StudyGuide1 - Study Questions for Exam #1 BCMB 401 I....

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Study Questions for Exam #1 BCMB 401 I. Water/noncovalent bonding 1. What are four types of non covalent interactions that occur between biomolecules? Give an example of each using amino acids. 2. Describe the properties of water and compare them to a non-polar solvent (e.g., benzene). Why is water more suited as a universal solvent for biochemical reactions? What is a dielectric constant and how does it determine the energetics of interaction between charged molecules? 3. In thermodynamic terms explain why sodium chloride readily dissolves in water with a negative Gibbs free energy (ΔG). Explain why a phenyl group would have a positive free energy for solvation by water. 4. Would you expect a hydrogen bond to be stronger in benzene or water? Explain. 5. What are the energetic driving forces for hydrophobic interactions (explain in terms of ΔG, ΔS and ΔH)? II. Amino Acids/Acid Base Chemistry 1. HCl (0.02 moles) is added to 300 ml solution of 0.1 M propionate base (pK a 4.87). Calculate the molarity of propionate and propionic acid in the solution. What is the pH of this solution? 2. What is the pH of a solution containing 0.1 M glutamate zwitterion and 0.05 M glutamate cation (use the pKa table at the end of the study guide)? 3. Phosphoric acid is tribasic with pK a ’s of 2.14, 6.86 and 12.4. Which form is predominant at pH = 3.2: (A) H 3 PO 4 . (B) H 2 PO 4 - . (C) HPO 4 2- . (D) PO 4 3- . Explain your answer. 4. For a weak acid with a pKa of 6.0, show how you would calculate the ratio of acid to conjugated base. 5. Know the structures of the twenty amino acids. a. Pick a pair of amino acids that have R groups capable of forming hydrogen bonds. Draw their structures and show how a hydrogen bond forms. b. Pick a pair of amino acids that have R groups capable of forming electrostatic bonds (salt bridges). Draw their structures and show how an electrostatic bond forms. c. What amino-acid R-groups form hydrophobic interactions? Show an example. 6. Pick one of the amino acids (any it is your choice) in each of the three classes given below. Show the titration curves of these amino acids and calculate their pIs. Compare the different behavior of these amino acids. (1) Amino acids with non-polar, aliphatic R groups. (2) Amino acids with positively charged R groups. (3) Amino acids with negatively charged R groups. 7. You wish to make a buffer at pH 6.5. Which amino acid would be the best choice to use in your buffer solution? Explain your choice. 8. Draw the structure of the following tetrapeptides that would be predominant at pH 7: S-G-P-D E-W-K-R a. Indicate on your structure the location of the amino terminus and the carboxyl terminus. b. At pH 7 which peptide will be negatively charged? Which will be positively charged? c.
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StudyGuide1 - Study Questions for Exam #1 BCMB 401 I....

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