ENZYMES introduction

Enzymes

•Almost every reaction that happen in the body involves

enzymes
•They function as a catalyst from physiological reaction
•Enzymes control in a selective manner reactants in chemical
reactions
•These reactants are called substrate
•Consequently, Enzymes mediate all metabolic interactions in
the body
 Chemical nature

 Enzymes are biological catalysts that speed

up the rate of the biochemical reaction.

 Most enzymes are three dimensional globular

proteins (tertiary and quaternary structure).

 Some RNA also act

enzymes
special species are Ribozymes as
hammerhead
and ribozyme.
called e.g.

Hammerhead enzyme
 STRUCTURE OF ENZYMES

 The active site of an enzyme is the region that binds

substrates, co-factors and prosthetic groups and contains
residue that helps to hold the substrate.

 Active sites generally occupy less than 5% of the total surface

area of enzyme.

 Active site has a specific shape due to tertiary structure of

protein.

 A change in the shape of protein affects the shape of active

site and function of the enzyme.
 Active Sites
Substrate molecule:
Substrate molecules are the
chemicals that an enzyme
acts on. They are drawn
Active site:
into the cleft of the enzyme.
The active site contains both binding
and catalytic regions. The substrate
is drawn to the enzyme’s surface and
the substrate molecule(s) are
positioned in a way to promote a
reaction: either joining two molecules
Enzyme molecule: together or splitting up a larger one.
The complexity of the
active site is what makes
each enzyme so specific
(i.e. precise in terms of
the substrate it acts on).

This model (above) is an enzyme called

Ribonuclease S, that breaks up RNA
molecules. It has three active sites
(arrowed).
Properties of enzymes
 1. Active site specificity

•Each enzyme has a unique empty space within its structure

named the active site
•The active site contains amino acids portion that participate in
the substrate interactions to form enzyme–substrate (ES)
complex
•This binding catalyzes the substrate via structural
transformation
 ACTIVE SITE

o Active site can be further divided into:

Active Site

Binding Site Catalytic Site

It chooses the substrate It performs the catalytic

and binds it to active site. action of enzyme.
 2. Catalytic efficiency

•Efficiency is one of the most important properties of enzymes

•When enzymes are not catalyzing a reaction, it takes 108
longer
•The amount of byproduct that results from the catalytic
reaction is called the turnover number
•This number range between 102-104 product per second
 3. Coenzymes and Cofactors

•Some enzymes can not facilitate a catalytic reaction with a

substrate without the presence of certain molecules
•When these molecules composed of metallic ions such as Zn2+
or Fe2+, it is called cofactors
•On the other hand, if the extra molecules organic in nature it is
denoted as coenzymes. E.g. vitamins B1
 CO-
FACTORS
o Co-factor is the non protein molecule which carries out
chemical reactions that can not be performed by standard 20
amino acids.

o Co-factors are of two types:

 Organic co-factors
 Inorganic cofactors
 INORGANIC CO-FACTORS
o These are the inorganic molecules required for the
proper
activity of enzymes.
Examples: ++
 Enzyme carbonic anhydrase requires Znfor it‟s activity.
 Hexokinase has co-factor
++
Mg

ORGANIC CO-FACTORS
o These are the organic molecules required for the
proper activity of enzymes.
Example:
 Glycogen phosphorylase requires the small
organic molecule pyridoxal phosphate.
 TYPES OF ORGANIC CO-FACTORS

Prosthetic Group Coenzyme

o A prosthetic group is a tightly bind with enzyme … can be

organic or inorganic ( heme, metal ion)
o A coenzyme is loosely with ezyme….totally organic e.g.

Flavins, NAD+, biotin.

 Types of co-factors

 An with it‟ co-factor removed is designated

enzyme s as
apoenzyme.
 The complete complex of a protein with all necessary small
organic molecules, metal ions and other components is
termed as holoenzyme of holoprotein.
 4. Location

•Enzymatic reactions take place in specific location within a cell

•This aspect of enzyme compartmentalization provide the
specify of enzymes
•Since there are thousands of enzymes within a cell, isolating
enzymes from their substrates into specific organelles helps in
organizing the huge number of pathways
 INTRACELLULAR AND
EXTRACELLULAR ENZYMES
o Intracellular enzymes are synthesized and retained in the cell
for the use of cell itself.
o They are found in the cytoplasm, nucleus, mitochondria and
chloroplast.
Example :
 Oxydoreductase catalyses biological oxidation.
 Enzymes involved in reduction in the mitochondria.

o Extracellular enzymes are in the cell but

synthesized secreted from the cell to work
externally.
 Example
Digestive :
enzyme produced by the pancreas, are not used by
the cells in the pancreas but are transported to the
duodenum.
 SUBSTRAT
E

 The reactant in biochemical reaction is termed as substrate.

 When a substrate binds to an enzyme it forms an enzyme-

substrate complex.

Substrate Joins Enzyme

 SITES OF ENZYME SYNTHESIS

o Enzymes are synthesized by ribosomes which are attached to

the rough endoplasmic reticulum.

o Information for the synthesis of enzyme is carried by DNA.

o Amino acids are bonded together to form specific

enzyme
according to the DNA‟s codes.
 NOMENCLATURE OF ENZYMES

o An enzyme is named according to the name of the substrate it

catalyses.
o Some enzymes were named before a systematic way
of
naming enzyme was formed.
Example: pepsin, trypsin and rennin
Recommended name
o By adding suffix -ase at the end of the name of
the
substrate, enzymes are named.
o Enzyme for catalyzing the hydrolysis is termed as

hydrolase.
maltose + water
Example : maltase glucose + glucose
 EXAMPLES

substrate enzymes products

lactose lactase glucose + galactose

maltose maltase Glucose

cellulose cellulase Glucose

lipid lipase Glycerol + fatty acid

starch amylase Maltose

protein protease Peptides +

polypeptide
 Nomenclature “Systematic name

•According to this nomenclature, all enzymes are classified

under 6 classes
•For any enzyme, the suffix “ase” is part of the chemical
modification initialed by the enzyme
•Additionally, all the involved substrates written a head of the
chemical reaction, e.g. lactate :NAD+ oxidoreductase
Nomenclature “Systematic naming system
 Nomenclature
• synthetase (requires ATP),

• synthase (no ATP required);

• phosphatase (uses water to remove phosphoryl

group), phosphorylase (uses Pi to break a bond
and generate a phosphorylated product);
•
• dehydrogenase (NAD+/FAD is an electron acceptor
in a redox reaction),

• oxidase (O2 is the acceptor, and oxygen atoms are

not incorporated into substrate),

• oxygenase (one or both oxygen atoms are

incorporated).
CLASSIFICATIO
N
 CLASSIFICATION OF ENZYMES

 A systematic classification of enzymes has been developed by

International Enzyme Commission.

 This classification is based on the type of reactions catalyzed

by enzymes.

 There are six major classes.

 Each class is further divided into sub classes, sub sub-classes

and so on, to describe the huge number of different enzyme-
catalyzed reactions.
 Classification of
enzymes
ENZYME CLASS REACTION TYPE EXAMPLES
Oxidoreductases Reduction-oxidation Lactate
(redox) dehydrogenase
Transferases Move chemical group Hexokinase
Hydrolases Hydrolysis; bond Lysozyme
cleavage with transfer of
functional group of water

Lysases Non-hydrolytic bond Fumarase

cleavage
Isomerases Intramolecular group Triose phosphate
transfer (isomerization) isomerase

Ligases Synthesis of new RNA polymerase

covalent bond between
substrates, using ATP
hydrolysis
Classification
 CHARACTERISTICS

 Enzymes speed up the reaction by lowering the

activation energy of the reaction.
 Their presence does not effect the nature and properties of
end product.
 They are highly specific in their action that is each enzyme
can catalyze one kind of substrate.
 Small amount of enzymes can accelerate chemical reactions.
 Enzymes are sensitive to change in pH, temperature
and substrate concentration.
 Turnover number is defined as the number of
substrate molecules transformed per minute by one enzyme
molecule.

Catalase turnover number = 6 x106/min

MECHANISM OF
ENZYME
ACTION
 Two models have been proposed to explain how an
enzyme binds its substrate: the lock-and –key
model and the induced-fit model.

Lock-and-Key Model of Enzyme-

Substrate Binding In this model, the
active site of the unbound enzyme is
complementary in shape to the
substrate.

"lock and key model" accounted for the

exquisite specificity of enzyme-
substrate interactions, the implied
rigidity of the enzyme's active site
failed to account for the dynamic
changes that accompany catalysis.
Induced-Fit Model of
Enzyme-Substrate Binding
In this model, the enzyme
changes shape on
substrate binding. The
active site forms a shape
complementary to the
substrate only after the
substrate has been bound.
When a substrate
approaches and binds to
an enzyme they induce a
conformational change, a
change analogous to
placing a hand (substrate)
into a glove (enzyme).
  Enzymes are catalysts and increase the speed of a chemical
reaction without themselves undergoing any permanent chemical
change. They are neither used up in the reaction nor do they
appear as reaction products.
 The basic enzymatic reaction can be represented as follows

 where E represents the enzyme catalyzing the reaction, S the

substrate, the substance being changed, and P the product of
the reaction.


 The mechanism of action of enzymes can be explained by

two
perspectives-
 Thermodynamic changes
 Processes at the active site
 MECHANISM OF ENZYME ACTION

 The catalytic efficiency of enzymes is explained by

two
perspectives:

Thermodynamic Processes at
changes the active
site
All enzymes accelerate reaction rates by
providing transition states with a lowered
∆G F for formation of the transition states.
The lower activation
energy means that more
molecules have the
required energy to
reach the transition
state.
 THERMODYNAMIC CHANGES

 Only a few substances cross the activation barrier and change

into products.
 That is why rate of uncatalyzed reactions is much slow.
 Enzymes provide an alternate pathway for conversion
of substrate into products.
 Enzymes accelerate reaction rates by forming
transitional
state having low activational energy.
 Hence, the reaction rate is increased many folds in
the presence of enzymes.
 The total energy of the system remains the same
and equilibrium state is not disturbed.