Problem Set #2: Amino Acids and Peptides

1) Given the following peptide: Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu

b) identify the non-polar amino acids

c) identify the amino acids that contain sulfur

d) identify the aromatic amino acids.

2) Draw the following amino acids in their fully protonated forms:

b) Cysteine

c) Glutamic acid

d) Histidine

e) Tyrosine

f) Leucine

3) For each of the amino acids in problem #2, indicate which protons are dissociable.

4) Using the pKa' values given in the attached table, for each of the amino acids listed in problem #2, indicate the ionic form which predominates at :

b) pH 7.0

c) pH 13

d) What is the net charge of the predominant form at each of these pH's?

5) Draw a titration curve for each of the amino acids given in problem #2.

6) Based on the information given in the attached table, is there any amino acid that could serve as a buffer at pH 8.0? If so which? Calculate the ratio of the two forms of this amino acid that would be present at this pH.

7) Draw the structure for each of the following peptides in their fully protonated forms. Indicate which protons are dissociable in the structure.

b) Tyr-Arg-Ser

8) Draw a titration curve for each of the peptides given in Problem #7.

9) For the peptides given in Problem #7, predict the ionic form that will predominate at

b) pH 7

c) pH 13.

10) Using the pK_a's given, calculate the isoelectric point for each of the following:

b) Ile

c) His

d) Tyr-Arg-Ser

e) Asp-Gly-Leu

11) The sequence of a 29 aa long peptide can be determined from the following data.

a) Treatment of the peptide with dansyl chloride reveals that the amino terminal is Val.
b) Trypsin digestion, separation of peptides and Edman degradation give sequences for peptide fragments as follows:
Val-Gly-Ala-His-Ala-Gly-Glu-Tyr-Gly-Ala-Glu-Ala-Thr-Glu
Ala-Ala-Trp-Gly-Lys
Val-Leu-Ser-Pro-Ala-Lys
Thr-Asn-Val-Lys
c) Chymotrypsin digestion, separation of peptides, and Edman degradation give the following sequences for fragments:
Gly-Ala-Glu-Ala-Thr-Glu
Gly-Lys-Val-Gly-Ala-His-Ala-Gly-Glu-Tyr
Val-Leu-Ser-Pro-Ala-Lys-Thr-Asn-Val-Lys-Ala-Ala-Trp

What is the sequence for the peptide?

12) Predict the fragments that will be generated from the treatment of the following peptide with: a) trypsin; b) chymotrypsin; c) and S. aureus V8 protease:

Gly-Ala-Trp-Arg-Asp-Ala-Lys-Glu-Phe-Gly-Gln

pKa's for the Acidic and Basic Constituents of the Free Amino Acids

Amino Acids	Carboxyl Group	Amino Group	Side Chain
Gly	2.4	9.8	---
Ala	2.4	9.9	---
Val	2.3	9.7	---
Leu	2.3	9.7	---
Ile	2.3	9.8	---
Met	2.1	9.3	---
Pro	2.0	10.6	---
Phe	2.2	9.3	---
Trp	2.5	9.4	---
Ser	2.2	9.2	---
Thr	2.1	9.1	---
Cys	1.9	10.7	8.4
Tyr	2.2	9.2	10.5
Asn	2.1	8.7	---
Gln	2.2	9.1	---
Asp	2.1	9.9	3.9
Glu	2.1	9.5	4.1
Lys	2.2	9.1	10.5
Arg	1.8	9.0	12.5
His	1.8	9.3	6.0

Adapted from Dawson, R. M. C., Elliot, D. C., and Jones, K. M. (1986) Data for Biochemical Research, 3rd. Ed. (Oxford: Clarendon Press)

Solutions to Problem Set 2:

Solution to #1
Solution to #2
Solution to #3
Solution to #4
Solution to #5
Solution to #6
Solution to #7
Solution to #8
Solution to #9
Solution to #10
Solution to #11
Solution to #12