Documenti di Didattica
Documenti di Professioni
Documenti di Cultura
HANDOUT
FOR
BIOCHEMISTRY
REVIEW PROPER 1: AMINO ACIDS
PART I: INTRODUCTION AND CHARACTERISTICS carboxyl groups. Thus, they are chiral. Based on
In the structural sense, amino acids are amino-group absolute stereochemistry:
containing carboxylic acids. L isomer - more commonly found in nature, with D
isomers existing but less common.
Glycine – only achiral amino acid of the 20.
An amino acid.
The general structure of all 20 amino acids. Glycine is the only achiral alpha amino acid.
.
Generally, an (alpha) amino acid is attached to
hydrogen and a R group in addition to the amino and
Zwitterionic form - +1 and -1 charge lying on the amino and carboxyl groups, respectively at neutral pH, giving a
net charge of 0. Amino acids always exist with at least one formal charge in the body.
NEUTRAL AMINO ACIDS Non-polar amino acids are listed in the sequence
Further classified in to non-polar and polar. The R aliphatic (G to M), aromatic (F, W) and finally the only
groups of polar amino acids only have a tendency to secondary amino acid (P); polar amino acids are listed
be charged in the neutral pH. in the sequence amides (N, Q), alcohols (S, T), thiol
(C), and phenol (Y).
NON-POLAR AMINO ACIDS Asparagine (N, asn)
Amino Acid Structure R: Carbamoyl (amide) +
Glycine (G, gly) methyl
R: Hydrogen
Amino acids can be titrated to achieve the zwitterionic form. At alterations in pH during titration, titratable groups
become protonated or deprotonated. For example, histidine has its carboxyl, amino and imidazole groups
protonated. As the pH increases, the carboxyl group becomes deprotonated, then the imidazole nitrogen, then
the amino group respectively.
At pH 1, the net charge is +2 because all three titratable groups are protonated (the nitrogen atom in the ring
possesses a positive charge). This charge becomes +1 then 0 and -1 as the pH increases. We should realize that
when charge becomes 0, zwitterionic form has been achieved.
The IpH can be computed by getting the average of the two pKa values that flank the 0 net charge. For histidine,
the IpH is 7.585 (IpH = (6.0 + 9.17) / 2).
PART 4: PEPTIDE BOND FORMATION: ENTRY TO PROTEINS
Peptide bond – bond between two amino acids. It is structurally an amide bond.
Condensation - a ANE reaction of two carboxylic acids to form the peptide bond. The carboxyl group of one
(nucleophile) attacks the amino group (electrophile) of the other, creating the pep tide bond and releasing water.
Thus, end products are trans-dipeptide and water.
Condensation reaction between two amino acids, leading to a dipeptide and water.
N-terminal – end of a peptide/protein with an exposed amino group.
C-terminal – end of a peptide/protein with an exposed carboxyl group.
Residue – R groups of the bonded amino acids in a peptide/protein.
Bonds in peptides
Psi (ψ) – bond between the alpha carbon and the carboxyl carbon
Phi (Φ) – bond between the alpha carbon and the amino nitrogen
Omega (ω) - AKA peptide bond
Condensing amino acids also changes their names. The –ine suffix is changed into –yl for most of the amino acids.
There are exceptions, namely: cysteinyl, tryptophanyl/ tryptophyl, asparagyl, glutaminyl (from glutamine;
glutamyl is used for glutamate), and aspartyl. For example, the nonapeptide CHEMISTRY is also known as
cysteinylhistidylglutamylmethionylisoleucylserylthreonylarginyltyrosine.
In tripeptide STC, there are three titratable groups, the amino group from serine, and the carboxyl and thiol group
from cysteine. They all become deprotonated at different pH values.
At pH 1, all titratable groups are protonated. This gives the tripeptide a net charge of +1. At pH 1.71, the carboxyl
group loses its protonation giving it a negative charge. This gives the tripeptide a net charge of 0, and the
zwitterionic form is achieved.
At pH 8.33, the thiol group loses its protonation. This gives the tripeptide a net charge of -1. At pH 9.15, the amino
group is deprotonated. This gives this tripeptide a net charge of -2 from the charged carboxyl and thiol groups.
- The IpH of the tripeptide is 5.02.
B) -pleated Sheet
D. - complexation – interaction of
aromatic molecules with each other
(stacking)
4. Myoglobin
Transport protein; globular
Also known as antibodies
Found mainly in the muscles
Defense proteins
Composed of only one protein chain with
a heme prosthetic group in the center Secreted by B-lymphocytes
Composed of two light chains and two
Myoglobin’s oxygen binding curve is
hyperbolic instead of sigmoidal heavy chains with constant and variable
regions (ex. VH is the heavy variable
region, CH is the heavy constant region)
Variable regions bind to the antigens
Constant regions activate immunological
defenses
Typically Y-shaped; some are monomers
(IgD, IgG, IgE), others are dimeric (IgA)
and pentameric (IgM)
Implications:
If the Km is low, it means that it takes just a few
amount of substrate to reach half the Vmax
(thus, the substrate greatly influences enzyme
activity) and vice-versa.
Turnover number - denotes how much
molecules of the substrate turn into product in
a given amount of time. Obviously, higher
PART 4: ENZYME INHIBITION
Recall that inhibition reduces the catalytic activity of enzymes. Be noted that this is not completely detrimental for
biological systems.
- Some enzymes have to be inactivated when the body calls for reduction in the products resulting from those
reactions that are catalyzed (if enzymes in the conversion of glucose to ATP are not inhibited, they may
produce too much that is not even needed by the body, leading to wastage of energy). When a product of the
enzyme or series of enzymes itself inhibits the progress, the inhibition is termed a feedback mechanism.
- Some enzymes from other microorganisms that may interfere with several physical/chemical processes such as
drug bioavailability (ex. penicillinase, an enzyme by several bacteria can destroy molecules of the penicillin
category of drugs). If they are inhibited, better therapeutic outcomes may be achieved.
- Of course, some inhibitions are really detrimental such as those which inhibit enzymes essential to our
maintenance of energy (ex. aconitase, an enzyme in Kreb’s cycle, is inhibited by fluoroacetate, which can lead
to poisoning).
Different types of inhibition in th eir Lineweaver-Burk plots (both x and y values of Michaelis-Menten plots reciproca ted). Y-
intercep t is th e recip rocal of Vmax.
=============================================================================================
Nomenclature for nucleosides Like proteins, nucleic acids have names for their
- Ribonucleosides: two ends: the 3’ end and the 5’ end.
For purines: Retain the name of the base, then
drop the “–ine” for “-osine”
NUCLEOSIDE
The bond between the sugar and the base is a
N- β -glycosidic bond.
STABILITY ISSUES
Electronegativity disturbances between adjacent
hydroxyl lone pairs may disrupt the stability of
the phosphodiester bonds of ribonucleic acids
only. 1. The sequence of nucleotides give rise to the
uniqueness in every species
PART 5: DNA Structure 2. The secondary structure of the DNA cannot
DNA – nucleic acid composed of be used to complete its purpose (expression)
deoxynucleotides.
- primary function is storage of genetic LINKING STRUCTURE TO FUNCTION
information. If DNA is to be function in the Central Dogma,
- present in eukaryotic and prokaryotic cells it must be read.
alike. DNA is readable only in primary structure.
- In eukaryotic cells, DNA are complexed with Double helices must be denatured to produce
basic histones. the individual and identical DNA strands. They
can be renatured after use in the central
LEVEL OF ORGANIZATION dogma.
1. Primary structure – consists of a single - heat
polynucleotide chain of deoxynucleotides. - enzymes
- Denotes the sequence of nucleotides
(specifically the bases) PART 6: RNA STRUCTURE
2. Secondary structure – the more well known RNA - nucleic acid composed of ribonucleotides.
helix structure of DNA, actually is the hydrogen - primary function is transfer and expression of
bonded complex of two intertwining genetic information.
deoxynucleotide strands. This is the more - present in eukaryotic and prokaryotic cells alike.
common level of organization in cells.
3. Tertiary structures have been proposed,
usually denoting a circular or intertwining double
helix. A common term associate to this would be
plasmids and topoisomerases.
- Some consider the complex of
deoxyribonucleic acids with histones as the LEVELS OF ORGANIZATION
quaternary level of organization. 1. Primary structure - consists of a single
polynucleotide chain of nucleotides.
PROPERTIES OF THE DOUBLE HELIX Denotes the sequence of nucleotides
1. Right-handed (specifically the bases)
2. Antiparallel – arranged in opposite
directions 2. Secondary structure - consists of
3. Double helix is stabilized by base pair interactions within the single strand of an
hydrogen bonds and stacking aromatic RNA. This includes hairpin turns, bulges,
bases (VDW) and loops.
Be informed that bases do not hydrogen Base pairs can only happen
bond randomly. They have specificities. intramolecularly, because RNA is always
Purine HBs with Pyrimidine single stranded.
TWO PROTEINS
1. The first enzyme (holoenzyme) is
important as it does most of the work in the
transcription process, spanning from 2. Rho-independent - uses the strong
initiation up to the end of the elongation. interactions between the base sequences in
2. The rho factor participates in one of the the single strand RNA sequence being
two ways to terminate the transcription created.
process. - folding into a hairpin loop results from a
stronger interaction usually in a palindrome
PART 1: INITIATION sequence, forcing the core enzyme out
The initiation starts by recognition of the without interference from the rho-factor.
origin. The holoenzyme does this by
observing two areas from the transcription
start site called promoter sites: -10
(pribnow box) and -35 area. This is a
consensus sequence among organisms.
PART 4: POST-TRANSCRIPTION
The holoenzyme starts the recognition Post-transcription consists of processes that
by closing on to the helix, then RNA undergo before being brought out for
unwinding it when the promoters have their specific purpose. In other words, RNA
been detected. The strands are not has to become mature.
copied at the same time; only one is
allowed. That used strand is called the Post-transcription depends on the RNA
template/antisense. The non-used or being produced because different RNA have
non-template strand is the sense different function, and consequently their
strand. structure. The most tackled is that of
The end of recognition practically ends mRNA.
initiation.
The sequence of mRNA post-transcription The ribosome is the site of protein
(RNA processing) is as follows: synthesis.
1. Capping at 5'-end and methylation It is located in the cytoplasm.
Approx. 66% RNA and 44% protein.
A ribosome has two subunits, one is
heavier and one is lighter.
In prokaryotes, it is called 70S ribosome
with 50S heavy and 30S light subunits.
In eukaryotes, it is called 80S ribosome
with 60S heavy and 40S light subunits.
3. Splicing
THE GENE
A part of the gene is equivalent to a single
amino acid. This part is a triplet of gene
nucleotides called a codon.
The tRNA which translates the gene reads
Introns are removed, and exons are fused. the correct codon by a complementary
anticodon.
- Participation of the small nuclear RNA As more codons are being read, more
(snRNA) amino acids are being connected together
- No snRNA, no stable mRNA to travel by tRNAs to form the primary structure of
the protein.
RNA is the end product of transcription. The reading of the gene proceeds from
the gene’s 5’-end to its 3’-end, and the
PHASE 3: TRANSLATION translated protein is produced from the N
- the language of nucleic acids is translated terminal to the C terminal.
into the language of proteins.
- mRNA directed protein synthesis Properties of gene translation:
- is the process by which the mature mRNA 1. Triplet and nonambiguous rule. A
codes for the polymerization of proteins in pattern of three nucleotides code for only
the ribosome. one amino acid.
2. Degenerate. An amino acid may have
• The gene (mRNA) produced by transcription more than one codon coding for it.
serves as the basis for the protein that will 3. Non-overlapping. Nucleotides for a
be produced. codon cannot be read again on the
• The sequence of the gene will dictate the succeeding codon.
sequence of the protein amino acids. 4. No punctuation. The nucleotide next to
• The nucleic acid sequence of the gene is the last nucleotide of a codon will
read by the corresponding tRNAs which automatically be the first nucleotide of the
creates the sequence of the amino acids for next codon.
protein synthesis. 5. Almost universal. Most species have the
common codon-amino acid correlation.
Translation occurs within the ribosomes,
and involves the following components: tRNA
1. Ribosomes tRNA reads the mRNA sequence while
2. Gene (mRNA) processing the amino acid sequence.
3. Activated tRNA tRNA further aids translation efficiency
4. Enzymes and accuracy by considering wrong
5. Guanosine and adenosine triphosphates codon sequences thru wobble bases.
THE RIBOSOME
A regions by the help of IF3 to form the 30S
initiation complex in prokaryotes
Prokaryotes – Shine-Dalgarno
Sequence – N-formylmethionine
Eukaryotes – AUG - methionine
3. The 50S subunit is binded with tRNA by
the guidance of IF2. The resulting complex
is called the 50S initiation complex.
4. The initiation complexes combine. The
resulting complex is called the 70S initiation
complex.
5. The tRNA for the first codon goes to the
P region and hydrogen bonds using the
respective anticodon
Usage of GTP
PART 2: INITIATION
1. The ribosomal subunits are separated
together by Initiation Factor (IF) 1.
2. mRNA combine with the lighter subunit
and place the first two codons to the P and
Modification
• The primary structure itself may be
enzymatically modified to its native
PART 3: TERMINATION form by the following ways:
1. Release factors recognize stop codons 1. The N-terminal amino acid is
2. A release factor goes to the A region trimmed away
3. The ester bond between the P tRNA and 2. Amino acid residues are
attached amino acid is cut off. modified to become other
residues (ex. Hydroxylation)
Synthesis stops and the initiation • The native protein may be modified to
complexes disassemble. its functional form by addition of
prosthetic groups or bonding with
other biomolecules.
Degradation
• Mutations in the gene may go through
the proofreading mechanism of tRNA
and create wrong sequences in
The protein (in primary level of proteins.
organization) is the end product of • Wrong proteins can be degraded by
translation and finally of the Central proteases/proteasomes.
Dogma. • Degradation is a well-controlled
process. They usually need molecular
PART 4: POST-TRANSLATIONAL PROCESSES signals that trigger these enzymes
These products of translation may undergo
• Ubiquitin-proteasome pathway –
several processes:
common pathway using ubiquitin as a
1. Folding towards the native form
signal for protease activation towards
2. Modification towards functional form
the protein it is binded to
3. Degradation
• Ubiquitin is a 76 amino acid
4. Protein targeting
polypeptide
FOLDING • Ubiquitin binds with a very positively
charged N-terminal of a non-functional
Most proteins are not yet functional
protein by help of E3 (ubiquitin ligase)
after translation because they need to
• E1 – ubiquitin-activating enzyme
go from primary level of organization to
• E2 – ubiquitin-conjugating enzyme
higher levels.
• Acidic N-terminal residues – addition
Most can self-fold into their native
of arginine by Arg-tRNA, consequently
form, but Some proteins cannot fold
attracting ubiquitin attack through
into their native form unless helped by
ubiquitin ligase
chaperones.
Protein Targeting • Golgi apparatus - final transport
• Proteins that are mature and fully of all proteins for delivery.
functional must be delivered to the
right parts of the cell.
• Proteins may be delivered toward the
cytoplasm or through membrane-
bound organelles.
• Amino acid sequences within the
protein (signal sequences) trigger
transfer by the proper organelles.
• Endoplasmic reticulum – site where
ribosomes produce proteins that have
to go through membranes, lysosomes
or export.
- further modification of protein by removal
of nonfunctional signal sequences or
attachment of other biomolecules
PART 1: MUTATION
Mutation – are changes in the base
sequence of DNA.
- organisms that induce mutation are called
mutagens or genotoxins.
3. Waxes - the backbone is a long chain Other lipids that we would give even less
monohydroxy alcohol (in contrast to importance in general biochemistry are pigments
glycerol and sphingolipid, which has which reflect (and thus, show us) colors of many
multiple hydroxyl groups). Their linear living creatures, and terpenes (a wide array of lipids
structure powerfully increases their non- with wide array of functions originating from the
polarity (why waxes are used as water building unit isoprene; cholesterol is one terpenoid
repellants, in example for fruits) compound).
Monosaccharide Classification
Monosaccharides have the general formula CnH2nOn
(and take note that only monosaccharides can have
such formula). Monosaccharide nomenclature An aldose and a ketose.
consists of two parts: the prefix and the suffix. The
prefix is based on the number of carbons in the Thus, the complete nomenclature of a
sugar as well as functional group present, and the monosaccharide consists of its functional group,
general carbohydrate suffix -ose. carbon length prefix, and –ose.
a) b)
Table of a) aldoses and b) ketoses, respectively.
Another essential thing to note In discussing carbohydrates is that we use two structural formulas to draw them.
The first one also used in the aldoses/ketoses chart above is called the Fischer Projection Formula, which is used
for the linear form of carbohydrates.
Fischer projection of glucose.
The second structural formula is the Haworth Projection Formula, which is used for the cyclic form of
carbohydrates.
2. Cyclic – in aqueous environment, carbohydrates turn into cyclic compounds, using an oxygen bridge to form
usually either a five-membered furan-derived compound (a furanose) or a six-membered pyran-derived
compound (a pyranose). Be noted that the #C in a carbohydrate does not dictate the members in its cyclic form.
(ex. Fructose has 6 carbons but its stable cyclic form is a furanose, a 5 carbon cyclic compound).
The carbon with the functional group turns chiral and thus will have another group of isomers, specifically
anomers (alpha, beta). The anomeric carbon can also be defined either as 1) the carbonyl carbon of the linear
carbohydrate or 2) the carbon of the cyclic form that is bonded to two oxygens.
Conformational isomers of carbohydrates are simply shape-based isomers of the exactly same cyclic
carbohydrate. The envelope configuration exists for pentoses, while the chair and boat configurations exist for
hexoses.
A carboxylic acid product of sugar oxidation can cyclicize, this time, doing esterification by S NAcyl (same concept as
hemiacetal formation, but this time with carboxyl instead of keto or formyl group). The product cyclic ester is also
called a lactone. However, the requirement for oxidation of cyclics is the presence of a free anomeric carbon.
3. Acetal/Ketal Formation – reacting a hydroxyl compound with a cyclic sugar (hemiacetal/hemiketal), thus
forming an acetal/ketal which is now called a glycoside.
Glycosides – compounds wherein there is addition of an alcohol to a free anomeric carbon; an acetal/ketal
• Energy investment phase – Glucose is broken into two molecules of G3P (Glyceraldehyde-3-phosphate).
It consists of the first 5 steps of glycolysis.
• Energy payoff phase – G3P molecules are turned into pyruvate. It consists of the last 5 steps of
glycolysis.
A critical stage after glycolysis is the transfer of NADH from the cytoplasm into the electron transport chain to
produce the promised number of ATPs from it. With its size, NADH must be supported by a shuttle to enter the
mitochondrial membrane, where ETC is located. Two shuttles exist: Malate-aspartate (MA) shuttle, and Glycerol-
phosphate (GP) shuttle. MA Shuttle requires no energy, while GP shuttle requires one mole of ATP per mole of
NADH. Thus, variations in the total number of ATP after the ETC result from this shuttle.
Glycogen enters a slightly different catabolic pathway (glycogenolysis), being catabolized into glucose-1-
phosphate by phosphorylase enzyme, then isomerized into glucose-6-phosphate, both without using energy. G3P
then enters the usual glycolytic pathway. The ATP consumption for phosphorylation of glucose to glucose-6-
phosphate (step 1) is then conserved.
Hexokinase targets hexoses in general, not just glucose, and thus will produce the same energy output with
hexoses other than glucose.
After glycolysis, pyruvic acid enters two pathways: an oxygen-including Tricarboxylic Acid Cycle or anaerobic
respiration. Obligate anaerobes and facultative aerobes engage in a form of respiration that is much unlike that
of aerobic respiration. In addition, anaerobic respiration usually discussed in books are very simple compared to
their aerobic counterpart. They always start with glycolysis to produce the pyruvic acid, and continue to the
following steps.
The Ethanol fermentation process utilizes Pyruvate, first decarboxylating it to form Ethanal (Acetaldehyde),
then finally reducing it through NADH to produce Ethyl Alcohol.
The Lactate fermentation directly reduces pyruvate through NADH to produce Lactate or Lactic acid.
It must be noted that fermentation happens only in the absence of oxygen. In its presence, pyruvate proceeds to
the Tricarboxylic acid cycle.
One important detail of the cycle is that it can accommodate only one acetyl-CoA at a time. Only after
the complete transformation to oxaloacetate can another acetyl-CoA enter the cycle. The process is not
simultaneous.
PDH Complex
Pyruvate acetyl-CoA
NAD ->NADH
O
Note: RCSCoA = fatty acyl -CoA
The special factor in the catabolism of fatty acids is that for a single acid, the cycle presented will repeat several
times, until finally all of the carbon chain is turned into acetyl-CoA. Thus, the cycle will equate to the number of
acetyl-CoA products minus one.
Although the fatty acid metabolism produces a much larger amount of acetyl-CoA that can translate to a large bulk
of ATP, the fact that the TCA cycle is non-simultaneous may just promote unproductive build-up of unused acetyl-
CoA. Moreover, acetyl-CoA is a precursor for cholesterol and ketone bodies, both producing unfavorable effects
on the body.
Appendix: Accounting Section
To count number of ATPs from a reactant to product, start adding ATPs produced per step from the table immediately below the reactant row.
Pathway, Product ATPs produced per ATPs produced per Net ATPs produced
reaction # step (double) step (singular) (from hexose or fatty
MA Shuttle/ GP MA Shuttle/ GP Shuttle acid)
Shuttle MA Shuttle/ GP Shuttle
G1 Glucose-6-phosphate -1 -1 -1
G3 Fructose-1,6-bisphosphate -1 -1 -2
G6 1,3-bisphosphoglycerate +5/ +3 + 2.5/ + 1.5 +3/ +1
G7 3-phosphoglycerate +2 +1 + 5/ 3
G10 Pyruvic acid (end of glycolysis) +2 +1 + 7/ 5 (entire glycolysis)
PTCA Acetyl-CoA +5 + 2.5 + 12/ 10
TCA3 Alpha-Ketoglutarate +5 + 2.5 + 17/ 15
TCA4 Succinyl-CoA +5 + 2.5 + 22/20
TCA5 Succinate +2 +1 + 24/ 22
TCA6 Fumarate +3 + 1.5 + 27/ 25
TCA8 Oxaloacetate (end of TCA) +5 + 2.5 + 32/ 30 overall
For entire TCA:
+20 / hexose
+10 / acetyl-CoA
PBOC Acyl-CoA -2 for each fatty acid
βOC1 Enoyl-CoA 1.5 x #C/2 1.5 x #cycles
#C = carbons in acid + (10 x number of acetyl
CoA produced)
- 2 (for pre-βO cycle)
βOC2 1, β -hydroxyacyl + 2.5 multiplied by 4 x #cycles
dehydrogenase #C/2 (- 2) + (10 x number of acetyl
#C = carbons in acid CoA produced)
- 2 (for pre-βO cycle)
NOTE: The double ATP column was meant to reflect the amount of ATP produced per step for EVERY hexose (since
each hexose is split into TWO after the first half of glycolysis).
References:
1. Campbell, M., Farell, S. (2012). Biochemistry 7th Edition. Belmont, CA: Thomson Brooks/Cole.
2. Mauseth, J.D. (2009). Botany: An Introduction to Plant Biology Fourth Edition. Sudbury, MA: Jones and
Bartlett Publishers, Inc.
3. Nelson, D., Cox, M. (2008). Lehninger principles of Biochemistry Fifth Edition. New York: W.H. Freeman and
Company.
4. Boyer, R. (2006). Concepts in Biochemistry 3rd Edition. New York: John Wiley & Sons.