probset_7_2009

probset_7_2009 - (e) Identify the proteins that contain...

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BMB 100A Fall, 2009 Problem Set #7 Name_________________ 1. Write the primary structure of the peptide RDHQWMI, indicating the predominant ionization forms that would be found for the sidechains at pH 5. 2. For the peptide GKDLC, what will its approximate NET charge (rounded off to the nearest whole integer) be at: (a) pH 7 (b) pH 1 (c) pH 13 3. Draw the maximally hydrogen-bonded interactions between the SIDE CHAINS of the following pairs of amino acids: (a) Gln and Asn (b) Arg and Asp
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4. There are pictures of protein structures in your text. For each of the ones listed below, find one end of the polypeptide chain, and trace it through to the other end. Then: (a) Identify the number of domains. (b) Classify the type of domain structure of each domain. (β-barrel, helical bundle, α-β, etc.) (c) Indicate whether the β-strands are parallel or antiparallel. (d) For the parallel β-strands, identify the crossovers, and indicate which type of crossovers they are (α or loops, right- or left-handed).
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Unformatted text preview: (e) Identify the proteins that contain -helices. What approximate angles are made between the different pairs of adjacent -helices? Myoglobin (p. 244) Concanavalin A (p. 245) Glyceraldehyde-3-phosphate dehydrogenase (p. 248) Retinol binding protein (p. 251) Triose phosphate isomerase (p. 253) Protein GB1 (p. 280) Rop protein (p. 281) Bacteriorhodopsin (p. 399) Omp F protein (p. 401) 6. Propose a specific mechanism for recognition of an A-T base pair in the major groove of DNA by the side chain of Asn in a regulatory protein, with a structural drawing. 7. Compare the geometry of A-form RNA, B-form DNA helices and protein -helices and -sheets, with respect to the following parameters: A-form RNA B-form DNA -helices -sheets (a) spacing of monomers along the helical axis (b) pitch (helical repeat) (c) diameter (d) monomers per helical repeat (e) twist angle per monomeric repeat...
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probset_7_2009 - (e) Identify the proteins that contain...

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