Chapter Two edition 6: Protein Structure and Function
Use the following to answer questions 1-10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) L-amino acids
b) water
c) protons
d) Zwitterions e) secondary structure
f) tertiary structure
g) Ramachandran
h) cysteine
i) extracellular
j) Histidine
k) Proline
l) Sanger
m) D-amino acids
1. Chiral type of amino acids found in proteins.
Answer: a
2. Another name for dipolar molecules.
Answer: d
3. Disulfide bonds are formed by pairs of which amino acid?
Answer: h
4. The amino acid with a pK near neutral pH.
Answer: j
5. When a peptide bond is formed, what molecule is also made?
Answer: b
6. Where are proteins with extensive disulfide links likely to be found?
Answer: i
7. The amino acid with a distinct structure, causing it to affect protein backbone structure.
Answer: k
8. Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.
Answer: g
9. The type of structure to which alpha helices, beta sheets, and turns are referred.
Answer: e
10. The overall structure of a protein is referred to as
Answer: f
11. What determines a protein’s function?
A) structure
D) none of the above
B) gene sequence
E) all of the above
C) N-terminal amino acids
Answer: A
12. Key properties of proteins include
A) a wide range of functional groups.
B) an ability to possess either rigid or flexible structures as dictated by functional requirements.
C) the ability to interact with other proteins.
D) a and b.
E) all of the above.
Answer: E
For questions about charges of amino acids you can use Table 3.1 p. 50 (This table will be given at the examination
if appropriate)
106748154
-1-
13. What charged group(s) are present in glycine at a pH of 7?
A) NH3+
B) COOC) NH2+
D) a and b
E) a, b, and c
Answer: D
14. At a pH of 12, what charged group(s) are present in glycine?
A) NH3+
B) COOC) NH2+
D) a and b
E) a, b, and c
Answer: B
15. What is the utility of Beer’s law and light absorbance near 280 nm in protein studies?
A) determining the size of proteins
D) estimating the amount of DNA contaminant
B) determining protein purity
E) none of the above
C) estimating protein concentration
Answer: C
16. Which amino acids contain reactive aliphatic hydroxyl groups?
A) serine and methionine
D) cysteine and methionine
B) serine and threonine
E) cysteine and threonine
C) methionine and threonine
Answer: B
17. Name three amino acids that are positively charged at a neutral pH.
A) lys, arg, and his
D) lys, arg, and pro
B) his, arg, and cys
E) arg, glu, and his
C) cys, arg, and met
Answer: A
18. In the following peptide, which amino acid is the N-terminus? Phe-Ala-Gly-Arg
A) Ala
B) Phe
C) Phe and Arg
D) Arg
E) none of the above
Answer: B
19. What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other
protein modifications.)
A) 20000
B) 11000
C) 220000
D) 222000
E) none of the above
Answer: C. The mean molecular weight of an amino acid residue is about 110 Dalton.
20. Sequencing the protein insulin means that?
A) One has determined the cystine bonds
B) One has determined the amino acid composition
C) One has determined the amino acid sequence
Answer: C
21. Why is the peptide bond planar?
A) Bulky side chains prevent free rotation around the bond.
B) It contains partial double bond character, preventing rotation.
C) Hydrogen bonding between the NH and C=O groups limits movement.
D) None of the above.
E) All of the above.
Answer: B
22. The configuration of most alpha-carbon atoms of amino acids linked in a peptide bond is
A) cis.
B) circular.
C) parallel.
D) trans.
E) perpendicular.
Answer: D
106748154
-2-
23. The angles of rotation about the peptide bond are called
A) phi and alpha.
D) alpha and beta.
B) psi and alpha.
E) beta and psi.
C) phi and psi.
Answer: C
24. Secondary structure elements in proteins are?
A) alpha helix B) beta sheet C) beta turns D) a, b, and c
Answer: D
E) a and b
25. An alpha helix is stabilized by?
A) hydrogen bonds between CO and NH groups of adjacent amino acid residues
B) hydrogen bonds between CO and NH groups of amino acid residues separated by two residues
C) hydrogen bonds between CO and NH groups of amino acid residues separated by three residues
D) hydrogen bonds between CO and NH groups of amino acid residues separated by four residues
Answer: D
26. Where are omega and beta turns and loops often found?
A) in a hydrophobic pocket
D) on the surface of proteins
B) on the interior cleft
E) none of the above
C) at the protein interface with ligand
Answer: D
27. The spatial arrangement of protein subunits is called
A) quaternary structure.
D) primary structure.
B) tertiary structure.
E) none of the above.
C) secondary structure.
Answer: A
28. How does a protein’s amino acid sequence influence the tertiary structure?
Answer: A protein will spontaneously fold into a three dimensional structure determined by the amino acid
sequence.
Section: Introduction
29. What is the advantage of having 20 different amino acids available to form proteins?
Answer: The amino acids provide a rich diversity of functional groups, which can independently contribute to
protein structure and function. In addition, many can be modified, increasing the diversity of functional groups.
30. What is the advantage of protein interaction and assembly with other proteins?
Answer: When proteins interact or assemble, new functions and specificity become available. Protein interactions
allow new binding sites at the assembly interface, as well as providing multifunctional activity and specificity, such
as found in polymerases and signal transduction.
31. How do amino acids vary from one another?
Answer: Amino acids vary in shape, charge, size, hydrogen-bonding character, chemical reactivity, and
hydrophobic character.
32. How does proline differ in structure from the other amino acids?
Answer: Proline contains an aliphatic side chain, but its side chain is linked in a ring containing the amino group.
33. What are the three aromatic amino acids?
Answer: Phenylalanine, tyrosine, and tryptophan.
34. Which amino acid side chains are capable of ionization? (use table 3.1 p.50)
Answer: The amino acids are: Asp, Glu, His, Cys, Tyr, Lys, and Arg.
106748154
-3-
35. How does the protein backbone add to structural stability?
Answer: The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups.
Hydrogen bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.
36. How can the amino acid sequence of a protein be important in molecular pathology?
Answer: Examination of amino acid sequences often reveals that mutations in the primary protein sequence cause
abnormalities in the protein structure, resulting in disease.
37. What clues can be gleaned from a protein’s amino acid sequence?
Answer: The sequence can be used for comparison to other known protein sequences, thus determining its possible
function, and providing clues as to its evolutionary history. Programs that analyze the characteristics of the amino
acid sequences can be used to predict the protein conformation.
38. Why are all the theoretical combinations of phi and psi not possible?
Answer: Steric hindrances of the side chains make certain combinations and angles impossible.
39. Describe some of the features of an alpha helix.
Answer: The alpha helix is coil stabilized by intrachain hydrogen bonds. There are 3.6 amino acids per turn. The
hydrogen bonds are between amino acids that have two intervening amino acids, thus the first is bonded to the
fourth residue, and these amino acids are found on the same side of the coil. The helix is almost always righthanded, although left-handed helices are, in theory, possible.
40. What is a protein domain?
Answer: A domain is a defined region of a protein. Often, a domain is defined by a particular function.
41. What was shown by the denaturation and refolding of ribonuclease?
Answer: Anfinson used ribonuclease to prove that the ability of a protein to fold properly is determined by the
protein’s amino acid sequence.
42. In the ribonuclease experiments performed by Anfinson, what was the significance of the presence of the
reducing agent beta-mercaptoethanol?
Answer: The reducing agent allowed the transient formation of the disulfide bonds, until the most stable
conformation of the protein had been obtained.
43. How can beta sheets be in a parallel or antiparallel form?
Answer: The hydrogen bonds in beta sheets form between adjacent strands. The strand can be aligned in either a
parallel structure (each is written N
C terminus) or in an antiparallel structure (the strands run in
opposite directions).
106748154
-4-