CYL456: Chemistry of Life An Introduction

Biomolecules
1

Enzymes
Instructor: Yashveer Singh, PhD
General, Organic, and Biological Chemistry, HS Stoker,
Brooks/Cole
Lehningers Principles of Biochemistry, DL Nelson and MM Cox,
WH Freeman
Molecular Cell Biology, H Lodish, A Berk, CA Kaiser, M Krieger,
MP Scott, A Bretscher, H Ploegh, P. Matsudaira, WH Freeman
18 October 2014

Enzymes

Enzymes acts as catalysts for biochemical reactions. Each cell in the

body contains thousands of different enzymes

Enzymes cause cellular reactions to occur millions of time faster than

corresponding uncatalyzed reactions
The word enzyme comes from the Greek words en, which means in,
and zyme, which means yeast

Most enzymes are globular proteins. Some are simple proteins,

consisting entirely of amino acid chains. Others are conjugated proteins,
containing additional chemical components. Earlier, it was thought
that all enzymes were proteins, which is no more true. Catalytic RNA
(ribozymes) catalyzing cellular reactions have been discovered

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Enzyme structure
Enzymes are simple or conjugated
A simple enzyme is an enzyme composed only of protein and a
conjugated enzyme is an enzyme that has a nonprotein part too.
Neither the protein part nor the nonprotein portion alone will have
catalytic properties
An apoenzyme is the protein part of a conjugated enzyme. A cofactor is
the nonprotein part of a conjugated enzyme. A holoenzyme is the
biochemically active conjugated enzyme produced from an apoenzyme
and a cofactor
A cofactor is generally either a small organic molecule or an inorganic
ion (usually a metal ion). When the cofactor is a small organic molecule
(vitamins), it is referred to as coenzyme and not cofactor

Typical cofactors include Zn2+, Mg2+, Mn2+, and Fe2+. The nonmetallic
Cl- ion occasionally acts as a cofactor. Dietary minerals are an important
source of inorganic ion cofactors
Stokers General, Organic, and Biological Chemistry, 5 Ed.

Enzyme nomenclature and classification

The suffix -ase identifies a substance as an enzyme (urease, sucrase, and

lipase). The suffix -in is still found in the names of some of the first
enzymes studied, mainly digestive enzymes (trypsin, chymotrypsin, and
pepsin)

The type of reaction catalyzed by an enzyme is often noted with a

prefix. An oxidase enzyme catalyzes an oxidation reaction, and a
hydrolase enzyme catalyzes a hydrolysis reaction
The identity of the substrate is often noted in addition to the type of
reaction. E.g., glucose oxidase, pyruvate carboxylase, and succinate
dehydrogenase

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Modern enzyme nomenclature and classification

Oxidoreductase: Catalyzes an oxidationreduction reaction

Transferase: Catalyzes the transfer of a functional group from one

molecule to another

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Modern enzyme nomenclature and classification

Hydrolase: A hydrolase enzyme catalyzes a hydrolysis reaction

Lyase: Catalyzes the addition of groups to double bonds or removal of

groups from double bond (not hydrolysis or oxidation)

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Modern enzyme nomenclature and classification

Isomerase: Catalyzes the isomerization of a substrate

Ligase: Catalyzes the joining of two molecules into one using ATP

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Models of enzyme action: active site and

enzyme-substrate complex
Active site. The active site is the
relatively small part of an
enzymes structure that is actually
involved in catalysis.

Enzyme-substrate
complex.
Catalysts offer an alternative
pathway with lower activation
energy through which a reaction
can occur. In enzyme-controlled
reactions, this alternative pathway
involves the formation of an
enzymesubstrate complex

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Models of enzyme action: lock and key

The lock-and-key model assumes that the active site in the enzyme has a
fixed and rigid geometrical conformation. Only substrates with a
complementary geometry can be accommodated at such a site

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Models of enzyme action: induced fit

The induced-fit model allows for small changes in the shape or geometry
of the active site of an enzyme to accommodate a substrate

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Models of enzyme action: induced fit

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Molecular interaction involved in the formation

of enzyme-substrate complex

The forces that draw the substrate into the active site are the same forces
that maintain tertiary structure in the folding of peptide chainselectrostatic interactions, hydrogen bonds, and hydrophobic
interactions
Stokers General, Organic, and Biological Chemistry, 5 Ed.

Enzyme specificity
Absolute specificity: An enzyme will catalyze a particular reaction for
only one substrate. Not very common (e.g., urease)
Stereochemical specificity: An enzyme can distinguish between
stereoisomers (L-amino-acid oxidase will catalyze reactions of L-amino
acids only)
Group specificity: Such specificity involves structurally similar
compounds that have the same functional groups (e.g., carboxypeptidase
cleaves an amino acid at a time, from the C-terminal)
Linkage specificity: An enzyme is selective for a particular type of bond,
irrespective of the structural characteristics in the vicinity of the bond (e.g.,
phosphatases hydrolyze phosphate ester bonds in all types of phosphate
esters). Most common

13
Stokers General, Organic, and Biological Chemistry, 5 Ed.

Factors affecting enzyme activity: temperature

The rate of enzyme catalyzed

reaction increases with an increase
in temperature
Increase beyond a certain point
will disrupt the tertiary structure of the
enzyme (denaturation), thus impeding
the rate of reaction
The temperature that produces
maximum activity for an enzyme is
called the optimum temperature for
that enzyme, which is 37 oC for
humans

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Factors affecting enzyme activity: pH

Similar

to temperature, most
enzymes exhibit maximum activity
over a very narrow pH range, which is
7.07.5 (physiological pH range) in
humans and known as optimum pH
Notable exceptions are digestive
enzymes pepsin and trypsin. Pepsin is
active in the stomach and functions
best at a pH of 2.0. Trypsin, in the
small intestine, functions best at a pH
of 8.0

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Factors affecting
concentration

enzyme

activity:

substrate

If the concentration of an enzyme

is constant and the concentration of
substrate increases, a saturation
curve is obtained
Enzyme activity increases up to a
certain substrate concentration
and then remains constant
At saturation point, an enzyme is
working at full capacity, which
implies that all active sites have been
engaged

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Factors affecting
concentration

enzyme

activity:

enzyme

The enzymes are not consumed

in the reaction and the cell
usually keeps the concentration
of enzymes much lower than
substrates
At a constant amount of
substrate, the rate of reaction
increases with increase in
enzyme concentration

Stokers General, Organic, and Biological Chemistry, 5 Ed.

Enzymes turnover number

An enzymes turnover number is the number of substrate molecules

transformed per minute by one molecule of enzyme under optimum

conditions of temperature, pH, and saturation

Stokers General, Organic, and Biological Chemistry, 5 Ed.