Where do the electrons and protons formed from biological reactions go? In a reaction like disulphide bond formation protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons and protons?

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I've reproduced the diagram that you linked to. It shows the oxidation of a pair of thiols to create a disulphide. What is missing from this scheme is the accompanying oxidising agent. So for example this could be carried out without catalysis in a reaction with molecular oxygen, in which case hydrogen peroxide would be formed. So the electrons and protons have ended up on the oxygen.

In a biological system this oxidation would usually be carried out by an enzyme, in which case the oxidising agent would probably be FAD (flavin adenine dinucleotide) or NAD+(nicotinamide adenine dinucleotide). These are by far the most commonly used redox cofactors. In a typical eukaryotic cell these would end up either (a) being reduced either by the mitochondrial electron transport chain (in which case the ultimate electron acceptor would again be oxygen); or (b) when they were used as a reducing agent in a metabolic reaction.