CChheemm 44334433First Exam Sept. 28th, 2005 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 glutamic acid, 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 overallneutral2. (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 ofaniline in aqueous solutions.(ii) Draw the potential energy diagram, i.e. a plot of the energy as ∆H versus the change indistance, 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, witha first pKa (i.e. removing the first proton) value of 1.2 and a second pKa value of 6.6. Proposean explanation for why the pKa value is so low and first the second pKa value is so much greaterthan the first.OHHNa+ROOHNH2OOHpKa=2.2pKa=9.7pKa=4.2OHOHOHOOPOHOOHA**NH2aniline3. (i) By drawing appropriate structures predict what effect the solvent hexane would have on a cellmembrane :(ii) The drawing below represents the release of oxygen from hemoglobin, Hb, at low pH:Hb.4O2↔ Hb + 4O2By drawing a structure for X give a complete explanation for how the oxygen is expelled by thehemoglobin.(iii)carboxylic acids, such as the molecule drawn below, exist as dimmers i.e. two moleculesbound by non-covalent interactions. Draw the dimeric structure for A.4. (i) Each of the following actions results in the denaturation of double helical DNA. Explain in terms of forces :LOWERING THE pHADDING ACETONEREMOVING Mg2+X4O2OOAsp-pH<74O2NNHHis- AspOOOOHAhexaneCH3-CH2-CH2-CH2-CH2-CH3(ii) A protein Y binds to DNA using the amino acid glutamine as shown below. What does thisdiagram tell you about the binding of Y to DNA and identify where on the DNA this mightoccur(iii) In samples of DNA isolated from two species of bacteria adenine makes up 32% (species A)composition in one species and 17% (species B) in the other. One species of bacterium lives in ahot spring environment at temperatures of 64oC. Identify , giving your reasoning, which speciesoriginates in the hot spring.5. (i) Single strands of DNA are isolated from three species of organism: X, Y and Z. Doublestranded 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 :Duplex TMX + Y 80oCX + Z 87oCY + Z 83OC(ii) 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 onthe stability of DNA 2o structure(iii) When dimethyladenosine, shown below, is widely substituted for adenosine in double strandedDNA the secondary structure remains largely intact. Explain this observation in terms of forces.NRRN,N-dimethyladenosineRiboseNNNNNMe2For 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 thesolution of the acid will be 6(ii) If the pH of a solution of an acid is 4, and the pKa of the acid is 5 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 3, then the pH of the solutionwill be 3.5(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 buffersComment7. 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 acidsComment8. Which, if any, of the following statements are true concerning the following process involving anucleic 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.CommentHA(aq)H+(aq)A-(aq)+pKa = -log (