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CChheemm 44334433 Exam #1 Sept 23rd, 2009 Name : Answer any seven of questions 1-8 . Each question is worth 15 points for a total of 105 points. 1. (i) For the amino acid lysine, the pKa’s for the various acidic and basic groups are given below draw the dominant structure found at pH values of 1, 5 and 10. (ii) Calculate, showing your method, the pH at which 50% of the lysine molecules have a +2 net charge and 50% have a +1 net charge (iii) The pKa values for citric acid below are 3.10, 4.80 and 5.40 for pKa1, pKa2 and pKa3, respectively. Calculate, showing your method, the pH at which 99% of the molecules have a -2 net charge 2. (i) Aspirin, A, has a PKa of 3.5 and absorbed into the bloodstream through the lining of the stomach and the small intestine. If the pH of stomach acid is 1.5 and the pH in the small intestine is about 6 determine, giving your justification, where the majority of aspirin in the blood comes from and give the pH at which 99% of the aspirin from the bloodstream is absorbed across the lining of the organ (ii) Table salt dissolves spontaneously in water as shown in the diagram below. Explain all of the factors that contribute to this process. (CH2)4H2N COOH2HNPKa=10.0PKa=2.2PKa=9.0OOOHOHO OHOH(iii) The scheme below represents reversible phosphorylation, an important mechanism for controlling a biomolecule’s function. Explain how this change can first alter the biomolecule’s structure. 3. (i)A melting analysis, i.e. a plot of UV absorbance at 260 nm versus temperature in oC, for two samples of DNA yields a TM for sample A of 74o C and for sample B of 87o C. From this result identify as many features of the structures of A and B that you can and give your reasoning (i) Identify how each of the following actions affects the TM for of double helical DNA. Explain in terms of forces : ADDING UREA (2NH-CO-NH2) ADDING ACETONE REMOVING Mg2+ (iii) A protein X binds specifically to a …GA… DNA sequence. Using the structures below draw an example of the forces used to bind protein X to the bases identifying specifically what atoms on the bases are used in this interaction 4 (i) The nucleic acid 1o structure shown to the right adopts a 2o structure corresponding to a single helix. Identify, with explanation and a drawing, all the forces that would stabilize this 2o structure. T yr O-HT yr O POO-O-ATPADP(ii) For the renaturation of single stranded DNA shown on the right draw plots of : absorbance of light at 260 nm for this process against increasing temperature and∆G for this process against increasing temperature . (iii) Single strands of DNA are isolated from three species of organism: X, Y and Z. Double stranded duplexes are formed by mixing these strands and the TM for each duplex is given below.Give two reasons why the duplex formed by mixing X and Z results in the highest TM : 5. (i) A single strand of a hybrid nucleic acid, mixed DNA and RNA, is shown on the right. Write down, do not draw , the sequence for the complementary strand. (ii) The plot on the right can be evaluated using the formula : Tm = 94.3 - 0.41(X) where X is either (%A + %T) or (%C + %G) Identify, giving your reasoning, which term applies to X and explain why the composition cannot be: A : 28% G : 22 % T : 31% C : 19% (iii) Based on the thermodynamic data given draw structures for the right hand side for each equation: Duplex TM X + Y 80oC X + Z 87oC Y + Z 83OC 2acetonewater∆H = -ve∆S = -ve∆H = -ve∆S = +ve2acetonewater∆H = -ve∆S = -ve∆H = -ve∆S = +veFor Questions 6-8 circle all answers (i) through (v) that are correct. For the carbonic acid-bicarbonate buffer system shown above which of the following statements are true(i) maintaining physiological pH demands a [HCO3-] : [H2CO3] ratio of 10 : 1 : (ii) maintaining physiological pH demands a [HCO3-] : [H2CO3] ratio of 1 : 10 (iii) raising the CO2 concentration raises the pH of the system (iv) adding water to the system raises the pH of the system (v) adding sodium bicarbonate at a concentration of 10x[CO2] lowers the pH by one unit Comment 7. For nucleic acid structure and function which, if any, of the following statements are true: (i) a single codon codes for multiple amino acids. (ii) at the end of translation a fully functional protein is formed (iii) the zinc finger is the name given to a palindromic sequence of DNA responsible for specific binding (iv) the mRNA sequence CGCGAAGUC codes for the amino acid sequence Arg-Glu-Val (v) the mRNA sequence (3’)CUGAAGCGC(5’) codes for the amino acid sequence Arg-Glu-Val Comment 8. For the process shown : (i) The process of going from the top to the bottom structure structure is spontaneous with a –ve ∆S. (ii) The process of going from the bottom structure to the top structure is spontaneous with a +ve ∆S. (iii) The process of going from the bottom structure to the top structure is favored by adding Mg2+ and lowering the temperature (iv) Going from from the top structure to the bottom structure involves must be exothermic (v) Going from from the top structure to the bottom structure involves changes in 1o, 2o and 3o structure Comment: H2CO3H++ HCO3-pH = 6.4 + log


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ST. EDWARDS CHEM 4343 - Study Notes

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