Question 1

Which of the following best describes the primary structure of a protein?

Accepted Answer

The linear sequence of amino acids from the N-terminus to the C-terminus.

Question 2

Why is it necessary to cleave disulfide bonds before sequencing a protein?

Accepted Answer

To separate polypeptide chains and prevent refolding into the native structure.

Question 3

Which reagent is commonly used to cleave proteins specifically at methionine residues?

Accepted Answer

Cyanogen bromide ($$\mathrm{CNBr})$$

Question 4

A protein is digested with trypsin and produces several peptide fragments. What is the specificity of trypsin cleavage?

Accepted Answer

Cleaves at the carboxyl side of lysine (K) and arginine (R), unless followed by proline (P).

Question 5

Which analytical technique allows for the determination of the mass-to-charge ratio ($$m/z) of $$peptide fragments and is commonly used in protein sequencing?

Accepted Answer

Mass spectrometry

Question 6

What is the main disadvantage of using Dansyl chloride for N-terminal sequencing?

Accepted Answer

It requires strong acid hydrolysis, which destroys all peptide bonds.

Question 7

Which of the following statements about Edman degradation is TRUE?

Accepted Answer

It sequentially removes one amino acid at a time from the N-terminus.

Question 8

A peptide is analyzed by tandem mass spectrometry (MS/MS). Which ion series retains the charge on the C-terminus?

Accepted Answer

x, y, and z ions

Question 9

Why is it important to use more than one cleavage reagent (e.g., trypsin and cyanogen bromide) when sequencing a protein?

Accepted Answer

To generate overlapping fragments that allow reconstruction of the full sequence.

Question 10

Which of the following amino acids is most likely to be destroyed during acid hydrolysis of a protein?

Accepted Answer

Tryptophan (Trp)

Question 11

A protein sample is analyzed by an amino acid analyzer after hydrolysis. What is the purpose of derivatizing the amino acids before analysis?

Accepted Answer

To make the amino acids detectable by colorimetric or fluorescence methods.

Question 12

Which of the following best explains why the primary structure of a protein is crucial for its function?

Accepted Answer

It determines the way the protein folds into its functional three-dimensional structure.

Question 13

Which enzyme would you use to selectively remove amino acids from the C-terminus of a peptide?

Accepted Answer

Carboxypeptidase A

Question 14

A researcher wants to compare the primary structure of a protein from two different species. Which resource would be most useful?

Accepted Answer

A protein sequence database such as UniProt

Question 15

Which of the following is a common reason for sequencing a protein in a clinical or pharmaceutical context?

Accepted Answer

To identify mutations that may cause disease or affect drug response.

Question 16

Which of the following statements about protein mass spectrometry is FALSE?

Accepted Answer

It cannot distinguish between peptides that differ by a single amino acid.

Question 17

Which of the following best describes the role of overlapping peptide fragments in protein sequencing?

Accepted Answer

They allow the reconstruction of the full protein sequence by aligning shared regions.

Question 18

Which of the following amino acids is LEAST likely to be found in high abundance in most proteins, based on amino acid composition analysis?

Accepted Answer

Tryptophan (Trp)

Question 19

A peptide is subjected to Edman degradation, but after several cycles, multiple amino acids are detected in each cycle. What is the most likely explanation?

Accepted Answer

The reaction efficiency is less than 100%, leading to incomplete removal of the N-terminal residue.

Question 20

Which of the following is a direct application of knowing the primary structure of a protein in biotechnology?

Accepted Answer

Designing enzyme inhibitors that target specific amino acid residues.

Primary Protein Structure and Sequencing: Study Notes for Biochemistry

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