In order to analyze peptides by using mass spectrometry, they need to be turned

Question

In order to analyze peptides by using mass spectrometry, they need to be turned into ions. Instead of making the radical cation, M+, like is commonly done, it is easier to protonate them, to make and [M+H]+. An important question that needs to be considered is, where is the proton? That information can be used to help determine the amino acids that are present in the peptide. One thing that has been found is that if the peptide contains the amino acids arginine (arg), histidine (his) or lysine(lys), the proton ends up on that amino acid (arg, his or lys).

a) Explain why arg, his and lys in peptides are more basic that other amino acids.

b) Suppose a peptide contains a combination of arg, his and/or lys. Rank the three amino acids according to their basicity, and explain why they have the order they do.

Explanation / Answer

a)Explain why arg, his and lys in peptides are more basic that other amino acids.

Explaination . Arginine, histidine and lysine have excess Nitrogen atom which can easily abstract the proton. This is reason they have shown the high basicity compare to other amino acid.

b) Suppose a peptide contains a combination of arg, his and/or lys. Rank the three amino acids according to their basicity, and explain why they have the order they do.

Increasing order of basicity: histidine <lysine < arginine

Explaination.

Histide has two nitrogen atom but they are the part of aromatic syntem (imidazole), therefore their availibily of electron pair is less to bind with proton compare to free amino group in lysine. Same time arginine has three free nitroge which can easily bind with proton, thus, the the arginine is highly basic than others amino acids.

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