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Multiple Choice problems based on the Primary, Secondary and Tertiary structures of Proteins.

1. In an α helix, the R groups on the amino acid residues:
a. Alternate between the outside and the inside of the helix.
b. Are found on the outside of the helix spiral.
c. Cause only right-handed helices to form.
d. Generate the hydrogen bonds that form the helix.
e. Stack within the interior of the helix.

2. A d-amino acid would interrupt a α helix made of l-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of:
a. a negatively charged Arg residue.
b. a nonpolar residue near the carboxyl terminus.
c. a positively charged Lys residue.
d. a Pro residue.
e. two Ala residues side by side.

3. A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):
a. Antiparallel β sheet.
b. Parallel β sheet.
c. α helix.
d. α sheet.
e. β turn.

4. Which of the following statements is false?
a. Collagen is a protein in which the polypeptides are mainly in the α-helix conformation.
b. Disulfide linkages are important for keratin structure.
c. Gly residues are particularly abundant in collagen.
d. an α-keratin chain contains 7-residue pseudo-repeats of nonpolar/polar arrangements.
e. α-keratin is a protein in which the polypeptides are mainly in the α-helix conformation.

5. Determining the precise spacing of atoms within a large protein is possible through the use of:
a. Cryo-electron microscopy.
b. Light microscopy.
c. Small angle neutron scattering.
d. Ramachandran plots.
e. X-ray diffraction of protein crystals.

6. Experiments on denaturation and renaturation after the reduction and reoxidation of the -S-S- bonds in the enzyme ribonuclease (RNase) have shown that:
a. Folding of denatured RNase into the native, active conformation requires the input of energy in the form of hat.
b. Native ribonuclease does not have a unique secondary and tertiary structure.
c. The completely unfolded enzyme, with all -S-S- bonds broken, is still enzymatically active.
d. The enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase.
e. The primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.

7. Diseases caused by protein misfolding include:
a. Mad cow disease.
b. Alzheimer's.
c. cancer.
d. all of the above.
e. a & b only.

8. A tandem mass spectrometer can sequence short peptides by:
1. hydrolysis of peptide bonds with a strong acid and identifying the amino acids by HPLC.
2. fragmenting the peptide and comparing the fragment masses.
3. determining the absorbance of the peptide at 280 nm.
4. measuring the molecular mass of the whole peptide.
5. the transfer of magnetization from one nuclei to another.

10. Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
a. Cα-C and N-Cα
b. C=O and N-C
c. C=O and N-Cα
d. N-C and Cα-C
e. N-Cα and N-C

11. Which of the following statements concerning the process of spontaneous folding of proteins is false?
i. It may be an essentially random process.
ii. It may be defective in some human diseases.
iii. It may involve a gradually decreasing range of conformational species.
iv. It may involve initial formation of a highly compact state.
v. It may involve initial formation of local secondary structure.

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