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Exam 4: Protein Structure and Function

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Question 41

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Indicate whether the following statements are TRUE or FALSE.If a statement is false, explain why it is false.

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The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

False

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

True

The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

Premises

The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

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False

True

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Premises

Responses

The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

Premises

The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

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Question 42

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Typical folded proteins have a stability ranging from 7 to 15 kcal/mole at 37°C.Stability is a measure of the equilibrium between the folded (F) and unfolded (U) forms of the protein.For a protein with a stability of 7.1 kcal/mole, calculate the fraction of protein molecules that would be unfolded at equilibrium at 37°C.The equilibrium constant (K_eq) is related to the standard free energy (ΔG°) by the equation K_eq = 10^{−ΔG°/1.42}. $F \rightleftharpoons U$ $K _ { e q } = \frac { [ U ] } { [ F ] }$ Figure 4-56

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The ΔG° of the unfolding react...

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Question 43

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Indicate whether the following statements are TRUE or FALSE.If a statement is false, explain why it is false.

Fill in the blanks with the labels in the list below to identify various parts of the antibody structure in Figure 4-80. A.constant domain of the light chain B.constant domain of the heavy chain C.antigen-binding site D.variable domain of the heavy chain E.variable domain of the light chain Figure 4-80

For each polypeptide sequence listed, choose from the options given below to indicate which secondary structure the sequence is most likely to form upon folding.The nonpolar amino acids are italicized. A.Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile B.Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile C.Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp amphipathic α helix hydrophilic β sheet amphipathic β sheet hydrophobic α helix hydrophilic α helix

Knowing that there are 20 different possible amino acids that can be used at each position in a polypeptide, calculate the number of different polypeptides that could theoretically be produced for a protein that is 180 amino acids in length.Do you expect to find all of these possible protein sequences produced in living systems? Explain your answer.

The process of generating monoclonal antibodies is labor-intensive and expensive.An alternative is to use polyclonal antibodies.A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography.Which type of chromatography is used for this purpose?

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes?

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure 4-33.You are able to show that E inhibits enzyme V, and H inhibits enzyme X.Which biosynthetic product is most likely the inhibitor of enzyme T? Figure 4-33

Which of the following statements is TRUE?

Drawn below are segments of β sheets, which are rigid pleated structures held together by hydrogen bonds between the peptide backbones of adjacent strands (Figure 4-79).The amino acid side chains attached to the α-carbons are omitted for clarity. (A) (B) Figure 4-79 A.For panel (A) and for panel (B), indicate whether the structure is parallel or antiparallel. B.Draw the hydrogen bonds as dashed lines (||||||).