1. When free water molecules are excluded from an enzyme's catalytic pocket, is a catalytic -OH group a stronger or weaker nucleophile? Explain your reasoning.
2. A histidine residue in the active site of aspartate transcarbamoylase is thought to be important in stabilizing the negatively-charged transition state of the bound substrates. Predict the pH dependence of the catalytic rate, assuming that this interaction is essential and dominates the pH-activity profile of the enzyme. Sketch a graph of the predicted behavior (enzyme activity vs. pH) and provide a brief rationale for your prediction.
3. In the serine protease triad, the proximity of an aspartate carboxylate group to the imidazole group of histidine raises the latter's pKa. Explain why.
4. AChE contains a catalytic triad with the residues His, Glu, and Ser. The nerve agent sarin is an extremely potent inactivator of AChE. Sarin irreversibly inhibits AChE by covalently modifying the serine residue in the active site.
a. Diagram the expected arrangement of the amino acids in teh catalytic triad
b. Draw a mechanism for the covalent modification of AChE by sarin.
c. How would sarin affect the apparent Km and Vmax of a sample of AChE? (Assume there is still detectable enzyme activity)