Talk:Uroporphyrinogen III

Mechanism of swapping the two chains

When the enzyme changes the two side chains in the last pyrrole ring, does it actually swap the chains? Or does it flip the last pirrole ring over? Or does it do something more complicated, like transferring a methylene bridge, or replacing the two original chains by new ones, or swapping the side chains on three rings while leaving one unchanged, or ...? — Preceding unsigned comment added by Jorge Stolfi (talk • contribs) 18:20, 10 March 2019 (UTC)

Do enzymes act on the acids, or on the anions?

I understand that, for chemists, the names of this and other porphyrin-related compounds refer to the complete neutral molecules, with all the −COOH groups in protonated form. However, it seems that biochemists, who are always thinking of things dissolved in water, would use the names to mean the anions, with some or all of those groups ionized as −COO⁻.
Thus, one question is which picture should be at the top right of the article: the neutral acid, or the anion?
A more important question is whether the reaction diagrams, such as the formation of uroporphyrinogen III from prouroporphirinogen, should show the neutral acids or the anions. Are the carboxyls fully deprotonated when that reaction occurs? Does the enzyme act only on the fully deprotonated cations, or only on the neutral acid, or on either indfferently?
--Jorge Stolfi (talk) 18:30, 10 March 2019 (UTC)