Peptide bonds and zwitterions?

[I_am_not_bad]

Please can you clarify this for me, it drives me nuts ;-P
Forget about side chains and the H and just look at the amino group and carboxylgroup of AAs
H2N and COOH. Because one is a weak base and the other a weak acid, they act at physiolocal pH at proton acceptor/donor making it H3N+ and COO-, the usual zwitterionic form of AAs
( Hope I got it right so far)
Now in peptide bonds ( lets just look at the bonds and forget about the rest) the COOH forms with the next NH2 (of the next AA) a CONH +H2O bond
But you write a peptide bond starting with H3N.......
but where does the extra H come from? It could come from its own ( in zwitterionic form) , but then peptide bonds are not possible because the H from the COOH would be missing
Or do peptide bonds only happen well below pI?
Sorry if I ask such a basic question, but I look and search and cant find an answer.
Thanks

[Kunal Pandya]

Re: Where does the H come from in peptide bonds?

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Hi

During making of peptide we use two amino acid. In which one having Protected amino part while other one having protected carboxyl group so you can proceed to go for desire reaction.

Example

Boc-Gly-COOH + NH2-Gly-COOMe + Coupling reagent

So what you get is
Boc-Gly-CO-NH-Gly-COOMe (i.e. OH from Carboxyl part while H is from Amino part gives H2O)

Thus to form peptide bond you must have to break zwitter ion other wise it not participate in reaction.It break during protection of Amino or carboxyl part. So buring deprotection of Boc with TFA we get protonated amino site .while if we use any other group cleaved under basic condition then you get just free amino site.

Regards
Kunal Pandya