Which residue will form hydrogen bonds with residue 3

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Unformatted text preview: than 0.429 [rev. 9/20]. Name: _____________________________________________________ 4 Helical wheel the following sequence: 4. [17 pt] An unspecified protein contains a 12- residue long α- helix with of raw::/geninf/prog/www/htdocs/tools/embo... Sun 9 Sep 2012 19:32:42 1 2 3 4 5 6 7 8 9 10 11 12 1 T 8 12 A V T S K N E F E A L D V V – 5 E 4 N A. (4 pts) How many hydrogen bonds exist between the backbone 9 V L 11 atoms in this helix? Explain your reasoning. S 2 There will be hydrogen bonds between 1 and 5, 2 and 6… 8 and 12. 8 total. 7 –E F 6 K 3 D 10 + – B. (4 pts) Which residue(s) would form ionic interaction(s) with residue #3 within the helix. Assume pH 7. K3 is positively charged. It will not form an interaction with E5 since it’s on the other side of the helix. It will form with E7. It will not form with 10 since it is too far away (2 pitches down). Tuesday, September 18, 12 C. (3pts) Is this helix amphipathic? Select one. 1) Yes 2) No 3) It depends on pH. No. There are hydrophobic residues and polar residues mixed around the helix. pH may change the charge of some residues, but still they remain polar either charged or neutral. Two β- strands given below interact with each other to form an anti- parallel β- sheet. Strand A Strand B 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 V S L N I A F Q F D V N L A F K D. (3 pts) Residue #5 of strand A forms hydrogen bond with residue #5 of B. Which residue will form hydrogen bond(s) with residue #3 of strand A? Strand B#7 E. (3 pts) Is this β- sheet amphipathic? Select one. 1) Yes 2) No 3) It depends on pH. Yes. Hydrophobic residues are facing one side and polar residues are facing another side. AT N V E L V S E K F D Name: _____________________________________________________ 5. [13 pts] Here is a Ramachandran diagram for "allowable" (Φ,Ψ) angles for Ala residues in proteins. The following table gives values for the phi (Φ) & psi (Ψ) angles of residues 24 to 54 of a protein: 5 Res. # 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 Amino acid Gly Φ ( o) Ψ ( o) –60 –49 –67 –58 –60 –57 –62 –61 –59 –60 –63 –61 –55 68 79 –90 –70 –89 –137 –142 –141 –135 –102 –60 –91 –45 –137 –136 –143 –138 67 147 –32 –34 –49 –42 –46 –...
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This test prep was uploaded on 02/25/2014 for the course BIOC 462A taught by Professor Ziegler,baldwin during the Spring '08 term at University of Arizona- Tucson.

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