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CChheemm 44334433Exam #1 Oct. 1st, 2003 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 givenbelow:(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) Identify, explaining your choice, which, if any, of the forms in (i) above could act as abuffer at physiological pH2. (i) The molecule oxalic acid is often used as a buffer in biochemical experiments due to itsreaction: R-COOH ↔ R-COO-+H+If the pKa of the R-COOH fragment of oxalic acid is 4.3 calculate, showing your method, the %fraction of oxalic acid present in its deprotonated (R-COO-) form at pH 5.3 (ii) Explain the observation that at pH of 7 tryptophan crosses a cell membrane about a 1000 times more slowly than the closely realted molecule indole, A below:tryptophanCαNHNH2OHOindoleNHOOHNH2OOHpKa=2.2pKa=9.7pKa=4.2(iii) The scheme below represents reversible phosphorylation, an important mechanism forcontrolling a biomolecule’s function. Explain how this change can first alter the biomolecule’s structure.3. (i) Each of the following actions results in the denaturation of double helical DNA. Explain in terms of forces :LOWERING pHADDING ACETONEREMOVING Mg2+(ii)A melting analysis, i.e. a plot of UV absorbance at 260 nm versus temperature in oC, for twosamples of DNA yields a TM for sample A of 74o C and for sample B of 87o C. Explain(iii)A researcher isolates DNA from an organism, performs a melting analysis but observes less thana 10% hypochromic effect. Propose an explanation for their finding.Tyr O-HTyr O POO-O-ATPADP4. Using the following structures to answer parts (i)-(iii) below:(i) Cruciform shapes, such as that shown above, often occur in double-helical DNA. Identify one featureof the primary structure that must be present for such a cruciform shape to occur(ii) Adenine can tautomerize to the imino form and then pair with cytosine, as shown above. If this wereto happen extensively what effect would this change have on the structure of double-helical DNA andhow might you detect such a change.(iii) Positively charged histones, shown above, are used to stabilize the tertiary structure of DNA,Acetylation, also shown, often occurs prior to denaturation of the DNA. Explain in terms of forces.For Questions 5-8 indicate all answers (i) through (v) that are correct.5. Which, if any, of the following statements are true concerning the process of denaturation:(i) denaturation always involves loss of the macromolecules native structure(ii) denaturation will often involve destruction of the primary structure(iii) denaturation is irreversible(iv) denaturation is favored by heat(i) denaturation is favored by entropyComment 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(ii) 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. For the genetic code which, if any, of the following statements are true:(i) multiple codons code for a single amino acid.(ii) a single codon codes for multiple amino acids.(iii) at the end of translation a fully functional protein is formed(iv) the mRNA sequence CGCGAAGUC codes for the amino acid sequence Arg-Glu-Val(v) the mRNA sequence (3’)CGCGAAGUC(5’) codes for the amino acid sequence Arg-Glu-ValComment8. Which of the following statements concerning energy and thermodynamics are true :(i) ATP can act as a reservoir and source of energy for biological processes(ii) ATP is metastable due to the presence of a kinetic barrier to dissociation of a phosphate bond(iii) ATP is metastable due to the energy released upon dissociation of a phosphate bond(iv) for a molecule to adopt a stable 3-D structure the sum of all interactions must yield a +ve ∆G(iv) for a molecule to adopt a stable 3-D structure the sum of all interactions must yield a -ve ∆GComment:HA(aq)H+(aq)A-(aq)+pKa = -log (


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ST. EDWARDS CHEM 4343 - Study Notes

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