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 
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. 
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

Typically, the interior of a water-solub

Question 4

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

Accepted Answer

Glycine and proline are often found with

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. 
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 
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 input question seems to be referring

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. 
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. 
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. 
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 greater stability of a polypeptide i

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

Once a protein has been denatured, meani

Question 13

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

Accepted Answer

A peptide bond is a covalent bond that f

Question 14

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

Accepted Answer

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

The Foundations of Biochemistry

Water

Amino Acids, Peptides, and Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

DNA-Based Information Technologies

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

DNA Metabolism

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

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: