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macromolecule: nucleic acids and proteins. Nucleic acids carry the genetic
information which is passed from parents to progeny, and which provides
the blueprint for a particular living organism. That blueprint is essentially a
set of instructions for making proteins.
This obviously means that proteins are the key molecules in the
processes of life, and it is now known that virtually all the activities which
sustain living organisms are carried out by proteins.
Proteins are constructed on a simple pattern, but that pattern allows for
an almost endless diversity of structure and function.
Proteins are the most abundant biological macromolecules, occurring in
all
cells and all parts of cells.
The following are a few examples of proteins and what they do:
All proteins, whether from the most ancient lines of bacteria or from the most
complex forms of life, are constructed from the same set of 20 amino acids,
covalently linked in characteristic linear sequences.
The helix
Chapter 3
Chapter 3
Chapter 3
Domains
Many proteins are composed of several discrete, independently folded,
compact units
called domains. Domains may consist of combinations of motifs. The
size of a domain varies from as few as 25 to 30 amino acid residues to more
than 300.
Chapter 3
Chapter 3
10
Tertiary structure
Chapter 3
11
Quaternary structure.
13
Common
motifs
Chapter 3
14
Common
domain folds
Chapter 3
15
Quaternary structure of
multidomain proteins
Chapter 3
16
Chapter 3
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Chapter 3
18
Globular proteins
Chapter 3
19
Fibrous proteins
Chapter 3
20
Chapter 3
21
Chapter 3
22
Column chromatography.
Chapter 3
23
SDSPAGE
Chapter 3
24
Isoelectric Points
In acidic solution, the carboxylate and amine are in
their conjugate acid forms, an overall cation
In basic solution, the groups are in their base forms,
an overall anion
In neutral solution cation and anion forms are present
This pH where the overall charge is 0 is the
isoelectric point, pI
25
Isoelectric Points
In acidic solution, the carboxylate and amine are in
their conjugate acid forms, an overall cation
In basic solution, the groups are in their base forms,
an overall anion
In neutral solution cation and anion forms are present
This pH where the overall charge is 0 is the
isoelectric point, pI
27
Chapter 3
28
Chapter 3
29
Amino Acids
General Structure of Amino Acids
Chapter 3
31
Chapter 3
32
Chapter 3
33
Chapter 3
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Chapter 3
35
When the pH of the solution is below the the protonated form predominates and
the amino acid is then a true acid that is capable of donating a proton.
When the pH of the solution is above the of the ionizable group, the unprotonated
form of that group predominates and the amino acid exists as the conjugate base,
which is a proton acceptor.
Every amino acid has at least two values corresponding to the ionization of the
and groups.
Seven of the common amino acids have ionizable side chains with additional,
measurable values:
Chapter 3
36
When the pH of the solution is below the the protonated form predominates and
the amino acid is then a true acid that is capable of donating a proton.
When the pH of the solution is above the of the ionizable group, the unprotonated
form of that group predominates and the amino acid exists as the conjugate base,
which is a proton acceptor.
Every amino acid has at least two values corresponding to the ionization of the
and groups.
Seven of the common amino acids have ionizable side chains with additional,
measurable values:
Chapter 3
37
Chapter 3
38
Chapter 3
39
Stereoisomers
Chapter 3
41
Chapter 3
42
Assimilation of Ammonia
A. Ammonia Is Incorporated into Glutamate and Glutamine
B. Transamination Reactions
Biosynthesis of serine
Biosynthesis of glycine
G. Histidine
Synthesis of histidine from phosphoribosyl pyrophosphate (PRPP) and ATP. Histidine is derived
from PRPP (5 C atoms), the purine ring of ATP (1 N and 1 C), glutamine (1 N), and
glutamate (1 N).
Protein Turnover
Proteins are continually synthesized and degraded in all cells, a process
called turnover.
Their half-lives can vary from a few minutes to several weeks but the halflife of a given protein in different organs and species is generally similar.
Protein Degradation 2 ways:
1. Lysosomes
2. Ubiquitin Proteasome System (UPS), ATP dependent
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Electrophoresis
Proteins have an overall pI that depends on the
net acidity/basicity of the side chains
The differences in pI can be used for separating
proteins on a solid phase permeated with liquid
Different amino acids migrate at different rates,
depending on their isoelectric points and on the
pH of the aqueous buffer
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D. Threonine
F. Methionine
G. Cysteine
The major route of cysteine catabolism is a three-step pathway leading to pyruvate.
Therefore, cysteine is glucogenic. Cysteine is first oxidized to cysteinesulfinate, which
loses its amino group by transamination to form -sulfinylpyruvat.
Nonenzymatic desulfurylation produces pyruvate
I. Lysine
I. Lysine
The exchange of glucose and alanine between muscle and liver, called the
glucosealanine cycle , provides an indirect means for muscle to eliminate nitrogen
and replenish its energy supply.
Glucosealanine cycle
-Ketoglutarate 2- + 2 NH4+
Nitrogen is fixed in only a few species of bacteria and blue-green algae by the
nitrogenase-catalyzed reduction of atmospheric to ammonia. Plants and
microorganisms can reduce nitrate and nitrite to ammonia.
Ammonia is assimilated into metabolites by the reductive amination of to glutamate,
catalyzed by glutamate dehydrogenase. Glutamine, a nitrogen donor in
many biosynthetic reactions, is formed from glutamate and ammonia by the action of
glutamine synthetase.
The amino group of glutamate can be transferred to an acid in a reversible
transamination reaction to form and the corresponding acid.
Pathways for the biosynthesis of the carbon skeletons of amino acids begin with simple
metabolic precursors such as pyruvate and citric acid cycle intermediates.
Nonessential amino acids are those that animals can produce in quantities that are
sufficient for growth. These amino acids are generally formed by short, energetically
inexpensive pathways. Essential amino acids must be supplied
in the diets of animals; these amino acids are synthesized by bacteria and plants.
In addition to their role in protein synthesis, amino acids serve as precursors in a
number of other metabolic pathways.
Protein molecules in all living cells are continually synthesized and degraded.
Amino acids obtained from protein degradation or directly from food can be
catabolized. Catabolism begins with deamination, followed by modification of the
remaining carbon chains for entry into the central pathways of carbon metabolism.
The pathways for the degradation of amino acids lead to pyruvate, acetyl CoA, or
intermediates of the citric acid cycle. Amino acids that are degraded to citric acid
cycle intermediates are glucogenic. Those that form acetyl CoA are ketogenic.
In mammals, most nitrogen is excreted as urea, which is formed by the urea cycle in
the liver. The carbon atom of urea is derived from bicarbonate. One amino group is
derived from ammonia, and the other from aspartate.
The metabolism of glutamine in the kidneys produces the bicarbonate needed to
neutralize acids produced in the body.