#protein sequencing

Mass Spectroscopy

Which amino acid has a monoisotopic residue mass of 99 Da?

Amino acid residue mass equals monoisotopic molecular mass minus water lost during peptide bond formation. Valine molecular mass is 117.07 Da; subtracting 18.0106 Da for H2O yields 99.06 Da residue mass. Lysine residue is 128 Da, glycine 57 Da, serine 87 Da. This 99 Da value creates diagnostic mass difference between consecutive b or y ions in tandem mass spectra when valine is present in sequence. Knowledge of residue masses enables manual de novo sequencing, validation of proteomic database search results, and understanding of mass spectrometry fragmentation ladders in peptide identification.

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

In the Sanger method of protein sequencing, which reagent is used?

Dinitrofluorobenzene (DNFB) 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 Dinitrofluorobenzene (DNFB) directly address what is being asked. Among the other options, PITC, Hydrochloric acid, and Sodium hydroxide 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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Protein

Which reagent is used in Edman degradation for N-terminal sequencing?

Phenylisothiocyanate (PITC) 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 Phenylisothiocyanate (PITC) directly address what is being asked. Among the other options, Cyanogen bromide, Dithiothreitol, and Urea 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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Protein

Edman degradation is used to determine:

N-terminal amino acid sequence 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 N-terminal amino acid sequence directly address what is being asked. Among the other options, Protein secondary structure, Protein quaternary structure, and C-terminal amino acid sequence 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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Protein

Cyanogen bromide cleaves proteins at the C-terminal of which amino acid?

Methionine is the scientifically accurate answer to this question. Within the study of Protein, 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, Lysine, Arginine, and Proline 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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Protein

Which method is commonly used to sequence large proteins (>100 residues)?

Enzymatic digestion followed by sequencing is the scientifically accurate answer to this question. Within the study of Protein, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Enzymatic digestion followed by sequencing directly address what is being asked. Among the other options, Edman degradation, Sanger sequencing, and Chemical hydrolysis 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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Protein

The function of performic acid in protein sequencing is:

Breaking disulfide bonds is the accurate answer because it correctly identifies the biological function or role described in this question. In Protein, understanding the specific functions of molecules, enzymes, or structures is fundamental. Breaking disulfide bonds fulfills this particular biological role through its specific structural properties, biochemical activity, or physiological mechanism. The other options (Hydrolyzing peptide bonds, Identifying N-terminal amino acids, and Detecting aromatic residues) serve different biological functions or are associated with other processes, pathways, or structural roles within the cell or organism.

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

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Protein

Which reagent is used in the Dansyl chloride method for N-terminal sequencing?

Dansyl chloride is the scientifically accurate answer to this question. Within the study of Protein, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Dansyl chloride directly address what is being asked. Among the other options, Phenylisothiocyanate, 1-Fluoro-2,4-dinitrobenzene, and Cyanogen bromide 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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