1. Which amino acid has a net charge of â€œ+ 0.09â€ at pH 7? Show all calculations. Draw the structure of the amino acid that would predominate at this pH.

2. Palmitate is a sixteen-carbon fatty acid. We will study it further when we study lipids, later in the course. When palmitate is put into water, the following reaction occurs spontaneously:

a) Which weak bond(s) stabilize the formation of the micelle? Explain.
b) Which weak bond(s) destabilize the formation of the micelle? Explain.
c) Which weak bond(s) neither stabilize nor destabilize the formation of the micelle? Explain.
d) If we lowered the temperature of the system 10oC, which side of the equilibrium, if any, would be favored? Why?

3. Using the one-letter code, identify those amino acids whose R-groups can act as both hydrogen bond donors and acceptors, regardless of the pH.

4. We use the Henderson-Hasselbalch equation to determine how much strong base to add to a certain quantity of weak acid to make up a buffer at a given pH. Why do we use the Henderson-Hasselbalch equation? Why do we not just subtract or add molar amounts of acid and base?

5. What must the pH be if a 10 mM solution of arginine has a net charge of â€œ-0.65â€? Use the pKaâ€™s given in appendix VII of Biochemical Calculations.

6. Calculate the pI of cysteine. Use the pKa values given in Biochemical Calculations, appendix VII. What does this pI value tell you (i.e. of what use is it to know the pI)?

7. How many moles of OHâ€“ are required to raise the pH of 4.00 liters of 25 mM glycine, pH 1.90, to a final pH of 9.70? Assume that the addition of OHâ€“ does not change the volume of the solution. The pKaâ€™s of glycine are Î±-COOH group 2.34 and Î±-NH3+ group 9.60.

8. The following is an excellent buffer problem from Outlines of Biochemistry, 5th ed., John
Wiley & Sons, c1987, pg. 24. This question tests your understanding of several weak acid/base concepts.

â€œCalculate the compositions of two buffers. Each buffer is to be 0.10 M ethanolamine (H2NCH2CH2OH) and to contain acetic acid. One buffer is to be pH 5.0, the other 9.2. Which of these two buffers will have the greater buffering capacity?â€ Note: assume a volume of one liter for each buffer. The pKaâ€™s of ethanolammonium ion (the protonated form of ethanolamine) and acetic acid are 9.44 and 4.76, respectively.

9. You have isolated a new pentapeptide from a bacterium. A series of experiments reveals the following about your peptide:

a) the column elution profile from amino acid analysis of the pentapeptide yields five distinct peaks;
b) the pentapeptide strongly absorbs light at 280 nm;
c) the pentapeptide has a net charge of â€œ-0.5â€, to the nearest tenth, at pH 10.50;
d) bubbling oxygen into the pentapeptide solution for an extended period of time results in
decapeptides being formed. Note: a decapeptide contains ten amino acid residues.

Draw the structure of a pentapeptide, in the form that would predominate at pH 7.00, that conforms to all of the above information. Explain how your pentapeptide structure fits all of the observations.

10. An oligopeptide with the sequence A-P-C-K-R was obtained from blood plasma.

a) How many moles of NaOH would be required to titrate one mole of the fully protonated peptide to its fully unprotonated form?
b) If you had 100 ml of a 1.00 M solution of the fully unprotonated form of this peptide, what would the pH be?

11. An oligopeptide has the following properties:

a) amino acid analysis yields six distinct peaks;
b) one of the above peaks had to be detected at A440, instead of A570;
c) it has a net charge of â€œ+ 4â€ at pH 0, but a net charge of â€œ- 0.83â€ at pH 13.2;
d) it contains an R-group that has a hydrophobicity between that of A and L;
e) it absorbs ultraviolet light.

Draw the structure of the above oligopeptide, in the form that would predominate at pH 7, and give your reasoning for how it satisfies the above five criteria.

1. Which amino acid has a net charge of â€œ+ 0.09â€ at pH 7? Show...

1. Which amino acid has a net charge of â€œ+ 0.09â€ at pH 7? Show...