Question 1

The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______.

Accepted Answer

A) 1° structure can determine 3° structure 
B) denaturation does not disrupt protein 2° structure 
C) disulfide bonds do not stabilize folded proteins 
D) All of the above. 
E) None of the above 
A) 1° structure can determine 3° structure 
B) denaturation does not disrupt protein 2° structure 
C) disulfide bonds do not stabilize folded proteins 
D) All of the above. 
E) None of the above

Question 2

A chaperonin

Accepted Answer

A) helps fold some proteins in their lowest energy state. 
B) is required for all proteins to fold properly. 
C) mediates the unfolding of proteins. 
D) is required for protein denaturation. 
E) counteracts the laws of thermodynamics. 
A) helps fold some proteins in their lowest energy state. 
B) is required for all proteins to fold properly. 
C) mediates the unfolding of proteins. 
D) is required for protein denaturation. 
E) counteracts the laws of thermodynamics.

Question 3

For$\beta$-sheets, the terms 'parallel' and 'antiparalllel' refer to ___________.

Accepted Answer

A) the 'direction' of the associated peptide strands 
B) the orientation of the amide cross-links 
C) the quaternary structure of the protein 
D) the orientation of the hydrogen bonding 
E) the topology of the reverse turns 
A) the 'direction' of the associated peptide strands 
B) the orientation of the amide cross-links 
C) the quaternary structure of the protein 
D) the orientation of the hydrogen bonding 
E) the topology of the reverse turns

Question 4

In a Ramachandran diagram the region representing the angles of $\varPhi$and $\varPsi$  that correspond to those commonly made by an amino acid that favors a left-handed $\alpha$ helix are different from those angles commonly made by an amino acid that favors right-handed $\alpha$ helix formation.Which of the following statements provides a plausible explanation for this difference?

Accepted Answer

A) Groups which would normally undergo high steric hindrance in the right-handed arrangement are separated maximally in the left-handed arrangement. 
B) Left-handed helices have smaller pitch than right-handed helices. 
C) The peptide backbone can coil tighter in the left-handed helices than in the right-handed helices. 
D) Left-handed helices exhibit cyclic symmetry, while righthanded helices are asymmetric. 
E) All of the above are plausible explanations. 
A) Groups which would normally undergo high steric hindrance in the right-handed arrangement are separated maximally in the left-handed arrangement. 
B) Left-handed helices have smaller pitch than right-handed helices. 
C) The peptide backbone can coil tighter in the left-handed helices than in the right-handed helices. 
D) Left-handed helices exhibit cyclic symmetry, while righthanded helices are asymmetric. 
E) All of the above are plausible explanations.

Question 5

Hydrogen bonds and maximum separation of amino acid side chains make the _____very stable and energetically ______________.

Accepted Answer

A) α helix and β sheet, favorable 
B) α helix, unfavorable 
C) β sheet, unfavorable 
D) α helix, favorable 
E) β sheet, favorable 
A) α helix and β sheet, favorable 
B) α helix, unfavorable 
C) β sheet, unfavorable 
D) α helix, favorable 
E) β sheet, favorable

Question 6

Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation?

Accepted Answer

A) formation of a low energy state 
B) association of ordered subunits 
C) aggregation of hydrophobic regions in the protein 
D) tertiary structure refinement 
E) formation of a low entropy state 
A) formation of a low energy state 
B) association of ordered subunits 
C) aggregation of hydrophobic regions in the protein 
D) tertiary structure refinement 
E) formation of a low entropy state

Question 7

Evolutionary processes have

Accepted Answer

A) increased the stability of 4° structures. 
B) decreased the number of subunits. 
C) increased similarity amount 1° structures. 
D) enhanced efficient folding pathways. 
E) all of the above 
A) increased the stability of 4° structures. 
B) decreased the number of subunits. 
C) increased similarity amount 1° structures. 
D) enhanced efficient folding pathways. 
E) all of the above

Question 8

Examine the three sequences below for collagen-like proteins and their melting temperatures (Tm).(Note: Flp = fluoroproline; Hyp = hydroxyproline)Based on this data, what is the most important feature in determining the strength of the collagen protein? 
1)…-Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly-… Tm=60oC
2)…-Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly-… Tm=78oC
3)…-Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr-… Tm=30oC

Accepted Answer

A) hydrogen bonding 
B) inductive effect 
C) electrostatic effect 
D) electrostatic and Inductive effect are equal 
E) hydrogen bonding and inductive effect are equal 
A) hydrogen bonding 
B) inductive effect 
C) electrostatic effect 
D) electrostatic and Inductive effect are equal 
E) hydrogen bonding and inductive effect are equal

Question 9

Chaperonins such as the GroEL/ES system

Accepted Answer

A) function with thermophilic proteins only. 
B) are required at low pH. 
C) require ATP hydrolysis. 
D) in vitro only. 
E) function in a nonaqueous environment. 
A) function with thermophilic proteins only. 
B) are required at low pH. 
C) require ATP hydrolysis. 
D) in vitro only. 
E) function in a nonaqueous environment.

Question 10

The structure and sequence of a protein of unknown function was examined.Which of the following provides the best prediction of the protein's function?

Accepted Answer

A) the observation of several disordered α helical domains. 
B) the observation of multiple protein subunits. 
C) the observation of motif known as the Rossmann fold. 
D) the observation of a large number of random coil regions. 
E) All of the above offer excellent prediction of the protein's function. 
A) the observation of several disordered α helical domains. 
B) the observation of multiple protein subunits. 
C) the observation of motif known as the Rossmann fold. 
D) the observation of a large number of random coil regions. 
E) All of the above offer excellent prediction of the protein's function.

Question 11

Proteins can denature due to a change in

Accepted Answer

A) pH. 
B) temperature. 
C) ionic strength. 
D) all of the above 
E) none of the above 
A) pH. 
B) temperature. 
C) ionic strength. 
D) all of the above 
E) none of the above

Question 12

Matching
-In a ______, the $\varPhi$ and $\varPsi$ angles of the peptide backbone would orient atoms closer than their van der Waals distance.

Accepted Answer

A) tertiary structure 
B) keratin 
C) molecular chaperones 
D) hydropathy 
E) cis
F)trans
G)sterically forbidden conformation
H)regular secondary structure
I)collagen
J)peptide  bond
K)ribonuclease A (RNase 
A) 
L)alpha 
A) tertiary structure 
B) keratin 
C) molecular chaperones 
D) hydropathy 
E) cis
F)trans
G)sterically forbidden conformation
H)regular secondary structure
I)collagen
J)peptide  bond
K)ribonuclease A (RNase 
A) 
L)alpha

Question 13

Matching
-The _____________ of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein.

Accepted Answer

A) tertiary structure 
B) keratin 
C) molecular chaperones 
D) hydropathy 
E) cis
F)trans
G)sterically forbidden conformation
H)regular secondary structure
I)collagen
J)peptide  bond
K)ribonuclease A (RNase 
A) 
L)alpha 
A) tertiary structure 
B) keratin 
C) molecular chaperones 
D) hydropathy 
E) cis
F)trans
G)sterically forbidden conformation
H)regular secondary structure
I)collagen
J)peptide  bond
K)ribonuclease A (RNase 
A) 
L)alpha

Question 14

Which of the following lines in the figure at right indicates a $\beta$ hairpin structure?

Accepted Answer

A) A, C, D 
B) B and C 
C) A only 
D) A, B, and D 
E) C only 
A) A, C, D 
B) B and C 
C) A only 
D) A, B, and D 
E) C only

Question 15

A helix has hydrogen bonds between the carbonyl group from residue "n" and the amino group of residue "n+6," which of the following is TRUE?

Accepted Answer

A) It has 3.6 residues per turn. 
B) It is a random coil, not a helix. 
C) It is an α helix. 
D) It has more residues per turn than an α helix. 
E) It has fewer residues per turn than an α helix. 
A) It has 3.6 residues per turn. 
B) It is a random coil, not a helix. 
C) It is an α helix. 
D) It has more residues per turn than an α helix. 
E) It has fewer residues per turn than an α helix.

Question 16

Which of the following has (have)both a favorable hydrogen bonding pattern and $\varPhi$ and $\varPsi$ values that fall within the allowed Ramachandran conformational regions?

Accepted Answer

A) ($\alpha$ helix) 
B) collagen helix 
C) ($\beta$ sheet) 
D) all of the above 
E) none of the above 
A) ($\alpha$ helix) 
B) collagen helix 
C) ($\beta$ sheet) 
D) all of the above 
E) none of the above

Question 17

Native protein purifications often require multiple reaction steps in order to purify the protein of interest from other proteins.One method used for protein separation in purification procedures is a change from water to an organic solvent.Which of the following would be accomplished by this solvent change?

Accepted Answer

A) Proteins with hydrophobic groups on the interior would maintain their native state. 
B) Proteins with hydrophilic groups on the exterior would denature and likely precipitate. 
C) Proteins with exposed hydrophobic groups would maintain their structure and remain in solution. 
D) Both A and B would occur. 
E) Both B and C would occur. 
A) Proteins with hydrophobic groups on the interior would maintain their native state. 
B) Proteins with hydrophilic groups on the exterior would denature and likely precipitate. 
C) Proteins with exposed hydrophobic groups would maintain their structure and remain in solution. 
D) Both A and B would occur. 
E) Both B and C would occur.

Question 18

In general molecular chaperone proteins function by

Accepted Answer

A) mediating disulfide bond formation 
B) synthesizing new proteins when one is misfolded. 
C) preventing premature folding by binding hydrophobic regions of the protein. 
D) enhancing salt bridge formation. 
E) none of the above 
A) mediating disulfide bond formation 
B) synthesizing new proteins when one is misfolded. 
C) preventing premature folding by binding hydrophobic regions of the protein. 
D) enhancing salt bridge formation. 
E) none of the above

Question 19

Which of the following would be most stable based on the information you have learned about protein structure?

Accepted Answer

A) a loop region with 8 amino acids 
B) a β sheet region made up of amino acids Val, Ile, Phe 
C) an α helix made up of Cys, Pro, and Phe 
D) a β hairpin with 12 amino acids 
E) All have equal stability. 
A) a loop region with 8 amino acids 
B) a β sheet region made up of amino acids Val, Ile, Phe 
C) an α helix made up of Cys, Pro, and Phe 
D) a β hairpin with 12 amino acids 
E) All have equal stability.

Question 20

Which of the characteristics of collagen structure listed below contrubute to the tensi le strength of collagen?
I.Collagen is made up of a triplet helix where 3 left-handed helices twist together in a right handed sense.
II.Collagen includes at repeating sequence of amino acids with glycine every 3 amino acids in a helix with about 3 amino acids per turn.
III.The three left-handed helices are staggered to allow close packing between glycine residues and rigidity from the bulky and inflexible proline/hydroxyproline.

Accepted Answer

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

Exam 6: Proteins: Three-Dimensional Structure

The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______.

A chaperonin

For β\betaβ -sheets, the terms 'parallel' and 'antiparalllel' refer to ___________.

Hydrogen bonds and maximum separation of amino acid side chains make the _____very stable and energetically ______________.

Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation?

Evolutionary processes have

Chaperonins such as the GroEL/ES system

The structure and sequence of a protein of unknown function was examined.Which of the following provides the best prediction of the protein's function?

Proteins can denature due to a change in

Matching -In a ______, the Φ\varPhiΦ and Ψ\varPsiΨ angles of the peptide backbone would orient atoms closer than their van der Waals distance.

Matching -The _____________ of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein.

Which of the following lines in the figure at right indicates a β\betaβ hairpin structure?

A helix has hydrogen bonds between the carbonyl group from residue "n" and the amino group of residue "n+6," which of the following is TRUE?

Which of the following has (have)both a favorable hydrogen bonding pattern and Φ\varPhiΦ and Ψ\varPsiΨ values that fall within the allowed Ramachandran conformational regions?

In general molecular chaperone proteins function by

Which of the following would be most stable based on the information you have learned about protein structure?

Introduction to the Chemistry of Life

Water

Nucleotides, Nucleic Acids, and Genetic Information

Amino Acids

Proteins: Primary Structure

Protein Function Part I: Myoglobin and Hemoglobin

Carbohydrates

Lipids and Biological Membranes

Membrane Transport

Enzyme Catalysis

Enzyme Kinetics, Inhibition and Control

Biochemical Signaling

Introduction to Metabolism

Glycogen Metabolism and Gluconeogenesis

Glucose Catabolism

Citric Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Lipid Metabolism

Amino Acid Metabolism

Mammalian Fuel Metabolism: Integration and Regulation

Nucleotide Metabolism

Nucleic Acid Structure

Dna Replication, Repair and Recombination

Transcription and Rna Processing

Translation

Regulation of Gene Expression

Filters

For $\beta$ -sheets, the terms 'parallel' and 'antiparalllel' refer to ___________.

Hydrogen bonds and maximum separation of amino acid side chains make the _very stable and energetically __________.

Matching -In a ______, the $\varPhi$ and $\varPsi$ angles of the peptide backbone would orient atoms closer than their van der Waals distance.

Which of the following lines in the figure at right indicates a $\beta$ hairpin structure? $Which of the following lines in the figure at right indicates a \beta hairpin structure?$

Which of the following has (have)both a favorable hydrogen bonding pattern and $\varPhi$ and $\varPsi$ values that fall within the allowed Ramachandran conformational regions?