Problem Set 1
Note that amino acids and various functional groups may be shown in their uncharged forms in
some questions. Your answers should be based on the predominant form of the molecules in a
solution of pH 7.
1.
a) For each amino acid below, indicate whether the side chain (R-group) is hydrophobic or
hydrophilic. Note that the uncharged forms of the amino acids are shown.
I II III IV V
hydrophillic hydrophobic
hydrophillic hydrophobic hydrophobic
2+
b) A magnesium ion Mg binds to a certain protein by forming ionic bonds with the side chains
of two residues from the list above. Assume that the residues are not at the termini of the
polypeptide. Identify these residues by circling the corresponding Roman numerals below. If
the two residues are different, circle each one; if the two residues are the same, circle the
corresponding amino acid and state explicitly that the two residues are the same amino acid.
I II III IV V
2. A certain protein is treated with a powerful protease that hydrolyzes all of the protein’s
peptide bonds. When you analyze the result, you find that there are two amino acids that are
still linked by a covalent bond. These two amino acids are which of the following choices? (If the
two amino acids are different, circle two, if they are the same, circle one and indicate that this
answer applies to both amino acids.)
cant form disulfide bonds
3. The image below shows part of a beta sheet.
The white spheres are hydrogen atoms, the black spheres are carbon atoms, the dashed lines
are hydrogen bonds, and the green spheres with the letter R denote R groups.
The strands are: (circle the correct answer)
A. parallel
B. anti-parallel
As one moves up along the left strand towards the blue star at the top of the image one moves
towards the: (circle the correct answer)
A. N-terminus
B. C-terminus
N to C = C terminus
N to CR = N terminus
H
4. Part of the primary sequence of a certain enzyme is shown below.
- Gln - Val - Phe - Ile - Met - Arg - His - Gly - Asp -
Consider variants of this protein in which one of the above residues has been changed. Some
amino acid substitutions are more likely to affect protein function than others. In other words,
the probability that a substitution affects enzyme activity is higher for some substitutions than
for others. Each of the substitutions below can be put in one of two categories: more likely to
affect protein function or less likely to affect protein function. Select all of the substitutions that
fall in the category: less likely to affect protein function. (You may wish to consult the table of
amino acids at the end of this problem set.)
A. Val to Leu
B. Phe to Lys
C. Arg to Asp
D. Arg to Lys
5. Consider the peptide shown below.
9
This peptide has______ amino acid residues.
C
The N-terminal residue of this peptide is: _______. (Use the one-letter amino acid code. You
can find a table of at the end of this problem set.)
What is the net charge of this peptide at neutral pH?
positive