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Carnitine transports long-chain acyl groups from fatty acids into the mitochondrial matrix, so they can be broken down through β-oxidation to acetyl CoA to obtain usable energy via the citric acid cycle. Fatty acids must be activated before binding to the carnitine molecule to form 'acylcarnitine'. The free fatty acid in the cytosol is attached with a thioester bond to coenzyme A (CoA). This reaction is catalyzed by the enzyme fatty acyl-CoA synthetase and driven to completion by inorganic pyrophosphatase.

An Acylcarnitine profile can detect a variety of inborn errors of metabolism, depending on the carbon-number involved. For example, an increase in C3 can suggest propionic academia, while an increase in C5 might indicate isovaleric academia. Also, the ratio of carbon species, i.e. C8/C10 can be useful in interpreting disease states.

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