Question 1

The first step in the folding of disordered polypeptides into ordered functional protein is the formation of ______.

Accepted Answer

A) 1o structure 
B) 2° structure 
C) 3° structure 
D) 4° structure 
E) hydrogen bonds 
A) 1o structure 
B) 2° structure 
C) 3° structure 
D) 4° structure 
E) hydrogen bonds

Question 2

When considering fibrous proteins, which of the following statements is TRUE?

Accepted Answer

A) Noncovalent interactions contribute to the strength of all of these proteins. 
B) All of them consist of $\alpha$ helix structure. 
C) All of them require vitamin C. 
D) Decrease in amounts of any of them cause scurvy. 
E) All of these are true of fibrous proteins. 
A) Noncovalent interactions contribute to the strength of all of these proteins. 
B) All of them consist of $\alpha$ helix structure. 
C) All of them require vitamin C. 
D) Decrease in amounts of any of them cause scurvy. 
E) All of these are true of fibrous proteins.

Question 3

Which of the following gives the best example of a nonrepetitive structure in a protein?

Accepted Answer

A) a random sequence of 12 amino acids with high Pα values forming an α helix 
B) an amino acid sequence with the following pattern "…a-b-c-d-e-a-b-c-d-a-b-c-d…" 
C) a 13 residue α helix with a Gln at position n+12 which hydrogen bonds to a residue at position n+10 
D) All of the above statements describe nonrepetitive protein structures. 
E) None of the above describe nonrepetitive protein structures. 
A) a random sequence of 12 amino acids with high Pα values forming an α helix 
B) an amino acid sequence with the following pattern "…a-b-c-d-e-a-b-c-d-a-b-c-d…" 
C) a 13 residue α helix with a Gln at position n+12 which hydrogen bonds to a residue at position n+10 
D) All of the above statements describe nonrepetitive protein structures. 
E) None of the above describe nonrepetitive protein structures.

Question 4

Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)? 
Val - Cys - Lys - Val - Cys - Ala - Cys - Val - Cys - Lys - Val - Cys - Ala - Cys

Accepted Answer

A) ($\alpha$ keratin) 
B) β keratin 
C) collagen 
D) pleated collagen 
E) This sequence cannot be from any of the structural proteins. 
A) ($\alpha$ keratin) 
B) β keratin 
C) collagen 
D) pleated collagen 
E) This sequence cannot be from any of the structural proteins.

Question 5

Matching
-In vivo protein folding is often is assisted by ______.

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 6

Protein dynamics is a field of study that examines the movements with in a protein.Which type of protein structure determination would be most useful to study this type of change?

Accepted Answer

A) X-ray crystallography 
B) Nuclear Magnetic Resonance (NMR) 
C) X-ray absorption spectroscopy 
D) A and B 
E) B and C 
A) X-ray crystallography 
B) Nuclear Magnetic Resonance (NMR) 
C) X-ray absorption spectroscopy 
D) A and B 
E) B and C

Question 7

Which one of these characteristics is not true for the $\alpha$ helix?

Accepted Answer

A) There are 3.6 amino acids per turn. 
B) There is a requirement for glycine every third amino acid residue. 
C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the - NH group of the (n + 4)th amino acid residue. 
D) Proline is typically not found in the $\alpha$ helix. 
E) It is right-handed. 
A) There are 3.6 amino acids per turn. 
B) There is a requirement for glycine every third amino acid residue. 
C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the - NH group of the (n + 4)th amino acid residue. 
D) Proline is typically not found in the $\alpha$ helix. 
E) It is right-handed.

Question 8

In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:

Accepted Answer

A) lathyrism 
B) prion diseases 
C) amyloid formation 
D) scurvy 
E) allysine 
A) lathyrism 
B) prion diseases 
C) amyloid formation 
D) scurvy 
E) allysine

Question 9

Conventional one dimensional NMR spectroscopy is not generally an effective tool for determination of protein structure because…
I.Proteins (including small proteins)have a high number of hydrogen atoms.
II.NMR requires a high quality protein crystal.
III.The NMR spectra exhibit high peak overlap.

Accepted Answer

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

Question 10

Matching
-________ is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which forms an α helix with one hydrophobic side.

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 11

Matching
-In most peptide groups the ______ conformation is not sterically favored.

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 12

In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of $\varPhi$ and $\varPsi$ that are allowed in _____ rather than in ______ because there is greater opportunity for separation of amino acid side chains.

Accepted Answer

A) secondary structure…tertiary structure 
B) α helix…β sheet 
C) β sheet…α helix 
D) tertiary structure…secondary structure 
E) none of the above 
A) secondary structure…tertiary structure 
B) α helix…β sheet 
C) β sheet…α helix 
D) tertiary structure…secondary structure 
E) none of the above

Question 13

Which of these characteristics does not describe the $\beta$ sheet?

Accepted Answer

A) Amino acid side chains are located both above and below the sheet. 
B) ($\beta$ sheets have a pleated edge-on appearance.) 
C) They can exist in either parallel or antiparallel configurations. 
D) The sheets contain as few as two and as many as 22 polypeptide chains. 
E) Parallel $\beta$ sheets containing fewer than five chains are the most common. 
A) Amino acid side chains are located both above and below the sheet. 
B) ($\beta$ sheets have a pleated edge-on appearance.) 
C) They can exist in either parallel or antiparallel configurations. 
D) The sheets contain as few as two and as many as 22 polypeptide chains. 
E) Parallel $\beta$ sheets containing fewer than five chains are the most common.

Question 14

Which of the following changes would not alter the functional characteristics of α keratin?

Accepted Answer

A) Increasing the number of residues per turn to 4.1 while maintaining the same amino acid sequence. 
B) Substitution of a hydrophilic amino acid for a hydrophobic amino acid at position a and d of the 7-residue pseudorepeat. 
C) Decreasing the number of cysteine amino acids within each protofilament. 
D) Changing the environment surrounding the protein to one that is more reductive. 
E) All of the above would alter the functional characteristics of keratin. 
A) Increasing the number of residues per turn to 4.1 while maintaining the same amino acid sequence. 
B) Substitution of a hydrophilic amino acid for a hydrophobic amino acid at position a and d of the 7-residue pseudorepeat. 
C) Decreasing the number of cysteine amino acids within each protofilament. 
D) Changing the environment surrounding the protein to one that is more reductive. 
E) All of the above would alter the functional characteristics of keratin.

Question 15

When comparing similarities among multiple protein structures, which of the following is false?

Accepted Answer

A) Proteins with the same function from a different species are likely to have similar motifs. 
B) Proteins with the same function from different species are likely to be more similar in sequence than in structure. 
C) An effective protein motif isl likely be observed in multiple proteins. 
D) Proteins with the same motifs are likely to perform similar functions. 
E) None of the above statements are false. 
A) Proteins with the same function from a different species are likely to have similar motifs. 
B) Proteins with the same function from different species are likely to be more similar in sequence than in structure. 
C) An effective protein motif isl likely be observed in multiple proteins. 
D) Proteins with the same motifs are likely to perform similar functions. 
E) None of the above statements are false.

Question 16

When solving a protein structure using X-ray crystallography, the crystallographer generates a 3-D grid called an electron density map based on the observed diffraction pattern.The higher the resolution, the more detailed the electron density map and therefore the easier it is to identify what atoms (and therefore what amino acids)are in a given position.Based on the three choices below, in which of the following groups could the two of amino acids be the easiest to differentiate regardless of resolution?
I.Leucine vs.Isoleucine
II.Phenylalanine vs.Alanine
III.Glutamate vs.Glutamic acid

Accepted Answer

A) Those in both groups I and II could be differentiated 
B) Those in both groups I and III could be differentiated 
C) Only those in group II could be differentiated 
D) Only those in group III could be differentiated 
E) Only those in groupI could be differentiated 
A) Those in both groups I and II could be differentiated 
B) Those in both groups I and III could be differentiated 
C) Only those in group II could be differentiated 
D) Only those in group III could be differentiated 
E) Only those in groupI could be differentiated

Question 17

Which of the following contribute to the minimization of energy that occurs with protein folding?

Accepted Answer

A) orientating amino acid groups to maximize hydrogen bonding 
B) folding hydrophobic groups towards the exterior of the protein 
C) burying polar groups towards the interior of the protein 
D) extensive cavity formation 
E) all of the above 
A) orientating amino acid groups to maximize hydrogen bonding 
B) folding hydrophobic groups towards the exterior of the protein 
C) burying polar groups towards the interior of the protein 
D) extensive cavity formation 
E) all of the above

Question 18

Examine the three sequences below for collagen-like proteins.If hydrogen bonding were the most important feature in determining strength in fibrous proteins, which of the following sequences likely has the highest melting temperature and why? (Note: Flp = fluoroproline; Hyp = hydroxyproline)
I.Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly
II.Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly
III.Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr

Accepted Answer

A) "1" because Hyp has OH groups 
B) "1" because the electronegativity of oxygen is greater 
C) "2" because the electronegativity of proline is greater 
D) "2" because the electronegativity of the -OH group increases hydrogen bond strength 
E) "3" because Thr is a small amino acid which allows close packing 
A) "1" because Hyp has OH groups 
B) "1" because the electronegativity of oxygen is greater 
C) "2" because the electronegativity of proline is greater 
D) "2" because the electronegativity of the -OH group increases hydrogen bond strength 
E) "3" because Thr is a small amino acid which allows close packing

Question 19

The structure of hen egg white protein has been solved and the torsion angles $\varPhi$ and $\varPsi$ are shown for each residue in the table below.What structure motif most likely forms as a result of this protein sequence?

Accepted Answer

A) β strand connected to another β strand with a break (or loop/turn)in between 
B) α Helix connect to another α Helix with a break (or loop/turn)in between 
C) β strand connected to another β strand with a alpha helix in between 
D) α Helix connected to a β strand with a break (or loop/turn)in between 
E) None of the above are correct. 
A) β strand connected to another β strand with a break (or loop/turn)in between 
B) α Helix connect to another α Helix with a break (or loop/turn)in between 
C) β strand connected to another β strand with a alpha helix in between 
D) α Helix connected to a β strand with a break (or loop/turn)in between 
E) None of the above are correct.

Question 20

Noncovalent forces that stabilize protein structure include all of the following except __________.

Accepted Answer

A) the hydrophobic effect 
B) salt bridges 
C) electrostatic interactions with metal ions 
D) hydrogen bonding 
E) disulfide bridges 
A) the hydrophobic effect 
B) salt bridges 
C) electrostatic interactions with metal ions 
D) hydrogen bonding 
E) disulfide bridges

Exam 6: Proteins: Three-Dimensional Structure

The first step in the folding of disordered polypeptides into ordered functional protein is the formation of ______.

When considering fibrous proteins, which of the following statements is TRUE?

Which of the following gives the best example of a nonrepetitive structure in a protein?

Matching -In vivo protein folding is often is assisted by ______.

Protein dynamics is a field of study that examines the movements with in a protein.Which type of protein structure determination would be most useful to study this type of change?

Which one of these characteristics is not true for the α\alphaα helix?

In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:

Matching -________ is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which forms an α helix with one hydrophobic side.

Matching -In most peptide groups the ______ conformation is not sterically favored.

In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of Φ\varPhiΦ and Ψ\varPsiΨ that are allowed in _____ rather than in ______ because there is greater opportunity for separation of amino acid side chains.

Which of these characteristics does not describe the β\betaβ sheet?

Which of the following changes would not alter the functional characteristics of α keratin?

When comparing similarities among multiple protein structures, which of the following is false?

Which of the following contribute to the minimization of energy that occurs with protein folding?

The structure of hen egg white protein has been solved and the torsion angles Φ\varPhiΦ and Ψ\varPsiΨ are shown for each residue in the table below.What structure motif most likely forms as a result of this protein sequence?

Noncovalent forces that stabilize protein structure include all of the following except __________.

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

Which one of these characteristics is not true for the $\alpha$ helix?

In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of $\varPhi$ and $\varPsi$ that are allowed in _ rather than in __ because there is greater opportunity for separation of amino acid side chains.

Which of these characteristics does not describe the $\beta$ sheet?