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I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation of a peptide bond).

How come there are two variations? And also, if the starting amino acid has three hydrogens in its amino group, what is the mechanism for the part that the nitrogen bonded to the carbonyl ends up having one hydrogen attached to it?

I worked up the mechanism on the former condition, but starting with three hydrogens, I don't quite get it. I hope you someone can enlighten me.

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    $\begingroup$ I think it might be helpful to link to some of those video lectures/textbooks. They could be publishing errors fixed in another edition or acknowledged in an errata. $\endgroup$
    – user79161
    Feb 12 at 3:54
  • $\begingroup$ I'm reading Solomons' Org chem book and then I also watched a video from Khan. $\endgroup$
    – Ellie
    Feb 12 at 4:02
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    $\begingroup$ General advice for written communication: don't use ALL CAPS and make sure the title allows the reader to understand what exactly the question is about without opening it. $\endgroup$
    – andselisk
    Feb 12 at 6:07
  • $\begingroup$ Also the word is "protonated" not "with three hydrogens". $\endgroup$
    – Mithoron
    Feb 12 at 18:27
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In neutral aqueous solution, the amino group is protonated (3 bound hydrogen atoms ) and the carboxilic acid group deprotonated (no bound hydrogen atom). In other solvents, you might have both groups in the neutral form the name amino acid suggests.

The mechanism of peptide bond formation is complex and involves intermediates with tRNA in the cell and starting materials distinct from amino acids for synthesis in the lab.

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