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#peptide cleavage

3 public questions tagged with this topic.

Mass Spectroscopy

In peptide analysis, which cleavage forms b/y ions?

Peptide backbone contains three bonds repeating per residue: N-Cα, Cα-C carbonyl, and C-N amide peptide bond. Fragmentation nomenclature associates specific bond cleavage with ion type. Breaking the amide linkage CO-NH retains N-terminal portion as b ion and C-terminal portion as y ion, most common pathway under collision-induced dissociation due to relative bond weakness and proton mobility mechanism. Cleavage of N-Cα produces c/z ions characteristic of electron transfer dissociation, while Cα-CO yields a/x ions. Thus CO-NH scission directly generates b/y series used for sequence determination in proteomics data analysis routinely performed.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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Protein

Which enzyme cleaves peptide bonds at the C-terminal of lysine and arginine?

Trypsin is the accurate response regarding enzymatic activity or regulation described in this question. Enzymes are biological catalysts that accelerate reactions by lowering activation energy through specific substrate binding and transition state stabilization. In the context of Protein Degradation, Trypsin plays a specific catalytic or regulatory role determined by its active site configuration and mechanism of action. The other options (Chymotrypsin, Pepsin, and Elastase) are either different enzymes with distinct substrate specificities, act through different mechanisms, or are involved in separate metabolic pathways.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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Protein

Cyanogen bromide (CNBr) cleaves peptides at the C-terminal of:

Methionine is the scientifically accurate answer to this question. Within the study of Protein Degradation, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Methionine directly address what is being asked. Among the other options, Arginine, Lysine, and Glutamate do not correctly answer this question because they either refer to different concepts, describe properties of other molecules or processes, or represent common misconceptions about this topic.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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