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Chemical compound
Palmitoyl-CoA is an acyl-CoA thioester. It is an "activated" form of palmitic acid and can be transported into the mitochondrial matrix by the carnitine shuttle system (which transports fatty acyl-CoA molecules into the mitochondria), and once inside can participate in beta-oxidation. Alternatively, palmitoyl-CoA is used as a substrate in the biosynthesis of sphingosine (this biosynthetic pathway does not require transfer into the mitochondria). 
Biosynthesis.
Palmitoyl CoA formed from palmitic acid, in the reaction below. 
This reaction is often referred to as the "activation" of a fatty acid. 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. The reaction is driven to completion by the exergonic hydrolysis of pyrophosphate.
The activation of fatty acids occurs in the cytosol and beta-oxidation occurs in the mitochondria. However, long chain fatty acyl-CoA cannot cross the mitochondrial membrane. If palmitoyl-CoA is to enter the mitochondria, it must react with carnitine in order to be transported across: 
This transesterification reaction is catalyzed by carnitine palmitoyl transferase. 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. Unattached carnitine is then shuttled back to the cytosolic side of mitochondrial membrane.
Beta-oxidation.
Once inside the mitochondrial matrix, palmitoyl-CoA may undergo β-oxidation. The full oxidation of palmitic acid (or palmitoyl-CoA) results in 8 acetyl-CoA's, 7 NADH, 7 , and 7 FADH2. The full reaction is below: 
Sphingolipid biosynthesis.
Palmitoyl-CoA is also the starting substrate, along with serine, for sphingolipid biosynthesis. Palmitoyl CoA and serine participate in a condensation reaction catalyzed by serine C-palmitoyltransferase (SPT), in which 3-ketosphinganine is formed. These reactions occur in the cytosol.
References.
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