2. SUMMARY
ENZYMES
1. Chemical vs. biological catalysis. The mechanism
of enzyme reactions. The active site. Enzyme
specificity. Cofactors.
3. BIBLIOGRAPHY
• Frederick A. Bettelheim, William H. Brown,
and Mary K. Campbell. INTRODUCTION TO
GENERAL, ORGANIC AND BIOCHEMISTRY.
12th Ed. 2020.
• John T. Tansey. BIOCHEMISTRY: AN
INTEGRATIVE APPROACH WITH EXPANDED
TOPICS. 1st Ed. 2019.
• Donald Voet, Judith G Voet, and Charlotte
W. Pratt. FUNDAMENTALS OF
BIOCHEMISTRY INTEGRATED E-TEXT WITH
E-STUDENT COMPANION. 5th Ed. 2016.
4. Kinetics and Enzymes
• The rates of reactions are governed by the
parameters of KINETICS.
• Virtually every chemical reaction in a cell
occurs at a significant rate only because
of the presence of ENZYMES.
• ENZYMES are biomolecules that catalyse
reactions in biological systems.
5. ENZYMES
Practical Importance
• In some diseases, especially inheritable genetic
disorders, there may be a deficiency or even a total
absence of one or more enzymes.
• For other disease conditions, excessive activity of an
enzyme may be the cause.
• Measurements of the activities of enzymes in blood
plasma, erythrocytes, or tissue samples are
important in diagnosing certain illnesses.
• Many drugs exert their biological effects through
interactions with enzymes.
6. ENZYMES
Energy Diagram of a Reaction
• The path from reactant(s) to
product(s) almost invariably
involves an energy barrier,
called the Activation Barrier.
• The highest point in the
reaction coordinate diagram
represents the transition
state, and the difference in
energy between the
reactant in its ground state
and in its transition state is
the activation energy, ΔG‡.
7. ENZYMES
Catalysis in a Reaction
• Enzymes increase the rate
of the reaction by
decreasing this activation
energy.
• Enzyme-catalyzed
reactions commonly
proceed at rates greater
than 10 to12 times faster
than the uncatalyzed
reactions.
• The enzyme does not
change the energy level of
8. • Each enzyme catalyses a Specific Reaction, and each
reaction in a cell is catalysed by a different enzyme.
• The Efficiency of enzymes, their Specificity and their
susceptibility or Regulation give cells the capacity to
lower activation barriers selectively.
ENZYMES
Catalysis in a Reaction
10. Mechanism of Enzyme
Reaction
Enzymes are
usually Proteins
that act as
Catalysts,
compounds that
increase the rate
of chemical
reactions.
Cellular Catalysts
11. Enzyme-catalysed reactions have two basic
steps:
(1) Binding of substrate and release of product
(2) Conversion of bound substrate to bound product
E + S ES EP E + P
(1) (1)
(2)
Mechanism of Enzyme
Reaction
12. • The substrates and the enzyme form a Transition
State Complex, an unstable high-energy complex
with a strained electronic configuration that is
intermediate between substrate and product.
• The transition state complex decomposes to
products, which dissociate from the enzyme that
generally returns to its original form.
Mechanism of Enzyme
Reaction
13. • Enzymes increase the rate of the reaction by
Decreasing the Activation Energy.
• They use various Catalytic Strategies:
• Electronic stabilization of the transition state
complex
• Acid-base catalysis
• Covalent catalysis
• Metal ion catalysis
Mechanism of Enzyme
Reaction
14. Each enzyme is a Specific Catalyst of a biochemical
reaction:
Substrate Specificity: the ability of an enzyme to
select just one substrate and distinguish this
substrate from A group of very similar
compounds.
Action specificity: the enzyme converts the
substrate to just one product.
Mechanism of Enzyme
Reaction
16. • To catalyse a chemical
reaction, the enzyme
forms an Enzyme-
Substrate Complex in
its active catalytic site.
• The Active Site is
usually a cleft or
crevice in the enzyme
formed by one or
more regions of the
polypeptide chain.
The Active Site
17. • The amino acid residues
that bind and modify
the substrate can come
from very different
parts of the linear
amino acid sequence of
the enzyme.
• The catalytic activity
depends on the
integrity of the native
enzyme conformation: if
an enzyme is denatured
or dissociated into its
subunits, catalytic
activity is usually lost.
The Active Site
18. Within the active site, cofactors and functional groups
from the polypeptide chain participate in
transforming the bound substrate molecules into
products.
• Three-dimensional Structure: the three-
dimensional arrangement of peptide chain forms a
crevice that allows the reacting portions of the
substrates to approach each other from the
appropriate angles.
• Ambient Groups: create hydrophobic medium,
expelling water molecules from it.
• Fixation Groups: initially, the substrate molecules
bind to their substrate binding sites, also called
the substrate recognition sites.
• Catalytic Groups: the active site also contains
The Active Site
20. • Almost all of the polar amino acids participate
directly in catalytic sites in one or more enzymes.
• Serine, cysteine, lysine, and histidine can participate
in covalent catalysis.
• Histidine, because it can donate and accept a proton
at neutral ph, often participates in acid-base
catalysis.
The Active Site
22. Enzymes Specificity
Each enzyme is a Specific Catalyst of a biochemical
reaction:
1. Substrate Specificity: the ability of an enzyme to
select just one substrate and distinguish this
substrate from a group of very similar compounds.
2. Action Specificity: the enzyme converts the
substrate to just one product.
Enzyme specificity results from the three-dimensional
arrangement of specific amino acid residues in the
active site.
There are two models for substrate binding
mechanism:
1. The “lock-and-key” model
23. Enzyme Specificity
Lock and Key Model
In the lock-and-key model, the complementarity between
the substrate and its binding site is compared to that of a
key fitting into a rigid lock.
24. Enzyme Specificity
Induced Fit Model
• As the substrate binds,
enzymes undergo a
conformational change
(“induced fit”) that
repositions the side
chains of the amino acids
in the active site and
increases the number of
binding interactions.
• The substrate binding
site is not a rigid “lock”
but rather a dynamic
surface.
27. Cofactors
• Some enzymes require an
additional chemical
component called a
Cofactor —either one or
more inorganic ions
(Fe+2, Mg+2, Mn+2, or
Zn+2), or an organic
molecule called a
Coenzyme.
• When is very tightly or
even covalently bound to
the enzyme protein is
28. • A complete, catalytically active enzyme together
with its bound coenzyme and/or metal ions is called
a Holloenzyme.
• The protein part of such an enzyme is called the
Apoenzyme or Apoprotein.
Apoenzyme + Cofactor →
Holloenzyme
Cofactors
29. Cofactors
Coenzymes Characteristics
• Coenzymes are complex organic molecules.
• Most are derived from Vitamins, organic nutrients
required in small amounts in the diet.
• Coenzymes have very little activity in the absence of
the enzyme and very little specificity.
• Coenzymes act as Transient Carriers of specific
functional groups.
• Each coenzyme is involved in catalyzing a specific
type of reaction for a class of substrates with certain
structural features.
30.
31. Cofactors
Coenzymes in Catalysis
• Coenzymes can be divided into two general classes:
• Activation-transfer Coenzymes
• Oxidation-reduction Coenzymes
• The Activation-transfer Coenzymes usually
participate directly in catalysis by forming a covalent
bond with a portion of the substrate in order to
activate it for transfer, addition of water, or some
other reaction.
• The Oxidation-reduction Coenzymes are involved in
oxidation-reduction reactions catalysed by enzymes
categorized as oxidoreductases.
32. Common Features of Activation-transfer
Coenzymes
1) They have a specific chemical group involved in
binding to the enzyme.
2) Also a separate and different functional or reactive
group that participates directly in the catalysis of
one type of reaction by forming a covalent bond
with the substrate.
3) They have dependence on the enzyme for
additional specificity of substrate and additional
catalytic power.
Cofactors
33. Thiamine pyrophosphate.
• Synthesized in human cells from the vitamin
Thiamine (B1)
• The functional group that extends into the active
site is the reactive carbon atom with a dissociable
proton.
• In all of the enzymes that use thiamine
pyrophosphate, this reactive thiamine carbon
forms a covalent bond with a substrate keto
group while cleaving the adjacent carbon–carbon
bond.
Cofactors
34. Coenzyme A (COASH)
• Synthesized from the
vitamin Pantothenate
• Its functional group is
a sulfhydryl group at
the end of the
molecule, is a
nucleophile that always
attacks carbonyl
groups and forms acyl
thioesters.
Cofactors
35. Biotin.
• Its structure is a vitamin
• Its functional group is a Nitrogen Atom that
covalently binds a CO2 group in an energy-
requiring reaction.
• In the human, biotin functions only in
Carboxylation Reactions.
Cofactors
36. Pyridoxal Phosphate.
• Synthesized from the
vitamin Pyridoxine,
which is also called
Vitamin B6.
• The reactive aldehyde
group usually
functions in enzyme-
catalysed reactions
by forming a covalent
bond with the amino
groups on amino
acids.
Cofactors
37. Common features of oxidation-reduction
coenzymes
1) A large number of coenzymes are involved in
oxidation-reduction reactions catalysed by
enzymes categorized as Oxidoreductases.
2) Some coenzymes, such as Nicotinamide Adenine
Dinucleotide (NAD+) and Flavin Adenine
Dinucleotide (FAD), can transfer electrons
together with hydrogen and have unique roles in
the generation of ATP from the oxidation of fuels.
3) Other oxidation-reduction coenzymes work with
Metals to transfer single electrons to oxygen.
Cofactors
38. 4) Oxidation-reduction coenzymes follow the same
principles as activation-transfer coenzymes,
except that they do not form covalent bonds with
the substrate.
5) Each coenzyme has a unique functional group that
accepts and donates electrons and is specific for
the form of electrons it transfers (e.G., Hydride
ions, hydrogen atoms, oxygen).
Cofactors
Common features of oxidation-reduction
coenzymes
39. Vitamin E and vitamin C
Are oxidation-reduction
coenzymes that can act as
antioxidants and protect
against oxygen free radical
injury.
Vit C
Vit E
Cofactors
40. Nicotinamide Adenine
Dinucleotide (NAD+).
• Synthesized from the
vitamin Niacin (which
forms the Nicotinamide
ring), and from ATP
(which contributes an
AMP).
• The functional group of
NAD+ is the carbon on
the Nicotinamide ring
opposite the positively
charged nitrogen. This
carbon atom accepts the
hydride ion (a hydrogen
atom that has two
electrons) transferred
from a specific carbon
Cofactors
41. Metal Ions in Catalysis
Metal ions.
• As they have a positive charge, contribute to the
catalytic process by acting as Electrophiles
(electron-attracting groups).
• They assist in binding of the substrate, or they
stabilize developing anions in the reaction.
• They can also accept and donate electrons in
oxidation-reduction reactions.
For example, the phosphate groups of ATP are
usually bound to enzymes through Mg2+ chelation.
Cofactors
50. BASIC STEPS OF THE
MECHANISM
ENZYME-CATALYZED REACTIONS HAVE
TWO BASIC STEPS:
(1) BINDING OF SUBSTRATE AND RELEASE OF
PRODUCT
(2) CONVERSION OF BOUND SUBSTRATE TO
BOUND PRODUCT
E + S ES EP E +
P
(1) (1)
(2)
55. ASPIRIN AS AN INHIBITOR
• ASPIRIN
(ACETYLSALICYLAT
E) INHIBITS THE
ENZYME THAT
CATALYZES THE
FIRST STEP IN THE
SYNTHESIS OF
PROSTAGLANDINS,
COMPOUNDS
INVOLVED IN MANY
PROCESSES,
INCLUDING SOME
THAT PRODUCE
76. Isoenzymes
• Catalyzed the same reaction but are encoded in
different genes are called isoenzymes.
• Have the same enzymatic action with different
structures.
• Are tissue-specific forms of the same enzymes that
arose through gene duplication.
77. Biological Importance
1. Different metabolic patterns in different organs
E.G. Glycogen phosphorylase,
2. Different locations and metabolic roles for
isoenzymes in the same cell. E.G. Isocitrate
dehydrogenase isoenzymes
3. Different stages of development in embryonic or
fetal tissues and in adult tissues. E.G. LDH, which
changes as the organ develops
4. Different responses of isoenzymes to allosteric
modulators.
E.G. Hexokinase IV (glucokinase)
