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

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

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

Transition state analog

Covalent catalysis

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

Identifying the active site residues Serine was identified by chemical labeling

His was identified by affinity labeling

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

Substrate Specificity

Figure 11-30a

Figure 11-30b

Zymogens – inactive enzyme precursors

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.

Section 3 – Control of Enzyme Activity Allosteric regulation

T-state R-state

Figure 12-13

Covalent Modifications Phosphorylation is most common Ubiquitination important for protein degradation

Glycogen Phosphorylase

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

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

Mechanism of Penicillin

Bacterial Evolution Bacterial now produce an enzyme lactamase Inactivates penicillin

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…..

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

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

HIV protease mechanism

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

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

HIV T-cell – green HIV – red