Question

1.

a) Name the following (with full names): (a) The amino acid without a primary amino group

(b) An amino acid that could form a salt bridge with an Asp residue in a protein interior:

(c) The amino acid that contains sulfur that doesn’t make disulfide bonds:

(d) Name one of the three amino acids that have hydroxylated R groups:

e) Draw the structure of the tetrapeptide SKYP at a pH of 5, making sure you include the structures of all R groups and all charges and clearly indicate where they originate. Clearly indicate the net charge of the tetrapeptide. If you can’t remember one of the side chains just use R but try to indicate the charge regardless. furthermore, What would be the net charge on the molecule at pH 1 and 12? Don’t redraw the peptide, but do indicate the charges on each residue at the different pH’s so part marks can be assigned. It may help to know the following pKa values: N-terminal amino group: 8 C-terminal carboxyl group: 3.1 Lys R-group: 10.8 Tyr R-group: 10.9

Answer 1

Answer 1

a. Proline is an amino acid without any primary amino group. It has a scondary amino group. All other amino acids contain an -NH2 group, while proline contains an -NH group.

b. In protein-chemistry, a salt bridge is defined as a non-covalent interaction between two oppositely charged side chains of two amino acids. Therefore, the RCOO- group of the negatively charged amino acids (Asp or Glu) can form salt bridges with the RNH3+ group of positively charged amino acids (Lys or Arg). Therefore, an example of a salt bridge is Asp-Lys.

c. Methionine is the amino acid that can't form disulfide bonds despite containig S in the side chain. Cystine, the other amino acid, which contains -SH (sulfhydryl) group at the gamma position, can readily undergo oxidation and two Cys residues can form the -S-S- or disulfide bond. On the other hand, in methionine, The -S- at the delta position can't be reduced to -SH group and also can't form disulfide linkages.

d. There are three amino acids with hydroxylated R groups. Serine, threonine and tyrosine.

e. The tetra-peptide SKYP corresponds to Ser-Lys-Tyr-Proline. At the mentioned pH, the N-terminal amino group will be in the -NH3+ configuration, while the C-terminal carboxyl group will be in the -COO- configuration. Further, the Lys side chain will be in the -NH3+ configuration and the Tyrosine side chain will be in the -OH configuration.

Therefore, the net charge will +1 on the tetrapeptide at a pH of 5.0.

At pH 1, the the N-terminal amino group will be in the -NH3+ configuration, while the C-terminal carboxyl group will be in the -COOH configuration. The Lys side chain will be in the -NH3+ configuration and the Tyrosine side chain will be in the -OH configuration. Therefore, total charge will be +2

At pH 12, the the N-terminal amino group will be in the -NH2 configuration, while the C-terminal carboxyl group will be in the -COO- configuration. The Lys side chain will be in the -NH2 configuration and the Tyrosine side chain will be in the -OH configuration. Therefore, net charge will be -1