Module 5 Topics acids.

The amino acids are represented by a three-letter

● Amino Acids and Peptides notation such as gly for glycine and phe for
● Properties of proteins phenylalanine or the one capital letter notation such as
● Primary Structure G for glycine or F for phenylalanine.
● Secondary Structure
● Tertiary Structure
● Quarternary Structure
● Enzymes

Learning Outcomes:
Proteins are synthesized in the ribosome by translation
of the mRNA from the N- to the C-terminus. There are
four hierarchies of protein structure starting with the
primary structure, secondary structure, tertiary
structure, and quaternary structure determined by the
structural features of local segments of the protein, the
protein folding and refolding unto itself to attain its
native conformation as well as the association of 2 or
more polypeptides resulting in an oligomeric protein
complex. The native conformation determines the
biologic function of a protein which includes
maintenance of structure, protection, catalysis, Table 1. Amino acids and their abbreviations
regulation, transport, storage, and signal transduction.
Loss of native conformation caused by denaturing Because of the different electronic characteristics of the
agents such as temperature, pH, various chemicals, functional R groups, amino acids are classified as
and enzymes can lead to a loss of biologic function of a non-polar aliphatic, aromatic, polar negatively charged
protein. or acidic, and polar positively charged or basic amino
acids.

Amino Acids and Peptides Table 2. Classifications of amino acids

Figure 1. Amino acid structure

Amino acids are the building blocks or monomers of

proteins. It contains a basic amine functional group and
a carboxylic group.
H2N – CH (R) - COOH
There are 20 naturally occurring amino acids in protein
that differ in the alkyl group (R) attached to the alpha C
atom. These amino acids are called alpha amino

Figure 2. Structures and classification of amino acids
source: Stoker, 2010. Brooks/Cole. p659
Amino acids have the following general properties:
1. Generally soluble in water, insoluble in
non-polar solvents such as benzene and ether
2. High melting point and low vapor pressure
3. Large dipole moments and high dielectric
constants
4. Chiral (presence of an asymmetric C attached
to four different substituents) (except for
glycine)
5. Absorb light in the UV region (aromatic amino
acids, phe, F-260nm; trp,W-280nm;
tyr,Y-275nm)
Essential amino acids: HMATTILLVP
Amino acids that cannot be synthesized by humans
and have to be obtained from the diet
In proteins, amino acids are joined together by peptide
bonds. A peptide bond are covalent bond formed by
the nucleophilic addition-elimination reaction. The
condensation reaction between the carboxylic group of
one amino acid and the amino group of a second
amino acid results to an amide bond (A water molecule
is released, HOH). Both small peptides and large
proteins are made up of a linear linkage of amino acid
residues joined by the peptide bond which is referred to
as the primary structure of a peptide or protein. Each
amino acid is termed as a residue because of the loss
of a water molecule.
Figure 1a. Peptide bond formation. Condensation of the
amino group of the first amino acid and the carboxylic
acid of the second amino acid
source: https://peptideguide.org/peptide-bond.html
● Two amino acids joined by a peptide bond result
in a dipeptide
● Three amino acids result in a tripeptide
● Four amino acids result in a tetrapeptide and so
on.
Naming a peptide
The peptide is named after the amino acid residues
that comprise it starting from the N-terminal (amino
group) end up to the C-terminal (carboxylic) end.
Figure 2. N-terminal and C-terminal
Figure 3. By convention, the N-terminal is placed on the
left and the C-terminal on the right when drawn
horizontally.
Note: aspartic acid = aspartate,
glutamic acid=glutamate.
Glutamate and Aspartate are usually used when they
are in the C- terminal
Example:
S-A-D = serylalanylaspartate
M-E = methionylglutamate
Example: the tetrapeptide composed of aspartic acid
on the N-terminal end, followed by phenylalanine,
cysteine and lysine on the C-terminal end
Peptide bond formation – mechanism of nucleophilic
addition–elimination reaction
The amino group and carboxylic group forming the
peptide bond are not available for chemical reaction,
thus the chemical characteristics of the side chain R
group determines the role the amino acid plays in the
protein. By applying the principles in determining the pI
of individual amino acids, one can also solve for the pI
of a peptide and, for that matter, determine the net
charge of small or large peptides or proteins.
Properties of proteins
Proteins serve many functions, including the
following:
1. Structure: Collagen and keratin are the chief
constituents of skin, bone, hair, and nails.
2. Catalysts: Virtually all reactions in living systems are
catalyzed by proteins called enzymes.
3. Movement: Muscles are made up of proteins called
myosin and actin.
4. Transport: Hemoglobin transports oxygen from the
lungs to cells, other proteins transport molecules
across cell membranes.
5. Hormones: Many hormones are proteins, among
them insulin, oxytocin, and human growth hormone.
6. Protection: Blood clotting involves the protein
fibrinogen; the body used proteins called antibodies to
fight disease.
7. Storage: Casein in milk and ovalbumin in eggs store
nutrients for newborn infants and birds. Ferritin, a
protein in the liver, stores iron.
8. Regulation: Certain proteins not only control the
expression of genes, but also control when gene
expression takes place.
Proteins classification based on chemical composition:
Simple proteins - a protein in which only amino acid
residues are present.
Conjugated proteins- a protein that has one or more
non-amino acids entities present in its structure. These
non-amino acid structures are called prosthetic groups.
Table 1. Types of conjugated proteins based on the
prosthetic group present
Proteins classification based on shapes1
Fibrous proteins
● protein molecules with an elongated shape
● Tend to be long and thin
● Are usually structural proteins
● Examples: cytoskeleton proteins, elastin,
collagen
Globular proteins
● The peptide chains are folded into spherical or
globular shapres
● Compact, spherical, and flexible
● These usually have enzymatic activity
General Properties of Fibrous and Globular Proteins 8,9
● Generally, globular proteins dissolve in water
while fibrous proteins are insoluble in water.
This allows globular proteins to travel through
the body fluids where they are needed.
● Fibrous proteins are mainly found in a single
type of secondary structure while globular
proteins may take several types secondary
structure.
● Fibrous proteins are associated with structural
functions that provide support and external
protection, whereas globular proteins are
commonly involved in functions related to
metabolism such as catalysis transport, and
regulation.
● There are more types of globular proteins that
of the fibrous proteins. However, the total mass
of fibrous proteins in the body is greater than
the total mass of globular proteins.
Table 2. Fibrous and Globular proteins
Classification of Proteins based on functions
● Catalytic proteins. Proteins that act as
biochemical catalyst are called enzymes.
Because enzymes participate in almost all of
the metabolic reactions that occur in cells and
that the chemistry of human genetics is highly
dependent on enzymes, an entire branch of
chemistry is dedicated to the properties, activity
and significance of enzymes called Enzymology
.
● Defense proteins. Also known as
immunoglobulins or antibodies. These proteins
focus on the body’s immune system. They act
by acting on foreign substances, such as
bacteria and viruses, to help combat invasion
and infections.
● Transport proteins. Their primary function is to
bind to small biomolecules and transport to the
different locations in the body. The hemoglobin
is the most well-known example. Another
example is the transferrin, a transport protein
that carries iron from the lifer to the bone. High-
and low- density lipoproteins are the most
commonly known transport proteins that carries
cholesterol
● Messenger proteins. The function of these
proteins is to relay signals between different
cells and tissues in the body to facilitates
biochemical processes. Insulin and glucagon
are the common examples of the hormones that
regulate body processes.
● Contractile proteins. Actin and myosin are
examples contractile proteins that are found in
all types of muscles. They respond to nerve
stimuli that causes the contraction and
extension. The sperm cell is able to move
because of the long flagella made up of
contractile proteins.
● Structural proteins. These proteins provides
structure and protective covering to the
 fluid-like biochemical systems. Common
examples are the collagen , the component of
cartilage , and the keratin, the protective
covering in the hair and nails.
● Transmembrane proteins. These proteins help
control the movement of small molecules and
ions through the cell membrane.
● Storage proteins. Small molecules are bound
and stored by these proteins for future use.
Examples are the ferritin, an iron-storage
proteins and the myoglobin, an oxygen-storage
protein.
● Regulatory proteins. Often found in the
exterior surface of cell membranes and are
embedded to act as sites at which messenger
molecules bind and "relay the message". They
are also proteins that bind to enzymes which
turn "on" and "off" the enzymatic action.
● Nutrient proteins. Examples are casein, found
in milk, and ovalbumin, found in egg white, are
two examples of such proteins.
Protein Denaturation
Figure 1. Denaturation and renaturation of proteins
Protein folding
● results from the formation of secondary
structures driven by the hydrophobic effect
● occurs in seconds to minutes
Protein denaturation
● results in the unfolding and disorganization of a
protein’s secondary and tertiary structure
without hydrolysis of the peptide
● often insoluble and precipitate from solution
Denaturing Processes:
● Heat
● Mechanical disruption
● Drastic pH changes
Denaturing Agents:
Aqueous urea: Disrupts hydrogen bonding.
Surface-active agents: Detergents such as sodium
dodecylbenzenesulfate (SDS) disrupt the electrostatic
interactions and hydrogen bonding in some cases
Reducing agents: 2-Mercaptoethanol (HOCH2CH2SH)
cleaves disulfide bonds by reducing -S-S- groups to
-SH groups.
Heavy metal ions: Transition metal ions such as Pb2+,
Hg2+, and Cd2+ form water-insoluble salts with -SH
groups; Hg2+ for example forms -S-Hg-S-.
Alcohols: 70% ethanol penetrates bacteria and kills
them by coagulating their proteins. It is used to sterilize
skin before injections.
Primary Structure
● The primary level of organization is simply the
order of amino acids in the peptide chain
● The primary structure of protein (order of amino
acids) determines how the protein folds and
interacts at the other levels of interaction
● Peptide bond has partial double bond
characteristics therefore it is rigid
● α-carbon bonds are flexible
Many different proteins can be formed from different
sequences of 20 amino acids. By looking at its
arithmetic, we can calculate the total number of
possible peptides or proteins for a chain of n amino
acids by simply raising 20 to the nth power.
Example:
dipeptides (2 amino acids) : 20^2 = 400 different
peptides
tripeptides (3 amino acids): 20^3= 8,000 different
peptides
tetrapeptide (4 amino acids): 20^4= 160,000 different
peptides!
The Human Insulin
Difference in Amino Acid Sequence for Human, Bovine,
Hog and Sheep Insulin
A - Chain B - Chain
8 – 9 – 10 30
 ● α-helices, β-sheets, β-bends, nonrepetitive
Human – Thr – Ser – Ile – – Thr secondary structure, supersecondary structure
α-helix – it is a spiral structure consisting of a tightly
Bovine – Ala – Ser – Val – – Ala packed, coiled polypeptide backbone core, with the
side chains of the component amino acids extending
Hog – Thr – Ser – Ile – – Ala outward from the central axis to avoid interfering
sterically with each other
Sheep – Ala – Gly – Val – – Ala –Extensive hydrogen bonding
–3.6aa (amino acid) per turn
Despite the slight difference in the structure, perform
the same function and can even be used by humans.
However, none of the other three is quite as effective
as human insulin. For this reason, recombinant DNA
techniques were explored and are now used to produce
human insulin from bacteria.

Oxytocin and Vasopressin

Figure 1. Different helix structure representation

β-sheets– all of the peptide bond components are

involved in hydrogen bonding
–Surfaces are “pleated”

These two nonapeptides differ only in the amino acids

in position 2 and 7 yet their biological functions are
quite different.

The Sickle Cell Disease

Figure 2. Beta sheets

The α-helix and β-sheetsare the most common

secondary structures. They provide maximal
hydrogen bonding for peptide bond components
within interior of polypeptides and stability to the
secondary structure.
Secondary structures are 2-dimensional
● Globular proteins contain only short α-helices
structures formed due to hydrogen binding between
and β-sheets interspersed with randomly coiled
hydrogen of amine groups and oxygen of the carbonyl
regions
groups
● Fibrous proteins, the α-helices and β-sheets
● formed through hydrogen bonds between
tend to make the polypeptide rigid
backbone atoms.
other secondary structures
 ● β-bends (reverse turns/β-turns)– reverse the
direction of the polypeptide chain, helping it
form a compact globular shape. Generally, it is
composed of 4aa and mainly contain many
polar and charged amino acids.
● Nonrepetitive secondary structure- also called as
random coil. It is described as having a loop or coil,
and has less regular structures.
● supersecondary structures - called as MOTIFS.
It is the combination of secondary structural
elements producing a specific geometry or
motifs. It primary form the core region of the
molecule. It is connected by loop regions
Tertiary Structure
The tertiary protein structure is the overall
three-dimensional arrangement of a protein. This
results from the interactions between the side chains (R
groups of the amino acids) within a peptide chain. It
refers to both the folding of domains and to the final
arrangement (3D). It is usually determined by X-ray
crystallography and NMR (Nuclear Magnetic
Resonance Spectroscopy.
--Tertiary Structure is stabilized by:
● Disulfide bonds - the most often covalent bond
involved in the stabilization of the tertiary
structures
● Hydrophobic interactions
● Hydrogen bonds
● Ionic interactions (electrostatic attractions) -
also called salt bridges
Figure 1. Bonds that stabilize the tertiary structure
Chaperones
● Proteins that help newly synthesized
polypeptide chain assume the correct
secondary and tertiary structures. It helps
protein fold correctly.
● Molecular chaperones, also known as Heat
Shock Proteins (Hsp)
● Interact with the polypeptide by binding
hydrophobic regions
Figure 2. Chaperone help newly synthesized
polypeptide chains assume their correct folding

Figure 1. Four levels of protein structure

Quaternary structure is the highest level of

protein organization which applies to proteins with
multiple polypeptide chains.
● Determines how the different subunits of the
protein fit into one organized molecule
● The subunits are held together by the same
bonds that stabilizes the tertiary structures
● multimeric units of the polypeptide chain
● Commonly occurring examples are dimers,
trimers, tetramers

Fibrous proteins
● α-helices and β-sheets tend to make the
polypeptide rigid
● Tend to be long and thin
● Are usually structural proteins
● Examples: cytoskeleton proteins, elastin,
collagen
Globular proteins
● Contain only short α-helices and β-sheets
interspersed with randomly coiled regions
● Compact, spherical, and flexible
● These usually have enzymatic activity

Quaternary Structure
Figure 2. Four Levels of Protein Structure

Figure 3a Summary of Protein Structures
Figure 3b Summary of Protein Structures
Overview
Enzymes are the cells’ effective biological catalysts.
Most enzymes are proteins and all are globular
proteins. They are able to increase the rates of
chemical reactions in cells many fold over the rate of
the uncatalyzed reaction. They are highly specific.
Enzymes are classified according to the type of
chemical reaction they catalyze. They bind substrate in
the part of their structure known as the active site
forming the enzyme-substrate complex. Oftentimes,
enzymes are named by adding the suffix –ase after the
name of the substrate or the type of reaction catalyzed.
The enzyme activity is best described by Michaelis
and Menten model for a simple enzyme reaction with a
single substrate and a single product. This model also
holds true for enzyme catalyzed reactions with two or
more substrates. The model defines the values of Vmax
or the maximum velocity of the reaction and the KM or
Michaelis constant, the substrate concentration at half
maximal velocity of the reaction. However, in this
model, it is difficult to obtain the exact value of the Vmax
and consequently the KM. The exact values of the Vmax
and KM can be obtained by the transformation of the
Michaelis-Menten equation using the Lineweaver-Burk
double reciprocal plot. Inhibitors are substances that
interfere with enzyme action and reduce the rate of the
enzyme reaction. Enzyme inhibition can be reversible
or irreversible. There are three types of reversible
enzyme inhibitors, namely, competitive,
non-competitive and uncompetitive inhibitors.
Enzyme inhibition is best studied using the
Lineweaver-Burk plot.
Enzymes, one of the most important types of proteins,
are effective biological catalysts. Most enzymes, with
the exception of ribozymes or RNAs with catalytic
activity, are proteins and all are globular proteins. They
are able to increase the rates of chemical reactions in
cells in the order of 106 to 1020 over the rate of
uncatalyzed reaction. They are highly specific and not
used up in the chemical reaction. Because most are
proteins, they are biomolecules with high molecular
weight and are made up of amino acids joined by
peptide bonds. They can be denatured and precipitated
with salts, solvents, and other reagents. Some require
the presence of co-factors to exert their biological
activity.
Characteristics of enzymes:
● Not used up in reactions
● Highly specific
● Chemically recognize, bind and modify
substrates
● High molecular weight compounds made up
principally of chains of amino acids linked
together by peptide bonds
● Can be denatured and precipitated with salts,
solvents and other reagents
 ● May require the presence of other compounds -
cofactors - before their catalytic activity can be
exerted
Classification enzymes according to structure:
● Simple enzymes- composed of only protein (all
amino acids)
● Conjugated enzymes - has a protein and a
nonprotein part. Neither the protein nor the
protein part has a catalytic activity on its own.
■ Apoenzyme- the protein part of a
conjugated enzyme
■ cofactor- the nonprotein part of a
conjugated enzyme.
■ Prosthetic group - Tightly
bound small organic
molecules and inorganic
metal ions. Typical
inorganic ion cofactors
include Zn2+, Mg2+,
Mn2+, and Fe2+.
■ Coenzyme - loosely
bound small organic
molecule that serves as a
cofactor. Many vitamins
also function as
coenzymes.
■ Holoenzyme- the biochemically
active conjugated enzyme
(Apoenzyme + Cofactor =
Holoenzyme)
Figure 1. Effect of coenzyme on the shape of the
enzyme
Nomenclature of enzymes
Enzymes are named mostly on its function, rather than
its structure. They are either named by its type of
reaction or its substrate identity
■ Substrate- the substance
involved in the reaction catalyzed
by the enzyme.
enzyme-naming processes:
● Many enzymes are named after its substrate
and the suffix-ase is added such. Example:
Lactase; this enzyme catalyzes the hydrolysis
of lactose (the substrate). The suffix -in is still
used in the early discovered enzymes (mostly
digestive enzymes) such as pepsin, trypsin.
● An an enzyme may be named after the type of
reaction it catalyzes. Example: oxidase is an
enzyme that catalyzes oxidation reaction.
● The type of substrate may also be emphasized
in the name, in addition to the type of reaction.
Example: glucose oxidase
Table 1. Classification of enzymes according to the type
of reaction they catalyze and their subclasses
Source: Stoker, 2010. Brooks/Cole p702
Enzymes bind substrate in the part of their structure
known as the active site forming the enzyme-substrate
complex. Enzymes are highly specific: they catalyze
only one chemical reaction, having a specific substrate.
This specificity results from an enzyme’s specific
3-dimensional shape. The binding reduces the
activation energy for the reaction to occur thus
increasing the rate of the reaction. After the reaction is
complete, the substrate has formed a new product or
products and the enzyme is released to be reused.

Active Site - the part of the enzyme where the catalysis

takes place. This is the region where the substrates
"attach"
Enzyme-substrate complex is formed when the
substrate attach to the active site.

Figure 3. Induced fit model

Factors that affect Enzyme Activity

Figure 1. Substrate binds to the active site forming an
● Temperature
enzyme-substrate complex
Two mechanisms that try to explain how enzymes work
● Lock and Key Model
The lock and key model states that the active
site in the enzyme has a fixed and rigid
conformation and only substrates with the exact
complementary shape can bind to it. The
concept is similar to a lock and its key.
● pH
● Substrate Concentration
Figure 2. Lock and Key Model
● Induced-fit Model
An interaction between the enzyme and
substrate induces or changes the shape of the
molecules to produce a suitable fit.
○ As the temperature of an
enzyme-catalyzed reaction increases,
the rate of reaction also increases
○ The reaction will reach its optimum
temperature at which the enzyme
exhibits its maximum catalytic activity
○ When the temperature goes beyond this
point, the enzyme will start to denature.
Therefore, the enzymatic activity will
rapidly decrease.
○ Most enzymes operates on a very
narrow pH range
○ Small changes in pH can cause the
denaturation of the enzyme
○ Optimum pH is the pH at the enzyme
exhibits maximum activity.
○ As the substrate concentration
increases, the enzyme reaches it
maximum capability
○ Each substrate must occupy the active
site for a certain period and the products
must leave before it can be used by next
substrate. When enzymes are "fully
booked" the incoming enzymes must
"wait" for their turn. At this point, the
enzymes have reached its saturation
point.
 ○The rate of enzymatic activity is constant
under saturated conditions
● Enzyme Concentration
○ The higher the enzyme concentration,
the higher the enzyme activity
Figure 4. Enzyme Activity
The enzyme activity is best described by the model
devised by Michaelis and Menten for a simple enzyme
reaction with a single substrate and a single product.
● Michaelis - Menten model states that when the
rate or velocity of the reaction is examined
under varying substrate concentrations :
○ at low substrate concentration, the
reaction is first order. This implies that
the velocity is dependent on the
substrate concentration.
○ At high levels of substrate concentration,
the rate becomes zero order. This
means that the velocity is independent
of substrate concentration.
● If the rate or velocity of the reaction is plotted
against the substrate concentration, the
resulting curve is hyperbolic. This means that at
high substrate concentrations the active sites of
all enzyme molecules are saturated with
substrate.
● The model also defines the values of Vmax or the
maximum velocity of the reaction and the KM or
Michaelis constant
● Michaelis Constant is simply defined as the
substrate concentration at half maximal velocity
(rate of reaction).
Enzyme Regulation/Inhibition
There are two main reasons why an enzyme is
regulated.
● It is a waste of energy if the cell continuously
produce large amount of enzyme even when
the amount of substrates is very low. Therefore,
enzyme production must be "turned off"
● If the amount of product from the
enzyme-catalyzed reaction is already more than
what the cell needs, then it is a waste of energy
if the enzyme continues to catalyze the reaction.
The enzyme must be "turned off".
Mechanisms of Enzyme Regulation
● Feedback control
○ An enzyme regulation in which the
product inhibits one of the reactions in a
chain of enzyme-catalyzed reactions.
○ The final product usually inhibits the
activity of the first enzyme in the chain
by competitive inhibition,
non-competitive inhibition or some other
type of inhibition.
○ When the concentration of the final
product decreases, all of the reactions in
the chain proceeds. The accumulation of
the final product, however, inhibits the
action of the first enzyme
○ The final product serves as the
messenger if the first enzyme needs to
be shutdown or not.
Figure 1. Schematic representation of a pathway
showing feedback inhibition
source: Bettelheim et al. 2013. Brooks/Cole p645
● Proenzyme ○ The attachment of the regulator to the
○ Some enzymes are produced in their enzyme is noncovalent and reversible
inactive form. These inactive form are ○ Allosteric enzymes has two kinetic
called proenzyme or zymogens. states :
○ In order to activate these enzymes, a ■ R form (relaxed form)-
small part of their polypeptide chain This is more active form
must be removed of the enzyme
○ Proenzymes are produced rather than ■ T form (taut form)-This is
its active form to avoid random reactions the less active form of the
in the body. Example, Trypsin is a enzyme
protease, an enzyme that catalyzes the
hydrolysis of peptide bonds. It is
important in the digestion of the proteins
that we eat. Its inactive precursor,
trypsinogen, is produced in the
pancreas. If the trypsin was produced in
its full active form, it would result to the
random digestion of the proteins in our
body. Therefore, trypsinogen is
produced and only turns into its active
form when it enters the digestive tract.
○ Trypsin is an example of a proteolytic
enzyme. Proteolytic enzymes are
enzymes that catalyzes the breaking of
peptide bonds. Because they encourage
the breaking of the tissues that produce
them, they are generated in their Figure 2. Schematic representation of an allosteric
inactive form. Most digestive and enzyme and its regulator
blood-clotting enzymes are proteolytic
enzymes.
○ Examples of proenzyme or zymogens :
Trypsinogen, pepsinogen, procaspase,
prolipase.

● Allosterism
○ This regulation happens when a
substance binds to a certain part of the
enzyme (but not in its active site) and
changes the shape of its active site.
○ Enzymes that are regulated through this
mechanism are called allosteric
enzymes
○ The substance that attaches to the
allosteric enzyme is called a regulator
and the site to which it binds is called
the regulatory site.
○ A regulator may inhibit the enzyme
action (negative modulation) or may
stimulate the enzyme action (positive
modulation).

Figure 2. Negative and Positive Allosteric Control
Protein Modification / covalent modification
○ A chemical group is usually added to the
apoenzyme, changing the primary
structure of the enzyme.
○ Addition or removal of the chemical
group may cause the activation or
inhibition of an enzyme
○ Typical examples are the
phosphorylation and dephosphorylation
■ phosphorylation - process of
adding phosphate group.
Glycogen phosphorylase, an
enzyme that catalyzes the
breaking down of glycogen to
glucose, is activated by the
addition of phosphate group.
Glycogen synthase, the enzyme
involved in glycogen synthesis, is
deactivated by the presence of
phosphate group.
■ dephosphorylation - removal of
phosphate group.
● Isoenzyme
○ This type of modulation takes place
when the same enzyme catalyzing the
same substrate appear in a different
tissue but in different form.
○ The same enzyme appears in a different
location with a different combination of
subunits, therefore, having a different
quarternary structure.
○ isoenzymes allow very specific
metabolic reactions to meet the
particular needs of a given tissue or
developmental stage.
○ An example of this is the lactate
dehydrogenase (LDH). LDH has two
isoenzymes: The H4 and M4 isoenzyme.
■ The H4 isoenzyme is found in the
heart while the M4 isoenzyme is
found in the skeletal muscle
■ H4 isoenzyme functions in
aerobic condition while the M4
functions in anaerobic condition
Type of Enzyme Inhibitors
An enzyme inhibitor is a substance that decreases or
stops the catalytic function of an enzyme
● Reversible Competitive Inhibitor
○ A molecule that has the same shape
and charge distribution as the enzyme
substrates
○ It competes for occupancy at the binding
site. When the inhibitor is attached to the
enzyme, no reaction occurs. This results
to the decrease in enzyme activity.
○ The inhibition is reversible because it
only forms weak bonds. The
enzyme-inhibitor complex easily breaks
down (in a fraction of a second).
○ When the complex breaks, the inhibitor
leaves the active site. The enzyme is
then free and ready to use. The
substrate and inhibitor again competes
for the active site
○ The substance with the higher
concentration will dominate the
occupancy procedure. Therefore,
increasing the substrate concentration
will decrease the inhibitory effect
 ● Irreversible Inhibitor
○ A molecule that forms strong covalent
bond with the active site
○ The inhibitor-active site bond
permanently inactivates the enzyme.
○ Chemical warfare agents (nerve gases)
and organophosphate insecticides are
based on the action of irreversible
inhibitors.

● Reversible Noncompetitive Inhibitor

○ A molecule that binds to the enzyme
other than the active site
○ The substrate can still bind to the active
site but the noncompetitive inhibitor
prevents the enzyme from performing its
catalytic action
○ Increasing the substrate concentration
does not remove the inhibition. However, Figure 4. Enzyme inhibitor summary
decreasing the concentration of the
inhibitors will free up enzyme, allowing ● Uncompetitive Inhibitor
normal enzyme activity. ○ Binds to a enzyme-substrate complex
○ Allosteric inhibition and noncompetitive but not to a free enzyme complex
inhibition may sound the same but they ○ The inhibition cannot be removed by
have several differences. Here are some increasing the substrate concentration
key points:
■ Both allosteric inhibitor and
noncompetitive inhibitor binds to
a site in the enzyme other than
the active site.
■ Noncompetitive inhibitor changes
the conformation of the enzyme
but not the active site. This
allows the substrate to bind to
the enzyme even in the presence
of the inhibitor. However, the
catalytic function of the enzyme
is disrupted because of its
conformational change.
■ Allosteric inhibitor changes the
conformation of the enzyme and
its active site. This prevents the
substrate from binding to the
enzyme's active site.