Chapter 1

ENZYMES
BIO150
Metabolism & Cell Division

Learning Objectives
At the end of this topic, students should be able:
1. To state the general characteristics of enzymes
2. To relate between enzyme and activation energy
3. To describe the enzyme specificity based on:

Key and Lock Model

Induced Fit Model

To identify the factors affecting enzyme activities

5. To describe enzymes inhibition
6. To classify types of enzymes
4.

Enzymes
Enzyme
A protein molecule serving as a biological catalyst, that speed up

the rate of chemical reaction by lowering the activation energy

without being consumed by the reaction.

Substrate / Reactant
A substrate on which an enzyme works

Active Site
The specific portion of an enzyme that binds the substrate by

means of multiple weal interactions and that forms the pocket in

which catalysis occur.

General Characteristics of Enzymes

1.
2.
3.
4.
5.

Made up of globular protein and coded for by DNA.

Catalysts because they can speed up chemical reactions
but stay unchanged at the end of the reaction.
Have active site where at this location the reaction
occurs.
Very specific, that is an enzyme can catalyze only a single
reaction.
Have the ability to lower the activation energy of the
reactions they catalyze.

6.

Work very efficient, where a very small amount of

enzyme can change a large amount of substrate into
products.
Eg: A single molecule of enzyme catalase can breakdown 40
million of hydrogen peroxide (H2O2) per second!

The catalyzing reaction of enzyme is reversible.

8. The activity of enzyme is affected by many factors. (eg.
Enzyme concentration, temperature and pH)
9. The presence of enzyme does not change the
properties of the end-product of the reactions.
7.

EXTRA NOTES
The specificity of enzyme:
Enzymes are substrate specific.
Each enzyme has a unique 3D shape.
The 3D shape will recognize and bind only the specific
substrate. Enzyme active site must be 100% complementary
with the substrate.

Relationship Between Enzyme and

Activation Energy
Every chemical reaction between molecules involves both

bond breaking and bond forming.

Changing one molecule into another generally involves
contorting the starting molecule into a highly
unstable state before the reaction can proceed.
To reach the contorted state where bonds can change,
reactants molecules must absorb energy from their
surroundings.

 When the new bonds of the product molecules form,

energy is released as heat, and the molecules return

to stable shapes with lower energy then the contorted
state.
The amount of energy that reactants must absorb
before a chemical reaction will start (the energy
required to contort the reactants molecules so the bonds can
break), is known as free energy of activation or activation
energy, EA.

The reactants must absorb

enough energy from the
surroundings to reach the
unstable transition state,
where bonds can break.

After bonds have broken,

new bonds form, releasing
energy to the surrounding.
Transition
state

Energy profile of an exergonic reaction

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Enzyme Specificity relating to Key and

Lock Model

1.
2.

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3.
4.
5.
6.

Substrate enter active site.

Substrates are held in active site by weak interactions, such as
hydrogen bonds and ionic bonds.
Active site can lower EA and speed up the chemical reaction.
Substrates are converted to products.
Products are released.
Active site is available for new substrate molecule.

Enzyme Specificity relating to Induced

Fit Model

1.
2.
3.
4.
5.
6.
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Substrates enter active site, enzyme changes shape such that its active site
enfolds the substrates (induced fit).
Substrates are held in active site by weak interactions, such as hydrogen
bonds and ionic bonds.
Active site can lower EA and speed up the chemical reaction.
Substrates are converted to products.
Products are released.
The enzyme returns to its original shape and active site is available for new
substrate molecule.

Induced Fit Model vs Key & Lock Model

Two models of enzyme reaction have been proposed.

According to the lock and key model, when the key

(substrate) fits the lock (active site), the chemical change
begins.
However, modern X-ray crystallographic and spectroscopic
methods show that in many cases the enzyme changes shape
when the substrate lands at the active site.

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Factors Affecting Enzyme Activities

A. Enzyme Concentration
The higher the concentration of enzyme, the faster the
rate of reaction as more substrate reacted.
However, as a reaction proceeds, the rate of reaction will
decrease as substrate (the limiting factor) will get used up.

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More enzyme molecules can react with more substrate

molecules, so the reaction rate increases.
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B. Substrate Concentration
The higher the substrate concentration, the higher the rate of
reaction because more substrate molecules will be
colliding with enzyme molecules, so more product will
be formed.
However, after a certain concentration, any increase will have
no effect on the rate of reaction since the enzyme become
limited (limiting factor).
The enzymes become saturated, and will be working at their
maximum possible rate.
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C.Temperature
Each enzyme has an optimal temperature at which its
reaction rate is the greatest.
The rate of enzymatic reaction increases with increasing
temperature. However, above the optimal temperature, the
speed of enzymatic reaction drops sharply as the enzyme
denatured.

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D. pH
The activity of enzyme is strongly affected by changes of pH.
Different enzymes have different optimum pH values.
This is the pH value at which the bonds within them are
influenced by H+ and OH- ions in such a way that the shape
of their active site is the most complementary to the shape of
their substrate.
At the optimum pH, the rate of reaction is at an optimum.

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Negative Feedback Inhibition (Endproduct Inhibition)

How does cell regulate enzymatic activity?
If the product of a series of enzymatic reactions such as
amino acid, begins to accumulate within the cell, the
product act as an allosteric inhibitor and it may
specifically inhibit the action of the first enzyme
involved in its synthesis. Thus the product begins to switch
off its own production as it accumulates.
The process is self-regulatory.
When the product being used up, its production is switched
back on again.
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Negative Feedback Inhibition

For eg: the final product of enzyme 4 is histidine. An

increasing concentration of histidine slowly turn off the

activity of enzyme 1.

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Allosteric Regulation
Another method of enzymatic control is the binding

of a regulation molecule to a protein at one site that

affects the function of the protein at a different
site.
Other than the active site, some enzymes have a
receptor site, called an allosteric site.
Substrates that affect enzyme activity by binding to the
allosteric site are called allosteric regulators.
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Allosteric Enzymes
1. The allosteric means another space, and the

characteristics of such enzyme is that they can exist in

two different forms (active and inactive).
2. The inactive form is shaped in such a way that the
substrate will not fit into the active site. For the
enzyme to work, it must be converted into the
active form (changing shape), so that the substrate
will fit into the active site.
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3. The allosteric inhibitor prevents the enzyme

from changing its shape into the active form.

The binding of allosteric inhibitor to enzyme
resembles non-competitive reversible inhibition.
4. Some allosteric regulators are activators which
result in an enzyme with a functional active site.

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Inhibition
Certain chemicals selectively inhibit the action of specific

enzymes.
Competitive
Inhibition

Reversible
Non
competitive
Irreversible

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Competitive Inhibition
a) Competitive inhibitor
mimics substrate and
compete for active
site.

Noncompetitive Inhibition
a) Noncompetitive inhibitor
alters conformation of
enzyme so active site is no
longer fully functional.
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A. Competitive Inhibition
Competitive inhibitors are chemical agents that sufficiently

resemble the normal substrate.

The actual substrate thus competes for a position in the
active site. This prevents the formation of ES complex.
Eg: Succinic acid (actual substrate), malonic acid
(competitive inhibitor).

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Competitive inhibition. Malonic acid competes with succinate

for active sites of succinic dehydrogenase, an important
enzyme in the Krebs cycle

B. Non-competitive Reversible Inhibition

Occurs when an inhibitors form weak chemical bond

with the enzymes.

The inhibitors are chemical agents that bind to the site
other than active site, called an allosteric site.
It alters the shape of the enzyme, thus making the
enzyme unable to bind to the substrate.
Eg: cyanide (or potassium cyanide KCN) which combines
dehydrogenase with the cytochrome enzymes responsible
for the transfer of hydrogen atoms during cellular
respiration.
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C. Non-competitive Irreversible Inhibition

Occurs when the inhibitor first binds to the allosteric site

and then makes a covalent bond to the enzyme.

Since the inhibitor cannot fall off (bind permanently), it
changes the structure of the enzyme and makes it become
ineffective.
The enzyme thus undergoes denaturation.
Eg: Silver (Ag+), arsenic (As+)

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Enzyme Cofactors
Any non-protein molecule or ion that is required for the

proper functioning of an enzyme.

Cofactors can be permanently bound to the active site or
may bind loosely with the substrate catalysis.
It stays unchanged at the end of a reaction and can
be regenerated by a later process.

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3 Types of Cofactor
1. Inorganic ions

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Known as enzyme activators.

Shape up either the enzyme or the substrate into a shape
that causes the enzyme-substrate complex to be produced.
Thus, is increasing the rate of reaction catalyzed by the
specific enzyme.
Eg: K+, Na+, Cu2+

2. Prosthetic group

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Organic non-protein substrate which is tightly

bound to the enzyme, of which it is the important part.
It is a highly active part of the enzyme molecule.
Function is to take up chemical group from the
protein part of the enzyme.
Eg: enzyme cytochrome oxidase, that plays role in
respiration, has a prosthetic group haem that contain iron.

3. Coenzymes

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Non-protein organic molecules which act as cofactors

and bind to the enzyme like prosthetic group.
Coenzymes do not bind tightly to the enzyme and do
not remain attached to the enzyme between reactions.
Most coenzymes can be classified as transfer agents
(transfer some components from one molecule to
another).
Eg: transfer electrons such as NADH, NADPH and FADH2

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Enzyme Classification
1. Oxidoreductase
Catalyze biological oxidation and reduction by the

transfer of hydrogen, oxygen, or electrons from one

molecule to another.
Eg:
Ethanal + NADH2

Ethanol + NAD
alcohol dehydrogenase

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2. Transferases
Catalyze the transfer of a chemical group from one

substrate to another.
Eg:
Glutamic acid
+
Pyruvic acid
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Aminotransferase

- ketoglutaric acid
+
Alanine

3. Hydrolases
Catalyze the formation of 2 products from a larger

substrate molecule by hydrolytic reaction.

Eg:
Sucrose

Fructose + Glucose
sucrase

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4. Lyases
Catalyze non-hydrolytic addition or removal of parts

of substrate molecules.
Eg:
Pyruvic acid

Ethanol + CO2
pyruvate
decarboxylase

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5. Isomerases
Catalyze internal arrangement of substrate molecule or

isomerisation
Eg:
Glucose-1-phosphate

Glucose-6-phosphate
Phosphoglucomutase

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6. Ligases
Catalyze the joining together of two molecules with

simultaneous hydrolysis of ATP.

Eg:
Amino acid
+ Specific tRNA
+ ATP
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Amino-acyl-tRNA
synthetase

Amino acid-tRNA complex