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The best source of energy for eukaryotic organisms are fats. Glucose offers a ratio 6.3 moles of ATP per carbon while saturated fatty acids offer 8.1 ATP per carbon. Also the complete oxidation of fats yields enormous amounts of water for those organisms that do not have adequate access to drinkable water. Camels and killer whales are good example of this, they obtain their water requirements from the complete oxidation of fats.
There are four distinct stages in the oxidation of fatty acids. Fatty acid degradation takes place within the mitochondria and requires the help of several different enzymes. In order for fatty acids to enter the mitochondria the assistance of two carrier proteins is required, Carnitine acyltransferase I and II. It is also interesting to note the similarities between the four steps of beta-oxidation and the later four steps of the TCA cycle.
Most fats stored in eukaryotic organisms are stored as triglycerides as seen below. In order to enter into beta-oxidation bonds must be broken usually with the use of a Lipase. The end result of these broken bonds are a glycerol molecule and three fatty acids in the case of triglycerides. Other lipids are capable of being degraded as well.
A triglyceride molecule
Glycerol Fatty Acids (unsaturated)
A fatty acyl-CoA is oxidized by Acyl-CoA dehydrogenase to yield a trans alkene. This is done with the aid of an [FAD] prosthetic group.
The trans alkene is then hydrated with the help of Enoyl-CoA hydratase
The alcohol of the hydroxyacly-CoA is then oxidized by NAD+ to a carbonyl with the help of Hydroxyacyl-CoA dehydrogenase. NAD+ is used to oxidize the alcohol rather then [FAD] because NAD+ is capable of the alcohol while [FAD] is not.
Finally acetyl-CoA is cleaved off with the help of Thiolase to yield an Acyl-CoA that is two carbons shorter than before. The cleaved acetyl-CoA can then enter into the TCA and ETC because it is already within the mitochondria.