PS1-Answer+Key+Chem+135+Spring+2010 - Chem 135 Spring 2010...

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Chem 135 Spring 2010 Problem Set 1 Due Tuesday February 2 at the beginning of class 1. Draw the following peptide as an organic molecule (including stereochemistry) at pH 11. H 2 N-M-I-C-H-E-L-L-E-W-Y-Q-T-K-CO 2 a. What is the net charge? -5 b. What is its net charge at pH 3 and pH 7? +3 (pH 3); -1 (pH 7) 2. The histidine side chain usually has a pK a of 6.0 in aqueous solution. However, in a certain folded protein, the pK a of a His side chain was found to be 7.0. a. Draw the equilibrium reaction for the dissociation of a proton from the His side chain in a polypeptide (i.e. a linear, unfolded protein). Use “R” groups to represent the remainder of the peptide connected to the amino and carboxyl groups of the His residue that you draw. N H R' R O NH N N H R' R O NH + HN b. In which direction has the above equilibrium shifted in the folding of the polypeptide (assume pK a of His is normally 6.0) to the final protein mentioned above? Towards the charged, protonated form of histidine c. Briefly suggest two possible causes for this pK a alteration. (1) Close to a negatively charged residue such as E or D so the positively charged histidine can form an ion pair; (2) the hydrogen can be a donor in a hydrogen bond 3. As discussed in class, the planar amide bond can be considered to be trans or cis with respect to the peptide backbone substituents (shown here as “R” groups). For most amino acids, the trans:cis ration is 10,000:1.
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In contrast, peptide bonds involving proline display a trans:cis ratio of only 80:20. a. Draw the
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This note was uploaded on 03/16/2010 for the course CHEM 135 taught by Professor Francis during the Spring '08 term at University of California, Berkeley.

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PS1-Answer+Key+Chem+135+Spring+2010 - Chem 135 Spring 2010...

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