Homework 2 BCH2333 Winter 2017

Topics covered: pH, pKa, H-H equation, amino acids, nucleic acids

1. The -carboxyl group of Glu has a pKa of 4.3.

a. What fraction of the -carboxyl groups will be deprotonated (i.e., -COO- rather than
COOH) in a dilute solution of Glu at pH = 5.0?
b. At pH =3.8?
c. explain why this -carboxyl pKa is higher than the pKa of the -carboxyl group.

2. Calculate the pH of the following: 0.1 M HCl, 0.1 M NaOH, 3 10-5 M HNO3, 5 10-
5
M HClO4, and 2 10-8 M KOH. Show all work.

3. A hospital lab has 10 mL of stomach juice (hours after a meal, so no food is there as a
buffer) and it was titrated to neutrality with 7.2 mL of 0.1 M NaOH. What is the pH of
stomach juice (HCl)?

4. You have 100 mL of 0.08 M phosphate buffer at pH 6.0. By accident, 3.2 mL of 6 M

HCl was added. What is the resulting pH? The pkas of phosphate are 2.14, 6.86, 12.4.

5. Draw the structures, full names, three-letter names, and 1-letter symbols for all 20
amino acids. Indicate the pKas for each of the ionizable functional groups on each amino
acid.

6. Draw the Fischer projection formula for L-alanine. Rotate L-alanine and draw 4 other
rotation states of the molecule where at least two bonds are in the plane of the page.

7. For the dipeptide Glu-Ala write out the structure and estimate the pK of all ionizable
groups.

Using your assigned pK values, determine the net charge at pH 1, 3, 5, 7, 10, 11

8. Draw the following amino acid or oligopeptide structures:

a. The dipeptide Ala-His

b. The tripeptide Glu-Pro-Cys
c. Show how an oligopeptide of Leu and Lys can be either a branched-chain or a
straight-chain structure (only straight-chain structures occur in most natural
proteins).

9. What amino acid has a methyl alcohol attached to the -carbon? Draw it as a fisher
projection with the correct stereochemistry and with two bonds to the -carbon in the
plane of the page.

10. What amino acid has a guanidinium ion at pH 7? Draw the Fisher projection of this
amino acid with the correct stereochemistry and with two bonds to the -carbon in the
plane of the page.
Homework 2 BCH2333 Winter 2017

11. What is the net charge of the peptide DRAMA at pH 8? Draw the structure of this
pentapeptide.

12. Draw the structure of the artificial sweetener aspartame (L-aspartyl-L-phenylalanyl-

methyl ester) at pH 6. What is the charge on the peptide at pH 6?

13. Draw the structures of the 4 DNA nucleosides.

14. Draw the structure of the 4 RNA nucleotides.

15. What is the difference between a nucleoside and nucleotide?

16. Show the base pairing for G with C, A with T, and A with U. What non-covalent
forces are involved in these base pairings? Of these three base pair interactions, which
has the strongest non-covalent attraction and why?

17. Show the acid-base equilibrium reaction for adding the acid HA to water. Give the
equilibrium equation. Show the equation that defines the Ka of the acid. How do these
two equations differ?

18. Define the following and give an example of each as it relates to biochemistry:
Hydrophobic interaction
Hydrogen bonds
Disulfide bond
London Forces
Ionic interactions

19. Draw all the tautomers you can for the bases cytosine and uracil.

20. Draw the DNA sequence 5-GTACC-3.