As we learned in the earlier steps, when NAD⁺ is Reduced to form NADH it also gains high energy electrons (same in FADH₂). These high energy electrons are shuttled along membrane proteins called Protein Complexes (I, II, III and IV) until they reach their final receptor: Oxygen (forming water). Each subsequent protein complex has a higher electronegativity, allowing the electrons to be pulled from the previous carrier (ex. from the NADH to complex I, and then from complex I to II, etc... With every transfer of electrons, a Redox Reaction occurs with one molecule being Oxidized (loses electron) and the other being Reduced (gains electron). Because of this, the ATP produced here is called Oxidatitive Phospholylation (as opposed to Substrate-level Phosphorylation in Glycolysis and the Krebs Cycle).

Protein Complexes I, III and IV are Transmembrane Proteins that are actually Protein Pumps. Each time an electron is passed through these complexes, they pump out an H⁺ ions from the Matrix into the Intermembrane Space (space between Inner and Outer membranes). NADH attaches at Protein Complex I and its electrons pass through III and IV pumping H⁺ ions into this space, creating an Electrochemical Gradient. FADH₂ on the other hand attaches at Protein Complex II (a peripheral protein that is NOT a pump), and its electrons then pass to complex III and IV, pumping H⁺ ions at each site.