Alternatively, palmitoyl-CoA is used as a substrate in the biosynthesis of sphingosine (this biosynthetic pathway does not require transfer into the mitochondria).

The activation is catalyzed by palmitoyl-coenzyme A synthetase and the reaction proceeds through a two step mechanism, in which palmitoyl-AMP is an intermediate.

[5] Palmitoyl-Carnitine may translocate across the membrane, and once on matrix side, the reaction proceeds in reverse as CoA-SH is recombined with palmitoyl-CoA, and released.

The full oxidation of palmitic acid (or palmitoyl-CoA) results in 8 acetyl-CoA's, 7 NADH, 7 H+, and 7 FADH2.

[6] The full reaction is below: Palmitoyl-CoA is also the starting substrate, along with serine, for sphingolipid biosynthesis.