Question 1

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. E

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

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

Accepted Answer

The egg white of a boiled egg provides important insights into the concept of protein thermal denaturation. When an egg is boiled, the heat causes the proteins in the egg white to unfold and change their three-dimensional structure. This process, known as denaturation, is irreversible and results in the solidification of the egg white.

From this, we can infer several important concepts regarding protein thermal denaturation. Firstly, we can understand that proteins are sensitive to heat and that high temperatures can cause them to lose their functional shape. This highlights the importance of temperature control in food preparation and the potential impact of heat on the nutritional value of proteins.

Additionally, the irreversible nature of protein denaturation in the egg white demonstrates that once proteins have been denatured, they cannot return to their original state. This has implications for the cooking and processing of foods, as well as for the stability of proteins in various industrial and scientific applications.

Furthermore, the change in texture and appearance of the egg white after boiling illustrates how denaturation can alter the physical properties of proteins. This can be applied to understanding the behavior of proteins in various culinary, pharmaceutical, and biotechnological contexts.

In conclusion, the egg white of a boiled egg provides valuable insights into the concept of protein thermal denaturation, highlighting the sensitivity of proteins to heat, the irreversible nature of denaturation, and the impact of this process on the physical and functional properties of proteins.

Question 4

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 5

Which method would be MOST useful to solve the structure of a small, soluble protein that does not 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 6

Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure.

Accepted Answer

A)  primary 
B)  secondary 
C)  tertiary 
D)  quaternary 
E)  globular 
A)  primary 
B)  secondary 
C)  tertiary 
D)  quaternary 
E)  globular

Question 7

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

Accepted Answer

Silk fibroin, the core protein in silk f

Question 8

As humans age, their connective tissue, rich in collagen, becomes more rigid and brittle. What is the molecular cause of this change?

Accepted Answer

A)  Collagen fibrils change their degree of supercoiling over time. 
B)  Many older adults have vitamin C deficiencies that result in collagen oxidation. 
C)  As cells age, a variant of collagen is expressed. 
D)  Crosslinks between collagen fibrils accumulate over time. 
E)  UV damage to collagen accumulates over time. 
A)  Collagen fibrils change their degree of supercoiling over time. 
B)  Many older adults have vitamin C deficiencies that result in collagen oxidation. 
C)  As cells age, a variant of collagen is expressed. 
D)  Crosslinks between collagen fibrils accumulate over time. 
E)  UV damage to collagen accumulates over time.

Question 9

Which residues are MOST likely to be enriched in an intrinsically disordered protein that is soluble in water?

Accepted Answer

A)  Y, K, W 
B)  E, C, F 
C)  V, I, L 
D)  R, K, A 
E)  H, F, W 
A)  Y, K, W 
B)  E, C, F 
C)  V, I, L 
D)  R, K, A 
E)  H, F, W

Question 10

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

The primary sequence of a protein, which

Question 11

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 12

What is the CORRECT way to classify the protein below according to its secondary-structure elements?

Accepted Answer

A)  all $\beta$ 
B)  $\alpha$ + $\beta$ 
C)  $\alpha$/$\beta$0 
D) $\beta$/$\alpha$/$\beta$ 
E)  $\alpha$/$\beta$/$\alpha$ 
A)  all $\beta$ 
B)  $\alpha$ + $\beta$ 
C)  $\alpha$/$\beta$0 
D) $\beta$/$\alpha$/$\beta$ 
E)  $\alpha$/$\beta$/$\alpha$

Question 13

Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a _____ for protein S.

Accepted Answer

A)  proteasome 
B)  molecular chaperone 
C)  protein precursor 
D)  structural motif 
E)  supersecondary structural unit 
A)  proteasome 
B)  molecular chaperone 
C)  protein precursor 
D)  structural motif 
E)  supersecondary structural unit

Question 14

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and -180 degrees, respectively.

Accepted Answer

A)  right-handed$\alpha$ helix 
B)  left-handed $\alpha$ helix 
C)  $\beta$ sheet 
D)  twisted $\beta$ sheets 
E)  Amino acids will not adopt this conformation 
A)  right-handed$\alpha$ helix 
B)  left-handed $\alpha$ helix 
C)  $\beta$ sheet 
D)  twisted $\beta$ sheets 
E)  Amino acids will not adopt this conformation

Question 15

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and 60 degrees, respectively.

Accepted Answer

A)  right-handed $\alpha$ helix 
B)  left-handed $\alpha$ helix 
C)  $\beta$ sheet 
D)  twisted $\beta$sheets 
E)  Amino acids will not adopt this conformation. 
A)  right-handed $\alpha$ helix 
B)  left-handed $\alpha$ helix 
C)  $\beta$ sheet 
D)  twisted $\beta$sheets 
E)  Amino acids will not adopt this conformation.

Question 16

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

1. The @#LAT-DLM&-helical polypeptide structure pr

Question 17

Which method would be BEST to use to monitor protein secondary structure during the titration of a denaturing agent?

Accepted Answer

A)  x-ray crystallography 
B)  electron microscopy 
C)  circular dichroism 
D)  mass spectrometry 
E)  liquid chromatography 
A)  x-ray crystallography 
B)  electron microscopy 
C)  circular dichroism 
D)  mass spectrometry 
E)  liquid chromatography

Question 18

The dimensions of an $\alpha$ helix from a fibrous protein such as keratin differ slightly from an $\alpha$ helix from a globular protein. What is the reason for this difference in helical dimensions?

Accepted Answer

A)  An $\alpha$ helix from a fibrous protein is left-handed, not right-handed. 
B)  An $\alpha$ helix from a fibrous protein contains mainly hydrophobic residues, elongating the helix. 
C)  An $\alpha$ helix from a fibrous protein contains mainly polar residues, elongating the helix. 
D)  An$\alpha$ helix from a fibrous protein forms a coiled-coil, distorting the helix. 
E)  An $\alpha$ helix from a fibrous protein contains mainly Gly residues for more efficient packing. 
A)  An $\alpha$ helix from a fibrous protein is left-handed, not right-handed. 
B)  An $\alpha$ helix from a fibrous protein contains mainly hydrophobic residues, elongating the helix. 
C)  An $\alpha$ helix from a fibrous protein contains mainly polar residues, elongating the helix. 
D)  An$\alpha$ helix from a fibrous protein forms a coiled-coil, distorting the helix. 
E)  An $\alpha$ helix from a fibrous protein contains mainly Gly residues for more efficient packing.

Question 19

Which statement 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 20

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.

Exam 4: The Three-Dimensional Structure of Proteins

An α\alphaα helix would be destabilized most by:

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:

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

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

Which method would be MOST useful to solve the structure of a small, soluble protein that does not easily form a repeating structure?

Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure.

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

As humans age, their connective tissue, rich in collagen, becomes more rigid and brittle. What is the molecular cause of this change?

Which residues are MOST likely to be enriched in an intrinsically disordered protein that is soluble in water?

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."

An average protein will NOT be denatured by:

What is the CORRECT way to classify the protein below according to its secondary-structure elements?

Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a _____ for protein S.

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and -180 degrees, respectively.

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi and psi angles of -90 and 60 degrees, respectively.

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.

Which method would be BEST to use to monitor protein secondary structure during the titration of a denaturing agent?

The dimensions of an α\alphaα helix from a fibrous protein such as keratin differ slightly from an α\alphaα helix from a globular protein. What is the reason for this difference in helical dimensions?

Which statement about oligomeric proteins is FALSE?

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

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

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

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

The dimensions of an $\alpha$ helix from a fibrous protein such as keratin differ slightly from an $\alpha$ helix from a globular protein. What is the reason for this difference in helical dimensions?