Question 1

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 2

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 3

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

Question 4

Matching

-The overall arrangement of the regular structural elements such as the α helix and the β sheet in the protein are considered the protein's ______.

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 5

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 6

Which statement below does not describe fibrous proteins?

Accepted Answer

A) Domains have a globular fold. 
B) These proteins usually contain only one type of secondary structure. 
C) These proteins usually exhibit structural or protective characteristics. 
D) These proteins have usually elongated hydrophilic surfaces. 
E) These proteins are usually insoluble in water. 
A) Domains have a globular fold. 
B) These proteins usually contain only one type of secondary structure. 
C) These proteins usually exhibit structural or protective characteristics. 
D) These proteins have usually elongated hydrophilic surfaces. 
E) These proteins are usually insoluble in water.

Question 7

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 8

In a Ramachandran diagram the region representing the angles of $\phi$ 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 9

In a Ramachandran diagram,a larger area represents sterically allowed torsion angles of $\phi$ 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 10

Matching

-A rigid,planar structure between at least two amino acids consisting of about 40% double bond character is characteristic of a ______.

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

Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)?

Accepted Answer

A) aggregation of a misfolded protein. 
B) aggregation of random coil regions on a protein. 
C) ingestion of ammonium salts. 
D) the serious side effects of experimental treatment with Quinacrine 
E) All are potential causes Creutzfeld-Jakob disease. 
A) aggregation of a misfolded protein. 
B) aggregation of random coil regions on a protein. 
C) ingestion of ammonium salts. 
D) the serious side effects of experimental treatment with Quinacrine 
E) All are potential causes Creutzfeld-Jakob disease.

Question 12

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 13

-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 14

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 15

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 16

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 17

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 18

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 19

Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein?

Accepted Answer

A) Lys and Arg 
B) Cys and Glu 
C) Glu and Lys 
D) Gln and Glu 
E) Pro and Asp 
A) Lys and Arg 
B) Cys and Glu 
C) Glu and Lys 
D) Gln and Glu 
E) Pro and Asp

Question 20

Matching

-A historical experiment exploring denaturation upon β- mercaptoethanol reduction of disulfide bonds and spontaneous renaturation upon dialysis to remove the β- mercaptoethanol was carried out using the protein ______.This experiment demonstrated the importance of disulfide bonds and amino acid sequence in folding of proteins.

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

Exam 6: Proteins: Three-Dimensional Structure

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

Chaperonins such as the GroEL/ES system

Matching -The overall arrangement of the regular structural elements such as the α helix and the β sheet in the protein are considered the protein's ______.

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 statement below does not describe fibrous proteins?

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

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

Matching -A rigid,planar structure between at least two amino acids consisting of about 40% double bond character is characteristic of a ______.

Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)?

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?

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

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.

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

Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein?

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

Glucose Catabolism

Glycogen Metabolism and Gluconeogenesis

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

Protein Synthesis

Regulation of Gene Expression

Filters

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

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

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