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Why is NAD+ free to diffuse within the mitochondrion whereas FAD+ is not ? What biochemical properties cause this difference ?

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up vote 3 down vote accepted

As explained at the Wikipedia page for succinate dehydrogenase the FAD is covalently attached to one of the subunits of the protein. It is the first carrier in a short intramolecular redox chain involving Fe-S clusters, and possibly a haem, before the electrons derived from succinate are passed on to ubiquinone and on down the respiratory chain.

As you say, this contrasts with NAD which is a diffusible coenzyme.

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