neutral sidechain
positively-charged
environment
polar
environment
hydrogen
bond
hydrogen
bond
0 1 2 3 4 5 6 7
hydrophobic
environment
negatively-charged
environment
The diagram above shows a protein chain, with eight amino acid residues, at neutral pH. The
environment of the amino acids is indicated. Only the Ca atoms are shown for the peptide backbone, and
no hydrogen atoms or double bonds are shown. Heteroatoms (e.g., nitrogens, oxygens or sulfurs) are not
identified. Assume that the chemical structure and charge of the sidechains is appropriate for the given
environment, and that the pKa values of the sidechains are close to their normal values.
(i) Do all of the amino acids in the chain correspond to naturally occurring (i.e., genetically
encoded) amino acids? If not, specify which ones could not be genetically-encoded, and
explain your reasoning.
(ii)
Write down a list that shows, for each residue, the corresponding three-letter and one-letter
codes, and write out the chemical structure of the sidechain. Show all hydrogen atoms that
can participate in hydrogen bonds, and show the charge on the sidechain, if relevant. You
need not label carbon atoms, or show non-polar hydrogen atoms. If a sidechain does not
correspond to that of a natural (genetically-encoded) amino acid, write down "X" for that
residue. Your list should contain entries such as that shown below for the residue numbered
"0": Residue Number: 0, Ser, S
