Question 1

Calculate the pI for the following dipeptide using the pKas shown.

Accepted Answer

The answer of Calculate the pI for the following dipeptide...

Question 2

What is believed to be the underlying cause of prion protein plaque formation? A) The PrP^Scproteins are misfolded and aggregated from PrP^cproteins. B) The unstructured N-terminal region of PrP^cis thought to remain unfolded. C) The normal PrP^cproteins are aggregated. D) The PrP^Scprotein adheres to and inhibits cell membranes.

Accepted Answer

Prion protein plaque formation is believed to be caused by misfolded and aggregated Prion proteins (PrP^Sc) forming from normal Prion proteins (PrP^c). The misfolded proteins then clump together to form plaques.

Question 3

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT
A) hydrogen bonds.
B) electrostatic interactions.
C) hydrophobic interactions.
D) peptide bonds.

Accepted Answer

Peptide bonds refer to covalent bonds that link amino acids in a protein chain, so they do not directly contribute to the binding of different subunits in a multi-subunit protein. The binding between subunits is facilitated by non-covalent interactions, such as hydrogen bonds, electrostatic interactions, and hydrophobic interactions.

Question 4

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?
A) Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein.
B) Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected.
C) Hsp70 is most active during cell division phases.
D) Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.

Accepted Answer

Hsp70 uses the energy from ATP binding and hydrolysis to assist in the folding of a protein. This helps to prevent protein misfolding and aggregation, which can lead to diseases such as Alzheimer's and Parkinson's. Hsp70 binds to hydrophobic regions of unfolded or misfolded proteins and uses ATP to create a conformational change in the protein, allowing it to fold correctly.

Question 5

Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures?
A) mutant globule
B) hydrophobic collapse model
C) framework model
D) nucleation model

Accepted Answer

The hydrophobic collapse model describes protein folding as initially driven by the hydrophobic effect, where the non-polar (hydrophobic) amino acid residues move towards the interior, forming a disordered globule. This is followed by the ordering of secondary and tertiary structures.

Question 6

Which gives rise to a favorable enthalpic ($\Delta$S) driving force for protein folding?
A) The lining up of hydrogen bonds as the protein folds.
B) The limiting of possible conformations as the protein folds.
C) The decrease in ordered water molecules as hydrophobic amino acids pack together.
D) The stabilization caused by favorable electrostatic interactions of amino acid side chains.

Accepted Answer

As hydrophobic amino acids pack together, there is a decrease in the ordered water molecules surrounding these non-polar residues. This disruption in the hydrogen bonding network of water molecules leads to an entropy decrease (ΔS<0) which results in a favorable enthalpic (ΔH<0) driving force for protein folding. This phenomenon is known as the hydrophobic effect.

Question 7

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

Accepted Answer

The answer of The essential amino acids in adult humans...

Question 8

Draw the structure of the amino acid glutamate showing the predominant form found at pH 7.0 (assume -NH₃⁺pKa 9.0; Glu pK_R 4.0; -COOH pKa 2.0).

Accepted Answer

The answer of Draw the structure of the amino acid...

Question 9

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?
A) mutant globule
B) hydrophobic collapse model
C) framework model
D) nucleation model

Accepted Answer

The framework model describes protein folding as the initial formation of secondary structures, such as alpha helices and beta sheets, which then come together to form the final tertiary structure. This model emphasizes the importance of these secondary structures as a scaffold for the overall folding process.

Question 10

Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct?
A) GroEL-GroES requires the hydrolysis of multiple ATPs to assist in the folding of a protein.
B) GroEL-GroES recycles misfolded proteins by recovering individual amino acids.
C) GroEL-GroES assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
D) GroEL-GroES uses GroEL as a cap, trapping an unfolded protein in the GroES chamber.

Accepted Answer

GroEL-GroES functions as a molecular chaperone, requiring the hydrolysis of ATP to change its conformation and provide an environment for a protein to correctly fold. It does not recycle proteins into amino acids, assist in protein unfolding by hydrolyzing peptide bonds, or use GroEL as a cap with GroES as the chamber; rather, GroEL forms the chamber and GroES acts as a cap.

Question 11

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?
A) glutamate-aspartate.
B) leucine-aspartate.
C) glutamate-lysine.
D) phenylalaninelysine.

Accepted Answer

Glutamate-lysine interactions contribute to the stability of a dimer at the interface between subunits of a protein with quaternary structure due to the formation of ionic bonds between the negatively charged glutamate and the positively charged lysine.

Question 12

What is the difference between clamp-type and chamber-type chaperone proteins?
A) One uses ATP and the other does not.
B) One folds proteins, whereas the other just protects them from unfolding.
C) They are shaped differently.
D) One type is found extracellularly and one intracellularly.

Accepted Answer

The answer of What is the difference between clamp-type and...

Question 13

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?
A) Remove denaturant first and reductant second.
B) Simultaneously remove denaturant and reductant.
C) Remove reductant first, denaturant second, and then finally add back reductant.
D) Remove reductant first and denaturant second.

Accepted Answer

In the Anfinsen experiment, RNaseA was denatured with urea and beta-mercaptoethanol (reduction) to break disulfide bonds. To achieve an inactive protein, the reducing agent is removed first, followed by the denaturant. This allows disulfide bonds to reform in the incorrect configuration, resulting in an inactive protein. Therefore, the correct order is to remove reductant first and denaturant second.

Question 14

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?
A) detergent and salt
B) urea and $\beta$-mercaptoethanol
C) acid and base
D) ethanol and $\beta$-mercaptoethanol

Accepted Answer

Christian Anfinsen used urea and F1F1F1S1F1F1F10-mercaptoethanol in his experiment to unfold and refold a protein.

Question 15

Cells deal with misfolded proteins by
A) storing them for later energy use.
B) collecting and excreting them from the cell.
C) aggregating them to maintain the cell's structural integrity.
D) degrading them to individual amino acids.

Accepted Answer

Cells deal with misfolded proteins by degrading them to individual amino acids through a process called proteolysis. This is usually carried out by proteases, which are enzymes that break down proteins. Misfolded proteins can be toxic to cells and can lead to diseases such as Alzheimer's and Parkinson's, so degrading them is a crucial mechanism for maintaining cellular health.

Question 16

Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a disease.
A) loss-of-function protein folding
B) chaperonin-unassisted folding
C) gain-of-function protein folding
D) amyloid plaque-forming

Accepted Answer

Cystic fibrosis results from loss-of-function protein folding, where the misfolded proteins are unable to properly insert into the membranes of lung epithelial cells and perform their function.

Question 17

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may
A) waste excessive ATP in attempts to refold them.
B) aggregate and interfere with normal cellular function.
C) eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent.
D) be excreted from the cell rather than recycled for building blocks.

Accepted Answer

Misfolded proteins that are not degraded may aggregate and interfere with normal cellular function. This can lead to misfolding of other proteins, cellular stress, and ultimately cell death.

Question 18

What is a current hypothesis that explains the infectious nature of prion diseases?
A) The virus responsible for prion diseases is transmissible.
B) Unfavorable environmental factors negatively influence healthy cells.
C) The small molecule denaturants found in infected cells are passed on to healthy cells.
D) The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

Accepted Answer

The current hypothesis for the infectious nature of prion diseases is that an improperly folded prion protein known as PrPSc (scrapie form) promotes the misfolding of normal prion proteins (PrPC), leading to the accumulation of PrPSc and the gradual destruction of healthy cells in the brain and nervous system. This misfolding and accumulation process can spread from cell to cell and even between individuals, leading to the infectious nature of prion diseases. This hypothesis is supported by experimental evidence showing that purified PrPSc can promote the conversion of normal PrPC into the misfolded form in vitro, and that the accumulation of PrPSc correlates with the severity of the disease in vivo.

Question 19

The following amino acid is discovered in a newly isolated protein. What would it be called, and does it represent a new amino acid?

Accepted Answer

The answer of The following amino acid is discovered in...

Question 20

Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.

Accepted Answer

The answer of Shown is the titration curve for the...

Quiz 4: Protein Structure

Calculate the pI for the following dipeptide using the pKas shown.

What is believed to be the underlying cause of prion protein plaque formation?

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?

Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures?

Which gives rise to a favorable enthalpic ( $\Delta$ S) driving force for protein folding?

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

Draw the structure of the amino acid glutamate showing the predominant form found at pH 7.0 (assume -NH₃⁺pKa 9.0; Glu pK_R 4.0; -COOH pKa 2.0).

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct?

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

What is the difference between clamp-type and chamber-type chaperone proteins?

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?

Cells deal with misfolded proteins by

Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a disease.

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may

What is a current hypothesis that explains the infectious nature of prion diseases?

The following amino acid is discovered in a newly isolated protein. What would it be called, and does it represent a new amino acid?

Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.

Quiz 4: Protein Structure

Calculate the pI for the following dipeptide using the pKas shown.

What is believed to be the underlying cause of prion protein plaque formation?

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?

Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures?

Which gives rise to a favorable enthalpic ( Δ\DeltaΔ S) driving force for protein folding?

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

Draw the structure of the amino acid glutamate showing the predominant form found at pH 7.0 (assume -NH3+ pKa 9.0; Glu pKR 4.0; -COOH pKa 2.0).

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct?

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

What is the difference between clamp-type and chamber-type chaperone proteins?

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?

Cells deal with misfolded proteins by

Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a disease.

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may

What is a current hypothesis that explains the infectious nature of prion diseases?

The following amino acid is discovered in a newly isolated protein. What would it be called, and does it represent a new amino acid?

Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.

Which gives rise to a favorable enthalpic ( $\Delta$ S) driving force for protein folding?

Draw the structure of the amino acid glutamate showing the predominant form found at pH 7.0 (assume -NH₃⁺pKa 9.0; Glu pK_R 4.0; -COOH pKa 2.0).