problem_set_3 - Problem Set #3 BMB 401 Spring 2004 Problems...

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Unformatted text preview: Problem Set #3 BMB 401 Spring 2004 Problems from Lehninger: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 Problem 1 – Summarize the similarities and the differences between the α-helix and the β-pleated –sheet structures. In particular, how relevant are the various forces in nature that stabilize them. Problem 2 – Contrast the helices associated with the fibrous proteins keratin and collagen. Discuss the forces that give them extra stability. Problem 3 – Draw structures of peptide bonds having the following φ and ψ angles (in degrees). For each, discuss the problems associated with each of the conformations. (a) φ = 0, ψ = 180 (b) φ = 180, ψ = 0 (c) φ = 0, ψ = 0 (d) φ = 180, ψ = 180 Problem 4 – In a 3.613 helix, how many amino acids would be between two whose alpha carbons stacked exactly on top of each other along the peptide backbone? Problem 5: A sample (660 mg) of an oligomeric protein of molecular weight 132,000 was treated with an excess of 1-fluoro-2,4-dinitrobenzene. After acid cleavage of the peptide bond, the hydrolysate was determined to contain 5.5 mg of the compound shown below. Calculate the number of polypeptide chains in this protein. NO2 H3C CH3 CH O2N N H C H COOH Problem 6: Explain why tryptophan rings are usually completely immobile in proteins that have rapidly flipping phenylalanine and tyrosine rings. Problem 7: Discuss the possible effects of the following mutations in a protein. (a) L to F (b) K to E (c) V to T (d) G to A (e) M to P (f) D to N Problem 8: Muscle glycogen phosphorylase A elutes from a calibrated gelfiltration column at a position corresponding to a molecular weight of 360,000 g. SDS gel electrophoresis suggests a subunit molecular weight of 90,000 g. A microbiological assay on an enzymatically hydrolyzed sample of phosphorylase A disclosed the presence of 1.86 µg of pyridoxal (a cofactor of molecular weight 167.2 g) per milligram of protein. What conclusions about the quaternary structure and the stoichiometry of pyridoxal can you draw? Problem 9: What are the symmetry designations for the three following protein structures (e.g. C2, D2 etc)? ...
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