Deck 6: The Three-Dimensional Structure of Proteins

Question 1

Which of the following types of secondary structure has a non-integer value of residues per turn?

A)antiparallel $\beta$ -sheet
B)parallel $\beta$ -sheet
C) $\alpha$ -helix
D)3₁₀ helix
E)polyproline II helix

Answer 1

$\alpha$ -helix

Question 2

Which of the following would contribute to tertiary structure?

A)charge-charge interaction between lysine and aspartic acid
B)disulfide bond
C)hydrogen bond between serine hydroxyl group and amide of glutamine
D)hydrophobic interaction between leucine and valine
E)all of the above

Answer 2

E

Question 3

Which of the following is considered a dead-end complex (and therefore dangerous due to its resistance to proteolytic cleavage)in the protein-folding pathway?

A)disordered aggregate
B)molten globule state
C)prefibrillar species
D)amyloid fibril
E)unfolded protein

Answer 3

D

Question 4

Which of the following causes denaturation of a protein when disulfide bonds are present?

A)heat
B)pH changes
C)reducing agent
D)detergent
E)all of the above

Question 5

What type of interaction occurs between the $\beta$ -sheets of fibroin?

A)charge-dipole interaction
B)dipole-dipole interaction
C)dipole-induced dipole interaction
D)van der Waals interaction
E)hydrogen bonding

Question 6

Which of the following correctly defines the angles $\varPhi$ and $\Psi$ ?

A) $\varPhi$ : N-C _$\alpha$ ; $\Psi$ : C _$\alpha$ -C _$\beta$
B) $\varPhi$ : N-C _$\alpha$ ; $\Psi$ : C _$\alpha$ -C_carbonyl
C) $\varPhi$ : C_carbonyl-N_{(i + 1)}; $\Psi$ : N-C _$\alpha$
D) $\varPhi$ : C_carbonyl-N_{(i + 1)}; $\Psi$ : C _$\alpha$ -C_carbonyl
E) $\varPhi$ : C _$\alpha$ -C _$\beta$ ; $\Psi$ : N-C _$\alpha$

Question 7

A protein with five disulfide bonds was treated with $\beta$ -mercaptoethanol and urea. Once the protein was denatured, the $\beta$ -mercaptoethanol and urea were removed by dialysis. What is the likelihood that all five disulfide bonds will reform correctly?

A)1/5 or 20%
B)1/10 or 10%
C)1/10² or 4%
D)1/5! = 1/120 or 0.83%
E)1/945 or 0.11%

Question 8

Which of the following could contribute to quaternary structure?

A)charge-charge interaction between arginine and glutamic acid
B)disulfide bond
C)hydrogen bond between threonine hydroxyl group and imidazole ring of histidine
D)hydrophobic interaction between phenylalanine and tryptophan
E)all of the above

Question 9

Which of the following is true regarding $\beta$ -sheet structures?

A)hydrogen bonds in an parallel sheet are non-linear
B)hydrogen bonds in an antiparallel sheet are non-linear
C)the rise per residue is greater for a parallel sheet than for an antiparallel sheet
D) $\beta$ -sheets are an n=3 helix with each residue rotated 120 ^$\circ$ with respect to its neighbors
E)none of the above

Question 10

Which of the following is a highly compact structure that is very commonly used to transition from one region of secondary structure to another in a globular protein?

A) $\alpha$ bend
B) $\beta$ turn
C) $\alpha$ / $\beta$ hairpin
D)high-glycine loop
E)none of the above

Question 11

The two amino acids most often found in a polyproline II helix are proline and _______.

A)alanine
B)glycine
C)serine
D)lysine
E)histidine

Question 12

In an $\alpha$ -helix, a hydrogen bond is formed between the carbonyl oxygen of the i^th residue and the amide hydrogen _____ residues away

A)i + 1
B)i + 2
C)i + 3
D)i + 4
E)i + 5

Question 13

The presence of a hydrophobic amino acid at every third or fourth residue in $\alpha$ -keratin results in which of the following?

A)a random placement of hydrophobic amino acids within the helix
B)a strip of hydrophobic surface area that, when combined with another monomer, results in the formation of a dimer through hydrophobic interactions
C)a strip of hydrophobic surface area that causes individual $\alpha$ -keratin molecules to fold back on themselves through hydrophobic interactions
D)represents a deleterious mutation that causes the $\alpha$ -keratin molecules to aggregate and form plaques
E)none of the above

Question 14

Which of the following contributes to a positive $\Delta$ G for protein folding?

A)conformational entropy
B)hydrophobic effect
C)charge-charge interactions
D)internal hydrogen bonds
E)van der Waals interactions

Question 15

Of the following proteins that aid in the folding process, which is exclusively involved in the interconversion of cis and trans bonds?

A)prolyl isomerase
B)protein disulfide isomerase
C)Hsp60
D)Hsp70
E)GroEl-ES complex

Question 16

Which of the following structural proteins is correctly paired with the modified amino acid or cross-link that is an integral part of that protein?

A)collagen: 5-hydroxylysine
B)elastin: hydroxyproline
C) $\alpha$ -keratin: cross link formed by oxidation of lysine, then aldol condensation
D)collagen: desmosine
E)fibroin: cross-link formed by dehydration of serine residues

Question 17

In a typical Ramachandran plot, _____ is plotted vs _____ to illustrate _______.

A) $\varPhi$ ; $\Psi$ ; dependence of $\Psi$ upon $\varPhi$
B) $\Psi$ ; $\varPhi$ ; dependence of $\varPhi$ upon $\Psi$
C) $\varPhi$ ; $\Psi$ ; allowable combinations of $\Psi$ and $\varPhi$
D) $\Psi$ ; $\varPhi$ ; allowable combinations of $\Psi$ and $\varPhi$
E)none of the above

Question 18

If a peptide was composed entirely of $\alpha$ -helical structure and found to contain an integer number of complete turns, which of the following would be a possible number of amino acid residues in the peptide?

A)12
B)20
C)32
D)36
E)60

Question 19

Which amino acid is often referred to as a "helix-breaker" due to its absence from $\alpha$ -helices but is often found in structures such as $\beta$ -turns?

A)Val
B)Met
C)Pro
D)Phe
E)Leu

Question 20

Which of the following statements regarding structural proteins is true?

A)silk fibroin is made from a repeat of three amino acids where each third amino acid is Gly
B) $\beta$ -keratin is composed of peptides that contain mostly $\alpha$ -helical structure with the exception of short sequences where the peptide folds back on itself
C)collagen has its own helical structure where three individual peptides are wound around each other in a left-handed helix
D)generally speaking, structural proteins are soluble in water
E)none of the above

Question 21

If two protein subunits produced the following structure, what term would be used to describe the interactions that hold the two peptides together?

A)point-group symmetry interactions
B)dyad axis symmetry interactions
C)isologous interactions
D)dihedral symmetry interactions
E)none of the above

Question 22

Show the most likely interaction that would occur between a serine residue and a glutamine residue.

Question 23

Draw a section of antiparallel $\beta$ -sheet showing two sheets with three residues in each sheet. Clearly show the hydrogen bond pattern between the two sheets.

Question 24

Show the reaction catalyzed by prolyl isomerase. Indicate the configuration of both substrate and product.