Biology Student’s Companion Resources SB 025

CHAPTER 4: BIOCATALYSIS

SUBTOPIC : 4.1 Properties of enzymes and mechanism of actions

LEARNING OUTCOMES:
a) State the properties of enzymes.
b) State the six classes of enzyme according to IUBMB classification
c) Explain how enzyme lowering activation energy.
d) Illustrate to explain the mechanism of action based on induced fit model.
e) State the factors that affect the enzymatic reaction
MAIN IDEAS
EXPLANATION NOTES
/KEY POINT

Enzymes • An organic catalyst (usually a protein)

• that speeds up / accelerates a specific chemical reaction
• by lowering activation energy (EA) required for that reaction
• without itself being affected or consumed by the reaction

Properties of 1. Required only in small amount.

enzymes 2. They are not altered irreversibly during the course of reaction.
3. They (the active site) are highly specific to their substrates.
4. They have no effect on the thermodynamics of the reaction.
5. Denatured by high temperature and extreme pH.
6. Speed up the chemical reactions (by lowering the activation energy)

Classification • A systematic nomenclature for enzymes was recommended by the

of enzymes International Union of Biochemistry and Molecular Biology
(IUBMB).
• Each enzyme was allocated a trivial name:
o The name of the substrate act upon the enzyme
o The type of reaction catalyzed
o The suffix –ase
o E.g: urase, sucrase, protease.

Enzyme Type of reaction Enzyme examples

Group catalyzed

1.Oxidoreductases Transfer of O and H • Dehydrogenase

atoms between • Oxidase
substances. • Catalase
All oxidation-
reduction reactions.

2. Transferases Transfer of a • Transaminase

functional group from • Phosphorylase
one substance to • Kinase
another.
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MAIN IDEAS
EXPLANATION NOTES
/KEY POINT
3. Hydrolases Hydrolysis reactions • Peptidase
• Lipase
• Amylase

4. Lyases Addition or removal • Pyruvate

of a functional group decarboxylase
without addition of
water

5. Isomerases Catalyze geometric or • Phosphoglucomutase

structural • Mutase
rearrangement within • Isomerase
one molecule

6. Ligases Formation of bonds • Synthetase

between two • DNA ligase
molecules using
energy derived from
the breakdown of
ATP

Activation • The initial energy needed to start a chemical reaction is called the
energy free energy of activation, or activation energy (EA).
• Activation energy is often supplied in the form of heat from the
surroundings

How do • Enzyme lowers the activation energy (EA) (or barrier) necessary to
enzymes initiate a chemical reaction
works

Mechanism of • The reactant that an enzyme acts on is called the enzyme’s

enzymes substrate.
action. • The active site is the region on the enzyme where the substrate
binds.
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MAIN IDEAS
EXPLANATION NOTES
/KEY POINT
• In an enzymatic reaction, the substrate binds to the active site of the
enzyme
• Forming an enzyme-substrate complex.
• Substate converted into product.
• Product no longer fit the active site and product are release
• The active site of enzyme is available for another substrate.

Catalysis in • The active site can lower an EA barrier by:

the Enzyme’s o Orienting substrates correctly
Active Site o Straining and weaken substrate bonds
o Facilitate breaking of bonds in substrate or formation of new bonds
o Providing a favorable microenvironment
o Covalently bonding to the substrate

Induced Fit Model

Mechanism of
enzyme action

Induced Fit
Model

1. Active site (enzyme) is able to change its shape to enfold a substrate

molecule.
• Distorted enzyme molecule in turn distorts the substrate molecule.
• Straining or twisting the bonds.
• Substrates less stable and thus lowering EA.

2. Products that formed no longer bind to the active site are then released.
❖ Enzyme returns to its original shape.
❖ Ready to bind the next substrate molecule

Factors that • The rate of an enzyme-catalyzed reaction is affected by four factors.

affect the • Chemical and physical factors that alter the enzyme’s 3-D shape are:
enzymes ▪ Temperature
reactions ▪ pH
▪ Concentration of substrate.
▪ Concentration of enzyme.

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Effect of Each enzyme has an optimal temperature at which an enzyme produces the
temperature highest production rate.

▪ Optimal conditions favor the most active shape for the enzyme.
▪ Effects the movement of enzyme.
▪ Increase temperature: The rate of an enzymatic reactions will
increase.
▪ Substrates collide with active sites more frequently.
▪ Fastest conversion of the reactants to product molecules.
▪ Above optimal temperature: Enzymes become denatured
▪ Because high temperature causes the atoms making up the enzyme
molecule to vibrate or have great kinetic energy
▪ The vibration breaks the hydrogen bonds and other bonds that hold
the enzyme
▪ Rate of reaction drops sharply

Effect of pH ▪ Different enzymes, different optimum pH.

Example: Pepsin and Trypsin
▪ Enzymes prefer to work at an optimum pH.
▪ Outside of its pH range the enzyme is denatured because high or low pH
may disrupt hydrogen bonding or ionic interactions and thus change the
shape of active site.

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Effect of ▪ The amount of substrate will affect the rate of reaction.

substrate ▪ Substrate concentration increases, rate of reaction will increase
concentration proportionally.
▪ Then it will level off
▪ All the enzyme molecules (active sites) are occupied

Effect of ▪ At low enzyme concentration, the rate of reaction is low.

enzyme ▪ Great competition for the active sites.
concentration ▪ As the enzyme concentration increases, the reaction can proceed at a
faster rate.
▪ more active sites provided.
▪ Substrate as a limiting factor.

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SUBTOPIC : 4.2 Cofactors

LEARNING OUTCOMES:
• Define cofactor
• Explain the three types of cofactors and functions of:
• i. Metal ion activators (example Mg2+).
• ii. Coenzyme (example NAD+)
• iii. Prosthetic group (example haem group)

MAIN IDEAS
EXPLANATION NOTES
/KEY POINT

Cofactors ▪ One or more non protein components required by enzymes

in order to function efficiently.
▪ Atom or molecules that are not part of the enzyme’s primary
structure.

Types of There are three types of cofactors:

cofactors
No Cofactors Examples
1. Metal Ions/Activator • e.g Ca2+, Zn2+, Mg2+, Cl-
(Inorganic)

2. Coenzymes ▪ Vitamin B6 and B12, NAD+

(from the niacin vitamin)
3. Prosthetic group • e.g haem group
and FAD

Metal ion • Non-protein inorganic substances.

• Assist in forming ES complex by bind temporarily either
enzyme or substrate molecule into more suitable shape.

• Non-protein organic or organometallic substances.

Coenzymes • Tightly or weakly bound to the enzyme.
• Most vitamins act as coenzymes or raw material from which
coenzymes are made.

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MAIN IDEAS
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Prosthetic • A metal or Coenzymes that are covalently or noncovalently
group bound very tightly to the enzyme.
• Example: prosthetic group of electron carrier cytochrome and
enzyme catalase. FAD (riboflavin) - prosthetic group of the
electron carrier cytochrome. It takes part in oxidation-
reduction reactions.

Functions of • Aassist in forming the enzyme-substrate complex by altering

cofactors the active site into a more suitable shape.
• May function to withdraw electrons from the substrate.
• May involve in transfer of electrons / atoms / chemical groups
in enzyme reactions.

SUBTOPIC : 4.3 Inhibitors

LEARNING OUTCOMES:
• Define inhibitor.
• Explain the roles and types of inhibitors:
i. competitive inhibitors
ii. non competitive inhibitors.
• Analyze graph related to competitive and non competitive inhibition.

MAIN IDEAS
EXPLANATION NOTES
/KEY POINT

Inhibitors • A substance that binds to an enzyme and decreases its activity.

Types of There are TWO types of inhibitors:

inhibitors 1. Competitive Inhibitor
2. Non-competitive Inhibitor

• Has close structural similarity to the normal substrate.

Competitive • Inhibitor & substrate “compete” for active site.
inhibitor • Bind reversibly to the active site (loosely bind).

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MAIN IDEAS
EXPLANATION NOTES
/KEY POINT
• Effect is temporarily to the enzyme.
• Enzyme can be reused again (do not destroy and do not
denatured).
• Causes No Permanent Damage to the enzyme

Non- • Shape of inhibitor is NOT SIMILAR to the shape of

competitive substrate.
inhibitor • Inhibitor will DO NOT directly compete with the substrate
to bind to the enzyme at the active site.
• Inhibitor binds to site other than active site which is
Allosteric site (Regulatory site)
• When the inhibitor is present, it fits into its site.
• Causes enzyme (active site) to change shape
(Conformational change).
• The substrate cannot bind with the enzyme.

Graph related
to competitive
and non-
competitive
inhibition.

Rate of reaction with competitive inhibitor is higher than rate of

reaction with non competitive inhibitor.

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