The document discusses the mechanisms of enzymatic catalysis, highlighting how enzymes enhance reaction rates, specificity, and regulate conditions. It elaborates on different types of catalysis, including acid-base, covalent, and metal ion catalysis, as well as the significance of active sites and transition states in enzyme action. Examples of various proteases and their catalytic mechanisms are also provided, emphasizing their evolutionary relationships.

1. Mechanism of Enzymatic
Catalysis
Moderator: Dr. S. K. Gupta
Presenter: Dr. Karthikeyan

2. Enzymes increases the rate of reaction

3. • Higher reaction rates, 106-1012
• Milder reaction conditions (temp, pH, …)
• Greater reaction specificity (no side products)
• Capacity for regulation
Chemical catalyst Vs. Biological catalyst

4. Chemical catalyst Vs. Biological catalyst
1.Temperature of 400°C
2.Pressure of 200 atm
3.Iron catalyst

5.  Proximity
 Straining
 Orientation Change
 Change of environment
 Transition state stabilization
How does enzymes increase the rate ?

6.  Acid Base Catalysis
 Covalent Catalysis
 Metal Ion Catalysis
What are all the modes of catalysis ?

9. Active Site
• 3 dimensional cleft
• Unique microenvironment
• Nature of binding
• Specificity

11. Changes during and after E-S complex
E-S Complex
Multiple, Reversible, Weak
Interactions
Binding Energy
Helps in attainment of transition state
Products

13. Transition state
• Fleeting, Momentary, Unstable chemical
species
• Evidence for existence
• Meaning of Transition State stabilization

14. Enzymes lower ΔG‡

16. Stabilization of transition state is
the mechanism of enzyme
action.

17. Transition State Vs. Intermediate

18. Active site is more complementary to transition
state than substrate.
So, Transition state analogues are better
competitive inhibitors than substrate
analogues

19. • higher their concentration, the more
frequently they will encounter one
another
• Concept of effective molarity
Proximity Effect

20. Proximity
Effect

21. Straining

22. Chemical Reactions
• Nucleophilic Substitutions
• Cleavage Reactions
• Oxidation–Reduction Reactions

23. Nucleophilic Substitutions

24. denotes movement of electrons

25. Acid-Base catalysis

26. Why fossils of RNA world
NOT found ?

27. Structure of RNA

28. RNAse A

29. RNAse A

49. Why RNAse can’t act on DNA ?

50. Covalent catalysis

51. Serine proteases

52. Chymotrypsin
Hydrophobic pocket

53. Trypsin
Deep groove with negatively
charged aspartate inside

54. Elastase
Shallow groove

55. Catalytic Triad

57. Ser-195 becomes a nucleophile

58. Tetrahedral intermediate
Ser-195 attacks the carbonyl group

59. Acyl enzyme intermediate

60. Binding of Water

61. Tetrahedral intermediate

62. Regeneration of enzyme

63. Other Serine Proteases
• Subtilisin
• Wheat germ Serine carboxy peptidase II
• E.coli Clp protease (caseinolytic peptidase)

64. Serine proteases are example for
both convergent and divergent
evolution !

65. Aspartic protease
• HIV PROTEASE
• Pepsin
• Rennin
• Lysosomal cathepsins.

66. Aspartic protease
• Catalysis involves two conserved aspartyl residues
which act as acid-base catalysts
• 2 different active site aspartates act simultaneously
as a general base or as a general acid.
• This is possible because their immediate
environment favours ionization of one but not the
other.

67. Metal Ion catalysis

68. Charge Shielding by metals

71. Binding to zinc lowers the pKa of water
from 15.7 to 7

73. Ogston’s 3 Point Attachment Theory

74. Enzymes react stereo-specifically
with chiral compounds

78. • Worked under Nobel laureate H. Gobind Khorana
• A prominent scientific journal rejected his work as "a
technological development of no general interest“.
Michael Smith

79. Vitalistic
Theory