2021-05-25

Enzyme Structure, Classification

and
Mechanism of Action

Importance of Enzymes
• Enzymes play an important role in Metabolism,
Diagnosis, and Therapeutics.

• All biochemical reactions are enzyme catalyzed in the

living organism.

• Levels of enzymes in blood are of diagnostic

importance e.g. it is a good indicator in disease such as
myocardial infarction.

• Enzyme can be used therapeutically such as digestive

enzymes.

1
 2021-05-25

Enzymes as Biological Catalysts

• Enzymes are proteins
that increase the rate of
reaction by lowering the
energy of activation.

• They catalyze nearly all

the chemical reactions
taking place in the cells
of the body.

• Enzymes have unique

three-dimensional
shapes that fit the
shapes of reactants
(substrates).

Naming Enzymes
• The name of an enzyme identifies the reacting
substance. Enzyme names usually ends in –ase
E.g. Sucrase catalyzes the hydrolysis of sucrose.
• The name also describes the function of the enzyme
For example, oxidases catalyze oxidation reactions.
• Sometimes common names are used, particularly for
the digestion enzymes such as pepsin and trypsin
• Some names describe both the substrate and the
function.
E.g. Alcohol dehydrogenase oxidizes ethanol.

2
 2021-05-25

Classification of Enzymes

• Enzymes are classified according to the type of

reaction they catalyze:

Class Reactions catalyzed

 Oxidoreductases Oxidation-reduction
 Transferases Transfer groups of atoms
 Hydrolases Hydrolysis
 Lyases Add atoms/remove atoms
to/from a double bond
 Isomerases Rearrange atoms
 Ligases Use ATP to combine molecules

1. Oxidoreductases
Catalyze oxidation-reduction reactions
• The oxidases
• Peroxidases
• Dehydrogenases

3
 2021-05-25

2. Transferases
Catalyze group transfer reactions

• Transfer a functional groups (e.g. methyl or

phosphate) between donor and acceptor molecules.

3. Hydrolases
Catalyze hydrolysis reactions where water is the
acceptor of the transferred group.

Eamples: esterases, peptidases, glycosidases

4
 2021-05-25

4. Lyases
Cleave various bonds by means other than hydrolysis
and oxidation.

Examples: Fumarase, Carbonic anhydrase.

5. Isomerases

Catalyse isomerization changes within a single molecule.

Examples: Isomerase, Mutase

5
 2021-05-25

6. Ligases (synthetases)

Catalyze ligation, or joining of two substrates.

Require chemical energy (e.g. ATP).

Examples: Acetyl~CoA Carboxylase.

Glutamine synthetase

• The active site is a region Active Site

within an enzyme that fits
the shape of substrate
of an Enzyme
molecules.
• Amino acid side-chains
align to bind the
substrate through
hydrogen-bonding, salt-
bridges, hydrophobic
interactions, etc.
• Products are released
when the reaction is
complete (they no longer
fit well in the active site).

6
 2021-05-25

Enzyme Specificity
• Enzymes have varying degrees of specificity for
substrates
• Enzymes may recognize and catalyze:
- a single substrate
- a group of similar substrates
- a particular type of bond

Models of Enzyme Action

a) Lock-and-Key Model
b) Induced Fit Model

7
 2021-05-25

Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- the active site has a rigid shape.
- only substrates with the matching shape can fit.
- the substrate is a key that fits the lock of the active
site.
• This is an older model. However, it does not work for
all enzymes.

Induced Fit Model

• In the induced-fit model of enzyme action:
- the active site is flexible, not rigid.
- the shapes of the enzyme, active site and substrate
adjust to maximize the fit, which improves catalysis.
- there is a greater range of substrate specificity.
• This model is more consistent with a wider range of
enzymes.

8
 2021-05-25

Apoenzyme and Holoenzyme

• The enzyme without its non protein moiety is termed

as apoenzyme and it is inactive.

• Holoenzyme is an active enzyme with its non protein

component.

Important Terms to Understand Biochemical

Nature and Activity of Enzymes

• Cofactor : This is a non-protein chemical compound

that is bound (either tightly or loosely) to an enzyme
and is required for catalysis.

• Types of Cofactors
a) Coenzymes
b) Prosthetic groups.

9
 2021-05-25

Types of Cofactors

Coenzyme: The non-protein component, loosely bound

to apoenzyme by non-covalent bond.

Examples : vitamins or compound derived from

vitamins.

Prosthetic group: The non-protein component, tightly

bound to the apoenzyme by covalent bonds is called a
Prosthetic group.

Structure of enzymes
Enzymes

Complex or holoenzymes (protein part Simple (only protein)

and nonprotein part – cofactor)

Apoenzyme (protein part) Cofactor

Prosthetic groups Coenzyme

-usually small inorganic -large organic

molecule or atom; molecule

-usually tightly bound to -loosely bound to

apoenzyme apoenzyme

10
 2021-05-25

Enzyme Catalyzed Reactions

• When a substrate (S) fits properly in an active site, an
enzyme-substrate (ES) complex is formed:
E + S  ES
• Within the active site of the ES complex, the reaction
occurs to convert substrate to product (P):
ES  E + P
• The products are then released, allowing another
substrate molecule to bind the enzyme. This cycle can
be repeated several times per minute.
• The overall reaction for the conversion of substrate to
product can be written as follows:
E + S  ES  E + P

Example of an Enzyme Catalyzed Reaction

• The reaction for the sucrase catalyzed hydrolysis of
sucrose to glucose and fructose can be written as
follows:
E + S  ES  E + P1 + P2
where E = sucrase, S = sucrose,
P1 = glucose and P2 = fructose

11
 2021-05-25

Isoenzymes

• Isoenzymes are different forms of an enzyme that

catalyze the same reaction in different tissues in the
body.

• They have slight variations in the amino acid

sequences of the subunits of their quaternary
structure.

• For example, lactate dehydrogenase (LDH), which

converts lactate to pyruvate, consists of five
isoenzymes.

12
 2021-05-25

Diagnostic Enzymes

• The levels of diagnostic enzymes in the blood can be

used to determine the amount of damage in specific
tissues

Factors that affect enzyme activity

1. Environmental Conditions: E.g temperature, pH,

substrate concentration, etc

2. Cofactors and Coenzymes: Inorganic substances

(zinc, iron) and vitamins.

3. Enzyme Inhibitors.

13
 2021-05-25

Temperature and Enzyme Activity

• Enzymes are most active at an optimum temperature
(usually 37°C in humans).
• They show little activity at low temperatures.
• Activity is lost at high temperatures as denaturation
occurs.

pH and Enzyme Activity

• Enzymes are most active at optimum pH.
• Amino acids with acidic or basic side-chains have the
proper charges when the pH is optimum.
• Activity is lost at low or high pH as tertiary structure
is disrupted.

14
 2021-05-25

Optimum pH for Selected Enzymes

• Most enzymes of the body have an optimum pH of about 7.4

• However, in certain organs, enzymes operate at lower and

higher optimum pH values.

Enzyme Concentration and Reaction Rate

• The rate of reaction increases as enzyme
concentration increases (at constant substrate
concentration).
• At higher enzyme concentrations, more enzymes are
available to catalyze the reaction (more reactions at
once).
• There is a linear relationship between reaction rate
and enzyme concentration (at constant substrate
concentration).

15
 2021-05-25

Substrate Concentration and Reaction Rate

• The rate of reaction increases as substrate

concentration increases (at constant enzyme
concentration).

• Maximum activity occurs when the enzyme is

saturated (when all enzymes are binding substrate).

• The relationship between reaction rate and substrate

concentration is exponential, and asymptotes (levels
off) when the enzyme is saturated.

Substrate Concentration and Reaction Rate

16
 2021-05-25

Enzyme Inhibitors
• Inhibitors (I) are molecules that cause a loss of
enzyme activity.

• They prevent substrates from fitting into the active

site of the enzyme:

E + S  ES  E + P
E + I  EI  no P formed

Reversible Inhibitors (Competitive Inhibition)

• A reversible inhibitor goes on and off, allowing the

enzyme to regain activity when the inhibitor
leaves.

• A competitive inhibitor is reversible and has a

structure like the substrate.

• It competes with the substrate for the active site.

• Its effect is reversed by increasing substrate

concentration.

17
 2021-05-25

Reversible Inhibitors (Competitive Inhibition)

Example of a Competitive Inhibitor

• Malonate is a competitive inhibitor of succinate
dehydrogenase.
- it has a structure that is similar to succinate
- inhibition can be reversed by adding succinate

18
 2021-05-25

Reversible Inhibitors (Noncompetitive Inhibition)

• A noncompetitive inhibitor has a structure that is
different than that of the substrate.

• It binds to an allosteric site rather than to the active

site.

• It distorts the shape of the enzyme, which alters the

shape of the active site and prevents the binding of the
substrate.

• The effect can not be reversed by adding more

substrate.

Non competitive inhibitors are usually reversible,

but are not influenced by concentrations of the
substrate unlike reversible competitive inhibitor.

19
 2021-05-25

Reversible Inhibitors (Noncompetitive Inhibition)

Irreversible Inhibitors
• An irreversible inhibitor destroys enzyme activity,
usually by bonding with side-chain groups in the
active site.

20