Final 3 Spring 02

Final 3 Spring 02 - 1) Identify the protein domain...

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1) Identify the protein domain displayed on the screen. Where is the ligand binding site? Provide an example of the biological function of that domain, and justify your choice. Be precise and specific. Graded by Andrew On the screen was displayed two different views of an SH3 domain. The ligand binding site is at the top, in a cleft created by the loops at the end of the Beta sheet (the ligand was shown at the top as the green backbone of a peptide with the many Prolines displayed). The biological function is either 1) to act as an adaptor protein (see question 9, part A for a definition of an adaptor protein), or 2) to bind poly-Proline helix- containing proteins. The justification is that the ligand, a poly-Proline helix, was shown within its binding site, which clearly indicates that an SH3 domain is involved.
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2) Paper # 2 = “Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3 Å resolution.” Graded by Roger (A). The photosynthetic reaction center was observed at 3Å resolution. What are the features that can be detected at this level of resolution? - trace the path of the polypeptide chain = 1 pt. - fit a known amino acid sequence to the map = 1 pt. - 1 pt. (B). Would a hydropathy plot analysis of the reaction center complex provide useful information? If yes, what region of the reaction center complex does the plot show, and which subunits make up the region? If no, then explain why. - yes - transmembrane helices = 0.5 pt. - L, M, and H subunits = 0.5 pt. (C). Briefly outline the steps involved in electron transfer to the reaction center complex and within the reaction center complex, starting from the absorption of a photon by the light-harvesting complex (also show in which step electrons start to move). = 4 pt.s - photons absorbed by LH2 LH1 “ special pair” chlorophylls electrons moved from special pair to accessory chlorophylls one of the pheophytins quinone A iron atom quinone B (D). Which subunits of the reaction center are involved in forming the central four helix bundle in which the “special pair” of chlorophylls is located. Be specific = 2 pt.s : L and M subunits, specifically the D and E alpha helices of L and M
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3) Paper # 3 = “Acetylcholine receptor channel imaged in the open state.” Graded by Bryant Answers = B, C, D, A, B 1. The acetylcholine receptor consists of: = 1 pt. for 5 subunits, 1 extra point for a) 4 subunits, _____ b) c) 6 subunits, ______ d) 6 subunits, ______ e) None of the above collectively termed: a) M5 b) B64 c) M2 = 1.5 pt.s d) M3 e) None of the above 3. Which residue is pr a) Ile b) Ser c) Thr d) Leu = 1.5 pt.s e) None of the above 4. Which portion of the acetylcholine receptor is most similar in both the open and closed states? a) Channel mouth/rim
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Final 3 Spring 02 - 1) Identify the protein domain...

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