NADH is oxidized into NAD, H ions, and electrons by an enzyme. FADH is also oxidized into H ions, electrons, and FAD. As those electrons travel farther through the electron transport chain in the inner membrane, energy is gradually released and used to pump the hydrogen ions from the splitting of NADH and FADH into the space between the inner membrane and the outer membrane (called the intermembrane space), creating an electrochemical gradient.
This electrochemical gradient creates potential energy (see ) across the inner mitochondrial membrane known as the proton-motive force. As a result, chemiosmosis occurs, and the enzyme ATP synthase produces ATP from ADP and a phosphate group. This harnesses the potential energy from the concentration gradient formed by the amount of H ions. H ions passively pass into the mitochondrial matrix by the ATP synthase, and later help to re-form HO (water).
The electron transport chain requires a varying supply of electrons in order to properly function and generate ATP. However, the electrons that have entered the electron transport chain would eventually pile up like cars traveling down a blocked one-way street. Those electrons are finally accepted by oxygen (O). As a result, they form two molecules of water (HO). By accepting the electrons, oxygen allows the electron transport chain to continue functioning. The chain is organized in the cristae lumen membrane, i.e. the membrane inside the junction.
The electrons from each NADH molecule can form a total of 3 ATP's from ADPs and phosphate groups through the electron transport chain, while each FADH molecule can produce a total of 2 ATPs.
As a result, 10 NADH molecules (from glycolysis and the Krebs cycle), along with 2 FADH molecules, can form a total of 34 ATPs during aerobic respiration (from a single electron transport chain). This means that combined with the Krebs Cycle and glycolysis, the efficiency for the electron transport chain is about 65%, as compared to only 3.5% efficiency for glycolysis alone.