1. Fundamentals of Biochemistry
Third Edition
Donald Voet • Judith G. Voet • Charlotte W. Pratt
Chapter 11
Enzymatic Catalysis
Copyright © 2008 by John Wiley & Sons, Inc.

2. Section 4 – Lysozyme NAG = N-acetylglucosamine
NAM = N-acetylmuramic acid

6. Non-polar environment
Glu – pKR = much higher than 4.07
Asp – normal pKR = 3.09

12. Transition state analog

13. Covalent catalysis

14. Section 5 – Serine Proteases
Highly reactive serine
Many digestive enzymes use this mechanism
Inhibiting serine proteases can be very toxic

15. Identifying the active site residues
Serine was identified by chemical labeling

16. His was identified by affinity labeling

17. Trypsin with leupeptin inhibitor
Chymotrypsin
Elastase also have similar
Structures
Asp is very important
Catalytic triad
Asp, His, Ser

18. Substrate Specificity

25. Figure 11-30a

26. Figure 11-30b

27. Zymogens – inactive enzyme precursors

28. Fundamentals of Biochemistry
Third Edition
Donald Voet • Judith G. Voet • Charlotte W. Pratt
Chapter 12
Enzyme Kinetics, Inhibition, and Control
Copyright © 2008 by John Wiley & Sons, Inc.

29. Section 3 – Control of Enzyme Activity
Allosteric regulation

31. T-state
R-state

32. Figure 12-13

33. Covalent Modifications
Phosphorylation is most common
Ubiquitination important for protein degradation

35. Glycogen Phosphorylase

38. Penicillin Penicillin – 1928 Alexander Fleming
Disrupts synthesis of peptidoglycans by transpeptidase
Used for bacterial cell walls
Lactam ring is highly reactive

40. Types of Penicillin First, injection only Acid stable, orally
Most widely used

41. Mechanism of Penicillin

42. Bacterial Evolution Bacterial now produce an enzyme lactamase
Inactivates penicillin

43. Human response Create inhibitor of β-lactamase Clavulanic acid
Augmentin – combination of both amoxicillin and clavulanic acid
New bateria resistant to both
The battle continues…..

44. HIV Retrovirus – RNA genome
Make a polyprotein consisting of 3 proteins
Reverse transcriptase, integrase, protease
Drugs for all enzymes
Drugs for attachment

45. Protease mechanisms Serine proteases (chymotrypsin) Cysteine proteases
Aspartyl proteases (HIV protease)
Metalloproteases

46. HIV protease mechanism

47. HIV protease inhibitors
OH – mimics stable intermediate, benzene ring mimics hydrophobic aa

48. Other HIV drug targets Integrase inhibitors
FDA approved in 2007 (raltegravir)
Inhibits strand transfer of viral DNA into host genome
Reverse Transcriptase Inhibitors
AZT 1987
Nucleoside inhibitors (terminate DNA chain)
Non-nucleoside inhibitors (irreveribily bind to RT)
Coming soon…
Viral fusion, maturation

49. HIV
T-cell – green
HIV – red