different mechanisms used by enzymes at their catalytic site

1. Submitted By: Gokul Arora
M.Sc. Medical biochemistry 2nd year
MECHANISMS INVOLVED
AT CATALYTIC SITE

2. CATALYTIC MECHANISMS
• Catalysis is a process that increases the rate at
which a reaction approaches equilibrium.
• catalyst stabilizes the transition state with
respect to the uncatalyzed reaction.
• Q. What apparently make enzymes such
powerful catalysts?
• Ans. Their specificity of substrate binding
combined with their optimal arrangement of
catalytic groups.

3. CATALYTIC MECHANSIMS
The types of catalytic mechanisms that enzymes employ
have been classified as:
• 1. Acid–base catalysis.
• 2. Covalent catalysis.
• 3. Metal ion catalysis.
• 4. Electrostatic catalysis.
• 5. Proximity and orientation effects.
• 6. Preferential binding of the transition state complex.

4. ACID-BASE CATALYSIS
• General acid catalysis is a process in which partial
proton transfer from a Brønsted acid lowers the
free energy of a reaction’s transition state.
• A reaction may also be stimulated by general base
catalysis if its rate is increased by partial proton
abstraction by a Brønsted base.
• Some reactions may be simultaneously subject to
both processes: a concerted general acid–base
catalyzed reaction.

6. Concerted Acid-Base Catalysis
• Many types of biochemical reactions are
susceptible to acid/or base catalysis.
• These include the hydrolysis of peptide and
esters, the reactions of phosphate groups,
tautomerizations, and additions to carbonyl
groups.

9. COVALENT CATALYSIS
• Covalent catalysis involves rate acceleration through the
transient formation of a catalyst–substrate covalent
bond.
• Reaction mechanisms are somewhat arbitrarily classified
as occurring with either nucleophilic catalysis or
electrophilic catalysis depending on which of these
effects provides the greater driving force for the
reaction.
• several coenzymes, most notably thiamine
pyrophosphate and pyridoxal phosphate , function in
association with their apoenzymes mainly as covalent
catalysts.

10. Lysozyme reaction mechanism
R group = N-acetyl group
R’ group = CH3CHCOO-

11. METAL IONS
• Nearly one-third of all known enzymes require the presence
of metal ions for catalytic activity.
• On the basis of ion-protein interaction:-
1. Metalloenzymes contain tightly bound metal ions , most
commonly transition metal ions such as Fe2+, Fe3+, Cu2+ etc.
2. Metal-activated enzymes loosely bind metal ions from
solution, usually the alkali and alkaline earth metal ions Na+,
K+,Mg2+, or Ca2+.

12. Metal ions participate in the catalytic process in three
major ways:
• 1. By binding to substrates so as to orient them
properly for reaction.
• 2. By mediating oxidation–reduction reactions through
reversible changes in the metal ion’s oxidation state.
• 3. By electrostatically stabilizing or shielding negative
charges.
METAL IONS

13. The decarboxylation of dimethyloxaloacetate,
as catalyzed by metal ions such as Cu2+ and
Ni2+, is a nonenzymatic example of catalysis by
a metal ion.

14. Electrostatic Catalysis
 Charge distributions about the active sites of enzymes
are arranged to stabilize the transition states of the
catalyzed reactions. Such a mode of rate enhancement is
termed electrostatic catalysis.
 Some examples-
-providing lower dielectric constant in active site.
-stabilizing a particular conformation of critical groups in
active site by electrostatic interactions.

15. Catalysis using proximity and
orientation effects
 Reactants must come together with the proper
spatial relationship for a reaction to occur.
 Proximity Alone Contributes Relatively Little to
Catalysis.
 Properly Orienting Reactants and Arresting
Their Relative Motions Can Result in Large
Catalytic Rate Enhancements.

16. oThe intramolecular reaction of Imidazole is 24 times faster than bimolecular
reaction of Imidazole and p-Nitrophenylacetate.
oThis rate enhancement has contributions from both proximity and orientation.

17. Catalysis by Preferential
Transition State Binding
 An enzyme binds the transition state of the
reaction with greater affinity than its substrate
or products.
 When taken together with the previously
described catalytic mechanisms, preferential
transition state binding rationalizes the
observed rates of enzymatic reactions.

18. Transition State Analogs
This reaction is catalyzed by Proline
racemase Clostridium sticklandii
Proline racemase is competitively inhibited by the
planar analogs of proline, pyrrole-2-carboxylate
and -1-pyrroline-2-carboxylate

19. REFERENCES
• Biochemistry Book by Donald Voet and Judith
G. Voet
• Nelson, D.L. and Cox, M.M. (2017) Lehninger
Principles of Biochemistry. 7th Edition, W.H.
Freeman, New York, 1328.

20. THANK YOU