MCB124-ANSWERS_SET1_F07

MCB124-ANSWERS_SET1_F07 - MCB124 Enoch Baldwin Proteins...

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MCB124 Proteins Structure and Function Enoch Baldwin ANSWERS SET I page 1 I. AMINO ACIDS 1. Protein Sequencing Using only chemical cleavage, proteases (Table 1.5, and carboxypeptidases) , Edman degradation HPLC purification of peptides AND amino acid analysis, design a strategy to completely sequence the following peptide- HOWEVER because you are in poorly equipped lab in you can only get 3 residues from an Edman degradation. Ac-Met-Asp-Lys-Leu-Ala-Asn-Gly-Lsu-Val-Glu-Arg-Phe-Leu-Lys-Ala-Arg-Arg There are three main points: 1) Using the various reagents (Table 1.5), cleave the peptide into2-4 amino acid fragments that can be sequenced from the N-terminus wth Edman degradation(3 residues max) and 1 residue from the C-terminus. Single residue products from cleavage can be identified from amino acid analysis. 2)However, since cleavage reactions don’t allow you to now the length of the peptide, or how the fragments are connected, it is necessary to develop a separate overlapping set of peptides. 3) Amino acid analysis (the percentage of particular residues in a peptide) should be used as a cross-check and to identify residues in longer peptides that are more than three from the N- terminus and 1 from the C-terminus. Of course, this alone does not yield the order. 2. Amino acid properties M-W P-G L-A H-I R-D A-V E-H W-K Q- D-F A-G G-D H-K Y-T C-Y Arrange the above amino acid dipeptides in order of Volume (Table 1.1) AG, Q, GD, PG, AV, LA, HI, DF, RD, HK, YT, EH~CY, WK, MW Hydrophobcity (Table 4.8, I used the Flaucere and Pliska scale) RD, HK, GD, EH, Q, AG, PG, DF, YT, WK, AV, HI, LA, CY, MW Helicity (Table 5.3) PG, GD, YT, HI, Q, CY, DF, HK, AG, RD, AV, MW, WK, LA Charges at (Table 1.2) pH 2 HK WK HI RD EH [PG Q AV LA MW AG] YT~CY DF GD pH 5.5 HK WK HI RD EH [PG Q AV LA MW AG] YT CY DF GD pH 10 HK ~ WK RD HI [PG, Q AV LA MW AG] YT EH CY DF GD
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MCB124 Proteins Structure and Function Enoch Baldwin ANSWERS SET I page 2 II. POLYPEPTIDES 1 . A) Sketch a tri-peptide Ile-Gly-Pro in the extended conformation . B) draw two boxes around the atoms contained within the two complete peptide planes C) indicate the bonds that correspond to the Gly phi and psi torsion angles which describe the relative positions of the two planes \D) Draw a Ramachandran plot on back using the above as a guide. Use it to answer the questions a. Indicate the backbone phi-psi angles for a right-handed helix with an "A" b. Indicate the backbone phi-psi angles for a beta-sheet with a B c. Where would you most likely find an alanine residue (mark it with "Ala") d. Where would find only (almost) glycine (mark it with a "Gly)
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MCB124 Proteins Structure and Function Enoch Baldwin ANSWERS SET I page 3 2 . a. Sketch the bonds and atoms of the following peptide sequence (N to C terminal). Note that this peptide was isolated under oxygen-free conditions. Cys-Trp-Asp-Arg-His
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MCB124-ANSWERS_SET1_F07 - MCB124 Enoch Baldwin Proteins...

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