Score for the page Chemistry 271, Section 21xx Your Name: University of Maryland, College Park Your SID #: General Chemistry and Energetics Prof. Jason Kahn Exam II (100 points total) May 2, 2007 You have 53 minutes for this exam. Exams written in pencil or erasable ink will not be re-graded under any circumstances. Explanations should be concise and clear. I have given you more space than you should need. There is extra space on the last page if you need it. You will need a calculator for this exam. No other study aids or materials are permitted. Generous partial credit will be given, i.e., if you don’t know, guess. Many useful equations are given on page 9. Honor Pledge: At the end of the examination time , please write out the following sentence and sign it, or talk to me about it: “I pledge on my honor that I have not given or received any unauthorized assistance on this examination.” 1. DNA Thermodynamics (25 pts) The formation of the double-stranded DNA 20-mer oligonucleotide below from the separated single strands has been measured to proceed with ∆H° = –128 kcal/mole and ∆S° = –346 cal/moleK. Assume a total strand concentration of 3 µM (1.5 µM for each strand). 5’-TATTAAGCGACCACACATAA ATAATTCGCTGGTGTGTATT-5’ (a; 7 pts) What is the Tm for this oligonucleotide? What is the value of ∆G° at the Tm?Chemistry 271, section 21xx Exam II, 5/2/07 2/9 Score for the page (b; 8 pts) Briefly explain why ∆H° and ∆S° are each negative for the hybridization reaction. (c; 6 pts) Briefly and qualitatively explain how the nearest-neighbor rules for prediction of DNA melting thermodynamics are analogous to the bond-energy approximation used to estimate ∆H°f for previously unknown organic compounds.Chemistry 271, section 21xx Exam II, 5/2/07 3/9 Score for the page (d; 4 pts) The DNA microarrays sold by Affymetrix typically use 25-mer DNA probes. One application is to detect the amount of a known mRNA sequence in a clinical sample. Each target mRNA (or fluorescently labeled copy of same) typically hybridizes to 20 or so different probe oligonucleotides on the array. Each of these perfect match probe oligos is accompanied by a “mismatch probe” on a nearby spot, with the idea being that the target mRNA will hybridize preferentially to the target probe over the mismatch probe. One doesn’t want to operate these sensitive and expensive machines at very high temperatures. Why don’t they use sequences much longer than 25 nucleotides long on the arrays? 2. Anaerobic Metabolism (25 pts) The “Anammox” reaction (anaerobic ammonia oxidation) is carried out by bacteria in the Black Sea. The Anammox bacteria are chemolithoautotrophs, which is considered an advantage for their possible use in wastewater treatment because they don’t have to be fed reduced carbon. (a; 8 pts) The Anammox reaction is as follows: NH4+(aq) + NO2–(aq) → N2(g) + 2H2O(l) Write down separate oxidative and reductive reactions for the individual conversions of ammonium and nitrite to elemental nitrogen. The beauty part is that the electrons and protons needed for Anammox are balanced. (b; 4 pts) ∆G°′ = –357 kJ/mole for the Anammox reaction as written above. What is E°′?Chemistry 271, section 21xx Exam II, 5/2/07 4/9 Score for the page (c; 2 pts) Is the Anammox reaction assimilative or dissimilative? (Circle one.) (d; 8 pts) The source of nitrite (NO2–) for the Anammox reaction is other bugs who reduce nitrate to nitrite as follows: NO3–(aq) + 2 H+(aq) + 2 e– → NO2–(aq) + H2O(l) This is an example of syntrophy. Briefly define syntrophy. It is obvious what the recipient in a syntrophic relationship gains. What is the advantage to the donor? (e; 3 pts) We have discussed the metabolism of methanogens, which transfer electrons from hydrogen to carbon dioxide to produce methane. They live on the edge of starvation, because the free energy available from this reaction is low. Why don’t the methanogens just burn the methane that they make and live high on the hog?Chemistry 271, section 21xx Exam II, 5/2/07 5/9 Score for the page 3. Redox Reactions to Live By (12 pts) The Breathalyzer works on the principle of oxidizing ethanol to acetic acid, with concurrent reduction of orange dichromate Cr2O72– to green Cr3+. Standard reduction potentials: CH3COOH(aq) + 4 H+(aq) + 4 e- → CH3CH2OH(aq) + H2O(l) E° = 0.058 V Cr2O72–(aq)+ 14 H+(aq) + 6 e– → 2 Cr3+(aq) + 7 H2O(l) E° = 1.33 V (a; 4 pts) What is the balanced overall reaction? (b; 2 pts) What is E° for the overall reaction? (c; 6 pts) What is the actual cell voltage E, at 25 °C, if all reagents are in their chemical standard states (1 M everything) except that the pH is 4?Chemistry 271, section 21xx Exam II, 5/2/07 6/9 Score for the page 4. Electrochemistry (14 pts) The Leclanché cell (misnamed the dry cell) shown at the right has a zinc anode (the negative terminal). The cathode is MnO2 dispersed in graphite throughout the body of the cell, with the central graphite electrode acting to return the electrons from the external circuit. The chloride in the picture is a spectator ion. (a; 10 pts) The anodic half-reaction for this galvanic cell is Zn(s) → Zn2+ (aq) + 2 e–. The cathodic half-reaction is 2 MnO2(s) + 2 NH4+ (aq) + n e– → Mn2O3(s) + 2 NH3 (aq) + H2O. Who is being reduced here? Calculate n for the reduction half-reaction. Write down the overall net galvanic reaction. (b; 4 pts) The Leclanché cell is headed for obsolescence, in part because its voltage drops off with time. It is being replaced by the alkaline cell with the overall reaction below, which uses the same redox couple. Why does the voltage of the Leclanché cell decline with use, whereas the voltage of the alkaline cell is constant until it is nearly dead (you need not calculate E°s)? Zn(s) + 2 MnO2(s) + H2O(l) → Zn(OH)2(s) + Mn2O3(s)Chemistry 271, section 21xx Exam II, 5/2/07 7/9 Score for the page 5. Kinetics (24 pts): NO CALCULUS REQUIRED Kinetic partitioning describes the distribution of products for reactions under kinetic control, such as correct and incorrect base incorporation by DNA polymerases. For the elementary reaction A -> B, the differential rate law is –d[A]/dt = k[A]. (a; 3 pts) What is the integrated rate law for a the first-order reaction A -> B assuming that we start with 100 % A at