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17.2: Oxidation of Fatty Acids

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    Some of this article derives from the sources below.

    Biochemistry, Fatty Acid Oxidation.  Jacob T. Talley; Shamim S. Mohiuddin.   Creative Commons Attribution 4.0 International License (,


    Fatty acids, esterified to glycerol in triacylglycerides, are the major source of stored energy in organisms.  As we burn fossil fuels to produce energy to drive our society, so can we "burn" fatty acids to produce energy for heat, to drive biosynthetic reactions and to do work.  As discussed in an earlier chapter, fatty acids are highly reduced so their oxidation by dioxgen is highly favored both enthapically (exothermic reaction) and entropically.  Of course, the biological oxidation reactions occur in stepwise fashion using not O2 directly, but rather less potent oxidizing agents like NAD+ and FAD.   We'll focus first on fatty acid oxidation in animals (humans) and later describe the differences in fatty acid catabolism in plants, prokaryotes and archea.

    As we discussed in the previous section, fatty acids released from triglyceride stores on signaling by epineprhine and glucagon in exercise and between meals) are used for energy when glycogen stores are low and without breaking down protein in muscles to produce energy.  Some fatty acids are broken in the normal process of membrane turnover and removal of xenobiotic lipids.

    Most fatty acids are oxidized in the mitochondria, where the oxidation reaction occurs at the beta-carbon of the acyl chain, as shown in the figure below.  This pathway is also called β-oxidation.  Fatty acids containing double bonds and those containing a 2-methyl branch at carbon 2 are oxidized in a step wise fashion by this pathway.  In each repetitive cycle of this pathway, acetyl-CoA and one CO2 is released.


    In addition, oxidation can occur at both the alpha- and beta-carbons when oxidized in an organelle called the peroxisome.  The α-oxidation pathway is used for fatty acid branched at carbon 3 releasing one CO2 until the beta oxidation pathway can be used. The peroxisome degrades fatty acids that can't be oxidized in the mitochondria.  These include very long chain fatty acids (VLCFAs) like 24:0 and 26:0, some fatty acids from dietary sources such as pristanic acid (an odd-chain 15:0 fatty acid methylated at carbons 2, 6, 10, and 14).  The α-oxidation pathway can't be use to completely oxidized fatty acids in the peroxisome.  At some point in the oxidative stepwise pathway, the resulting shorter fatty acids are exported to the mitochondria for β-oxidation.

    Also enzymes in the endoplasmic reticulum can oxidized fatty acids at the omega or terminal carbon.  The enzyme used is a cytochrome P450 that uses one oxygen from O2 to hydroxylate the ω-carbon.  

    Peroxisomes - An underappreciated organelle

    These organelles, initially called microbodies, are vital to cellular metabolism and health. In the Zellweger syndrome spectrum, there is a several disorder in the formation of peroxisomes which is often lethal.   The are important metabolically in lipid metabolism, synthesis of myelin sheath lipids, and metabolism of reactive oxygen species like peroxides. In fact, the enzymes catalase and urate oxidase are found in such high concentrations they often form crystal "bodies" in the matrix of the peroxisome.  Additional roles include responses to pathogens and virus. Effectively that are a protective organelle.

    In contrast to mitochondria, peroxisomes, like most other organelles, have a single bilayer and have no DNA, from which transcription of RNA and translation of proteins occur.  All proteins are hence imported from the cytoplasm after synthesis on free ribosomes.  Imported proteins have a peroxisome targeting sequence (PTS) of serine-lysine and leucine (SKL) near their C-terminus which facilitates binding of the proteins to a PTS receptor in the peroxisome membrane. These organelles oxidize very long chain fatty acids (VLFA), make and break down hydrogen peroxide(hence the name) but also synthesize plasmalogens. The enzymes involved in the stepwise cycle of reactions in the peroxisome β-oxidation pathway use enzymes different from those used in the mitochondria for β-oxidation.

    For those more inclined towards chemistry than biology, yet another organelle with its own structures and function may seems like one to many.  However this less discussed organelle is critically important in its own right.  One interesting feature is its relationship with different organelles in cells, as shown in the left figure below.    Some proteins involved in organelle functions are shown as well (right panel).


    Islinger, M., Voelkl, A., Fahimi, H.D. et al. The peroxisome: an update on mysteries 2.0. Histochem Cell Biol 150, 443–471 (2018).  Creative Commons Attribution 4.0 International License (

    The peroxisome (PO, green) has binding interactions (redinterfaces) with the endoplasmic reticulum (ER) lysosomes, mitochondria, lipid droplets (a pseudoorganelle) and also itself (left figure).  Some of the key membrane proteins (which we have discussed previously) involved in peroxisome function include the ABC transporter proteins ABCD1-3 for fatty acids transport, OCTN3 for organic and cation/carnitine transport, and MCT1/2 for monocarboxylate transport.  In addition, peroxisomes have receptors for protein import mediated by PTSs and for peroxisome movement along microtubules in the cell.


    Mitochondrial β-Oxidation

    Mitochondrial β-oxidation in muscle generates acetyl-CoA, which enters the citric acid cycle for subsequent production of ATP through mitochonrial electron transport and oxidative phosphorylation. In liver, the generated acetyl-CoA is used for ketone body production under fasting states.  The figure below shows the β-oxidation pathway for 16:0, a saturated fatty acid, starting with its import from the cytoplasm.


    The figure below shows an abbreviated comparison of the β-oxidation pathways in the mitochondria and peroxisomes. Peroxisomal beta-oxidation is used to metabolizes very-long-chain fatty acids (VLCFAs), which are composed of 24-26 carbon units as well as branched chain fatty acids (BRCHAs). 



    Fransen, Marc & Lismont, Celien & Walton, Paul. (2017). The Peroxisome-Mitochondria Connection: How and Why?. International Journal of Molecular Sciences. 18. 1126. 10.3390/ijms18061126. DOI: 10.3390/ijms18061126.  Commons Attribution (CC BY) license (


    Comparison and interplay of peroxisomal and mitochondrial fatty acid β-oxidation (for details, see Section 4.1). Fatty acid β-oxidation, the NAD(H) redox shuttles, the tricarboxylic acid cycle, and the electron transfer chain are respectively depicted in blue, purple, red, and pink. 1a, acyl-CoA oxidase; 1b, acyl-CoA dehydrogenase; 2, enoyl-CoA hydratase; 3, 3-hydroxyacyl-CoA dehydrogenase; 4, 3-ketoacyl-CoA thiolase. ABCD, ATP-binding cassette transporters of subfamily D; ADP, adenine dinucleotide phosphate; BRCFA, branched-chain fatty acid; CAC, carnitine-acylcarnitine carrier; FAD, flavin adenine dinucleotide; FADH2, reduced FAD; LCFA, long-chain fatty acid; MCFA, medium-chain fatty acid; NAD, nicotinamide adenine dinucleotide; NADH, reduced NAD; NRS, NAD(H) redox shuttles; OXPHOS, oxidative phosphorylation; TCA, tricarboxylic acid; VLCFA, very-long-chain fatty acid
    (16) (PDF) The Peroxisome-Mitochondria Connection: How and Why?. Available from: [accessed Aug 20 2021].


    Mitochondrial nicotinamide adenine dinucleotide transporter SLC25A51 is recently been shown to be a NAD+/NADH mitochondria transporter

    Peroxisomal α-Oxidation

    Alpha oxidation of fatty acids occurs in the peroxisome as well; this metabolic pathway exists to degrade by-products of chlorophyll, a component of green vegetables in the diet. Phytanic acid is the primary molecule that requires the enzymes dedicated to alpha-oxidation. It derives from chlorophyll within ingested plant matter.



     As previously mentioned, omega-oxidation, the third and final fatty acid oxidation pathway, occurs in the endoplasmic reticulum. This pathway exists to process large, water-insoluble fatty acids that would otherwise be toxic to the cell in higher concentrations.

    Omega oxidation


    "The cytochrome P450 gene 4 family (CYP4) consists of a group of over 63 members that omega-hydroxylate the terminal carbon of fatty acids. In mammals, six subfamilies have been identified and three of these subfamily members show a preference in the metabolism of short (C7-C10)-CYP4B, medium (C10-C16)-CYP4A, and long (C16-C26)-CYP4F, saturated, unsaturated and branched chain fatty acids. These omega-hydroxylated fatty acids are converted to dicarboxylic acids, which are preferentially metabolized by the peroxisome beta-oxidation system to shorter chain fatty acids that are transported to the mitochondria for complete oxidation or used either to supply energy for peripheral tissues during starvation or in lipid synthesis."

    fig from  recreate





    Important concepts pertaining to the regulation of mitochondrial beta-oxidation, cellular handling, and transport of fatty acids will be discussed here. As the other forms of fatty acid oxidation are substrate-dependent and are not regulated by feedback or substrate concentrations, they will not receive the same level of discussion as mitochondrial beta-oxidation.

    Fatty acid beta-oxidation is regulated by the cell’s energy requirements. These molecules become more available in times of increased energy demand of prolonged fasting due to stimulation of hormone-sensitive lipase in adipose tissue epinephrine and glucagon. Serum-free fatty acids increase under the influence of these molecules and enter target cells. Other factors that regulate beta-oxidation include adequate oxygen supply for the continued electron acceptance from carrier substrates produced, namely FAD(H2) and NADH, to maintain a pool of electron acceptors available. Expression of enzymes involved in fatty acid oxidation becomes upregulated through fatty acids behaving as ligands that bind to peroxisome proliferator-activated receptors (PPARs); these transcription factors form homo-/heterodimers and translocate to the nucleus, where they alter gene expression involved in the production of proteins required for beta-oxidation and mitochondrial biogenesis. 

    First, free fatty acids must be taken up in cells by a transporter-mediated mechanism involving the membrane fatty acid-binding protein (FABPpm). Then, fatty acids within target cells must undergo multiple steps to arrive at previously mentioned cellular locations for oxidation to occur. The steps and enzymes involved in this process are highly site and substrate-specific. The major steps involve activation and transportation into cellular compartments.

    Activation of fatty acids requires the formation of a thioester bond with Coenzyme A, an ATP-dependent process carried out by acyl-CoA synthetases. Site and substrate specificity are demonstrated by the fact that long-chain acyl-CoA synthetase is located in the outer mitochondrial membranes, peroxisomal membranes, and endoplasmic reticulum membrane and demonstrates activity towards fatty acids of 12 to 20 carbons in length. However, in the case of VLCFAs, a specific synthetase is required for their activation and is only located in the membrane of peroxisomes, as this is the only location with the enzymatic profile suitable for their oxidation. Similarly, medium-chain acyl-CoA synthetases are only present in the mitochondrial matrix. The production of these smaller, diffusible compounds will be discussed in the section headed “Molecular.”

    Transportation of long-chain fatty acids into the mitochondrial matrix requires three enzymes, in addition to acyl-CoA synthetase. The transport of fatty acyl-CoA across the outer mitochondrial membrane occurs by carnitine:palmitoyltransferase I (CPT I); this enzyme simultaneously converts fatty acylcarnitine. This step is heavily regulated by the energy status of the cell; malonyl-CoA levels rise during the synthesis of fatty acids and function to inhibit mitochondrial beta-oxidation at this point in the pathway. The enzymatic transportation and conversion completed by CPT I is the rate-limiting step of fatty acid oxidation in the mitochondria. Fatty acyl-carnitine molecules are then transported into the mitochondrial matrix in exchange for carnitine by carnitine:acylcarnitine translocase through an antiport mechanism. The pool of carnitine available to this transporter depends on the functioning of carnitine:palmitoyltransferase II (CPT II), which serves to convert acylcarnitine to fatty acyl CoA, trapping the molecules within the mitochondrial matrix.

    In contrast to this involved, regulated transport mechanism, VLCFAs are not dependent on carnitine for transport into peroxisomes; the transport of branched-chain fatty acids destined for alpha-oxidation is similar to this process, and as previously mentioned, is substrate-dependent. VLCFAs and phytanic acid are transported into peroxisomes by the ABCD1-3 transporters by an ATP-dependent process; deficiencies of these transporters have demonstrated to have severe implications and are discussed below in “Clinical Significance.” 



    In a similar fashion to previous sections, the process and enzymatic steps of the beta-oxidation spiral will primarily undergo discussion with alternative oxidation pathways mentioned later, as they pertain to and produce metabolic products destined for mitochondrial beta-oxidation. Variation of fatty acid molecular structure and additional required enzymes will also be discussed.

    Mitochondrial beta-oxidation of fatty acids requires four steps, all of which occur in the mitochondrial matrix, to produce three energy storage molecules per round of oxidation, including one NADH, one FAD(H2), and one acetyl CoA molecule.

    Step 1. The first enzyme required is called acyl CoA dehydrogenase, and as other enzymes involved in the handling of fatty acids, it is specific to chain length. Members of this enzyme family include long-chain, medium-chain, and short-chain acyl CoA dehydrogenases (LCAD), (MCAD), and (SCAD), respectively. These enzymes catalyze the formation of a trans double bond between the alpha and beta carbons on acyl CoA molecules by removing two electrons to produce one molecule of FAD(H2), which eventually accounts for 1.5 ATP molecules produced in the electron transport chain (ETC).

    Step 2. Next, the enzyme, enoyl CoA hydratase, performs a hydration step of the double bond between the alpha and beta carbons; this results in the addition of a hydroxyl (OH-) group to the beta carbon and a proton (H+) to the alpha carbon. There is no energy production associated with this step.

    Step 3. Following hydration, the next step is carried out by beta-hydroxyl acyl CoA dehydrogenase; as the name implies, electrons and two protons are removed from the hydroxyl group, and the attached beta carbon to oxidize the beta carbon and produce a molecule of NADH. Each molecule of NADH will result in the production of 2.5 ATP molecules from the ETC.

    Step 4. The final step in Beta oxidation involves cleavage of the bond between the alpha and beta carbon by CoASH. This step is catalyzed by beta-keto thiolase and is a thiolytic reaction. The reaction produces one molecule of acetyl CoA and a fatty acyl CoA that is two carbons shorter. The process may repeat until the even chain fatty acid has completely converted into acetyl CoA.

    Steps 1 through 4 refer to the beta-oxidation of a saturated fatty acid with an even-numbered carbon skeleton. Unsaturated fatty acids, such as oleate (18:1) and linoleate (18:2), contain cis double bonds that must be isomerized to the trans configuration (enoyl CoA isomerase) or reduced at the expense of an NADPH molecule (2,4-dienoyl CoA reductase).

    Odd-chain fatty acids undergo beta-oxidation in the same manner as even chain fatty acids; however, once a five-carbon chain remains, the final spiral of beta-oxidation will yield one molecule of acetyl CoA and one molecule of propionyl CoA. This three-carbon molecule can be enzymatically converted to succinyl CoA, forming a bridge between the TCA cycle and fatty acid oxidation.

    VLCFA beta-oxidation in peroxisomes occurs by a process similar to mitochondrial beta-oxidation; however, some key differences exist, including the fact that different genes encode fatty acid oxidation enzymes in peroxisomes, which is significant is certain inborn errors of metabolism. The enzyme responsible for the production of a double bond between the alpha and beta carbon in the first step of the peroxisomal pathway is an oxidase and donates electrons to molecular oxygen to produce hydrogen peroxide, rather than storing electrons in FAD(H2) as reducing the potential for the ETC. The remaining three steps are similar to the mitochondrial steps. Another notable difference involves the extent to which beta-oxidation occurs; it may occur to completion, ending in the production of acetyl CoA molecules than are able to enter the cytosol or be transported to the mitochondria bound to carnitine. Carnitine may also transfer short to medium-chain fatty acids to the mitochondrial matrix for the completion of oxidation.

    Branched-chain fatty acids also require additional enzymatic modification to enter the alpha-oxidation pathway within peroxisomes. Phytanic acid, 3,7,11,14-tetramethylhexadecanoic acid, requires additional peroxisomal enzymes to undergo beta-oxidation. Phytanic acid initially activates to phytanyl CoA; then, phytanyl CoA hydroxylase (alpha-hydroxylase), encoded by the PHYH gene, introduces a hydroxyl group to the alpha carbon. The alpha carbon-hydroxyl bond then undergoes two successive rounds of oxidation to pristanic acid. Pristanic acid undergoes beta-oxidation, which produces acetyl CoA and propionyl CoA in alternative rounds. As with peroxisomal beta-oxidation of VLCFAs, this process generally ends when the carbon chain length reaches 6-8 carbons, at which point the molecule is shuttled to the mitochondria by carnitine for complete oxidation to carbon dioxide and water.

    Omega-oxidation of fatty acids in the endoplasmic reticulum primarily functions to hydroxylate and oxidize fatty acids to dicarboxylic acids to increase water solubility for excretion in the urine. This enzymatic conversion relies on the cytochrome P450 superfamily to catalyze this reaction between xenobiotic compounds and molecular oxygen. Deficiencies in some enzymes of fatty acid oxidation may result in accumulation. Thus, up-regulation of omega-oxidation, increased serum, and or urine medium-chain dicarboxylic acids can be diagnostic of certain deficiencies and will be discussed under the “Clinical Significance” section.


    Clinical Significance

    Listed below are a few select diseases that either directly involves defective fatty acid metabolism through intrinsic enzyme deficiencies or indirectly prevent the proper functioning of fatty acid metabolism through extrinsic enzyme deficiencies. Many, but not all, deficiencies of enzymes involved in fatty acid oxidation result in abnormal neurological development and or function early in life; a brief list of signs and symptoms appears under the selected diseases mentioned. 

    MCAD Deficiency

    Medium-chain acyl dehydrogenase is the most common inherited defect of fatty acid oxidation in humans; as one would expect, medium-chain, 6-8 carbon molecules accumulate in this disease. Clinical manifestations of MCAD deficiency primarily present during fasting conditions and include lethargy, weakness, diaphoresis, and hypoketotic hypoglycemia, most commonly in children under the age of 5. Serum measurements of octanoyl carnitine are usually elevated in these patients and can aid in the diagnosis. These abundant molecules then undergo oxidation by the cytochrome P450 system involved in omega-oxidation, resulting in a dicarboxylic acidemia and dicarboxylic aciduria. This clinical syndrome must be differentiated from Reye’s Syndrome, as salicylates compete with medium-chain fatty acids for binding sites on MCAD.

    Zellweger Syndrome

    Zellweger syndrome results from autosomal recessive mutations in the PEX genes; these DNA sequences code for peroxin proteins, which are involved in the assembly of peroxisomes. Almost 70% of all peroxisomal biogenesis disorders (PBDs) result from a PEX1 gene mutation. Many different fatty acid compounds can accumulate without the oxidative machinery of peroxisomes, including VLCFAs and phytanic acid. Manifestations of this disease generally include the brain, kidneys, and skeleton.

    X-Linked Adrenoleukodystrophy (X-ALD)

    X-ALD is a genetic deficiency of the ABCD transporters in the membrane of peroxisomes, as mentioned previously, resulting in the pathological accumulation of phytanic acid and VLCFAs within cells and is most clinically significant when the ABCD1 transporter is absent. The disease presents with neurodegenerative and adrenal abnormalities.

    Refsum Disease

    Refsum disease results from a genetic deficiency of the enzyme phytanyl CoA 2-hydroxylase, which, as previously mentioned, is involved in the alpha-oxidation of phytanic acid, a breakdown product of chlorophyll. Notable clinical manifestations of Refsum disease include cardiac malfunction and defective functioning of the olfactory and auditory nerves due to the accumulation of phytanic acid.









    Add section in plants and prokaryotes, archea.  Use these referecnes

    Molecules 201823(10), 2583;



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