Fundamentals of Biochemistry

Third Edition

Fundamentals of Biochemistry

Third Edition

Chapter 11Enzymatic Catalysis

Chapter 11Enzymatic Catalysis

Copyright © 2008 by John Wiley & Sons, Inc.Copyright © 2008 by John Wiley & Sons, Inc.

Donald Voet • Judith G. Voet • Charlotte W. Pratt

Donald Voet • Judith G. Voet • Charlotte W. Pratt

Section 4 – Lysozyme

NAG = N-acetylglucosamineNAM = N-acetylmuramic acid

Asp – normal pKR = 3.09

Non-polar environmentGlu – pKR = much higher than 4.07

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

ChymotrypsinElastase also have similarStructures

Asp is very important

Catalytic triadAsp, His, Ser

Substrate Specificity

Figure 11-30a

Figure 11-30b

Zymogens – inactive enzyme precursors

Fundamentals of Biochemistry

Third Edition

Fundamentals of Biochemistry

Third Edition

Chapter 12Enzyme Kinetics, Inhibition, and Control

Chapter 12Enzyme Kinetics, Inhibition, and Control

Copyright © 2008 by John Wiley & Sons, Inc.Copyright © 2008 by John Wiley & Sons, Inc.

Donald Voet • Judith G. Voet • Charlotte W. Pratt

Donald Voet • Judith G. Voet • Charlotte W. Pratt

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

Acid stable, orallyMost widely used

Mechanism of Penicillin

Bacterial Evolution

Bacterial now produce an enzyme lactamase

Inactivates penicillin

Human response

Create inhibitor of β-lactamaseClavulanic 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