Chapter 9 Catalytic Strategies 7 6 What supports the theory that a catalytic triad strategy is an effective means to accomplish hydrolysis of peptides? Ans:A number of different enzymes,including the peptidase family,some esterases,and others,have similar mechanisms of actions.While the strategy is similar,the actual participating amino acids differ,suggesting a mechanism commonly employed as a result of convergent evolution. Section:9.1 7 What is common strategy for cysteine,metallo,and aspartyl proteases? Ans:All employ a mechanism whereby a nucleophile is generated that attacks the carbonyl of the peptide bond. Section:9.1 8 What is the common nucleophile found in cysteine,metallo,and aspartyl proteases? Ans:The common nucleophile is water. Section:9.1 9 Designing drugs to inhibit enzymes is a large part of pharmaceutical research.What are some of the enzymatic features that would be important? Ans:The enzyme could be inhibited by interaction of a potential drug at the active site or at a site that alters conformation or regulation of the enzyme.The structure of natural substrates and activators,and their binding sites,would be useful features to study a new drug design.The binding affinity and specificity would be important,and standard enzyme assays would be used to determine the effect of the inhibitors on Keat,KM,and Vmax. Section:9.1 10 How is the bicarbonate formed when carbonic anhydrase is present? Ans:The zinc promotes formation of a hydroxide ion,which attacks the carbon dioxide. Section:9.2 11 What features of carbonic anhydrase allow the rapid hydration of carbon dioxide? Ans:Bringing the two reactants(carbon dioxide and water)facilitates the rapid reaction rate into proximity,and the presence of a buffer system aids in proton transfer and release. Section:9.2 12 What mechanism is responsible for restriction endonuclease cleavage of DNA? Ans:An activated water molecule directly attacks the phosphorous atom in a single displacement reaction. Section:9.3 13 The sequence 6 bp restriction cleavage site for EcoRV is GATXXX.What is the complete sequence of the double stranded restriction site? Ans:GATATC CTATAG Section:9.3Chapter 9 Catalytic Strategies 7 6 What supports the theory that a catalytic triad strategy is an effective means to accomplish hydrolysis of peptides? Ans: A number of different enzymes, including the peptidase family, some esterases, and others, have similar mechanisms of actions. While the strategy is similar, the actual participating amino acids differ, suggesting a mechanism commonly employed as a result of convergent evolution. Section: 9.1 7 What is common strategy for cysteine, metallo, and aspartyl proteases? Ans: All employ a mechanism whereby a nucleophile is generated that attacks the carbonyl of the peptide bond. Section: 9.1 8 What is the common nucleophile found in cysteine, metallo, and aspartyl proteases? Ans: The common nucleophile is water. Section: 9.1 9 Designing drugs to inhibit enzymes is a large part of pharmaceutical research. What are some of the enzymatic features that would be important? Ans: The enzyme could be inhibited by interaction of a potential drug at the active site or at a site that alters conformation or regulation of the enzyme. The structure of natural substrates and activators, and their binding sites, would be useful features to study a new drug design. The binding affinity and specificity would be important, and standard enzyme assays would be used to determine the effect of the inhibitors on Kcat, KM, and Vmax. Section: 9.1 10 How is the bicarbonate formed when carbonic anhydrase is present? Ans: The zinc promotes formation of a hydroxide ion, which attacks the carbon dioxide. Section: 9.2 11 What features of carbonic anhydrase allow the rapid hydration of carbon dioxide? Ans: Bringing the two reactants (carbon dioxide and water) facilitates the rapid reaction rate into proximity, and the presence of a buffer system aids in proton transfer and release. Section: 9.2 12 What mechanism is responsible for restriction endonuclease cleavage of DNA? Ans: An activated water molecule directly attacks the phosphorous atom in a single displacement reaction. Section: 9.3 13 The sequence 6 bp restriction cleavage site for EcoRV is GATXXX. What is the complete sequence of the double stranded restriction site? Ans: GATATC CTATAG Section: 9.3