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 91 - 100 of 48700 pathways
SMPDB ID Pathway Chemical Compounds Proteins

SMP0000588

Pw000564 View Pathway
Physiological

Striated Muscle Contraction

Tubular striated muscle cells (i.e. skeletal and cardiac myocytes) are composed of bundles of rod-like myofibrils. Each individual myofibril consists of many repeating units called sarcomeres. These functional units, in turn, are composed of many alternating actin and mysoin protein filaments that produce muscle contraction. The muscle contraction process is initiated when the muscle cell is depolarized enough for an action potential to occur. When acetylcholine is released from the motor neuron axon terminals that are adjacent to the muscle cells, it binds to receptors on the sarcolemma (muscle cell membrane), causing nicotinic acetylcholine receptors to be activated and the sodium/potassium channels to be opened. The fast influx of sodium and slow efflux of potassium through the channel causes depolarization. The resulting action potential that is generated travels along the sarcolemma and down the T-tubule, activating the L-type voltage-dependent calcium channels on the sarcolemma and ryanodine receptors on the sarcoplasmic reticulum. When these are activated, it triggers the release of calcium ions from the sarcoplasmic reticulum into the cytosol. From there, the calcium ions bind to the protein troponin which displaces the tropomysoin filaments from the binding sites on the actin filaments. This allows for myosin filaments to be able to bind to the actin. According to the Sliding Filament Theory, the myosin heads that have an ADP and phosphate attached binds to the actin, forming a cross-bridge. Once attached, the myosin performs a powerstroke which slides the actin filaments together. The ATP and phosphate are dislodged during this process. However, ATP now binds to the myosin head, which causes the myosin to detach from the actin. The cycle repeats once the attached ATP dissociates into ADP and phosphate, and the myosin performs another powerstroke, bringing the actin filaments even closer together. Numerous actin filaments being pulled together simultaneously across many muscles cells triggers muscle contraction.

SMP0121029

Pw122296 View Pathway
Physiological

Pancreas Function - Alpha Cell

Alpha cells are a type of islet cell found in the pancreas that release glucagon. Glucagon counteracts insulin and functions to maintain glucose homeostasis when detected glucose levels are low. Glucagon is contained in granules in the cell as a reserve ready to be released. Extracellular glucose levels and ion channels regulate the secretion of glucagon. Glucose undergoes glycolysis to increase ATP in the cell. The moderate activity of potassium ATP channels causes the membrane potential to be around -70mV. The alpha cell then becomes electrically active due to the closure of potassium channels. The cell membrane becomes depolarized due to voltage dependent sodium, potassium and calcium channels. This causes an increase in action potentials and opens voltage gate calcium channels causing an increase of calcium into the cell. This triggers the exocytosis of glucagon from the cell. Conversely, an increase in extracellular glucose leads to an increase in ATP production and inhibition of potassium ATP channels. The membrane depolarizes to a membrane potential that inactivates voltage dependent calcium channels. This results in decreased intracellular calcium and inhibits exocytosis of glucagon.

SMP0121124

Pw122397 View Pathway
Metabolic

Eumelanin Biosynthesis

Melanin is the term used for multiple pigments found in many organisms, and specifically our skin, hair and iris tissues. There are three types of melanin, eumelanin, pheomelanin and neuromelanin. Eumelanin is the most common, and can be brown or black. Melanin is produced by melanocytes, and is a polymer made of smaller components, so there are many types with different polymerization patterns and proportions of components. To begin, this pathway takes L-dopachrome from the L-dopa and L-dopachrome biosynthesis pathways and, in the melanosome, it can either spontaneously form 5,6-dihydroxyindole, or can form 5,6-dihydroxyindole-2-carboxylic acid using L-dopachrome tautomerase as the catalyst. Both 5,6-dihydroxyindole and 5,6-dihydroxyindole-2-carboxylic acid use tyrosinase as a catalyst to form indole-5,6-quinone and indole-5,6-quinone-2-carboxylate respectively. Finally, some combination of 5,6-hydroxyindole, indole-5,6-quinone, 5,6-dihydroxyindole-2-carboxylic acid and indole-5,6-quinone-2-carboxylate combine to form melanochrome, an intermediate in the formation of eumelanin, and finally forms eumelanin, the final product of this pathway.

SMP0000067

Pw000002 View Pathway
Metabolic

Aspartate Metabolism

Aspartate is synthesized by transamination of oxaloacetate by aspartate aminotransferase or amino acid oxidase. Aspartyl-tRNA synthetase can then couple aspartate to aspartyl tRNA for protein synthesis. The aspartate content in human proteins is about 7%. Asparagine synthase can convert aspartate to the polar amino acid asparagine. Aspartate is also a precursor for cellular signaling compounds such as, N-acetyl-aspartate, beta-alanine, adenylsuccinate, arginino-succinate and N-carbamoylaspartate. Aspartate is also a metabolite in the urea cycle and involved in gluconeogenesis. Additionally, aspartate carries the reducing equivalents in the mitochondrial malate-aspartate shuttle, which utilizes the ready interconversion of aspartate and oxaloacetate. The conjugate base of L-aspartic acid, aspartate, also acts as an excitatory neurotransmitter in the brain which activates NMDA receptors.

SMP0121055

Pw122323 View Pathway
Metabolic

Mevalonate Pathway

The Mevalonate Pathway is a necessary pathway that occurs in archaea, eukaryotes and select bacteria. It has mainly been studied with regard to cholesterol biosynthesis and how it relates to cardiovascular disease in humans, but has recently garnered attention for its many other essential roles within human pathology. The pathway begins in the cytoplasm with acetyl-CoA and acetoacetyl-CoA, which interact with acetyl-CoA acetyltransferase, coenzyme A and water to synthesize hydroxymethylglutaryl-CoA synthase. In turn, this synthase teams up with coenzyme A and a hydrogen ion in the endoplasmic reticulum to create 3-hydroxy-3-methylglutaryl-CoA. 3-Hydroxy-3-methylglutaryl-CoA then pairs with 2NADPH, 2 hydrogen ions and is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase to produce (R)-mevalonate, also producing byproducts CoA and NADP. Exiting the endoplasmic reticulum, and entering the peroxisome, (R)-mevalonate uses the help of ATP and mevalonate kinase to create mevalonic acid (5P). This piece is especially important to the human species as decreased activity of the enzyme mevalonate kinase has been found to be a direct link to two auto-inflammatory disorders: MVA and HIDS. Using phosphomevalonate kinase and ATP, the pathway re-enters the cytoplasm and mevalonic acid (5P) converts to (R)-mevalonic acid-5-pyrophosphate and ADP. (R)-mevalonic acid-5-pyrophosphate, ATP and diphosphomevalonate decarboxylase work together to create phosphate, carbon dioxide, ADP and isopentenyl pyrophosphate. Re-entering the peroxisome, isopentenyl diphosphate delta isomerase 1 is waiting to propel isopentenyl pyrophosphate into dimethylallylpyrophosphate. This pushes the pathway back into the cytoplasm, where another isopentenyl pyrophosphate molecule and the enzyme farnesyl pyrophosphate synthase create pyrophosphate and geranyl-PP. Yet another isopentenyl pyrophosphate molecules works with farnesyl pyrophosphate synthase to produce pyrophosphate and farnesyl pyrophosphate. Now in the endoplasmic reticulum membrane, 2 farnesyl pyrophosphate molecules with the help of NADPH and a hydrogen ion catalyze with squalene synthase and create squalene. This is an important first step in the specific hepatic cholesterol pathway. Remaining in the endoplasmic reticulum membrane, squalene, FMNH, oxygen and squalene monooxygenase synthesize (S)-2,3-epoxysqualene. This comes along with the byproducts of flavin mononucleotide, a hydrogen ion and water. In the final reaction within this pathway, lanesterol synthase converts (S)-2,3-epoxysqualene to lanosterin. Not pictured in this pathway, lanosterin will eventually be converted to cholesterol, an important part of many functions in the human body.

SMP0000072

Pw000003 View Pathway
Metabolic

Glutamate Metabolism

Glutamate is one of the non-essential amino acids that is produced by the body. Glutamate is precursor for many nucleic acids and proteins in addition to its role in the central nervous system. It is an excitatory neurotransmitter and has a role in neuronal plasticity, affecting memory and learning. Glutamate plays a role in numerous metabolic pathways. Dysfunctional glutamate metabolism may cause disorders such as: gyrate atrophy, hyperammonemia, γ-hydoxybutyric aciduria, hemolytic anemia, and 5-oxoprolinuria.

SMP0000045

Pw000008 View Pathway
Metabolic

Amino Sugar Metabolism

Amino sugars are sugar molecules containing an amine group. They make up many polysaccharides including, glycosaminoglycans or mucopolysaccharides.

SMP0000054

Pw000022 View Pathway
Metabolic

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.

SMP0000455

Pw000027 View Pathway
Metabolic

Homocysteine Degradation

Homocysteine is an amino acid and homologue of cysteine that appears in the body as a result of the degradation of methionine. In mammals, homocysteine is used to biosynthesize cysteine via the following pathway. First the enzyme cystathionine beta-synthetase irreversibly condenses homocysteine with L-serine, forming L-cystathionine. The L-cystathionine is then cleaved by cystathionine gamma-lyase, producing 2-oxobutanoate, L-cysteine, and ammonia. The 2-oxobutanoate is further broken down via the 2-oxobutanoate degradation pathway, producing citric acid cycle intermediates, while the L-cysteine goes to the cysteine metabolism pathway. The homocysteine degradation pathway composes a part of the larger methionine metabolism pathway.

SMP0000459

Pw000034 View Pathway
Metabolic

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.
Showing 91 - 100 of 48700 pathways