UNIT-II

Chemical biology

Books: Biochemistry, Voet and Voet
Principles of Biochemostry, Lehninger

Enzymes (History)
First discovered by Eduard Buchner in 1897
who observed that yeast extracts can ferment
sugar to alcohol
This proved that fermentation was promoted
by molecules that continued to function when
removed from cells
The first enzyme to be purified and
crystallized was urease in 1926; these
crystals consisted entirely of protein
Later, pepsin, trypsin and other digestive
proteins were isolated and determined to be
purely protein as well

Enzymes are the catalysts of nature.

With the exception of catalytic RNA, all enzymes are
proteins.

Catalyst alter the rate of a chemical reaction without
undergoing a permanent change in structure.

Catalytic activity is dependant upon native
conformation; if it is lost, then catalytic activity is
lost as well

All levels of protein architecture must be intact and
correct for enzymes to perform their functions

They range in molecular weights from 12,000 to over
1 million

Enzymes
Simple Enzymes: composed of whole proteins

Complex Enzymes: composed of protein plus a relatively small
organic molecule

holoenzyme = apoenzyme + prosthetic group / coenzyme

A prosthetic group describes a small organic or metalloorganic molecule
bound to the apoenzyme by covalent bonds.

When the binding between the apoenzyme and non-protein
components is non-covalent, the small organic molecule is called a
coenzyme.

Coenzymes serve as transient carriers of specific functional groups.

They often come from vitamins (organic nutrients required in small amounts in the
diet)
Enzyme Classification

Oxidoreductases Act on many chemical groupings to add or remove
hydrogen atoms (transfer of electrons).
Transferases Transfer functional groups between donor and
acceptor molecules. Kinases are specialized
transferases that regulate metabolism by
transferring phosphate from ATP to other
molecules.
Hydrolases Add water across a bond, hydrolyzing it.
Lyases Add water, ammonia or carbon dioxide across
double bonds, or remove these elements to
produce double bonds.
Isomerases Carry out many kinds of isomerization: L to D
isomerizations, mutase reactions (shifts of
chemical groups) and others.
Ligases Catalyze reactions in which two chemical groups
are joined (or ligated) with the use of energy from
ATP.
International Classification of Enzyme
How enzymes work
Enzymes provide specific environments in which
chemical reactions that dont normally proceed under
neutral pH, mild temperature, and aqueous
environment conditions can occur
This region is a pocket on the enzyme known as the
active site
The molecule that is bound to the active site and
acted upon by the enzyme is called the substrate
The two together form what is known as the enzyme-
substrate complex
The function of an enzyme catalyst is to increase the
rate of a chemical reaction, not affect is equilibrium
Therefore, enzymes dont make more product, they
just make product faster


Active Site
The area of an enzyme that binds to the substrate
Structure has a unique geometric shape that is designed to
fit the molecular shape of the substrate
Each enzyme is substrate specific
Thus the active site that is complementary to the geometric
shape of a substrate molecule


Active site is lined with residues and sometimes contains a co-
factor
Active site residues have several important properties:
Charge [partial, dipoles, helix dipole]
pKa
Hydrophobicity
Flexibility
Reactivity
Substrate Binding specificity
Complementarity
Geometric
Electronic (electrostatic)
Stereospecificity (enzymes and
substrates are chiral)
1. Lock and Key model
2. Induced Fit model
Enzyme active site
Chymotrypsin (Cuts next to Hydrophobic Groups)
Trypsin (Cuts next to Arg & Lys)
Elastase (Cuts next to Val & Thr)
An enzyme binds a substrate in a region called the active site
Only certain substrates can fit the active site
Amino acid R groups in the active site help substrate bind

Lock and Key Model
Enzyme structure flexible, not rigid
Enzyme and active site adjust shape to bind substrate
Increases range of substrate specificity
Shape changes also improve catalysis during reaction
- transition-state like configuration

Induced Fit Model
Enzyme-Substrate Interaction

Sucrose Glucose and Fructose

sucrase
hydrolysis
Hexokinase undergoes a conformational change upon
binding to a substrate
red: before substrate-binding
green: after substrate-binding
Effect of Temperature
Effect of pH
The pH-rate profile of an enzyme is a function of the
pK
a
values of the catalytic groups in the enzyme
a group is
catalytically
active in its basic
form
a group is
catalytically
active in its acidic
form
Dependence of lysozyme activity on the pH of the reaction
Asp 52
Glu 35
The pH at which
enzyme is 50% active
Carboxypeptidase A catalyzes the hydrolysis of the
C-terminal peptide