Mechanism of enzyme catalysis

1. Mechanism of Enzyme catalysis
Gaurav
19mslsbf03
M.Sc Life science (Bioinformatics)

2. How Enzymes operate?
 An enzyme accelerates the rate of chemical reaction several times as
compared to uncatalyzed reaction.
 Enzyme increases the rate of chemical reaction by lowering the
activation energy.
 Enzyme does not change the free energies of the initial and final states.
 The free energy of reaction G, remains unchanged in the presence of
enzymes, so the relative amounts of reactants and products remain
unchanged.

3. Figure adapted from : An Introduction to Medicinal Chemistry By G. L. Patrick

4. We all know Enzymes lower the activation energy
But
Where does the energy to lower the activation energy
come from????

5. The Binding energy released due to the interactions between the enzyme and the
substrate lowers the activation energy.
 Only the correct substrate can form maximum interactions and thus maximize
binding energy.
 Maximum binding energy is released when the enzyme facilitates the formation of
transition state.
Transition state is the highest point of free energy , in which the reactants are
partially converted to products.

6. First step towards Enzyme Catalysis : Formation of enzyme substrate complex
Active site : It is the portion of enzyme where substrate binds and catalysis occurs.
 The substrate binds to the active site of an enzyme by multiple weak non-covalent
interactions like hydrophobic interactions, H-bonds, ionic interactions and reversible
covalent bonds.
Binding energy : It is the free energy released in the formation of large number of weak
interactions between enzyme and substrate.

7. Two models for describing enzyme – substrate binding
1. Lock-and-Key model :
 It assumes a high degree of complementarity between the shape of the substrate and
the geometry of the binding site on the enzyme.
 This model was proposed by Emil Fischer in 1894.

8. 2. Induced fit model :
According to this model Enzymes are flexible and that the shapes of the active sites can be
markedly modified by the binding of substrate.
 The binding of the substrate induces a conformational change in the enzyme that results in a
complementary fit once the substrate is bound.

10. BIOCHEMICAL MECHANISMS
The types of catalytic mechanisms that enzymes employ have been
classified as:
1. Acid–base catalysis
2. Covalent catalysis
3. Metal ion catalysis

11. ACID–BASE CATALYSIS
 General acid catalysis is a process in which proton transfer from an
acid lowers the free energy of a reaction’s transition state.
 The ionisable functional groups of amino acyl side chains and
(where present) of prosthetic groups contribute to catalysis by acting
as acids or bases.
The ability of enzymes to arrange several catalytic groups around
their substrates makes concerted acid–base catalysis a common
enzymatic mechanism.
The catalytic activity of these enzymes is sensitive to pH, since the
pH influences the state of protonation of side chains at the active site.
RNase A Is an Acid–Base Catalyst. Bovine pancreatic RNase A
provides an example of enzymatically mediated acid–base catalysis.
This digestive enzyme is secreted by the pancreas into the small
intestine, where it hydrolyzes RNA to its component nucleotides.

13. COVALENT CATALYSIS
The process of covalent catalysis involves the formation of a
covalent bond between the enzyme and one or more substrates.
Covalent catalysis accelerates reaction rates through the transient
formation of a catalyst– substrate covalent bond.
Usually, this covalent bond is formed by the reaction of a
nucleophilic group on the catalyst with an electrophilic group on the
substrate, and hence this form of catalysis is often also called
nucleophilic catalysis.

14. Covalent catalysis can be conceptually decomposed into three stages:
1. The nucleophilic reaction between the catalyst and the substrate to form a
covalent bond.
2. The withdrawal of electrons from the reaction center by the now
electrophilic catalyst.
3. The elimination of the catalyst, a reaction that is essentially the reverse of
stage 1.
Functional groups in proteins that act in this way include:
 The unprotonated amino group of Lysine,
 The imidazole group of Histidine,
 The thiol group of Cysteine,
 The carboxyl group of Aspartic acid ,
 And the hydroxyl group of Serine.

15. Examples of enzymes that participate in covalent catalysis
include the proteolytic enzyme chymotrypsin and trypsin
in which the nucleophlie is the hydroxyl group on the
serine.

16. METAL ION CATALYSIS
 Nearly one-third of all known enzymes require metal ions for catalytic
activity. This group of enzymes includes the metalloenzymes.
Most common transition metal ions include Fe2+ , Fe 3+, Cu 2+ , Mn 2+ or,
Co 2+ .
Ionic interactions between an enzyme-bound metal and a substrate can
help orient the substrate for reaction or stabilize charged reaction
transition states.
Metal ions participate in the catalytic process in three major ways:
1. By binding to substrates 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.

17. An excellent example of this phenomenon occurs in the catalytic
mechanism of carbonic anhydrase a widely occurring enzyme
that catalyzes the reaction:
CO2 + H2O ⇌ HCO3
- + H+

18. References:
 Introduction to Medicinal chemistry : “ Graham L. Patrick” ; ISBN-
978-0-19-923447-9 ; Oxford university press.
 https://www.slideshare.net/DavidEnoma/enzyme-catalysis-
mechanisms-involved?qid=a72901a0-d9bf-4814-8144-
786aa8d736df&v=&b=&from_search=1
 Life science fundamentals : “Mina.U., kumar.P.”; ISBN:
9789380473185; Pathfinder publications.