SolutionSet5 2008

SolutionSet5 2008 - BMB100B Winter 2008 Rubin Solution Set...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
BMB100B Winter 2008 Rubin Solution Set #5 Due Tuesday, February 19 th 10:00 A.M. 1) Recall that the active site of HIV protease contains two aspartic acids. The pKa values for these acids are tuned in the protein such that one is in the deprotonated state. a) Propose a mechanism for acid/base catalyzed hydrolysis of a peptide bond by this important enzyme. Use the following picture as the beginning (ES complex) state and draw the tetrahedral intermediate and product states. Be sure to indicate movement of electrons with arrows and all formal charges.
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
BMB100B Winter 2008 Rubin b) The serine protease mechanism (e.g. chymotrypsin, etc.) is often characterized as covalent catalysis. Would you characterize the acid protease mechanism as covalent catalysis? What is the key difference between this mechanism and the serine protease mechanism? The acid protease mechanism is not considered covalent catalysis because there is no covalent intermediate formed between the enzyme and the substrate. In serine proteases, the nucleophilic serine attacks the substrate and forms an acyl intermediate that is then eliminated by water. In the mechanism above, the water and carbonyl are activated by acid/base chemistry so the water directly hydrolyzes the substrate. 2) Leupeptin is a common protease inhibitor. Here is its structure: Use the structure of trypsin bound to leupeptin (PDB ID: 1JRT) to answer the following:
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 7

SolutionSet5 2008 - BMB100B Winter 2008 Rubin Solution Set...

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online