Question 1

Which of the following is not an appropriate description for van der Waals interactions?

Accepted Answer

A) They involve dipole-dipole interactions. 
B) Their strength depends on the distance between the two interacting atoms. 
C) They are highly specific. 
D) An individual van der Waals interaction does not contribute significantly to the stability of a protein. 
E) They can involve hydrophobic amino acids. 
A) They involve dipole-dipole interactions. 
B) Their strength depends on the distance between the two interacting atoms. 
C) They are highly specific. 
D) An individual van der Waals interaction does not contribute significantly to the stability of a protein. 
E) They can involve hydrophobic amino acids.

Question 2

Why is silk fibroin so strong,but at the same time so soft and flexible?

Accepted Answer

Unlike collagen and keratin,silk fibroin

Question 3

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

Accepted Answer

Hydrophobic amino acid residues cluster

Question 4

Proteins often have regions that can fold and function as an independent entity from the whole protein.These regions are called:

Accepted Answer

A) domains. 
B) oligomers. 
C) peptides. 
D) sites. 
E) subunits. 
A) domains. 
B) oligomers. 
C) peptides. 
D) sites. 
E) subunits.

Question 5

Thr and/or Leu residues tend to disrupt an $\alpha$ helix when they occur next to each other in a protein because:

Accepted Answer

A) an amino acids like Thr is highly hydrophobic. 
B) covalent interactions may occur between the Thr side chains. 
C) electrostatic repulsion occurs between the Thr side chains. 
D) steric hindrance occurs between the bulky Thr side chains. 
E) the R group of Thr can form a hydrogen bond. 
A) an amino acids like Thr is highly hydrophobic. 
B) covalent interactions may occur between the Thr side chains. 
C) electrostatic repulsion occurs between the Thr side chains. 
D) steric hindrance occurs between the bulky Thr side chains. 
E) the R group of Thr can form a hydrogen bond.

Question 6

Experiments on denaturation and renaturation after the reduction and reoxidation of the -S-S- bonds in the enzyme ribonuclease (RNase)have shown that:

Accepted Answer

A) folding of denatured RNase into the native,active conformation,requires the input of energy in the form of heat. 
B) native ribonuclease does not have a unique secondary and tertiary structure. 
C) the completely unfolded enzyme,with all -S-S- bonds broken,is still enzymatically active. 
D) the enzyme,dissolved in water,is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. 
E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure. 
A) folding of denatured RNase into the native,active conformation,requires the input of energy in the form of heat. 
B) native ribonuclease does not have a unique secondary and tertiary structure. 
C) the completely unfolded enzyme,with all -S-S- bonds broken,is still enzymatically active. 
D) the enzyme,dissolved in water,is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. 
E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.

Question 7

Any given protein is characterized by a unique amino acid sequence (primary structure)and three-dimensional (tertiary)structure.How are these related?

Accepted Answer

The three-dimensional structure is deter

Question 8

Each of the following reagents or conditions will denature a protein.For each,describe in one or two sentences what the reagent/condition does to destroy native protein structure.
(a)urea
(b)high temperature
(c)detergent
(d)low pH

Accepted Answer

(a)Urea acts primarily by disrupting hyd

Question 9

Which of the following statements concerning protein domains is true?

Accepted Answer

A) They are a form of secondary structure. 
B) They are examples of structural motifs. 
C) They consist of separate polypeptide chains (subunits). 
D) They have been found only in prokaryotic proteins. 
E) They may retain their correct shape even when separated from the rest of the protein. 
A) They are a form of secondary structure. 
B) They are examples of structural motifs. 
C) They consist of separate polypeptide chains (subunits). 
D) They have been found only in prokaryotic proteins. 
E) They may retain their correct shape even when separated from the rest of the protein.

Question 10

Describe three of the important features of a $\beta$ sheet polypeptide structure.Provide one or two sentences for each feature.

Accepted Answer

In the @#LAT-DLM& sheet structure,several extended

Question 11

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 12

Explain (succinctly)the theoretical and/or experimental arguments in support of this statement: "The primary sequence of a protein determines its three-dimensional shape and thus its function."

Accepted Answer

Anfinsen showed that a complet

Question 13

Which of the following statements concerning the process of spontaneous folding of proteins is false?

Accepted Answer

A) It may be an essentially random process. 
B) It may be defective in some human diseases. 
C) It may involve a gradually decreasing range of conformational species. 
D) It may involve initial formation of a highly compact state. 
E) It may involve initial formation of local secondary structure. 
A) It may be an essentially random process. 
B) It may be defective in some human diseases. 
C) It may involve a gradually decreasing range of conformational species. 
D) It may involve initial formation of a highly compact state. 
E) It may involve initial formation of local secondary structure.

Question 14

Pauling and Corey's studies of the peptide bond showed that:

Accepted Answer

A) at pH 7,many different peptide bond conformations are equally probable. 
B) peptide bonds are essentially planar,with no rotation about the C-N axis. 
C) peptide bonds in proteins are unusual,and unlike those in small model compounds. 
D) peptide bond structure is extraordinarily complex. 
E) primary structure of all proteins is similar,although the secondary and tertiary structure may differ greatly. 
A) at pH 7,many different peptide bond conformations are equally probable. 
B) peptide bonds are essentially planar,with no rotation about the C-N axis. 
C) peptide bonds in proteins are unusual,and unlike those in small model compounds. 
D) peptide bond structure is extraordinarily complex. 
E) primary structure of all proteins is similar,although the secondary and tertiary structure may differ greatly.

Question 15

What are two mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?

Accepted Answer

Chaperones protect unfolded po

Question 16

In superhelical proteins,such as collagen,several polypeptide helices are intertwined.What is the function of this superhelical twisting?

Accepted Answer

The superhelical twisting of m

Question 17

Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.

Accepted Answer

To obtain an x-ray picture of a biomolec

Question 18

An $\alpha$helix would be destabilized most by:

Accepted Answer

A) an electric dipole spanning several peptide bonds throughout the $\alpha$ helix. 
B) interactions between neighboring Asp and Arg residues. 
C) interactions between two adjacent hydrophobic Val residues. 
D) the presence of an Arg residue near the carboxyl terminus of the $\alpha$ helix. 
E) the presence of two Lys residues near the amino terminus of the $\alpha$ helix. 
A) an electric dipole spanning several peptide bonds throughout the $\alpha$ helix. 
B) interactions between neighboring Asp and Arg residues. 
C) interactions between two adjacent hydrophobic Val residues. 
D) the presence of an Arg residue near the carboxyl terminus of the $\alpha$ helix. 
E) the presence of two Lys residues near the amino terminus of the $\alpha$ helix.

Question 19

An average protein will not be denatured by:

Accepted Answer

A) a detergent such as sodium dodecyl sulfate. 
B) heating to 90°C. 
C) iodoacetic acid. 
D) pH 10. 
E) urea. 
A) a detergent such as sodium dodecyl sulfate. 
B) heating to 90°C. 
C) iodoacetic acid. 
D) pH 10. 
E) urea.

Question 20

How can changes in pH alter the conformation of a protein?

Accepted Answer

Changes in pH can influence the extent t

Exam 4: The Three-Dimensional Structure of Proteins

Which of the following is not an appropriate description for van der Waals interactions?

Why is silk fibroin so strong,but at the same time so soft and flexible?

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

Proteins often have regions that can fold and function as an independent entity from the whole protein.These regions are called:

Thr and/or Leu residues tend to disrupt an α\alphaα helix when they occur next to each other in a protein because:

Experiments on denaturation and renaturation after the reduction and reoxidation of the -S-S- bonds in the enzyme ribonuclease (RNase)have shown that:

Any given protein is characterized by a unique amino acid sequence (primary structure)and three-dimensional (tertiary)structure.How are these related?

Each of the following reagents or conditions will denature a protein.For each,describe in one or two sentences what the reagent/condition does to destroy native protein structure. (a)urea (b)high temperature (c)detergent (d)low pH

Which of the following statements concerning protein domains is true?

Describe three of the important features of a β\betaβ sheet polypeptide structure.Provide one or two sentences for each feature.

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):

Explain (succinctly)the theoretical and/or experimental arguments in support of this statement: "The primary sequence of a protein determines its three-dimensional shape and thus its function."

Which of the following statements concerning the process of spontaneous folding of proteins is false?

Pauling and Corey's studies of the peptide bond showed that:

What are two mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?

In superhelical proteins,such as collagen,several polypeptide helices are intertwined.What is the function of this superhelical twisting?

Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.

An α\alphaα helix would be destabilized most by:

An average protein will not be denatured by:

How can changes in pH alter the conformation of a protein?

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

Thr and/or Leu residues tend to disrupt an $\alpha$ helix when they occur next to each other in a protein because:

Describe three of the important features of a $\beta$ sheet polypeptide structure.Provide one or two sentences for each feature.

An $\alpha$ helix would be destabilized most by: