When for example hydrogen ions are pumped against a chemical gradient and then used to power ATP synthase are these hydrogen ions naked protons or are they attached to a water molecule and form hydronium ions?

Hydrogen ions in any solvent at all will stick to a molecule (or several molecules) of that solvent.

It's typically something like H₉O₄+
As part of the process of being pumped, a proton might temporarily be stuck to a protein.

 

Thank you 

 

A decrease in pH within a cell may manifest itself as an increase in the relative amount of H₂PO₄^1- to HPO₄^2-.  As a proton is actively transported across a membrane, there are side-chains that can bind and release protons.  These include glutamate, histidine, and lysine residues.

Edited May 23, 20187 yr by BabcockHall

Good point- at physiological pH it might also be bicarbonate/ carbonate rather than a "free" proton.

So as the hydrogen ion is fueling the phosphorylation of ADP in ATP synthase it is being transferred from one protein to another and is really never a naked proton?

 

http://science.sciencemag.org/content/354/6319/1552.full

This is a link to a paper on bacteriorhodopsin, which is a light-driven proton pump.  It might give you a general picture of how protons and proteins interact.  Groups such as Asp85 and Asp96 transiently bind to the proton that is being actively transported.  This protein was put into artificial vesicles with ATP synthase.  Light cause bR to create a proton gradient, which was able to drive the synthesis of ATP, an early demonstration that the Mitchell chemiosmotic hypothesis was correct.  My understanding is that protons that are not bound to side-chains on a protein are frequently bound to buffering species.  The concentration of free protons is small.

Edited May 24, 20187 yr by BabcockHall

Thanks