Practice Quiz 1 Chapters 1-5

Question 1

Which of the following statements about cystine is correct?

a) Cystine forms when the –CH₂–SH R group is oxidized to form a –CH₂–S–S–CH₂– disulfide bridge between two cysteines.
b) Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids.
c) Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
d) Cystine is formed through a peptide linkage between two cysteines.
e) Two cystines are released when a –CH₂–S–S–CH₂– disulfide bridge is reduced to –CH₂–SH

Answer 1

a) Cystine forms when the –CH₂–SH R group is oxidized to form a –CH₂–S–S–CH₂– disulfide bridge between two cysteines.

Question 2

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):

a) antiparallel ß sheet
b) parallel ß sheet
c) alpha-helix
d) alpha-sheet
e) ß turn

Answer 2

e) ß turn

Question 3

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

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.

Answer 3

c) They are highly specific

Question 4

Which of the tripeptides:

1) is most negatively charged at pH 7?
2) will yield DNP-tyrosine when reacted with 1-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
3) contains the largest number of nonpolar R groups?
4) contains sulfur?
5) will have the greatest light absorbance at 280 nm?

Answer 4

1) D
2) A
3) E
4) A
5) C

aromatic amino acids, to different degrees, absorb UV light. Tyrosine and tryptophan absorb more than do Phenylalanine. Tryptophan is responsible for most of the absorbance of UV light (280 nm) by proteins.

Question 5

Which of the following is not correct concerning cooperative binding of a ligand to a protein?

a) it is usually a form of allosteric interaction
b) it is usually associated with proteins with multiple subunits
c) it rarely occurs in enzymes
d) it results in a nonlinear Hill plot
e) it results in a sigmoidal binding curve

Answer 5

c) it rarely occurs in enzymes

Question 6

Which of the following statements about allosteric control of enzymatic activity is false?

a) allosteric effectors give rise to sigmoidal V₀ vs [S] kinetic plots
b) Allosteric proteins are generally composed of several subunits.
c) An effector may either inhibit or activate an enzyme.
d) Binding of the effector changes the conformation of the enzyme molecule.
e) Heterotropic allosteric effectors compete with substrate for binding sites.

Answer 6

e) Heterotropic allosteric effectors compete with the substrate for binding sites.

an allosteric protein is one in which the binding of a ligand to one site affects the binding properties of another site on the same protein

Question 7

Give the general Henderson-Hasselbalch equation.

sketch a properly labeled titration curve for leucine titrated with NaOH; indicate where the pH = pK and the region(s) in which buffering occurs.

Leucine has two dissociable protons: one with a pK_a of 2.3, the other with a pK_a of 9.7

Answer 7

Henderson-Hasselbalch: pH = pK_a + log ([A^–]/[HA])

pI = the pH at which the net electric charge is zero (pH = pK_a)

1/2 (pK₁ + pK₂) = 1/2 (2.3+9.7) = 6

buffering regions occur at pH values of pK_a ±1

Question 8

Draw the dipeptide Gly-Ser chemical structure and label the peptide bond and the bonds for the phi, psi, and omega dihedral angles.

Which dihedral angle is normally a rigid, fixed angle, and why?

What is its normal conformation in proteins?

Answer 8

phi: N–C_a
psi: C_a–C

Omega: each peptide bond has some double-bond character due to resonance and cannot rotate. Therefore, it is normally a rigid and fixed angle

Trans is the normal conformation in proteins. This is the most thermodynamically stable conformation where it allows the least amount of steric hindrance. The trans conformation allows a lot of space between R groups that differ in size and charge.

Question 9

What fraction of ligand binding sites are occupied when [L] = K_d?

Show your work

Answer 9

1/2

Question 10

Describe briefly the two principal models for the cooperative binding of ligands to proteins with multiple binding sites

Answer 10

concerted model: binding of a ligand to one subunit of the protein results in an allosteric effect that switches the remaining subunits to the high-affinity conformation. Only two conformations are possible where all of the subunits are in the low- or high-affinity state

sequential model: ligand binding induces a change of conformation in an individual subunit. There are many possible conformations with different combinations of low- and high-affinity subunits.