Chapter 6: Proteins: Three Dimensional Structue

Draw a cis peptide bond and identify the groups that experience steric interference.

Describe the hydropathic index plot for a fibrous protein such as collagen or keratin.

Question: Experiments in mice suggest that pyro glutamylation (see Problem 19 ) increases the rate of aggregation of $\mathbf{amyloid}\mathbf{-}\mathbf{\beta }$protein. Propose an explanation for this observation.

Describe the forces that stabilize proteins, and rank their relative importance.

Helices can be described by the notation $\mathit{n}\mathit{m}$ , where$\mathit{n}$ is the number of residues per helical turn and$\mathit{m}$ is the number of atoms, including$\mathit{H}$ , in the ring that is closed by the hydrogen bond.

(a) What is this notation for the helix?

(b) Is the$\mathbf{\text{310}}$ helix steeper or shallower than the helix?

Hydrophobic residues usually appear at the first and fourth positions in the seven-residue repeats of polypeptides that form coiled coils.

(a) Why do polar or charged residues usually appear in the remaining five positions?

(b) Why is the sequence$\mathbf{\text{Ile–Gln–Glu–Val–Glu–Arg–Asp}}$ more likely than the sequence$\mathbf{\text{Trp–Gln–Glu–Tyr–Glu–Arg–Asp}}$ to appear in a coiled coil?

Why would it be advantageous for a protein or a segment of a protein to lack defined secondary or tertiary structure?

Which of the following polypeptides is most likely to form an α helix?

(a) CRAGNRKIVLETY

(b) SEDNFGAPKSILW

(c) QKASVEMAVRNSG

Question: Which of the peptides in Problem 23 is least likely to form a β strand?

Explain why it is important for protein disulfide isomerase to catalyze both the breaking and formation of disulfide bonds.