Chapter 6 Part 2

Which pairs of amino acid side chains could not interact in the interior of a protein by hydrogen bonding? Asp, Asn Ser, His Gln, Thr Ala, Lys

Ala, Lys The side chain of Ala is unable to make a hydrogen bond.

Which of the following is not a disease that is caused by protein misfolding? Bovine spongiform encephalopathy. Alzheimer's disease. Creutzfeldt-Jakob disease. Down's syndrome.

Down's syndrome.

Which of the following sequences of amino acids is most likely to be at the surface of a water-soluble globular protein? Glu-Asp-Lys Gly-Tyr-Val Pro-Phe-Thr Ile-Ser-Met Ala-Leu-Phe

Glu-Asp-Lys All three of these amino acids have polar, charged side chains

Which of the following statements about quaternary structure is FALSE? Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits. Quaternary structure is stabilized primarily by hydrophobic interactions. Quaternary structure exists only in proteins containing more than one polypeptide. Quaternary structure is fine-tuned by ion pairs, disulfide bonds, and hydrogen bonds.

Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits This statement is false. Quaternary structure does not require four subunits

Which pairs of amino acid side chains could interact in the interior of a protein only via van der Waals interactions? Entry field with correct answer Gln, His. Ser, Ser. Arg, Thr. Val, Leu

Val, Leu. Val, Leu are both aliphatic side chains whereas the other pairs shown can hydrogen bond.

Which of the following series of amino acids is most likely to be buried in the center of a water-soluble globular protein? Glu, Asp, Lys Pro, Gln, His Ala, Leu, Phe Gly, Asn, Ser

Ala, Leu, Phe YES, THIS IS THE MOST LIKELY SEQUENCE. Ala, Leu and Phe all have nonpolar side chains and so this series is highly likely to be buried in the hydrophobic core of a water-soluble globular protein.

Which statement about disulfide bonds is false? Disulfide bonds help stabilize extracellular proteins. Disulfide bonds are rare in intracellular proteins because the cytoplasm is a reducing environment. Disulfide bonds can occur between two different polypeptide chains. Disulfide bonds can occur between either Cys or Met residues. Disulfide bonds are not essential for stabilizing a folded protein. Can be reductively cleaved by 2-mercaptoethanol. Disulfide bonds can occur within a polypeptide chain.

Disulfide bonds can occur between either Cys or Met residues Only Cys residues can form disulfide bonds - as two thiol (SH) functional group are required to form a disulfide bond. Met has a thioether (RSR) functional group that cannot form disulfide bonds.

Which one of the following sequences of five amino acids would most likely be located on the surface of a soluble globular protein? Tyr-Phe-Glu-Asn-Leu Glu-Asn-Ser-Thr-Gln Met-Phe-Pro-Ile-Leu Val-Thr-Val-Glu-Val

Glu-Asn-Ser-Thr-Gln All five of these amino acids are polar, and so this sequence is the most likely to be found at the surface of a soluble globular protein.

Which treatment is least likely to cause a protein to denature? High concentrations of detergents like SDS. Extremes of pH. Temperatures approaching 100oC. High concentrations of salts. High concentrations of chaotropic agents like urea or the guanidinium ion.

High concentrations of salts.

Which pair of amino acid side chains could form an ion pair? Glu, Gly Asp, Gln His, Asp Lys, Arg

His, Asp His can become positive, while Asp can become negative.

The short amino acid sequence shown below occurs within the longer amino acid sequence of a large protein. This specific portion of the amino acid sequence adopts an -helical conformation. ............Ala-Val-Ala-Val-Ala-Val-Ala-Val-Ala-Val............... When the protein has adopted its tertiary conformation, which of the following hydrogen bonds are most likely to be formed by groups on the amino acid residues in this short segment? Hydrogen bonds with other residues in the same -helix. None, because Ala and Val side chains are unable to form hydrogen bonds. Hydrogen bonds with water molecules at the surface of the protein. Hydrogen bonds with residues in a neighbouring -helix.

Hydrogen bonds with other residues in the same -helix An -helix is stabilized by hydrogen bonds within the helix. These occur between groups in the polypeptide backbone that are part of the amino acid residues in the polypeptide. Thus the amino group of an Ala residue might make a hydrogen bond with the carbonyl group of a Val residue.

Why does a decrease in pH alter/disrupt the tertiary structure of an enzyme? It deprotonates prosthetic groups. It promotes proteolytic cleavage of peptide bonds. It disrupts ion pairs/salt bridges. It reduces hydrophobic interactions. It reduces disulphide bonds.

It disrupts ion pairs/salt bridges. Ion pairs/salt bridges are relatively weak, non-covalent interactions between charged R groups which play a role in fine-tuning protein tertiary structure. Because the charge of some amino acid R groups is sensitive to pH, changes in pH may disrupt these bonds and alter the protein's tertiary structure.

Which one of the following sequences of five amino acids would most likely be located in the interior of a water soluble globular protein? Tyr-Phe-Glu-Asn-Leu Met-Phe-Pro-Ile-Leu Val-Ala-Val-Glu-Val Glu-Asn-Ser-Thr-Gln

Met-Phe-Pro-Ile-Leu Yes, this is the most likely sequence. All five of the amino acids in the sequence are nonpolar.

Which statement is not a consequence of the hydrophobic effect? Nonpolar side chains are buried in the interior of a protein. The folding of proteins is generally a favorable process. The entropy of water increases when proteins fold. Metal ions can function to stabilize folded proteins.

Metal ions can function to stabilize folded proteins.

Which of the following statements is true because of the hydrophobic effect? Charged polar residues R, H, K, E, and D are usually found on the surfaces of proteins. Nonpolar residues V, L, I, M, and F are found in the interior of proteins. Uncharged polar residues S, T, N, Q, and Y are usually found on the surface of proteins, but may also be found in the interior. The interior of proteins is packed very densely.

Nonpolar residues V, L, I, M, and F are found in the interior of proteins. The hydrophobic effect causes nonpolar side chains to be buried inside proteins

What is the major factor that "drives" the folding of proteins into their tertiary structure? Formation of the maximum number of hydrophilic interactions. Placement of hydrophobic amino acid residues within the interior of the protein. Formation of the maximum number of ionic interactions. Placement of polar amino acid residues on the surface of the protein.

Placement of hydrophobic amino acid residues within the interior of the protein. This placement occurs through the hydrophobic effect which is the primary "driving force" in protein folding

Which of the following is TRUE about prosthetic groups? Prosthetic groups are bound and released by the protein as needed. Prosthetic groups are amino acids with additional reactivity. Prosthetic groups are inorganic. Prosthetic groups are an integral part of the three dimensional structure of the protein.

Prosthetic groups are an integral part of the three dimensional structure of the protein. The tertiary structure of a protein describes the precise atomic positioning of all its atoms, including those in prosthetic groups.

Which of the following statements about prosthetic groups is INCORRECT? Heme is an example of a prosthetic group. Prosthetic groups increase the inherent chemical reactivity of proteins. Prosthetic groups are not amino acids. Prosthetic groups form an integral part of the secondary structure of proteins

Prosthetic groups form an integral part of the secondary structure of proteins This statement is false. Prosthetic groups form an integral part of the tertiary structure of proteins.

Which is NOT a conclusion drawn from the experiments of Christian Anfinsen about renaturation of Ribonuclease A? A protein's primary structure can determine its tertiary structure. A protein can fold spontaneously to its native structure without the presence of other factors. Proteins are marginally stable in solution. A protein can fold rapidly to its native structure.

Proteins are marginally stable in solution. This experiment did not address the magnitude of the protein's stability.

Which statement about the families of protein folding patterns is false? Folding patterns that are commonly found are those which are likely to tolerate substitutions, insertions, and deletions in the amino acid sequence. The number of folding patterns seems to be much smaller than the number of proteins. Proteins of similar primary structure tend to have similar tertiary structure. Proteins of similar tertiary structure tend to have a very similar primary structure.

Proteins of similar tertiary structure tend to have a very similar primary structure. Proteins of similar tertiary structure tend to have a very similar primary structure is the False statement: Some families of similar tertiary structure have many members of unrelated primary structure.

Which of the following statements about quaternary structure is TRUE? Quaternary structure exists only in proteins containing prosthetic groups. Quaternary structure requires covalent interactions between polypeptide chains. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure. Quaternary structure is defined as the 3D structure of proteins with four subunits.

Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure

Which of the following statements about quaternary structure is TRUE? Quaternary structure requires covalent interactions between polypeptide chains. Quaternary structure exists in monomeric proteins. Quaternary structure is defined as the precise, 3-D arrangement of polypeptide backbones in proteins with more than one subunit. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.

Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.

Which of the following describes the entire three-dimensional structure of a single polypeptide? Primary structure Quaternary structure Secondary structure Tertiary structure

Tertiary structure

Which of the following is not a requirement for the structural determination of a protein using two-dimensional (2D) NMR spectroscopic techniques such as NOESY? Known geometric constraints such as covalent bond distances and angles. A low molecular mass no greater than ~40 kD. The ability of the protein to crystallize. The protein's primary amino acid sequence.

The ability of the protein to crystallize.

In the experiment of Christian Anfinsen, which condition permitted Ribonuclease A to renature? Entry field with correct answer Exposure to high temperatures during renaturation. The use of 8 M urea to denature the protein. The presence of O2 at pH 8.0 during renaturation. The presence of 2-mercaptoethanol during denaturation

The presence of O2 at pH 8.0 during renaturation. These conditions allowed the simultaneous and reversible re-oxidation and refolding of the polypeptide chain that is necessary to refold to the native state.

What ultimately determines the unique three dimensional structure of soluble globular proteins? The prosthetic groups. The exact number of disulfide bonds. The sequence of the amino acid residues. The number of subunits. The exact number of H-bonds.

The sequence of the amino acid residues. The sequence of amino acids in a polypeptide determines the structure of that polypeptide.

Which of the following statements about domains found in multi-domain proteins is false? They resemble small, globular proteins. They often have specialized functions. They contain 20-50 amino acids. They are often structurally independent.

They contain 20-50 amino acids. Domains usually contain 100-200 amino acids.

What is the major role played by prosthetic groups in proteins? They bind to the enzyme, participate in the catalytic reaction, and then leave the active site. They provide reactive groups not found in amino acid side chains. They provide flexibility in the enzyme structure. They maintain protein solubility. They are required to promote induced-fit by substrates.

They provide reactive groups not found in amino acid side chains. Prosthetic groups confer chemical reactivity on the protein which is not found in any amino acid R group.

A domain is: the same as a protein's tertiary structure. always a motif. an -helix, β-sheet or irregular secondary structure. a folded segment of polypeptide with a separate hydrophobic core

a folded segment of polypeptide with a separate hydrophobic core.

Which of the following pairings of a supersecondary structure / motif and a statement describing it is INCORRECT: immunoglobulin fold: two B- a- B - a - B units that combine to form a dinucleotide-binding site. a-a motif: two successive antiparallel a -helices packed against each other with their axes slightly inclined. B - a -B motif: an a -helix connecting two parallel strands of a B-sheet. B-hairpin motif: two anti-parallel B-strands connected by a tight turn. B-barrels: B-sheets that are rolled-up to form a continuous, circular sheet, with the first strand adjacent to the last strand.

immunoglobulin fold: two B- a- B - a - B units that combine to form a dinucleotide-binding site. An immunoglobulin fold (Fig. 6-29b in the text) involves a large proportion of B-sheets and is devoid of a-helices.