COMPREHENSIVE

HANDOUT
FOR

BIOCHEMISTRY
Prepared by:
Ser Loisse R. Mortel
with major contributions from Justin Redd B. Mapalo

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REVIEW PROPER 1: AMINO ACIDS

PART I: INTRODUCTION AND CHARACTERISTICS
In the structural sense, amino acids are amino-group
containing carboxylic acids.

carboxyl groups. Thus, they are chiral. Based on

absolute stereochemistry:
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.
However, we do not consider all amino acids as
important for discussion. In biochemistry, we only
use 20: only those which are essential for the
creation of proteins. They are specifically called alpha
amino acids, because the amino and carboxyl groups
lie on the same (alpha) carbon.

The general structure of all 20 amino acids.

.
Generally, an (alpha) amino acid is attached to
hydrogen and a R group in addition to the amino and

The chirality of the tetrahedral alpha amino acid.

Glycine is the only achiral alpha amino acid.

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.

Even with a positive and negative charge, the zwitterionic form of

an amino acid is electrically neutral.

PART II: THE 20 AMINO ACIDS

An amino acid may be distinguished from all others by their R groups.
They can be grouped together according to what charge their R group possesses in the neutral pH (neutral, basic,
acidic). Sometimes they are grouped based on the structural similarities among their R groups (aromatic, aliphatic,
amidic, etc.)

NEUTRAL AMINO ACIDS

Further classified in to non-polar and polar. The R
groups of polar amino acids only have a tendency to
be charged in the neutral pH.

Non-polar amino acids are listed in the sequence

aliphatic (G to M), aromatic (F, W) and finally the only
secondary amino acid (P); polar amino acids are listed
in the sequence amides (N, Q), alcohols (S, T), thiol
(C), and phenol (Y).
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NON-POLAR AMINO ACIDS

Amino Acid
Structure
Glycine (G, gly)
R: Hydrogen

Asparagine (N, asn)

R: Carbamoyl (amide) +
methyl

Alanine (A, ala)

R: Methyl

Glutamine (Q, gln)

R: Carbamoyl + ethyl

Valine (V, val)

R: Isopropyl

Leucine (L, leu)

R: Isobutyl

Isoleucine (I, ile)

R: sec-Butyl

Methionine (M, met)

R: Methylthioethyl

Serine (S, ser)

R: Hydroxymethyl (a
primary alcohol group)

Threonine (T, thr)

R: 1-hydroxyethyl (a
secondary alcohol group)

Cysteine (C, cys)

R: Thiomethyl
C forms a disulfide
linkage when reacted
with another C
molecule, the product
being named cystine.
Tyrosine (Y, tyr)
R: Phenol + methyl (or 4hydroxymethyl)

Phenylalanine (F, phe)

R: Benzyl (phenylmethyl)

CHARGED AMINO ACIDS

Tryptophan (W, trp)
R: Indole ring + methyl

Proline (P, pro)

R: Propyl closing on the
alpha nitrogen to form a
pyrrolidone ring

Further classified in to acidic and basic. The R groups

of acidic amino acids are negative in neutral pH;
those of basic amino acids are positive in neutral pH.
ACIDIC AMINO ACIDS
Amino Acid
Structure
Aspartic Acid (D, asp)
R: Carboxyl + methyl

Glutamic Acid (E, glu)

R: Carboxyl + ethyl

POLAR AMINO ACIDS

Amino Acid
Structure

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BASIC AMINO ACIDS

Amino Acid
Structure
Lysine (K, lys)
R: Aminobutyl

Arginine (R, arg)

R: Guanidopropyl

Histidine (H, his)

R: Imidazole ring +
methyl

Essential and Non-essential Amino Acids: A

Nutritional Classification
In the nutritional standpoint, amino acids have two
main classifications based on whether they can be
spontaneously produced by the body or not.
Non-essential - can be produced by the body without
requiring any additional dietary intake of food, and
therefore the food containing these are not essential
to assure that the body has sufficient amino acid
count.
Essential - can not be produced spontaneously by the
body, and food that contain these are required for
intake because lack of them will cause amino acid
deficiency in the body. There are ten essential amino
acids, given a common acronym PVT TIM HALL

One letter
Amino acid
abbreviation
P
P henylalanine
V
V aline
T
T hreonine
W
T ryptophan
I
I soleucine
M
M ethionine
H
H istidine
A
A rginine
L
L eucine
K
L ysine
The ten essential amino acids.

PART 3: TITRATIONS AND THE ISOELECTRIC PH

Titratable group any part of the amino acid that can be protonated (or deprotonated) at a given pH.
Recall that protonation happens when there are many protons around AKA acidic pH.
Isoelectric pH (abbreviated IpH or PI) - pH at which the amino acid possesses no NET charge (aka their zwitterionic
form)
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).
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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 peptide 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 ( ) bond between the alpha carbon and the carboxyl carbon
Phi () bond between the alpha carbon and the amino nitrogen
Omega () - AKA peptide bond

The bonds existing within peptides.

PART 5: NAMING POLYPEPTIDES
Peptides are classified according to the number of amino acid residues they possess (dipeptide if two AA,
tetrapeptide if 4 AA). A polypeptide refers to a chain of amino acids. An oligopeptide refers to a chain of 30-50
amino acid residues. A protein refers to a chain containing more than 50 residues.
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.
PART 6: TITRATING POLYPEPTIDES
Polypeptides, like amino acids, can be titrated as well. Most amino acids have only two titratable groups, the
amino and carboxyl groups. But some amino acids R groups are titratable as well ( ONLY for D, E, H, C, Y, K, and R).
When the pH goes beyond the pKa of a titratable group, it becomes deprotonated.
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.
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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.

REVIEW PROPER 2: PROTEIN STRUCTURE AND CHARACTERIZATION

PART I: INTRODUCTION
Proteins serve different biological functions.
Examples of which are: catalytic proteins or
enzymes; regulatory proteins like the hormones
insulin and glucagon; transport proteins like
myoglobin and hemoglobin; structural proteins like
collagen and elastin; and defense proteins known
as the immunoglobulins.
Before we enumerate several useful proteins, its
better to review first their structure.
PART 2: LEVELS OF ORGANIZATION OF PROTEINS
1. PRIMARY LEVEL OF ORGANIZATION
The order/sequence of amino acids of the
peptide chain and the number of amino
acids present
In other words, the linking of the amino
acids by peptide bonds already makes the
primary level
2. SECONDARY LEVEL OF ORGANIZATION
Refers to the hydrogen-bonded arrangement
of the polypeptide chain.
A) -helix
A polypeptide chain forms hydrogen
bonds with itself (intrapolypeptidal Hbonding), forming a helix
Helix may be right-handed or lefthanded

The alpha helix.

Pitch the vertical distance in one turn
(5.4 )
There are 3.6 residues per turn (13
atoms)
Rise distance between amino acids
(rise = pitch / 3.6)
Proline cannot be found in an -helix
because its cyclic nature and absence of
hydrogen bonding ability causes a bend
that restricts rotation.
The proximity of side chains with similar
charges causes electrostatic repulsion
therefore causing a strain on the helix.
The proximity of bulky side chains to
each other causes steric crowding
causing straining of the helix.

B) -pleated Sheet

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D. - complexation interaction of
aromatic molecules with each other
(stacking)
4. QUATERNARY LEVEL OF ORGANIZATION
Same interactions occur but between two
or more polypeptide chains.

Parallel and anti-parallel sheets.

Hydrogen bonding between one or two
peptide chains (interpolypeptidal Hbonding)
May be parallel or anti-parallel
1. Parallel - the C-terminals of the two
chains are going the same direction
2. Antiparallel - the C-terminals of the
two chains are going different
directions
-bulge - localized disruptions of the
polypeptide
chain;
non-repetitive,
irregular motifs in the anti-parallel
position
Glycine and Proline cause reverse turns
that change the direction of the
polypeptide chain.

Supersecondary Structures
Combinations of -helices and -pleated
sheets (ex. , -hairpin, -meander,
Greek Key, -barrell etc.)
Domains independently folded
structures
Motifs repeated supersecondary
structures

In simplified form, helices are drawn as they are, while

pleated sheets are drawn as arrows. Domains are the
lines connecting helices o r sheets

3. TERTIARY LEVEL OF ORGANIZATION

3-D arrangement of all the atoms in the
polypeptide chain with the side chains,
determined by covalent and non-covalent
interactions within the chain such as:
A. Electrostatic attractions and hydrogen
bonding between R groups
B. Disulfide linkages
C. Metal-ion coordination

PART 3: PROTEIN CONFORMATION AND

DENATURATION
1. Fibrous Proteins rod-like; insoluble because
of high molecular weights; unaffected by pH
and temperature
2. Globular Proteins spherical or ellipsoid;
somewhat soluble because of the exposed
polar groups and unexposed, insoluble inner
core; affected by pH and temperature (ex.
enzymes)
Proteins, in nature, have a native conformation.
When they take on this conformation, they are
biologically ACTIVE.
Chaperones - assist in the correct folding of
proteins (ex. Hsp70).
Ways of disrupting protein organization
Degrading protein structure may disable them of
the activities they perform in native conformation.
However, this can be used as advantage for
practical purposes (ex. egg white becomes more
edible and easier to digest as in cooked form, hair is
easier to style upon heating) and analytical
purposes.
1) Denaturation - process by which a protein loses
its natural conformation by disruption of its
structural order be it quaternary, tertiary, or
secondary, but never primary.
Denaturation may be reversible or irreversible.
Denaturing agents include:
a) Heat - disrupt hydrophobic interactions
b) Detergents such as sodium dodecyl sulfate disrupt hydrophobic interactions as well
c) Urea or guanidine - disrupt hydrogen
bonding
d) Mercaptoethanol - reduces disulfide bonds.
e) Large changes in pH alter electrostatic
attractions between side chains especially with
the acidic and basic amino acids.
2) Hydrolysis destruction of primary structure
through hydrolysis of peptide bonds.

PART 4: PROTEINS IN VERTEBRATES

While it is now known that thousands and
thousands of different proteins exist in living
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systems such as our human bodies, those below

comprise very large percentages of our bodily
biochemical composition:
1.

3.

Collagen
Structural protein; filamentous
Left-handed triple helix containing 3.3
residues per turn
Contains 800 residues
Distinctive peptide chains containing a
proline or hydroxyproline residue bound
between a glycine residue and another
amino acid (x pro gly or x hyp gly)
Proline is converted into hyroxyproline by
an enzyme known as hydroxylase which
is catalyzed by Vitamin C.

Heme. Each 5-membered ring with

nitrogen at the four corners is called a
pyrrole ring.

Synthesis of Collagen:
i. Translation into
preprocollagen.
ii. Hydroxylation: formation of
hydroxyproline and
hyroxylysine
iii. Release from ribosomes
and addition of
endoplasmic reticulum
sugars like galactose and
glucose at hydroxylysine.
iv. Formation of the triple
helix and folding of
globular domains;
transformation into
procollagen
v. Secretion from cell
vi. Removal of N and C
terminal domains;
transformation into
tropocollagen
vii. Deamination of lysine to
form allysine
viii. Cross-linkage of allysine
with a Lysine residue, or
another allysine residue to
form collagen.

2.

Elastin

Structural protein; filamentous

Found in ligaments and arterial blood
vessels
Non-repetitive coil
Rich in G, A, V, P, but not in
hydroxyproline and hydroxylysine
Four lysine residues (or four allysine
residues) (or two lysine and two allysine)
residues condense to form the desmosine
or isodesmosine crosslink giving elastin
its rubbery characteristic

Hemoglobin
Transport protein; globular
Complex of heme, an iron containing
prosthetic group, and globin, the protein
portion which prevents the oxidation of
Fe 2+ into Fe3+

Tetramer made of four different protein

subunits each wrapped around a heme
molecule; It has two alpha chains and two
beta chains
Types of Hemoglobin:
i. Hb + O2 Oxyhemoglobin
ii. Hb O2 Deoxyhemoglobin
iii. Hb + CO2
Carbaminohemoglobin
iv. Hb + CO Carboxyhemoglobin
v. Hb + Fe 3+
Ferrihemoglobin/Methemoglobin
vi. Hb + Fe 2+ Ferrohemoglobin
Heme is made of four pyrrole rings that
form one porphyrin ring. It is also known
as an iron protoporphyrin. Each pyrrole
ring forms the first four coordination sites
of heme.
Histidine F8, or the proximal histidine,
binds the iron strongly to the heme. This
forms the fifth coordination site under
the heme molecule.
Histidine E7 distal histidine, forms the
sixth coordination site, allows the
hydrogen bonding of oxygen or carbon
monoxide to the molecule.
Hemoglobins oxygen binding curve is
sigmoidal because it exhibits positive
cooperation. This means, the binding of
one O2 molecule to one coordination site
enhances the attachment of O 2 to the
other sites.
Hemoglobin is an allosteric protein. That
means, it is affected by H+, CO2, and 2,3bisphosphoglycerate which decreases O2
affinity to hemoglobin.
HbA is the normal hemoglobin which
has six glutamic acid residues on its beta
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4.

chain. HbS - hemoglobin of patients with

sickle cell anemia.
In sickle cell anemia, valine replaces
glutamic acid. The ionic interactions of
glutamic
acid
are
replaced by
hydrophoblic interactions of valine. The
cells clump because of this and oxygen
flow gets blocked.

7.

Myoglobin
Transport protein; globular
Found mainly in the muscles
Composed of only one protein chain with
a heme prosthetic group in the center
Myoglobins oxygen binding curve is
hyperbolic instead of sigmoidal

Immunoglobulins

Comparisons in structure and oxygen binding curves

of myoglobin and hemoglobin.

5.

6.

Also known as antibodies

Defense proteins
Secreted by B-lymphocytes
Composed of two light chains and two
heavy chains with constant and variable
regions (ex. V H 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)

PART VII: PROTEIN PURIFICATION

Before we can characterize or describe proteins,
experimental procedures first require us to assure
that the sample we are getting is the pure protein.
Purification techniques below isolate proteins
based on the following properties they possess:
1.

SOLUBILITY/POLARITY
a. Isoelectric Precipitation adjusting the
pH of the solution until the protein
reaches its IpH and becomes insoluble
b. Salting Out removing water from
proteins by adding an excess amount of a
salt; makes the protein less soluble
(salting in increases the solubility of
proteins in water by adding a sufficient
amount of a salt)
c. Normal and Reversed Phase
Chromatography protein separation
based on affinities with the mobile or
stationary phases; in normal phase
chromatography, the polar proteins are
the last to be eluted
d. High Performance Liquid
Chromatography (HPLC) uses a column
pre-packed with the stationary phase and
is pressurized

2.

MOLECULAR SIZE/WEIGHT
a. Dialysis movement of particles through
a semi-permeable membrane; large MW
proteins will remain inside the dialysis bag
b. Ultrafiltration filtration using a vacuum
c. Ultracentrifugation centrifugating a
solution at various speeds will separate its

Insulin
Regulatory protein/ hormone
Produced from the -cells of the Islets of
Langerhans
Composed of two polypeptide chains,
containing 51 amino acid residues, linked
together
by
intermolecular
and
intramolecular disulfide linkages
Also known as hypoglycemic hormone
Breaks down glucose in a process known
as glycolysis to synthesize pyruvate then
ATP
Converts glucose into glycogen, to be
stored in the liver, through a process
known as glycogenesis
Aids in fatty acid synthesis and protein
synthesis
Glucagon
Also a regulatory protein/hormone
Brings about glycogenolysis
Produced from the -cells of the Islets of
Langerhans
Single polypeptide chain composed of 29
amino acid residues

Released when blood glucose levels are

below normal; hyperglycemic hormone

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d.

e.

molecular components; high MW proteins

will settle at a high speed, while low MW
proteins need a higher speed to settle at
the bottom
Gel Filtration Chromatography (or Size
Exclusion or Molecular Sieve) uses
porous gel beads such as agarose
(Sepharose) or dextran (Sephadex) which
trap smaller molecules leaving the larger
molecules to be eluted first
SDS-PAGE (Sodium Dodecyl Sulfate
Polyacrylamide Gel Electrophoresis)
utilizes a detergent, SDS, which imparts a
negative charge to the proteins; smaller
protein molecules treated with the
detergent move faster towards the
positively charged anode

3.

CHARGE
a. Electrophoresis separates the proteins
(or amino acids) based on their attraction
towards the negatively charged cathode
or the positively charged anode at a
specific pH
b. Ion Exchange Chromatography uses
cation or anion exchangers (resins); when
a cation exchanger is used, positively
charged amino acids are eluted last

4.

BINDING AFFINITY
a. Affinity Chromatography a ligand acts
as the stationary phase to entrap the
protein of interest
b. Precipitation by Antibodies

PART VIII: PROTEIN CHARACTERIZATION

TECHNIQUES
Proteins may be characterized by the types of amino
acids they possess. Complete hydrolysis, using strong
acids or bases, cleaves all peptide bonds leaving
individual amino acids. Incomplete hydrolysis
involves reagents or enzymes which are more
specific and cleave peptide bonds at certain places
only.
1. Edman Reagent phenyl isothiocyanate
(PTH) reagent; cleaves the carboxyl side of
the N-terminal amino acid; the products are
the N-terminal amino acid attached to
phenylthiohydantoin (PTH), and the
remaining peptide
Ex. STC + Edman Reagent (PTH+S) + T-C
2. Cyanogen bromide cleaves the carboxyl
side of methionine
Ex. BIOCHEMISTRY + Cyanogen Bromide
BIOCHEM + ISTRY
3. Proteinases/Proteases/Proteolytic Enzymes
a. Exopeptidases cleave off terminal
amino acids

i. Aminopeptidase cleaves off the Nterminal amino acid

ii. Carboxypeptidase cleaves off the Cterminal amino acid
b. Endopeptidases cleave peptide chains
from the inside
i. Trypsin cleave off the carboxyl side
of basic amino acids lysine and
arginine
ii. Chymotrypsin cleave off the
carboxyl side of aromatic amino acids
phenylalanine,
tyrosine,
and
tryptophan
Ex. Give the correct sequence of a nonapeptide
containing arg, ser, asp, gly, trp, met, ala, phe,
cys.
Edman Reagent: G + PTH
Cyanogen bromide: pentapeptide: M, F, D, S, G
tetrapeptide: W, C, R, A
Aminopeptidase: G
Carboxypeptidase: A
Trypsin: octapeptide: D, M, W, C, G, S, R, F
single alanine residue
Chymotrypsin: tripeptide: F, G, S
tripeptide: M, W, D
tripeptide: C-R-A
Sequence: _ _ _ _ _ _ _ _ _
1. We start by placing G and A at the N and Cterminals respectively based on the
reactions with the Edman reagent,
aminopeptidase and carboxypeptidase.
G ___ __ _ _A
2. The reaction with chymotrypsin yielded a
tripeptide
C-R-A.
G ___ __ CRA
3. The reaction with chymotrypsin yielded two
other tripeptides containing F, G, S and M,
W, D respectively. We know that G is the Nterminal AA so the tripeptide containing M,
W, D must be somewhere in the middle. We
also know that chymotrypsin cleaves the
carboxyl side of W. We place it beside C.
G ___ _W CRA
4. The reaction with cyanogen bromide yielded
two peptide chains. We know that cyanogen
bromide cleaves at the carboxyl side of M.
We therefore place M beside W.
G ___ MW CRA
5. The reaction with chymotrypsin shows that
the amino acids M, W, and D come as one
tripeptide. We therefore place D beside M.
G __DM W CRA
6. Lastly, we know that chymotrypsin cleaves
the carboxyl side of F. We therefore place
the last two amino acids at their rightful
positions.
G SFDMW CRA
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REVIEW PROPER 3: ENZYME STRUCTURE AND FUNCTION

PART I: INTRODUCTION
Chemical processes essential to maintain the life of
living systems are not all innately fast enough to
keep up with the needs of the body system. Some
processes that would maintain life or prevent death
would be too slow for their purpose unless their
rates increase. Elementary chemical kinetics tells us
of four factors that influence the rate of a reaction:
1. Temperature transition state theory suggests
that the reactants have to elicit enough energy
(energy of activation) to reach a state wherein
bonds break and new bonds form to create the
products.
2. Concentration of reactants more reactant
molecules increase tendency of colliding with
each other and consequently the total energy
being in a reaction, making the energy of
activation more achievable.
3. Orientation of reactants the electric charges
of the reactants must face each other in a
position where the attractive forces of
opposing charges are at a maximum.
4. Catalyst lowers the total amount of energy
required to reach the transition state without
being used in the reaction.
Enzyme a biological catalyst. They are the most
efficient catalysts ever known.
Note that while an increase of concentration in
reactants may exponentially raise the rate of a
certain reaction, some catalysts are so efficient that
the effect of concentration on reaction rates is
negligible compared to the effect that catalysts do.
PART 2: ENZYME STRUCTURE AND FUNCTION
Most enzymes are proteins. Some enzymes are
powered by nonprotein components which may
be metal ions or additional chemical groups called
the prosthetic groups. The pure protein part of the
enzyme is called the apoenzyme. Most enzymes
are globular.
Structure-Function relationship
In the body, the enzyme molecules have to make
contact with the reactants that the particular
enzyme catalyzes. The assisted reactant is called
the substrate.
Thus, the enzyme can only help the substrates
when they touch each other through reversible
forces of attraction.
Active (or receptor) site - area of the enzyme
where the substrate makes contact.

The resulting system is called the enzyme-substrate

(ES) complex. Upon release of the substrates after
the complex, they must have been turned into
products by the enzyme.
Specificity property of enzyme to accept only a
single or few substrates due to the molecular
geometry of its receptor site (only molecules with a
shape that fits the site can interac)
Some are absolute (accept only one chemical
entity, not even any of its isomers no matter how
similar) while some are not absolute and thus have
group specificity/ selectivity (accept a group of
similarly shaped compounds, usually with different
results per molecule).
The dynamism of proteins in the enzyme has raised
the issue of whether the enzyme moves in the act
of forming the ES complex or not. Two models have
been raised in regard to this:
1. Lock and key model the enzyme is rigid at the
time the substrate arrives to form the ES
complex. This means the substrate must be in
perfect shape complementary to the active
site.
2. Induced-fit model the substrate need not be
in perfect shape complementary to the active
site because the enzyme can alter its
arrangement to fit the substrate better once
the enzyme and substrate get closer to each
other.
The consequence of having enzymes that are
not particular to one specific substrate is that
some very unrelated molecules with similar
shapes can form the ES complex but produce no
products or even block enzyme activity. This is
called inhibition.
Allosteric effect movement of the enzymes 3D
arrangement in response to the formation of the ES
complex. For enzymes with multiple active sites,
this movement may increase the ability of the
enzyme (allosteric activation) or [more often]
decrease the ability of the enzyme (allosteric
inhibition). This can be observed in hemoglobin.
Enzymes may be classified according to the
mechanism of the reactions they catalyze:
1. Oxidoreductase performs oxidation or
reduction reactions on a substrate.
2. Transferase performs transfer of functional
groups.
3. Hydrolases performs hydrolysis.

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4. Lyase performs addition or elimination

reactions.
5. Isomerase

performs
rearrangement
reactions.
6. Ligases performs condensation reactions
along with the expense of energy in the form of
ATP.

turnover numbers mean a more efficient

enzyme.
2. Enzyme given that substrate amount does
not decline, any increase in enzyme will
prevent the saturation point in the entire
mixture of enzymes and substrates. Thus, firstorder kinetics is maintained (linear).

PART 3: ENZYME ACTIVITY KINETICS

The kinetics of the enzymes catalytic action is
dependent on factors that would either alter
proportions of enzyme to the substrate or that
would alter the native conformation of the enzyme
(considering it is a protein):
1. Substrate increasing concentration of
reactants increase collision between molecules,
but only as long as there is space for the
reaction to go through.
At first, the rate of reaction will increase in
equal proportion to the amount of substrate
added (first order kinetics = linear), but when
substrates fill up all enzymes (saturation), the
rate will become constant at its maximum
capacity (maximum velocity, Vmax). At Vmax,
the kinetics is called a zero order kinetics (= flat
line) because the substrate does not anymore
affect the rate regardless of how many it is (no
more free enzymes to accommodate them).
Total graph is hyperbolic (if not under allosteric
influence)

3. Temperature heat is one of the denaturing

agents of proteins. Initial heating activates the
enzymes by increasing collision, but too much
heat denatures the enzymes, leading to a
decline in a quick pace. The temperature at
which the enzyme has the greatest turnover
number is called the optimum temperature.

4. pH upon alteration of pH, the tertiary or

quaternary structures of protein enzymes may
rearrange and inhibit their activity.

Michaelis constant (Km) amount of substrate

that drives the reaction velocity to half of
Vmax.

The pH at which the enzyme has the greatest

turnover number is called the optimum pH.
Any deviation from the optimum pH (either
increase or decrease) will reduce the turnover
at an increasing pace at equal amounts from
the optimum pH down or up the scale. This
produces a bell-shaped curve.

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

SLRM/JRBM | 12

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 Krebs cycle, is inhibited by fluoroacetate, which can lead
to poisoning).
Here, we discuss the different types of enzyme inhibition:
1. Irreversible inhibition a covalent bond forms between the inhibitory substance (we cant call it a substrate)
and an enzyme. The enzyme will forever be removed of its function.
2. Reversible inhibition the bond formed between the inhibitory substance and enzyme can be taken away,
and leave the enzyme active yet again.
a. Competitive inhibition the inhibitor targets the target site of the substrate (E). This means substrates
are blocked. [Only either ES or EI complexes are possible)
b. Noncompetitive inhibition the inhibitor targets another site of the enzyme (E+I is possible). The
substrates are not blocked of their own active sites (E+S is possible), but the ES complex with the inhibitor
(E+S+I) will not produce any desired product. (ES, EI, or ESI complexes are possible)
c. Uncompetitive inhibition the inhibitor targets only to the ES complex (E+S and E+S+I are possible E+I is
not). The substrates are not blocked again, and unless ES complexes exist, the uncompetitive inhibitor will
find no use. Uncompetitive inhibition thus depends on a higher concentration of ES complexes. (Only ES
and ESI complexes are possible)

Different types of inhibition in their Lineweaver-Burk plots (both x and y values of Michaelis-Menten plots reciproca ted). Yintercep t is th e recip rocal of Vmax.
=============================================================================================

REVIEW PROPER 4: PATHWAY AND CHANGES OF NUCLEIC ACIDS

REVIEW SUBPROPER 1: STRUCTURE OF
NUCLEIC ACIDS
PART 1: INTRODUCTION
Nucleic acid are acidic compounds commonly
found in the nucleus of eukaryotic cells.

- biomolecules responsible for the storage,

transfer, and expression of genetic traits.
- more commonly known as two substances,
Ribonucleic acid (RNA) and Deoxyribonucleic
acid (DNA)
SLRM/JRBM | 13

PART 2: STRUCTURE
Nucleic acids consist building blocks called
nucleotides.
Nucleotides
have
three
components:
1. NITROGENOUS BASE
Pyrimidines: Cytosine, Thymine, Uracil
Purines: Adenine, Guanine
2. FIVE-CARBON SUGAR
RNA: D-Ribose; DNA: 2-Deoxy-D-Ribose
3. PHOSPHATE GROUP

Figure . A N- -glycosidic bond is emphasized

in this drawing.
A nucleoside attached to a phosphate group is

the nucleo ide.

Nomenclature for nucleotides
The nomenclature is simpler, because all that
is needed is to add a ____phosphate suffix to
the nucleoside name (1 phosphate
monophosphate; 2 phosphates diphosphate;
3 phosphates triphosphate).
An alternate is using -ylic acid suffix (ex.
Adenosine monophosphate can also be called
adenylic acid).

Figure . Complete structure of a nucleotide.

PART 3: NOMENCLATURE OF NUCLEIC ACIDS
- the bonded product of the nitrogenous base
and five-carbon sugar is called a nucleoside.
- two general classification of nucleosides exist,
depending on the sugar used.
a. Ribonucleosides use ribose
b. Deoxyribonucleosides use deoxyribose

Figure . Nomenclature systems for

nucleosides and nucleotides.
- Nucleotides are the monomeric units of
nucleic acids, joined by linkage of 5 and 3.
- 5 is already one phosphate ester with the
sugar; the 5 to 3 bond is another phosphate
ester (which makes TWO). Thus the bond
between monomers is called the 3-5
phosphodiester bond.

PART 4: BASIC STRUCTURE OF NUCLEIC ACIDS

Simply, the nucleic acid structure is simply a
polymer of many nucleotide units.
Nomenclature for nucleosides
- Ribonucleosides:
For purines: Retain the name of the base, then
drop the ine for -osine

Like proteins, nucleic acids have names for their

two ends: the 3 end and the 5 end.

For pyrimidines: Retain the first prefix and add

idine
- Deoxyribonucleosides are named the same,
the only difference being a deoxy- prefix.
NUCLEOSIDE
The bond between the sugar and the base is a
N- -glycosidic bond.

STABILITY ISSUES
Electronegativity disturbances between adjacent
hydroxyl lone pairs may disrupt the stability of
SLRM/JRBM | 14

the phosphodiester bonds of ribonucleic acids

only.
PART 5: DNA Structure
DNA

nucleic
acid
composed
of
deoxynucleotides.
- primary function is storage of genetic
information.
- present in eukaryotic and prokaryotic cells
alike.
- In eukaryotic cells, DNA are complexed with
basic histones.
LEVEL OF ORGANIZATION
1. Primary structure consists of a single
polynucleotide chain of deoxynucleotides.
- Denotes the sequence of nucleotides
(specifically the bases)
2. Secondary structure the more well known
helix structure of DNA, actually is the hydrogen
bonded complex
of two intertwining
deoxynucleotide strands. This is the more
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
quaternary level of organization.
PROPERTIES OF THE DOUBLE HELIX
1. Right-handed
2. Antiparallel arranged in opposite
directions
3. Double helix is stabilized by base pair
hydrogen bonds and stacking aromatic
bases (VDW)
Be informed that bases do not hydrogen
bond randomly. They have specificities.
Purine HBs with Pyrimidine

1. The sequence of nucleotides give rise to the

uniqueness in every species
2. The secondary structure of the DNA cannot
be used to complete its purpose (expression)
LINKING STRUCTURE TO FUNCTION
If DNA is to be function in the Central Dogma,
it must be read.
DNA is readable only in primary structure.
Double helices must be denatured to produce
the individual and identical DNA strands. They
can be renatured after use in the central
dogma.
- heat
- enzymes
PART 6: RNA STRUCTURE
RNA - nucleic acid composed of ribonucleotides.
- primary function is transfer and expression of
genetic information.
- present in eukaryotic and prokaryotic cells alike.

LEVELS OF ORGANIZATION
1. Primary structure - consists of a single
polynucleotide chain of nucleotides.
Denotes the sequence of nucleotides
(specifically the bases)
2. Secondary structure - consists of
interactions within the single strand of an
RNA. This includes hairpin turns, bulges,
and loops.
Base pairs can only happen
intramolecularly, because RNA is always
single stranded.

BASE PAIRS FOR NUCLEIC ACIDS

Adenosine is to Thymine (DNA)
Adenosine is to Uracil (RNA)
Cytosine is to Guanine (both)
Secondary structures/ Double helices have
had different models, differing only in the
number of bases per turn and the pitch.
Watson and Crick, the discoverers of the
secondary structure proposed the B-DNA
mode.
Others such as A-DNA and Z-DNA are
known in most biochemistry textbooks,
but are said to be inactive.
DNA participates in the first phase of the
Central Dogma of Molecular Biology:
Replication. These are essential for practical
understanding of DNA:

TYPES OF RNA
RNA has varying designations in the Central
Dogma, unlike DNA. We can apply RNA in the
Central Dogma if we understand the different
types along with the introduction of the
Dogma itself:

SLRM/JRBM | 15

1. mRNA is the closest RNA to DNA such that it

comes from DNA. It is the product of
transcription and source for translation.
2. tRNA serves as the adaptor or bridge
between the nitrogenous base language of
nucleic acids and amino acid language of
proteins.

REVIEW SUBPROPER 2: PATHWAY

THE CENTRAL DOGMA OF
MOLECULAR BIOLOGY
Introduction
The central dogma of mol FINISHPLEASE

PHASE 1: REPLICATION
DNA -----------> RNA -----------> Protein

DNA yields itself

DNA-directed DNA synthesis
Semi-conservative each resulting
double strand has one of those
strands replicated and one of those
part of the original.
Consists of three major phases:
Initiation,
Elongation,
and
Termination
Its only components are 1) the DNA,
2) enzymes, and 3) RNA primers

PART 1: INITIATION
An origin of replication is recognized
in the DNA.
A replication bubble will then expose
the two separate individual strands to
enzyme action.

3. snRNA is a requirement for RNA processing

(post-transcription). This is important because
no mRNA, no translation, no protein, no
growth of organism.
4. RNA can actually catalyze reactions. They
are called ribozymes.

This cannot be possible if the parts of the

new strands are now possible, of course the
nucleotides
(strictly
deoxynucleotide
triphosphate)
Mg++ is used to amplify polar
compatibility towards phosphodiester
bonds
Leading strand will need one primer at the
origin and will proceed in a straight manner.
Lagging strands need several primers. In
the backward manner of elongation, lagging
strands form okazaki fragments.

Because DNA is vital for genetic expression,

it must be accurate. Sometimes mismatch
of bases occur, and there must be a
proofreading to correct the mismatch. Only
3-5 nuclease action is able to do this.

REPLICATION IS SPECIFIC PROCEEDING

FROM 5-END TO THE 3-END.
The leading strand follows this sequence,
but the lagging strand goes the opposite,
and replication is slower (lagged) there.

Helicase unwinds to make DNA readable

DNA gyrase compensates the physical
instability by relieving torsional strain.
Single-strand binding proteins (SSB)
compensate for the chemical instability to
possible N-B-glycosidic hydrolysis.
Finally as introduction for elongation,
primase introduces to the leading and
lagging strands the RNA primers.
PART 2: ELONGATION
DNA Polymerase III dominates the next
step, elongating the primer just inserted
into the leading and lagging strands
towards the creation of their new partner
strands.

5-3 exonuclease primer removal and

replacement
3-5 exonuclease proofreading (because
opposite)
PART 3: TERMINATION
Nick translation on the okazaki
fragments to assure uniformity of
deoxynucleotides (that is, removal of
primers), done by the 5-3 nuclease
action of DNA polymerase I.
The removal of primers also include the
phosphodiester formation between the
replacements dNTPs.
DNA ligase to seal the very last
phosphodiester bond.
DNA is the end product of replication.
SLRM/JRBM | 16

PHASE 2: TRANSCRIPTION
the code for translation is understood
before decoding
DNA directed RNA synthesis
is the process by which the DNA serves
its purpose as a storage information
towards production of transfer and
expression material (genes) for the last
phase of the Central Dogma
Consists of four major phases: Initiation,
Elongation, and Termination, and Posttranscription

Transcription is a more performed reaction

in the Central Dogma. Thus it is assumed
that many RNA copies can come from a
single DNA molecule, and that fidelity of
transcription is not as heavy as that of
replication.
- Its only components are 1) the DNA, 2) the
necessary proteins
TWO PROTEINS
1. The first enzyme (holoenzyme) is
important as it does most of the work in the
transcription process, spanning from
initiation up to the end of the elongation.
2. The rho factor participates in one of the
two ways to terminate the transcription
process.
PART 1: INITIATION
The initiation starts by recognition of the
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.

The holoenzyme starts the recognition

by closing on to the helix, then
unwinding it when the promoters have
been detected. The strands are not
copied at the same time; only one is
allowed. That used strand is called the
template/antisense. The non-used or
non-template strand is the sense
strand.
The end of recognition practically ends
initiation.

PART 2: ELONGATION
The elongation starts by the release of
the holoenzyme sub-unit called the
sigma sub-unit. This hints the purpose
of the said sub-unit.
The core enzyme left continues the
whole elongation, using the necessary
nucleotides and Mg++ again to promote
phosphodiester bond formation.
Elongation proceeds in the 5'-3'
direction again.
PART 3: TERMINATION
Termination in transcription, unlike in
replication, can end in two ways:
1. Rho-dependent - using rho-factor to
dissociate the core enzyme from the RNA
sequence being created

2. Rho-independent - uses the strong

interactions between the base sequences in
the single strand RNA sequence being
created.
- folding into a hairpin loop results from a
stronger interaction usually in a palindrome
sequence, forcing the core enzyme out
without interference from the rho-factor.

PART 4: POST-TRANSCRIPTION
Post-transcription consists of processes that
RNA undergo before being brought out for
their specific purpose. In other words, RNA
has to become mature.
Post-transcription depends on the RNA
being produced because different RNA have
different function, and consequently their
structure. The most tackled is that of
mRNA.
SLRM/JRBM | 17

The sequence of mRNA post-transcription

(RNA processing) is as follows:
1. Capping at 5'-end and methylation

The ribosome is the site of protein

synthesis.
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.

2. Poly-adenylation at 3'-end so that

when the RNA goes to cytoplasm, the
attacking enzymes will chop off the adenylyl
tails first, preserving the mRNA
3. Splicing

Introns are removed, and exons are fused.

- Participation of the small nuclear RNA
(snRNA)
- No snRNA, no stable mRNA to travel
RNA is the end product of transcription.

PHASE 3: TRANSLATION
-

the language of nucleic acids is translated

into the language of proteins.
mRNA directed protein synthesis
is the process by which the mature mRNA
codes for the polymerization of proteins in
the ribosome.
The gene (mRNA) produced by transcription
serves as the basis for the protein that will
be produced.
The sequence of the gene will dictate the
sequence of the protein amino acids.
The nucleic acid sequence of the gene is
read by the corresponding tRNAs which
creates the sequence of the amino acids for
protein synthesis.
Translation occurs within the ribosomes,
and involves the following components:
1. Ribosomes
2. Gene (mRNA)
3. Activated tRNA
4. Enzymes
5. Guanosine and adenosine triphosphates

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
the correct codon by a complementary
anticodon.
As more codons are being read, more
amino acids are being connected together
by tRNAs to form the primary structure of
the protein.
The reading of the gene proceeds from
the genes 5-end to its 3-end, and the
translated protein is produced from the N
terminal to the C terminal.
Properties of gene translation:
1. Triplet and nonambiguous rule. A
pattern of three nucleotides code for only
one amino acid.
2. Degenerate. An amino acid may have
more than one codon coding for it.
3. Non-overlapping. Nucleotides for a
codon cannot be read again on the
succeeding codon.
4. No punctuation. The nucleotide next to
the last nucleotide of a codon will
automatically be the first nucleotide of the
next codon.
5. Almost universal. Most species have the
common codon-amino acid correlation.
tRNA
tRNA reads the mRNA sequence while
processing the amino acid sequence.
tRNA further aids translation efficiency
and accuracy by considering wrong
codon sequences thru wobble bases.

THE RIBOSOME
SLRM/JRBM | 18

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

Only methionine and tryptophan are the

two amino acids with only one codon.
PREPREQUISITE: AMINO ACID ACTIVATION
tRNA serves as an adaptor for amino acids
and must be connected to them to be able
to equate them with the correct codon
upon reading.
tRNA with an attached amino acid is
said to be activated.
tRNA is activated by Aminoacyl-tRNA
synthetases.

Aminoacyl tRNA transferase Class I 2

hydroxyl
Aminoacyl tRNA trasnferase Class II 3
hydroxyl
This enzyme is the primary proofreading
mechanism of translation.

PART 2: ELONGATION
1. Elongation factor detects functional
codon
The tRNA for the first codon moves
toward the A region thru the elongation
factor (uses GTP)
2. A peptide bond between the first and
second amino acids held by the first and
second tRNAs is catalyzed by peptidyl
transferase; tRNA on P (the first one) is cut
from its amino acid
At this point, the second tRNA on the A
site holds both amino acids
3. Translocation of second tRNA from A to
P, where the first tRNA goes from P to E to
exit (uses GTP)
4. Arrival of new tRNA on A by elongation
factors and process repeats for many times

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
SLRM/JRBM | 19

PART 3: TERMINATION
1. Release factors recognize stop codons
2. A release factor goes to the A region
3. The ester bond between the P tRNA and
attached amino acid is cut off.
Synthesis stops and the initiation
complexes disassemble.

The protein (in primary level of

organization) is the end product of
translation and finally of the Central
Dogma.
PART 4: POST-TRANSLATIONAL PROCESSES
These products of translation may undergo
several processes:
1. Folding towards the native form
2. Modification towards functional form
3. Degradation
4. Protein targeting
FOLDING
Most proteins are not yet functional
after translation because they need to
go from primary level of organization to
higher levels.
Most can self-fold into their native
form, but Some proteins cannot fold
into their native form unless helped by
chaperones.

Modification
The primary structure itself may be
enzymatically modified to its native
form by the following ways:
1. The N-terminal amino acid is
trimmed away
2. Amino acid residues are
modified to become other
residues
(ex. Hydroxylation)
The native protein may be modified to
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
proteins.
Wrong proteins can be degraded by
proteases/proteasomes.
Degradation is a well-controlled
process. They usually need molecular
signals that trigger these enzymes

Ubiquitin-proteasome pathway
common pathway using ubiquitin as a
signal for protease activation towards
the protein it is binded to
Ubiquitin is a 76 amino acid
polypeptide
Ubiquitin binds with a very positively
charged N-terminal of a non-functional
protein by help of E3 (ubiquitin ligase)
E1 ubiquitin-activating enzyme
E2 ubiquitin-conjugating enzyme
Acidic N-terminal residues addition
of arginine by Arg-tRNA, consequently
attracting ubiquitin attack through
ubiquitin ligase

SLRM/JRBM | 20

Protein Targeting
Proteins that are mature and fully
functional must be delivered to the
right parts of the cell.
Proteins may be delivered toward the
cytoplasm or through membranebound 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

Golgi apparatus - final transport

of all proteins for delivery.

REVIEW SUBPROPER 3: CHANGES

MUTATION AND MANIPULATION
PART 1: MUTATION
Mutation are changes in the base
sequence of DNA.
- organisms that induce mutation are called
mutagens or genotoxins.
Mutation can cause lesions in the cell,
which may be followed by any of the
following:
1. Repair due to anti-mutation
mechanisms
2. Cell death
3. Escaping repair existing and remains
unfixed, ready to spread throughout,
causing any of the ff:
a. Cancer in the somatic cells;
b. Sterility/genetic disorder to
reproductive cells; and
c. Teratogenesis in newborns
Mutations are of two general types:
1. Spontaneous no outside physical or
chemical force, only due to the
chemical/physical stability of the DNA itself
2. Induced with outside physical or
chemical forces.
Some examples covering all classification of
mutagens will be presented.
TYPES OF MUTATIONS
I. Spontaneous
1. Base pair tautomerization

Changes in proton arrangement can cause

different base pairing due to different
hydrogen bonding.
Transition pyr to pyr; pur to pur
Transversion pyr to pur
Nonsense mutation of a base causes
the formation of a stop codon (UAG UGA
UAA)
Missense mutation causes changes in
coded amino acid
Silent mutation does not affect amino
acid (corrected by wobble base)
2. Simple misalignment/ frameshift
mutation change in triplet sequencing
3. Repetitive sequence misalignment
4. Palindomic sequence misalignment
5. Metabolism of quasi palindromes
6. Insertion mutagenesis
II. Induced
1. Physical
a. UV Light cyclobutane ring

b. Ionizing Radiation - dimerization

c. Heat/X-Ray - dipositivity
SLRM/JRBM | 21

2. Chemical
a. Superoxide species apyrimidinic site
b. Alkoxy free radicals - dimerization
c. Amino acid pyrolysates adduct with
guanine
d. Nitrosoamines apurinic site/misreading
e. Polycyclic aromatic hydrocarbons
disrupts the DNA helix
f. Hydrazines creates rigid loop
g. Caffeine may disrupt repair system
h. Bisulfite (HSO-) can cause misreading of
C as U
j. Dibromoethylene dipositivity
k. Aflatoxin

- utilizes plasmids extensively.

Steps in Genetic Engineering:
1. The DNA with the desired gene is isolated
and cut into pieces
2. Identical clones are made
3. Desired gene is isolated
4. Transgene is inserted into organism

PROTECTION AND REPAIR AGAINST

MUTATION
I. Protection Mechanisms
1. Enzymes
a. Superoxide dismutase (SOD)
b. Glutathione peroxidase (Se activated)
c. Glutathione transferase
d. Sulfitase (Mo containing)
e. Demethylase (suicidal)
2. Water - for epoxides
3. Vitamins against free radicals (A,D,E)
4. Riboflavin (Vitamin B2)

Recombinant DNA are usually plasmids

having new fragments of DNA from other
species. The cutting of the DNA and plasmid
is the action of a restriction endonuclease.
Restriction endonuclease can produce
sticky ends or blunt ends upon cutting.
Sticky ends are shown to be more used and
effective.
The process of combining two different
DNA fragments is called transformation.

Selectable markers which is undisturbed

imparts immunity of an organism to a
certain antibacterial agent.

5. Nicotinic acid has a negative charge

6. Mineral cations like Zn, Ca, Fe, Mg, Cu

7. Acetyl CoA
II. Repair Mechanisms
1. Insertase for apurinic sites
2. DNA photolyase for cyclobutane ring
3. Gap filling mechanism error prone
4. Copy editing enzyme 5. Excision repair - can excise base only or
nucleotide
PART 2: GENETIC ENGINEERING
- produces recombinant DNA or a chimeric
transgene, an organism whose genome
comes from more than one gene source.

Polymerase Chain Reaction project that

aims to amplify or duplicate millions of
copies of DNA for several purposes of
several departments.
- Uses a thermocycler, with the following
ingredients:
1. dNTP + Mg++
2. Taq polymerase
3. Buffer and nuclease-free water
4. The DNA itself
Steps in polymerase chain reaction (PCR):
1. Denaturation at around 94 to 96 deg. C
2. Annealing at 55 to 60 deg. C
- duration depends on length of sample
3. Extension at around 72 deg. C

SLRM/JRBM | 22

REVIEW PROPER 5: LIPIDS

PART 1: INTRODUCTION
Lipids are known to many as fats (the solid form) or
oils (the liquid form), but they are not readily easy to
define based on their structure. While the reality is
that the structure of different lipids can be very
diverse, their common denominator lies in that they
are extremely non-polar, and thus insoluble in polar
solvents like water.
Given that lipids have diverse structure, they have
different diverse physiological uses:
- Creation of cell membranes (phospholipids)
- Storage of energy in bulk (triacylglycerols,
steroids)
- Formation of myelin sheaths in brian
(sphingolipids)
- Vitamins (A, D, E, K)
- Control of body processes by hormones
(steroidal hormones)
- Trigger of pain and asthma responses
(prostaglandins and leukotrienes)
PART 2: STRUCTURE AND PROPERTIES
Lipids are too diverse to classify under one scheme.
Lipids can be divided by structure (if the lipid contains
fatty acids or not) or by function (storage, structural,
physiological)
Fatty acid long chain carboxylic acids
- their non-polar hydrocarbon portion
outweighs the polar carboxyl portion
- can be further divided into two: saturated
and unsaturated
Physical Properties:
1. Polarity/Solubility as the carbon length
increases, fatty acids become even less
polar and less soluble in polar solvents such
as water (medium lengths are sufficient
enough to induce immiscibility)
2. Melting and boiling points increasing
carbon length increases their melting and
boiling points.

In natural fatty acids, the double bond

elicits a cis-isomer. This produces a bend in
the linear structure, and reduces area for
forces of attraction. This is why unsaturated

fatty acids have significantly lower boiling

and melting points.
3. Compaction straight chain (saturated)
fatty acids induce a very large area for
attractive forces and the longer chain
saturated fatty acids are solids in room
temperature.
The bends produced by cis unsaturated
fatty acids greatly reduce area for these
forces and thus are almost always found
as liquids in room temperature.
No fatty acid is small enough to have
forces weak enough to make them
appear as gas in room temperature; they
are either only liquid (oils) or solid (fats).
Reactivity:
1. Addition reactions the most significant is
hydrogenation, where in the addition of
hydrogen we remove double bonds of a
fatty acid.
2. Substitution reaction the most significant
is esterification, because it allows the fatty
acids to become the lipids that are most
essential in biological systems (ex.
Triacylglycerols, sphingolipids etc.)
3. Oxidation the most significant is auto
oxidation (rancidification) wherein fatty
acids are oxidized by atmospheric oxygen to
produce acids and aldehydes that give the
unpleasant taste/color and unusual color in
oils exposed to air in a long time.
PART 3: CLASSIFICATION
Storage fatty acid derivatives
1. Triacylglycerols three (tri) fatty acid
groups (acyl) are esterified to a glycerol
molecule. Triacylglycerols, as esters, have
no polar portion and along with cholesteryl
esters are very non-polar lipids found
stored in the body tissues. These are used
when the primary sources of energy
(sugars) are depleted.

Structural fatty acid derivatives

1. Glycerophospholipids here, fatty acids
(lipids) are esterified to glycerol (glycerol)
SLRM/JRBM | 23

wherein ONE carbon of the glycerol is

bonded to PHOSPHATE instead of a fatty
acid, further bonded to a head group X.
These are the most abundant lipids in
molecules. The phosphate group grants
additional
polarity
to
the
glycerophospholipids.

The head groups give the difference between

different glycerophospholipids.
Lecithin contains the head group choline (thus,
they are called phosphatidylcholines) which is
the most abundant phospholipid in membrane.
Other glycerophospholipids are cardiolipins,
cephalins and phosphoinositides.
2. Sphingholipids instead of glycerol, the 18C alcohol sphingosine takes place. One
sphingolipid is called sphingomyelin (head
group being choline) because it is an
abundant lipid in nerve myelin sheaths.
Some sphingolipids have carbohydrates
attached to them (cerebroside = one
carbohydrate, ganglioside = several
carbohydrates).

The other lipids are not fatty acid derivatives, and

usually are those which induce a physiological effect
on the body (hormone-like, etc)
1. Eicosanoids wide array of physiological lipids
that originate from arachidonic acid
a. Leukotrienes eicosanoids that contract
smooth muscle. Targets of some antiasthma
drugs (ex. Montelukast)
b. Thromboxanes promote platelet
aggregation and vasoconstriction.
c. Prostaglandins most known to induce
inflammation, and thus are targets of some
anti-inflammatory drugs (ex. Aspirin)
2. Vitamins vital amines known to assist in
maintenance of many biochemical processes.
Most of these are used as cofactors in enzymes
that catalyze reactions in the body essential for it
to remain living. (ex. Vitamin C assists in collagen
formation, keeping skin tight and stable)
3. Steroids lipids having a polycyclic backbone
(cyclopentanoperhydrophenanthrene).

Some steroids have very important physiological

functions such as cholesterol (stabilizes fluidity in
cell membrane) and cholesterol derived steroid
hormones (ex. Cortisone, progesterone,
testosterone) with powerful endocrine effects.
3. Waxes - the backbone is a long chain
monohydroxy alcohol (in contrast to
glycerol and sphingolipid, which has
multiple hydroxyl groups). Their linear
structure powerfully increases their nonpolarity (why waxes are used as water
repellants, in example for fruits)

Other lipids that we would give even less

importance in general biochemistry are pigments
which reflect (and thus, show us) colors of many
living creatures, and terpenes (a wide array of lipids
with wide array of functions originating from the
building unit isoprene; cholesterol is one terpenoid
compound).

REVIEW PROPER 6: CARBOHYDRATES (EXCLUDING POLYSACCHARIDES)

PART 1: INTRODUCTION
Many know carbohydrates by their name sugars.
Unlike lipids, carbohydrates have a general
identifiable structure, which, even just based on its
name, is obviously composed of mainly carbon,
oxygen, and hydrogen.
Like lipids, the term carbohydrate may refer to a
single identifiable monomer or to a long chain of
monomers unlike proteins and nucleic acids which
have different names for their building blocks. Thus,

we can classify carbohydrates first based on their

length:
1) Monosaccharides the monomeric form of a
carbohydrate; building blocks of larger
carbohydrates
2) Oligosaccharides carbohydrates composed of
two to ten (2-10) monosaccharide units. Thus,
disaccharides fall in this category.

SLRM/JRBM | 24

3) Polysacharides carbohydrates composed of

more than ten monosaccharide units (can reach
up to dozens or hundreds).
Monosaccharide Classification
Monosaccharides have the general formula CnH2nOn
(and take note that only monosaccharides can have
such formula). Monosaccharide nomenclature
consists of two parts: the prefix and the suffix. The
prefix is based on the number of carbons in the
sugar as well as functional group present, and the
general carbohydrate suffix -ose.
Number of carbons
General name
3
Triose
4
Tetrose
5
Pentose
6
Hexose
7
Heptose
Nomenclature for monosaccharides based on
carbon chain length.
Monosaccharide nomenclature is complicated by
the fact that there are two functional groups that
exist in monosaccharides: the formyl and carbonyl
groups. Carbohydrates with formyl groups are
called aldoses and those with the carbonyl group
are called ketoses. Aldoses can spontaneously
isomerizes into their ketose isomers.

a)

An aldose and a ketose.

Thus, the complete nomenclature of a
monosaccharide consists of its functional group,
carbon length prefix, and ose.
# Carbons
With formyl
With carbonyl
3
Aldotriose
Ketotriose
4
Aldotetrose
Ketotetrose
5
Aldopentose
Ketopentose
6
Aldohexose
Ketohexose
6
Aldoheptose
Ketoheptose
Complete nomenclature for monosaccharides.

Glucose, an aldohexdose.

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.

SLRM/JRBM | 25

Fischer projection of glucose.

The second structural formula is the Haworth Projection Formula, which is used for the cyclic form of
carbohydrates.

Haworth projection of D-glucopyranose.

Part 3: CARBOHYDRATE STEREOCHEMISTRY
General formula: CnH2nOn
Carbohydrates have several isomers, resulting in quite a lot of prefixes and suffixes after the base name of the
carbohydrate. The first is the existence of linear and cyclic forms of a single sugar.
# of isomers = 2n where n = number of chiral carbons
I. Linear - usually drawn in the Fischer projection formula.
- Aldoses always have the C1 as formyl carbon, and ketoses have C2 as keto carbon.
- The final carbon is always primary alcohol.
- The following isomers exist:
1. Enantiomers/ Mirror images the being a D- or L- isomer of a sugar is based on its penultimate
carbon. (ex. D-glucose and L-glucose)
2. Epimers (differing in configuration of only one hydroxyl) (ex. Glucose and galactose)
3. Functional isomers configuration of all hydroxyl are the same, and differs only in the functional
group (one is an aldose, the other is a ketose) (ex. Glucose and Fructose)
4. Diastereomers isomers that cannot fall under the first three isomerisms. (ex. Ribose and lyxose)
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).

1) Furan. 2) Pyran. 3) Pyranose formation, based on the hemiacetal/hemiketal A N reaction.

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.

SLRM/JRBM | 26

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.

Part 4: REACTIONS OF CARBOHYDRATES

Carbohydrates undergo the following reactions to yield the corresponding carbohydrate derivatives.
1. Oxidation - of linear monosaccharides
Weak oxidizing (Cupric ions) Aldonic acid with formyl turned carboxyl (ex. Glucose to gluconic acid)
Strong oxidizing (HNO3) Aldaric acid with formyl + primary alcohol to carboxyl (ex. Glucose to glucaric acid)
Strong + Protecting group Alduronic acid with primary alcohol only to carboxyl (ex. Glucose to glucuronic acid)
Aldonic acid

Alduronic acid

Aldaric acid

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.
2. Reduction polyhydroxy alcohols/alditol if carbonyl is reduced (ex. Glucose to glucitol(sorbitol) below)
- deoxy sugars if hydroxyl is reduced/removed (ex. Deoxyribose below, where C2 OH is reduced to H)

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

If alcohol used is another sugar, the carbohydrate chain expands

If it reaches polysaccharide quantity of monomers, it is homopolysaccharide if there is only one monomer
unit; heteropolysaccharide if more than one.
Sugar derivatives other than oligo/polysaccharides which are glycosides include amino sugars,
glycoproteins, peptidoglycans, and glycosaminoglycans, among others.
Technically, all non-monosaccarides are glycosides or acetals/ketals.
NOTE: Its also good-to-know info to memorize the monomers of the common polysaccharides in other
references (ex. dextran, chitin, chondroitin, heparin, etc.)

SLRM/JRBM | 27

REVIEW PROPER 7: INTRODUCTION TO METABOLISM

PART 1. INTRODUCTION TO METABOLISM
Metabolism is the way through which an organism
maintains itself through internal chemical
processes. There are two types of such: 1)
Anabolism, or building up of molecules from
smaller ones, and 2) Catabolism, or breaking down
of molecules from larger ones. The greatest
contrast between the two is in the way that energy
is involved: Anabolism uses energy, while
catabolism produces energy.
GLYCOLYSIS

and extent to which energy is produced in the

different catabolic pathways are given stress.
Remember that energy cannot be expressed
without having a suitable measurement. In the
biochemical language, energy equates to Adenosine
Triphosphate (ATP). It can be directly produced, or
may be produced from electron carriers such as
Nicotinamide Adenine Dinucleotide Phosphate
(NADP), Flavine Adenine Dinucleotide (FAD), and
other DNPs such as GTP.

CITRIC ACID CYCLE

Glucose
Energy investment

NADH and FADH2

Energy payoff

ELECTRON TRANSPORT CHAIN

G3P

Electron carriers go down the electron transport

chain to produce the amount of ATP promised from
the potential chemical energy that they posses.

Pyruvate
ATP
Decarboxylation of Pyruvate

The anabolic and catabolic pathways are very much

intertwined. Intermediate products in an anabolic
pathway may be utilized in another catabolic
pathways, and vice-versa.
For example, carbohydrates used for catabolism
may be synthesized into amino acids used for
anabolic synthesis of proteins.

Electron carrier

ATPs produced

NADH (same as NADH + H+)

2.5 (or 3)

FADH 2

1.5 (or 2)

GTP

NOTE: In the boards, they usually use 3 (NADH) and

2(FADH)
The source of these energy carriers or ATP will be the
energy containing biomolecules that exist in the body,
particularly those which are also used in the anabolic
processes, the carbohydrates, lipids, and proteins.

Anabolic pathways are not always building up

compounds. Although some do (like photosynthesis
and fatty acid synthesis), some convert a
biomolecule into another, such as protein or fat into
sugar in gluconeogenesis or into ketone bodies in
ketogenesis.

However, much as the scope of basic biochemistry

syllabi concentrate solely on catabolism, the way

The interesting factor between catabolism of the

biomolecules is that they share a common
intermediate, acetyl-CoA.
SLRM/JRBM | 28

PART 2. GLYCOLYTIC AND ANAEROBIC PATHWAYS

Glycolysis (Embden-Meyerhof pathway) is the first step of both aerobic and anaerobic respiration. Its goal is to
transform glucose into two molecules of pyruvic acid (or pyruvate). It has nine notable steps, but in order to
grasp the essence of it, we can reduce the main steps into two phases:

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.

Glycolysis occurs in the cytoplasm (cytosol) of the cell.

Step and Reaction type

Enzyme

1, phosphorylation
2, isomerization
3, phosphorylation
4, cleavage and oxidation

Hexokinase
Phosphoglucose isomerase
Phosphofructokinase
Aldolase

5, isomerization

Triose phosphate isomerase

Product
Glucose-6-phosphate
Fructose-6-phosphate
Fructose-1,6-bisphosphate
Glyceraldehyde-3-phosphate
(G3P);
Dihydroxyacetone
Glyceraldehyde-3-phosphate

Energy carrier
involved

- 1 ATP
-1 ATP

SLRM/JRBM | 29

6, oxidative phosphorylation
7, substrate-level
phosphorylation (of ATP)
8, isomerization
9, dehydration
10, substrate-level
phosphorylation (of ATP)

G3P dehydrogenase
Phosphoglycerate kinase

1,3-bisphosphoglycerate
3-phosphoglycerate

+ 1 NADH
+ 1 ATP

Phosphoglycerate mutase
Enolase
Pyruvate kinase

2-phosphoglycerate
Phosphoenolpyruvate (PEP)
Pyruvate

+ 1 ATP

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 Glycerolphosphate (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-1phosphate 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-6phosphate (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.
Pyruvate decarboxylase

Pyruvate

Alcohol dehydrogenase

Acetaldehyde

Ethyl Alcohol
NADH NAD

The Ethanol fermentation process utilizes Pyruvate, first decarboxylating it to form Ethanal (Acetaldehyde),
then finally reducing it through NADH to produce Ethyl Alcohol.

Lactat e deh ydrogenase

Pyruvate

Lactic Acid
NADH NAD

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.

PART 3. TRICARBOXYLIC ACID CYCLE

The Tricarboxylic Acid Cycle/ Citric Acid Cycle is the second primary step of Aerobic Respiration. It aims
to use pyruvate as a medium for production of ATP, NADH and FADH. These electrons serve as receivers
and carriers of electrons for the electron transport chain. The TCA Cycle occurs at the mitochondrial
matrix.
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.
SLRM/JRBM | 30

PDH Complex

Pyruvate

acetyl-CoA
NAD -> NADH

Step and Reaction type

Enzyme

Product

Energy carrier
involved

Pre-TCA Cycle, Oxidative

decarboxylation
1, condensation
2, [dehydration + rehydration]
= isomerization (net)
3, oxidative decarboxylation
4, oxidative decarboxylation

Pyruvate dehydrogenase
(PDH) complex
Citrate synthase
Aconitase

Acetyl-CoA

Isocitrate decarboxylase

-ketoglutarate
Succinyl-CoA

+1 NADH
+1 NADH

5, substrate-level
phosphorylation (of ATP)
6, dehydrogenation (oxidation)
7, dehydrogenation
8, oxidative dehydrogenation

Succinate thiokinase

Succinate

+1 GTP

Succinate dehydrogenase
Fumarase
Malate dehydrogenase

Fumarate
Malate
Oxaloacetate

+1 FADH2

-ketoglutarate
dehydrogenase complex

+1 NADH

Citric acid
Cis-aconitate -> Isocitrate

+1 NADH

PART 4. FATTY ACID METABOLISM

Upon scarcity of carbohydrates, the body can utilize fatty acids within it to produce energy. Fortunately, the
enzymes needed for metabolism of fatty acids exist in the mitochondrial matrix, the same place where the
enzymes for TCA Cycle exist. The catabolic pathway of fatty acids towards production of acetyl-CoA intermediate is
called -oxidation. The first 4 steps consist an acyclic (nonrepeating pathway), where the next steps consist a
cyclic pathway.

SLRM/JRBM | 31

Pre--oxidation cycle:

O
Note: RCSCoA = fatty acyl-CoA

Step and Reaction type

Pre--oxidation (1-4),
esterification (net)
5, dehydrogenation
6, hydration
7, oxidation
9, cleavage

Enzyme
Fatty acyl-CoA synthetase, Carnitine
acyltransferases I and II
Acyl-CoA dehydrogenase
Enoyl-CoA hydratase
L-3 hydroxyacyl-CoA dehydrogenase
3-ketoacyl-CoA thiolase

Product

Energy carrier
involved

Acyl-CoA

- 2 ATP

Enoyl-CoA
L-3 hydroxyacyl-CoA
3-ketoacyl-CoA
Acetyl-CoA and Acyl-CoA 2
carbons shorter than
original

+1 FADH2
+1 NADH

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 acetylCoA. Moreover, acetyl-CoA is a precursor for cholesterol and ketone bodies, both producing unfavorable effects
on the body.

SLRM/JRBM | 32

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,
reaction #

G1
G3
G6
G7
G10
PTCA
TCA3
TCA4
TCA5
TCA6
TCA8

Product

Glucose-6-phosphate
Fructose-1,6-bisphosphate
1,3-bisphosphoglycerate
3-phosphoglycerate
Pyruvic acid (end of glycolysis)
Acetyl-CoA
Alpha-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Oxaloacetate (end of TCA)

ATPs produced per

step (double)
MA Shuttle/ GP
Shuttle
-1
-1
+5/ +3
+2
+2
+5
+5
+5
+2
+3
+5

ATPs produced per

step (singular)
MA Shuttle/ GP Shuttle
-1
-1
+ 2.5/ + 1.5
+1
+1
+ 2.5
+ 2.5
+ 2.5
+1
+ 1.5
+ 2.5

Net ATPs produced

(from hexose or fatty
acid)
MA Shuttle/ GP Shuttle
-1
-2
+3/ +1
+ 5/ 3
+ 7/ 5 (entire glycolysis)
+ 12/ 10
+ 17/ 15
+ 22/20
+ 24/ 22
+ 27/ 25
+ 32/ 30 overall
For entire TCA:
+20 / hexose
+10 / acetyl-CoA

PBOC
OC1

Acyl-CoA
Enoyl-CoA

-2 for each fatty acid

1.5 x #C/2
#C = carbons in acid

OC2

1, -hydroxyacyl
dehydrogenase

+ 2.5 multiplied by
#C/2 (- 2)
#C = carbons in acid

1.5 x #cycles
+ (10 x number of acetyl
CoA produced)
- 2 (for pre-O cycle)
4 x #cycles
+ (10 x number of acetyl
CoA produced)
- 2 (for pre-O 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.

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