Question 1

Which of the following would contribute to tertiary structure?

Accepted Answer

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 
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 E

Question 2

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?

Accepted Answer

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

Question 3

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

Accepted Answer

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

Question 4

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?

Accepted Answer

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

Question 5

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?

Accepted Answer

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

Question 6

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

Accepted Answer

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 
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 7

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

Accepted Answer

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

Question 8

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

Accepted Answer

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

Question 9

Which of the following statements regarding structural proteins is true?

Accepted Answer

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 
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 10

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

Accepted Answer

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 
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 11

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?

Accepted Answer

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% 
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 12

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

Accepted Answer

A)  $\varPhi$: N-C$\alpha$;  $\Psi$: C$\alpha$-C$\beta$ 
B)  $\varPhi$: N-C$\alpha$;  $\Psi$: C$\alpha$-Ccarbonyl 
C)  $\varPhi$: Ccarbonyl-N(i + 1);  $\Psi$: N-C$\alpha$ 
D)  $\varPhi$: Ccarbonyl-N(i + 1);  $\Psi$: C$\alpha$-Ccarbonyl 
E)  $\varPhi$: C$\alpha$-C$\beta$;  $\Psi$: N-C$\alpha$ 
A)  $\varPhi$: N-C$\alpha$;  $\Psi$: C$\alpha$-C$\beta$ 
B)  $\varPhi$: N-C$\alpha$;  $\Psi$: C$\alpha$-Ccarbonyl 
C)  $\varPhi$: Ccarbonyl-N(i + 1);  $\Psi$: N-C$\alpha$ 
D)  $\varPhi$: Ccarbonyl-N(i + 1);  $\Psi$: C$\alpha$-Ccarbonyl 
E)  $\varPhi$: C$\alpha$-C$\beta$;  $\Psi$: N-C$\alpha$

Question 13

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

Accepted Answer

the structure below

Question 14

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

Accepted Answer

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

Question 15

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

Accepted Answer

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 
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 16

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

Accepted Answer

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

Question 17

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

Accepted Answer

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

Question 18

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

Accepted Answer

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

Question 19

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

Accepted Answer

The answer of Show the reaction catalyzed by prolyl isomerase....

Question 20

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

Accepted Answer

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

Exam 6: The Three-Dimensional Structure of Proteins

Which of the following would contribute to tertiary structure?

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?

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

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?

If a peptide was composed entirely of α\alphaα -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?

Which of the following is true regarding β\betaβ -sheet structures?

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

In an α\alphaα -helix, a hydrogen bond is formed between the carbonyl oxygen of the ith residue and the amide hydrogen _____ residues away

Which of the following statements regarding structural proteins is true?

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

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

Which of the following correctly defines the angles Φ\varPhiΦ and Ψ\PsiΨ ?

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

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

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

What type of interaction occurs between the β\betaβ -sheets of fibroin?

Which of the following contributes to a positive Δ\DeltaΔ G for protein folding?

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

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

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

The Scope of Biochemistry

The Matrix of Life: Weak Interactions in an Aqueous Environment

The Energetics of Life

Nucleic Acids

Introduction to Proteins: the Primary Level of Protein Structure

Protein Function and Evolution

Contractile Proteins and Molecular Motors

Carbohydrates: Sugars, Saccharides, Glycans

Lipids, Membranes and Cellular Transport

Enzymes: Biological Catalysts

Chemical Logic of Metabolism

Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Citric Acid Cycle and Glyoxylate Cycle

Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

Photosynthesis

Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

Lipid Metabolism Ii: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

Nucleotide Metabolism

Mechanisms of Signal Transduction

Genes, Genomes and Chromosomes

DNA Replication

DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

Information Readout: Transcription and Post-Transcriptional Processing

Information Decoding: Translation and Post-Translational Protein Processing

Regulation of Gene Expression

Filters

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?

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

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

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

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?

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

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

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

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