MCB124-PROBLEM_SET1

MCB124-PROBLEM_SET1 - MCB 124 Enoch Baldwin Protein 1, 2, 3...

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MCB 124 Protein 1˚, 2˚, 3˚ and 4˚ Structure Enoch Baldwin PROBLEM SET I page 1 I. AMINO ACIDS 1. Protein Sequencing Using only chemical cleavage, proteases, and carboxypeptidases (Table 1.5, PrimaryStructure.pdf from Lecture 1), 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, you can only get 3 residues from an Edman degradation. Ac-Met-Asp-Lys-Leu-Ala-Asn-Gly-Leu-Val-Glu-Arg-Phe-Leu-Lys-Ala-Arg-Arg 2. Amino acid properties Arrange the following amino acid dipeptides in order of Volume, Hydrophobcity Statistical tendency to be in a helix Charges at pH 2, pH 5.5 pH 10 (most positive to most negative) 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 (Hint: see the tables in PrimaryStructure.pdf) 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) E) Draw the Ramachandran plot look like for D-amino acids? 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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This note was uploaded on 04/06/2011 for the course MCB 124 taught by Professor Baldwin during the Summer '09 term at UC Davis.

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MCB124-PROBLEM_SET1 - MCB 124 Enoch Baldwin Protein 1, 2, 3...

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