LECTURE 03:

Biological Catalysis
LECTURE 03:

Biological Catalysis

❑Introduction to Enzymology
❑Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
LECTURE 03:

Biological Catalysis
❑ What are enzymes and their significance in biological systems?
❑ How are enzymes named and classified?
❑ What are the different parts of an enzyme and what are their roles in
❑ Structure and Properties of Enzymes catalysis?
❑ How is a cofactor similar or different from a coenzyme?
❑ Why do we have to acquire vitamins and minerals from our diet?
LECTURE 03:

Biological Catalysis

❑Introduction to Enzymology
❑Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
BIOLOGICAL CATALYSIS
A catalyst is a chemical agent which
makes a chemical reaction faster without
itself being consumed in the process
In biological systems, catalysts exist in form of enzymes
which are large assemblies of proteins that specifically
process their substrates and turn them into products
Majority of enzymes are proteins and not all
proteins are enzymes
In biological systems, catalysts exist in form of enzymes
which are large assemblies of proteins that specifically
process their substrates and turn them into products
Majority of enzymes are proteins and not all
proteins are enzymes
Due to the existence of various R groups,
proteins have the capacity to specifically
bind to different types of molecules
through a repertoire of intermolecular
forces

Most of the time, these interactions

are just weak enough to carry on
catalytic
action
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
❑Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
❑Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
Classification of Enzymes
1.Oxidoreductases – catalyze oxidation-reduction
processes such as dehydrogenases, oxidases,
oxygenases, peroxidases and hydroxylases.

2.Transferases – involved in transfer of groups from

one source to another such as transaminases,
transcarboxylases and transmethylases.

3.Hydrolases – catalyze reactions in which bonds are

broken through addition of water like the esterases,
phosphatases and peptidases
Classification of Enzymes

1.Lyases – catalyze reactions with groups like

H2O, CO2 and NH3 are removed to form a
double bond. This group includes
decarboxylases, hydratases, deaminases and
synthases.

2.Isomerases – catalyze rearragements within a

molecule such as epimerases and mutases
3.Ligases – catalyze bond formation between two
substrate molecules. Most are synthases.
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
❑Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
Nomenclature of Enzymes
Named by adding the suffix –ase. To eliminate confusion, the
International Union of Biochemists instituted a naming scheme for
enzymes with E.C. numbers
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
✓Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
✓Enzyme Nomenclature
❑Structure and Properties of Enzymes
❑Cofactors and Coenzymes
Some Terms to Remember
•Binding site – made up of amino acids that facilitate
interaction with the substrate and hold it all throughout the
catalytic process.

•Catalytic site – composed of few amino acid residues that

carry out series of chemical reactions that converts the
substrate into products.

•Allosteric site – a portion of the enzyme, other than the

substrate’s binding site in which other modulator molecules
may bind and cause conformational change.

•Conformational change – a change in three-dimensional

positioning and arrangement of amino acids in an enzyme
Substrate Binding / Active Site

Substrate Active Site

Substrate Binding Site

Lysozyme
Properties of Enzymes
1.High Specificity in binding substrates

2.High Efficiency without production of

side products through maximizing
interactions by excluding water from the
active site

3.Able to Stabilize a transition state

through energy minimization
Models of Enzyme Specificity: Lock and Key
Model
Postulated by Organic chemist Emil Fischer
Models of Enzyme Specificity:
Induced Fit
Postulated by Daniel
Koshland

Includes the binding of

substrate into the
enzyme’s binding site
followed by a
conformational change

This change in structure

allows interaction of
substrate with the
catalytic site
Enzymatic Reaction
Substrate ‘A’
Substrate ‘B’

Enzyme
Enzymatic Reaction

Substrate ‘A’

Substrate ‘B’

Enzyme

ES Complex
Enzymatic Reaction

Enzyme Changes Result

in Reaction
Between Substrates A
and B

ES* Complex
Substrates Affect Enzymes on Binding

‘A’ Has Become ‘C’ ‘B’ Has Become ‘D’

Part of ‘A’
Has Moved to
‘B’

EP Complex
Substrates Affect Enzymes on Binding

Product D Released
Product C Released

Enzyme Freed to Bind More Substrates

E+P
 Steps In Catalysis

E+S
Free Enzyme

<=>
& Substrates

ES
Substrate Binding

<=>
Reversible
ES* Reaction

<=>
EP
Product Formation
<=>
E+P
Release of Products
 Enzymes lower activation energy
Enzymes catalyze reversible reactions
Enzymes do not change overall energy
Enzymes do not change equilibrium
concentrations Enzymes speed achieving
equilibrium
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
✓Enzyme Nomenclature
✓Structure and Properties of Enzymes
❑Cofactors and Coenzymes
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
✓Enzyme Nomenclature
✓Structure and Properties of Enzymes
❑Cofactors and Coenzymes
Enzymes require Co-factors for them to be active
and perform their biological functions.

Co-factors are non-protein parts of an enzyme,

including metallic ions and organic compounds.
When they are tightly bound to enzymes, they are
referred to as prosthetic groups.
Coenzymes are organic molecules that work
hand-in-hand with enzymes such the vitamins
that carry functional groups for transfer
LECTURE 03:

Biological Catalysis

✓Introduction to Enzymology
✓Classification of Enzymes
✓Enzyme Nomenclature
✓Structure and Properties of Enzymes
✓Cofactors and Coenzymes