Most of the ATP of Cell is produced in the Mitochondria. This a complex and multi-step process. The following is an attempt to step through this process.
The Role of Hydrogen in the Process
Coenzymes NAD+ and FAD act as carriers of electrons and protons in the form of Hydrogen atoms to the Electron Transport Chain (ETC).
The following is a diagram of first the reduction of NAD+when it captures atoms from the oxidation of glucose and then the oxidation of NADH + H+ when it releases atom to the ETC. Notice how the is then recycled to pick up more.
The protons and electrons from the Hydrogen atoms are then used to power the proton pump of the electron transport chain.