Biological Sciences 102

Homework #1b

SQ13

Note: pKa of the side chain R-groups are: D (3.9), E (4.2), H (6.0), C (8.3), Y (10.1), K (10.5) and R (12.5). pKa of the Amino acid -carboxyl group 2.1; -amino group 9.6 pKa of the Oligopeptide N-terminal amino group 7.4; Oligopeptide C-terminal carboxyl group 3.6 pKa values of phosphoric acids are 2.15, 7.20, 12.40.
1. We have discussed the biological function of the proteins in the lecture, a) which type of protein does not perform any obvious chemical transformation, but control the ability of other proteins to carry out their physiological functions are? b) give an example of the protein described in (a): c) What type of function does Hemoglobin perform as a protein: d) What type of protein does Collagen belong to: e) What type of function does Chymotrypsin perform:

2. An oligopeptide X was obtained from blood plasma with the sequence W-P-T-I-H-E. (a) Draw the structure of this X oligopeptide in the form that would predominate at pH 7.0 (b) Calculate the overall net charge of X oligopeptide at that pH (7.0) to the nearest 0.01 (with a precision of two decimal places)? (c) In running through an ion-exchange column made up of sulphate S-resin, what pH fraction would this X oligopeptide be expected in a gradient of acid-to-base elution. Show your work to receive full credit in MT1.

Biological Sciences 102

Homework #1b

SQ13

3. Amino acid analysis of an oligopeptide seven residues long gave Asp Leu Lys Met Phe Tyr. The following facts were observed: a. Trypsin treatment had no apparent effect. b. The phenylthiohydantoin released by Edman degradation was c. Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. d. Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide?

4. A student performs one cycle of the Edman chemistry on an unknown peptide. The student expects one PTH-a.a. as the result. a) However, what would you conclude if you found no PTH-a.a.? b) What would you conclude if you found two PTH-a.a.s in the first cycle? Assume that the steps in the Edman procedure were run correctly. If there is more than one possible explanation, then give them all.

Biological Sciences 102

Homework #1b

SQ13

5. One surface protein of an isolated virus contains a remarkably long alpha-helix with 53 amino acids. (a) How many turns does this alpha-helix have? (b) What would be the main stabilizing force behind this secondary structure formation? (c) How long is this alpha-helix?

6. What characteristic of proline makes it both an -helix breaker and a common component of -turns

7. There are five amino acids, aspartate, histidine, isoleucine, valine and lysine, known to compose a peptide. Describe the expected elution pattern for a mixture of amino acids hydrolyzed from this pentapeptide on a column of a) a Dowex-50 cation exchanger column (use the pKa values given in Table 4.1, Garrett & Grisham, Biochemistry); b) explain your reason of the elution pattern; and c) what about the elution pattern of an anion exchange column.