CChheemm 44334433 First Exam Sept. 22nd, 2010 Name : Answer any seven of questions 1-8 . Each question is worth 15 points for a total of 105 points. 1. For the amino acid shown the pKa’s for the various acidic and basic groups are given. (i) Draw the dominant structure found at pH values of 1, 5 and 10. (ii) Estimate, showing your method, the isolelectric point for Glutamic acid (iii) At a pH of 5.2 calculate, showing your method, the % of glutamic acid that is overall neutral 2. (i) For the amine, aniline, shown you are told it has a pKa of 4.6 and is poorly soluble in water. Decide, giving your reasoning, what should be added to the water to increase the solubility of aniline in aqueous solutions. (ii) Draw the potential energy diagram, i.e. a plot of the energy as ∆H versus the change in distance, R from zero to infinity, for the following system: (iii) The molecule α-D-ribose-5-phosphate, A shown below , has two ionizable OH groups, with a first pKa (i.e. removing the first proton) value of 1.2 and a second pKa value of 6.6. Propose an explanation for why the pKa value is so low and first the second pKa value is so much greater than the first. OHHNa+ROOHNH2OOHpKa=2.2pKa=9.7pKa=4.2OHOHOHOOPOHOOHA**NH2aniline3 (i) For the C:G base pair shown below describe an additional role played by the lone pairs on the oxygen at position 6 and the nitrogen at position 7 in the function of DNA. Hypoxanthine, shown on the right, is a purine base that can be accidently incorporated into human DNA instead of guanosine. Determine what effect this might have on DNA structure (iii) Each of the following actions results in the denaturation of double helical DNA Explain in terms of forces : LOWERING THE pH ADDING ACETONE REMOVING Mg2+ (iii) Acridine, shown below, binds to double stranded DNA and is often used for DNA detection. Based on its structure identify exactly how acridine binds and what effect this binding would have the TM of DNA 4 (i) For the 1o structure of RNA shown on the right and by focusing on the underlined bases identify, giving your reasoning, any possible element of 2o structure NHNONNNNNHNOHHHHH67N RR(ii) The molecule below binds in the major grove of DNA. By circling at the appropriate places identify those interactions responsible for stabilizing the DNA/molecule complex. (iii) The following table summarizes the transcription and translation of a double-helical strand of DNA. By identify the appropriate nucleotide fill in as many boxes as possible 5. (i) Based on the thermodynamic data given draw structures for the right hand side for each equation: (ii) Draw the reaction energy diagram, i.e. a plot of the energy as ∆H versus the change in going from left to right for the system: ADP + Pi ---> ATP (iii) For the two systems shown on the right identify the forces operating in the circled areas a and b.2acetonewater∆H = -ve∆S = -ve∆H = -ve∆S = +ve2acetonewater∆H = -ve∆S = -ve∆H = -ve∆S = +ve abFor Questions 6-8 indicate all answers (i) through (v) that are correct. 6. For the system : (i) If the pKa of an acid is 5, when the concentrations of [A-] and [HA] are equal the pH of the solution of the acid will be 6 (ii) If the pH of a solution of an acid is 5, and the pKa of the acid is 4 then the ratio of [A-] / [HA] will be 10 (i) If the ratio of [A-] / [HA] is 10 and the pKa of the acid is 4, then the pH of the solution will be 4.5 (iv) If the pKa of the acid is 4 and the pH is 6, the ratio of [A-] / [HA] will be 100 (v) All acids are capable of functioning as physiological buffers Comment 7. Which of the following statements are true regarding nucleic acids (i) DNA will always exhibit a hypochromic effect. (ii) DNA and RNA differ only in secondary and tertiary structure (iii) the melting temperature TM double-helical DNA increases with strand length (iv) the % of bases (A+C) always equals % of bases (G+T) in double-helical DNA (v) the same codon can code for different amino acids Comment 8. Which, if any, of the following statements are true concerning the following process involving a nucleic acid : (i) this process is favored by entropy (ii) UV-Vis spectroscopy can be used to follow this process (iii) the base sequence for this nucleic acid must be palindromic (iv) if the above process is disfavored by free energy ∆H for this process must be positive (v) lowering the temperature will make this process more favorable. Comment HA(aq)H+(aq)A-(aq)+ pKa = -log (