Amino Acid/Protein Problem Set



1. Consider the 8 residue oligopeptide FWQKSLHR



a) Starting from the N-terminus, draw the two-dimensional chemical structure at pH 7 (draw the predominant ionization state). Indicate correct stereochemistry at the Calpha's.



b) With the symbol "x", mark the Calpha atom(s) of the residue(s) that could readily form covalent cross-link(s) to a second peptide of the same sequence.



c) Draw a box around two adjacent groups of six coplanar atoms.



d) With labels phi and psi, label the two rotational degrees of freedom relating these two boxes.



e) Redraw any residue that changes ionization state when the pH drops to 5. Draw the predominant ionization state of that residue at pH 5.



f) Assuming this peptide is embedded in an infinitely long alpha-helix, mark every backbone atom that is a hydrogen bond donor within the alpha-helix, with a lower case letter "d".



g) Assuming this peptide is embedded in an infinitely long alpha-helix, mark every backbone atom that is a hydrogen bond acceptor within the alpha-helix, with a lower case letter "a".



h) Assuming this peptide forms a completely isolated 8-residue alpha-helix, with an upper case letter "A", mark every backbone atom that is a hydrogen bond acceptor.



h) Assuming this peptide forms a completely isolated 8-residue alpha-helix, with with an upper case letter "D", mark every backbone atom that is a hydrogen bond donor.



2. Draw the amino acid S, with proper stereochemistry, with the N, Calpha, C' in the plane of the paper. Rotate this amino acid (by 120 degrees) about the Calpha-Cbeta bond. Redraw it.



3. Consider the peptide:



-Ala-Met-Ile-Phe-



Would you expect to find this sequence element on the interior or exterior of a globular protein? Explain why.



4. Gatechase A is a 174 residue protein with no disulfide bonds.



Which of following aqueous conditions might you expect to denature Techase A?



0.2 M Sodium Chloride



8.0 MUrea



0.1 M 2-Mercaptoethanol



saturated O2



100degreesC .



5. Gatechase B is an enzyme with four disulfide (-S-S-) bonds. A sample of Gatechase B is denatured and reduced.



a) If the protein is oxidized then renatured, what fraction of the activity will be regained.



< 0.1% / 0.1-1% / 1-10% / 10-50% / >50%
(circle one)



b) (5 points) If the protein is first renatured, then oxidized, what fraction of the activity will be regained.



< 0.1% / 0.1-1% / 1-10% / 10-50% / >50%
(circle one)