Problem set 1 - ANSWERS

Problem set 1 - ANSWERS - BIOCHEMISTRY 403 Problem Set 1...

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BIOCHEMISTRY 403: Problem Set 1 ENZYME MECHANISMS: ANSWERS 1. 20 + 30 = 50 kJ mol -1 of transition state stabilization would result in a ~6 x 10 8 fold rate acceleration. k cat /k uncat = exp(50000 J mol -1 /298 K x 8.314 JK -1 mol -1 ) 2. Properties that distinguish enzymes from other catalysts include increasing the reaction rates to a greater extent; acting under mild "physiological" conditions (temperatures below 100 o C, atmospheric pressure, near-neutral pH); having a high degree of selectivity and specificity for their substrates and reaction products; and being regulated at many levels (inhibition, activation, cooperativity, gene expression, proteolytic turn over etc) 3. (a) For each of the ionizable side chains, assume their pK a is in the typical range. If an enzyme reaction has a pH optimum of 7, what type of catalyst (general acid or base) would you expect each type of amino acid to play in this enzyme? Tyrosine (general acid; predominantly protonated at pH 7); Lysine (neither, predominantly protonated at pH 7 but amino group is not a good general acid due to its high pK a ); Cysteine (predominantly protonated at pH 7, although some of the unprotonated form may exist; general acid; weak general base); Histidine (both protonated and unprotonated forms exist at pH 7; thus a good general acid and general base); Asp/Glu (predominantly deprotonated at pH 7; general base). (b) The hydrophobic environment would destabilize the charged form of the amino acid side chain. For example, pK a of lysine and histidine would tend to decrease; that of Asp/Glu would tend to increase. Therefore, in this environment, an aspartic acid side chain may act as a general acid in a reaction with a pH optimum of 7 if its pK a is increased to just above 7. Or a lysine could act as a general base, if its pK a is decreased to just below the pH optimum of 7. 4. His12 has pK of 5.4, since it is active when unprotonated in the first stage of the reaction (acts as general base). It would lose activity when the pH decreases. His119 has a pK of 6.4 since it is active when protonated in the first stage of the reaction (acts as a general acid). It would lose activity when the pH increases. 5. Tyr14 first acts as a general acid, then a base. Asp28 first acts as a general base then an acid. Bifunctional catalysis refers to the simultaneous protonation (by Tyr14) and deprotonation (by Asp 28) of a substrate, such that an energetically unfavourable intermediate is avoided. In this case, if Asp 28 acted alone to deprotonate the ketone substrate to an enolate intermediate in the first step, it would require removal of a proton with a very high pK a (18-20; i.e., very difficult!). Simultaneous protonation by Tyr14 creates an energetically more favourable enol intermediate, which is more easily converted to product.
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6. The carboxylic acid will be protonated at pH 4, and thus intramolecular general acid
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Problem set 1 - ANSWERS - BIOCHEMISTRY 403 Problem Set 1...

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