Question 1

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

Accepted Answer

Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents,removal of those conditions will reestablish the original aqueous environment,often permitting the protein to fold once again into its native conformation.If the protein does not renature,it may be because the denaturing treatment removed a required prosthetic group,or because the normal folding pathway requires the presence of a polypeptide chain binding protein or molecular chaperone.The normal folding pathway could also be mediated by a larger polypeptide,which is then cleaved (e.g. ,insulin).Denatured insulin would not refold easily.

Question 2

In an aqueous solution,protein conformation is determined by two major factors.One is the formation of the maximum number of hydrogen bonds.The other is the:

Accepted Answer

A) formation of the maximum number of hydrophilic interactions. 
B) maximization of ionic interactions. 
C) minimization of entropy by the formation of a water solvent shell around the protein. 
D) placement of hydrophobic amino acid residues within the interior of the protein. 
E) placement of polar amino acid residues around the exterior of the protein. 
A) formation of the maximum number of hydrophilic interactions. 
B) maximization of ionic interactions. 
C) minimization of entropy by the formation of a water solvent shell around the protein. 
D) placement of hydrophobic amino acid residues within the interior of the protein. 
E) placement of polar amino acid residues around the exterior of the protein. D

Question 3

How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.

Accepted Answer

The protein is crystallized,and the crystal structure is determined by x-ray diffraction.The pattern of diffracted x-rays yields,by Fourier transformation,the three-dimensional distribution of electron density.By matching electron density with the known sequence of amino acids in the protein,each region of electron density is identified as a single atom.Sometimes,the three-dimensional structure of a small protein or peptide can be determined in solution by sophisticated analysis of the NMR spectrum of the polypeptide.This technique can also reveal dynamic aspects of protein structure such as conformational changes.Computer analysis of multi-dimensional NMR spectra can be used to generate a picture of the three-dimensional structure of a protein.A three dimensional structure can also be determined by cryo-electron microscopy.

Question 4

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

In the unfolded polypeptide,there are or

Question 5

Which of the following best represents the backbone arrangement of two peptide bonds?

Accepted Answer

A) C $\alpha$ -N-C $\alpha$ -C-C $\alpha$ -N-C $\alpha$ -C 
B) C $\alpha$ -N-C-C-N-C $\alpha$   
C) C-N-C $\alpha$ -C $\alpha$ -C-N 
D) C $\alpha$ -C-N-C $\alpha$ -C-N 
E) C $\alpha$ -C $\alpha$ -C-N-C $\alpha$ -C $\alpha$ -C 
A) C $\alpha$ -N-C $\alpha$ -C-C $\alpha$ -N-C $\alpha$ -C 
B) C $\alpha$ -N-C-C-N-C $\alpha$   
C) C-N-C $\alpha$ -C $\alpha$ -C-N 
D) C $\alpha$ -C-N-C $\alpha$ -C-N 
E) C $\alpha$ -C $\alpha$ -C-N-C $\alpha$ -C $\alpha$ -C

Question 6

Pauling and Corey showed that in small peptides,six atoms associated with the peptide bond all lie in a plane.Draw a dipeptide of two amino acids in trans linkage (side-chains can be shown as -R),and indicate which six atoms are part of the planar structure of the peptide bond.

Accepted Answer

The N and H of the amino and t

Question 7

Which of the following statements about oligomeric proteins is false?

Accepted Answer

A) A subunit may be similar to other proteins. 
B) All subunits must be identical. 
C) Many have regulatory roles. 
D) Some oligomeric proteins can further associate into large fibers. 
E) Some subunits may have nonprotein prosthetic groups. 
A) A subunit may be similar to other proteins. 
B) All subunits must be identical. 
C) Many have regulatory roles. 
D) Some oligomeric proteins can further associate into large fibers. 
E) Some subunits may have nonprotein prosthetic groups.

Question 8

Kendrew's studies of the globular myoglobin structure demonstrated that:

Accepted Answer

A) "corners" between $\alpha$-helical regions invariably lacked proline residue. 
B) highly polar or charged amino-acid residues tended to be located interiorally. 
C) myoglobin was completely different from hemoglobin,as expected. 
D) the structure was very compact,with virtually no internal space available for water. 
E) the $\alpha$ helix predicted by Pauling and Corey was not found in myoglobin. 
A) "corners" between $\alpha$-helical regions invariably lacked proline residue. 
B) highly polar or charged amino-acid residues tended to be located interiorally. 
C) myoglobin was completely different from hemoglobin,as expected. 
D) the structure was very compact,with virtually no internal space available for water. 
E) the $\alpha$ helix predicted by Pauling and Corey was not found in myoglobin.

Question 9

Which of the following is least likely to result in protein denaturation?

Accepted Answer

A) Altering net charge by changing pH 
B) Changing the salt concentration 
C) Disruption of weak interactions by boiling 
D) Exposure to detergents 
E) Mixing with organic solvents such as acetone 
A) Altering net charge by changing pH 
B) Changing the salt concentration 
C) Disruption of weak interactions by boiling 
D) Exposure to detergents 
E) Mixing with organic solvents such as acetone

Question 10

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

Accepted Answer

Hydrophobic amino acid residue

Question 11

The $\alpha$-keratin chains indicated by the diagram below have undergone one chemical step.To alter the shape of the $\alpha$-keratin chains-as in hair waving-what subsequent steps are required?

Accepted Answer

A) Chemical oxidation and then shape remodeling 
B) Chemical reduction and then chemical oxidation 
C) Chemical reduction and then shape remodeling 
D) Shape remodeling and then chemical oxidation 
E) Shape remodeling and then chemical reduction 
A) Chemical oxidation and then shape remodeling 
B) Chemical reduction and then chemical oxidation 
C) Chemical reduction and then shape remodeling 
D) Shape remodeling and then chemical oxidation 
E) Shape remodeling and then chemical reduction

Question 12

Protein secondary structure $\beta$ 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 13

The major reason that antiparallel $\beta$-stranded protein structures are more stable than parallel $\beta$-stranded structures is that the latter:

Accepted Answer

A) are in a slightly less extended configuration than antiparallel strands. 
B) do not have as many disulfide crosslinks between adjacent strands. 
C) do not stack in sheets as well as antiparallel strands. 
D) have fewer lateral hydrogen bonds than antiparallel strands. 
E) have weaker hydrogen bonds laterally between adjacent strands. 
A) are in a slightly less extended configuration than antiparallel strands. 
B) do not have as many disulfide crosslinks between adjacent strands. 
C) do not stack in sheets as well as antiparallel strands. 
D) have fewer lateral hydrogen bonds than antiparallel strands. 
E) have weaker hydrogen bonds laterally between adjacent strands.

Question 14

What important concepts regarding protein thermal denaturation can be inferred from the egg white of a boiled egg?

Accepted Answer

1)Denatured proteins often pre

Question 15

Describe three of the important features of the $\alpha$-helical polypeptide structure predicted by Pauling and Corey.Provide one or two sentences for each feature.

Accepted Answer

The @#LAT-DLM&-helical structure of a polypeptide

Question 16

Draw the hydrogen bonding typically found between two residues in an $\alpha$ helix.

Accepted Answer

Hydrogen bonds occur between e

Question 17

A d-amino acid would interrupt an $\alpha$ helix made of l-amino acids.Another naturally occurring hindrance to the formation of an$\alpha$ helix is the presence of:

Accepted Answer

A) a negatively charged Arg residue. 
B) a nonpolar residue near the carboxyl terminus. 
C) a positively charged Lys residue. 
D) a Pro residue. 
E) two Ala residues side by side. 
A) a negatively charged Arg residue. 
B) a nonpolar residue near the carboxyl terminus. 
C) a positively charged Lys residue. 
D) a Pro residue. 
E) two Ala residues side by side.

Question 18

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 19

What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?

Accepted Answer

Each different polypeptide requires a se

Question 20

In the $\alpha$ helix the hydrogen bonds:

Accepted Answer

A) are roughly parallel to the axis of the helix. 
B) are roughly perpendicular to the axis of the helix. 
C) occur mainly between electronegative atoms of the R groups. 
D) occur only between some of the amino acids of the helix. 
E) occur only near the amino and carboxyl termini of the helix. 
A) are roughly parallel to the axis of the helix. 
B) are roughly perpendicular to the axis of the helix. 
C) occur mainly between electronegative atoms of the R groups. 
D) occur only between some of the amino acids of the helix. 
E) occur only near the amino and carboxyl termini of the helix.

Exam 4: The Three-Dimensional Structure of Proteins

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

In an aqueous solution,protein conformation is determined by two major factors.One is the formation of the maximum number of hydrogen bonds.The other is the:

How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.

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?

Which of the following best represents the backbone arrangement of two peptide bonds?

Pauling and Corey showed that in small peptides,six atoms associated with the peptide bond all lie in a plane.Draw a dipeptide of two amino acids in trans linkage (side-chains can be shown as -R),and indicate which six atoms are part of the planar structure of the peptide bond.

Which of the following statements about oligomeric proteins is false?

Kendrew's studies of the globular myoglobin structure demonstrated that:

Which of the following is least likely to result in protein denaturation?

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

The α\alphaα -keratin chains indicated by the diagram below have undergone one chemical step.To alter the shape of the α\alphaα -keratin chains-as in hair waving-what subsequent steps are required?

Protein secondary structure β\betaβ turn are:

The major reason that antiparallel β\betaβ -stranded protein structures are more stable than parallel β\betaβ -stranded structures is that the latter:

What important concepts regarding protein thermal denaturation can be inferred from the egg white of a boiled egg?

Describe three of the important features of the α\alphaα -helical polypeptide structure predicted by Pauling and Corey.Provide one or two sentences for each feature.

Draw the hydrogen bonding typically found between two residues in an α\alphaα helix.

A d-amino acid would interrupt an α\alphaα helix made of l-amino acids.Another naturally occurring hindrance to the formation of an α\alphaα helix is the presence of:

Which statement about intrinsically disordered proteins is true?

What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?

In the α\alphaα helix the hydrogen bonds:

The Foundations of Biochemistry

Water

Amino Acids, peptides, and Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

Recombinant Dna Technology

Lipids

Biological Membranes and Transport

Biosignaling

Principles of Bioenergetics

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

Integration and Hormonal Regulation of Mammalian Metabolism

Genes and Chromosomes

Dna Metabolism

Rna Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

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

Protein secondary structure $\beta$ turn are:

The major reason that antiparallel $\beta$ -stranded protein structures are more stable than parallel $\beta$ -stranded structures is that the latter:

Describe three of the important features of the $\alpha$ -helical polypeptide structure predicted by Pauling and Corey.Provide one or two sentences for each feature.

Draw the hydrogen bonding typically found between two residues in an $\alpha$ helix.

A d-amino acid would interrupt an $\alpha$ helix made of l-amino acids.Another naturally occurring hindrance to the formation of an $\alpha$ helix is the presence of:

In the $\alpha$ helix the hydrogen bonds: