In the light-dependent reactions of photosynthesis, H+ ions pass to the thylakoid space. Where do these protons come from?
The photolysis of water is coupled to the reduction of plastaquinone (Q) in photosystem II (PSII) as summarized in this diagram, adapted from Berg et al.:
The overall reaction (which balances) is:
2 H2O + 2 Q + 4 H+ = O2 + 2 QH2 + 4 H+
But the 4 H+ on both sides of the equation are not the same. The generation of the hydrogen ions in the thylakoid lumen is coupled to the uptake of hydrogen ions from the stroma as the plastoquinone is reduced. This is made possible because of the membrane disposition of the components of photosystem II. Hence an electochemical gradient is established that can be used for generating the ATP needed for photosynthesis.