fundamentals of biochemistry third edition fundamentals of biochemistry third edition chapter 11...
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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