Name : ______________________ ID # : ______________________ Signature : _____________________ Chem & Biochem 153A-1 Summer 2004 Midterm I (100 pt, 50 min) 11) Short answers. a. (12 pt) Draw the complete structure of the tri-peptide Met-Ser-Lys in its predominant form at pH 7. b. (6 pt) Which of the standard amino acids would you expect to be negatively charged at pH 13? Explain. c. (6 pt) Is the peptide bond longer or shorter than a typical C-N bond? Explain. d. (6 pt) H-bonding is a special type of dipole-dipole interaction. Explain the difference between an H-bond and a typical dipole-dipole interaction. 232) A protein in influenza virus contain a long α-helix of 53 residues. Based on what you know about α-helix structure, answer the following. a. (5 pt) How long is this helix (in Angstrom)? Explain or illustrate your reasoning. b. (5 pt) How many turns does this helix have? Explain or illustrate your reasoning. c. (10 pt) Each amino acid in an α-helix is involved in 2 H-bonding interaction that stabilizes the helix. How many H-bonds would we expect to find in this helix (ignore side chains)? Explain or illustrate your reasoning.43) As a budding protein chemist, consider the following amino acid sequence. 1 2 3 4 5 6 7 8 9 10 Ala – Glu – Pro – Asp – His – Ile – Cys – His – Ala – Asp – 11 12 13 14 15 16 17 18 19 20 Asn – Gln – Val – Glu – Cys – Ser – Leu – Ala – Tyr – Gly – 21 22 23 24 25 26 27 28 29 30 Gln – Trp – Ser – Met – Gln – Met – Ile – Phe – Val – Ile – a. (10 pt) At which amino acid(s) would you predict the occurrence of β-bend(s)/turn(s). Explain your reasoning in each case. b. (10 pt) Where might intra-chain disulfide cross linkages be formed? Explain and illustrate the mechanism by drawing out the relevant structures of the amino acid(s) involved and show a reasonable electron pushing mechanism. Include relevant structures of the product. c. (5 pt) In a soluble globular protein, where might you predict amino acids 26-30 to be located (surface or inside protein)? Explain.54) Given the pKa of glycine’s ionizable groups to be 9.60 and 2.34 for the α-amino and carboxyl groups respectively. a. (5 pt) The pI of glycine (~ 5.97) is defined as the pH at which it is electrically neutral. Would glycine make a good buffer at its pI? Explain. b. (15 pt) At what pH would glycine have a net positive charge of 0.25? Explain or illustrate your reasoning and any assumptions made. c. (5 pt) Would glycine make a good buffer at this pH (pH calculated in part b)?
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