Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group 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.
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.