ENZYMES- Naming, classification, mechanism, models, enzyme activity, transition state diagram, enzyme inhibitors

2.  Is a biocatalyst that increases the rate of
chemical reactions without itself being
changed in the overall process
 Virtually all cellular reactions or processes
are mediated by enzymes
 It has several properties which makes them
unique

3. 1. Most but not all enzymes are proteins. With the
exception of small group of catalytic RNA
molecule, all enzymes are protein
2. Enzymes are highly specific. They are
specialized proteins and have a high degree of
specificity for their substrates
3. They exhibit enormous catalytic power. It
increases the rate of reaction by lowering the
activation energy
4. They do not change the equilibrium state of a
biochemical reaction. It changes only the rate
at which equilibrium is achieved

4. proteinaceous enzymes
Simple enzymes
Consists entirely of amino acids
Conjugated enzymes
Consists of proteins as well as non
protein components
Non protein component is called
cofactor, which is required for
catalytic activity.
Removal of cofactor form a
conjugated enzyme leaves only
protein component called as
apoenzyme which is generally
biologically inactive
The complete biologically active
conjugated enzyme is called a
holoenzyme

5. vitamin Coenzyme form Reaction/ process
promoted
thiamine Thiamine pyrophosphate decarboxylation,
aldehyde group transfer
riboflavin FAD and FMN Redox reaction
pyridoxine Pyridoxal phosphate Amino group transfer
Nicotinic acid NAD+ and NADP+ Redox reaction
Pantothenic acid Coenzyme A Acyl group transfer
biotin bicytin carboxylation
Folic acid Tetrahydrofolic acid One carbon group
transfer
Vitamin B12 deoxyadenosylcobalami
n
Intramolecular
rearrangements

6.  Many enzymes have common names
 Ex. Trypsin a proteolytic enzymes, is secreted
by the pancreas
 Common names- provide little information about
their reactions that enzyme catalyze
 Many enzymes are named for their substrates
and for reactions that they catalyze, with the
suffix –ase added
 Ex. ATPase that helps breaking down ATP
whereas
 ATP synthase which helps in synthesis of ATP

7.  International commission of enzymes was established to
create a systematic basis for enzyme nomenclature
 Rules for naming enzymes-
 Each enzyme is classified and named according to the
type of chemical reaction it catalyze
 The ENZYME COMMISSION (EC)has given each enzyme
a number with 4 parts, like, EC 2.7.1.2 (hexokinase)
 The 1st 3 numbers define major class, subclass and sub-
subclass respectively
 The last number is a serial number in the sub- class,
indicating the order in which each enzyme is added to the
list

8.  Common name and EC number of some
enzymes
Alcohol dehydrogenase EC 1.1.1.1
phosphofructokinase EC 2.7.1.11
Glutamine synthetase EC 6.3.1.2
Acetyl cholinesterase EC 3.1.1.7

9.  The first integer in the EC number
designates the class of enzymes
 There are 6 classes to which different
enzymes belong. These classes are-
 EC1 oxidoreductase
 EC 2 transferase
 EC 3 hydrolases
 EC 4 lyases
 EC 5 isomerases

10.  EC 1 OXIDOREDUCTASE
 Catalyzes oxidation reduction reactions
 A(red) + B(ox)A(ox) + B(red)
 Ex. Oxidases. Dehydrogenases,
oxygenases, peroxidases

11.  EC 2 TRANSFERASES
 Catalyzes reactions that involve the transfer of
groups from one molecule to another. Examples
of such groups include amino, carboxyl,
carbonyl, methyl, phosphoryl and acyl common
trivial names for the transferases often include
the prefix trans
 A-B + C A + B-C
 Ex. Transcarboxylases, kinases,
transaminases, phosphorylases

12.  EC 3 HYDROLASES
 Catalyzes reactions in which the cleavage of
bond is accomplished by adding water
 A-B + H2O A-H + B-OH
 Ex. Phosphodiesterases, phosphatases,
peptidases

13.  EC 4 LYASES
 Catalyzes the breaking of C-C, C-O, C-N, C-
S and other bonds by means other than
hydrolysis or oxidation
 A=B + HX  A-X + B-H
 Ex. aldolases, synthases, dehydratases,
decarboxylases

14.  EC 5 ISOMERASES
 Catalyzes several types of intramolecular
rearrangements and yield isomeric forms
 A-B B-A
 Ex. Mutases, cis trans isomerases,
epimerases, racemases

15.  EC 6 LIGASES
 Catalyzes the formation of C-C, C-S, C-O,
C-N bonds with simultaneous hydrolysis of
ATP
 A+ B+ ATP  A-B + ADP
 Ex. Carboxylases

16.  It increases the rate of a chemical reaction by
lowering the activation energy
 The free energy of reaction, ∆G, remains
unchanged in the presence of an enzyme, so
the relative amounts of reactants and products
at equilibrium are unchanged it only accelerates
the attainment of equilibria but do not shift their
positions
 The formation of an enzyme- substrate complex
is the first step in enzymatic catalysis

17. The binding between the enzyme and substrate is highly specific
The given enzyme usually binds to only one kind of substrate
Active site is the region of the enzyme where substrate binds and catalysis occurs
The substrate binds to active site of an enzyme by multiple weak
non covalent interactions
Formation of an enzyme substrate complex
Enzyme first binds to the substrate, the compound to be
catalyzed

18.  LOCK AND KEY MODEL
 Assumes a high degree of complementarity
between the shape of the substrate and
geometry of binding site on the enzyme
 The complementarity between enzymes and
their substrates is the basis of the lock and
key model of enzyme function
 This model was proposed by Emil Fischer

20.  INDUCED FIT MODEL
 Enzymes are flexible and that the shapes of
the active site can be markedly modified by
binding of substrate
 The binding of substrate induces a
conformational change in the enzyme that
results in a complementary fit once the
substrate is bound the binding site has a
different 3 dimensional shape before the
substrate is bound

22. An enzyme catalyzed chemical
reaction in which substrate S
changes into product
P goes through transition state
The substrate and product
correspond to low free energy
structures
The point of highest free energy is
the transition state in which the
substrates are partially converted to
products

23.  Amounts of enzymes can either be expressed
as molar amounts or measured in terms of
activity
 Enzymes are usually present in very small
quantities so a convenient method of enzyme
quantification is a measurement of catalytic
activity
 There are 2 standard units to express enzyme
activity
 Enzyme unit –U
 Katal - KAT

24.  Inhibition of enzyme activity may be reversible or
irreversible
 In reversible inhibition, inhibitor called irreversible
inhibitor binds tightly to the enzyme
 Inhibitor dissociates very slowly from the enzyme
and enzyme’s catalytic activity is permanently
inhibited
 The antibiotic penicillin acts as an irreversible
inhibitor of the enzyme glycopeptide transpeptidase
 Aspirin binds covalently with enzyme
cyclooxygenase, reducing the synthesis of
prostaglandin

25.  In reversible inhibitions, inhibitors called
reversible inhibitor binds non covalently to
the enzyme and dissociates rapidly from the
enzyme the effect of a reversible inhibitor is
reversed after dissociation of inhibitor from
enzyme
 There are 3 types of reversible inhibition
 Competitive
 Uncompetitive
 Non competitive

26.  The structure of a competitive inhibitor closely
resembles that of the enzyme’s normal substrate.
Because of its structure, a competitive inhibitor
binds reversibly to the enzyme’s active site
 The inhibitor forms an enzyme- inhibitor
complex(EI) that is equivalent to the ES complex
the effect of a competitve inhibitor on activity can
be reversed by increasing the concentration of
substrate
 At high S all the active sites are filled with substrate
and reaction velocity reaches the value observed
without an inhibitor

27.  The inhibitor binds to the enzyme at a site other than the
active site
 Inhibitor binding alters the enzyme’s 3 dimensional
configuration and blocks the reaction
 There are 2 types of non competitive inhibition- pure and
mixed
 In pure non competitive inhibition- substrate and inhibitor
binds at different sites on enzyme and binding of inhibitor
does not affect binding of substrate
 In mixed non competitive inhibition- the binding of inhibitor
with enzyme influences the binding of substrate with
enzyme

28.  The inhibitor binds at the site distinct from
the substrate
 It will bind only to the ES complex
 On the other hand non competitive inhibitor
binds to either free enzyme or the ES
complex