sample problems for exam II

Chem 4511/6501 Protein Structure Sample Questions1) In the figure belowa) label all the atoms of the backbone (as N, Cα, C’ or O, neglect the r-groups)b) draw all hydrogen bondsc) give the sequence (give a best estimate, it may be ambiguous at some residues)d) draw boxes around two adjacent sets of coplaner backbone atomse) label phi and psi for two residuesf) estimate these phi and psi anglesg) draw the dipole moments of each peptide grouph) draw the net dipole moment of the whole peptidei) label the N and C terminij) sketch a phi/psi map for this structurek) number the residues from 1 to n, starting at the N terminus (number each Cα)l) draw the peptide as a 2D structure (i.e. as a chemical structure), from N to Cm) number the residues of the 2D structuren) draw the hydrogen bonds on the 2D structure.2) Using only phenylalanine and lysine, design an amphiphilic α-helix of 12 residues inlength. Give the sequence. Draw a helical wheel.2a) Using only phenylalanine and lysine, design an amphiphilic β-sheet of 3 strands, 12residues in length each. Give the three sequences. Sketch the sheet (make it antiparallel).

3) In the figure below (all the side-chains have been omitted)o) label all the atoms of the backbones (as N, Cα, C’ or O, neglect the r-groups)p) draw all hydrogen bondsq) draw boxes around two adjacent sets of coplaner backbone atomsr) label phi and psi for two residuess) estimate these phi and psi anglest) draw the dipole moments of each peptide bond of one strandu) label the N and C terminiv) sketch a phi/psi map of for this structurew) add the sidechains (as R groups), indicating correct stereochemistry’s at the Cα’atoms.