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ProblemSet5 - reaction Use the picture as the beginning(ES...

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BMB100B Winter 2009 Rubin Problem Set #5 Due Tuesday, February 17 th 10:00 A.M. 1) 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: a) Explain the mechanism of leupeptin inhibition. b) Design a leupeptin analog that would inhibit chymotrypsin. 2) In the absence of inhibitor, what effect on the catalytic activity of trypsin would you expect from the mutations below and why? Using the 1JRT trypsin structure (imagining no inhibitor) may help. a) D102N (i.e. mutate D102 to an N). b) D102E c) D189K d) S195C 3) Another type of protease that carries out the same peptide hydolysis reaction as serine proteases is the Zn protease. Below is a schematic of the active site containing the Zn, an activated water, and a Glu. Propose a mechanism for the Zn protease catalyzed hydrolysis
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Unformatted text preview: reaction. Use the 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. BMB100B Winter 2009 Rubin 4) Explain why most enzyme active sites are buried within the interior of proteins as opposed to on the protein surface. Try to give three reasons. 5) Aldolase catalyzes cleavage of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehydes 3-phosphate ( read from right to left below ). Aldolase has a catalytic lysine that acts as a nucleophile (think Schiff base intermediate) and residues in the active site that can act as acid/base proton acceptors and donors. Write down a mechanism describing the reaction that contains intermediates, movement of electrons and protons, etc....
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ProblemSet5 - reaction Use the picture as the beginning(ES...

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