BioChemistry: Learning Curve Chapter 4

What is a difference between γ and β turns? a. γ turns have three amino acids; β turns have four amino acids b. γ turns contain disulfide bonds; β turns have hydrogen bonds c. γ turns rarely contain glycine; β turns frequently contain glycine d. γ turns have trans proline; β turns have cis proline

a. γ turns have three amino acids; β turns have four amino acids

Which of the following amino acids would be located on the exterior of a protein and not part of the hydrophobic protein core? a. Trp b. Ser c. Leu d. Val

b. Ser

A change in _____ changes the spatial arrangement of atoms in a protein, but does not involve the breaking of covalent bonds. a. configuration b. conformation c. primary structure d. stereoisomer

b. conformation

Which amino acids are particularly common in β turns? a. glycine and alanine b. glycine and proline c. serine and threonine d. alanine and proline

b. glycine and proline

What role does vitamin C play in the synthesis of collagen? a. the formation of disulfide bonds b. the hydroxylation of proline and lysine c. vitamin C has no role in the synthesis of collagen d. the assembly of the three-stranded superhelix

b. the hydroxylation of proline and lysine

Which amino acid is most favored in an α-helical conformation? a. Arg b. Asp c. Ala d. Gly e. Asn

c. Ala

Which is not made of fibrous protein? a. hair b. silk c. collagen d. myoglobin

d. myoglobin

The C-N bond in the peptide backbone of a protein would have a bond that is _____ the C-N bond in CH3-NH3+. a. longer than b. weaker than c. identical to d. the same length as e. shorter than

e. shorter than

Which statement does not apply to intrinsically disordered proteins? a. They are usually al α structures. b. They lack a hydrophobic core and have a high density of charged amino acids. c. They can interact with many protein partners. d. Some serve as scavengers.

a. They are usually al α structures.

Of the following secondary structures, which has not been observed in a protein before? a. Type II β turn b. Left-handed α helix c. Antiparallel β conformation d. Type I β turn

b. Left-handed α helix

Which of the following plays a large role in maintaining the secondary structure of proteins? a. hydrophobic interactions b. ionic bonds c. hydrogen bonds d. peptide bonds

c. hydrogen bonds

Numerous weak interactions are responsible for stabilizing protein conformation. Of the following, _____ are the major contributors to stabilizing the conformation of most soluble proteins. a. ionic interactios b. hydrogen bons c. hydrophobic interactions d. van der Waals interactions

c. hydrophobic inteactions

What feature of a disease classifies it as a prion disease? a. if it affects the central nervous system b. if it results from protein aggregation c. if the infectious agent is a protein d. if the diseases are fatal e. none of these define prion diseases

c. if the infectious agent is a protein

A regular secondary structure occurs in a protein chain segment when _____. a. the segment is primarily composed of aromatic amino acids b. the pH is near 7.0 c. the φ and ψ angles are the same, or nearly so, throughout the segment d. the dihedral angle is near 0°

c. the φ and ψ angles are the same, or nearly so, throughout the segment

Which of the following combinations of φ and ψ dihedral angles would be allowed in a poly-Alanine polymer? a. +180°, -180° b. +120°, -120° c. +120°, +120° d. -120°, -120° e. -120°, +120°

e. -120°, +120°

Which of the following is true regarding troponin C? a. It has 2 calcium-binding domains. b. It has 2 amino and 2 carboxyl termini. c. It has quaternary structure. d. It has many protein fibers cross-linked together.

a. It has 2 calcium-binding domains.

How does urea denature proteins? a. by disrupting both hydrogen bonding and hydrophobic interactions b. by disrupting hydrophobic interactions c. by disrupting hydrogen bonding d. by breaking disulfide bonds

a. by disrupting both hydrogen bonding and hydrophobic interactions

The cell has a number of mechanisms to protect against the accumulation of misfolded proteins when the endoplasmic reticulum's capacity to fold proteins is overwhelmed. Which of the following does not describe the way a cell would respond during that situation? a. increase the rate of overall protein synthesis b. degrade proteins by the ubiqutin-proteasome system c. increase the number of chaperone proteins d. degrade misfolded proteins by autophagy

a. increase the rate of overall protein synthesis

Which of the following best defines the term secondary structure with respect to proteins? a. the local spatial arrangement of the main-chain atoms in a segment of a polypeptide chain b. the three-dimensional conformation of a protein in its native folded state c. a description of the covalent backbone of a protein, including the sequence of the amino acids d. the three-dimensional structure of a multisubunit protein

a. the local spatial arrangement of the main-chain atoms in a segment of a polypeptide chain

Ehlers-Danlos syndrome and osteogenesis imperfecta are caused by _____ in collagen. a. the substitution of glycine with larger residues such as cysteine or serine b. insufficient hydroxylation of proline residues c. chemical toxins causing the formation of carbon-carbon double bonds d. an increase in dehydrohydroxylsinonorleucine cross-links

a. the substitution of glycine with larger residues such as cysteine or serine

Ramachandran plots describe the combinations of φ and ψ dihedral angles that are or are not permitted in a peptide backbone. Which of the following statements is INCORRECT regarding φ and ψ angles? a. φ involves C-N-Cα-C bonds. b. ψ involves the N-Cα-C-N bonds. c. Both angles are defined as +/- 90 degrees when the polypeptide is fully extended and all peptide groups are in the same plane. d. Steric hinderance between atoms in the polypeptide backbone and amino acid side chains limit the values of φ and ψ.

c. Both angles are defined as +/- 90 degrees when the polypeptide is fully extended and all peptide groups are in the same plane.

Which of the following is a deficiency disease characterized by general degeneration of connective tissue, and is caused by a lack of vitamin C? a. Ehlers-Danlos syndrome b. Osteogenesis imperfecta c. Scurvy d. Myotonic dystrophy

c. Scurvy

What is proteostasis? a. The process of cooperative folding of a protein. b. The collective list of all proteins in a given cell. c. The continuous maintenance of an active set of cellular proteins. d. The set of all reactions catalyzed by protein enzymes.

c. The continuous maintenance of an active set of cellular proteins.

Which does not apply to the most common kind of α helix? a. has about 3.6 amino acid residues per helix turn b. is stabilized by hydrogen bonding c. can be a mixture of L and D amino acids d. is right-handed

c. can be a mixture of L and D amino acids

Which type of hydrogen bond stabilizes most secondary structures? (The hydrogen bond is represented by dots, ... .) a. H-N...C=O b. C=O...C=O c. C=O...N-Cα d. C=O...H-N

d. C=O...H-N

Why are salt bridges much stronger when they occur at the interior of a protein as compared to its surface? a. Because a salt bridge neutralizes the charges on each ionic group and makes it very non-polar, so it also interacts by hydrophobic forces. b. Salt bridges become covalent at the core of a protein because there are no other charges around. c. A salt bridge inside a protein causes induced dipoles to interact with the ions. d. The interior of the protein has a much lower dielectric constant than the solvent so there is no shielding of the charges. e. There is no difference in strength between salt bridges at the surface and the core of a protein.

d. The interior of the protein has a much lower dielectric constant than the solvent so there is no shielding of the charges.

An active protein was purified to homogeneity using gel filtration and analyzed for its amino terminal residue using dabsyl chloride as described in Chapter 3. After multiple tries, the researcher gave up because there appeared to be four different amino terminal residues in the protein. What would you conclude about this protein? a. The protein has not been purified properly. b. The protein had Lys, Arg, and His residues that were reacting in the dabsyl chloride. c. The protein had been degraded. d. The protein was made of four unique subunits. e. none of the above

d. The protein was made of four unique subunits.

Which of the following types of proteins are exceptions to the two simple rules of protein folding: (1) Hydrophobic residues are found buried in the interior of a protein; and (2) the number of hydrogen bonds and ionic interactions within the protein are maximized? a. globular proteins b. transmembrane proteins c. proteins with intrinsically disordered segments d. both b and c

d. both b and c

Which of the following types of proteins are exceptions to the two simple rules of protein folding: (1) Hydrophobic residues are found buried in the interior of a protein; and (2) the number of hydrogen bonds and ionic interactions within the protein are maximized? a. globular proteins b. transmembrane proteins c. proteins with intrinsically disordered segments d. both b and c

d. both b and c

Autophagy of amyloid fibers includes _____. a. aggregation to form larger insoluble structures b. elongation of the fibers and the formation of additional disulfide links c. the action of heat shock proteins to refold the proteins d. degradation by encapsulation followed by docking with a lysosome

d. degradation by encapsulation followed by docking with a lysosome

What is unique about proline that is part of a β turn? a. it is more protonated than other prolines. b. its ring structure is broken. c. it is in the D configuration. d. its N-terminal peptide bond is cis.

d. its N-terminal peptide bond is cis.

If a disulfide bond connects two polypeptide chains in a protein, the highest level of protein organization this protein has is _____. a. primary structure b. secondary structure c. tertiary structure d. quaternary structure

d. quaternary structure