Amino Acids & Polypeptides

[MedPR]

So in a single amino acid, the amine, carboxylic acid, and side chain (if acidic/basic) can be protonated/deprotonated. In a protein, however, only the C-terminus and N-terminus and all acidic/basic side chains can be protonated.

Why can't the peptide bond be protonated or deprotonated?

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[aSagacious]

The carboxyl and amino groups concatenate between amino acids to form the backbone of the polypeptide (see below). In addition to forming covalent bonds (which are already fairly stable) the backbone exhibits resonant stabilization from the carbonyls, which makes the protons associated with the backbone unavailable for (de)protonation.

 

[MedPR]

The carboxyl and amino groups concatenate between amino acids to form the backbone of the polypeptide (see below). In addition to forming covalent bonds (which are already fairly stable) the backbone exhibits resonant stabilization from the carbonyls, which makes the protons associated with the backbone unavailable for (de)protonation.

That makes sense, but doesn't the nitrogen still have a lone pair? Couldn't it be protonated?

 

[aSagacious]

That makes sense, but doesn't the nitrogen still have a lone pair? Couldn't it be protonated?

No, because of resonance with the adjacent carbonyl it behaves as if it is has half of a pi bond.

 

[SaintJude]

What a coincidence! Was just reading in Kaplan how the limited rotation around the C-N peptide bond adds rigidity and stability around backbone of proteins...

 

[pfaction]

A large amount of aqueous acid does clip it apart, though. It reverses the dehydration process, according to TPR. But yes, what everyone else said: due to partial resonance, the pi electrons aren't able to pick up the protons needed.

 

[MedPR]

No, because of resonance with the adjacent carbonyl it behaves as if it is has half of a pi bond.

What a coincidence! Was just reading in Kaplan how the limited rotation around the C-N peptide bond adds rigidity and stability around backbone of proteins...

Right, thanks I forgot those details were related.

This TBR section on amino acids and isoelectric point is amazing. Glad I came back to it.

Also histidine-argining-lysine means N-terminal of histidine and C-terminal of lysine are exposed. Had to type that out because I've been having trouble remembering the convention.

 

[kasho11]

Resonance is legitimately the answer to everything... involving molecules... usually. No but it is important, always follow the electrons.

 

[MedPR]

Resonance is legitimately the answer to everything... involving molecules... usually. No but it is important, always follow the electrons.

Yea probably so. Just like hydrogen bonding is the answer to almost every solvent question on the mcat.