Question 1

Which mutation would be MOST likely to result in amyloid formation?

Accepted Answer

A)  Lys $\rightarrow$ Arg 
B)  Gln $\rightarrow$ Glu 
C)  Lys $\rightarrow$ Phe 
D)  Tyr $\rightarrow$ His 
E)  Trp $\rightarrow$ Ile

Question 2

Which statement does NOT describe a feature of the E. coli GroEL/GroES chaperonin system?

Accepted Answer

A)  The conformational changes in GroEL/GroES do not require external energy input. 
B)  An unfolded protein binds to the hydrophobic surface of the GroEL chamber. 
C)  Constraining a protein inside the GroEL chamber restricts the conformational space a protein can explore while folding. 
D)  Constraining a protein inside the GroEL chamber prevents protein aggregation. 
E)  All of these function in the process of the GroEL/GroES chaperonin.

Question 3

What is typically found in the interior of a water-soluble globular protein?

Accepted Answer

The answer of What is typically found in the interior...

Question 4

Why are glycine and proline often found within a $\beta$ turn?

Accepted Answer

The answer of Why are glycine and proline often found...

Question 5

Which statement about intrinsically disordered proteins is TRUE?

Accepted Answer

A)  They contain small hydrophobic cores. 
B)  They represent misfolded conformations of cellular proteins. 
C)  They have no stable three-dimensional structure and therefore have no cellular function. 
D)  They are responsible for proteostasis. 
E)  They can interact with multiple protein-binding partners and are central to protein interaction networks.

Question 6

Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water?

Accepted Answer

A)  N, Y, and K 
B)  I, M, and V 
C)  V, T, and R 
D)  M, S, and Y 
E)  F, Y, and W

Question 7

In a $\beta$$\alpha$$\beta$ loop, and describe what is found in the interior of the loop.

Accepted Answer

The answer of In a $\beta$$\alpha$$\beta$ loop, and describe what...

Question 8

Amino acid residues commonly found in the middle of $\beta$ turn are:

Accepted Answer

A)  Ala and Gly. 
B)  hydrophobic. 
C)  Pro and Gly. 
D)  those with ionized R-groups. 
E)  two Cys.

Question 9

A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):

Accepted Answer

A)  antiparallel $\beta$ sheet. 
B)  parallel $\beta$  sheet. 
C)  $\alpha$ helix. 
D)  $\alpha$ sheet. 
E)  $\beta$ turn.

Question 10

Which disease is NOT one characterized by or associated with an unfolded protein aggregate?

Accepted Answer

A)  Alzheimer disease 
B)  diabetes 
C)  Parkinson disease 
D)  scurvy 
E)  All of these diseases are linked to unfolded protein aggregates.

Question 11

When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

Accepted Answer

The answer of When a polypeptide is in its native...

Question 12

Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

Accepted Answer

The answer of Once a protein has been denatured, how...

Question 13

Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C-N bond.

Accepted Answer

The answer of Describe the resonance structure of a peptide...

Question 14

Proteins in their functional, folded conformation are called _____ proteins.

Accepted Answer

A)  native 
B)  unique 
C)  intrinsic 
D)  inherent 
E)  natural

Question 15

Which peptide could form an amphipathic $\alpha$helix?

Accepted Answer

A)  Nterm-RIFHKVAE-Cterm 
B)  Nterm-RIHFKMEA-Cterm 
C)  Nterm-RHKEMVAI-Cterm 
D)  Nterm-ALIWSQDK-Cterm 
E)  None of the answers is correct.

Question 16

Proteins are classified within families or superfamilies based on similarities in:

Accepted Answer

A)  evolutionary origin. 
B)  physico-chemical properties. 
C)  structure and/or function. 
D)  subcellular location. 
E)  subunit structure.

Question 17

Which method would be MOST useful to solve the atomic resolution structure of a protein that happens to easily form a repeating structure?

Accepted Answer

A)  NMR 
B)  x-ray crystallography 
C)  mass spectrometry 
D)  circular dichroism 
E)  electron microscopy

Question 18

The image below plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement?

Accepted Answer

A)  The addition of GdnHCl has little effect on protein secondary structure. 
B)  Increasing temperature causes the protein to become unfolded. 
C)  Unfolding of this protein is a cooperative process. 
D)  Ribonuclease A is a heat-stable protein. 
E)  The peptide bonds of the protein are broken around 3.4 M GdnHCl.

Question 19

Which factor is NOT known to be involved in the process of assisted folding of proteins?

Accepted Answer

A)  chaperonins 
B)  disulfide interchange 
C)  heat shock proteins 
D)  peptide bond condensation 
E)  peptide bond isomerization

Question 20

A protein is highly unlikely to have both $\phi$  and $\Psi$ angles equal to zero degrees due to:

Accepted Answer

A)  steric hindrance between the side chain and the peptide backbone. 
B)  polarity differences between adjacent side chains. 
C)  hydrophobic interactions between adjacent side chains. 
D)  steric hindrance between adjacent side chains. 
E)  too few van der Waals contacts for proper folding.

Exam 4: The Three-Dimensional Structure of Proteins

Which mutation would be MOST likely to result in amyloid formation?

Which statement does NOT describe a feature of the E. coli GroEL/GroES chaperonin system?

What is typically found in the interior of a water-soluble globular protein?

Why are glycine and proline often found within a $\beta$ turn?

Which statement about intrinsically disordered proteins is TRUE?

Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water?

In a $\beta$ $\alpha$ $\beta$ loop, and describe what is found in the interior of the loop.

Amino acid residues commonly found in the middle of $\beta$ turn are:

A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n) :

Which disease is NOT one characterized by or associated with an unfolded protein aggregate?

When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C-N bond.

Proteins in their functional, folded conformation are called _____ proteins.

Which peptide could form an amphipathic $\alpha$ helix?

Proteins are classified within families or superfamilies based on similarities in:

Which method would be MOST useful to solve the atomic resolution structure of a protein that happens to easily form a repeating structure?

The image below plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement?

Which factor is NOT known to be involved in the process of assisted folding of proteins?

A protein is highly unlikely to have both $\phi$ and $\Psi$ angles equal to zero degrees due to:

Exam 4: The Three-Dimensional Structure of Proteins

Which mutation would be MOST likely to result in amyloid formation?

Which statement does NOT describe a feature of the E. coli GroEL/GroES chaperonin system?

What is typically found in the interior of a water-soluble globular protein?

Why are glycine and proline often found within a β\betaβ turn?

Which statement about intrinsically disordered proteins is TRUE?

Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water?

In a β\betaβα\alphaαβ\betaβ loop, and describe what is found in the interior of the loop.

Amino acid residues commonly found in the middle of β\betaβ turn are:

A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n) :

Which disease is NOT one characterized by or associated with an unfolded protein aggregate?

When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C-N bond.

Proteins in their functional, folded conformation are called _____ proteins.

Which peptide could form an amphipathic α\alphaα helix?

Proteins are classified within families or superfamilies based on similarities in:

Which method would be MOST useful to solve the atomic resolution structure of a protein that happens to easily form a repeating structure?

The image below plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement?

Which factor is NOT known to be involved in the process of assisted folding of proteins?

A protein is highly unlikely to have both ϕ\phiϕ and Ψ\PsiΨ angles equal to zero degrees due to:

Why are glycine and proline often found within a $\beta$ turn?

In a $\beta$ $\alpha$ $\beta$ loop, and describe what is found in the interior of the loop.

Amino acid residues commonly found in the middle of $\beta$ turn are:

Which peptide could form an amphipathic $\alpha$ helix?

A protein is highly unlikely to have both $\phi$ and $\Psi$ angles equal to zero degrees due to: