Amino Acids

Question 1

The hydrophobic affect is largely responsible for the correct protein folding and the association of lipids into bilayers and other structures. The basis of the hydrophobic effect is:
A) vibration of water molecules adjacent to non- polar molecules
B) attraction of closely packed non-polar groups due to van der waals interactions
C) increased hydrogen bonding in water molecules surrounding non-polar molecules
D) increased dielectric constant of water relative to non- polar solvents.
E) increased water entropy due to minimized contact of water with non- polar groups

Answer 1

E) increased water entropy due to minimized contact of water with non- polar groups

Question 2

The side chain of aspatic acid normally has a pka of 3.9. At which value would you expect about 90% of the ASP side chains to be in the negatively charged (COO-) form?
A) pH 2.9
B) pH 3.9
C) pH 4.9
D)pH 5.9
E) pH 8.6

Answer 2

C) pH 4.9
According to the Henderson-hasselbach equitation, the value of log [A-]/[HA] is 10, or about 90 % of ASP side chains in the carboxylate form, corresponding to a pH value of one unit above the pka.

Question 3

Only the amino acid …. Can spontaneously for covalent bonds between two different polypeptide chains, while …. Is often used to monitor protein purification because of its ability to absorb UV light.
A) proline; tyrosine
B)cysteine, tryptophan
C) methionine, cysteine
D) glutamic acid, valine
E) methionine, histadine

Answer 3

B) cysteine, tryptophan
When oxidized, two cysteine residues can form a disulfide bond between (or within) polypeptide chains, while tryptophan has the highest UV absorbance of all the amino acids ( at 280nm)

Question 4

Solutions of four different lure amino acids were titrated, and the pka values of the solutes were determined:
Solution Pk1. Pk2. Pk3
1 2.10. 3.86. 9.82
2. 2.10. 4.07. 9.47
3. 2.32. 9.76. Not applicable
4. 2.18. 9.04. 12.48
Which solution contains an amino acid that when incorporated into the surface of a proteins would most likely become capable of binding an anionic ligand at physiological pH?
A)solution 1
B)solution 2
C)solution 3
D)solution 4
E) none of the above

Answer 4

D) solution 4
The correct answer is Solution 4. You can deduce that solutions 1 and 2 likely contain the amino acids glutamate or aspartate, as two of the pka values are well below 7, corresponding to the alpha and side chain carboxyl groups. These side chains would be negatively charged at physiological pH. The amino acid in solution 3 must have a non- ionizable side chain, are there are only two pka values (corresponding to the free alpha carboxyl and amino groups). In contrast, the compound in solution 4 has two pka values well above pH 7, likely corresponding to the alpha amino group and guanidium side chain of arginine, which would carry a full positive charge at pH 7. The Arg side chain could thus assist binding of an anionic (negatively charged) molecule through ionic attraction. (Remember: the alpha amino and carboxyl groups of amino acids are no longer charged in the peptide bond; only the ionizable side chains be charged within a polypeptide chain).