NOMENCLATURE OF

ENZYMES

Ms M. Mombeshora
Biochemistry Lecture 1
 Enzyme definition
• Protein catalyst that increases the velocity of a
chemical reaction and are not consumed during
the reaction
NB
• Some types of RNA act like enzymes (ribozymes)
 Usually catalysing the cleavage and synthesis of
phosphodiester bonds
 Less commonly encountered compared to protein
catalysts
 Importance of enzymes
• Enzymes play an important role in
Metabolism, Diagnosis, and Therapeutics
• All biochemical reactions are enzyme
catalysed in the living organism
• Level of enzyme 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
Diagnostic Enzymes
Serum enzymes used in
diagnosis of tissue damage
 Shared properties with chemical
catalyst
1. Enzymes are neither consumed or produced
during the course of the reaction
2. Enzyme do not cause reaction to take place
But they greatly enhance the rate of the
reaction that would proceed much slower in
their absence
They alter the rate not eqm constants of the
reactions
Differences between enzymes and
chemical catalysts
1. Enzymes are proteins

2. Enzymes are highly specific and produce only expected

products from the given substrates
 There are no side reactions

3. Enzymes may show high specificity towards one substrate

 Or exhibit a broad specificity, using more than one substrate

4. Enzymes usually function within moderate pH and

temperature
 Basic functions of enzymes in
biological object
They are catalytic and regulatory
Catalytic efficiency
• Most enzyme-catalysed reactions are highly
efficient
• Proceeding from 103 to 108 times faster than
uncatalysed reactions
• Typically, each enzyme molecule is capable of
transforming 100 to 1000 substrate molecules
into product s-1
• The number of molecules of substrate converted
to product per enzyme molecule s-1 is called the
turnover number
 Basic functions of enzymes in
biological object
Regulation
• Enzyme activity can be regulated
• Enzymes can be activated or inhibited
• Rate of product formation responds to the
needs of the cell
 Substrate
• The reactant in a biochemical reaction is
termed a substrate
• When a substrate binds to an enzyme it forms
a substrate-enzyme complex
 Active sites

• Enzyme molecules contain a special pocket or

cleft called the active sites.
 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:
– A cofactor is a non-protein chemical
compound that is bound (either tightly or
loosely) to an enzyme and is required for
catalysis
– Types of Cofactors:
• Coenzymes
• Prosthetic groups
 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
 Enzyme Specificity

• Enzymes have varying degrees of specificity

for substrates
• Enzymes may recognize and catalyse:
- a single substrate
- a group of similar substrates
- a particular type of bond
Types of enzyme specificity
 Mechanism of Action of Enzymes
• Enzymes increase reaction rates by
decreasing the Activation energy:
• Enzyme-Substrate Interactions:
‒ Formation of Enzyme substrate complex by:
‒ Lock-and-Key Model
‒ Induced Fit Model
 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, and does

not work for all enzymes
Lock-and-Key Model
 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 maximise the fit, which
improves catalysis
there is a greater range of substrate specificity

• This model is more consistent with a wider

range of enzymes
Induced Fit Model
 Enzyme-substrate complex
• Step 1:
• Enzyme and substrate combine to form
complex
• E + S ES
• Enzyme Substrate Complex

+
 Enzyme-product complex
• Step 2:
• An enzyme-product complex is formed

• ES EP

ES transition EP
state
 Reversible competitive inhibition
A competitive inhibitor:
• Has a structure like the substrate
• Competes with the substrate for the active
site
• Has its effects reversed by increasing the
substrate concentration
Competitive and noncompetitive
inhibition
 Noncompetitive inhibition

A noncompetitive inhibitor:
• Has a structure different from the substrate
• Distorts the shape of the enzyme, which alters
the shape of the active site
• Prevents the binding of the substrate
• Cannot have its effects reversed by adding more
substrate
 Naming Enzymes

• The name of an enzyme in many cases end in –ase

• For example, sucrase catalyses the hydrolysis of

sucrose

• The name describes the function of the enzyme

For example, oxidases catalyse oxidation reactions
 Naming Enzymes

Trivial names
• Sometimes common names are used, particularly for
the digestion enzymes such as pepsin , thrombin
and trypsin
• Gives no idea of source, function or reaction
catalysed by the enzyme
 Naming Enzymes

Systematic name
• According to the International Union of Biochemistry an
enzyme name has two parts:
– First part is the name of the substrates for the enzyme
– Second part is the type of reaction catalyzed by the enzyme
– This part ends with the suffix “ase”
• Some names describe both the substrate and the
function
• For example, alcohol dehydrogenase oxidises ethanol
 Naming Enzymes

EC number
• Enzymes are classified into six different groups
according to the reaction being catalysed
• All enzymes are assigned an “EC” number
• The classification does not take into account amino
acid sequence (i.e, homology), protein structure, or
chemical mechanism
 Enzyme classification
• Classified into six functional classes (EC number
Classification) by the International Union of
Biochemists (I.U.B.).
• On the basis of the types of reactions that they
catalyse
• EC 1. Oxidoreductases
• EC 2. Transferases
• EC 3. Hydrolases
• EC 4. Lyases
• EC 5. Isomerases
• EC 6. Ligases
 Principle of the international
classification

Each enzyme has classification number

consisting of four digits:
Example, EC: (2.7.1.1) HEXOKINASE
EC: (2.7.1.1) these components indicate the
following groups of enzymes:

• 2. is class (Transferase)

• 7. is subclass (Transfer of phosphate)

• 1. is sub-sub class (Alcohol is phosphate acceptor)

• 1. specific name
ATP,D-HEXOSE-6-PHOSPHOTRANSFERASE (Hexokinase)
 6 CH2OH 6 CH OPO 2
2 3
ATP ADP
5 O 5 O
H H H H
H H
4 1 4 H 1
OH H OH
Mg2+
OH OH OH OH
3 2 3 2
H OH Hexokinase H OH
glucose glucose-6-phosphate

1. Hexokinase catalyses:
Glucose + ATP  glucose-6-P + ADP
 Oxidoreductases

• Involved in oxidation and reduction

Ared + Box Aox + Bred

 Examples of subclasses of
Oxidoreductases
a. Oxidases
 Use oxygen as an electron acceptor but do not
incorporate it into the substrate
b. Dehydrogenases
 Use molecules other than oxygen (e.g NAD+) as an
electron acceptor
c. Oxygenases
 Directly incorporate oxygen into the substrate
d. Peroxidases
 Use H2O2 as an electron acceptor
 Example of Oxidoreductase
• catalyse oxidation-reduction reactions
 Transferases

• Transfer functional groups e.g amino or

phosphate groups

A-B + C A + B-C
 Examples of subclasses of
Transferases
a. Methyltransferases
 Transfer one-carbon units between substrates

b. Aminotransferases
 Transfer NH2 from amino acids to keto acids

c. Kinases
-
 Transfer PO3 from ATP to a substrate

d. Phosphorylases
-
 Transfer PO3 from inorganic phosphate (Pi) to a
substrate
 Example of Transferase

•catalyse group transfer reactions

 Hydrolases

• Transfer of water i.e catalyse the hydrolysis of

a substrate

А-В + Н2О А-Н + В-ОН

Examples of subclasses of Hydrolases
• Peptidases

• Lipases

• Amylases
 Example of Hydrolase

•catalyse hydrolysis reactions where water is the

acceptor of the transferred group
 Lyases

• Cleave various bonds by means other than

hydrolysis and oxidation
• Add or remove the elements of water,NH3,
CO2 to/from double bonds
 Examples of subclasses of lyases
a. Decarboxylases
 Produce CO2 via elimination reactions

b. Aldolases
 Produce aldehydes via elimination reactions

c. Synthases
 Link two molecules without involvement of ATP
Examples of Lyase
 Isomerases

• Catalyse rearrangement of atoms within a

molecule

А-В В-А
• Product has same molecular formula as
substrate
• Only differs in bond connectivity or spatial
arrangement
• Carry out many kinds of isomerisation:
• L to D isomerisations
• Mutase reactions (Shifts of chemical groups)
 Examples of subclasses of
Isomerases

a. Racemases
Interconvert L and D stereoisomers

b. Mutases
Transfer groups between atoms within a molecule
 Example of Isomerase
• Catalyses isomerisation reactions
 Ligases
• Join two molecules

А+В + ATP А-В + ADP + Pi

 Examples of subclasses of Ligases

a. Carboxylases
• Use CO2as a substrate

a. Synthetases
Link two molecules via an ATP-dependent reaction
 Example of Ligase
• catalyse ligation, or joining of two substrates
• Require chemical energy (e.g. ATP)