydrate found in many plants and
plant parts. The molecule is a disaccharide combination of the monosaccharides glucose and fructose with the formula C12H22O11.
In sucrose, the components glucose and fructose are linked via an acetal bond between
C1 on the glucosyl subunit and C2 on the fructosyl unit. The bond is called a glycosidic
linkage. Glucose exists predominantly as two isomeric "pyranoses" ( and ), but only
one of these forms links to the fructose. Fructose itself exists as a mixture of "furanoses", each of which having and isomers, but only one particular isomer links to the
glucosyl unit. What is notable about sucrose is that, unlike most disaccharides, the glycosidic bond is formed between the reducing ends of both glucose and fructose, and
not between the reducing end of one and the nonreducing end of the other. This linkage inhibits further bonding to other saccharide units. Since it contains no anomeric
hydroxyl groups, it is classified as a non-reducing sugar.
Hydrolysis breaks the glycosidic bond converting sucrose into glucose and fructose. Hydrolysis is, however, so slow that solutions of sucrose can sit for years with negligible
change. If the enzyme sucrase is added, however, the reaction will proceed rapidly. Hydrolysis can also be accelerated with acids, such as cream of tartar or lemon juice, both
weak acids. Likewise, gastric acidity converts sucrose to glucose and fructose during digestion the bond between them being an acetal bond which can be broken by an acid.
https://en.wikipedia.org/wiki/Sucrose
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Sucrose Synthase
Sucrose synthase (EC 2.4.1.13) is an enzyme that catalyzes the chemical react
NDP-glucose + D-fructose <=> NDP + Sucrose
The reaction is reversible and can be used to split the two sugars of sucrose.
Index
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Sugar
Sugar is the generalized name for sweet, short-chain, soluble carbohydrates, many of
which are used in food. They are composed of carbon, hydrogen, and oxygen. There
are various types of sugar derived from different sources. Simple sugars are called
monosaccharides and include glucose (also known as dextrose), fructose, and galactose. The table or granulated sugar most customarily used as food is sucrose, a disaccharide. (In the body, sucrose hydrolyzes into fructose and glucose.) Other disaccharides include maltose and lactose. Longer chains of sugars are called oligosaccharides.
Chemically-different substances may also have a sweet taste, but are not classified as
sugars. Some are used as lower-calorie food substitutes for sugar described as artificial
sweeteners.
Since the latter part of the twentieth century, it has been questioned whether a diet
high in sugars, especially refined sugars, is good for human health. Sugar has been
linked to obesity, and suspected of, or fully implicated as a cause in the occurrence of
diabetes, cardiovascular disease, dementia, macular degeneration, and tooth decay. Numerous studies have been undertaken to try to clarify the position, but with varying results, mainly because of the difficulty of finding populations for use as controls that do
not consume or are largely free of any sugar consumption.
https://en.wikipedia.org/wiki/Sugar
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Sugar Alcohol
Sugar alcohols are organic compounds, typically derived from sugars, that comprise a
class of polyols. Contrary to what the name may suggest, a sugar alcohol is not a sugar
nor an alcoholic beverage. They are white, water-soluble solids that can occur naturally
or be produced industrially from sugars. Sugar alcohols are used widely in the food industry as thickeners and sweeteners. In commercial foodstuffs, sugar alcohols are commonly used in place of table sugar (sucrose), often in combination with high intensity
artificial sweeteners to counter the low sweetness. Xylitol is perhaps the most popular
sugar alcohol due to its similarity to sucrose in visual appearance and sweetness.
As a group, sugar alcohols are not as sweet as sucrose, and they have less food energy
than sucrose. Their flavor is like sucrose, and they can be used to mask the unpleasant
aftertastes of some high intensity sweeteners. Sugar alcohols are not metabolized by
oral bacteria, and so they do not contribute to tooth decay. They do not brown or caramelize when heated.
In addition to their sweetness, some sugar alcohols can produce a noticeable cooling
sensation in the mouth when highly concentrated, for instance in sugar-free hard
candy or chewing gum. This happens, for example, with the crystalline phase of sorbitol, erythritol, xylitol, mannitol, lactitol and maltitol. The cooling sensation is due to
the dissolution of the sugar alcohol being an endothermic (heat-absorbing) reaction,
one with a strong heat of solution.
Sugar alcohols are usually incompletely absorbed into the blood stream from the small
intestines which generally results in a smaller change in blood glucose than "regular"
sugar (sucrose). This property makes them popular sweeteners among diabetics and
people on low-carbohydrate diets. However, like many other incompletely digestible
substances, overconsumption of sugar alcohols can lead to bloating, diarrhea and flatulence because they are not absorbed in the small intestine. Some individuals experience such symptoms even in a single-serving quantity. With continued use, most people develop a degree of tolerance to sugar alcohols and no longer experience these
symptoms. As an exception, erythritol is actually absorbed in the small intestine and
excreted unchanged through urine, so it contributes no calories even though it is rather
sweet.
Shown below - erythritol
https://en.wikipedia.org/wiki/Sugar_alcohol
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Sugars
Sugar is the generalized name for sweet, short-chain, soluble carbohydrates, many of
which are used in food. They are composed of carbon, hydrogen, and oxygen. There
are various types of sugar derived from different sources. Simple sugars are called
monosaccharides and include glucose (also known as dextrose), fructose, and galactose. The table or granulated sugar most customarily used as food is sucrose, a disaccharide. (In the body, sucrose hydrolyses into fructose and glucose.) Other disaccharides include maltose and lactose. Longer chains of sugars are called oligosaccharides.
Chemically-different substances may also have a sweet taste, but are not classified as
sugars. Some are used as lower-calorie food substitutes for sugar described as artificial
sweeteners.
Since the latter part of the twentieth century, it has been questioned whether a diet
high in sugars, especially refined sugars, is good for human health. Sugar has been
linked to obesity, and suspected of, or fully implicated as a cause in the occurrence of
diabetes, cardiovascular disease, dementia, macular degeneration, and tooth decay. Numerous studies have been undertaken to try to clarify the position, but with varying results, mainly because of the difficulty of finding populations for use as controls that do
not consume or are largely free of any sugar consumption.
https://en.wikipedia.org/wiki/Sugar
Index
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Suicide Inhibition
Suicide inhibition, also known as suicide inactivation or mechanism-based inhibition,
is an irreversible form of enzyme inhibition that occurs when an enzyme binds a substrate analogue and forms an irreversible complex with it through a covalent bond during the "normal" catalysis reaction. The inhibitor binds to the active site where it is
modified by the enzyme to produce a reactive group that reacts irreversibly to form a
stable inhibitor-enzyme complex. This usually uses a prosthetic group or a coenzyme,
forming electrophilic alpha and beta unsaturated carbonyl compounds and imines.
Some clinical examples of suicide inhibitors include:
Aspirin, which inhibits cyclooxygenase 1 and 2 enzymes.
Penicillin, which inhibits DD-transpeptidase from building bacterial cell walls.
Sulbactam, which prohibits penicillin-resistant strains of bacteria from metabolizing
penicillin.
Allopurinol, which inhibits uric acid production by xanthine oxidase in the treatment
of gout.
AZT (zidovudine) and other chain-terminating nucleoside analogues used to inhibit
HIV-1 reverse transcriptase in the treatment of HIV/AIDS.
https://en.wikipedia.org/wiki/Suicide_inhibition
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Sulfate
The sulfate or ion is a polyatomic anion SO4= .Sulfates are salts of sulfuric acid and
many are prepared from that acid. The anion consists of a central sulfur atom surrounded by four equivalent oxygen atoms in a tetrahedral arrangement. The symmetry
is the same as that of methane. The sulfur atom is in the +6 oxidation state while the
four oxygen atoms are each in the 2 state. The sulfate ion carries a negative two
charge and is the conjugate base of the bisulfate (or hydrogen sulfate) ion, HSO4-,
which is the conjugate base of H2SO4, sulfuric acid. Organic sulfate esters, such as dimethyl sulfate, are covalent compounds and esters of sulfuric acid.
https://en.wikipedia.org/wiki/Sulfate
Index
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Sulfates
The sulfate or ion is a polyatomic anion SO4= .Sulfates are salts of sulfuric acid and
many are prepared from that acid. The anion consists of a central sulfur atom sur
is the same as that of methane. The sulfur atom is in the +6 oxidation state while t
four oxygen atoms are each in the 2 state. The sulfate ion carries a negative two
charge and is the conjugate base of the bisulfate (or hydrogen sulfate) ion, HSO4-,
which is the conjugate base of H2SO4, sulfuric acid. Organic sulfate esters, such as
methyl sulfate, are covalent compounds and esters of sulfuric acid.
https://en.wikipedia.org/wiki/Sulfate
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Sulfhydryl
Thiol is an organosulfur compound that contains a carbon-bonded sulfhydryl or sulphydryl (CSH or RSH) group (where R represents an alkyl or other organic substituent). Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of oxygen
in the hydroxyl group of an alcohol). The SH functional group itself is referred to as
either a thiol group or a sulfhydryl group.
Many thiols have strong odors resembling that of garlic or rotten eggs. Thiols are used
as odorants to assist in the detection of natural gas (which in pure form is odorless),
and the "smell of natural gas" is due to the smell of the thiol used as the odorant.
https://en.wikipedia.org/wiki/Thiol
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Sulfite
A compound that contains the sulfite ion (or the sulfate (IV) ion, from its correct systematic name), SO3=.
The structure of the sulfite anion can be described with three equivalent resonance
structures. In each resonance structure, the sulfur atom is double-bonded to one oxygen atom with a formal charge of zero (neutral), and sulfur is singly bonded to the
other two oxygen atoms, which each carry a formal charge of 1, together accounting
for the 2 charge on the anion. There is also a non-bonded lone pair on the sulfur, so
the structure predicted by VSEPR theory is trigonal pyramidal, as in ammonia (NH3).
In the hybrid resonance structure, the S-O bonds are equivalently of bond order one
and one-third.
Sulfites occur naturally in all wines to some extent. Sulfites are commonly introduced
to arrest fermentation at a desired time, and may also be added to wine as preservatives to prevent spoilage and oxidation at several stages of the winemaking. Sulfur dioxide (SO2, sulfur with two atoms of oxygen) protects wine from not only oxidation, but
also from bacteria. Without sulfites, grape juice would quickly turn to vinegar.
Organic wines are not necessarily sulfite-free, but generally have lower amounts and
regulations stipulate lower maximum sulfite contents for these wines. In general, white
wines contain more sulfites than red wines and sweeter wines contain more sulfites
than drier ones.
https://en.wikipedia.org/wiki/Sulfite
Index
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G-G
Chapter 6 - Metabolism: Amino Acids and the Urea Cycle
Chapter 9 - Point by Point: Metabolism
Sumoylation
Small Ubiquitin-like Modifier (or SUMO) proteins are a family of small proteins that
are covalently attached to and detached from other proteins in cells to modify their
function. SUMOylation is a post-translational modification involved in various cellular
processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis,
protein stability, response to stress, and progression through the cell cycle.
SUMO proteins are similar to ubiquitin, and SUMOylation is directed by an enzymatic
cascade analogous to that involved in ubiquitination. In contrast to ubiquitin, SUMO is
not used to tag proteins for degradation. Mature SUMO is produced when the last four
amino acids of the C-terminus have been cleaved off to allow formation of an isopeptide bond between the C-terminal glycine residue of SUMO and an acceptor lysine on
the target protein.
SUMO modification of proteins has many functions. Among the most frequent and
best studied are protein stability, nuclear-cytosolic transport, and transcriptional regulation. Typically, only a small fraction of a given protein is SUMOylated and this modification is rapidly reversed by the action of deSUMOylating enzymes. SUMOylation of
target proteins has been shown to cause a number of different outcomes including altered localization and binding partners. The SUMO-1 modification of RanGAP1 (the
first identified SUMO substrate) leads to its trafficking from cytosol to nuclear pore
complex. The SUMO modification of hNinein leads to its movement from the centrosome to the nucleus. In many cases, SUMO modification of transcriptional regulators
correlates with inhibition of transcription.
https://en.wikipedia.org/wiki/SUMO_protein
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Super-secondary Structures
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Supercoil
DNA supercoiling refers to the over- or under-winding of a DNA strand. Relative to the
winding of relaxed B-DNA (10.5 bp per turn), over- or under-winding (making fewer or
more bp/turn, respectively) creates strain on the strands in a duplex. Supercoiling
(winding of the duplex with itself0 occurs, then, to relieve the strain.
Supercoiling is important in a number of biological processes, such as compacting
DNA, and by regulating access to the genetic code, DNA supercoiling strongly affects
DNA metabolism and possibly gene expression. Additionally, certain enzymes such as
topoisomerases are able to change DNA topology to facilitate functions such as DNA
replication or transcription. Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA.
In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.410.5 base pairs of sequence. Adding or subtracting twists, as
some enzymes can do, imposes strain. If a DNA segment under twist strain were closed
into a circle by joining its two ends and then allowed to move freely, the circular DNA
would contort into a new shape, such as a simple figure-eight. Such a contortion is a supercoil. The noun form "supercoil" is often used in the context of DNA topology.
Positively supercoiled (overwound) DNA is transiently generated during DNA replication and transcription, and, if not promptly relaxed, inhibits (regulates) these processes. The simple figure eight is the simplest supercoil, and is the shape a circular DNA
assumes to accommodate one too many or one too few helical twists. The two lobes of
the figure eight will appear rotated either clockwise or counterclockwise with respect to
one another, depending on whether the helix is over- or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about
their axis. As a general rule, the DNA of most organisms is negatively supercoiled.
Shown below - relaxed (left) and supercoiled (right) DNA.
https://en.wikipedia.org/wiki/DNA_supercoil
Superoxide
A superoxide, is a compound that contains the superoxide anion with the chemical formula O2-. Superoxide anion is particularly important as the product of the oneelectron reduction of dioxygen O2, which occurs widely in nature. Whereas molecular
oxygen (dioxygen) is a diradical containing two unpaired electrons, the addition of a
second electron fills one of its two degenerate molecular orbitals, leaving a charged
ionic species with single unpaired electron and a net negative charge of 1. Both dioxygen and superoxide ion are free radicals that exhibit paramagnetism.
Superoxide is biologically quite toxic and is deployed by the immune system to kill invading microorganisms. In phagocytes, superoxide is produced in large quantities by
the enzyme NADPH oxidase for use in oxygen-dependent killing mechanisms of invading pathogens. Mutations in the gene coding for the NADPH oxidase cause an immunodeficiency syndrome called chronic granulomatous disease, characterized by extreme
susceptibility to infection, especially catalase-positive organisms. In turn, microorganisms genetically engineered to lack superoxide dismutase (SOD) lose virulence.
Superoxide is also deleterious when produced as a byproduct of mitochondrial respiration (most notably by Complex I and Complex III), as well as several other enzymes,
for example xanthine oxidase.
Because superoxide is toxic, nearly all organisms living in the presence of oxygen contain isoforms of the superoxide-scavenging enzyme superoxide dismutase, or SOD.
SOD is an extremely efficient enzyme. It catalyzes the neutralization of superoxide
nearly as fast as the two can diffuse together spontaneously in solution. Other proteins
that can be both oxidized and reduced by superoxide (e.g., hemoglobin) have weak
SOD-like activity. Genetic inactivation ("knockout") of SOD produces deleterious phenotypes in organisms ranging from bacteria to mice and have provided important clues
as to the mechanisms of toxicity of superoxide in vivo.
Yeast lacking both mitochondrial and cytosolic SOD grow very poorly in air, but quite
well under anaerobic conditions. Absence of cytosolic SOD causes a dramatic increase
in mutagenesis and genomic instability. Mice lacking mitochondrial SOD (MnSOD) die
around 21 days after birth due to neurodegeneration, cardiomyopathy, and lactic acidosis. Mice lacking cytosolic SOD (CuZnSOD) are viable but suffer from multiple pathologies, including reduced lifespan, liver cancer, muscle atrophy, cataracts, thymic involution, haemolytic anemia and a very rapid age-dependent decline in female fertility.
Superoxide may contribute to the pathogenesis of many diseases (the evidence is particularly strong for radiation poisoning and hyperoxic injury), and perhaps also to aging via the oxidative damage that it inflicts on cells. While the action of superoxide in
the pathogenesis of some conditions is strong (for instance, mice and rats overexpressing CuZnSOD or MnSOD are more resistant to strokes and heart attacks), the role of
superoxide in aging must be regarded as unproven for now. In model organisms (yeast,
the fruit fly Drosophila and mice), genetically knocking out CuZnSOD shortens lifespan and accelerates certain features of aging (cataracts, muscle atrophy, macular degeneration, thymic involution). But the converse, increasing the levels of CuZnSOD,
does not seem (except perhaps in Drosophila), to consistently increase lifespan. The
most widely accepted view is that oxidative damage (resulting from multiple causes, including superoxide) is but one of several factors limiting lifespan.
https://en.wikipedia.org/wiki/Superoxide
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Superoxide Dismutase
Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme that alternately catalyzes the dismutation (or partitioning) of the superoxide (O2) radical into either ordinary molecular oxygen (O2) or hydrogen peroxide (H2O2). Superoxide is produced as a by-product
of oxygen metabolism and, if not regulated, causes many types of cell damage. Hydrogen peroxide is also damaging, but less so, and is degraded by other enzymes such as
catalase. Thus, SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus plantarum and related lactobacilli,
which use a different mechanism to prevent damage from reactive (O2).
SOD enzymes deal with the superoxide radical by alternately adding or removing an
electron from the superoxide molecules it encounters, thus changing the O2 into one
of two less damaging species: either molecular oxygen (O2) or hydrogen peroxide
(H2O2). This SOD-catalyzed dismutation of superoxide may be written, for Cu,Zn
SOD, with the following half-reactions:
Cu2+-SOD + O2 Cu+-SOD + O2
The general form, applicable to all the different metal-coordinated forms of SOD, can
be written as follows:
M(n+1)+-SOD + O2 Mn+-SOD + O2
Mn+-SOD + O2 + 2H+ M(n+1)+-SOD + H2O2
where M = Cu (n=1); Mn (n=2); Fe (n=2); Ni (n=2).
In a series of such reactions, the oxidation state and the charge of the metal cation oscillates between n and n+1: +1 and +2 for Cu, or +2 and +3 for the other metals.
https://en.wikipedia.org/wiki/Superoxide_dismutase
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Superoxide Dismutases
Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme that alternately catalyzes the dismutation (or partitioning) of the superoxide (O2) radical into either ordinary molecular oxygen (O2) or hydrogen peroxide (H2O2). Superoxide is produced as a by-product
of oxygen metabolism and, if not regulated, causes many types of cell damage. Hydrogen peroxide is also damaging, but less so, and is degraded by other enzymes such as
catalase. Thus, SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus plantarum and related lactobacilli,
which use a different mechanism to prevent damage from reactive (O2).
SOD enzymes deal with the superoxide radical by alternately adding or removing an
electron from the superoxide molecules it encounters, thus changing the O2 into one
of two less damaging species: either molecular oxygen (O2) or hydrogen peroxide
(H2O2). This SOD-catalyzed dismutation of superoxide may be written, for Cu,Zn SOD,
with the following half-reactions:
Cu2+-SOD + O2 Cu+-SOD + O2
The general form, applicable to all the different metal-coordinated forms of SOD, can
be written as follows:
M(n+1)+-SOD + O2 Mn+-SOD + O2
Mn+-SOD + O2 + 2H+ M(n+1)+-SOD + H2O2
where M = Cu (n=1); Mn (n=2); Fe (n=2); Ni (n=2).
In a series of such reactions, the oxidation state and the charge of the metal cation oscillates between n and n+1: +1 and +2 for Cu, or +2 and +3 for the other metals.
https://en.wikipedia.org/wiki/Superoxide_dismutase
Index
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Supersecondary Structure
Index
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Surfactants
Surfactants are compounds that lower the surface tension (or interfacial tension) between two liquids or between a liquid and a solid. Surfactants may act as detergents,
wetting agents, emulsifiers, foaming agents, and dispersants.
Surfactants are usually organic compounds that are amphiphilic, meaning they contain
both hydrophobic groups (their tails) and hydrophilic groups (their heads). Therefore,
a surfactant contains both a water-insoluble (or oil-soluble) component and a watersoluble component. Surfactants will diffuse in water and adsorb at interfaces between
air and water or at the interface between oil and water, in the case where water is
mixed with oil. The water-insoluble hydrophobic group may extend out of the bulk water phase, into the air or into the oil phase, while the water-soluble head group remains
in the water phase.
https://en.wikipedia.org/wiki/Surfactant
Svedberg Units
A svedberg unit (symbol S, sometimes Sv) is a non-SI unit for sedimentation rate. The
sedimentation rate for a particle of a given size and shape measures how fast the particle 'settles', the sedimentation. It is often used to reflect the rate at which a molecule
travels to the bottom of a test tube under the centrifugal force of a centrifuge. The svedberg is actually a measure of time. It is defined as exactly 1013 seconds (100fs).
The Svedberg unit (S) offers a measure of particle size based on its rate of travel in a
tube subjected to high g-force. The Svedberg coefficient is a nonlinear function. A particle's mass, density, and shape will determine its S value. It depends on the frictional
forces retarding its movement, which, in turn, are related to the average crosssectional area of the particle.
The sedimentation coefficient is the ratio of the speed of a substance in a centrifuge to
its acceleration in comparable units. A substance with a sedimentation coefficient of
26S (261013s) will travel at 26 micrometers per second (26106 m/s) under the influence of an acceleration of a million gravities (107m/s2). Centrifugal acceleration is
given as r2, where r is the radial distance from the rotation axis and is the angular
velocity in radians per second.
Bigger particles tend to sediment faster and so have higher svedberg values.
Svedberg units are not directly additive since they represent a rate of sedimentation,
not weight.
https://en.wikipedia.org/wiki/Svedberg
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Symport(er)
A symporter is an integral membrane protein that is involved in the transport of many
differing types of molecules across the cell membrane. The symporter works in the
plasma membrane and molecules are transported across the cell membrane at the
same time, and is, therefore, a type of co-transporter. The transporter is called a symporter, because the molecules will travel in the same direction in relation to each other.
This is in contrast to the antiport transporter. Typically, the ion(s) will move down the
electrochemical gradient, allowing the other molecule(s) to move against the concentration gradient. The movement of the ion(s) across the membrane is facilitated diffusion,
and is coupled with the active transport of the molecule(s).
https://en.wikipedia.org/wiki/Symporter
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Synaptic Cleft
Synapses are functional connections between neurons, or between neurons and other
types of cells. A typical neuron gives rise to several thousand synapses, although there
are some types that make far fewer. Most synapses connect axons to dendrites, but
there are also other types of connections, including axon-to-cell-body, axon-to-axon,
and dendrite-to-dendrite. Synapses are generally too small to be recognizable using a
light microscope except as points where the membranes of two cells appear to touch,
but their cellular elements can be visualized clearly using an electron microscope.
Chemical synapses pass information directionally from a presynaptic cell to a postsynaptic cell and are therefore asymmetric in structure and function. The presynaptic
terminal, or synaptic bouton, is a specialized area within the axon of the presynaptic
cell that contains neurotransmitters enclosed in small membrane-bound spheres
called synaptic vesicles (as well as a number of other supporting structures and organelles, such as mitochondria and endoplasmic reticulum). Synaptic vesicles are docked
at the presynaptic plasma membrane at regions called active zones.
Immediately opposite is a region of the postsynaptic cell containing neurotransmitter
receptors. For synapses between two neurons, the postsynaptic region may be found
on the dendrites or cell body. Immediately behind the postsynaptic membrane is an
elaborate complex of interlinked proteins called the postsynaptic density (PSD).
Proteins in the PSD are involved in anchoring and trafficking neurotransmitter receptors and modulating the activity of these receptors. The receptors and PSDs are often
found in specialized protrusions from the main dendritic shaft called dendritic spines.
Synapses may be described as symmetric or asymmetric. When examined under an
electron microscope, asymmetric synapses are characterized by rounded vesicles in the
presynaptic cell, and a prominent postsynaptic density. Asymmetric synapses are typically excitatory. Symmetric synapses in contrast have flattened or elongated vesicles,
and do not contain a prominent postsynaptic density. Symmetric synapses are typically
inhibitory.
https://en.wikipedia.org/wiki/Chemical_synapse
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Synaptic Vesicles
Synaptic vesicles store various neurotransmitters that are released at the synapse. The
release is regulated by a voltage-dependent calcium channel. Vesicles are essential for
propagating nerve impulses between neurons and are constantly recreated by the cell.
Synaptic vesicles contain two classes of obligatory components: transport proteins involved in neurotransmitter uptake, and trafficking proteins that participate in synaptic
vesicle exocytosis, endocytosis, and recycling.
Transport proteins are composed of proton pumps that generate electrochemical gradients, which allow for neurotransmitter uptake, and neurotransmitter transporters
that regulate the actual uptake of neurotransmitters. The necessary proton gradient is
created by V-ATPase, which breaks down ATP for energy. Vesicular transporters
move neurotransmitters from the cells' cytoplasm into the synaptic vesicles. Vesicular
glutamate transporters, for example, sequester glutamate into vesicles by this process.
Trafficking proteins are more complex. They include intrinsic membrane proteins, peripherally bound proteins, and proteins such as SNAREs. These proteins do not share
a characteristic that would make them identifiable as synaptic vesicle proteins, and
little is known about how these proteins are specifically deposited into synaptic vesicles. Many but not all of the known synaptic vesicle proteins interact with nonvesicular proteins and are linked to specific functions.
Some neurotoxins, such as batrachotoxin, are known to destroy synaptic vesicles. The
tetanus toxin damages vesicle-associated membrane proteins (VAMP), a type of vSNARE, while botulinum toxins damage t-SNARES and v-SNARES and thus inhibit
synaptic transmission. A spider toxin called -Latrotoxin binds to neurexins, damaging vesicles and causing massive release of neurotransmitters.
In the figure below, 1 = mitochondrion; 2 = synaptic vesicle with neurotransmitters; 3
= autoreceptor; 4 = synapse with neurotransmitter released; 5 = postsynaptic receptors activated by neurotransmitter (induction of a postsynaptic potential); 6 = calcium
channel; 7 = exocytosis of a vesicle; 8 = recaptured neurotransmitter.
https://en.wikipedia.org/wiki/Synaptic_vesicle
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Syndecans
Syndecans are single transmembrane domain proteins that are thought to act as coreceptors, especially for G protein-coupled receptors. These core proteins carry three to
five heparan sulfate and chondroitin sulfate chains, which allow for interaction with a
large variety of ligands including fibroblast growth factors, vascular endothelial growth
factor, transforming growth factor-beta, fibronectin and antithrombin-1. Interactions
between fibronectin and some syndecans can be modulated by the extracellular matrix
protein tenascin C.
Functions of syndecan can be categorized in four ways. First is growth-factor-receptor
activation. Glycosaminoglycans attached to the syndecan help binding of the various
growth factors for activation of important cellular signaling mechanisms. Growth factors such as FGF2, HGF, EGF, VEGF, neuregulins and others interact with syndecans.
For example, at the site of tissue injury, the soluble syndecan-1 ectodomains are
cleaved by heparanases, producing heparin-like fragments that activate bFGF.
Whereas most growth factors interact with syndecans via heparan sulfate chains, the
prosecretory mitogen lacritin requires heparanase to both expose and create a binding
site in the N-terminus of syndecan 1.
The second function is matrix adhesion. Syndecans bind to structural extracellular matrix molecules such as collagens I, III, V, fibronectin, thrombospondin, and tenascin to
provide structural support for the adhesion.
A third function is cellcell adhesion. Evidence for syndecans role in cellcell adhesion comes from the human myeloma cell line. These myeloma cells had a deficiency in
the ability to adhere to one another in a rotation-mediated aggregation matrix. This deficiency is attributed to the lack of syndecan 1 expression. Syndecan 4 also interacts
with integrin proteins for cellcell adhesion.
A final role is in tumor suppression and progression. Syndecans act as tumor inhibitors
by preventing cellular proliferation of tumor cell lines. For example, in the epithelialderived tumor cell line, S115, the syndecan 1 ectodomain suppresses the growth of S115
cells without affecting the growth of normal epithelial cells. However, syndecan 1 expression also has a role in tumor progression in myeloma and other cancers.
https://en.wikipedia.org/wiki/Syndecan
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Synovial Fluid
Synovial fluid is a viscous, non-Newtonian fluid found in the cavities of synovial joints.
With its egg whitelike consistency, the principal role of synovial fluid is to reduce friction between the articular cartilage of synovial joints during movement.
The inner membrane of synovial joints is called the synovial membrane and secretes
synovial fluid into the joint cavity. Synovial fluid is an ultrafiltrate from plasma, and
contains proteins derived from the blood plasma and proteins that are produced by
cells within the joint tissues. The fluid contains hyaluronan secreted by fibroblast-like
cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood
plasma. This fluid forms a thin layer (roughly 50 m) at the surface of cartilage and
also seeps into microcavities and irregularities in the articular cartilage surface, filling
all empty space. The fluid in articular cartilage effectively serves as a synovial fluid reserve. During movement, the synovial fluid held in the cartilage is squeezed out mechanically to maintain a layer of fluid on the cartilage surface (so-called weeping lubrication). The functions of the synovial fluid include:
reduction of friction synovial fluid lubricates the articulating joints
shock absorption as a dilatant fluid, that possesses rheopectic properties, becoming more viscous under applied pressure. The synovial fluid in diarthrotic joints becomes thick the moment shear is applied in order to protect the joint and subsequently, thins to normal viscosity instantaneously to resume its lubricating function
between shocks.
nutrient and waste transportation the fluid supplies oxygen and nutrients and removes carbon dioxide and metabolic wastes from the chondrocytes within the surrounding cartilage
molecular sieving - pressure within the joint forces hyaluronan in the fluid against
the synovial membrane forming a barrier against cells migrating into, or fluid migrating out of, the joint space. This function is dependent on the molecular weight of the
hyaluronan.
https://en.wikipedia.org/wiki/Synovial_fluid
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T-cell Receptor
The T cell receptor or TCR is a molecule found on the surface of T lymphocytes (or T
jor histocompatibility complex (MHC) molecules. The binding between TCR and ant
gen peptides is of relatively low affinity and is degenerate: that is, many TCRs recog-
nize the same antigen peptide and many antigen peptides are recognized by the same
TCR.
The TCR is composed of two different protein chains (that is, it is a heterodimer). In
humans, in 95% of T cells the TCR consists of an alpha () and beta () chain, where
in 5% of T cells the TCR consists of gamma and delta (/) chains. This ratio changes
during ontogeny and in diseased states as well as in different species.
When the TCR engages with antigenic peptide and MHC (peptide/MHC), the T lym-
phocyte is activated through signal transduction, that is, a series of biochemical even
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T-SNARES
SNARE proteins (an acronym derived from "SNAP (Soluble NSF Attachment P
yeast and mammalian cells. The primary role of SNARE proteins is to mediate
fusion, that is, the fusion of vesicles with their target membrane bound compa
(such as a lysosome). The best studied SNAREs are those that mediate dockin
aptic vesicles with the presynaptic membrane in neurons. These SNAREs are t
gets of the bacterial neurotoxins responsible for botulism and tetanus.
SNAREs can be divided into two categories: vesicle or v-SNAREs, which are in
rated into the membranes of transport vesicles during budding, and target or
gests that t-SNAREs form stable subcomplexes which serve as guides for v-SN
binding to complete the formation of the SNARE complex.
https://en.wikipedia.org/wiki/SNARE_(protein)
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T-state
The Monod-Wyman-Changeux (MWC) model for concerted allosteric transitions
eplored the phenomenon of cooperativity based on thermodynamics and threedimensional conformations. It was originally formulated for oligomeric proteins with
symmetrically arranged, identical subunits, each of which has one ligand binding site.
According to this framework, two (or more) interconvertible conformational states of
an allosteric protein coexist in a thermal equilibrium. The states - often termed tense
(T) and relaxed (R) - differ in affinity for the ligand molecule. The ratio between the
two states is regulated by the binding of ligand molecules that stabilizes the higheraffinity state. Importantly, all subunits of a molecule change states at the same time, a
phenomenon known as "concerted transition".
https://en.wikipedia.org/wiki/Cooperative_binding
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Tamiflu
Oseltamivir, marketed under the trade name Tamiflu, is an antiviral medication used
to treat influenza A and influenza B (flu), and to prevent flu after exposure. It was the
first orally administered neuraminidase inhibitor commercially developed.
The prodrug oseltamivir is itself not virally effective. However, once in the liver it is hydrolyzed to its active metabolite the free oseltamivir carboxylate.
Oseltamivir is a neuraminidase inhibitor, serving as a competitive inhibitor of the activity of the viral neuraminidase (NA) enzyme upon sialic acid, found on glycoproteins on
the surface of normal host cells. By blocking the activity of the enzyme, oseltamivir prevents new viral particles from being released through the cleaving of terminal sialic
acid on glycosylated hemagglutinin and thus fail to facilitate virus release.
https://en.wikipedia.org/wiki/Oseltamivir
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Tardigrade
Tardigrades (also known as water bears or moss piglets) are water-dwelling, eight-
legged, segmented micro-animals. They were first discovered by the German pastor J
hann August Ephraim Goeze in 1773. The name Tardigrada (meaning "slow stepper"
was given three years later by the Italian biologist Lazzaro Spallanzani. They have be
found everywhere from mountaintops to the deep sea, from tropical rain forests to th
Antarctic.
Tardigrades are notable for being perhaps the most durable of known organisms: the
can survive extreme conditions that would be rapidly fatal to nearly all other known
life forms. They can withstand temperature ranges from 1K (458F; 272C) to
about 420K (300F; 150C), pressures about six times greater than those found in
the deepest ocean trenches, ionizing radiation at doses hundreds of times higher than
the lethal dose for a human, and the vacuum of outer space. They can go without food
or water for more than 30 years, drying out to the point where they are 3% or less wa
ter, only to rehydrate, forage, and reproduce.
https://en.wikipedia.org/wiki/Tardigrade
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TATA Box
In molecular biology, the TATA box (also called the Goldberg-Hogness box) is a DNA
sequence (cis-regulatory element) found in the promoter region of genes in archaea
and eukaryotes. Approximately 24% of human genes contain a TATA box within the
core promoter.
Considered to be the core promoter sequence, it is the binding site of either general
transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA
polymerase.
The TATA box has the core DNA sequence 5'-TATAAA-3' or a variant, which is usually
followed by three or more adenine bases[citation needed]. It is usually located 25-35
base pairs upstream of the transcription start site. The sequence is believed to have remained consistent throughout much of the evolutionary process, possibly originating
in an ancient eukaryotic organism.
During the process of transcription, the TATA binding protein (TBP) normally binds to
the TATA-box sequence, which unwinds the DNA and bends it through 80. The ATrich sequence of the TATA-box facilitates easy unwinding, due to weaker base-pairing
interactions between A and T bases, as compared to between G and C. The TBP is an
unusual protein in that it binds to the minor groove and binds with a sheet.
The TATA box is usually found at the binding site of RNA polymerase II. TFIID, a transcription factor, binds to the TATA box, followed by TFIIA binding to the upstream
part of the TFIID protein. TFIIB then binds to the downstream part of TFIID. RNA polymerase can then recognize this multi-protein complex and bind to it, along with various other transcription factors such as TFIIF, TFIIE and TFIIH. Transcription is then
initiated, and the polymerase moves along the DNA strand, leaving TFIID and TFIIA
bound to the TATA box. These can then facilitate the binding of additional RNA polymerase II molecules.
This cluster of RNA polymerase II and various transcription factors is known as a basal
transcriptional complex or BTC. In this state, it only gives a low level of transcription.
Other factors must stimulate the BTC to increase transcription levels. One such example of a BTC stimulating region of DNA is the CAAT box.
Most genes lack a TATA box and use an initiator element or downstream core promoter instead. Nevertheless, TBP is always involved and is forced to bind without sequence specificity. A genome-wide study put the fraction of TATA-dependent human
promoters at ~10%. An earlier study of ~1,000 genes found 32% of the promoters had
a TATA box.
https://en.wikipedia.org/wiki/TATA_box
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Tau Protein
Tau proteins (or proteins, after the Greek letter by that name) are protein
lize microtubules. They are abundant in neurons of the central nervous syst
less common elsewhere, but are also expressed at very low levels in CNS ast
heimer's disease and Parkinson's disease are associated with tau proteins t
come defective and no longer stabilize microtubules properly.
The tau proteins are the product of alternative splicing from a single gene th
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Taurocholic Acid
For commercial use, taurocholic acid is manufactured from cattle bile, a byproduct of
the meat-processing industry. This acid is also one of the many molecules in the bod
that has cholesterol as its precursor.
https://en.wikipedia.org/wiki/Taurocholic_acid
Tautomerize
Tautomers are constitutional isomers of organic compounds that readily interconvert
with each other. The chemical reaction interconverting the two is called tautomerization. This reaction commonly results in the formal migration of a hydrogen atom or
proton, accompanied by a switch of a single bond and adjacent double bond. The concept of tautomerizations is called tautomerism. Because of the rapid interconversion,
tautomers are generally considered to be the same chemical compound. Tautomerism
should be distinguished from resonance, where two structures differing only in the position of electrons coexist in quantum superposition, rather than as a rapidlyinterconverting mixture. Tautomerism is a special case of structural isomerism and
can play an important role in non-canonical base pairing in DNA and especially RNA
molecules.
https://en.wikipedia.org/wiki/Tautomer
Taxadiene
ate in the synthesis of taxol. Six hydroxylation reactions, and a few others, are neede
to convert taxadiene to baccatin III.
https://en.wikipedia.org/wiki/Taxadiene
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TBP
The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30
base pairs upstream of the transcription start site in some eukaryotic gene promoters.
TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a
sequence-specific manner, it helps position RNA polymerase II over the transcription
start site of the gene. However, it is estimated that only 1020% of human promoters
have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II.
TBP is involved in DNA melting (double strand separation) by bending the DNA by
80 (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a sheet.
TBP is a subunit of the eukaryotic transcription factor TFIID. TFIID is the first protein
to bind to DNA during the formation of the pre-initiation transcription complex of
RNA polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the promoter
region of the gene initiates the recruitment of other factors required for RNA Pol II to
begin transcription. Some of the other recruited transcription factors include TFIIA,
TFIIB, and TFIIF. Each of these transcription factors is formed from the interaction of
many protein subunits, indicating that transcription is a heavily regulated process.
TBP is also a component of RNA polymerase I and RNA polymerase III and is therefore involved in transcription initiation by all three RNA polymerases. In specific cell
types or on specific promoters TBP can be replaced by one of several TBP-related factors.
When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting
amino acid side-chains between base pairs, partially unwinding the helix, and doubly
kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the
DNA backbone through positively charged lysine and arginine amino acid residues.
The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.
The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands.
https://en.wikipedia.org/wiki/TATA-binding_protein
Telomerase
Telomerase, also called terminal transferase, is a ribonucleoprotein that adds a
species-dependent telomere repeat sequence to the 3' end of telomeres. A telomere is a
region of repetitive sequences at each end of a eukaryotic chromatid, which protects
the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Telomerase, active in normal stem cells, is normally absent from, or at very
low levels in, most somatic cells.
Telomerase is a reverse transcriptase enzyme that carries its own RNA molecule (e.g.,
with the sequence "CCCAAUCCC" in vertebrates) which is used as a template when it
elongates telomeres.
The human telomerase enzyme complex consists of two molecules each of human telomerase reverse transcriptase (TERT), telomerase RNA (TR or TERC), and dyskerin
(DKC1).
By using TERC, TERT can add a six-nucleotide repeating sequence, 5'-TTAGGG (in vertebrates, the sequence differs in other organisms) to the 3' strand of chromosomes.
These TTAGGG repeats (with their various protein binding partners) are called telomeres. The template region of TERC is 3'-CAAUCCCAAUC-5'.
Telomerase can bind the first few nucleotides of the template to the last telomere sequence on the chromosome, add a new telomere repeat (5'-GGTTAG-3') sequence, let
go, realign the new 3'-end of telomere to the template, and repeat the process. Telomerase reverses telomere shortening.
https://en.wikipedia.org/wiki/Telomerase
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Telomeres
A telomere is a region of repetitive nucleotide sequences at each end of a chromosome,
which protects the end of the chromosome from deterioration or from fusion with
neighboring chromosomes. For vertebrates, the sequence of nucleotides in telomeres is
TTAGGG. This sequence of TTAGGG is repeated approximately 2,500 times in humans.
During chromosome replication, the enzymes that duplicate DNA cannot continue
their duplication all the way to the end of a chromosome, so in each duplication the
end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). The telomeres are
disposable buffers at the ends of chromosomes which are truncated during cell division; their presence protects the genes before them on the chromosome from being
truncated instead.
For vertebrates, the sequence of nucleotides in telomeres is TTAGGG. Most prokaryotes, lacking this linear arrangement, do not have telomeres. Telomeres compensate for
incomplete semi-conservative DNA replication at chromosomal ends. A protein complex known as shelterin serves as protection against double-strand break(DSB) repair
by homologous recombination(HR) and non-homologous end joining(NHEJ).
In most prokaryotes, chromosomes are circular and, thus, do not have ends to suffer
premature replication termination. A small fraction of bacterial chromosomes (such as
those in Streptomyces, Agrobacterium, and Borrelia) are linear and possess telomeres, which are very different from those of the eukaryotic chromosomes in structure
and functions. The known structures of bacterial telomeres take the form of proteins
bound to the ends of linear chromosomes, or hairpin loops of single-stranded DNA at
the ends of the linear chromosomes.
While replicating DNA, the eukaryotic DNA replication enzymes (the DNA polymerase
protein complex) cannot replicate the sequences present at the ends of the chromosomes (or more precisely the chromatid fibers). Hence, these sequences and the information they carry may get lost. This is the reason telomeres are so important in context of successful cell division: They "cap" the end-sequences and themselves get lost in
the process of DNA replication. But the cell has an enzyme called telomerase, which
carries out the task of adding repetitive nucleotide sequences to the ends of the DNA.
Telomerase, thus, "replenishes" the telomere "cap" of the DNA. In most multicellular
eukaryotic organisms, telomerase is active only in germ cells, some types of stem cells
such as embryonic stem cells, and certain white blood cells. Telomerase can be re activated and telomeres reset back to an embryonic state by somatic cell nuclear transfer.
There are theories that claim that the steady shortening of telomeres with each replication in somatic (body) cells may have a role in senescence and in the prevention of cancer. This is because the telomeres act as a sort of time-delay "fuse", eventually running
out after a certain number of cell divisions and resulting in the eventual loss of vital genetic information from the cell's chromosome with future divisions.
https://en.wikipedia.org/wiki/Telomere
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Template
In copying a DNA, the word template refers to the strand being copied by a polymerase
using the rules of base-pairing. The word template is appropriate for making DNA or
for making RNA and the strand being copied can be DNA or RNA, depending on the
system. For transcription, where only one strand of a DNA duplex, the strand being
copied is known as the template strand and the other strand is known as the coding
strand.
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Termination of Transcription
In genetics, a transcription terminator is a section of nucleic acid sequence that marks
the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized mRNA
that trigger processes which release the mRNA from the transcriptional complex.
These processes include the direct interaction of the mRNA secondary structure with
the complex and/or the indirect activities of recruited termination factors. Release of
the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
Termination is part of the process of transcribing RNA. In eukaryotes, a termination
factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat
followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop
structure which destabilizes binding by the RNA polymerase and causes independent transcription termination.
The most extensively studied transcriptional termination factor is the (rho) protein
of E. coli. The protein recognizes a cytosine-rich region of the elongating mRNA, but
the exact features of the recognized sequences remain unknown. forms a ring-shaped
hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5'
to 3' with respect to the mRNA). When the protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA.
The structure, as well as the activity, of the Rho protein is similar to that of the F1
subunit of ATP synthase, supporting the theory that the two share an evolutionary link.
The antibiotic bicyclomycin works by inhibiting .
The process of transcriptional termination is less well understood in eukaryotes, which
have extensive post-transcriptional RNA processing. Each of the three types of eukaryotic RNA polymerase has a different termination system. Eukaryotic termination factors bind to the termination signal region and disturb RNA polymerase II as it moves
by, causing it to fall off the DNA strand within the next 300 base pairs. This 300 bp region is removed during processing, before poly(A)tailing.
https://en.wikipedia.org/wiki/Termination_factor
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Terminator Site
In genetics, a transcription terminator is a section of nucleic acid sequence that marks
the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized mRNA
that trigger processes which release the mRNA from the transcriptional complex.
These processes include the direct interaction of the mRNA secondary structure with
the complex and/or the indirect activities of recruited termination factors. Release of
the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
Termination is part of the process of transcribing RNA. In eukaryotes, a termination
factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat
followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop
structure which destabilizes binding by the RNA polymerase and causes independent transcription termination.
The most extensively studied transcriptional termination factor is the (rho) protein
of E. coli. The protein recognizes a cytosine-rich region of the elongating mRNA, but
the exact features of the recognized sequences remain unknown. forms a ring-shaped
hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5'
to 3' with respect to the mRNA). When the protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA.
The structure, as well as the activity, of the Rho protein is similar to that of the F1
subunit of ATP synthase, supporting the theory that the two share an evolutionary link.
The antibiotic bicyclomycin works by inhibiting .
The process of transcriptional termination is less well understood in eukaryotes, which
have extensive post-transcriptional RNA processing. Each of the three types of eukaryotic RNA polymerase has a different termination system. Eukaryotic termination factors bind to the termination signal region and disturb RNA polymerase II as it moves
by, causing it to fall off the DNA strand within the next 300 base pairs. This 300 bp region is removed during processing, before poly(A)tailing.
https://en.wikipedia.org/wiki/Termination_factor
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Terpenes
Terpenes are a large and diverse class of organic compounds, produced by a variety of
plants, particularly conifers, though also by some insects such as termites or swallowtail butterflies, which emit terpenes from their osmeteria. They are often strongsmelling. They may protect the plants that produce them by deterring herbivores and
by attracting predators and parasites of herbivores. Many terpenes are aromatic hydrocarbons and thus may have had a protective function. The difference between terpenes
and terpenoids is that terpenes are hydrocarbons, whereas terpenoids contain additional functional groups.
They are the major components of resin, and of turpentine produced from resin. The
name "terpene" is derived from the word "turpentine". In addition to their roles as
end-products in many organisms, terpenes are major biosynthetic building blocks
within nearly every living creature. Steroids, for example, are derivatives of the triterpene squalene.
When terpenes are modified chemically, such as by oxidation or rearrangement of the
carbon skeleton, the resulting compounds are generally referred to as terpenoids.
Some authors will use the term terpene to include all terpenoids. Terpenoids are also
known as isoprenoids.
Terpenes and terpenoids are the primary constituents of the essential oils of many
types of plants and flowers. Essential oils are used widely as fragrances in perfumery,
and in medicine and alternative medicines such as aromatherapy. Synthetic variations
and derivatives of natural terpenes and terpenoids also greatly expand the variety of
aromas used in perfumery and flavors used in food additives. Vitamin A is a terpene.
https://en.wikipedia.org/wiki/Terpene
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Terpineol
Terpineol is a naturally occurring monoterpene alcohol that has been isolated fro
variety of sources such as cajuput oil, pine oil, and petitgrain oil. There are four i
mers, -, -, -terpineol, and terpinen-4-ol. - and -terpineol differ only by the
tion of the double bond. Terpineol is usually a mixture of these isomers with terpineol as the major constituent.
https://en.wikipedia.org/wiki/Terpineol
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Tertiary Structure
Biomolecular structure is the intricate folded, three-dimensional shape that is formed
by a protein, DNA, or RNA molecule, and that is important to its function. The structure of these molecules is frequently decomposed into primary structure, secondary
structure, tertiary structure, and quaternary structure. The scaffold for this structure is
provided by secondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of protein structure and nucleic acid
structure, including secondary structure like hairpin loops, bulges and internal loops
for nucleic acids, and alpha helices and beta sheets for proteins.
The tertiary structure of a protein or any other macromolecule is its three-dimensional
structure, as defined by the atomic coordinates. Proteins and nucleic acids are capable
of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse
and seemingly complex, they are composed of recurring, easily recognizable tertiary
structure motifs that serve as molecular building blocks. Tertiary structure is considered to be largely determined by the biomolecule's primary structure, or the sequence
of amino acids or nucleotides of which it is composed. Efforts to predict tertiary structure from the primary structure are in general known as structure prediction.
https://en.wikipedia.org/wiki/Biomolecular_structure#Tertiary_structure
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Testosterone
Testosterone is a steroid hormone from the androgen group and is found in humans
and other vertebrates. In humans and other mammals, testosterone is secreted primarily by the testicles of males and, to a lesser extent, the ovaries of females. Small
amounts are also secreted by the adrenal glands. It is the principal male sex hormone
and an anabolic steroid.
In men, testosterone plays a key role in the development of male reproductive tissues
such as the testis and prostate as well as promoting secondary sexual characteristics
such as increased muscle and bone mass, and the growth of body hair. In addition, testosterone is essential for health and well-being as well as the prevention of osteoporosis.
In general, androgens promote protein synthesis and growth of those tissues with androgen receptors. Testosterone effects can be classified as virilizing and anabolic,
though the distinction is somewhat artificial, as many of the effects can be considered
both.
Anabolic effects include growth of muscle mass and strength, increased bone density
and strength, and stimulation of linear growth and bone maturation.
Androgenic effects include maturation of the sex organs, particularly the penis and
the formation of the scrotum in the fetus, and after birth (usually at puberty) a deepening of the voice, growth of the beard and axillary hair. Many of these fall into the category of male secondary sex characteristics.
https://en.wikipedia.org/wiki/Testosterone
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Tetrahedral
In a tetrahedral molecular geometry, a central atom is located at the center
substituents that are located at the corners of a tetrahedron. The bond angle
109.5 when all four substituents are the same, as in methane (CH4). The pe
metrical tetrahedron belongs to point group Td, but most tetrahedral molec
have lower symmetry. Tetrahedral molecules can be chiral.
https://en.wikipedia.org/wiki/Tetrahedral_molecular_geometry
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Tetrahedral Structure
In a tetrahedral molecular geometry, a central atom is located at the center
substituents that are located at the corners of a tetrahedron. The bond angl
109.5 when all four substituents are the same, as in methane (CH4). The pe
metrical tetrahedron belongs to point group Td, but most tetrahedral molec
have lower symmetry. Tetrahedral molecules can be chiral.
https://en.wikipedia.org/wiki/Tetrahedral_molecular_geometry
Tetrahedron
posed of four triangular faces, six straight edges, and four vertex corners. The te
dron is the simplest of all the ordinary convex polyhedra and the only one that h
fewer than 5 faces.
The tetrahedron is the three-dimensional case of the more general concept of a
ean simplex.
https://en.wikipedia.org/wiki/Tetrahedron
Tetrahydrofolate
Tetrahydrofolic acid, or tetrahydrofolate, is a folic acid derivative that is produced
from dihydrofolic acid by dihydrofolate reductase. This reaction is inhibited by
methotrexate. It is converted into 5,10-methylenetetrahydrofolate by serine hydroxymethyltransferase.
Tetrahydrofolate is a cofactor in many reactions, especially in the metabolism of amino
acids and nucleic acids. It acts as a donor of a group with one carbon atom. It gets this
carbon atom by sequestering formaldehyde produced in other processes. A shortage in
tetrahydrofolic acid (FH4) can cause megaloblastic anemia.
https://en.wikipedia.org/wiki/Tetrahydrofolic_acid
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Tetraterpenes
Tetraterpenes are terpenes consisting of eight isoprene units and have the m
Index
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TFIIA
Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase IIdependent transcription of DNA. TFIIA is one of several general (basal) transcription
factors (GTFs) that are required for all transcription events that use RNA polymerase
II. Other GTFs include TFIID, a complex composed of the TATA binding protein TBP
and TBP-associated factors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and
TFIIH. Together, these factors are responsible for promoter recognition and the formation of a transcription pre-initiation complex (PIC) capable of initiating RNA synthesis
from a DNA template.
TFIIA interacts with the TBP subunit of TFIID and aids in the binding of TBP to
TATA-box containing promoter DNA. Interaction of TFIIA with TBP facilitates formation of and stabilizes the pre-initiation complex. Interaction of TFIIA with TBP also results in the exclusion of negative (repressive) factors that might otherwise bind to TBP
and interfere with PIC formation. TFIIA also acts as a co-activator for some transcriptional activators, assisting with their ability to increase, or activate, transcription. The
requirement for TFIIA in vitro transcription systems has been variable, and it can be
considered either as a GTF and/or a loosely associated TAF-like co-activator. Genetic
analysis in yeast has shown that TFIIA is essential for viability.
https://en.wikipedia.org/wiki/Transcription_factor_II_A
TFIIB
Transcription Factor II B (TFIIB) is a general transcription factor that is involved in
the formation of the RNA polymerase II preinitiation complex (PIC) and aids in stimulating transcription initiation. TFIIB is localized to the nucleus and provides a platform
for PIC formation by binding and stabilizing the DNA-TBP (TATA-binding protein)
complex and by recruiting RNA polymerase II and other transcription factors. It is encoded by the TFIIB gene.
There are six steps in the mechanism of TFIIB action in the formation of the PIC and
transcription initiation:
1 The DNA is recruited to RNA polymerase II through the B ribbon and it is then positioned by the B core.
2 DNA opening occurs aided by the B linker, the template strand is then placed into
the RNA polymerase II cleft and the bubble is stabilized by the B reader (open complex
formation).
3 RNA polymerase II and B reader scan the DNA for the Inr in order to position the
transcription start site.
4 The first phosphodiester bond is formed.
5 Production of short abortive transcripts due to clashes with the B reader loop.
6 The growth of nascent RNA chain to 12-13 bases leads to ejection of TFIIB due to further clashes with TFIIB.
https://en.wikipedia.org/wiki/Transcription_factor_II_B
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TFIID
Transcription factor II D (TFIID) is one of several general transcription factors
eral transcription factors, and regulatory proteins known as SRB proteins. Befo
Serves as the scaffold for assembly of the remainder of the transcription comp
Acts as a channel for regulatory signals
https://en.wikipedia.org/wiki/Transcription_factor_II_D
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TFIIE
TFIIF
TFIIF binds to RNA PolII when the enzyme is already unbound to any othe
tion factor, thus avoiding it from contacting DNA outside the promoter. Fur
TFIIF stabilizes the RNA polymerase II while it's contacting TBP and TFIIB
https://en.wikipedia.org/wiki/Transcription_factor_II_F
TFIIH
Transcription factor II Human (TFIIH) is one of several general transcription factors
that make up the RNA polymerase II preinitiation complex. TFIIH consists of ten
subunits, 7 of which (XPD, XPB, p62, p52, p44, p34 and TTDA) form the core complex.
The cyclin activating kinase-subcomplex (CDK7, MAT1, and cyclin H) is linked to the
core via the XPD protein. Two of the subunits, ERCC2/XPD and ERCC3/XPB, have
helicase and ATPase activities and help create the transcription bubble. In a test tube
these subunits are only required for transcription if the DNA template is not already denatured or if it is supercoiled.
Two other TFIIH subunits, CDK7 and cyclin H, phosphorylate serine amino acids on
the RNA polymerase II C-terminal domain and possibly other proteins involved in the
cell cycle. Next to a vital function in transcription initiation, TFIIH is also involved in
nucleotide excision repair.
It is responsible for giving the 'go' signal which is why it is assembled last.
https://en.wikipedia.org/wiki/Transcription_factor_II_H
THC
Tetrahydrocannabinol (THC, dronabinol by INN), or more precisely its main isomer
nabinoid) of cannabis. It can be an amber or gold colored glassy solid when cold, whi
becomes viscous and sticky if warmed.
sesses high UV-B (280315nm) absorption properties, which, it has been speculated
could protect the plant from harmful UV radiation exposure.
https://en.wikipedia.org/wiki/Tetrahydrocannabinol
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Thermogenin
Thermogenin (called uncoupling protein by its discoverers and now known as uncoupling protein 1, or UCP1) is an uncoupling protein found in the mitochondria of brown
adipose tissue (BAT). It is used to generate heat by non-shivering thermogenesis, and
makes a quantitatively important contribution to countering heat loss in neonates
which would otherwise occur due to the high surface area-volume ratio.
UCPs are transmembrane proteins that decrease the proton gradient generated in oxidative phosphorylation. They do this by increasing the permeability of the inner mitochondrial membrane, allowing protons that have been pumped into the intermembrane space to return to the mitochondrial matrix. UCP1-mediated heat generation in
brown fat uncouples the respiratory chain, allowing for fast substrate oxidation with a
low rate of ATP production.
UCPs are transmembrane proteins that decrease the proton gradient generated in oxidative phosphorylation. They do this by increasing the permeability of the inner mitochondrial membrane, allowing protons that have been pumped into the intermembrane space to return to the mitochondrial matrix. UCP1-mediated heat generation in
brown fat uncouples the respiratory chain, allowing for fast substrate oxidation with a
low rate of ATP production. UCP1 is related to other mitochondrial metabolite transporters such as the adenine nucleotide translocator, a proton channel in the mitochondrial inner membrane that permits the translocation of protons from the mitochondrial intermembrane space to the mitochondrial matrix. UCP1 is restricted to brown
adipose tissue, where it provides a mechanism for the enormous heat-generating capacity of the tissue.
https://en.wikipedia.org/wiki/Thermogenin
Thermolysin
Thermolysin is a thermostable neutral metalloproteinase enzyme produced by the
Gram-positive bacteria Bacillus thermoproteolyticus. It requires one zinc ion for enzyme activity and four calcium ions for structural stability. Thermolysin specifically
catalyzes the hydrolysis of peptide bonds containing hydrophobic amino acids. However thermolysin is also widely used for peptide bond formation through the reverse
teinases produced by various Bacillus species. These enzymes are also termed 'neutra
proteinases or thermolysin -like proteinases (TLPs).
In contrast to many proteins that undergo conformational changes upon heating and
denaturation, thermolysin does not undergo any major conformational changes unti
at least 70C. The thermal stability of members of the TLP family is measured in term
of a T50 temperature. At this temperature incubation for 30 minutes reduces the enzymes activity by half. Thermolysin has a T50 value of 86.9C, making it the most
thermo stable member of the TLP family.
https://en.wikipedia.org/wiki/Thermolysin
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Thiamine
Thiamine was named as the "thio-vitamine" ("sulfur-containing vitamin") is a vitamin
of the B complex. First named aneurin for the detrimental neurological effects if not
present in the diet, it was eventually assigned the generic descriptor name vitamin B1.
Its phosphate derivatives are involved in many cellular processes. The bestcharacterized form is thiamine pyrophosphate (TPP), a coenzyme in the catabolism of
sugars and amino acids. In yeast, TPP is also required in the first step of alcoholic fermentation.
All living organisms use thiamine, but it is synthesized only in bacteria, fungi, and
plants. Animals must obtain it from their diet, and thus, for humans, it is an essential
nutrient. Insufficient intake in birds produces a characteristic polyneuritis. In mammals, deficiency results in Korsakoff's syndrome, optic neuropathy, and a disease
called beriberi that affects the peripheral nervous system (polyneuritis) and/or the cardiovascular system. Thiamine deficiency has a potentially fatal outcome if it remains
untreated. In less severe cases, nonspecific signs include malaise, weight loss, irritability and confusion.
ThDP is a coenzyme for several enzymes that catalyze the transfer of two-carbon units
and in particular the dehydrogenation (decarboxylation and subsequent conjugation
with coenzyme A) of 2-oxoacids (-keto acids).
https://en.wikipedia.org/wiki/Thiamine
Thiamine Diphosphokinase
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Thiamine Pyrophosphate
Thiamine pyrophosphate (TPP or ThPP), or thiamine diphosphate (ThDP), or cocarboxylase is a thiamine (vitamin B1) derivative which is produced by the enzyme thiamine diphosphokinase. Thiamine pyrophosphate is a cofactor that is present in all living systems, in which it catalyzes several biochemical reactions. It was first discovered
as an essential nutrient (vitamin) in humans through its link with the peripheral nervous system disease Beriberi, which results from a deficiency of thiamine in the diet.
TPP works as a coenzyme in many enzymatic reactions, such as:
2-hydroxyphytanoyl-CoA lyase
Transketolase
https://en.wikipedia.org/wiki/Thiamine_pyrophosphate
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Thiazole Ring
Thiazole, or 1,3-thiazole, is a heterocyclic compound that contains both sulfur and nitrogen. The term 'thiazole' also refers to a large family of derivatives. Thiazole itself is
a pale yellow liquid with a pyridine-like odor and the molecular formula C3H3NS. The
thiazole ring is notable as a component of the vitamin thiamine (B1).
Thiazole rings are planar and aromatic. Thiazoles are characterized by larger pielectron delocalization than the corresponding oxazoles and have therefore greater aromaticity.
Thiazoles are members of the azoles, heterocycles that include imidazoles and oxazoles. Thiazole can also be considered a functional group. Oxazoles are related compounds, with sulfur replaced by oxygen. Thiazoles are structurally similar to imidazoles, with the thiazole sulfur replaced by nitrogen.
Thiazole rings are planar and aromatic. Thiazoles are characterized by larger pielectron delocalization than the corresponding oxazoles and have therefore greater aromaticity. This aromaticity is evidenced by the chemical shift of the ring protons in proton NMR spectroscopy (between 7.27 and 8.77 ppm), clearly indicating a strong diamagnetic ring current. The calculated pi-electron density marks C5 as the primary site
for electrophilic substitution, and C2 as the site for nucleophilic substitution.
https://en.wikipedia.org/wiki/Thiazole
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Thioester
Thioesters are compounds with the functional group CSCOC. They are the pr
mation and degradation of fatty acids and mevalonate, precursor to steroids. Exam
https://en.wikipedia.org/wiki/Thioester
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Thioesterase
Thioesterases exhibit esterase activity (splitting of an ester into acid and alc
Thiol
phydryl (CSH or RSH) group (where R represents an alkyl or other organic sub-
stituent). Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of
oxygen in the hydroxyl group of an alcohol), and the word is a portmanteau of "thion
+ "alcohol," with the first word deriving from Greek (theion) = "sulfur". The
functional group itself is referred to as either a thiol group or a sulfhydryl group.
Many thiols have strong odors resembling that of garlic or rotten eggs. Thiols are us
as odorants to assist in the detection of natural gas (which in pure form is odorless),
and the "smell of natural gas" is due to the smell of the thiol used as the odorant.
https://en.wikipedia.org/wiki/Thiol
Thiolase
which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate path
Thiolases are ubiquitous enzymes that have key roles in many vital biochemical p
ways, including the oxidation pathway of fatty acid degradation (where they cat
family can be divided into two broad categories: degradative thiolases and biosyn
thiolases.
https://en.wikipedia.org/wiki/Thiolase
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Thiolytic Cleavage
Thioredoxin
Thioredoxin is a class of small redox proteins known to be present in all organisms. It
plays a role in many important biological processes, including redox signaling. In humans, it is encoded by the TXN gene. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo. Although not entirely understood, thioredoxin plays a central role in humans and is increasingly linked to medicine through their response to reactive oxygen species (ROS).
In plants, thioredoxins regulate a spectrum of critical functions, ranging from photosynthesis to growth, flowering and the development and germination of seeds. It has
also recently been found to play a role in cell-to-cell communication.
Thioredoxins act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms
and are essential for life in mammals.
The thioredoxins are kept in the reduced state by the flavoenzyme thioredoxin reductase, in a NADPH-dependent reaction. Thioredoxins act as electron donors to peroxidases and ribonucleotide reductase. The related glutaredoxins share many of the functions of thioredoxins, but are reduced by glutathione rather than a specific reductase.
The benefit of thioredoxins to reduce oxidative stress is shown by transgenic mice that
overexpress thioredoxin, are more resistant to inflammation, and live 35% longer
supporting the free radical theory of aging. However, the controls of this study were
short lived, which may have contributed to the apparent increase in longevity.
https://en.wikipedia.org/wiki/Thioredoxin
Thioredoxin Reductase
Thioredoxin reductases (TR, TrxR) are the only known enzymes to reduce t
(Trx). Two classes of thioredoxin reductase have been identified: one class i
and some eukaryotes and one in animals. Both classes are flavoproteins wh
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Threonine
Threonine (abbreviated as Thr or T) encoded by the codons ACU, ACC, ACA, and ACG
is an -amino acid that is used in the biosynthesis of proteins. It contains an -amino
group (which is in the protonated NH3+ form under biological conditions), an carboxylic acid group (which is in the deprotonated COO form under biological conditions), and an alcohol containing side chain, classifying it as a polar, uncharged(at
physiological pH) amino acid. It is essential in humans, meaning the body cannot synthesize it, and must be ingested in our diet. Threonine is synthesized from aspartate in
bacteria such as E. coli.
As an essential amino acid, threonine is not synthesized in humans, hence we must ingest threonine in the form of threonine-containing proteins. In plants and microorganisms, threonine is synthesized from aspartic acid via -aspartyl-semialdehyde and homoserine. Homoserine undergoes O-phosphorylation; this phosphate ester undergoes
hydrolysis concomitant with relocation of the OH group.
Threonine is metabolized in two ways:
It is converted to pyruvate via threonine dehydrogenase. An intermediate in this pathway can undergo thiolysis with CoA to produce acetyl-CoA and glycine.
In humans, it is converted to -ketobutyrate in a less common pathway via the enzyme serine dehydratase, and thereby enters the pathway leading to succinyl-CoA.
https://en.wikipedia.org/wiki/Threonine
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Threonine Deaminase
Threonine ammonia-lyase, also commonly referred to as threonine deaminase or threonine dehydratase, is an enzyme responsible for catalyzing the conversion of Lthreonine into alpha-ketobutyrate and ammonia. -ketobutyrate can be converted into
L-isoleucine, so threonine ammonia-lyase functions as a key enzyme in BCAA synthesis. It employs a pyridoxal-5-phosphate cofactor, similar to many enzymes involved in
amino acid metabolism. It is found in bacteria, yeast, and plants, though most research
to date has focused on forms of the enzyme in bacteria. This enzyme was one of the
first in which negative feedback inhibition by the end product of a metabolic pathway
was directly observed and studied. The enzyme serves as an excellent example of the
regulatory strategies used in amino acid homeostasis.
Threonine ammonia-lyase has been shown to not follow Michaelis-Menten kinetics,
rather, it is subject to complex allosteric control. The enzyme is inhibited by isoleucine,
the product of the pathway it participates in, and is activated by valine, the product of a
parallel pathway. Thus, an increase in isoleucine concentration shuts off its production, and an increase in valine concentration diverts starting material (HydroxyethylTPP) away from valine production. The enzyme has two binding sites for isoleucine.
One has a high affinity for isoleucine and the other has a low affinity. The binding of
isoleucine to the high affinity site increases the binding affinity of the low affinity site,
and enzyme deactivation occurs when isoleucine binds to the low affinity site. Valine
promotes enzyme activity by competitively binding to the high affinity site, preventing
isoleucine from having an inhibitory effect. The combination of these two feedback
methods balances the concentration of BCAAs.
https://en.wikipedia.org/wiki/Threonine_ammonia-lyase
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Threonine Protease
Threnonine proteases are a family of proteolytic enzymes harboring a threonine (Thr)
residue within the active site. The prototype members of this class of enzymes are the
catalytic subunits of the proteasome, however the acyltransferases convergently
evolved the same active site geometry and mechanism.
Threonine proteases use the secondary alcohol of their N-terminal threonine as a nucleophile to perform catalysis. The threonine must be N-terminal since the terminal
amide of the same residue acts as a general base by polarizing an ordered water which
deprotonates the alcohol to increase its reactivity as a nucleophile.
Catalysis takes place in two steps:
Firstly the nucleophile attacks the substrate to form a covalent acyl-enzyme intermediate, releasing the first product.
Secondly the immediate is hydrolized by water to regenerate the free enzyme and release the second product.
In ornithine acyltransferase, instead of water, the substrate ornithine (the acceptor)
performs the second nucleophilic attack and so leaves with the acyl group.
https://en.wikipedia.org/wiki/Threonine_protease
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Threonine Synthase
Threonine synthase is an enzyme that catalyzes the chemical reaction:
O-phospho-L-homoserine + H2O L-threonine + Pi
Index
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Thrombin
Thrombin is a serine protease that, in humans, is encoded by the F2 gene. Prothrombin (coagulation factor II) is proteolytically cleaved to form thrombin in the coagulation cascade, the clotting process. Thrombin in turn acts as a serine protease that converts soluble fibrinogen into insoluble strands of fibrin, as well as catalyzing many
other coagulation-related reactions.
In the blood coagulation pathway, thrombin acts to convert factor XI to XIa, VIII to
VIIIa, V to Va, fibrinogen to fibrin, and XIII to XIIIa. Factor XIIIa is a transglutaminase that catalyzes the formation of covalent bonds between lysine and glutamine residues in fibrin. The covalent bonds increase the stability of the fibrin clot. Thrombin interacts with thrombomodulin. As part of its activity in the coagulation cascade, thrombin also promotes platelet activation and aggregation via activation of proteaseactivated receptors on the cell membrane of the platelet.
https://en.wikipedia.org/wiki/Thrombin
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Thromboxane A2
Thromboxane A2 (TXA2) is a type of thromboxane that is produced by activated platelets and has prothrombotic properties: it stimulates activation of new platelets as well
as increases platelet aggregation. This is achieved by increasing expression of the glycoprotein complex GPIIb/IIIa on the cell membrane of platelets. The same effect is also
achieved by ADP in platelet stimulation, which is blocked by clopidogrel. Circulating
fibrinogen binds these receptors on adjacent platelets, further strengthening the clot.
Thromboxane A2 is also a known vasoconstrictor and is especially important during tissue injury and inflammation. It is also regarded as responsible for Prinzmetal's angina.
TXA2 is generated from prostaglandin H2 by thromboxane-A synthase in a metabolic
reaction which generates approximately equal amounts of 12hydroxyheptadecatrienoic acid (12-HHT). Aspirin irreversibly inhibits platelet cyclooxygenase 1 preventing the formation of prostaglandin H2, and therefore thromboxane
A2.
https://en.wikipedia.org/wiki/Thromboxane_A2
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Thromboxanes
Thromboxane is a member of the family of lipids known as eicosanoids. The two major
thromboxanes are thromboxane A2 and thromboxane B2. The distinguishing feature of
thromboxanes is a 6-membered ether-containing ring. Thromboxane is named for its
role in clot formation (thrombosis).
Thromboxane is a vasoconstrictor and a potent hypertensive agent, and it facilitates
platelet aggregation. It is in homeostatic balance in the circulatory system with prostacyclin, a related compound. The mechanism of secretion of thromboxanes from platelets is still unclear. They act in the formation of blood clots and reduce blood flow to
the site of a clot.
It is believed that the vasoconstriction caused by thromboxanes plays a role in Prinzmetal's angina. -3 fatty acids are metabolized to produce higher levels of TxA,3 which is
relatively less potent than TxA2 and PGI3. Therefore, there is a balance shift toward inhibition of vasoconstriction and platelet aggregation. It is believed that this shift in balance lowers the incidence of myocardial infarction (heart attack) and stroke. Vasoconstriction and, perhaps, various proinflammatory effects exerted by TxA on tissue microvasculature, is probable reason why the TxA is pathogenic in various diseases, such as
ischemia-reperfusion injury, hepatic inflammatory processes, acute hepatotoxicity etc.
TxB2, a stable degradation product of TxA2, plays a role in acute hepatoxicity induced
by acetaminophen.
Thromboxane A2
Thromboxane B2
https://en.wikipedia.org/wiki/Thromboxane
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Thylakoid Membrane
The thylakoid membrane is the site of the light-dependent reactions of photosynthesis
with the photosynthetic pigments embedded directly in the membrane. It is an alternating pattern of dark and light bands measuring each 1 nanometre. The thylakoid lipid
bilayer shares characteristic features with prokaryotic membranes and the inner chloroplast membrane. For example, acidic lipids can be found in thylakoid membranes, cyanobacteria and other photosynthetic bacteria and are involved in the functional integrity of the photosystems.
The thylakoid membranes of higher plants are composed primarily of phospholipids
and galactolipids that are asymmetrically arranged along and across the membranes.
Thylakoid membranes are richer in galactolipids rather than phospholipids. Also they
predominantly consist of hexagonal phase II forming monogalacotosyl diglyceride
lipid. Despite this unique composition, plant thylakoid membranes have been shown
to assume largely lipid-bilayer dynamic organization. Lipids forming the thylakoid
membranes, richest in high-fluidity linolenic acid are synthesized in a complex pathway involving exchange of lipid precursors between the endoplasmic reticulum and inner membrane of the plastid envelope and transported from the inner membrane to
the thylakoids via vesicles.
In higher plants thylakoids are organized into a granum-stroma membrane assembly.
A granum (plural grana) is a stack of thylakoid discs. Chloroplasts can have from 10 to
100 grana. Grana are connected by stroma thylakoids, also called intergranal thylakoids or lamellae. Grana thylakoids and stroma thylakoids can be distinguished by
their different protein composition. Grana contribute to chloroplasts' large surface
area to volume ratio. Different interpretations of electron tomography imaging of thylakoid membranes has resulted in two models for grana structure. Both posit that lamellae intersect grana stacks in parallel sheets, though whether these sheets intersect in
planes perpendicular to the grana stack axis, or are arranged in a right-handed helix is
debated.
https://en.wikipedia.org/wiki/Thylakoid
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Thylakoid Space
The thylakoid lumen (space) is a continuous aqueous phase enclosed by the thylakoid
membrane. It plays an important role for photophosphorylation during photosynthesis. During the light-dependent reaction, protons are pumped across the thylakoid
membrane into the lumen making it acidic down to pH 4.
https://en.wikipedia.org/wiki/Thylakoid
Index
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Thylakoids
Index
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Thymidine
Thymidine is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T,
which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used
to synchronize the cells in G1/early S phase. Thymidine occurs almost exclusively in
DNA but also occurs in the T-loop of tRNA.
In its composition, deoxythymidine is a nucleoside composed of deoxyribose (a pentose sugar) joined to the pyrimidine base thymine. Deoxythymidine can be phosphorylated with one, two or three phosphoric acid groups, creating respectively dTMP, dTDP
or dTTP (deoxythymidine mono- di- or triphosphate).
Deoxythymidine is non-toxic and as part of one of the four nucleotides in DNA it is a
naturally occurring compound that exists in all living organisms and DNA viruses.
RNA has uridine (uracil joined to ribose) instead. Uracil is chemically very similar to
thymine, the latter being 5-methyluracil. Since thymine nucleotides are precursors of
DNA, not RNA, the prefix "deoxy" is often left out, i.e., deoxythymidine is often just
called thymidine.
https://en.wikipedia.org/wiki/Thymidine
Thymidylate Synthetase
Thymidylate synthetase (TS) is an enzyme that catalyzes the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP).
Thymidine is one of the nucleotides in DNA. With inhibition of TS, an imbalance of deoxynucleotides and increased levels of dUTP arise. Both cause DNA damage.
The following reaction is catalyzed by thymidylate synthetase:
5,10-methylenetetrahydrofolate + dUMP Dihydrofolate + dTMP
This provides the sole de novo pathway for production of dTMP and is the only enzyme
in folate metabolism in which the 5,10-methylenetetrahydrofolate is oxidized during
one-carbon transfer. The enzyme is essential for regulating the balanced supply of the
four DNA precursors in normal DNA replication: defects in the enzyme activity affecting the regulation process cause various biological and genetic abnormalities, such as
thymineless death. The enzyme is an important target for certain chemotherapeutic
drugs. Thymidylate synthase is an enzyme of about 30 to 35 Kd in most species except
in protozoan and plants where it exists as a bifunctional enzyme that includes a dihydrofolate reductase domain. A cysteine residue is involved in the catalytic mechanism
(it covalently binds the 5,6-dihydro-dUMP intermediate). The sequence around the active site of this enzyme is conserved from phages to vertebrates.
The use of TS inhibitors has become a main focus of using TS as a drug target. The
most widely used inhibitor is 5-Fluorouracil (5-FU), which acts as an antimetabolite
that irreversibly inhibits TS by competitive binding. However, due to a low level of 5FU found in many patients, it has been discovered that in combination with leucovorin
(LV), 5-FU has greater success in down regulating tumor progression mechanisms and
increasing immune system activity.
https://en.wikipedia.org/wiki/Thymidylate_synthase
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Thymine
Thymine is one of the four nucleobases in the nucleic acid of DNA that are represented
by the letters GCAT. The others are adenine, guanine, and cytosine. Thymine is
also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced
by the nucleobase uracil.
As its alternate name (5-methyluracil) suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases.
In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thereby stabilizing
the nucleic acid structures.
Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is
synonymous with the term thymidine. Thymidine can be phosphorylated with one,
two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP
(thymidine mono-, di-, or triphosphate).
One of the common mutations of DNA involves two adjacent thymines or cytosine,
which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in
the DNA molecule that inhibit normal function.
Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment.
5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively dividing cells.
Thymine bases are frequently oxidized to hydantoins over time after the death of an organism.
https://en.wikipedia.org/wiki/Thymine
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Thymosin
Thymosins are small proteins present in many animal tissues. They are nam
ins because they were originally isolated from the thymus, but most are now
of which have already progressed from the laboratory to the clinic. In relati
eases, thymosins have been categorized as biological response modifiers.
https://en.wikipedia.org/wiki/Thymosins
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Thyroglobulin
Thyroglobulin (Tg) is a 660 kDa, dimeric protein produced by the follicular cells of the
thyroid and used entirely within the thyroid gland. Thyroglobulin protein accounts for
approximately half of the protein content of the thyroid gland.
The protein is a precursor of the thyroid hormones. These are produced when thyroglobulin's tyrosine residues are combined with iodine and the protein is subsequently
cleaved. Each thyroglobulin molecule contains approximately 100-120 tyrosine residues, but only a small number (20) of these are subject to iodination by thyroperoxidase in the follicular colloid. Therefore, each Tg molecule forms only approximately 10
thyroid hormone molecules.
Tg is used by the thyroid gland to produce the thyroid hormones thyroxine (T4) and
triiodothyronine (T3). The active form of triiodothyronine, 3, 5, 3' triiodothyronine, is
produced both within the thyroid gland and in the periphery by 5'-deiodinase (which
has been referred to as tetraiodothyronine 5' deiodinase). It is presumed that Tg and
thyroid are also an important storage of iodine for all body needs, in particular, for
many iodine-concentrating organs such as breast, stomach, salivary glands, thymus,
choroid plexus and cerebrospinal fluid, etc.
Tg is produced by the thyroid epithelial cells, called thyrocytes, which form spherical
follicles. Tg is secreted and stored in the follicular lumen.
https://en.wikipedia.org/wiki/Thyroglobulin
Thyroid Hormones
The thyroid hormones, triiodothyronine (T3) and its prohormone, thyroxine (T4), are
tyrosine-based hormones produced by the thyroid gland that are primarily responsible
for regulation of metabolism. T3 and T4 are partially composed of iodine. A deficiency
of iodine leads to decreased production of T3 and T4, enlarges the thyroid tissue and
will cause the disease known as simple goiter. The major form of thyroid hormone in
the blood is thyroxine (T4), which has a longer half-life than T3. In humans, the ratio of
T4 to T3 released into the blood is between 14 to 1 and 20 to 1. T4 is converted to the active T3 (three to four times more potent than T4) within cells by deiodinases (5'iodinase).
These are further processed by decarboxylation and deiodination to produce iodothyronamine (T1a) and thyronamine (T0a). All three isoforms of the deiodinases are
selenium-containing enzymes, thus dietary selenium is essential for T3 production.
The thyroid hormones act on nearly every cell in the body. They act to increase the basal metabolic rate, affect protein synthesis, help regulate long bone growth (synergy
with growth hormone) and neural maturation, and increase the body's sensitivity to
catecholamines (such as adrenaline) by permissiveness. The thyroid hormones are essential to proper development and differentiation of all cells of the human body. These
hormones also regulate protein, fat, and carbohydrate metabolism, affecting how human cells use energetic compounds. They also stimulate vitamin metabolism. Numerous physiological and pathological stimuli influence thyroid hormone synthesis.
https://en.wikipedia.org/wiki/Thyroid_hormone
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Thyroxine
The thyroid hormones, triiodothyronine (T3) and its prohormone, thyroxine (T4), are
tyrosine-based hormones produced by the thyroid gland that are primarily responsible
for regulation of metabolism. T3 and T4 are partially composed of iodine (see molecular
model). A deficiency of iodine leads to decreased production of T3 and T4, enlarges the
thyroid tissue and will cause the disease known as simple goiter. The major form of thyroid hormone in the blood is thyroxine (T4), which has a longer half-life than T3. In humans, the ratio of T4 to T3 released into the blood is between 14 to 1 and 20 to 1. T4 is
converted to the active T3 (three to four times more potent than T4) within cells by deiodinases (5'-iodinase).
These are further processed by decarboxylation and deiodination to produce iodothyronamine (T1a) and thyronamine (T0a). All three isoforms of the deiodinases are
selenium-containing enzymes, thus dietary selenium is essential for T3 production.
https://en.wikipedia.org/wiki/Thyroid_hormone
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Tight Coupling
means one cannot occur without the other. The flow of electrons through th
transport chain, from electron donors such as NADH to electron acceptors
dergonic process, which requires an input of energy. Both the electron trans
and the ATP synthase are embedded in a membrane, and energy is transfer
https://en.wikipedia.org/wiki/Oxidative_phosphorylation#Overview_of_e
sfer_by_chemiosmosis
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Tight Junctions
Tight junctions are the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates. The corresponding junctions that occur in invertebrates are septate junctions.
Tight junctions are composed of a branching network of sealing strands, each strand
acting independently from the others. Therefore, the efficiency of the junction in preventing ion passage increases exponentially with the number of strands. Each strand is
formed from a row of transmembrane proteins embedded in both plasma membranes,
with extracellular domains joining one another directly.
Tight junctions perform vital functions:
They hold cells together.
Barrier function, which can be further subdivided into protective barriers and
functional barriers serving purposes such as material transport and maintenance of osmotic balance:
Tight Junctions help to maintain the polarity of cells by preventing the lateral
diffusion of integral membrane proteins between the apical and lateral/basal surfaces,
allowing the specialized functions of each surface (for example receptor-mediated endocytosis at the apical surface and exocytosis at the basolateral surface) to be preserved.
This aims to preserve the transcellular transport.
Tight Junctions prevent the passage of molecules and ions through the space between plasma membranes of adjacent cells, so materials must actually enter the cells
(by diffusion or active transport) in order to pass through the tissue. Investigation using freeze-fracture methods in electron microscopy is ideal for revealing the lateral extent of tight junctions in cell membranes and has been useful in showing how tight
junctions are formed. The constrained intracellular pathway exacted by the tight junction barrier system allows precise control over which substances can pass through a
particular tissue. (Tight junctions play this role in maintaining the bloodbrain barrier.) At the present time, it is still unclear whether the control is active or passive and
how these pathways are formed. In one study for paracellular transport across the tight
junction in kidney proximal tubule, a dual pathway model is proposed: large slit breaks
formed by infrequent discontinuities in the TJ complex and numerous small circular
pores.
https://en.wikipedia.org/wiki/Tight_junction
Tightly Coupled
means one cannot occur without the other. The flow of electrons through th
transport chain, from electron donors such as NADH to electron acceptors
dergonic process, which requires an input of energy. Both the electron trans
and the ATP synthase are embedded in a membrane, and energy is transfer
https://en.wikipedia.org/wiki/Oxidative_phosphorylation#Overview_of_e
sfer_by_chemiosmosis
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Titin
Titin also known as connectin, is a protein that, in humans, is encoded by the TTN
gene. Titin is a giant protein, greater than 1 m in length, that functions as a molecular
spring which is responsible for the passive elasticity of muscle. It is composed of 244
individually folded protein domains connected by unstructured peptide sequences.
These domains unfold when the protein is stretched and refold when the tension is removed.
Titin is important in the contraction of striated muscle tissues. It connects the Z line to
the M line in the sarcomere. The protein contributes to force transmission at the Z line
and resting tension in the I band region. It limits the range of motion of the sarcomere
in tension, thus contributing to the passive stiffness of muscle. Variations in the sequence of titin between different types of muscle (e.g., cardiac or skeletal) have been
correlated with differences in the mechanical properties of these muscles.
After myosin and actin, titin is the third most abundant protein in muscle and an adult
human contains approximately 0.5kg of titin. With its length of ~27,000 to ~33,000
amino acids (depending on the splice isoform), titin is the largest known protein. Furthermore, the gene for titin contains the largest number of exons (363) discovered in
any single gene, as well as the longest single exon (17,106 bp).
https://en.wikipedia.org/wiki/Titin
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Titration
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Titration Curve
A titration curve is a curve in the plane whose x-coordinate is the volume of titrant
added since the beginning of the titration, and whose y-coordinate is the concentration
of the analyte at the corresponding stage of the titration (in an acid-base titration, the
y-coordinate is usually the pH of the solution).
In an acid-base titration, the titration curve reflects the strength of the corresponding
acid and base. For a strong acid and a strong base, the curve will be relatively smooth
and very steep near the equivalence point. Because of this, a small change in titrant volume near the equivalence point results in a large pH change and many indicators
would be appropriate (for instance litmus, phenolphthalein or bromothymol blue).
Titrations are often recorded on graphs called titration curves, which generally contain
the volume of the titrant as the independent variable and the pH of the solution as the
dependent variable (because it changes depending on the composition of the two solutions).
The equivalence point on the graph is where all of the starting solution (usually an
acid) has been neutralized by the titrant (usually a base). It can be calculated precisely
by finding the second derivative of the titration curve and computing the points of inflection (where the graph changes concavity). However, in most cases, simple visual
inspection of the curve will suffice.
https://en.wikipedia.org/wiki/Titration_curve
Tm
The melting point (or, rarely, liquefaction point) of a solid is the temperature a
solid and liquid phase exist in equilibrium. The melting point of a substance d
on pressure and is usually specified at standard pressure.
https://en.wikipedia.org/wiki/Melting_point
Nucleic acid thermodynamics is the study of how temperature affects the nucl
structure of double-stranded DNA (dsDNA). The melting temperature (Tm) is
as the temperature at which half of the DNA strands are in the random coil or
stranded (ssDNA) state. Tm depends on the length of the DNA molecule and it
nucleotide sequence.
https://en.wikipedia.org/wiki/Nucleic_acid_thermodynamics
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Tocopherols
Tocopherols (TCP) are a class of organic chemical compounds (more precisely, various
methylated phenols), many of which have vitamin E activity. Because the vitamin activity was first identified in 1936 from a dietary fertility factor in rats, it was given the
name "tocopherol" from the Greek words "" [tkos, birth], and "", [phrein, to bear or carry] meaning in sum "to carry a pregnancy," with the ending "-ol" signifying its status as a chemical alcohol.
An essential nutrient for the body, vitamin E is made up of four tocopherols (, , , )
and four tocotrienols (, , , ). The slight difference between tocotrienols and tocopherols lies in the unsaturated side chain of tocotrienols, having three double bonds in
its farnesyl isoprenoid tail.
-Tocopherol is the main source found in supplements and in the European diet,
where the main dietary sources are olive and sunflower oils, while -tocopherol is the
most common form in the American diet due to a higher intake of soybean and corn
oil.
Tocotrienols, which are related compounds, also have vitamin E activity. All of these
various derivatives with vitamin activity may correctly be referred to as "vitamin E". Tocopherols and tocotrienols are fat-soluble antioxidants but also seem to have many
other functions in the body.
Shown below is a-tocopherol
https://en.wikipedia.org/wiki/Tocotrienol
Tocotrienols
Tocotrienols are members of the vitamin E family. An essential nutrient for the body,
vitamin E is made up of four tocopherols (, , , ) and four tocotrienols (, , , ).
The slight difference between tocotrienols and tocopherols lies in the unsaturated side
chain of tocotrienols, having three double bonds in its farnesyl isoprenoid tail.
Tocotrienols are natural compounds found in select vegetable oils, including rice bran
oil and palm oil, wheat germ, barley, saw palmetto, anatto, and certain other types of
seeds, nuts, grains, and the oils derived from them. This variant of vitamin E typically
only occurs at very low levels in nature.
Chemically, vitamin E in all of its forms functions as an antioxidant. All of the tocotrienol and tocopherol isomers have this antioxidant activity due to the ability to donate a
hydrogen atom (a proton plus electron) from the hydroxyl group on the chromanol
ring, to a free radical in the body. This process inactivates ("quenches") the free radical
by effectively donating a single unpaired electron (which comes with the hydrogen
atom) to the radical. Thus, one model for the function of vitamin E in the body is that it
protects cell membranes, active enzyme sites, and DNA from free radical damage. Although the many vitamers of vitamin E have different distributions and metabolic
fates, there is as yet no accepted evidence that any of the active forms of vitamin E are
able to do any essential function in the body that each of the others is not also able to
do. Specifically, symptoms caused by -tocopherol deficiency can be alleviated by tocotrienols. Thus, tocotrienols may be viewed as being members of the natural vitamin E
family not only structurally but also functionally.
While the majority of research on vitamin E has focused on -tocopherol, studies into
tocotrienols account for less than 1% of all research into vitamin E. More recently, tocotrienols have been the subject of increased scientific attention, with research on tocotrienols accounting for nearly 30% of all peer-reviewed articles published on vitamin E
between 2009 and 2010.
The human body makes cholesterol in the liver. Tocotrienols can decrease the liver's
capacity to manufacture cholesterol. They do so by inhibiting HMG-CoA reductase, the
enzyme responsible for cholesterol synthesis.
https://en.wikipedia.org/wiki/Tocotrienol
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Topoisomerases
Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA.
The winding problem of DNA arises due to the intertwined nature of its double-helical
structure. During DNA replication and transcription, DNA becomes overwound ahead
of a replication fork. If left unabated, this torsion would eventually stop the ability of
RNA & DNA polymerase involved in these processes to continue down the DNA
strand.
In order to prevent and correct these types of topological problems caused by the double helix, topoisomerases bind to either single-stranded or double-stranded DNA and
cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be
untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again. Since the overall chemical composition and connectivity of the DNA do
not change, the tangled and untangled DNAs are chemical isomers, differing only in
their global topology, thus their name. Topoisomerases are isomerase enzymes that act
on the topology of DNA.
The double-helical configuration that DNA strands naturally reside, makes them difficult to separate and yet they must be separated by helicase enzymes, if other enzymes
are to transcribe the sequences that encode proteins, or if chromosomes are to be replicated. In so-called circular DNA, in which double-helical DNA is bent around and
joined in a circle, the two strands are topologically linked, or knotted. Otherwise identical loops of DNA, having different numbers of twists, are topoisomers, and cannot be
interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting or unkinking of DNA by creating transient breaks in the DNA using a conserved Tyrosine as the catalytic residue.
https://en.wikipedia.org/wiki/Topoisomerase
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Trans fats
Trans fats, or trans-unsaturated fatty acids, trans fatty acids, are a type of unsaturated
fat that is uncommon in nature but became commonly produced industrially from vegetable fats for use in margarine, snack food, packaged baked goods and frying fast food
starting in the 1950s. Trans fat has been shown to consistently be associated, in an
intake-dependent way, with increased risk of coronary heart disease, a leading cause of
death in Western nations.
Fats contain long hydrocarbon chains, which can either be unsaturated, i.e. have double bonds, or saturated, i.e. have no double bonds. In nature, unsaturated fatty acids
generally have cis as opposed to trans configurations. In food production, liquid cisunsaturated fats such as vegetable oils are hydrogenated to produce saturated fats,
which have more desirable physical properties, e.g. they melt at a desirable temperature (3040C). Partial hydrogenation of the unsaturated fat converts some of the cis
double bonds into trans double bonds by an isomerization reaction with the catalyst
used for the hydrogenation, which yields a trans fat. Although trans fats are edible,
consumption of trans fats has shown to increase the risk of coronary heart disease in
part by raising levels of the lipoprotein LDL (so-called "bad cholesterol"), lowering levels of the lipoprotein HDL ("good cholesterol"), increasing triglycerides in the bloodstream and promoting systemic inflammation.
https://en.wikipedia.org/wiki/Trans_fat
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Transaldolase
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Transaminases
In biochemistry, a transaminase or an aminotransferase is an enzyme that catalyzes a
type of reaction between an amino acid and an -keto acid. They are important in the
synthesis of amino acids, which form proteins. In medicine, they are an important indicator of liver damage.
An amino acid contains an amine (NH2) group. A keto acid contains a keto (=O) group.
In transamination, the NH2 group on one molecule is exchanged with the =O group on
the other molecule. The amino acid becomes a keto acid, and the keto acid becomes an
amino acid.
https://en.wikipedia.org/wiki/Transaminase
Transamination
Most amino acids are deaminated by transamination, a chemical reaction that transfers an amino group to a ketoacid to form new amino acids. Transamination in biochemistry is accomplished by enzymes called transaminases or aminotransferases. ketoglutarate acts as the predominant amino group acceptor and produces glutamate
as the new amino acid.
Amino acid + -ketoglutarate -keto acid + Glutamate
Glutamate's amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate.
Glutamate + Oxaloacetate -ketoglutarate + Aspartate
The product of transamination reactions depend on the availability of -keto acids.
The products usually are either alanine, aspartate or glutamate, since their corresponding -keto acids are produced through metabolism of fuels. Lysine proline and threonine are the only three amino acids that do not always undergo transamination.
https://en.wikipedia.org/wiki/Transamination
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Transcription
Transcription is the first step of gene expression, in which a particular segment of DNA
is copied into RNA (mRNA) by the enzyme RNA polymerase. Both RNA and DNA are
nucleic acids, which use base pairs of nucleotides as a complementary language. The
two can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by an RNA polymerase, which
produces a complementary, antiparallel RNA strand called a primary transcript.
Transcription proceeds in the following general steps:
1 One or more sigma factor protein binds to the RNA polymerase holoenzyme, allowing it to bind to promoter DNA.
2 RNA polymerase creates a transcription bubble, which separates the two strands of
the DNA helix. This is done by breaking the hydrogen bonds between complementary
DNA nucleotides.
3 RNA polymerase adds matching RNA nucleotides to the complementary nucleotides
of one DNA strand.
4 RNA sugar-phosphate backbone forms with assistance from RNA polymerase to
form an RNA strand.
5 Hydrogen bonds of the untwisted RNADNA helix break, freeing the newly synthesized RNA strand.
6 If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.
7 The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear
pore complex.
The stretch of DNA transcribed into an RNA molecule is called a transcript. If the gene
transcribed encodes a protein, messenger RNA (mRNA) will be transcribed, and the
mRNA will in turn serve as a template for the protein's synthesis through translation.
Alternatively, the transcribed gene may encode for either non-coding RNA (such as microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes. Overall, RNA helps synthesize, regulate, and process proteins;
it therefore plays a fundamental role in performing functions within a cell.
https://en.wikipedia.org/wiki/Transcription_(genetics)
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Transcription Bubble
A transcription bubble is a molecular structure that occurs during the transcription of
DNA when a limited portion of the DNA double strand is unwound. RNA polymerase
may then bind to the exposed DNA and begin synthesizing a new strand of RNA. As
RNA polymerase progresses down the DNA strand in the 5' to 3' direction, more of the
DNA double strand is unwound downstream of the polymerase while DNA upstream of
the polymerase re-anneals, moving a transcription bubble in the process that may be
seen with specialized staining techniques, spectroscopy or microscopy.
https://en.wikipedia.org/wiki/Transcription_bubble
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Transcription Factor
In molecular biology and genetics, a transcription factor (sometimes called a sequencespecific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby
controlling the rate of transcription of genetic information from DNA to messenger
RNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of
RNA polymerase (the enzyme that performs the transcription of genetic information
from DNA to RNA) to specific genes.
A defining feature of transcription factors is that they contain one or more DNAbinding domains (DBDs), which attach to specific sequences of DNA adjacent to the
genes that they regulate. Additional proteins such as coactivators, chromatin remodelers, histone acetylases, deacetylases, kinases, and methylases, while also playing crucial roles in gene regulation, lack DNA-binding domains, and, therefore, are not classified as transcription factors.
Transcription factors are essential for the regulation of gene expression and are, as a
consequence, found in all living organisms. The number of transcription factors found
within an organism increases with genome size, and larger genomes tend to have more
transcription factors per gene.
There are approximately 2600 proteins in the human genome that contain DNAbinding domains, and most of these are presumed to function as transcription factors,
though other studies indicate it to be a smaller number. Therefore, approximately 10%
of genes in the genome code for transcription factors, which makes this family the single largest family of human proteins. Furthermore, genes are often flanked by several
binding sites for distinct transcription factors, and efficient expression of each of these
genes requires the cooperative action of several different transcription factors (see, for
example, hepatocyte nuclear factors). Hence, the combinatorial use of a subset of the
approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development.
https://en.wikipedia.org/wiki/Transcription_factor
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Transcription Factors
RNA Polymerase
https://en.wikipedia.org/wiki/Transcription_(genetics)
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Transcription-coupled Repair
There are two general categories of nucleotide excision repair (NER) - Transcriptioncoupled repair (TC-NER) and global genomic repair (GG-NER). At any given time,
most of the genome in an organism is not undergoing transcription. There is a difference in nucleotide excision repair (NER) efficiency between transcriptionally silent
and transcriptionally active regions of the genome. For many types of lesions, NER repairs the transcribed strands of transcriptionally active genes faster than it repairs
non-transcribed strands and transcriptionally silent DNA.
TC-NER and GG-NER differ only in the initial steps of DNA damage recognition. The
principal difference between TC-NER and GG-NER is that TC-NER does not require
XPC or DDB proteins for distortion recognition in mammalian cells. Instead TC-NER
initiates when RNA polymerase stalls at a lesion in DNA: the blocked RNA polymerase
serves as a damage recognition signal, which replaces the need for the distortion recognition properties of the XPC-RAD23B and DDB complexes. CS proteins (CSA and CSB)
bind some types of DNA damage instead of XPC-Rad23B.
TC-NER initiates when RNA polymerase stalls at a lesion in DNA, whereupon protein
complexes help move the polymerase backwards. Mutations in TC-NER machinery are
responsible for multiple genetic disorders including:
Trichothiodystrophy (TTD): some individuals are photosensitive, ichthyosis, mental/
physical retardation
Cockayne syndrome (CS): photosensitivity, mental retardation, progeria-like features, microcephaly
https://en.wikipedia.org/wiki/Nucleotide_excision_repair#Transcription_coupled_r
epair_.28TC-NER.29
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Transcriptomics
The transcriptome is the set of all messenger RNA molecules in one cell or a po
tion of cells. It differs from the exome in that it includes only those RNA molecu
found in a specified cell population, and usually includes the amount or concen
of each RNA molecule in addition to the molecular identities.
The transcriptomes of stem cells and cancer cells are of particular interest to re
ers who seek to understand the processes of cellular differentiation and carcino
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Transferase
cule (called the donor) to another (called the acceptor). They are involved in
Transferrin
Transferrins are iron-binding blood plasma glycoproteins that control the level of free
iron in biological fluids. Human transferrin is encoded by the TF gene.
Transferrin glycoproteins bind iron tightly, but reversibly. Transferrin has a molecular
weight of around 80 KDa and contains two specific high-affinity Fe(III) binding sites.
The affinity of transferrin for Fe(III) is extremely high (association constant is 1020
M1 at pH 7.4) but decreases progressively with decreasing pH below neutrality.
When a transferrin protein loaded with iron encounters a transferrin receptor on the
surface of a cell (e.g., to erythroid precursors in the bone marrow), it binds to it and, as
a consequence, is transported into the cell in a vesicle by receptor-mediated endocytosis. The pH of the vesicle is reduced by hydrogen ion pumps (H+ ATPases) to about 5.5,
causing transferrin to release its iron ions. The receptor (with its ligand, transferrin,
bound) is then transported through the endocytic cycle back to the cell surface, ready
for another round of iron uptake. Each transferrin molecule has the ability to carry two
iron ions in the ferric form (Fe3+).
https://en.wikipedia.org/wiki/Transferrin
Transferrin Receptor
Transferrin receptor (TfR) is a carrier protein for transferrin. It is needed for the import of iron into the cell and is regulated in response to intracellular iron concentration. It imports iron by internalizing the transferrin-iron complex through receptormediated endocytosis.
Low iron concentrations promote increased levels of transferrin receptor, to increase
iron intake into the cell. Thus, transferrin receptor maintains cellular iron homeostasis.
TfR production in the cell is regulated according to iron levels by iron-responsive
element-binding proteins, IRP1 and IRP2. In the absence of iron, one of these proteins
(generally IRP2) binds to the hairpin like structure (IRE) that is in the 3' UTR of the
TfR mRNA. Once binding occurs, the mRNA is stabilized and degradation is inhibited.
https://en.wikipedia.org/wiki/Transferrin_receptor
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Transformation
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Transglutaminase
A transglutaminase is an enzyme that catalyzes the formation of an isopeptide bond between a free amine group (e.g., protein- or peptide-bound lysine) and the acyl group at
the end of the side chain of protein- or peptide-bound glutamine. The reaction also produces a molecule of ammonia. Bonds formed by transglutaminase exhibit high resistance to proteolytic degradation (proteolysis).
Transglutaminases form extensively cross-linked, generally insoluble protein polymers. These biological polymers are indispensable for an organism to create barriers
and stable structures. Examples are blood clots (coagulation factor XIII), as well as
skin and hair.
The catalytic reaction is generally viewed as being irreversible, and must be closely
monitored through extensive control mechanisms.
Deficiency of blood factor XIII (a rare genetic condition) predisposes to hemorrhage.
Concentrated enzyme can be used to correct the abnormality and reduce bleeding risk.
Anti-transglutaminase antibodies are found in celiac disease and may play a role in the
small bowel damage in response to dietary gliadin that characterises this condition. In
the related condition dermatitis herpetiformis, in which small bowel changes are often
found and which responds to dietary exclusion of gliadin-containing wheat products,
epidermal transglutaminase is the predominant autoantigen.
Recent research indicates that sufferers from neurological diseases like Huntington's
and Parkinson's may have unusually high levels of one type of transglutaminase, tissue
transglutaminase. It is hypothesized that tissue transglutaminase may be involved in
the formation of the protein aggregates that causes Huntington's disease, although it is
most likely not required.
Mutations in keratinocyte transglutaminase are implicated in lamellar ichthyosis.
https://en.wikipedia.org/wiki/Transglutaminase
Transketolase
Transketolase is an enzyme of both the pentose phosphate pathway in all organisms
and the Calvin cycle of photosynthesis. It catalyzes two important reactions, which operate in opposite directions in these two pathways.
GLYAL-3-P + F6P
Xu-5-P + R-5-P
In mammals, transketolase connects the pentose phosphate pathway to glycolysis, feeding excess sugar phosphates into the main carbohydrate metabolic pathways. Its presence is necessary for the production of NADPH, especially in tissues actively engaged
in biosyntheses, such as fatty acid synthesis by the liver and mammary glands, and for
steroid synthesis by the liver and adrenal glands.
https://en.wikipedia.org/wiki/Transketolase
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Translation
In molecular biology and genetics, translation is the process in which cellular ribosomes create proteins. In translation, messenger RNA (mRNA)produced by transcription from DNAis decoded by a ribosome to produce a specific amino acid chain,
or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino
acids that are chained together into a polypeptide as the mRNA passes through and is
"read" by the ribosome. The entire process is a part of gene expression.
In brief, translation proceeds in three phases:
1 - Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon.
2 - Elongation: The tRNA transfers an amino acid to the tRNA corresponding to the
next codon. The ribosome then moves (translocates) to the next mRNA codon to continue the process, creating an amino acid chain.
3 - Termination: When a stop codon is reached, the ribosome releases the polypeptide.
In bacteria, translation occurs in the cell's cytoplasm, where the large and small
subunits of the ribosome bind to the mRNA. In eukaryotes, translation occurs in the cytosol or across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. In many instances, the entire ribosome/mRNA complex binds to the
outer membrane of the rough endoplasmic reticulum (ER); the newly created polypeptide is stored inside the ER for later vesicle transport and secretion outside of the cell.
The basic process of protein production is addition of one amino acid at a time to the
end of a protein. This operation is performed by a ribosome. The choice of amino acid
type to add is determined by an mRNA molecule. Each amino acid added is matched to
a three nucleotide subsequence of the mRNA. For each such triplet possible, the corresponding amino acid is accepted. The successive amino acids added to the chain are
matched to successive nucleotide triplets in the mRNA. In this way the sequence of nucleotides in the template mRNA chain determines the sequence of amino acids in the
generated amino acid chain. Addition of an amino acid occurs at the C-terminus of the
peptide and thus translation is said to be amino-to-carboxyl directed.
The mRNA carries genetic information encoded as a ribonucleotide sequence from the
chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes
for a specific amino acid.
The ribosome molecules translate this code to a specific sequence of amino acids. The
ribosome is a multisubunit structure containing rRNA and proteins. It is the "factory"
where amino acids are assembled into proteins. tRNAs are small noncoding RNA
chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a
site for amino acid attachment, and a site called an anticodon. The anticodon is an
RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.
https://en.wikipedia.org/wiki/Translation_(biology)
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Transmembrane Proteins
A transmembrane protein (TP) is a type of integral membrane protein that spans the
entirety of the biological membrane to which it is permanently attached. Many transmembrane proteins function as gateways to permit the transport of specific substances
across the biological membrane. They frequently undergo significant conformational
changes to move a substance through the membrane.
Transmembrane proteins are polytopic proteins that aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of
them (-barrels) can be also extracted using denaturing agents.
The other type of integral membrane protein is the integral monotopic protein that is
also permanently attached to the cell membrane but does not pass through it.
There are two basic types of transmembrane proteins: -helical and -barrels. helical proteins are present in the inner membranes of bacterial cells or the plasma
membrane of eukaryotes, and sometimes in the outer membranes. This is the major
category of transmembrane proteins. In humans, 27% of all proteins have been estimated to be -helical membrane proteins. -barrel proteins are so far found only in
outer membranes of gram-negative bacteria, cell wall of gram-positive bacteria, and
outer membranes of mitochondria and chloroplasts. All -barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism.
Transmembrane proteins are classified by topology. Types I, II, and III are single-pass
molecules, while type IV are multiple-pass molecules. Type I transmembrane proteins
are anchored to the lipid membrane with a stop-transfer anchor sequence and have
their N-terminal domains targeted to the ER lumen during synthesis (and the extracellular space, if mature forms are located on plasmalemma). Type II and III are anchored with a signal-anchor sequence, with type II being targeted to the ER lumen
with its C-terminal domain, while type III have their N-terminal domains targeted to
the ER lumen. Type IV is subdivided into IV-A, with their N-terminal domains targeted to the cytosol and IV-B, with an N-terminal domain targeted to the lumen. The
implications for the division in the four types are especially manifest at the time of
translocation and ER-bound translation, when the protein has to be passed through
the ER membrane in a direction dependent on the type.
Pictured below are bitopic -helix (1), polytopic -helix (2), and polytopic -barrel (3)
transmembrane proteins.
https://en.wikipedia.org/wiki/Transmembrane_protein
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Transmethylase
Methyltransferases (transmethylases) are a large group of enzymes that all methylate
their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a
Rossman fold for binding S-Adenosyl methionine (SAM).
The general mechanism for methyl transfer is a SN2-like nucleophilic attack where the
methionine sulfur serves as the nucleophile that transfers the methyl group to the enzyme substrate. SAM is converted to S-Adenosyl homocysteine (SAH) during this process. The breaking of the SAM-methyl bond and the formation of the substrate-methyl
bond happen nearly simultaneously. These enzymatic reactions are found in many
pathways and are implicated in genetic diseases, cancer, and metabolic diseases.
Methylation, as well as other epigenetic modifications, affects transcription, gene stability, and parental imprinting. It directly impacts chromatin structure and can modulate
gene transcription, or even completely silence or activate genes, without mutation to
the gene itself. Though the mechanisms of this genetic control are complex, hypo- and
hypermethylation of DNA is implicated in many diseases.
https://en.wikipedia.org/wiki/Methyltransferase
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a group of progressive conditions that affect the brain (encephalopathies) and nervou
system of many animals, including humans. According to the most widespread hy-
pothesis, they are transmitted by prions, though some other data suggest an involve-
ment of a Spiroplasma infection. Mental and physical abilities deteriorate and myria
tiny holes appear in the cortex causing it to appear like a sponge (hence spongiform)
when brain tissue obtained at autopsy is examined under a microscope. The disorder
kuru, and the recently discovered variably protease-sensitive prionopathy. These con
tions form a spectrum of diseases with overlapping signs and symptoms.
https://en.wikipedia.org/wiki/Transmissible_spongiform_encephalopathy
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Transporter Proteins
teins. That is, they exist permanently within and span the membrane acros
they transport substances. The proteins may assist in the movement of subs
Index
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Transporters
teins. That is, they exist permanently within and span the membrane acros
they transport substances. The proteins may assist in the movement of subs
Transposable Elements
A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's
genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel Prize in 1983.
Transposable elements make up a large fraction of the C-value of eukaryotic cells.
There are at least two classes of TEs: Class I TEs generally function via reverse transcription, while Class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been
shown that TEs are important in genome function and evolution. In Oxytricha, which
has a unique genetic system, these elements play a critical role in development. Transposons are also very useful to researchers as a means to alter DNA inside a living organism.
Transposable elements represent one of several types of mobile genetic elements. TEs
are assigned to one of two classes according to their mechanism of transposition,
which can be described as either copy and paste (Class I TEs) or cut and paste (Class II
TEs).
https://en.wikipedia.org/wiki/Transposable_element
Transverse Diffusion
Lipids in lipid bilayers can move in two ways. Movements within a leaflet of the
layer are called lateral diffusion and occur readily. Movements from one leaflet o
other are called transverse diffusion. They are rare and must be catalyzed by enz
called flippases, floppases, or scramblases.
https://en.wikipedia.org/wiki/Flippase
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Triacylglycerides
Fat is one of the three main macronutrients: fat, carbohydrate, and protein. Fats, also
known as triglycerides, triacylglycerides or triacylglycerols, are esters of three fatty
acid chains and the alcohol glycerol.
The terms "oil", "fat", and "lipid" are often confused. "Oil" normally refers to a fat with
short or unsaturated fatty acid chains that is liquid at room temperature, while "fat"
may specifically refer to fats that are solids at room temperature. "Lipid" is the general
term, as a lipid is not necessarily a triglyceride. Fats, like other lipids, are generally hydrophobic, and are soluble in organic solvents and insoluble in water.
Fat is an important foodstuff for many forms of life, and fats serve both structural and
metabolic functions. They are necessary part of the diet of most heterotrophs (including humans). Some fatty acids that are set free by the digestion of fats are called essential because they cannot be synthesized in the body from simpler constituents. There
are two essential fatty acids (EFAs) in human nutrition: -linolenic acid (an -3 fatty
acid) and linoleic acid (an -6 fatty acid). Other lipids needed by the body can be synthesized from these and other fats. Fats and other lipids are broken down in the body
by enzymes called lipases produced in the pancreas.
Fats and oils are categorized according to the number and bonding of the carbon atoms in the aliphatic chain. Fats that are saturated fats have no double bonds between
the carbons in the chain. Unsaturated fats have one or more double bonded carbons in
the chain. The nomenclature is based on the non-acid (non-carbonyl) end of the chain.
This end is called the omega end or the n-end. Thus -linolenic acid is called an -3
fatty acid because the 3rd carbon from that end is the first double bonded carbon in
the chain counting from that end.
Some oils and fats have multiple double bonds and are therefore called polyunsaturated fats. Unsaturated fats can be further divided into cis fats, which are the most common in nature, and trans fats, which are rare in nature. Unsaturated fats can be altered
by reaction with hydrogen effected by a catalyst. This action, called hydrogenation,
tends to break all the double bonds and makes a fully saturated fat. To make vegetable
shortening, then, liquid cis-unsaturated fats such as vegetable oils are hydrogenated to
produce saturated fats, which have more desirable physical properties e.g., they melt at
a desirable temperature (3040C), and store well, whereas polyunsaturated oils go
rancid when they react with oxygen in the air. However, trans fats are generated during hydrogenation as contaminants created by an unwanted side reaction on the catalyst during partial hydrogenation. Consumption of such trans fats has shown to increase the risk of coronary heart disease.
Saturated fats can stack themselves in a closely packed arrangement, so they can solidify easily and are typically solid at room temperature. For example, animal fats tallow
and lard are high in saturated fatty acid content and are solids. Olive and linseed oils
on the other hand are unsaturated and liquid.
Fats serve both as energy sources for the body, and as stores for energy in excess of
what the body needs immediately. Each gram of fat when burned or metabolized releases about 9 food calories (37 kJ = 8.8 kcal). Fats are broken down in the healthy
body to release their constituents, glycerol and fatty acids. Glycerol itself can be converted to glucose by the liver and so become a source of energy.
https://en.wikipedia.org/wiki/Fat
Triacylglycerol Lipase
Triacylglycerol lipase (EC 3.1.1.3) is the only regulated enzyme of fat breakd
acid from the fat. Diacylglyceride lipase removes the second one and monoa
eride lipase removes the third. As noted, only the first one is regulated and
to be the rate limiting reaction when active.
This enzyme catalyses the following reaction
Triacylglycerol + H2O <=> Diacylglycerol + Fatty acid
The pancreatic enzyme acts only on an ester-water interface.
https://en.wikipedia.org/wiki/Triacylglycerol_lipase
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Triiodothyronine
Triiodothyronine, also known as T3, is a thyroid hormone. It affects almost every
physiological process in the body, including growth and development, metabolism,
body temperature, and heart rate. Production of T3 and its prohormone thyroxine (T4)
is activated by thyroid-stimulating hormone (TSH), which is released from the pituitary gland.
As concentrations of these hormones decrease, the pituitary gland increases production of TSH, and by these processes, a feedback control system stabilizes the amount of
thyroid hormones that are in the bloodstream.
T3 is the true hormone. Its effects on target tissues are roughly four times more potent
than those of T4. Of the thyroid hormone that is produced, just about 20% is T3,
whereas 80% is produced as T4. Roughly 85% of the circulating T3 is later formed in
the liver and pituitary by removal of the iodine atom from the carbon atom number
five of the outer ring of T4. In any case, the concentration of T3 in the human blood
plasma is about one-fortieth that of T4. This is observed in fact because of the short
half-life of T3, which is only 2.5 days. This compares with the half-life of T4, which is
about 6.5 days.
https://en.wikipedia.org/wiki/Triiodothyronine
Trimethylamine-N-oxide
Trimethylamine N-oxide (TMAO) is the organic compound in the class of amine oxides
with the formula (CH3)3NO. This colorless solid is usually encountered as the dihydrate. It is a product of the oxidation of trimethylamine and a common metabolite in
animals. It is a protein stabilizer that may serve to counteract urea, the major osmolyte
of sharks, skates and rays. It is also higher in deep-sea fishes and crustaceans, where it
may counteract the protein-destabilizing effects of pressure. TMAO decomposes to trimethylamine (TMA), which is the main odorant that is characteristic of degrading seafood.
Trimethylamine oxide is used in protein folding experiments to counteract the unfolding effects of urea.
https://en.wikipedia.org/wiki/Trimethylamine_N-oxide
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Trinucleotide Repeat
Trinucleotide repeat disorders are a set of genetic disorders caused by trinucleotide repeat expansion, a kind of mutation where trinucleotide repeats in certain genes exceed
the normal, stable threshold, which differs per gene. The mutation is a subset of unstable microsatellite repeats that occur throughout all genomic sequences. If the repeat is
present in a healthy gene, a dynamic mutation may increase the repeat count and result in a defective gene.
Currently, nine neurologic disorders are known to be caused by an increased number
of CAG repeats, typically in coding regions of otherwise unrelated proteins. During protein synthesis, the expanded CAG repeats are translated into a series of uninterrupted
glutamine residues forming what is known as a polyglutamine tract ("polyQ"). Such
polyglutamine tracts may be subject to increased aggregation.
Trinucleotide repeat disorders generally show genetic anticipation, where their severity increases with each successive generation that inherits them. This is likely explained by the addition of further CAG repeats in the gene in the progeny of affected individuals. For example, Huntington's disease occurs when there are more than 35 CAG
repeats on the gene coding for the protein HTT. A parent with 35 repeats would be considered "normal" and never exhibit any symptoms of the disease. That parent's offspring, however, would be at an increased risk compared to the general population of
developing Huntington's, as it would take only the addition of one more CAG codon to
cause the production of mHTT (mutant HTT), the protein responsible for disease.
Huntington's very rarely occurs spontaneously. It is almost always the result of inheriting the defective gene from an affected parent.
https://en.wikipedia.org/wiki/Trinucleotide_repeat_disorder
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Triose Kinase
In enzymology, a triokinase is an enzyme that catalyzes the chemical reaction:
ATP + D-glyceraldehyde <---> ADP + D-glyceraldehyde 3-phosphate
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TPI has been found in nearly every organism searched for the enzyme, including animals such as mammals and insects as well as in fungi, plants, and bacteria. However,
some bacteria that do not perform glycolysis, like ureaplasmas, lack TPI.
Triose phosphate isomerase is a highly efficient enzyme, performing the reaction billions of times faster than it would occur naturally in solution. The reaction is so efficient that it is said to be catalytically perfect: It is limited only by the rate the substrate
can diffuse into and out of the enzyme's active site.
https://en.wikipedia.org/wiki/Triosephosphate_isomerase
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Triosephosphate Isomerase
Triose-phosphate isomerase (TPI or TIM) is an enzyme that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and Dglyceraldehyde 3-phosphate. TPI plays an important role in glycolysis and is essential
for efficient energy production.
TPI has been found in nearly every organism searched for the enzyme, including animals such as mammals and insects as well as in fungi, plants, and bacteria. However,
some bacteria that do not perform glycolysis, like ureaplasmas, lack TPI.
Triose phosphate isomerase is a highly efficient enzyme, performing the reaction billions of times faster than it would occur naturally in solution. The reaction is so efficient that it is said to be catalytically perfect: It is limited only by the rate the substrate
can diffuse into and out of the enzyme's active site.
https://en.wikipedia.org/wiki/Triosephosphate_isomerase
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Triterpenes
plants. Many terpenes are aromatic hydrocarbons and thus may have had a
function.
Triterpenes consist of six isoprene units and have the molecular formula C3
linear triterpene squalene, the major constituent of shark liver oil, is derive
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tRNA
A transfer RNA (abbreviated tRNA and archaically referred to as sRNA, for soluble
RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in
length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. It does this by carrying an amino acid to the protein synthetic machinery of a cell (ribosome) as directed by a three-nucleotide sequence (codon) in a
messenger RNA (mRNA). As such, tRNAs are a necessary component of translation,
the biological synthesis of new proteins according to the genetic code.
One end of the tRNA matches the genetic code in a three-nucleotide sequence called
the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each
of which is recognized by a particular tRNA. On the other end of the tRNA is a covalent
attachment to the amino acid that corresponds to the anticodon sequence. Each type of
tRNA molecule can be attached to only one type of amino acid, so each organism has
many types of tRNA (in fact, because the genetic code contains multiple codons that
specify the same amino acid, there are several tRNA molecules bearing different anticodons which also carry the same amino acid).
The covalent attachment to the tRNA 3 end is catalyzed by enzymes called aminoacyl
tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1
in eukaryotes), which aid in decoding the mRNA codon sequence. If the tRNA's anticodon matches the mRNA, another tRNA already bound to the ribosome transfers the
growing polypeptide chain from its 3 end to the amino acid attached to the 3 end of
the newly delivered tRNA, a reaction catalyzed by the ribosome.
A large number of the individual nucleotides in a tRNA molecule may be chemically
modified, often by methylation or deamidation. These unusual bases sometimes affect
the tRNA's interaction with ribosomes and sometimes occur in the anticodon to alter
base-pairing properties.
https://en.wikipedia.org/wiki/Transfer_RNA
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a tRNA precursor + 2 CTP + ATP a tRNA with a 3' CCA end + 3 diphosphate (ov
all reaction)
Individual reactions below:
(1a) a tRNA precursor + CTP a tRNA with a 3' cytidine end + diphosphate
(1b) a tRNA with a 3' cytidine + CTP a tRNA with a 3' CC end + diphosphate
(1c) a tRNA with a 3' CC end + ATP a tRNA with a 3' CCA end + diphosphate
The acylation of all tRNAs with an amino acid occurs at the terminal ribose of a 3' C
sequence.
https://en.wikipedia.org/wiki/CCA_tRNA_nucleotidyltransferase
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Tropocollagen
Topocollagen is a type of collegen formed by processing of a collagen fiber outside of a
cell. Steps in the process (that starts inside the cell) are as follows:
1 Inside the cell
1 Two types of alpha chains are formed during translation on ribosomes along the
rough endoplasmic reticulum (RER): -1 and -2 chains. These peptide chains (known
as preprocollagen) have registration peptides on each end and a signal peptide.
2 Polypeptide chains are released into the lumen of the RER.
3 Signal peptides are cleaved inside the RER and the chains are now known as
pro- chains.
4 Hydroxylation of lysine and proline amino acids occurs inside the lumen. This
process is dependent on ascorbic acid (vitamin C) as a cofactor.
5 Glycosylation of specific hydroxylysine residues occurs.
6 Triple alpha helical structure is formed inside the endoplasmic reticulum from
two -1 chains and one -2 chain.
7 Procollagen is shipped to the Golgi apparatus, where it is packaged and secreted
by exocytosis.
2 Outside the cell
1 Registration peptides are cleaved and tropocollagen is formed by procollagen
peptidase.
2 Multiple tropocollagen molecules form collagen fibrils, via covalent crosslinking (aldol reaction) by lysyl oxidase which links hydroxylysine and lysine residues.
Multiple collagen fibrils form into collagen fibers.
3 Collagen may be attached to cell membranes via several types of protein, including fibronectin and integrin.
Tropoelastin
Tropoelastin is a water-soluble molecule with a molecular weight of approximately
72,000 daltons. Multiple tropoelastin molecules covalently bind together with
crosslinks to form the protein elastin that is very prevalent in the body. There is only
one gene for this molecule. However, alternative splicing does produce tissue specific
elastin variants.
There are 36 small domains in tropoelastin and each weighs about 2 kilodaltons.
Within the exons, there are alternating hydrophobic and lysine-rich domains that are
important in forming elastin. Tropoelastin does not undergo cleavage and formation of
the microfibril is achieved by a self-association process termed coacervation.
Tropoelastin aggregates at physiological temperature due to interactions between hydrophobic domains. This process is reversible and thermodynamically controlled. The
coacervate is stabilized by cross-linking via lysyl oxidase. The coacervate then becomes
insoluble and the process is irreversible. It then condenses to form a cross-linked structure of 4 residues, either Desmosine or Isodesmosine.
https://en.wikipedia.org/wiki/Tropoelastin
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Tropomyosin
Tropomyosin is a two-stranded -helical coiled coil protein found in cell cytoskeletons.
Tropomyosins are a large family of integral components of actin filaments that play a
critical role in regulating the function of actin filaments in both muscle and nonmuscle
cells. These proteins consist of rod-shaped coiled-coil hetero- or homo-dimers that lie
along the -helical groove of most actin filaments. Interaction occurs along the length
of the actin filament, with dimers aligning in a head-to-tail fashion.
The binding of the myosin heads to the muscle actin is a highly regulated process. The
thin filament is made of actin, tropomyosin, and troponin. The contraction of skeletal
muscle is triggered by nerve impulses that in turn stimulate the release of Ca++. The release of Ca++ from the sarcoplasmic reticulum causes an increase in the concentration
of Ca++ in the cytosol. Calcium ions then bind to troponin, which is associated with tropomyosin. Binding causes changes in the shape of troponin and subsequently causes
the tropomyosin isoform to shift its position on the actin filament. This shifting in position exposes the myosin-binding sites on the actin filament, allowing the myosin heads
of the thick filament to bind to the thin filament.
Structural and biochemical studies suggest that the position of tropomyosin and troponin on the thin filament regulates the interactions between the myosin heads of the
thick filament and the binding sites on the actin of the thin filament. X-ray diffraction
and cryoelectron microscopy suggest that tropomyosin sterically blocks the access of
myosin to the actin filament.
Although this model is well-established, it is unclear as to whether the movement of
tropomyosin directly causes the myosin head to engage the actin filament. As such, an
alternative model has emerged, whereby the movement of the tropomyosin in the filament functions as an allosteric switch that is modulated by activating myosin binding
but does not function solely by regulating myosin binding.
https://en.wikipedia.org/wiki/Tropomyosin
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Troponin
Troponin is a complex of three regulatory proteins (troponin C, troponin I, and troponin T) that is integral to muscle contraction in skeletal muscle and cardiac muscle,
but not smooth muscle.
An increased level of the cardiac protein isoform of troponin circulating in the blood
has been shown to be a biomarker of heart disorders, the most important of which is
myocardial infarction. Raised troponin levels indicate cardiac muscle cell death as the
molecule is released into the blood upon injury to the heart.
Troponin is attached to the protein tropomyosin and lies within the groove between actin filaments in muscle tissue. In a relaxed muscle, tropomyosin blocks the attachment
site for the myosin crossbridge, thus preventing contraction. When the muscle cell is
stimulated to contract by an action potential, calcium channels open in the sarcoplasmic membrane and release calcium into the sarcoplasm. Some of this calcium attaches
to troponin, which causes it to change shape, exposing binding sites for myosin (active
sites) on the actin filaments. Myosin's binding to actin causes crossbridge formation,
and contraction of the muscle begins.
Troponin activation (see figure below). Troponin C (red) binds Ca++, which stabilizes
the activated state, where troponin I (yellow) is no longer bound to actin. Troponin T
(blue) anchors the complex on tropomyosin.
Troponin is found in both skeletal muscle and cardiac muscle, but the specific versions
of troponin differ between types of muscle. The main difference is that the TnC subunit
of troponin in skeletal muscle has four calcium ion-binding sites, whereas in cardiac
muscle there are only three. Views on the actual amount of calcium that binds to troponin vary from expert to expert and source to source.
https://en.wikipedia.org/wiki/Troponin
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Troponins
Troponin is a complex of three regulatory proteins (troponin C, troponin I, and troponin T) that is integral to muscle contraction in skeletal muscle and cardiac muscle,
but not smooth muscle.
An increased level of the cardiac protein isoform of troponin circulating in the blood
has been shown to be a biomarker of heart disorders, the most important of which is
myocardial infarction. Raised troponin levels indicate cardiac muscle cell death as the
molecule is released into the blood upon injury to the heart.
Troponin is attached to the protein tropomyosin and lies within the groove between actin filaments in muscle tissue. In a relaxed muscle, tropomyosin blocks the attachment
site for the myosin crossbridge, thus preventing contraction. When the muscle cell is
stimulated to contract by an action potential, calcium channels open in the sarcoplasmic membrane and release calcium into the sarcoplasm. Some of this calcium attaches
to troponin, which causes it to change shape, exposing binding sites for myosin (active
sites) on the actin filaments. Myosin's binding to actin causes crossbridge formation,
and contraction of the muscle begins.
Troponin activation (see figure below). Troponin C (red) binds Ca++, which stabilizes
the activated state, where troponin I (yellow) is no longer bound to actin. Troponin T
(blue) anchors the complex on tropomyosin.
Troponin is found in both skeletal muscle and cardiac muscle, but the specific versions
of troponin differ between types of muscle. The main difference is that the TnC subunit
of troponin in skeletal muscle has four calcium ion-binding sites, whereas in cardiac
muscle there are only three. Views on the actual amount of calcium that binds to troponin vary from expert to expert and source to source.
https://en.wikipedia.org/wiki/Troponin
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Trp Operon
The trp operon is an operon a group of genes that are used, or transcribed, together
that codes for the components for production of tryptophan. The trp operon is present in many bacteria, but was first characterized in Escherichia coli. The operon is
regulated so that when tryptophan is present in the environment, the genes for tryptophan synthesis are not expressed. It was an important experimental system for learning about gene regulation, and is commonly used to teach gene regulation.
The operon operates by a negative repressible feedback mechanism. The repressor for
the trp operon is produced upstream by the trpR gene, which is constitutively expressed at a low level. Synthesized TrpR monomers associate into tetramers. These tetramers are inactive and are dissolved in the nucleoplasm. When tryptophan is present,
these tryptophan repressor tetramers bind to tryptophan, causing a change in the repressor conformation, allowing the repressor to bind to the operator. This prevents
RNA polymerase from binding to and transcribing the operon, so tryptophan is not produced from its precursor. When tryptophan is not present, the repressor is in its inactive conformation and cannot bind the operator region, so transcription is not inhibited by the repressor.
Attenuation is a second mechanism of negative feedback in the trp operon. The repression system targets the intracellular trp concentration whereas the attenuation responds to the concentration of charged tRNAtrp. Thus, the trpR repressor decreases
gene expression by altering the initiation of transcription, while attenuation does so by
altering the process of transcription that's already in progress. While the TrpR repressor decreases transcription by a factor of 70, attenuation can further decrease it by
a factor of 10, thus allowing accumulated repression of about 700-fold. Attenuation is
made possible by the fact that in prokaryotes (which have no nucleus), the ribosomes
begin translating the mRNA while RNA polymerase is still transcribing the DNA sequence. This allows the process of translation to affect transcription of the operon directly.
https://en.wikipedia.org/wiki/Trp_operon
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Trypsin
Trypsin is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins. Trypsin is formed in the small
intestine when its proenzyme form, the trypsinogen produced by the pancreas, is activated. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when either is followed by proline. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or
trypsinization, and proteins that have been digested/treated with trypsin are said to
have been trypsinized.
In the duodenum, trypsin catalyzes the hydrolysis of peptide bonds, breaking down proteins into smaller peptides. The peptide products are then further hydrolyzed into
amino acids via other proteases, rendering them available for absorption into the blood
stream. Tryptic digestion is a necessary step in protein absorption as proteins are generally too large to be absorbed through the lining of the small intestine.
Trypsin is produced as the inactive zymogen trypsinogen in the pancreas. When the
pancreas is stimulated by cholecystokinin, it is then secreted into the first part of the
small intestine (the duodenum) via the pancreatic duct. Once in the small intestine, the
enzyme enteropeptidase activates trypsinogen into trypsin by proteolytic cleavage.
Auto catalysis can happen with trypsin using trypsinogen as the substrate. This activation mechanism is common for most serine proteases, and serves to prevent autodegradation of the pancreas.
https://en.wikipedia.org/wiki/Trypsin
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Trypsinogen
mucosa, to form trypsin. Once activated, the trypsin can activate more tryps
into trypsin. Trypsin cleaves the peptide bond on the carboxyl side of basic
such as arginine and lysine.
https://en.wikipedia.org/wiki/Trypsinogen
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Tryptophan
Tryptophan (abbreviated as Trp or W; encoded by the codon UGG) is an -amino acid
that is used in the biosynthesis of proteins. It contains an -amino group (which is in
the protonated NH3+ form under biological conditions), an -carboxylic acid group
(which is in the deprotonated COO form under biological conditions), and a side
chain indole, classifying it as a non-polar, aromatic amino acid. It is essential in humans, meaning the body cannot synthesize it and thus it must be obtained from the
diet.
For many organisms (including humans), tryptophan is needed to prevent illness or
death, but cannot be synthesized by the organism and must be ingested; in short, it is
an essential amino acid. Amino acids, including tryptophan, act as building blocks in
protein biosynthesis, and proteins are required to sustain life. In addition, tryptophan
functions as a biochemical precursor for the following compounds):
Serotonin (a neurotransmitter), synthesized via tryptophan hydroxylase. Serotonin,
in turn, can be converted to melatonin (a neurohormone), via N-acetyltransferase and
5-hydroxyindole-O-methyltransferase activities.
Niacin, also known as vitamin B3, is synthesized from tryptophan via kynurenine and
quinolinic acids as key biosynthetic intermediates.
Auxin (a phytohormone), is mainly synthesized from tryptophan via indole-3pyruvic acid.
The disorder fructose malabsorption causes improper absorption of tryptophan in the
intestine, reduced levels of tryptophan in the blood, and depression. Some studies did
not find reduced tryptophan in cases of lactose maldigestion.
In bacteria that synthesize tryptophan, high cellular levels of this amino acid activate a
repressor protein, which binds to the trp operon. Binding of this repressor to the tryptophan operon prevents transcription of downstream DNA that codes for the enzymes involved in the biosynthesis of tryptophan. So high levels of tryptophan prevent tryptophan synthesis through a negative feedback loop and, when the cell's tryptophan levels
are reduced, transcription from the trp operon resumes. The genetic organization of
the trp operon thus permits tightly regulated and rapid responses to changes in the
cell's internal and external tryptophan levels.
https://en.wikipedia.org/wiki/Tryptophan
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Tubulin
Tubulin can refer either to the tubulin protein superfamily of globular proteins, or one
of the member proteins of that superfamily. - and -tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. Microtubules function in
many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation
and therefore cell division.
- and -tubulin polymerize into dynamic microtubules. In eukaryotes, microtubules
are one of the major components of the cytoskeleton, and function in many processes,
including structural support, intracellular transport, and DNA segregation.
- and -tubulin polymerize into dynamic microtubules. In eukaryotes, microtubules
are one of the major components of the cytoskeleton, and function in many processes,
including structural support, intracellular transport, and DNA segregation.
Microtubules are assembled from dimers of - and -tubulin. These subunits are
slightly acidic with an isoelectric point between 5.2 and 5.8. Each has a molecular
weight of approximately 50,000 Daltons.
To form microtubules, the dimers of - and -tubulin bind to GTP and assemble onto
the (+) ends of microtubules while in the GTP-bound state. The -tubulin subunit is exposed on the plus end of the microtubule while the -tubulin subunit is exposed on the
minus end. After the dimer is incorporated into the microtubule, the molecule of GTP
bo