Enzymes-Module-Coabaxxnbxzbpy-sent (2).ppt

ENZYMES
Enzymes are inseparable from living
organisms. They are the largest group of
proteins and they catalyze almost every
reaction that occurs in living organisms.
They exhibit extraordinary catalytic powers.
© 2007 Paul Billiet ODWS

 much greater than that of synthetic
catalysts. They exhibit a high degree
of specificity & they function in dilute
aqueous solutions under very mild
conditions of temperature and
pressure.

ENZYME
 An enzyme is an organic compound
that acts as a catalyst for a
biochemical reaction.
 They are the largest and the most
highly specialized class of proteins.

Enzyme structure
 Enzymes are
proteins
 They have a
globular shape
 A complex 3-D
structure
Human pancreatic amylase
© Dr. Anjuman Begum

Structure of Enzyme
It has two general structural classes
Simple enzymes
Conjugated enzymes

Structure of Enzyme
 Simple enzymes
are enzymes composed only of protein
(amino acid chains)
 Conjugated enzymes
are enzyme that has a non-protein part
in addition to its protein part

Structure of Enzyme
 Coenzyme
is a small organic molecule that serves as a
cofactor in a conjugated enzyme

Cofactors
 An additional non-
protein molecule that is
needed by some
enzymes to help the
reaction
 Tightly bound cofactors
are called prosthetic
groups
 Cofactors that are bound
and released easily are
called coenzymes
 Many vitamins are
coenzymes Nitrogenase enzyme with Fe, Mo and ADP cofactors
Jmol from a RCSB PDB file © 2007 Steve Cook
H.SCHINDELIN, C.KISKER, J.L.SCHLESSMAN, J.B.HOWARD, D.C.REES
STRUCTURE OF ADP X ALF4(-)-STABILIZED NITROGENASE COMPLEX AND ITS
IMPLICATIONS FOR SIGNAL TRANSDUCTION; NATURE 387:370 (1997)

Nomenclature and Classification
of Enzymes
 Enzymes are most commonly named by
using a system that attempts to provide
information about the function rather than
the structure of the enzyme
 Substrate
is the reactant in an enzyme-catalyzed
reaction

Important aspects of enzyme-
naming process
 The suffix –ase identifies a substance as an
enzyme (urease, sucrase & lipase)
 The suffix –in is still found in the names of
some of the first enzymes studied, many of
which are digestive enzymes
(trypsin,chymotrypsin & pepsin)
 The type of reaction catalyzed by an
enzyme is often noted with a prefix (oxidase
&hydrolase)

Important aspects of enzyme-
naming process
 The identity of the substrate is often noted in
addition to the type of reaction (glucose
oxidase, pyruvate carboxylase and
succinate dehydrogenase)
 Sometimes, the substrate but not the
reaction type is given ( urease & lactase), in
such names, the reaction involved is
hyrdolysis

Predict the function of the
following enzyme
 Cellulase
 cellulase catalyzes hydrolysis of cellulose
 Sucrase
 sucrase catalyzes hydrolysis of the
disaccharide sucrose
 L-amino acid oxidase
 catlayzes the oxidation of L-amino acids

Predict the function of the
following enzyme
 Aspartate aminotransferase
 aspartate aminotransferase catalyzes the
transfer of an amino group from aspartate
to a different molecule of L-amino acids

Six major classes of enzymes on the basis
of the types of reactions they catalyze
 An oxidoreductase
an enzyme that catalyzes an oxidation-reduction
reaction

 A transferase
an enzyme that catalyzes the transfer of a
functional group from one molecule to another
 It has two major subtypes
1. transaminases
2. kinases

 Transaminases
transferase that catalyzes the transfer of an
amino group from one molecule to
another
 Kinases
transferase that play a major role in metabolic
energy- production reaction, catalyze
the transfer of a phosphate group from
ATP to ADP and a phosphorylated product

 Kinases
transferase that plays a major role in metabolic energy-
production. The reaction catalyzes the transfer of a
phosphate group from ATP to ADP and a phosphorylated
product

 Lyase
is an enzyme that catalyzes the addition of a
group to a double bond or the removal of a group
to form a double bond in a manner that does not
involve hyrdrolysis or oxidation (ex. dehydratase &
hydratase)

 hydrolase
is an enzyme that catalyzes a hydrolysis
reaction in which the addition of water
molecule to a bond causes the bond to
break
Maltase

 Isomerase
is an enzyme that catalyzes the
isomerization (rearrangement of atoms)
of a substrate in a reaction, into a
molecule isomeric with itself
there is only one reactant and product in
reactions where isomerases are
operative

 Isomerase

 Ligase
is an enzyme that catalyzes the bonding
together of two molecules into one with the
participation of ATP
 ATP is required because such reactions are
generally energetically unfavorable and
they require the simultaneous input of
energy obtained by hydrolysis reaction in
which ATP is converted to ADP

 Ligase

MODEL OF ENZYME ACTION
The active site
 One part of an enzyme,
the active site, is
particularly important
 The shape and the
chemical environment
inside the active site
permit a chemical
reaction to proceed
more easily
© H.PELLETIER, M.R.SAWAYA
ProNuC Database

MODEL OF ENZYME ACTION
The active site
 A small portion of an
enzyme molecule that
pariticipates in the
interaction with a
substrate/s during the
reaction
 It is actually the part of
the enzyme that is
involved in the
catalysis
© H.PELLETIER, M.R.SAWAYA
ProNuC Database

The substrate
 The substrate of an enzyme is the reactant
that is activated by the enzyme
 Enzymes are specific to their substrates
 The specificity is determined by the active
site

The Lock and Key Hypothesis
 Fit between the substrate and the active site of the enzyme is
exact
 Like a key fits into a lock very precisely
 The key is analogous to the enzyme and the substrate
analogous to the lock.
 Temporary structure called the enzyme-substrate complex
formed
 Products have a different shape from the substrate
 Once formed, they are released from the active site
 Leaving it free to become attached to another substrate

Enzyme may
be used again
Enzyme-
substrate
complex
E
S
P
E
E
P
Reaction coordinate

 This explains enzyme specificity
 This explains the loss of activity when
enzymes denature

The Induced Fit Hypothesis
 Some proteins can change their shape
(conformation)
 When a substrate combines with an enzyme, it
induces a change in the enzyme’s conformation
 The active site is then moulded into a precise
conformation
 Making the chemical environment suitable for the
reaction
 The bonds of the substrate are stretched to make the
reaction easier (lowers activation energy)

The Induced Fit Hypothesis
 This explains the enzymes that can react with a
range of substrates of similar types
Hexokinase (a) without (b) with glucose substrate
http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/enzyme_mechanism.html

Factors affecting Enzymes
 substrate concentration
 pH
 temperature
 inhibitors

Substrate concentration: Non-enzymic reactions
 The increase in velocity is proportional to the
substrate concentration
Reaction
velocity
Substrate concentration

Substrate concentration: Enzymic reactions
 Faster reaction but it reaches a saturation point when all the
enzyme molecules are occupied.
 If you alter the concentration of the enzyme then Vmax will
change too.
Reaction
velocity
Substrate concentration
Vmax

The effect of pH
Optimum pH values
Enzyme
activity Trypsin
Pepsin
pH
1 3 5 7 9 11

The effect of pH
 Extreme pH levels will produce denaturation
 The structure of the enzyme is changed
 The active site is distorted and the substrate
molecules will no longer fit in it
 At pH values slightly different from the enzyme’s
optimum value, small changes in the charges of the
enzyme and it’s substrate molecules will occur
 This change in ionization will affect the binding of
the substrate with the active site.

The effect of temperature
 Q10 (the temperature coefficient) = the increase in
reaction rate with a 10°C rise in temperature.
 For chemical reactions the Q10 = 2 to 3
(the rate of the reaction doubles or triples with every
10°C rise in temperature)
 Enzyme-controlled reactions follow this rule as they
are chemical reactions
 But at high temperatures proteins denature
 The optimum temperature for an enzyme controlled
reaction will be a balance between the Q10 and
denaturation.

Temperature / °C
Enzyme
activity
0 10 20 30 40 50
Q10 Denaturation

 For most enzymes the optimum temperature is about
30°C
 Many are a lot lower,
cold water fish will die at 30°C because their
enzymes denature
 A few bacteria have enzymes that can withstand very
high temperatures up to 100°C
 Most enzymes however are fully denatured at 70°C

Inhibitors
 Inhibitors are chemicals that reduce the rate
of enzymic reactions.
 The are usually specific and they work at low
concentrations.
 They block the enzyme but they do not
usually destroy it.
 Many drugs and poisons are inhibitors of
enzymes in the nervous system.

The effect of enzyme inhibition
 Irreversible inhibitors: Combine with the
functional groups of the amino acids in the
active site, irreversibly.
Examples: nerve gases and pesticides,
containing organophosphorus, combine with
serine residues in the enzyme acetylcholine
esterase.

 Reversible inhibitors: These can be washed
out of the solution of enzyme by dialysis.
There are two categories.

1. Competitive: These
compete with the
substrate molecules for
the active site.
The inhibitor’s action is
proportional to its
concentration.
Resembles the substrate’s
structure closely.
Enzyme inhibitor
complex
Reversible
reaction
E + I EI

Succinate Fumarate + 2H+
+ 2e-
Succinate dehydrogenase
CH2COOH
CH2COOH CHCOOH
CHCOOH
COOH
COOH
CH2
Malonate

2. Non-competitive: These are not influenced by the
concentration of the substrate. It inhibits by binding
irreversibly to the enzyme but not at the active site.
Examples
 Cyanide combines with the Iron in the enzymes
cytochrome oxidase.
 Heavy metals, Ag or Hg, combine with –SH groups.
These can be removed by using a chelating agent such
as EDTA.

Allosteric Regulation
 Allosteric regulation is a form of non-
competitive inhibition. It involves an
oligomeric enzyme (more than one
polypeptide protein) which contains sites at
which substrate molecules can bind (active
site) & sites at which inhibitor molecules can
bind (allosteric site). There is an interaction
between the substrate and the inhibitor such
that when an inhibitor occupies an allosteric

Allosteric Regulation
 site the active site changes conformation. If
the change effects an increase in the rate of
the reaction, the inhibitor also called
allosteric effector is properly referred to as
positive effector or allosteric activator.
 It is called negative effector or allosteric
inhibitor if reaction rate is decreased.

Applications of inhibitors
 Negative feedback: end point or end product
inhibition
 Poisons snake bite, plant alkaloids and nerve
gases.
 Medicine antibiotics, sulphonamides,
sedatives and stimulants

Chemical reactions
 Chemical reactions need an initial input of energy =
THE ACTIVATION ENERGY
 During this part of the reaction the molecules are
said to be in a transition state.

Reaction pathway

Making reactions go faster
 Increasing the temperature makes molecules move
faster
 Biological systems are very sensitive to temperature
changes.
 Enzymes can increase the rate of reactions without
increasing the temperature.
 They do this by lowering the activation energy.
 They create a new reaction pathway “a short cut”

An enzyme controlled pathway
 Enzyme controlled reactions proceed 108
to 1011
times faster
than corresponding non-enzymic reactions.

Enzymes-Module-Coabaxxnbxzbpy-sent (2).ppt

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