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Think of it like this: Every time the electron is handed to another cytochrome, it pumps H+ across a membrane to create a gradient. NADH sticks the electron in higher up the chain than FADH2 does so the NADH electron pumps more protons since it is passed between more cytochromes than the FADH2 electrons. Since every proton pumped across is an ADP-->ATP reaction, the more protons an electron can pump, the more energy you get from that electron. FADH2 is around because it has roles in other areas like synthesis, so by being a little more multifunctional than NADH it sacrifices some in the electron transport role.

-Jelanen

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