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

Explanation / Answer

The protanation is carried out on N-terminal i.e on terminal amino group in peptides.

The proton ends up on Arginine becouse terminal amino group is in conjugation with imino group.

The order of Basicity is given by ,

Lysine > Arginine > Histidine

Reason = As pKa values increases the basicity increases & as number of electron donating group is more then basicity is also more, therefore,

The pKa of lysine is 2.18 and having connected to four elctron donating CH2 groups.

The pKa of Arginine is 2.17 and having connected to three elctron donating CH2 groups.

  The pKa of Histidine is 1.82 and having connected to only one elctron donating CH2 groups.

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