Page 1
Chapter 4
Enzymes and
Bioenergetics
4.1. Enzymes:
Classi??cation and
Mode of Action
4.2. Brief Introduction to
Bioenergetics
4.1 Enzym Es : Classifi Cation and m od E
of a Ction Enzymes are biocatalysts which catalyse the biochemical
reactions both in vivo as well as in vitro. These are highly
speci??c to substrates and have great catalytic power,
i.e., they enhance the rate of reaction tremendously
without being changed. All enzymes are proteins with
exception of some small group of catalytic RNA molecules
called ribozymes. Like proteins, the molecular weight of
enzymes ranges from about 2000 to more than one million
Dalton. Enzymatic activity of proteinaceous enzymes may
be affected depending on the conformational structure as
well as its denaturation. There are many enzymes which
require cofactors for their catalytic activity. The cofactor
may be a complex organic molecule called coenzyme
(Table 4.1) or it may be a metal ion such as Fe
2+
, Mn
2+
,
Zn
2+
, Mg
2+
(Table 4.2). An enzyme plus its cofactor is called
holoenzyme. In such cases, the protein component in
cofactor requiring enzyme is called apoenzyme.
Chapter 4 enzymes and Bioengertics.indd 85 09/01/2025 15:22:06
Reprint 2025-26
Page 2
Chapter 4
Enzymes and
Bioenergetics
4.1. Enzymes:
Classi??cation and
Mode of Action
4.2. Brief Introduction to
Bioenergetics
4.1 Enzym Es : Classifi Cation and m od E
of a Ction Enzymes are biocatalysts which catalyse the biochemical
reactions both in vivo as well as in vitro. These are highly
speci??c to substrates and have great catalytic power,
i.e., they enhance the rate of reaction tremendously
without being changed. All enzymes are proteins with
exception of some small group of catalytic RNA molecules
called ribozymes. Like proteins, the molecular weight of
enzymes ranges from about 2000 to more than one million
Dalton. Enzymatic activity of proteinaceous enzymes may
be affected depending on the conformational structure as
well as its denaturation. There are many enzymes which
require cofactors for their catalytic activity. The cofactor
may be a complex organic molecule called coenzyme
(Table 4.1) or it may be a metal ion such as Fe
2+
, Mn
2+
,
Zn
2+
, Mg
2+
(Table 4.2). An enzyme plus its cofactor is called
holoenzyme. In such cases, the protein component in
cofactor requiring enzyme is called apoenzyme.
Chapter 4 enzymes and Bioengertics.indd 85 09/01/2025 15:22:06
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Biotechnology 86
Table 4.1: Some coenzymes and their precursor vitamins and their role
Coenzyme Precursor vitamin Role in the catalytic reaction
Biocytin Biotin (vitamin B7) Transfer of CO
2
Coenzyme B12 (5'-adenosylcobalamin) Vitamin B12 Transfer of an alkyl group
Flavin adenine dinucleotide (FAD) Ribo??avin (vitamin B2) Transfer of electrons
Coenzyme A
Pantothenic acid
(vitamin B5)
Transfer of acyl and alkyl group
Nicotinamide adenine dinucleotide (NAD) Niacin (vitamin B3) Transfer of hydride (:H
-
)
Pyridoxal phosphate Pyridoxine (vitamin B6) Transfer of amino group
Thiamine pyrophosphate Thiamine (vitamin B1) Transfer of aldehydes
Tetrahydrofolate Folic acid (vitamin B9) Transfer of one carbon group
Coenzymes take part in catalysis transiently and are
carriers of speci??c functional groups. Most of the
coenzymes are derived from vitamins (organic nutrients
required in small amounts in diet).
Table 4.2: Metal ions that serve as cofactors for enzymes
Metal Ions Enzyme name
Fe
2+
or Fe
3+
Catalase, peroxidase, cytochrome oxidase
Cu
2+
Cytochrome oxidase
Mg
2+
DNA polymerase
Mn
2+
Arginase
K
+
Pyruvate kinase
Mo
2+
Nitrogenase, nitrate reductase
Zn
2+
Carbonic anhydrase, alcohol dehydrogenase
Ni
2+
Urease
When a coenzyme or metal ion is tightly bound through
covalent bond with the enzyme protein, it is called a
prosthetic group.
4.1.1 Classi??cation of enzymes
In order to have a systematic study and to avoid ambiguities
considering the fact that new enzymes may also be
Chapter 4 enzymes and Bioengertics.indd 86 09/01/2025 15:22:07
Reprint 2025-26
Page 3
Chapter 4
Enzymes and
Bioenergetics
4.1. Enzymes:
Classi??cation and
Mode of Action
4.2. Brief Introduction to
Bioenergetics
4.1 Enzym Es : Classifi Cation and m od E
of a Ction Enzymes are biocatalysts which catalyse the biochemical
reactions both in vivo as well as in vitro. These are highly
speci??c to substrates and have great catalytic power,
i.e., they enhance the rate of reaction tremendously
without being changed. All enzymes are proteins with
exception of some small group of catalytic RNA molecules
called ribozymes. Like proteins, the molecular weight of
enzymes ranges from about 2000 to more than one million
Dalton. Enzymatic activity of proteinaceous enzymes may
be affected depending on the conformational structure as
well as its denaturation. There are many enzymes which
require cofactors for their catalytic activity. The cofactor
may be a complex organic molecule called coenzyme
(Table 4.1) or it may be a metal ion such as Fe
2+
, Mn
2+
,
Zn
2+
, Mg
2+
(Table 4.2). An enzyme plus its cofactor is called
holoenzyme. In such cases, the protein component in
cofactor requiring enzyme is called apoenzyme.
Chapter 4 enzymes and Bioengertics.indd 85 09/01/2025 15:22:06
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Biotechnology 86
Table 4.1: Some coenzymes and their precursor vitamins and their role
Coenzyme Precursor vitamin Role in the catalytic reaction
Biocytin Biotin (vitamin B7) Transfer of CO
2
Coenzyme B12 (5'-adenosylcobalamin) Vitamin B12 Transfer of an alkyl group
Flavin adenine dinucleotide (FAD) Ribo??avin (vitamin B2) Transfer of electrons
Coenzyme A
Pantothenic acid
(vitamin B5)
Transfer of acyl and alkyl group
Nicotinamide adenine dinucleotide (NAD) Niacin (vitamin B3) Transfer of hydride (:H
-
)
Pyridoxal phosphate Pyridoxine (vitamin B6) Transfer of amino group
Thiamine pyrophosphate Thiamine (vitamin B1) Transfer of aldehydes
Tetrahydrofolate Folic acid (vitamin B9) Transfer of one carbon group
Coenzymes take part in catalysis transiently and are
carriers of speci??c functional groups. Most of the
coenzymes are derived from vitamins (organic nutrients
required in small amounts in diet).
Table 4.2: Metal ions that serve as cofactors for enzymes
Metal Ions Enzyme name
Fe
2+
or Fe
3+
Catalase, peroxidase, cytochrome oxidase
Cu
2+
Cytochrome oxidase
Mg
2+
DNA polymerase
Mn
2+
Arginase
K
+
Pyruvate kinase
Mo
2+
Nitrogenase, nitrate reductase
Zn
2+
Carbonic anhydrase, alcohol dehydrogenase
Ni
2+
Urease
When a coenzyme or metal ion is tightly bound through
covalent bond with the enzyme protein, it is called a
prosthetic group.
4.1.1 Classi??cation of enzymes
In order to have a systematic study and to avoid ambiguities
considering the fact that new enzymes may also be
Chapter 4 enzymes and Bioengertics.indd 86 09/01/2025 15:22:07
Reprint 2025-26
e nzym e s and Bio e n e rg e tics 87
discovered, International Union of Biochemistry (I.U.B.)
in 1964 has adopted classi??cation of enzymes depending
on the type of reactions they catalyze. According to this
commission, all enzymes are classi??ed into 6 major
classes, but recently, another class of enzymes namely
translocase has been added (Table 4.3).
Table 4.3: Classi??cation of enzymes adopted by I.U.B.
Class
No.
Class name Type of reaction catalyze
1. Oxidoreductases Oxidation-reduction reactions (transfer of electrons)
2. Transferases Transfer of groups
3. Hydrolases Hydrolytic reactions (transfer of functional groups to water)
4. Lyases Addition or removal of groups to form double bonds
5. Isomerases Transfer of groups within molecules to yield isomeric forms
6. Ligases Condensation of two molecules coupled through ATP hydrolysis
7. Translocase Transfer of ion/molecules across the membrane
Isozymes
Many enzymes are present in multiple forms (more than
one molecular form) in the same species, tissue or even
in the same cell. These enzymes are called isoenzymes
or isozymes. Isoenzymes catalyse the same reaction but
have different amino acid composition, hence, possess
different physicochemical properties. For example, a
glycolytic enzyme, hexokinase exists in four isozyme forms
in various tissues. Similarly, lactate dehydrogenase (LDH),
involved in anaerobic glucose metabolism has five isozyme
forms in human.
Enzyme active site
The catalytic reaction performed by enzymes occurs at a
particular site on the enzyme. This site is called active
site, and represents only small part of the total size of
the enzyme. The active site is a clearly de??ned pocket or
cleft in the enzyme molecule where the whole or a portion
of substrate can ??t. Active site has a three-dimensional
structure since it consists of portions of a polypeptide
chain. Various non-covalent bonds involved in enzyme
substrate binding are electrostatic interactions, hydrogen
bonds, Van der Waals forces and hydrophobic interactions.
Chapter 4 enzymes and Bioengertics.indd 87 09/01/2025 15:22:07
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Page 4
Chapter 4
Enzymes and
Bioenergetics
4.1. Enzymes:
Classi??cation and
Mode of Action
4.2. Brief Introduction to
Bioenergetics
4.1 Enzym Es : Classifi Cation and m od E
of a Ction Enzymes are biocatalysts which catalyse the biochemical
reactions both in vivo as well as in vitro. These are highly
speci??c to substrates and have great catalytic power,
i.e., they enhance the rate of reaction tremendously
without being changed. All enzymes are proteins with
exception of some small group of catalytic RNA molecules
called ribozymes. Like proteins, the molecular weight of
enzymes ranges from about 2000 to more than one million
Dalton. Enzymatic activity of proteinaceous enzymes may
be affected depending on the conformational structure as
well as its denaturation. There are many enzymes which
require cofactors for their catalytic activity. The cofactor
may be a complex organic molecule called coenzyme
(Table 4.1) or it may be a metal ion such as Fe
2+
, Mn
2+
,
Zn
2+
, Mg
2+
(Table 4.2). An enzyme plus its cofactor is called
holoenzyme. In such cases, the protein component in
cofactor requiring enzyme is called apoenzyme.
Chapter 4 enzymes and Bioengertics.indd 85 09/01/2025 15:22:06
Reprint 2025-26
Biotechnology 86
Table 4.1: Some coenzymes and their precursor vitamins and their role
Coenzyme Precursor vitamin Role in the catalytic reaction
Biocytin Biotin (vitamin B7) Transfer of CO
2
Coenzyme B12 (5'-adenosylcobalamin) Vitamin B12 Transfer of an alkyl group
Flavin adenine dinucleotide (FAD) Ribo??avin (vitamin B2) Transfer of electrons
Coenzyme A
Pantothenic acid
(vitamin B5)
Transfer of acyl and alkyl group
Nicotinamide adenine dinucleotide (NAD) Niacin (vitamin B3) Transfer of hydride (:H
-
)
Pyridoxal phosphate Pyridoxine (vitamin B6) Transfer of amino group
Thiamine pyrophosphate Thiamine (vitamin B1) Transfer of aldehydes
Tetrahydrofolate Folic acid (vitamin B9) Transfer of one carbon group
Coenzymes take part in catalysis transiently and are
carriers of speci??c functional groups. Most of the
coenzymes are derived from vitamins (organic nutrients
required in small amounts in diet).
Table 4.2: Metal ions that serve as cofactors for enzymes
Metal Ions Enzyme name
Fe
2+
or Fe
3+
Catalase, peroxidase, cytochrome oxidase
Cu
2+
Cytochrome oxidase
Mg
2+
DNA polymerase
Mn
2+
Arginase
K
+
Pyruvate kinase
Mo
2+
Nitrogenase, nitrate reductase
Zn
2+
Carbonic anhydrase, alcohol dehydrogenase
Ni
2+
Urease
When a coenzyme or metal ion is tightly bound through
covalent bond with the enzyme protein, it is called a
prosthetic group.
4.1.1 Classi??cation of enzymes
In order to have a systematic study and to avoid ambiguities
considering the fact that new enzymes may also be
Chapter 4 enzymes and Bioengertics.indd 86 09/01/2025 15:22:07
Reprint 2025-26
e nzym e s and Bio e n e rg e tics 87
discovered, International Union of Biochemistry (I.U.B.)
in 1964 has adopted classi??cation of enzymes depending
on the type of reactions they catalyze. According to this
commission, all enzymes are classi??ed into 6 major
classes, but recently, another class of enzymes namely
translocase has been added (Table 4.3).
Table 4.3: Classi??cation of enzymes adopted by I.U.B.
Class
No.
Class name Type of reaction catalyze
1. Oxidoreductases Oxidation-reduction reactions (transfer of electrons)
2. Transferases Transfer of groups
3. Hydrolases Hydrolytic reactions (transfer of functional groups to water)
4. Lyases Addition or removal of groups to form double bonds
5. Isomerases Transfer of groups within molecules to yield isomeric forms
6. Ligases Condensation of two molecules coupled through ATP hydrolysis
7. Translocase Transfer of ion/molecules across the membrane
Isozymes
Many enzymes are present in multiple forms (more than
one molecular form) in the same species, tissue or even
in the same cell. These enzymes are called isoenzymes
or isozymes. Isoenzymes catalyse the same reaction but
have different amino acid composition, hence, possess
different physicochemical properties. For example, a
glycolytic enzyme, hexokinase exists in four isozyme forms
in various tissues. Similarly, lactate dehydrogenase (LDH),
involved in anaerobic glucose metabolism has five isozyme
forms in human.
Enzyme active site
The catalytic reaction performed by enzymes occurs at a
particular site on the enzyme. This site is called active
site, and represents only small part of the total size of
the enzyme. The active site is a clearly de??ned pocket or
cleft in the enzyme molecule where the whole or a portion
of substrate can ??t. Active site has a three-dimensional
structure since it consists of portions of a polypeptide
chain. Various non-covalent bonds involved in enzyme
substrate binding are electrostatic interactions, hydrogen
bonds, Van der Waals forces and hydrophobic interactions.
Chapter 4 enzymes and Bioengertics.indd 87 09/01/2025 15:22:07
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Biotechnology 88
Fischer’s Lock and Key Model
In 1894, the introduction of Lock and Key Model for the
substrate and enzyme interaction was proposed by Emil
Fischer. According to this model, complementary structural
features are present between enzyme and substrate, and
the active site is pre-shaped to ??t the substrate. The
substrate can ??t into its complementary site on the enzyme
as a key ??ts into a lock. This results in the formation of an
enzyme-substrate complex (Fig. 4.1).
Koshland’s Induced Fit Model
Daniel Koshland in 1958 proposed Induced Fit Hypothesis.
He suggested that the structure of a substrate may be
complementary to that of the active site in the enzyme-
substrate complex but not in the free enzyme. The interaction
between the substrate and the enzyme induces
conformational changes in the enzyme which aligns the
amino acid residues or other groups for substrate binding,
catalysis, or both (Fig 4.2). The relationship between a
substrate and an active site resembles hand and glove.
During interaction, the structure of one component, i.e.,
substrate or hand remains rigid and the shape of the second
+
Enzyme Substrate Enzyme Substrate
complex
Fig. 4.1: Interaction between an enzyme and its substrate accord-
ing to lock and key model
Fig. 4.2: Interaction between an enzyme and its substrate according
to induced ??t model
+
Enzyme Substrate Enzyme Substrate
complex
Chapter 4 enzymes and Bioengertics.indd 88 09/01/2025 15:22:07
Reprint 2025-26
Page 5
Chapter 4
Enzymes and
Bioenergetics
4.1. Enzymes:
Classi??cation and
Mode of Action
4.2. Brief Introduction to
Bioenergetics
4.1 Enzym Es : Classifi Cation and m od E
of a Ction Enzymes are biocatalysts which catalyse the biochemical
reactions both in vivo as well as in vitro. These are highly
speci??c to substrates and have great catalytic power,
i.e., they enhance the rate of reaction tremendously
without being changed. All enzymes are proteins with
exception of some small group of catalytic RNA molecules
called ribozymes. Like proteins, the molecular weight of
enzymes ranges from about 2000 to more than one million
Dalton. Enzymatic activity of proteinaceous enzymes may
be affected depending on the conformational structure as
well as its denaturation. There are many enzymes which
require cofactors for their catalytic activity. The cofactor
may be a complex organic molecule called coenzyme
(Table 4.1) or it may be a metal ion such as Fe
2+
, Mn
2+
,
Zn
2+
, Mg
2+
(Table 4.2). An enzyme plus its cofactor is called
holoenzyme. In such cases, the protein component in
cofactor requiring enzyme is called apoenzyme.
Chapter 4 enzymes and Bioengertics.indd 85 09/01/2025 15:22:06
Reprint 2025-26
Biotechnology 86
Table 4.1: Some coenzymes and their precursor vitamins and their role
Coenzyme Precursor vitamin Role in the catalytic reaction
Biocytin Biotin (vitamin B7) Transfer of CO
2
Coenzyme B12 (5'-adenosylcobalamin) Vitamin B12 Transfer of an alkyl group
Flavin adenine dinucleotide (FAD) Ribo??avin (vitamin B2) Transfer of electrons
Coenzyme A
Pantothenic acid
(vitamin B5)
Transfer of acyl and alkyl group
Nicotinamide adenine dinucleotide (NAD) Niacin (vitamin B3) Transfer of hydride (:H
-
)
Pyridoxal phosphate Pyridoxine (vitamin B6) Transfer of amino group
Thiamine pyrophosphate Thiamine (vitamin B1) Transfer of aldehydes
Tetrahydrofolate Folic acid (vitamin B9) Transfer of one carbon group
Coenzymes take part in catalysis transiently and are
carriers of speci??c functional groups. Most of the
coenzymes are derived from vitamins (organic nutrients
required in small amounts in diet).
Table 4.2: Metal ions that serve as cofactors for enzymes
Metal Ions Enzyme name
Fe
2+
or Fe
3+
Catalase, peroxidase, cytochrome oxidase
Cu
2+
Cytochrome oxidase
Mg
2+
DNA polymerase
Mn
2+
Arginase
K
+
Pyruvate kinase
Mo
2+
Nitrogenase, nitrate reductase
Zn
2+
Carbonic anhydrase, alcohol dehydrogenase
Ni
2+
Urease
When a coenzyme or metal ion is tightly bound through
covalent bond with the enzyme protein, it is called a
prosthetic group.
4.1.1 Classi??cation of enzymes
In order to have a systematic study and to avoid ambiguities
considering the fact that new enzymes may also be
Chapter 4 enzymes and Bioengertics.indd 86 09/01/2025 15:22:07
Reprint 2025-26
e nzym e s and Bio e n e rg e tics 87
discovered, International Union of Biochemistry (I.U.B.)
in 1964 has adopted classi??cation of enzymes depending
on the type of reactions they catalyze. According to this
commission, all enzymes are classi??ed into 6 major
classes, but recently, another class of enzymes namely
translocase has been added (Table 4.3).
Table 4.3: Classi??cation of enzymes adopted by I.U.B.
Class
No.
Class name Type of reaction catalyze
1. Oxidoreductases Oxidation-reduction reactions (transfer of electrons)
2. Transferases Transfer of groups
3. Hydrolases Hydrolytic reactions (transfer of functional groups to water)
4. Lyases Addition or removal of groups to form double bonds
5. Isomerases Transfer of groups within molecules to yield isomeric forms
6. Ligases Condensation of two molecules coupled through ATP hydrolysis
7. Translocase Transfer of ion/molecules across the membrane
Isozymes
Many enzymes are present in multiple forms (more than
one molecular form) in the same species, tissue or even
in the same cell. These enzymes are called isoenzymes
or isozymes. Isoenzymes catalyse the same reaction but
have different amino acid composition, hence, possess
different physicochemical properties. For example, a
glycolytic enzyme, hexokinase exists in four isozyme forms
in various tissues. Similarly, lactate dehydrogenase (LDH),
involved in anaerobic glucose metabolism has five isozyme
forms in human.
Enzyme active site
The catalytic reaction performed by enzymes occurs at a
particular site on the enzyme. This site is called active
site, and represents only small part of the total size of
the enzyme. The active site is a clearly de??ned pocket or
cleft in the enzyme molecule where the whole or a portion
of substrate can ??t. Active site has a three-dimensional
structure since it consists of portions of a polypeptide
chain. Various non-covalent bonds involved in enzyme
substrate binding are electrostatic interactions, hydrogen
bonds, Van der Waals forces and hydrophobic interactions.
Chapter 4 enzymes and Bioengertics.indd 87 09/01/2025 15:22:07
Reprint 2025-26
Biotechnology 88
Fischer’s Lock and Key Model
In 1894, the introduction of Lock and Key Model for the
substrate and enzyme interaction was proposed by Emil
Fischer. According to this model, complementary structural
features are present between enzyme and substrate, and
the active site is pre-shaped to ??t the substrate. The
substrate can ??t into its complementary site on the enzyme
as a key ??ts into a lock. This results in the formation of an
enzyme-substrate complex (Fig. 4.1).
Koshland’s Induced Fit Model
Daniel Koshland in 1958 proposed Induced Fit Hypothesis.
He suggested that the structure of a substrate may be
complementary to that of the active site in the enzyme-
substrate complex but not in the free enzyme. The interaction
between the substrate and the enzyme induces
conformational changes in the enzyme which aligns the
amino acid residues or other groups for substrate binding,
catalysis, or both (Fig 4.2). The relationship between a
substrate and an active site resembles hand and glove.
During interaction, the structure of one component, i.e.,
substrate or hand remains rigid and the shape of the second
+
Enzyme Substrate Enzyme Substrate
complex
Fig. 4.1: Interaction between an enzyme and its substrate accord-
ing to lock and key model
Fig. 4.2: Interaction between an enzyme and its substrate according
to induced ??t model
+
Enzyme Substrate Enzyme Substrate
complex
Chapter 4 enzymes and Bioengertics.indd 88 09/01/2025 15:22:07
Reprint 2025-26
e nzym e s and Bio e n e rg e tics 89
component, i.e., active site or glove ??exible to become
complementary to that of the ??rst.
Enzyme speci??city
The enzymes are highly speci??c in action. In fact, the
properties that make enzymes such a strong catalyst
are their speci??city of substrate binding and their ideal
arrangement of catalytic groups. Various types of enzyme
speci??city are: group speci??city, absolute speci??city,
stereospeci??city, and geometrical speci??city. When
enzymes act on several different closely related substrates
then it is called group speci??city . When enzymes act
only on one particular substrate, it is called absolute
speci??city . Stereochemical or optical speci??city
occurs when substrate exists in two stereochemical forms
(chemically identical but different arrangement of atoms
in three-dimensional space) then only one of the isomers
will undergo reaction by particular enzyme. For example,
D-amino acid oxidase catalyses oxidation of the D-amino
acids to keto acids. In geometrical speci??city , enzymes
are speci??c towards cis and trans forms. For example,
fumarase catalyses the interconversion of fumarate and
malate.
4.1.2 Factors affecting enzyme activity
Rate of enzyme catalysed reactions is
in??uenced by changing the environmental
conditions. The important factors that
in??uence the velocity of enzyme catalysed
reactions are temperature, pH, substrate
concentration, and modulators.
1. Temperature
The rate of an enzyme catalysed reaction
increases with the increase in temperature
up to a maximum and then falls. When
a graph is plotted between temperature
versus enzyme activity, a bell-shaped curve
is obtained (Fig. 4.3). The temperature at
which the maximum rate of reaction occurs
is called the enzyme’s optimum temperature.
The optimum temperature is different
for different enzymes; but for most of the
Optimum
temperature
Reaction velocity
Tem erature (ºC) p
Fig. 4.3: Effect of temperature on enzyme
activity
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