CChheemm 44334433Exam #1 Sept 24th, 2004 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 lysine, the pKa’s for the various acidic and basic groups are given below:(i) Draw the dominant structure found at pH values of 1, 5 and 10.(ii) Estimate, showing your method, the isolelectric point for Lysine(iii) Calculate, showing your method, the pH at which 50% of the molecules have a +2 netcharge and 50% have a +1 net charge2. (i) Table salt dissolves spontaneously in water as shown in the diagram below. Explain all of the factors that contribute to this process.(ii) Explain the observation that at pH of 7 tryptophan crosses a cell membrane about a1000 times more slowly than the closely related molecule indole below:tryptophanCαNHNH2OHOindoleNH(CH2)4H2N COOH2HNPKa=10.0PKa=2.2PKa=9.0(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 :ADDING UREA (2NH-CO-NH2)ADDING ACETONEREMOVING Mg2+(ii) The E. Coli chromosome adopts a structure similar to that shown below. Identify this level ofstructure and the purpose that it serves for the organism(iii) A protein X binds to DNA using the amino acid glutamine as shown below. What does this diagramtell you about the binding of X to DNA and identify where on the DNA this might occurTyr 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. 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’)CUGAAGCGC(5’) codes for the amino acid sequence Arg-Glu-ValComment6. For the follwing pair of molecules:(i) at physiological pH naphthol will pass through the membrane bilayer faster than phenol(ii) at physiological pH phenol will pass through the membrane bilayer faster than naphthol(iiii) an aqueous solution of pH=11 will dissolve both naphthol and phenol(iv) an aqueous solution of pH=6 will dissolve both naphthol and phenol(v) at physiological pH=9 naphthol will pass through the membrane bilayer slower than phenolComment7. Which, if any, of the following statements are true concerning the following process involving anucleic acid :(i) this process is favored by entropy(ii) the % of base A equals % of base T for the structure on the right above(iii) the base sequence for this nucleic acid must be palindromic(iv) if the above process is favored by free energy ∆H for this process must be negative(v) if the above process is not favored by free energy ∆H for this process must be positiveComment8. Under strongly acidic conditions several of the DNA bases become protonated e.g. at N1 and N7of adenine, N7 of guanine , N3 of cytosine and O4 of thymine (see page 86 of text for numberingsystem). Which of the following occurs at low pH:(i) double-helical DNA becomes denatured due to loss of base pairing(ii) double-helical DNA becomes denatured due to loss of hydrophobic effect(iii) double-helical DNA becomes more stable due to enhanced solubility in water(iv) TM for double-helical DNA increases at low pH(v) TM for double-helical DNA decreases at low pHComment:2-naphtholOHphenolOHPKa = 10.0PKa =