Protons ( H + ) accumulate in the thylakoid space during electron transport between photosystems II and I. Which of the following describes what will happen to these protons next? The protons will raise the pH of the thylakoid space until it becomes alkaline at which point the protons are pumped out of the thylakoid, generating ATP. The protons will move from the thylakoid space to the stroma through an ATP synthase complex that generates ATP. The protons will diffuse out of the lipid layer surrounding the thylakoid and exit the plant during gas exchange. The protons will reenter the electron transport chain and be used to generate water. The protons will be used to oxidize NADPH to NADH, generating ATP in the process..