1. The level of protein structure that is stabilized primarily by non-covalent interactions between the side chains within a single polypeptide chain is refered to as its:
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) none of the above
2. Collagen, a strong fibrous protein found in connective tissue, bone, and the extracellular matrix, has a structure in which three left-handed helices wind around each other to form a right-handed triple helix. The primary structure of collagen has a repeat unit of -(Gly-X-Pro)- Which of the following bonds stabilize the collagen triple helix? (mark all that apply)
A) Hydrogen bonds between hydroxyproline residues
B) Hydrogen bonds between N-H and C=O
C) Ionic bonds between amino acid side chains
D) Hydrogen bonds between charged amino acids
3. The non-covalent forces that stabilize the Beta-strand conformation of peptides include:
A) H-bonds between amide C=O and amide NH
B) Van der Waals packing between the peptide backbone atoms
C) Van der Waals packing due to side chain interdigitation
D) Only A and B above
E) None of the above
4. What is the approximate length difference of a 22-kDa single-stranded ?-helical protein segment vs. a 22-kDa single-stranded ?-strand protein segment? Assume a mean residue mass of 110 Da. Show work.
5. Circular dichroism measurements have shown that the peptide backbone of poly-l-lysine (KKKKKKK) adopts a random coil conformation at pH 7.0, but becomes ?-helical as the pH is raised above 10. This observation is known as the ‘helix-coil' transition. Predict the helix-coil transition of the poly-L-glutamate (EEEEEEE).
A) Helix below pH 4.4 and coil above pH 4.4
B) Coil below pH 4.4 and helix above pH 4.4
C) Helix above pH 10 and coil below pH 10.2
D) Helix below pH 10 and coil above pH 10.2
E) Will not undergo a helix-coil transition
6. The super secondary structural motif known as the greek key consists of two hairpin motifs that can be arranged 24 different ways, although only two of those ways are commonly observed. This motif is comprised of what secondary structure elements?
A) coiled-coils.
B) ?-sheets
C) B-barrels.
D) alpha-helices.
E) bends.
F) CD spectroscopy.
7. In the 1950s, Christian Anfinsen demonstrated the renaturation of the protein ribonuclease (RNase) in vitro. To get the protein into an unfolded state, he first added the reducing reagent ?-mercaptoethanol and then added urea (to denature the protein). After removing the urea and then the reducing agent, the protein refolded, with greater than 90% activity. If the urea were removed after oxidation occurred, the protein had less than 5% activity. Why would the protein not refold correctly if the urea were removed after the reducing agent was removed? Choose the best answer.
A) Disulfide bonds are not positioned correctly unless weak bonding interactions are present.
B) The protein would not fully unfold (denature)
C) Urea would participate in weak bonding interactions with RNase, preventing oxidation of CYS
residues.
D) Contaminants in the RNase preparation would form covalent bonds with the protein, preventing
reactivation.