Problem Set 1

1. Why are polar covalent bonds and the resulting permanent dipoles so important in biology? 2. Why could covalent bonds not be used in place of noncovalent bonds to mediate most of the interactions of macromolecules? 3. Hydrogen bonds and van der Waals attractions are important in the interactions between molecules in biology. What are the differences and similarities between van der Waals attractions and hydrogen bonds. 4. Five students in your class always sit together in the front row. This could be because 1) they really like each other or 2) nobody else in your class wants to sit next to them. Which explanation holds for the assembly of a lipid bilayer? Explain your answer. If the lipid bilayer assembled for the opposite reason, how would its properties differ? 5. What is the pKa of the weak acid HA if a solution containing 0.1 M HA and 0.2 M Ahas a pH of 6.5? 6. Inside cells the two most important buffer systems are provided by phosphate and proteins. The quantitative aspects of a buffer system pertain to both the effective buffering range (how near the pH is to the pKa for the buffer) and the overall concentration of the buffering species (which determines the number of protons that can be handled). H2PO4 HPO42- has a pKa of 6.9 with an overall intracellular phosphate concentration of about 1 mM. In red blood cells the concentration of globin chains (molecular weight = 15,000) is about 100 mg/mL and each has 10 histidines, with pKa values between 6.5 and 7.0. Which of these two buffering systems do you think is quantitatively the more important in red blood cells, and why do you think so?

7. The three molecules in the Figure on the right contain the seven most common reactive groups in biology. Most molecules in the cell are built from these functional groups. Indicate and name the functional groups in these molecules.

8. Suggest a rank order for the pKa values (from lowest to highest) for the carboxyl group on the aspartate side chain in the following environments on a protein. Explain your ranking. A. an aspartate side chain on the surface of a protein with no other ionizable groups nearby; B. an aspartate side chain buried in a hydrophobic pocket on the surface of a protein; C. an aspartate side chain in a hydrophobic pocket adjacent to a glutamate side chain; D. an aspartate side chain in a hydrophobic pocket adjacent to a lysine side chain. 9. Proline differs from the other 19 amino acids in proteins in that it has a ______ amino group. 10. The two amino acids with amide-containing side chains are asparagine and ______. 11. The two amino acids containing sulfur are ______ and methionine. 12. Which of the following amino acids has a charged polar side chain at pH 7? A) Leu B) Ala C) Met D) Trp E) Glu 13. Which of the following amino acids has an uncharged polar side chain at pH 7? A) Arg B) Thr C) Glu D) Pro E) Ile 14. At pH 7, arginine (pKs are -carboxylate 1.82, -amino 8.99, guanidino 12.48) would be charged as follows: A) 0 -carboxylate, 0 -amino, +1 guanidino, +1 net charge B) +1 -carboxylate, 0 -amino, 1 guanidino, 0 net charge C) +1 -carboxylate, 1 -amino, 1 guanidino, 1 net charge D) 1 -carboxylate, +1 -amino, +1 guanidino, +1 net charge E) 1 -carboxylate, 0 -amino, +1 guanidino, 0 net charge 15. At pH 7, aspartic acid (pKs are -carboxylate 1.99, -amino 9.9, -carboxylate 3.9 ) would be charged as follows: A) 0 -carboxylate, +1 -amino, 0 -carboxylate, +1 net charge B) 1 -carboxylate, +1 -amino, 1 -carboxylate, 1 net charge C) 0 -carboxylate, 1 -amino, 0 -carboxylate, 1 net charge D) +1 -carboxylate, 1 -amino, +1 -carboxylate, +1 net charge

E)

+1 -carboxylate, +1 -amino, +1 -carboxylate, +3 net charge

16. At pH 11, glutamic acid (pKs are -carboxylate 2.1, -amino 9.47, -carboxylate 4.07) would be charged as follows: A) +1 -carboxylate, 0 -amino, +1 -carboxylate, +2 net charge B) 1 -carboxylate, +1 -amino, 1 -carboxylate, 1 net charge C) 0 -carboxylate, 0 -amino, 0 -carboxylate, 0 net charge D) +1 -carboxylate, 1 -amino, +1 -carboxylate, +1 net charge E) 1 -carboxylate, 0 -amino, 1 -carboxylate, 2 net charge 17. At pH 4, histidine (pKs are -carboxylate 1.8, -amino 9.33, 6.04 imidazole) would be charged as follows: A) +1 -carboxylate, 0 -amino, 1 imidazole, 0 net charge B) 1 -carboxylate, +1 -amino, 0 imidazole, 0 net charge C) +1 -carboxylate, +1 -amino, 1 imidazole, +1 net charge D) 1 -carboxylate, +1 -amino, +1 imidazole, +1 net charge E) 0 -carboxylate, + -amino, +1 imidazole, +2 net charge 18. At pH 1, lysine (pKs are -carboxylate 2.16, -amino 9.06, -amino 10.54 ) would be charged as follows: A) 0 -carboxylate, 1 -amino, 1 -amino, 2 net charge B) 1 -carboxylate, +1 -amino, +1 -amino, +1 net charge C) +1 -carboxylate, +2 -amino, +2 -amino, +5 net charge D) 0 -carboxylate, +1 -amino, +1 -amino, +2 net charge E) +2 -carboxylate, +1 -amino, +1 -amino, +4 net charge 19. At pH 14, lysine (pKs are -carboxylate 2.16, -amino 9.06, -amino 10.54 ) would be charged as follows: A) 0 -carboxylate, 1 -amino, 1 -amino, 2 net charge B) 1 -carboxylate, 0 -amino, 0 -amino, 1 net charge C) +1 -carboxylate, +2 -amino, +2 -amino, +5 net charge D) 0 -carboxylate, +1 -amino, +1 -amino, +2 net charge E) +2 -carboxylate, +1 -amino, +1 -amino, +4 net charge 20. The disulfide bond between two cysteine molecules: A) is a peptide bond. B) is an ionic bond that is stable at physiological pH. C) is a covalent bond formed by oxidation. D) is a hydrogen bond between the two sulfhydryl groups. E) is a weak ion-induced dipole attraction. 21. How is the pK of the -carboxylate group of an amino acid influenced by the amino group on the same molecule?

22. If you were to design a small peptide with acidic character, which amino acid residues should predominate? 23. If you were to design a small peptide with a large net positive charge at physiological pH, which amino acid residues should predominate? 24. What is usually the origin of a non-standard amino acid residue found in a polypeptide chain?