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2 Sample questions from previous exam Part 1 1) The chirality of most amino acids results from the presence of four different groups on the 2) The only one of the standard 20 amino acids which is not optically active is 3) In the tripeptide ala-ala-ala, how many bonds in the backbone do not have free rotation? 4) How many atoms are co-planar in a peptide bond? 5) In the α -helix the hydrogen bonds are parallel to 6) An anomer of α -D-galactopyranose is beta D galactose (why not galactopyranose though?) 7) The enzyme carboxypeptidase cleaves those peptide bonds in a polypeptide which are located next to 8) N-terminal amino analysis of a pure protein gave both alanine and serine. The protein probably has more than one. 9) How many α -D-aldopentofuranoses are theoretically possible? 4 10) The higher affinity of fetal hemoglobin for O 2 is probably the result of its lower ability to bind 11) In the disaccharide lactose [galactosyl (1-4) glucose] there are 2 anomers of the monosaccharide unit but only one anomer of the monosaccharide unit. Glucose, galactose 12) The favorable free energy change for the formation of hydrophobic interactions in proteins results primarily from favorable entropy change in the structure of 13) An important function of the protein portion of myoglobin and hemoglobin is to protect the Fe ++ from upon binding of O 2. 14) Draw the structure and give the name of an amino acid with a sulphur-containing R group

3 15) Draw the structure and give the name of an amino acid with a nitrogen-containing R group 16) LDL binds to the on the cell surface. Ldl receptor 17) Glycerolipids contain fatty acids only in an ester linkage whereas sphingolipids usually also contain fatty acids in a(n) linkage. amide 18) The difference between the various classes of liproteins which results in the difference in their densities is percentage of lipid and protein 19) The amphipathic nature of cholesterol is primarily due to the presence of a single group in the molecule. -OH 20) Triglycerides are mainly carried in the blood in the class of lipoproteins. chylomicron Part 2 1) A ligand (L) binds to a single binding site on a protein (P): P + L (P.L) An experiment was carried out in which a series of solutions contained P and varying concentrations of L. The mixtures were allowed to reach equilibrium and the concentration of protein with a ligand bound was measured. The following data were obtained: [L] (mm) Fraction of protein molecules with bound L

4 a) Determine the Keq for the binding reaction as written (i.e. the Ka). b) Predict the result (i.e. the Fraction of protein molecules with bound L) if the above experiment were carried out with [L] = 0.3 mm. c) Determine the Keq for the binding reaction (as written) if the above experiment experiment were carried out with P at a concentration of 20 mm. 2) Mutant forms of a protein were isolated from three individuals with genetic diseases. Each mutant protein was found to differ from the normal protein by only one amino acid, as indicated below. On the diagram below the electrophoretic mobility (at ph=8) of the wild type (normal) protein is indicated by the letter W. Using the letters A, B and C, indicate on the diagram the likely mobility of each mutant protein. (Note: assume that the difference in molecular weights is insignificant). Explain the reasons for the difference or lack of difference in mobility from the normal protein. (No points without an explanation). - Electrode W + Electrode Mutant Protein A: arginine instead of valine. Mutant Protein B: aspartic acid instead of valine Mutant Protein C: isoleucine instead of valine 3) a) What is the physiological rationale for the cooperative binding of O 2 to hemoglobin? b) What is the effect of ph on the affinity of hemoglobin for O 2?

5 c) What is the physiological rationale for the effect of ph on the affinity of hemoglobin for O 2?

6 Part 1 1) α -carbon 2) glycine 3) 2 4) 6 5) the axis 6) β -D-galactose 7) carboxyl terminus 8) subunit [polypeptide] 9) 4 10) BPG 11) glucose; galactose 12) water 13) oxidation 14) see book 15) see book 16) LDL receptor 17) amide 18) percentage of lipid and protein 19) OH 20) chylomicron Part 2

7 1) a) 5; b) 0.6; c) 5 2) Protein A closer to electrode since contains a + charged amino acid instead of an uncharged amino acid Protein B closer to + electrode since contains a - charged amino acid instead of an uncharged amino acid Protein C same as W since also contains an uncharged amino acid. 3) a) In order to be able to bind O 2 tightly at high O 2 partial pressure in the lungs and release O 2 at the lower partial pressure in the tissues. b) the affinity decreases with decreasing ph c) under conditions of high metabolism in a tissue (with need for more O 2 ) CO 2 is generated which generates H + by the reaction of carbonic anhydrase: CO 2 + H 2 O H 2 CO 3 HCO H + Because this decrease in ph results in a decrease in the affinity of Hb for O 2, it releases more O 2 in the tissue.