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2002mcb200f2 - University of Cape Town Department of...

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University of Cape Town Department of Molecular & Cell Biology Course Code: MCB200F Course Name: Intro to Biochemistry Paper: 2 (Theory) Date: 18 June 2002 No.of pages: 6 Marks: 120 Time: 3 Hours Venue: Zoo 1 - a.m. Attachments: 2 pages & graph paper ANSWER ALL THE QUESTIONS In the interest of economy please write on both sides of the exam script Please answer each section in a different answer book. Section 1 Amino acids and proteins Total marks: 32 1. A binding site on a protein depends critically on the pK a of a single glutamic acid residue. What would the effect on the pK a be (increases or decreases), if the following changes were made to this critical glutamic acid? (a) An arginine side-chain was brought into close proximity. (b) A C-terminal carboxyl group was brought into close proximity. (c) Moving the glutamic acid residue from the outside to the hydrophobic interior of the protein. [6] 2. Given the following peptide: Asn-Ala-Lys (a) Draw the complete structure of this tripeptide at pH 7.0 , with the side chains oriented in the trans configuration (show every atom including hydrogens). (6) (b) Estimate the approximate charge of this peptide at pH 7.0. (2) (c) Circle any one of the internal phi torsion angles. (1) [9] 3. What role does cysteine play in stabilizing the tertiary structure of secretory proteins as opposed to proteins found in the cytoplasm of eukaryotic cells? (hint: intracellular milieu of cells is highly reducing and proteases compartmentalized). [4] 4. Nearly every third amino acid residue in the primary structure of collagen is glycine. Another abundant amino acid that is present is proline. (a) Which weak non-covalent force is mainly responsible for stabilizing the collagen triple helix? (1) (b) Name the amino acid residue that plays an important role in stabilizing the triple helix as alluded to in (a)? (2) [3] 1
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5. Determine the amino acid sequence of the following oligopeptide about which the following data are known: (a) The amino acid composition is found to be (Ala, Lys, Phe, Met, Gly, Cys).
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