Question 1

Proteins unfold (denature) under various experimental conditions, such as heat or presence of _______ in the buffer.

Accepted Answer

Proteins can denature under various conditions, including extreme pH levels, the presence of chemicals like β-mercaptoethanol, urea, and guanidinium hydrochloride. These agents disrupt the non-covalent interactions holding the protein's secondary, tertiary, or quaternary structure, leading to denaturation.

Question 2

Unfolded (denatured) proteins can be re-folded by removing the chemicals in a process called _________.

Accepted Answer

Dialysis is the process used to remove denaturing agents from a solution, allowing proteins to refold into their native conformations.

Question 3

Proteins can be denatured using $\beta$-mercaptoethanol, since this reagent will _____________.

Accepted Answer

?-mercaptoethanol is used to reduce disulfide bonds in proteins, leading to their denaturation by disrupting the protein's tertiary structure.

Question 4

Proteins containing ________ residues may not re-fold properly.

Accepted Answer

Proteins with numerous cysteine residues may not re-fold properly because cysteine can form disulfide bonds, which are crucial for the protein's tertiary structure. If a protein is denatured and then attempts to refold, incorrect disulfide bonds can form, leading to improper folding.

Question 5

Given a peptide: Salt bridges will form in this peptide in a buffer at pH 7 between: I. the amino terminus -NH₃⁺ and the carboxy terminus -COO^- II. the side chain of Asp6 and the amino terminus -NH₃⁺ III. the side chains of Ser6 and Gln9 IV. the side chain of His13 and the carboxy terminus -COO^- V. the side chains of Gln9 and His13

Accepted Answer

The answer of Given a peptide: 
Salt bridges will form...

Question 6

Given a peptide:  Disulfide bonds will form between the side chains of ______ in a buffer at pH 7 (under oxidizing conditions).

Accepted Answer

The answer of Given a peptide:  Disulfide bonds will...

Question 7

Given a peptide: 
Hydrogen bonds will form in this peptide in a buffer at pH 7 between:

Accepted Answer

The answer of Given a peptide: 
Hydrogen bonds will form...

Question 8

Several neurodegenerative diseases (Alzheimer's, Parkinson's, etc.) present __________ structures at the molecular level.

Accepted Answer

The answer of Several neurodegenerative diseases (Alzheimer's, Parkinson's, etc.) present...

Question 9

The 3D solution structure of a 20mer peptide could be determined by_________.

Accepted Answer

Multidimensional NMR (Nuclear Magnetic Resonance) spectroscopy is a powerful technique for determining the 3D structure of small proteins and peptides in solution, making it suitable for a 20mer peptide.

Question 10

The thermodynamic stabilization of the protein in folded state is partly due to the hydrophobic effect that accompanies protein folding. The hydrophobic effect in proteins is manifested in ________ and _________.

Accepted Answer

The hydrophobic effect in proteins involves the burial of exposed hydrophobic side chains away from the aqueous environment and the release of water molecules that were previously structured around these hydrophobic regions. This process contributes to the thermodynamic stability of the folded protein structure.

Question 11

Forming bonds _______ energy. Thus, formation of numerous _______ during protein folding contributes to the stability of the folded structure.

Accepted Answer

Forming bonds releases energy, and hydrogen bonds are significant contributors to the stability of protein structures during folding.

Question 12

During protein folding the entropy of the solvent molecules _______.

Accepted Answer

During protein folding, the entropy of the solvent molecules, typically water, increases. This is because as the protein folds into its native structure, hydrophobic amino acid residues tend to be buried in the interior of the protein, reducing their contact with water. This leads to a more ordered arrangement of water molecules around the hydrophobic regions when they are exposed, and as these regions become buried, the water molecules are no longer as constrained and can move more freely, thus increasing the entropy of the solvent.

Question 13

The most stable 3D protein structure has the ______ free energy, and is therefore assumed to be the native conformation of the protein.

Accepted Answer

The most stable 3D protein structure is the one with the lowest free energy, as this indicates a state of minimal energy and maximal stability, which is characteristic of the native conformation of a protein.

Question 14

The ___________ sequence is needed to predict the 3D structure of a relatively small protein using de novo structure prediction software.

Accepted Answer

The amino acid sequence of a protein is essential for predicting its 3D structure using de novo structure prediction software. This is because the sequence of amino acids determines the protein's folding and ultimately its function.

Question 15

_____ of protein structures is a useful tool in building 3D structures for proteins that do not have a solved x-ray structure. It uses the x-ray structure of a related protein as a template and the amino acid sequence of the protein of interest.

Accepted Answer

Homology modeling is the correct answer because it involves using the structure of a related protein (the template) to predict the 3D structure of another protein based on its amino acid sequence. This method is particularly useful for proteins that do not have a solved x-ray crystallography structure.

Question 16

Molecular dynamics simulations can be used to model the sequence in which the _____ structure of a protein forms during protein folding.

Accepted Answer

The answer of Molecular dynamics simulations can be used to...

Question 17

Protein folding can be described in terms of energy, and visualized by an energy funnel diagram .The width of the funnel is given by the________.

Accepted Answer

The width of the energy funnel in protein folding diagrams represents the number of conformational states of the protein. As the protein folds, it explores a variety of conformations, with the width of the funnel indicating the diversity of these states at different energy levels.

Question 18

Depositing falsified protein structure data into the Protein Data Bank, PDB, is a huge disservice to the scientific community because it leads to ___________.

Accepted Answer

Depositing falsified protein structure data into the Protein Data Bank (PDB) can mislead scientific research and drug discovery efforts, leading to incorrect conclusions about protein-drug interactions. This not only wastes time and financial resources but can also result in the retraction of publications based on incorrect data, affecting the entire scientific community negatively.

Question 19

Whistleblowers are in general protected from being fired from the job by __________.

Accepted Answer

The answer of Whistleblowers are in general protected from being...

Quiz 20: Designer Proteins and Protein Folding

Proteins unfold (denature) under various experimental conditions, such as heat or presence of _______ in the buffer.

Unfolded (denatured) proteins can be re-folded by removing the chemicals in a process called _________.

Proteins can be denatured using $\beta$ -mercaptoethanol, since this reagent will _____________.

Proteins containing ________ residues may not re-fold properly.

Given a peptide: Disulfide bonds will form between the side chains of ______ in a buffer at pH 7 (under oxidizing conditions) .

Given a peptide: Hydrogen bonds will form in this peptide in a buffer at pH 7 between:

Several neurodegenerative diseases (Alzheimer's, Parkinson's, etc.) present __________ structures at the molecular level.

The 3D solution structure of a 20mer peptide could be determined by_________.

The thermodynamic stabilization of the protein in folded state is partly due to the hydrophobic effect that accompanies protein folding. The hydrophobic effect in proteins is manifested in and _.

Forming bonds _ energy. Thus, formation of numerous _ during protein folding contributes to the stability of the folded structure.

During protein folding the entropy of the solvent molecules _______.

The most stable 3D protein structure has the ______ free energy, and is therefore assumed to be the native conformation of the protein.

The ___________ sequence is needed to predict the 3D structure of a relatively small protein using de novo structure prediction software.

_____ of protein structures is a useful tool in building 3D structures for proteins that do not have a solved x-ray structure. It uses the x-ray structure of a related protein as a template and the amino acid sequence of the protein of interest.

Molecular dynamics simulations can be used to model the sequence in which the _____ structure of a protein forms during protein folding.

Protein folding can be described in terms of energy, and visualized by an energy funnel diagram .The width of the funnel is given by the________.

Depositing falsified protein structure data into the Protein Data Bank, PDB, is a huge disservice to the scientific community because it leads to ___________.

Whistleblowers are in general protected from being fired from the job by __________.

Quiz 20: Designer Proteins and Protein Folding

Proteins unfold (denature) under various experimental conditions, such as heat or presence of _______ in the buffer.

Unfolded (denatured) proteins can be re-folded by removing the chemicals in a process called _________.

Proteins can be denatured using β\betaβ -mercaptoethanol, since this reagent will _____________.

Proteins containing ________ residues may not re-fold properly.

Given a peptide: Disulfide bonds will form between the side chains of ______ in a buffer at pH 7 (under oxidizing conditions) .

Given a peptide: Hydrogen bonds will form in this peptide in a buffer at pH 7 between:

Several neurodegenerative diseases (Alzheimer's, Parkinson's, etc.) present __________ structures at the molecular level.

The 3D solution structure of a 20mer peptide could be determined by_________.

The thermodynamic stabilization of the protein in folded state is partly due to the hydrophobic effect that accompanies protein folding. The hydrophobic effect in proteins is manifested in ________ and _________.

Forming bonds _______ energy. Thus, formation of numerous _______ during protein folding contributes to the stability of the folded structure.

During protein folding the entropy of the solvent molecules _______.

The most stable 3D protein structure has the ______ free energy, and is therefore assumed to be the native conformation of the protein.

The ___________ sequence is needed to predict the 3D structure of a relatively small protein using de novo structure prediction software.

_____ of protein structures is a useful tool in building 3D structures for proteins that do not have a solved x-ray structure. It uses the x-ray structure of a related protein as a template and the amino acid sequence of the protein of interest.

Molecular dynamics simulations can be used to model the sequence in which the _____ structure of a protein forms during protein folding.

Protein folding can be described in terms of energy, and visualized by an energy funnel diagram .The width of the funnel is given by the________.

Depositing falsified protein structure data into the Protein Data Bank, PDB, is a huge disservice to the scientific community because it leads to ___________.

Whistleblowers are in general protected from being fired from the job by __________.

Proteins can be denatured using $\beta$ -mercaptoethanol, since this reagent will _____________.

The thermodynamic stabilization of the protein in folded state is partly due to the hydrophobic effect that accompanies protein folding. The hydrophobic effect in proteins is manifested in and _.

Forming bonds _ energy. Thus, formation of numerous _ during protein folding contributes to the stability of the folded structure.