Mcb 354 Exam 1

MCB 354 Fall 2008 Exam I Revision Checklist

1) Amino acid structures. a) know the general structure of an amino acid b) be able to draw most of the amino acids, in particular His, Asp, Glu, Lys Cys, Gly, Ala, Ser, Phe, Tyr, Asn, Gln, Val, Leu, Pro, (including chirality) c) be able to draw peptides containing these amino acids d) be able to draw the ionization states of amino acids and peptides e) know the three-letter and single letter abbreviations for the 20 standard amino acids 2) pKa and titrations. a) know the approximate values of pKas for: -Terminal carboxyl of free aa and aa in polypeptide (~2.2 and 3.2) -Terminal amino group of free aa and aa in polypeptide (~9.5 and 8.5) -Asp and Glu R-carboxyl (~4.5) -Histidine R-group (~6) -Lys side chain (~10.5) -Arg side chain (~12.5) If a precise pKa is important in a calculation (i.e. to be plugged into a calculation using the Henderson-Hasselbalch equation), it will be given. Otherwise, use the values above or from the lecture. b) memorize the Henderson-Hasselbalch equation and be able to apply it. c) be able to determine the pI of an amino acid or peptide d) know the significance of the inflection points on a titration curve 3) Peptides and secondary structure. a) be able to draw a peptide bond and know it has partial double bond character and is rigid and planar. b) know the bonds about which rotation is permitted (N-Calpha (phi angle) and Calpha-C (psi angle)); understand the meaning of a dihedral angel. c) be able to explain what a Ramachandran plot shows

d) be able to draw a simple version of an α-helix or a β-sheet, illustrating the hydrogen bonding e) know the impact of charge on alpha helix formation. Know which amino acids are destabilizing. f) know why Pro is a helix breaker g) know why Gly is unusual (too much conformational flexibility) 4) Protein purification. a) How gel filtration, ion exchange, affinity chromotography, and SDS-PAGE work. b) Know what specific activity means in the context of...