Question 1

Which of the following best explains the hydrophobic effect as it relates to protein folding?

Accepted Answer

Hydrophobic amino acids avoid water, causing water molecules to form ordered 'cages' around them, which drives the nonpolar residues to cluster together and minimizes the ordering of water.

Question 2

Refer to the titration curve of a weak acid (HA) shown. At what point on the curve does the solution act as the most effective buffer?

Accepted Answer

At the point where [HA] = [A^-] and pH = pK_a

Question 3

A solution of phosphoric acid (H₃PO₄) is titrated with NaOH. Which of the following statements is correct regarding the titration curve shown?

Accepted Answer

The curve shows three distinct buffering regions, each corresponding to a different pK_a value.

Question 4

Which of the following amino acids is NOT classified as hydrophobic based on the structures highlighted?

Accepted Answer

Serine

Question 5

In the context of polypeptide directionality, which end is considered the beginning of the chain, and why is this convention important?

Accepted Answer

The N-terminal end; it reflects the order of amino acid addition during protein synthesis.

Question 6

What does a Ramachandran plot illustrate in protein structure analysis?

Accepted Answer

The possible phi (φ) and psi (ψ) torsion angles for amino acid residues in a polypeptide chain.

Question 7

Which statement about the resonance structures of the peptide bond is correct?

Accepted Answer

Resonance gives the peptide bond partial double-bond character, making it planar and rigid.

Question 8

Which feature distinguishes hemoglobin from myoglobin based on their structures and functions?

Accepted Answer

Hemoglobin exhibits cooperative oxygen binding due to its quaternary structure, while myoglobin does not.

Question 9

What is the molecular basis for sickle cell anemia as illustrated in the formation of HbS aggregates?

Accepted Answer

A hydrophilic amino acid is replaced by a hydrophobic one, causing hemoglobin molecules to aggregate in the deoxygenated state.

Question 10

Which statement best describes the alpha helix structure shown?

Accepted Answer

Hydrogen bonds form between the carbonyl oxygen of one residue and the amide hydrogen four residues ahead.

Question 11

What is the significance of the protein folding funnel diagram?

Accepted Answer

It shows that proteins fold through a series of intermediates toward a single, lowest-energy native state.

Question 12

During collagen synthesis, which step requires vitamin C (ascorbic acid) as a cofactor, and what is the consequence of its deficiency?

Accepted Answer

Hydroxylation of proline and lysine residues; deficiency leads to unstable collagen and symptoms of scurvy.

Question 13

Which post-translational modification is essential for the activation of vitamin K-dependent clotting factors, and how does warfarin affect this process?

Accepted Answer

γ-carboxylation of glutamate residues; warfarin inhibits vitamin K epoxide reductase, preventing regeneration of active vitamin K.

Question 14

In gel filtration chromatography, which type of protein will elute first from the column?

Accepted Answer

The largest protein, because it cannot enter the pores and travels a shorter path.

Question 15

Which principle underlies the separation of proteins in ion exchange chromatography?

Accepted Answer

Proteins are separated based on their net charge at a given pH.

Question 16

What is the main advantage of high-performance liquid chromatography (HPLC) over traditional chromatography methods?

Accepted Answer

HPLC uses smaller beads and high pressure, resulting in greater resolving power and more efficient separation.

Question 17

In SDS-PAGE, what property of proteins determines their migration through the gel?

Accepted Answer

Their molecular weight, because SDS gives all proteins a uniform negative charge.

Question 18

Which statement best describes the role of the active site in enzyme catalysis?

Accepted Answer

The active site is a three-dimensional pocket that binds substrates and positions them for catalysis, often undergoing conformational changes (induced fit).

Biochemistry Study Guide: Protein Structure, Amino Acids, Buffers, and Protein Techniques

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