Biochemistry Chapter 4
A polypeptide has a high pI value. Which amino acids might compromise it?a. arginine and lysine residues b. aspartate and glutamate residues c. the large nonpolar amino acids d. a mixture of aspartate and arginine residues
A
Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a __________ disease. a. loss-of-function protein folding b. chaperonin-unassisted folding c. gain-of-function protein folding d. amyloid plaque-forming
A
The amino acid with the neutral side chain at neutral pH is a. asparagine. b. aspartate. c. arginine. d. glutamate.
A
The peptide bond is stronger than the ester bond. What structural feature of the peptide bond gives it additional bond strength? a. Resonance structures give the peptide bond some double bond character. b. The peptide bond is between carbon and nitrogen instead of carbon and oxygen atoms. c. The peptide bond is more polar. d. Peptide bonds can hydrogen bond.
A
To what organic reaction class does peptide bond formation belong? a. condensation b. isomerization c. oxidation d. addition
A
Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?a. NCCNCC b. NCCONCCO c. NCONCO d. CNCCNC
A
Using the table below, determine the kind of gene mutation illustrated. ATG_AAT_CAC → ATG_AAG_CAC *see 34* a. missense mutation b. nonsense mutation c. frameshift mutation d. silent mutation
A
What do Ramachandran plots show? a. Only some ψ and φ angles are commonly found in proteins. b. The chiral carbon in amino acids is found largely in the S configuration. c. Peptide backbones form mostly linear chains. d. The α-carbon is chiral.
A
What is believed to be the underlying cause of prion protein plaque formation? a. The PrPSc proteins are misfolded and aggregated from PrPc proteins. b. The unstructured N-terminal region of PrPc is thought to remain unfolded. c. The normal PrPc proteins are aggregated. d. The PrPSc protein adheres to and inhibits cell membranes.
A
What is the dominant secondary structure found in hair keratin? a. α-helices b. disulfide bonds c. β-sheets d. loop structures
A
Which amino acid side chain from the list below is the most polar? a. Gln b. Ala c. Leu d. Phe
A
Which of the following are negatively charged amino acids at pH = 7? a. Glu, Asp b. Gln, Asn c. Thr, Tyr d. Cys, Asn
A
Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct? a. GroEL-GroES requires the hydrolysis of multiple ATPs to assist in the folding of a protein. b. GroEL-GroES recycles misfolded proteins by recovering individual amino acids. c. GroEL-GroES assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds. d. GroEL-GroES uses GroEL as a cap, trapping an unfolded protein in the GroES chamber.
A
Which of the following statements about the clamp-type chaperone protein Hsp70 is correct? a. Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein. b. Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected. c. Hsp70 is most active during cell division phases. d. Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
A
Which of the following statements about β-sheet structures is true? a. The individual strands of all β-sheet structures are connected by turns, helices, or loops. b. All amino acid side chains in antiparallel and parallel β-sheet structures point to one side of the sheet. c. Parallel β-sheet structures have backbone amides that directly hydrogen bond between strands, whereas antiparallel β-sheets have hydrogen bonds that are offset. d. All β-sheet structures form a spiraling backbone chain.
A
Which statement about amino acids is true? a. Most common natural amino acids in proteins are L-amino acids. b. All naturally occurring amino acids in proteins are chiral. c. Most naturally occurring amino acids in proteins are D-amino acids. d. Naturally occurring amino acids in proteins occur as a mixture of enantiomers.
A
Which linear sequence of bonded atoms can be found in the backbone of polypeptides? a. C-N-N-C DIF: Medium REF: 4.1 DIF: Medium REF: 4.1 b. C-C-N-C c. N-C-C-C d. C-O-C-N
B
Which stabilizing force in protein tertiary structures is a covalent bonding force? a. ionic bonding b. disulfide bonding c. hydrophobic interactions d. van der Waals bonding
B
Which statement about the α-helix is true? a. The hydrophobic interior of α-helices is stabilized by the side chains of hydrophobic amino acids. b. The amino acid side chains point out to the sides with every third amino acid roughly lining up on one side of the helix. c. α-Helices have backbone amide groups that are hydrogen bonded to amino acid side chains. d. α-Helices have 5 amino acids per one turn of the helix.
B
Which gives rise to a favorable enthalpic (∆S) driving force for protein folding? a. The lining up of hydrogen bonds as the protein folds. b. The limiting of possible conformations as the protein folds. c. The decrease in ordered water molecules as hydrophobic amino acids pack together. d. The stabilization caused by favorable electrostatic interactions of amino acid side chains.
C
Which of the following statements is true about α-helices? a. The center of the helix is an open channel. b. There are about seven amino acids per helical turn. c. The amide backbone dipoles line up in one direction. d. The helical backbone structure is stabilized by ionic interactions.
C
Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure? a. mutant globule b. hydrophobic collapse model c. framework model d. nucleation model
C
Which of the following statements regarding protein domains is true? a. Each protein has one unique domain. b. Multiple domains require multiple subunits and a quaternary structure. c. A domain can be composed of smaller structural units called motifs. d. A domain is a region absent of α-helices and β-sheets.
C
Protein tertiary structures a. require the formation of disulfide bonds in order to achieve their native state. b. are always irreversibly destroyed by the addition of denaturants, such as urea and salts, even when the denaturants are subsequently removed. c. are often disrupted by the either very low pH or very high pH values as a result of alterations in the ionization states of acidic or basic amino acids. d. are generally poorly defined and cannot be determined experimentally.
C
The amino acid with the most hydrophobic side chain is a. asparagine. b. aspartate. c. valine. d. threonine.
C
The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they a. are fibrous proteins. b. are composed of repeating amino acid sequences. c. are composed of α-helical structures. d. play important structural roles in biology.
C
What is the approximate net charge of the molecule shown below at pH 7? *see 18* a. +1 b. 0 c. −1 d. −2
C
What is the difference between clamp-type and chamber-type chaperone proteins? a. One uses ATP and the other does not. b. One folds proteins, whereas the other just protects them from unfolding. c. They are shaped differently. d. One type is found extracellularly and one intracellularly.
C
What is the peptide sequence Asp-Gln-Gly-Ser, using one-letter abbreviations for the amino acids? a. AGYS b. DNGC c. DQGS d. EGYS
C
Which amino acid contains a hydroxyl group? a. valine b. cysteine c. threonine d. aspartate
C
All of the following are stabilizing forces in maintaining a stable protein tertiary (3°) structure, EXCEPT a. H bonds. b. temperature. c. hydrophobic interactions. d. electrostatic attractions.
B
An α-helix has the sequence: NH3+-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of a. Asp. b. Lys. c. Trp. d. Ala.
B
Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein? a. detergent and salt b. urea and β-mercaptoethanol c. acid and base d. ethanol and β-mercaptoethanol
B
Consider the whole amino acid alanine at pH =7. How many atoms (including Hs) are found in the molecule? a. 15 b. 13 c. 10 d. 8
B
For the alanine titration curve shown below, which best describes point A? *see pdf #4 for picture* a. a buffer region b. isoelectric point c. second equivalence point d. pH=pKa
B
How many β-turns or β-loops are required to construct a β-sheet composed of four antiparallel strands? a. 0 b. 3 c. 4 d. 5
B
If the isoelectric point (pI) for an amino acid is at point A, what is the charge on the amino acid at point B? *see #7 for pic* a. 0 b. −2 c. +2 d. −1
B
It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may a. waste excessive ATP in attempts to refold them. b. aggregate and interfere with normal cellular function. c. eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent. d. be excreted from the cell rather than recycled for building blocks.
B
Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures? a. mutant globule b. hydrophobic collapse model c. framework model d. nucleation model
B
The chirality of naturally occurring amino acids in proteins is a. R. b. L. c. D. d. the same as glyceraldehyde.
B
The peptide bond a. is most stable in the cis configuration. b. has a mix of single and double bond characters. c. can rotate around the carbonyl and N bond but not around the α-carbon and N bond. d. can function as a weak acid and weak base.
B
The points in the Ramachandran plot are derived by *see 30* a. counting the number of amino acids and placing points in allowed regions. b. measuring the φ and ψ angles in an experimentally determined protein crystal structure. c. placing each amino acid in regions commonly occupied by that amino acid. d. experimentally measuring the optical rotation of polarized light
B
The protein fold known as the Rossman fold is found in proteins that commonly bind a. α-helices. b. nucleotides. c. cytochromes. d. membranes.
B
The φ and ψ angles are the a. flatness of the peptide bond. b. torsion angles on either side of the α-carbon. c. angles of each amino acid side chain. d. peptide bond plane angle.
B
Use the table below to determine how many possible RNA sequences could code for the dipeptide Pro-Ala. *see 32* a. 1 b. 16 c. 8 d. 64
B
Using the pKas shown, what is the isoelectric point of the amino acid tyrosine? *see number 9* a. <1.0 b. 5.5 c. 7.0 d. 9.75
B
What is a difference between parallel and antiparallel β-sheet secondary structures? a. Antiparallel β-sheets have a larger number of stabilizing H bonds between backbone amides than parallel β-sheets. b. Parallel β-sheets require a larger loop connecting together the individual peptide strands in the sheet. c. Parallel β-sheets are longer than antiparallel sheets. d. Parallel β-sheets have amino acid side chains alternating up and down, whereas antiparallel side chains alternate down and up.
B
What is the minimum number of amino acids needed to make one turn of an α-helix? a. 3 b. 4 c. 6 d. 7
B
What is the pI of the dipeptide shown? (Use the pK as given.) *see number 10* a. 0 b. 5 c. 9 d. 10.5
B
Which class of protein structures does the protein shown below fit into? *see 51* a. predominantly α-helical b. predominantly β -sheet c. intermixed α-helix and β -sheet d. domains of α-helix adjacent to domains of β-sheet
B
Which interaction largely stabilizes protein secondary (2°) structures? a. disulfide bonds b. hydrogen bonding c. hydrophobic packing d. metal ions
B
*number 22* Which represents the correct arrangement of bonding in a peptide bond?
C
All of the following are types of protein secondary structure EXCEPT a. β-sheets. b. α-helixes. c. β-helixes. d. β-turns.
C
At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer? a. glutamate-aspartate. b. leucine-aspartate. c. glutamate-lysine. d. phenylalaninelysine.
C
At what point does the isoelectric point or pI occur? a. when all of the acidic protons are neutralized with base b. atpH=7.0 c. at the pH when all negative charges on a zwitterion counter the positive charges d. when the molecule has a single electric charge
C
How many possible protein primary structures are there for a tripeptide given the 20 amino acids? a. 3^20 b. 400 c. 20^3 d. 1.27 × 10^130
C
If the titration curve shown below is for the amino acid glycine, at which point in the curve is the pI? *see #6 for pic* a. A b. B c. C d. D
C
In a standard α-helix, __________ H bonds and __________ dipole moments are found per amino acid, which stabilizes the α-helical structure. a. 1;1 b. 1;2 c. 2;1 d. 2;2
C
Of the 20 common amino acids, how many have a chiral α-carbon? a. 0 b. 1 c. 19 d. 20
C
Which statement regarding protein secondary structures is correct? a. β-strands allow α-helices to interact with one another. b. Protein α-helices alternate with β-strands in stabilizing protein structure. c. Protein α-helices are left handed, whereas β-sheets are right handed in arrangement. d. Protein α-helices and β-strands differ in that α-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands.
D
A __________ mutation in a gene results in the least amount of damage to the resulting protein. a. missense b. nonsense c. frameshift d. silent
D
Cells deal with misfolded proteins by a. storing them for later energy use. b. collecting and excreting them from the cell. c. aggregating them to maintain the cell's structural integrity. d. degrading them to individual amino acids.
D
How many different protein folds are recognized in the formal system of organization, referred to as SCOP: Structure Organization of Proteins? a. 4 b. >10 c. >100 d. >1000
D
How many possible unique triplet codons could there be in a genome? a. 3 b. 20 c. 36 d. 64
D
In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT a. hydrogen bonds. b. electrostatic interactions. c. hydrophobic interactions. d. peptide bonds.
D
In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein? a. Remove denaturant first and reductant second. b. Simultaneously remove denaturant and reductant. c. Remove reductant first, denaturant second, and then finally add back reductant. d. Remove reductant first and denaturant second.
D
Protein secondary structures such as α-helices and β-sheets are stabilized mainly by a. ionic interactions. b. disulfide bond formation. c. van der Waals forces. d. hydrogen bond formation.
D
The common protein fold shown below is the __________ fold.*see 53* a. Greek key b. Rossman c. FERM domain d. α/ β barrel
D
The dipole moment associated with a peptide bond proceeds from which amide? a. the Ct o the O atom b. the C to the N atom c. the O to the H atom d. the H to the O atom
D
What are the three-letter and one-letter abbreviations for the amino acid tyrosine? a. Tyo, T b. Tyr, R c. Tro, Y d. Tyr, Y
D
What is a current hypothesis that explains the infectious nature of prion diseases? a. The virus responsible for prion diseases is transmissible. b. Unfavorable environmental factors negatively influence healthy cells. c. The small molecule denaturants found in infected cells are passed on to healthy cells. d. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.
D
Which amino acid has the highest pKa? a. glutamate b. asparagine c. cysteine d. lysine
D
Which of the following statements about Ramachandran plots is true? a. They are good predictors of protein tertiary structure. b. They are needed to determine the secondary structure of a protein. c. They show equal distributions of φ and ψ angles for α-helical and β-sheet containing proteins. d. They show that β-sheets and α-helices occupy different φ and ψ angles.
D
Which of the following statements about α-helices and β-sheets are FALSE? a. They are both incompatible with the amino acid proline. b. They both interact with other protein elements through amino acid side chains that stick out. c. They both contain a recurring pattern of hydrogen bonds from one peptide bond to another peptide bond. d. They both give rise to similar tertiary structures.
D
Which one of the following statements comparing alpha keratin and silk fibroin is true? a. Both have covalently cross-linked strands. b. Both are primarily α-helical in character. c. Both fibers are intracellularly located. d. Both fibers are heavily stabilized by hydrogen bonds.
D
