SolutionSet5-2 - BMB100B Winter 2010 Rubin Solution Set#5 1...

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BMB100B Winter 2010 Rubin Solution Set #5 1) Another type of protease that carries out the same peptide hydrolysis reaction as serine proteases is the Zn protease. Below is a schematic of the active site containing the Zn and a Glu. Propose a mechanism for the Zn protease catalyzed hydrolysis reaction. Use the picture and add a water to depict 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. Here are two answers: This first mechanism is simple and applies the key concepts that are important for you to know from lecture: Here the Glu acts as a base (take H 2 O proton) and acid (donate to leaving H 2 N-R’). The role of Zn is to activate water, i.e. make the H 2 O proton more acidic so that even the weak glutamate base can deprotonate it. The second answer is a more complicated (but more accurate according to the actual experiments done to determine the mechanism):
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BMB100B Winter 2010 Rubin This more detailed mechanism is somewhat similar to the simple first mechanism, but the Zn also stabilizes the negative charge that builds on the carbonyl O in the tetrahedral intermediate. Note that it has been determined that the tetrahedral intermediate O actually coordinates to the metal (metal-ligand bond) but this inorganic chemistry detail is beyond the scope of this course. If your answer looked like the first mechanism, you understand the catalysis concepts well! b) The serine protease mechanism (e.g. chymotrypsin, etc.) is often characterized as covalent catalysis. Would you characterize the zinc protease mechanism as covalent catalysis? What is the key difference between this mechanism and the serine protease mechanism? The metalloprotease mechanism is not considered covalent catalysis because there is
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This note was uploaded on 03/16/2010 for the course BIOC 100B taught by Professor Sethrubin during the Winter '10 term at UCSC.

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SolutionSet5-2 - BMB100B Winter 2010 Rubin Solution Set#5 1...

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