Quantitative metabolomics services for biomarker discovery and validation.
Specializing in ready to use metabolomics kits.
Your source for quantitative metabolomics technologies and bioinformatics.

Filter by Pathway Type:

Showing 101 - 110 of 605359 pathways
SMPDB ID Pathway Name and Description Pathway Class Chemical Compounds Proteins


Pw000173 View Pathway

Mitochondrial Beta-Oxidation of Long Chain Saturated Fatty Acids

Fatty acids and their CoA byproducts can be found in many places in the body, playing major roles in many basic functions of the body. These include signalling roles, energy creation roles and enzyme regulation. Beta-oxidation is a process that occurs in the peroxisomes and in the mitochondria, although this pathway is focused on the mitochondrial piece of that process. Depending on the length of the fatty acid, beta-oxidation will either begin in the peroxisomes or the mitochondria. Very long chain fatty acids, fatty acids that consist of more than 22 carbons, can be reduced in the peroxisome where they become octanyl-CoA before moving to the mitochondria for the rest of the oxidation process. Stearoylcarnitine is transported by a mitochondrial carnitine/acylcarnitine carrier protein into the mitochondrial matrix, where it is converted to stearoyl-CoA through the enzyme carnitine o-palmitoyltransferase 2. Stearoyl-CoA then is catalyzed into (2E)-octadecenoyl-CoA by the enzyme long-chain specific acyl-CoA dehydrogenase. Then, enoyl-CoA hydratase converts (2E)-octadecenoyl-CoA into (s)-hydroxyoctadecanoyl-CoA. The pathway continues as hydroxyacyl-coenzyme A dehydrogenase cleaves (s)-hydroxyoctadecanoyl-CoA into 3-oxooctadecanoyl-CoA. 3-oxooctadecanoyl-CoA then uses 3-ketoacyl-CoA thiolase to create acetyl-CoA (necessary for the citric acid cycle) and uses trifunctional enzyme subunits alpha and beta to create palmityl-CoA. This palmityl-CoA is then converted by long-chain specific acyl-CoA dehydrogenase to (2E)-hexadecenoyl-CoA. Enoyl-CoA then converts (2E)-hexadecenoyl-CoA to 3-hydroxyhexadecanoyl-CoA, which is then turned into 3-oxohexadecanoyl-CoA by the enzyme hydroxyacyl-coenzyme A dehydrogenase. 3-ketoacyl-CoA thiolase then creates acetyl-CoA with the help of trifunctional enzyme subunits alpha and beta, which also produce tetradecanoyl-CoA from 3-oxohexadecanoyl-CoA. Long-chain specific acyl-CoA dehydrogenase then converts tetradecanoyl-CoA to (2E)-tetradecenoyl-CoA. (2E)-tetradecenoyl-CoA is then converted by the enzyme enoyl-CoA hydratase into 3-hydroxytetradecanoyl-CoA, which then creates 3-oxotetradecanoyl-CoA through the enzyme hydroxyacyl-coenzyme A dehydrogenase. Finally, the 3 enzymes 3-ketoacyl-coA thiolase, trifunctional enzyme subunit alpha and trifunctional enzyme subunit beta convert 3-oxotetradecanoyl-CoA into acetyl-CoA and lauroyl-CoA which can then be beta-oxidized as medium chain saturated fatty acids.


Pw000154 View Pathway

Transfer of Acetyl Groups into Mitochondria

Acetyl-CoA is an important molecule, which is precursor to HMG CoA, which is a vital component in cholesterol and ketone synthesis. Acetyl CoA participates in the biosynthesis of fatty acids and sterols, in the oxidation of fatty acids and in the metabolism of many amino acids. It also acts as a biological acetylating agent. Acetyl-CoA is made in the mitochondria by metabolizing fatty acids, and the oxidation of pyruvate of acetyl-CoA. When the body has an excess of ATP, the energy in acetyl-Coa can be stored in the form of fatty acids. Acetyl-CoA must cross the mitochondrial membrane to the cytosol, where fatty acid synthesis takes place. Acetyl-CoA is combined with oxalacetic acid by the enzyme citrate synthase, creating citric acid. Citric acid is then transported out of the mitochondria, to the cytosol, where the enzyme citrate lyase converts citric acid back into acetyl-CoA and oxalacetic acid. Malate dehydrogenase reduces oxalacetic acid to malate, which then is either transported back into the mitochondria by the malate-alpha ketoglutarate transporter or oxidized to pyruvate by malic enzyme. Pyruvate can then be transported back into the mitochondria and undergo decarboxylation into oxalacetic acid. Malate can also be used to create NADH by the conversion of malate to oxalacetic acid by malate dehydrogenase.


Pw000034 View Pathway

Pyruvaldehyde Degradation

This Pyruvaldehyde degradation pathway (Methylglyoxal degradation;2-oxopropanal degradation), also known as the glyoxalase system, is probably the most common pathway for the degradation of pyruvaldehyde (methylglyoxal), a potentially toxic metabolite due to its interaction with nucleic acids and other proteins. Pyruvaldehyde is formed in low concentrations by glycolysis, fatty acid metabolism and protein metabolism. Pyruvaldehyde is catalyzed by the glyoxylase system, composed of the enzymes lactoylglutathione lyase (glyoxalase I) and glyoxylase II. Glyoxalase I catalyes the isomerization of the spontaneously formed hemithioacetal adduct between glutathione and pyruvaldehyde into S-lactoylglutathione. S-lactoylglutathione is then catalyzed by glyoxalase II into D-lactic acid and glutathione. D-lactic acid is then catalyzed by an unknown quinol in the membrane to pyruvic acid, which then enters pyruvate metabolism.


Pw000565 View Pathway

Gastric Acid Production

Gastric acid plays a key role in the digestion of proteins by activating digestive enzymes to break down long chains of amino acids. In addition, it aids in the absorption of certain vitamins and minerals and also acts as one of the body's first line of defence by killing ingested micro-organisms. This digestive fluid is formed in the stomach (specifically by the parietal cells) and is mainly composed of hydrochloric acid (HCl). However, it is also constituted of potassium chloride (KCl) and sodium chloride (NaCl). The main stimulants of acid secretion are histamine, gastrin, and acetylcholine which all, after binding to their respective receptors on the parietal cell membrane, trigger a G-protein signalling cascade that causes the activation of the H+/K+ ATPase proton pump. As a result, hydrogen ions are able to be pumped out of the parietal cell and into the lumen of the stomach. The hydrogen ions are available inside the parietal cell after water and carbon dioxide combine to form carbonic acid(the reaction is catalyzed by the carbonic anhydrase enzyme) which dissociates into a bicarbonate ion and a hydrogen ion. Moreover, the chloride and potassium ions are transported into the stomach lumen through their own channels so that hydrogen ions and/or potassium ions can form an ionic bond with chloride ions to form HCl and/or KCl, which are both constituents of stomach acid. In addition, the peptide hormone somatostatin is the main inhibitor to gastric acid secretion. Not only does it inhibit the G-protein signalling cascade that leads to proton pump activation, but it also directly acts on the enterochromaffin-like cells and G cells to inhibit histamine and gastrin release, respectively.


Pw000692 View Pathway

Methylhistidine Metabolism

Methylhistidine is a modified amino acid that is produced in myocytes during the methylation of actin and myosin. It is also formed from the methylation of L-histidine, which takes the methyl group from S-adenosylmethionine and forms S-adenosylhomocysteine as a byproduct. After its formation in the myocytes, methylhistidine enters the blood stream and travels to the kidneys, where it is excreted in the urine. Methylhistidine is present in the blood and urine in higher concentrations after skeletal muscle protein breakdown, which can occur due to disease or injury. Because of this, it can be used to judge how much muscle breakdown is occurring. Methylhistidine levels are also affected by diet, and may differ between vegetarian diets and those containing meats.


Pw000010 View Pathway

Arginine and Proline Metabolism

The arginine and proline metabolism pathway illustrates the biosynthesis and metabolism of several amino acids including arginine, ornithine, proline, citrulline, and glutamate in mammals. In adult mammals, the synthesis of arginine takes place primarily through the intestinal-renal axis (PMID: 19030957). In particular, the amino acid citrulline is first synthesized from several other amino acids (glutamine, glutamate, and proline) in the mitochondria of the intestinal enterocytes (PMID: 9806879). The mitochondrial synthesis of citrulline starts with the deamination of glutamine to glutamate via mitochondrial glutaminase. The resulting mitochondrial glutamate is converted into 1-pyrroline-5-carboxylate via pyrroline-5-carboxylate synthase (P5CS). Alternately, the 1-pyrroline-5-carboxylate can be generated from mitochondrial proline via proline oxidase (PO). Ornithine aminotransferase (OAT) then converts the mitochondrial 1-pyrroline-5-carboxylate into ornithine and the enzyme ornithine carbamoyltransferase (OCT -- using carbamoyl phosphate) converts the ornithine to citrulline (PMID: 19030957). After this, the mitochondrial citrulline is released from the small intestine enterocytes and into the bloodstream where it is taken up by the kidneys for arginine production. Once the citrulline enters the kidney cells, the cytosolic enzyme argininosuccinate synthetase (ASS) will combine citrulline with aspartic acid to generate argininosuccinic acid. After this step, the enzyme argininosuccinate lyase (ASL) will remove fumarate from argininosuccinic acid to generate arginine. The resulting arginine can either stay in the cytosol where it is converted to ornithine via arginase I (resulting in the production of urea) or it can be transported into the mitochondria where it is decomposed into ornithine and urea via arginase II. The resulting mitochondrial ornithine can then be acted on by the enzyme ornithine amino transferase (OAT), which combines alpha-ketoglutarate with ornithine to produce glutamate and 1-pyrroline-5-carboxylate. The mitochondrial enzyme pyrroline-5-carboxylate dehydrogenase (P5CD) acts on the resulting 1-pyrroline-5-carboxylate (using NADPH as a cofactor) to generate glutamate. Alternately, the mitochondrial 1-pyrroline-5-carboxylate can be exported into the kidney cell’s cytosol where the enzyme pyrroline-5-carboxylate reductase (P5CR) can convert it to proline. While citrulline-to-arginine production primarily occurs in the kidney, citrulline is readily converted into arginine in other cell types, including adipocytes, endothelial cells, myocytes, macrophages, and neurons. Interestingly, chickens and cats cannot produce citrulline via glutamine/glutamate due to a lack of a functional pyrroline-5-carboxylate synthase (P5CS) in their enterocytes (PMID: 19030957).


Pw000053 View Pathway

Vitamin B6 Metabolism

As is commonly known there are many vitamins, the vitamin B complex group being one of the most well known. An important vitamin B complex group vitamin is vitamin B6, which is water-soluble. Moreover, this vitamin comes in various forms, one of which is an active form, known by the name pyridoxal phosphate or PLP. PLP serves as cofactor in a variety of reactions including from amino acid metabolism, (in particular in reactions such as transamination, deamination, and decarboxylation). To complicate matters however, there are in fact seven alternate forms of this same vitamin. These include pyridoxine (PN), pyridoxine 5’-phosphate (PNP), pyridoxal (PL), pyridoxamine (PM), pyridoxamine 5’-phosphate (PMP), 4-pyridoxic acid (PA), and the aforementioned pyridoxal 5’-phosphate (PLP). One of these forms, PA, is in fact a catabolite whose presence is found in excreted urine. For a person to absorb some of these active forms of vitamin B6 such as PLP or PMP they must first be dephosphorylized. This done via an alkaline enzyme phosphatase. There are a wide variety of biproducts from the metabolism in question, most of which find there ways into the urine and from there are excreted. One such biproduct is 4-pyridoxic acid. In fact this last biproduct is found in such large quantities that estimates of vitamin B6 metabolism birproducts show that 4-pyridoxic acid is as much as 40-60% of all the biproducts.Of course, it is not the only product of metabolism. Others include,include pyridoxal, pyridoxamine, and pyridoxine.


Pw000039 View Pathway

Ubiquinone Biosynthesis

Ubiquinone is also known as coenzyme Q10. It is a 1,4-benzoquinone, where Q refers to the quinone chemical group, and 10 refers to the isoprenyl chemical subunits. Ubiquinone is a carrier of hydrogen atoms (protons plus electrons) and functions as an ubiquitous coenzyme in redox reactions, where it is first reduced to the enzyme-bound intermediate radical semiquinone and in a second reduction to ubiquinol (Dihydroquinone; CoQH2). Ubiquinone is not tightly bound or covalently linked to any known protein complex but is very mobile. In eukaryotes ubiquinones were found in the inner mito-chondrial membrane and in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. The benzoquinone portion of Coenzyme Q10 is synthesized from tyrosine, whereas the isoprene sidechain is synthesized from acetyl-CoA through the mevalonate pathway. The mevalonate pathway is also used for the first steps of cholesterol biosynthesis. The enzyme para-hydroxybenzoate polyprenyltransferase catalyzes the condensation of p-hydroxybenzoate with polyprenyl diphosphate to generate ubiquinone.


Pw000022 View Pathway

Fatty Acid Elongation in Mitochondria

Cells typically contain large amounts of C18 and C20 fatty acids. Longer chain fatty acids are found in certain specialized tissues (myelin contains high amounts of C22 and C24 components). Even longer chain fatty acids are derived from either dietary sources or from elongation of C16-CoA or C18-CoA formed by the cytoplasmic fatty acid synthetase system. All of the fatty acids needed by the body can be synthesized from palmitate (C16:0) except the essential, polyunsaturated fatty acids such as linoleate and linolenate. To create longer, shorter, oxidized, reduced fatty acids, palmitic acid is subjected to enzymatic reactions by reductases, hydroxylases, elongases and mixed function oxidases. There are 3 major processes that modify palmitic acid: elongation, desaturation and hydroxylation. Elongation of fatty acids may occur at endoplasmic reticulum where fatty acid molecules of length up to C24 may be produced. Mitochondrial elongation may result in fatty acids up to C16 in length. Fatty acid elongation in mitochondria is essentially the reverse of beta-oxidation for fatty acid oxidation. In particular, both pathways make use of acetyl-CoA acyltransferase, 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase. The final step of fatty acid elongation uses enoyl-CoA reductase (not part of the beta-oxidation pathway). The elongation takes place in the mitochondrial matrix. In liver and kidney fatty acid elongation operates best in the presence of both NADH and NADPH, whereas in heart and skeletal muscle, only NADH is required. The mitochondrial pathway is important for elongating fatty acids containing 14 or fewer carbon atoms. Short chain fatty acids (SCFA) are fatty acids with aliphatic tails of less than six carbons. Medium chain fatty acids (MCFA) are fatty acids with aliphatic tails of 6Š—–12 carbons. Long chain fatty acids (LCFA) are fatty acids with aliphatic tails longer than 12 carbons. Very Long chain fatty acids (VLCFA) are fatty acids with aliphatic tails longer than 22 carbons.


Pw000161 View Pathway

Beta Oxidation of Very Long Chain Fatty Acids

The degradation of fatty acids occurs is many ways, but for the most part in most species it occurs mainly through the beta-oxidation cycle. Take mammals for example, in this subset of species we find that beta-oxidation takes place not only in mitochondria, but in peroxisomes as well. In contrast, it tends to be the case that in plants and fungi beta-oxidation is only seen in peroxisomes. The reason the beta-oxidation cycle is found to occur in both mitochondria and peroxisomes in mammals is thought to be that extremely long chain fatty acids will in fact undergo oxidation in both locations, an initial or first oxidation in peroxisomes and second oxidation in the mitochondria. There is however a difference between the oxidation cycle which occurs in both these organelles. Namely, that the oxidation undergone in peroxisomes does not have any coupling to ATP synthesis, unlike the corresponding oxidation which occurs in the mitochondria. We find rather that electrons are passed to molecules of oxygen, which produces hydrogen peroxide. Moreover, there is an enzyme which is found only peroxisomes which ties into this process. It can turn hydrogen peroxide back into water and oxygen and is catalase. To expound further the differences between the oxidation cycle found in the peroxisomes and the mitchondria consider the following three key differences. One, in the peroxisome the beta-oxidation cycle takes as a necessary input a special enzyme called, peroxisomal carnitine acyltransferase, which is needed to move an activated acyl group from outside the peroxisome to inside it. In mitochondrial oxidation similar but different enzymes are used called carnitine acyltransferase I and II. Difference number two is that oxidation in the peroxisome commences with catalysis induced by an enzyme called acyl CoA oxidase. Also, it should be noted that another enzyme called beta-ketothiolase which aids in peroxisomal beta-oxidation has a substrate specificity which differs from that of the mitochondrial beta-ketothiolase. Turning now to how the oxidation cycle function in mitochondria, note that the mitochondrial beta-oxidation pathway is composed of four repeating reactions that take place with each fatty acid molecule. The oxidation of fatty acid chains is a process of progress through repetition. With each turn of the cycle two carbons are removed from the fatty acid chain and the energy of the chemical bonds once housed by the molecule is captured by the reduced energy carriers NADH and FADH2. Acetyl-CoA is created in this 4 step reaction beta-oxidation process and is sent to the TCA cycle. Once inside the TCA cycle, the process of oxidation continues until even the acetyl-CoA is oxidized to CO2. More NADH and FADH2 result.
Showing 101 - 110 of 65005 pathways