47. Match the reagents in Group I with their preferred cleavage sites in Group II.

Group I	Group II
P) Cyanogen bromide	1) Carboxyl side of methionine
Q) o-Iodosobenzoate	2) Amino side of methionine
R) Hydroxylamine	3) Carboxyl side of tryptophan
S) 2-Nitro-5-thiocyanobenzoate	4) Amino side of cysteine
	5) Asparagine–glycine bonds

(A) P-1, Q-3, R-5, S-4
(B) P-2, Q-3, R-1, S-4
(C) P-1, Q-2, R-5, S-4
(D) P-4, Q-2, R-5, S-3

---

Step-by-Step Matching With Explanation

P) Cyanogen bromide → Carboxyl side of methionine (1)

• Cyanogen bromide (CNBr) is a highly specific chemical cleavage reagent.

• It cleaves peptide bonds on the carboxyl (C-terminal) side of methionine residues.

• Widely used in protein sequencing and peptide mapping.

✅ Correct match: P–1

---

Q) o-Iodosobenzoate → Carboxyl side of tryptophan (3)

• o-Iodosobenzoate selectively oxidizes tryptophan residues.

• It cleaves peptide bonds at the carboxyl side of tryptophan.

• Useful for selective protein fragmentation.

✅ Correct match: Q–3

---

R) Hydroxylamine → Asparagine–glycine bonds (5)

• Hydroxylamine specifically cleaves Asn–Gly peptide bonds.

• This reaction occurs due to nucleophilic attack on the amide bond.

• Commonly tested in protein chemistry MCQs.

✅ Correct match: R–5

---

S) 2-Nitro-5-thiocyanobenzoate → Amino side of cysteine (4)

• This reagent reacts with cysteine residues.

• It causes peptide bond cleavage on the amino (N-terminal) side of cysteine.

• Used for selective modification and cleavage of cysteine-containing peptides.

✅ Correct match: S–4

---

✅ Final Correct Answer

Option (A)

P–1, Q–3, R–5, S–4

---

Introduction

The ability to match the reagents with their preferred cleavage sites is a high-yield topic in protein chemistry and molecular biology. Such MCQs frequently appear in exams like GATE, CSIR-NET, JAM, and CUET-PG, testing knowledge of chemical protein cleavage methods used in sequencing and structural analysis.

---

Explanation of Reagent–Cleavage Specificity

---

Cyanogen Bromide

Cyanogen bromide is one of the most important reagents in protein chemistry. It cleaves peptides specifically at the carboxyl side of methionine residues, producing predictable peptide fragments.

➡ Cleavage site: Carboxyl side of methionine

---

o-Iodosobenzoate

This reagent selectively targets tryptophan residues and cleaves peptide bonds on their carboxyl side. It is used for controlled fragmentation of proteins.

➡ Cleavage site: Carboxyl side of tryptophan

---

Hydroxylamine

Hydroxylamine exhibits remarkable specificity for Asparagine–Glycine (Asn–Gly) peptide bonds. This makes it useful for identifying specific sequence motifs.

➡ Cleavage site: Asparagine–glycine bonds

---

2-Nitro-5-thiocyanobenzoate

This reagent reacts with cysteine residues and cleaves peptide bonds on the amino side of cysteine, allowing selective disruption of cysteine-containing regions.

➡ Cleavage site: Amino side of cysteine

---

Correct Matching Summary

---

Final Answer

✅ Option (A): P–1, Q–3, R–5, S–4

---

Exam Tip

CNBr → Met (C-side), Hydroxylamine → Asn-Gly, o-Iodosobenzoate → Trp (C-side), Thiocyanobenzoate → Cys (N-side)
Memorizing these associations makes protein cleavage MCQs extremely easy.