Chemistry 595C Fall 2000 Exam 1 Written Answers 1. In the use of NMR to determine the structure of biomolecules the structural information is obtained primarily by measuring the nuclear Overhauser effect. a) Very briefly describe what the nuclear Overhauser effect results from and to what degree the effect depends upon distance. Give the maximum practical observable distance. b) Solving macromolecular structures by X-ray crystallography depends upon measurement of the electron density at each point within the unit cell. In turn, those measurements depend upon the intensities of the diffracted X-rays and the phases of the diffracted X-rays. Briefly describe two common methods (MIR and MAD) that can be used to solve the “phase problem.” c) Contrast the use of NMR and X-ray crystallography as applied to biomacromolecules. Address in particular the issues of any limitations on the size of the macromolecules whose structure can be determined by either technique; what types of information that can be determined by one technique and not the other and whether both techniques always give the same structure for a particular macromolecule (both proteins and nucleic acids). 2. From the amino acid structures listed below, answer the following questions:a. What is the name of amino acid A? ___________________________ b. Which of the above amino acids has the highest isoelectric point? ________________ c. Which of the above amino acids is classified as a basic amino acid? _______________ d. Which of the above amino acids absorbs light centered at 280 nm? _______________ e. What is the name of amino acid D? ______________________________ f. What is the name of amino acid B? _______________________________ g. Draw the structure of tryptophan showing the charge on the molecule as it would be at pH 7. h. Draw the structure of the dipeptide pro-his (at pH 7) i. Name 2 sulfur containing amino acids _________________________ ________________________ j. What is the approximate pK of the side chain amino group of lysine? _____________ 3. a) What is meant by the statement “stacking interactions are important in stabilizing the structures of nucleic acids”? Describe the nature of these interactions and give examples for both DNA and RNA molecules. (1/3 p) b) Which of the following stacking interactions will provide more stability : purine-purine or pyrimidine-pyrimidine? (1/3 p) c) Bound metals are often found in RNA structures. What kinds of roles can the metals play?(1/4 p) d) Hydrogen bonding also plays a role in nucleic acid structure stabilization. In what important ways does it differ from stacking and metal ion interactions? 5. a) Using the simple expression E + S ⇔ ES ⇒ E + P as a basis, describe the effect of competitive and uncompetitive inhibitors. b) With a brief description and diagrams show how these two types of inhibitors can be distinguished by Lineweaver-Burk plots. c) Using aspartate transcarbamoylase as an example, contrast feedback inhibition of an enzyme with simple competitive and uncompetitive inhibition. 6. Studies of oxygen transport in pregnant mammals have shown that the O2-saturation curves of fetal and maternal blood are markedly different when measured under the same conditions. Fetal erythrocytes contain a structural variant of hemoglobin, HbF, consisting of two α and two γ subunits (α2γ2), whereas maternal erythrocytes contain HbA (α2β2).(a) Which hemoglobin has a higher affinity for oxygen under physiological conditions, HbA or HbF? Explain. (b) What is the physiological significance of the different O2 affinities? (c) When all the BPG is carefully removed from samples of HbA and HbF, the measured O2-saturation curves (and consequently the O2 affinities) are displaced to the left. However, HbA now has a greater affinity for oxygen than does HbF. When BPG is reintroduced, the O2-saturation curves return to normal, as shown in the grwph. What is the effect of BPG on the O2 affinity of hemoglobin? How can the above information be used to explain the different O2 affinities of fetal and maternal hemoglobin? 7. You have a polypeptide that has been degraded with cyanogen bromide (cleaves on the C-terminal side of methionines) and trypsin (cleaves on the C-terminal side of lysines and arginines). The sequences of the fragments are listed below (using the one-letter codes). Is there enough information to derive the complete amino acid sequence of the polypeptide? If so list the complete sequence. If not, show how much of the sequence you can derive. In both cases show your methodology. What other treatments might be used to support such a deduced sequence, or complete the sequencing?Multiple Choice 1. One of the reasons that enzymes are such efficient catalysts is that a) the energy level of the enzyme-transition state complex is much higher than for an uncatalyzed reaction b) enzymes can lower the activation energy for the reaction c) the translational entropy of the substrate is greatly increased upon binding to the enzyme d) the enzyme typically binds the substrate much more strongly than the transition state e) enzymes can employ nucleophilic reaction mechanisms while reactions in free solution can only proceed by electrophilic mechanisms 2. For an enzyme reaction that shows typical Michaelis-Menten kinetics, doubling the concentration of enzyme will a. triple the Km b. double the Km c. halve the Km d. not alter the Km 3. If the following section of a polypeptide is folded into an α-helix, to which amino acid is the carbonyl group of alanine noncovalently bonded? ala-ser-val-asp-glu-leu-gly a. serine b. glutamic acid c. aspartic acid d. leucine 4. The Michaelis-Menten combined rate constant Km, is defined for the following kinetic mechanism as k1 k2 E + S ⇔ ES → E + P k-1 a. (k1 + k2)/k-1 b. (k-1 + k2)/k1 c. (k1 + k-1)k2 d. k-1/k1 4. For an enzyme which obeys Michaelis-Menten kinetics, what is the Vmax value in µmol/min if v = 35 µmol/min when [S] = Km? a. 50 b. 70 c. 45 d. 955. The highly charged 2,3-bisphosphoglycerate binds to hemoglobin a. on the exterior surface b. on the heme group c. at the Fe+2 ion d. in the interior cavity 6. At high altitudes, the concentration of