BIOCHEM CHAP 4
All of the following are considered “weak” interactions in proteins except:
Hydrogen bonds
Hydrophobic interactions
Ionic bonds
Peptide bonds
Van der waals forces
The most important contribution to the stability of a protein’s conformation appears to be the:
Entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
Maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
Sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.
Sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
Stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.
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:
Formation of the maximum number of hydrophilic interactions.
Maximization of ionic interactions.
Minimization of entropy by the formation of a water solvent shell around the protein.
Placement of hydrophobic amino acid residues within the interior of the protein.
Placement of polar amino acid residues around the exterior of the protein.
Which of the following is not an appropriate description for van der Waals interactions?
They involve dipole-dipole interactions.
Their strength depends on the distance between the two interacting atoms.
They are highly specific.
A) An individual van der Waals interaction does not contribute significantly to the stability of a protein.
A) They can involve hydrophobic amino acids.
Which statement about intrinsically disordered proteins is true?
They contain small hydrophobic cores.
They represent misfolded conformations of cellular proteins.
They have no stable three-dimensional structure and therefore have no cellular function.
They are responsible for proteostasis.
They can interact with multiple protein-binding partners and are central to protein interaction networks.
Pauling and Corey’s studies of the peptide bond showed that:
At pH 7, many different peptide bond conformations are equally probable.
Peptide bonds are essentially planar, with no rotation about the C—N axis.
Peptide bonds in proteins are unusual, and unlike those in small model compounds.
Peptide bond structure is extraordinarily complex.
Primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly.
In the diagram below, the plane drawn behind the peptide bond indicates the:
Absence of rotation around the C—N bond because of its partial double-bond character.
Plane of rotation around the C—N bond.
Region of steric hindrance determined by the large C=O group.
Region of the peptide bond that contributes to a Ramachandran plot.
Theoretical space between –180 and +180 degrees that can be occupied by the and angles in the peptide bond.
Which of the following best represents the backbone arrangement of two peptide bonds?
C—N—C—C—C—N—C—C
C—N—C—C—N—C
C—N—C—C—C—N
C—C—N—C—C—N
C—C—C—N—C—C—C
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
C—C and N—C
C=O and N—C
C=O and N—C
N—C and C—C
N—C and N—C
In the helix the hydrogen bonds:
A) are roughly parallel to the axis of the helix.
A) are roughly perpendicular to the axis of the helix.
A) occur mainly between electronegative atoms of the R groups.
A) occur only between some of the amino acids of the helix.
A) occur only near the amino and carboxyl termini of the helix.
In an helix, the R groups on the amino acid residues:
Alternate between the outside and the inside of the helix.
Are found on the outside of the helix spiral.
Cause only right-handed helices to form.
Generate the hydrogen bonds that form the helix.
Stack within the interior of the helix.
Thr and/or Leu residues tend to disrupt an helix when they occur next to each other in a protein because:
An amino acids like Thr is highly hydrophobic.
Electrostatic repulsion occurs between the Thr side chains.
Covalent interactions may occur between the Thr side chains.
Steric hindrance occurs between the bulky Thr side chains.
The R group of Thr can form a hydrogen bond.
A d-amino acid would interrupt an helix made of l-amino acids. Another naturally occurring hindrance to the formation of an helix is the presence of:
A negatively charged Arg residue.
A nonpolar residue near the carboxyl terminus.
A positively charged Lys residue.
A Pro residue.
Two Ala residues side by side.
An helix would be destabilized most by:
An electric dipole spanning several peptide bonds throughout the helix.
Interactions between neighboring Asp and Arg residues.
Interactions between two adjacent hydrophobic Val residues.
The presence of an Arg residue near the carboxyl terminus of the helix.
The presence of two Lys residues near the amino terminus of the helix.
The major reason that antiparallel -stranded protein structures are more stable than parallel -stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
A) do not have as many disulfide crosslinks between adjacent strands.
A) do not stack in sheets as well as antiparallel strands.
A) have fewer lateral hydrogen bonds than antiparallel strands.
A) have weaker hydrogen bonds laterally between adjacent strands.
Amino acid residues commonly found in the middle of turn are:
Ala and Gly.
Hydrophobic.
Pro and Gly.
Those with ionized R-groups.
Two Cys.
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):
Antiparallel sheet.
Parallel sheet.
ρ� helix.
ρ� sheet.
ρ� turn.
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
Generally near each other in sequence.
Always side by side.
Invariably restricted to about 7 of the 20 standard amino acids.
Usually near the polypeptide chain’s amino terminus or carboxyl terminus.
Often on different polypeptide strands.
The -keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the -keratin chains—as in hair waving—what subsequent steps are required?
Chemical oxidation and then shape remodeling
Chemical reduction and then chemical oxidation
Chemical reduction and then shape remodeling
Shape remodeling and then chemical oxidation
Shape remodeling and then chemical reduction
Which of the following statements is false?
Collagen is a protein in which the polypeptides are mainly in the -helix conformation.
Disulfide linkages are important for keratin structure.
Gly residues are particularly abundant in collagen.
Silk fibroin is a protein in which the polypeptide is almost entirely in the conformation.
ρ�-keratin is a protein in which the polypeptides are mainly in the -helix conformation.
Kendrew’s studies of the globular myoglobin structure demonstrated that:
�corners” between -helical regions invariably lacked proline residue.
Highly polar or charged amino-acid residues tended to be located interiorally.
Myoglobin was completely different from hemoglobin, as expected.
The structure was very compact, with virtually no internal space available for water.
The helix predicted by Pauling and Corey was not found in myoglobin.
Proteins often have regions that can fold and function as an independent entity from the whole protein. These regions are called:
Domains.
Oligomers
Peptides.
Sites
Subunits
Which of the following statements concerning protein domains is true?
They are a form of secondary structure.
They are examples of structural motifs.
They consist of separate polypeptide chains (subunits).
They have been found only in prokaryotic proteins.
They may retain their correct shape even when separated from the rest of the protein.
The structural classification of proteins (based on motifs) is based primarily on their:
Amino-acid sequence.
Evolutionary relationships.
Function.
Secondary structure content and arrangement.
Subunit content and arrangement.
Proteins are classified within families or superfamilies based on similarities in:
Evolutionary origin.
Physico-chemical properties.
Structure and/or function.
Subcellular location.
Structure
Which of the following statements about oligomeric proteins is false?
A subunit may be similar to other proteins.
All subunits must be identical.
Many have regulatory roles.
Some oligomeric proteins can further associate into large fibers.
Some subunits may have nonprotein prosthetic groups.
A repeating structural unit in a multimeric protein is known as a(n):
Domain
Motif
Oligomer.
Protomer
Subunit
Proteostasis is the cellular process by which:
A) proteins are synthesized.
B) proteins are folded.
C) proteins are modified.
D) proteins are degraded.
E) protein levels are maintained.
An average protein will not be denatured by:
A detergent such as sodium dodecyl sulfate.
Heating to 90°C.
Iodoacetic acid.
PH 10.
Urea
Which of the following is least likely to result in protein denaturation?
Altering net charge by changing pH
Changing the salt concentration
Disruption of weak interactions by boiling
Exposure to detergents
Mixing with organic solvents such as acetone
Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease (RNase) have shown that:
Folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat.
Native ribonuclease does not have a unique secondary and tertiary structure.
The completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active.
The enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase.
The primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.
Which of the following statements concerning the process of spontaneous folding of proteins is false?
It may be an essentially random process.
It may be defective in some human diseases.
It may involve a gradually decreasing range of conformational species.
It may involve initial formation of a highly compact state.
It may involve initial formation of local secondary structure.
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.
Proteasome
Molecular chaperone
Protein precursor
Structural motif
Supersecondary structural unit
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