Deck 4: The Three-Dimensional Structure of Proteins

Question 1

The $\alpha$ -keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the $\alpha$ -keratin chains-as in hair waving-what subsequent steps are required?

A) chemical oxidation and then shape remodeling
B) chemical reduction and then chemical oxidation
C) chemical reduction and then shape remodeling
D) shape remodeling and then chemical oxidation
E) shape remodeling and then chemical reduction

Answer 1

shape remodeling and then chemical oxidation

Question 2

The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:

A) always side by side.
B) generally near each other in sequence.
C) invariably restricted to about 7 of the 20 standard amino acids.
D) often on different polypeptide strands.
E) usually near the polypeptide chain's amino terminus or carboxyl terminus.

Answer 2

B

Question 3

A D-amino acid would interrupt an $\alpha$ helix made of L-amino acids. Another naturally occurring hindrance to the formation of an $\alpha$ 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.

Answer 3

a Pro residue.

Question 4

In an $\alpha$ 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.

Question 5

Pauling and Corey's studies of the peptide bond showed that:

A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C-N axis.
C) peptide bonds in proteins are unusual, and unlike those in small model compounds.
D) peptide bond structure is extraordinarily complex.
E) primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly.

Question 6

In the $\alpha$ helix, the hydrogen bonds:

A) are roughly parallel to the axis of the helix.
B) are roughly perpendicular to the axis of the helix.
C) occur mainly between electronegative atoms of the R groups.
D) occur only between some of the amino acids of the helix.
E) occur only near the amino and carboxyl termini of the helix.

Question 7

Which pairs of bonds within a peptide backbone show free rotation around both bonds?

A) C _$\alpha$ -C and N-C _$\alpha$
B) C=O and N-C
C) C=O and N-C _$\alpha$
D) N-C and C _$\alpha$ -C
E) N-C _$\alpha$ and N-C

Question 8

Which backbone arrangement BEST represents that of two peptide bonds?

A) C _$\alpha$ -N-C _$\alpha$ -C-C _$\alpha$ -N-C _$\alpha$ -C
B) C _$\alpha$ -N-C-C-N-C _$\alpha$
C) C-N-C _$\alpha$ -C _$\alpha$ -C-N
D) C _$\alpha$ -C-N-C _$\alpha$ -C-N
E) C _$\alpha$ -C _$\alpha$ -C-N-C _$\alpha$ -C _$\alpha$ -C

Question 9

An $\alpha$ helix would be destabilized most by:

A) an electric dipole spanning several peptide bonds throughout the $\alpha$ helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence of an Arg residue near the carboxyl terminus of the $\alpha$ helix.
E) the presence of two Lys residues near the amino terminus of the $\alpha$ helix.

Question 10

Roughly how many amino acids are there in one turn of an $\alpha$ helix?

A) 1
B) 2.8
C) 3.6
D) 4.2
E) 10

Question 11

In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:

A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic interactions.
C) minimization of entropy by the formation of a water solvent shell around the protein.
D) placement of hydrophobic amino acid residues within the interior of the protein.
E) placement of polar amino acid residues around the exterior of the protein.

Question 12

The major reason that antiparallel $\beta$ -stranded protein structures are more stable than parallel $\beta$ -stranded structures is that the latter:

A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslinks between adjacent strands.
C) do not stack in sheets as well as antiparallel strands.
D) have fewer lateral hydrogen bonds than antiparallel strands.
E) have weaker hydrogen bonds laterally between adjacent strands.

Question 13

Which statement is NOT an appropriate description for van der Waals interactions?

A) They involve dipole-dipole interactions.
B) Their strength depends on the distance between the two interacting atoms.
C) They are highly specific.
D) An individual van der Waals interaction does not contribute significantly to the stability of a protein.
E) They can involve hydrophobic amino acids.

Question 14

Which interactions are NOT considered to be "weak" in proteins?

A) hydrogen bonds
B) hydrophobic interactions
C) ionic bonds
D) peptide bonds
E) van der Waals forces

Question 15

Thr and/or Leu residues tend to disrupt an $\alpha$ helix when they occur next to each other in a protein because:

A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs between the Thr side chains.
D) steric hindrance occurs between the bulky Thr side chains.
E) the R group of Thr can form a hydrogen bond.

Question 16

The MOST important contribution to the stability of a protein's conformation appears to be the:

A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.
D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.

Question 17

Amino acid residues commonly found in the middle of $\beta$ turn are:

A) Ala and Gly.
B) hydrophobic.
C) Pro and Gly.
D) those with ionized R-groups.
E) two Cys.

Question 18

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 $\beta$ sheet.
B) parallel $\beta$ sheet.
C) $\alpha$ helix.
D) $\alpha$ sheet.
E) $\beta$ turn.

Question 19

Which statement about intrinsically disordered proteins is TRUE?

A) They contain small hydrophobic cores.
B) They represent misfolded conformations of cellular proteins.
C) They have no stable three-dimensional structure and therefore have no cellular function.
D) They are responsible for proteostasis.
E) They can interact with multiple protein-binding partners and are central to protein interaction networks.

Question 20

In the diagram below, the plane drawn behind the peptide bond indicates the:

A) absence of rotation around the C-N bond because of its partial double-bond character.
B) plane of rotation around the C _$\alpha$ -N bond.
C) region of steric hindrance determined by the large C=O group.
D) region of the peptide bond that contributes to a Ramachandran plot.
E) theoretical space between -180 and +180 degrees that can be occupied by the $\phi$ and $\Psi$ angles in the peptide bond.

Question 21

Which residues are MOST likely to be enriched in an intrinsically disordered protein that is soluble in water?

A) Y, K, W
B) E, C, F
C) V, I, L
D) R, K, A
E) H, F, W

Question 22

Proteins often have regions that can fold and function as an independent entity from the whole protein. These regions are called:

A) domains.
B) oligomers.
C) peptides.
D) sites.
E) subunits.

Question 23

A repeating structural unit in a multimeric protein is known as a(n):

A) domain.
B) motif.
C) oligomer.
D) protomer.
E) subunit.

Question 24

The structural classification of proteins (based on motifs) is based primarily on their:

A) amino-acid sequence.
B) evolutionary relationships.
C) function.
D) secondary structure content and arrangement.
E) subunit content and arrangement.

Question 25

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 heat.
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.

Question 26

Which statement concerning protein domains is TRUE?

A) They are a form of secondary structure.
B) They are examples of structural motifs.
C) They consist of separate polypeptide chains (subunits).
D) They have been found only in prokaryotic proteins.
E) They may retain their correct shape even when separated from the rest of the protein.

Question 27

Disulfide bonds are more likely to be formed _____ of the cell, due to the _____ environment there.

A) inside; oxidizing
B) inside; reducing
C) outside; oxidizing
D) outside; reducing
E) inside; hydrophobic

Question 28

A salt bridge would be MOST likely to be found:

A) in the interior of a protein of a bacterium that lives in humans.
B) on the exterior of a protein of a bacterium that lives in humans.
C) in the interior of a protein of a thermophilic archaeal organism.
D) on the exterior of a protein of a thermophilic archaeal organism.
E) A salt bridge would be equally likely to be found in any of these cases.

Question 29

Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a _____ for protein S.

A) proteasome
B) molecular chaperone
C) protein precursor
D) structural motif
E) supersecondary structural unit

Question 30

Which statement is FALSE?

A) Collagen is a protein in which the polypeptides are mainly in the $\alpha$ -helix conformation.
B) Disulfide linkages are important for keratin structure.
C) Gly residues are particularly abundant in collagen.
D) Silk fibroin is a protein in which the polypeptide is almost entirely in the $\beta$ conformation.
E) $\alpha$ -keratin is a protein in which the polypeptides are mainly in the $\alpha$ -helix conformation.

Question 31

Which factor is LEAST likely to result in protein denaturation?

A) altering net charge by changing pH
B) changing the salt concentration
C) disruption of weak interactions by boiling
D) exposure to detergents
E) mixing with organic solvents such as acetone

Question 32

An average protein will NOT be denatured by:

A) a detergent such as sodium dodecyl sulfate.
B) heating to 90°C.
C) iodoacetic acid.
D) pH 10.
E) urea.

Question 33

Which factor is NOT known to be involved in the process of assisted folding of proteins?

A) chaperonins
B) disulfide interchange
C) heat shock proteins
D) peptide bond condensation
E) peptide bond isomerization

Question 34

Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water?

A) N, Y, and K
B) I, M, and V
C) V, T, and R
D) M, S, and Y
E) F, Y, and W

Question 35

Proteostasis is the cellular process by which:

A) proteins are synthesized.
B) proteins are folded.
C) proteins are modified.
D) proteins are degraded.
E) protein levels are maintained.

Question 36

Which statement about oligomeric proteins is FALSE?

A) A subunit may be similar to other proteins.
B) All subunits must be identical.
C) Many have regulatory roles.
D) Some oligomeric proteins can further associate into large fibers.
E) Some subunits may have nonprotein prosthetic groups.

Question 37

Proteins in their functional, folded conformation are called _____ proteins.

A) native
B) unique
C) intrinsic
D) inherent
E) natural

Question 38

Which statement concerning the process of spontaneous folding of proteins is FALSE?

A) It may be an essentially random process.
B) It may be defective in some human diseases.
C) It may involve a gradually decreasing range of conformational species.
D) It may involve initial formation of a highly compact state.
E) It may involve initial formation of local secondary structure.

Question 39

Proteins are classified within families or superfamilies based on similarities in:

A) evolutionary origin.
B) physico-chemical properties.
C) structure and/or function.
D) subcellular location.
E) subunit structure.

Question 40

Kendrew's studies of the globular myoglobin structure demonstrated that:

A) "corners" between $\alpha$ -helical regions invariably lacked proline residue.
B) highly polar or charged amino-acid residues tended to be located interiorally.
C) myoglobin was completely different from hemoglobin, as expected.
D) the structure was very compact, with virtually no internal space available for water.
E) the $\alpha$ helix predicted by Pauling and Corey was not found in myoglobin.

Question 41

Which method would be BEST to use to monitor protein secondary structure during the titration of a denaturing agent?

A) x-ray crystallography
B) electron microscopy
C) circular dichroism
D) mass spectrometry
E) liquid chromatography

Question 42

The secondary structure shown below is an example of a(n):

A) parallel $\beta$ sheet.
B) antiparallel $\beta$ sheet.
C) right-handed $\alpha$ helix.
D) left-handed $\alpha$ helix.
E) $\beta$ turn.

Question 43

The dimensions of an $\alpha$ helix from a fibrous protein such as keratin differ slightly from an $\alpha$ helix from a globular protein. What is the reason for this difference in helical dimensions?

A) An $\alpha$ helix from a fibrous protein is left-handed, not right-handed.
B) An $\alpha$ helix from a fibrous protein contains mainly hydrophobic residues, elongating the helix.
C) An $\alpha$ helix from a fibrous protein contains mainly polar residues, elongating the helix.
D) An $\alpha$ helix from a fibrous protein forms a coiled-coil, distorting the helix.
E) An $\alpha$ helix from a fibrous protein contains mainly Gly residues for more efficient packing.

Question 44

As humans age, their connective tissue, rich in collagen, becomes more rigid and brittle. What is the molecular cause of this change?

A) Collagen fibrils change their degree of supercoiling over time.
B) Many older adults have vitamin C deficiencies that result in collagen oxidation.
C) As cells age, a variant of collagen is expressed.
D) Crosslinks between collagen fibrils accumulate over time.
E) UV damage to collagen accumulates over time.

Question 45

A protein is highly unlikely to have both $\phi$ and $\Psi$ angles equal to zero degrees due to:

A) steric hindrance between the side chain and the peptide backbone.
B) polarity differences between adjacent side chains.
C) hydrophobic interactions between adjacent side chains.
D) steric hindrance between adjacent side chains.
E) too few van der Waals contacts for proper folding.

Question 46

Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure.

A) primary
B) secondary
C) tertiary
D) quaternary
E) globular

Question 47

Which method would NOT increase the strength of a fibrous protein?

A) increasing the number of coiled-coils in the supercomplex
B) increasing the number of Pro residues in the polypeptide
C) increasing the number of Cys residues in the polypeptide
D) placing the protein in an oxidizing environment
E) All of these methods could increase the strength of a fibrous protein.

Question 48

Interactions between residues on separate polypeptide chains could be best classified as _____ structure.

A) primary
B) secondary
C) tertiary
D) quaternary
E) global

Question 49

A _____ protein will often have properties that allow it to be both strong and flexible.

A) macromolecular
B) fibrous
C) globular
D) helical
E) membrane

Question 50

The secondary structure shown below is an example of a(n):

A) parallel $\beta$ sheet.
B) antiparallel $\beta$ sheet.
C) right-handed $\alpha$ helix.
D) left-handed $\alpha$ helix.
E) $\beta$ turn.

Question 51

The difference between the stretching ability of silk and wool fibers, low and high ability to stretch, respectively, is due to their protein components. Which statement CORRECTLY attributes the secondary structure contributions to this stretch ability?

A) Both silk and wool fibers have roughly equal distributions of $\alpha$ helices and $\beta$ sheets, but they are arranged in different conformations.
B) Silk is mainly $\beta$ sheets; wool is mainly $\alpha$ helices.
C) Silk is mainly $\alpha$ helices; wool is mainly $\beta$ sheets.
D) Silk contains mainly $\beta$ barrels; wool contains mainly coiled-coil $\alpha$ helices.
E) Silk contains coiled-coil $\alpha$ helices; wool contains mainly $\beta$ barrels.

Question 52

The _____ secondary structure is formed more readily than other types of secondary structures, most likely due to _____.

A) $\beta$ turn; hydrogen bonds with solvent molecules
B) $\beta$ sheet; R-group contacts
C) $\beta$ sheet; internal hydrogen bonds
D) $\alpha$ helix; R-group contacts
E) $\alpha$ helix; internal hydrogen helical bonds

Question 53

Which amino acid is MOST likely to be found outside of the highlighted/shaded regions on a Ramachandran plot?

A) Met
B) Cys
C) Ala
D) Gly
E) His

Question 54

Which method would be MOST useful to solve the structure of a small, soluble protein that does not easily form a repeating structure?

A) NMR
B) x-ray crystallography
C) mass spectrometry
D) circular dichroism
E) electron microscopy

Question 55

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and 60 degrees, respectively.

A) right-handed $\alpha$ helix
B) left-handed $\alpha$ helix
C) $\beta$ sheet
D) twisted $\beta$ sheets
E) Amino acids will not adopt this conformation.

Question 56

Proline residues are infrequently found in _____ due to their _____.

A) $\alpha$ helices; decreased ability to serve as hydrogen-bond donors
B) $\alpha$ helices; large positive charge that disrupts the repeating structure
C) $\beta$ sheets; decreased ability to serve as hydrogen-bond donors
D) $\beta$ sheets; large positive charge that disrupts the repeating structure
E) $\beta$ turns; decreased flexibility as an amino acid

Question 57

Of the following bonds, which have freedom of rotation? I. N - C _$\alpha$
II) C _$\alpha$ - C
III) C - N
IV) R - C _$\alpha$

A) All of them
B) II, III, and IV
C) I, II, and IV
D) I, II, and III
E) I and IV

Question 58

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and -180 degrees, respectively.

A) right-handed $\alpha$ helix
B) left-handed $\alpha$ helix
C) $\beta$ sheet
D) twisted $\beta$ sheets
E) Amino acids will not adopt this conformation

Question 59

Which method would be MOST useful to solve the atomic resolution structure of a protein that happens to easily form a repeating structure?

A) NMR
B) x-ray crystallography
C) mass spectrometry
D) circular dichroism
E) electron microscopy

Question 60

Which peptide could form an amphipathic $\alpha$ helix?

A) N_term-RIFHKVAE-C_term
B) N_term-RIHFKMEA-C_term
C) N_term-RHKEMVAI-C_term
D) N_term-ALIWSQDK-C_term
E) None of the answers is correct.

Question 61

Which disease is NOT one characterized by or associated with an unfolded protein aggregate?

A) Alzheimer disease
B) diabetes
C) Parkinson disease
D) scurvy
E) All of these diseases are linked to unfolded protein aggregates.

Question 62

Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?

Question 63

Describe three of the important features of the $\alpha$ -helical polypeptide structure predicted by Pauling and Corey. Provide one or two sentences for each feature.

Question 64

Why are glycine and proline often found within a $\beta$ turn?

Question 65

Which mutation would be MOST likely to result in amyloid formation?

A) Lys $\rightarrow$ Arg
B) Gln $\rightarrow$ Glu
C) Lys $\rightarrow$ Phe
D) Tyr $\rightarrow$ His
E) Trp $\rightarrow$ Ile

Question 66

Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. On a dipeptide of two amino acids in trans linkage (side-chains can be shown as -R), which six atoms are part of the planar structure of the peptide bond?

Question 67

Provide a brief explanation for the statement "Soluble globular proteins can be distinguished from soluble intrinsically disordered proteins on the basis of their amino acid content."

Question 68

When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

Question 69

Which statement does NOT describe a feature of the E. coli GroEL/GroES chaperonin system?

A) The conformational changes in GroEL/GroES do not require external energy input.
B) An unfolded protein binds to the hydrophobic surface of the GroEL chamber.
C) Constraining a protein inside the GroEL chamber restricts the conformational space a protein can explore while folding.
D) Constraining a protein inside the GroEL chamber prevents protein aggregation.
E) All of these function in the process of the GroEL/GroES chaperonin.

Question 70

What is the CORRECT way to classify the protein below according to its secondary-structure elements?

A) all $\beta$
B) $\alpha$ + $\beta$
C) $\alpha$ / $\beta$ 0
D) $\beta$ / $\alpha$ / $\beta$
E) $\alpha$ / $\beta$ / $\alpha$

Question 71

Where are the hydrogen bonding typically found between two residues in an $\alpha$ helix?

Question 72

Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.

Question 73

Intrinsically disordered proteins may:

A) wrap around their targets.
B) have multiple interaction partners.
C) function as molecular "scavengers."
D) lack a hydrophobic core.
E) All of the answers are correct.

Question 74

The image below plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement?

A) The addition of GdnHCl has little effect on protein secondary structure.
B) Increasing temperature causes the protein to become unfolded.
C) Unfolding of this protein is a cooperative process.
D) Ribonuclease A is a heat-stable protein.
E) The peptide bonds of the protein are broken around 3.4 M GdnHCl.

Question 75

Describe three of the important features of a $\beta$ sheet polypeptide structure. Provide one or two sentences for each feature.

Question 76

Which statement about protein folding is NOT true?

A) Burial of hydrophobic residues requires at least two layers of secondary structure.
B) Generally, $\alpha$ helices and $\beta$ sheets are found in different layers of a protein structure.
C) Residues close together in primary structure are often close together in tertiary structure.
D) The $\beta$ conformation is most stable in a right-handed twist.
E) The backbone of a $\beta$ sheet cannot readily hydrogen bond to an adjacent $\alpha$ helix.

Question 77

If a protein is not folded correctly or becomes partially unfolded, what could NOT be a consequence?

A) The protein may form an inactive aggregate that leads to disease.
B) The protein may be remodeled by a chaperone.
C) The protein may be degraded by the proteasome.
D) The protein may be refolded.
E) All of these consequences are possible.

Question 78

Which image below shows that there are folding intermediates with substantial stability along nearly every folding pathway?

A) I
B) II
C) III
D) IV
E) None of the answers is correct.

Question 79

Which of the images below depict a protein-folding pathway with no stable folding intermediates?

A) I
B) III
C) IV
D) I and III
E) II and IV

Question 80

Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C-N bond.