ps2s - MIT Department of Biology 7.014 Introductory Biology...

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MIT Department of Biology 7.014 Introductory Biology, Spring 2004 Name:__________________________________________ Section: ______ Solutions to 7.014 Problem Set 2 Question 1 A schematic of the active site of an enzyme with its substrate bound is shown below. The side chains of the amino acids important to the function of that active site are shown as a-e. _ CH 3 H O C CH 2 a C N O C C NH O e CH 2 C NH 2 2 N C CH 3 O C C O HO CH b C C CH 3 CH 3 CH 3 CH 3 CH 3 CH 3 CH 2 CH CH CH 2 d c a) Identify each of the amino acids a-e and indicate the strongest type of non-covalent interaction it makes with the substrate. # Amino acid Interaction with substrate a aspartate Hydrogen bond b threonine Hydrogen bond c isoleucine van der Waals d leucine van der Waals e asparagine Hydrogen bond 1
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Name:__________________________________________ Section: ______ Question 1, continued The isolated substrate for this enzyme is shown below (rotated 90 ° to the left). For parts b) and c) below ignore size considerations. NH 2 O C C C N C H CH 3 C N C C C CH 3 CH 3 O b) For each of the following, indicate if the interaction with the enzyme would be stronger than that seen with the original substrate, the same as that seen with the original substrate, or weaker than that seen with the original substrate. For each, explain your reasoning. i) NH 2 O interaction (circle one): stronger weaker CH 3 H same C C reasoning: N C C This change is on a region of the substrate that does not bond to the enzyme. It does not change the interaction of enzyme with substrate. N C C C C CH 3 CH 3 CH 2 O CH 3 ii) NH 2 O interaction (circle one): stronger weaker same CH 3 H + C C reasoning: N C C The positive charge on the N can now form an ionic bond N C C C C with the side chain of amino acid (a) of the enzyme. CH 3 CH 3 O iii) NH 2 O interaction (circle one): stronger weaker same CH 3 H C C reasoning: N C C The SH group no longer forms a hydrogen bond C N C with the asparagine (amino acid e) of the enzyme. C C CH 3 CH 3 SH 2
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Name:__________________________________________ Section: ______ Question 1, continued c) The following modified substrate does not bind. You want to change one amino acid of the enzyme active site to allow this version of the substrate to bind. Your change should maximize the strength of the interaction between the substrate below and the enzyme. O _ NH 2 O H C C C O N C C C N C C C CH 3 CH 3 O i) Which amino acid would you change? You would change amino acid c. ii) To what would you change it and why? Change it to something positively charged such as lysine, histidine, or arginine because this would allow the formation of an ionic bond.
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