glucarate catabolism
glucarate breakdown
glucarate degradation

The chemical reactions and pathways resulting in the breakdown of glucarate, the anion of glucaric acid. [ISBN:0198506732]


butanoic acid catabolic process
butyrate catabolism
butanoic acid breakdown
butanoic acid catabolism
butyrate degradation
butanoic acid degradation
butyrate breakdown

The chemical reactions and pathways resulting in the breakdown of butyrate, the anion of butyric acid. [ISBN:0198506732]


2-oxobutyrate degradation
2-oxobutyrate breakdown
alpha-ketobutyrate catabolism
alpha-ketobutyrate catabolic process
2-oxobutyrate catabolism

The chemical reactions and pathways resulting in the breakdown of 2-oxobutyrate, the anion of the organic acid 2-oxobutyric acid, which contains a ketone group on carbon 2. [ISBN:0198506732]


galactonate breakdown
galactonate degradation
galactonate catabolism

The chemical reactions and pathways resulting in the breakdown of galactonate, the anion of galactonic acid. [GOC:ai]


galacturonate catabolism
galacturonate breakdown
galacturonate degradation

The chemical reactions and pathways resulting in the breakdown of galacturonate, the anion of galacturonic acid. [GOC:ai]


D-galacturonate catabolism
D-galacturonate degradation
D-galacturonate breakdown

The chemical reactions and pathways resulting in the breakdown of D-galacturonate, the D-enantiomer of galacturonate, the anion of galacturonic acid. [GOC:ai, GOC:jsg, GOC:mah]


glucuronate degradation
glucuronate catabolism
glucuronate breakdown

The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid. [GOC:go_curators]


glucuronate degradation to xylulose 5-phosphate

glucuronate breakdown to xylulose 5-phosphate

glucuronate catabolic process to xylulose 5-phosphate

The chemical reactions and pathways resulting in the breakdown of glucuronate into other compounds, including xylulose 5-phosphate. [GOC:go_curators]


propionate breakdown
propionate degradation
propionate catabolism

The chemical reactions and pathways resulting in the breakdown of propionate, the anion derived from propionic acid. [GOC:go_curators]


propionate degradation, 2-methylcitrate cycle

propionate breakdown, 2-methylcitrate cycle

propionate catabolic process, 2-methylcitrate cycle

The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle. [GOC:go_curators]


shikimate breakdown
shikimate catabolism
shikimate degradation

The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. [GOC:go_curators]


organomercury catabolism
organomercury breakdown
organomercury degradation

The chemical reactions and pathways resulting in the breakdown of organomercury compounds, any organic compound containing a mercury atom. [GOC:ai]


methylmercury catabolism
methylmercury degradation
methylmercury breakdown

The chemical reactions and pathways resulting in the breakdown of methylmercury (MeHg+), a highly toxic organometal. [GOC:ai]


pigment breakdown
pigment catabolism
pigment degradation

The chemical reactions and pathways resulting in the breakdown of a pigment, any general or particular coloring matter in living organisms, e.g. melanin. [ISBN:0198506732]


eye pigment degradation
eye pigment breakdown
eye pigment catabolism

The chemical reactions and pathways resulting in the breakdown of eye pigments, any general or particular coloring matter in living organisms, found or utilized in the eye. [GOC:ai]


rhodopsin catabolism
rhodopsin breakdown
rhodopsin degradation

The chemical reactions and pathways resulting in the breakdown of rhodopsin, a brilliant purplish-red, light-sensitive visual pigment found in the rod cells of the retinas. [ISBN:0198506732]


melanin degradation
melanin breakdown
melanin catabolism

The chemical reactions and pathways resulting in the breakdown of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom. [ISBN:0198506732]


ocellus pigment breakdown
ocellus pigment catabolism
ocellus pigment degradation

The chemical reactions and pathways resulting in the breakdown of ocellus pigments, any general or particular coloring matter in living organisms, found or utilized in the ocellus, a minute simple eye found in many invertebrates. [GOC:ai, PMID:15176085, PMID:18421706]


polyphosphate degradation
polyphosphate catabolism
polyphosphate breakdown

The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid. [GOC:go_curators, ISBN:0198506732]


regulation of catabolism
regulation of degradation
regulation of breakdown

Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. [GOC:go_curators]


negative regulation of catabolism
negative regulation of degradation
downregulation of catabolic process
down-regulation of catabolic process
negative regulation of breakdown
down regulation of catabolic process

negative regulation of catabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. [GOC:go_curators]


positive regulation of catabolism
upregulation of catabolic process
positive regulation of degradation
up-regulation of catabolic process
positive regulation of breakdown
up regulation of catabolic process

positive regulation of catabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. [GOC:go_curators]


regulation of glycolysis involved in cellular glucose homeostasis

Any process that modulates the frequency, rate or extent of glycolysis. [GOC:go_curators]


down-regulation of glycolysis
down regulation of glycolysis
downregulation of glycolysis

negative regulation of glycolytic process

Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis. [GOC:go_curators]


up-regulation of glycolysis
up regulation of glycolysis
upregulation of glycolysis

positive regulation of glycolytic process

Any process that activates or increases the frequency, rate or extent of glycolysis. [GOC:go_curators]


ribonucleoside catabolism
ribonucleoside degradation
ribonucleoside breakdown

The chemical reactions and pathways resulting in the breakdown of any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule. [GOC:jl]


terpene catabolism
terpene degradation
terpene breakdown

The chemical reactions and pathways resulting in the breakdown of terpenes, any of a large group of hydrocarbons made up of isoprene units. [GOC:ai]


alpha-pinene catabolism
alpha-pinene degradation
alpha-pinene breakdown

The chemical reactions and pathways resulting in the breakdown of alpha-pinene, a monoterpene that may be a significant factor affecting bacterial activities in nature. [GOC:ai]


limonene breakdown
limonene catabolism
limonene degradation

The chemical reactions and pathways resulting in the breakdown of limonene (4-isopropenyl-1-methyl-cyclohexene), a monocyclic monoterpene. [GOC:ai]


urate catabolism
urate degradation
uric acid catabolic process
urate breakdown

The chemical reactions and pathways resulting in the breakdown of urate, the anion of uric acid, 2,6,8-trioxypurine. [ISBN:0198506732]


vitamin degradation
vitamin breakdown
vitamin catabolism

The chemical reactions and pathways resulting in the breakdown of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. [GOC:ai]


fat-soluble vitamin catabolism
fat-soluble vitamin degradation
fat-soluble vitamin breakdown

The chemical reactions and pathways resulting in the breakdown of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. [GOC:jl, ISBN:0198506732]


vitamin D degradation
vitamin D catabolism
calciferol catabolic process
calciferol catabolism
vitamin D breakdown

The chemical reactions and pathways resulting in the breakdown of vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3). [GOC:mah, ISBN:0471331309]


water-soluble vitamin breakdown
water-soluble vitamin catabolism
water-soluble vitamin degradation

The chemical reactions and pathways resulting in the breakdown of any of a diverse group of vitamins that are soluble in water. [GOC:jl, http://www.indstate.edu/thcme/mwking/vitamins.html]


vitamin B7 catabolism
vitamin B7 catabolic process
biotin degradation
biotin catabolism
biotin breakdown
vitamin H catabolic process
vitamin H catabolism

The chemical reactions and pathways resulting in the breakdown of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid. [ISBN:0198506732]


L-ascorbic acid breakdown
vitamin C catabolic process
ascorbate catabolism
vitamin C catabolism
L-ascorbic acid degradation
L-ascorbic acid catabolism
ascorbate catabolic process

The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions. [GOC:go_curators]


thiamin catabolic process
vitamin B1 catabolism
thiamine degradation
thiamine breakdown
vitamin B1 catabolic process
thiamine catabolism

The chemical reactions and pathways resulting in the breakdown of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. [GOC:jl, ISBN:0198506732]


vitamin B2 catabolism
vitamin G catabolism
vitamin B2 catabolic process
riboflavin catabolism
riboflavin breakdown
riboflavin degradation
vitamin G catabolic process

The chemical reactions and pathways resulting in the breakdown of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). [GOC:jl, http://www.indstate.edu/thcme/mwking/vitamins.html]


coenzyme and prosthetic group metabolism


The chemical reactions and pathways involving 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA, a derivative of coenzyme A. [GOC:ai]


acetyl coenzyme A metabolic process
acetyl coenzyme A metabolism
acetyl-CoA metabolism

The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis. [ISBN:0198547684]


The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group. [ISBN:0198506732]


The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. [GOC:go_curators]


The chemical reactions and pathways involving coenzyme B (7-mercaptoheptanoylthreonine phosphate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes. [GOC:go_curators]


The chemical reactions and pathways involving coenzyme M (2-thioethansulfonate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes. [GOC:go_curators]


oxidized flavin-adenine dinucleotide metabolic process

oxidized flavin adenine dinucleotide metabolic process

oxidized flavin-adenine dinucleotide metabolism

oxidized flavin adenine dinucleotide metabolism

The chemical reactions and pathways involving FAD, the oxidized form of flavin adenine dinucleotide. [PMID:20822113]


The chemical reactions and pathways involving FMN, riboflavin 5'-(dihydrogen phosphate), a coenzyme for a number of oxidative enzymes including NADH dehydrogenase. [GOC:ai, PMID:20822113]


The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle. [ISBN:0198506732]


The chemical reactions and pathways involving coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester. [ISBN:0198547684]


The chemical reactions and pathways involving any phosphorylated nucleoside. [GOC:mah]


vitamin B5 metabolism
pantothenate metabolism
vitamin B5 metabolic process

The chemical reactions and pathways involving pantothenate, the anion of pantothenic acid, the amide of beta-alanine and pantoic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods. [GOC:ai, ISBN:0721662544]


iron-sulfur cluster biosynthesis
iron-sulphur cluster assembly

The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster. [GOC:jl, GOC:mah, GOC:pde, GOC:vw]


The chemical reactions and pathways involving L-methylmalonyl-CoA, the L-enantiomer of 2-carboxypropanoyl-CoA. S-methylmalonyl-CoA is an intermediate in the beta oxidation of odd-numbered fatty acids in animals. [GOC:jsg, GOC:mah, ISBN:0198506732]


The chemical reactions and pathways involving lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group. [GOC:go_curators]


lipoate metabolic process
lipoate metabolism
lipoic acid metabolism

The chemical reactions and pathways involving lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid. [GOC:ai, ISBN:0198506732]


reduced flavin adenine dinucleotide metabolic process

The chemical reactions and pathways involving the reduced form of flavin adenine dinucleotide. [GOC:ai]


The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. [GOC:jl]


The chemical reactions and pathways involving nicotinamide, pyridine-3-carboxamide, the amide of nicotinic acid. It is a member of the B complex of vitamins and occurs widely in living organisms. [ISBN:0198506732]


reduced nicotinamide adenine dinucleotide metabolic process

reduced nicotinamide adenine dinucleotide metabolism

The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. [GOC:jl, ISBN:0618254153]


reduced nicotinamide adenine dinucleotide oxidation

reduced nicotinamide adenine dinucleotide dehydrogenation

A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD. [GOC:ai]


reduced nicotinamide adenine dinucleotide regeneration

A metabolic process that generates a pool of NADH by the reduction of NAD+. [GOC:mah]


reduced nicotinamide adenine dinucleotide phosphate metabolic process

oxidized nicotinamide adenine dinucleotide phosphate metabolic process

reduced nicotinamide adenine dinucleotide phosphate metabolism

oxidized nicotinamide adenine dinucleotide phosphate metabolism

The chemical reactions and pathways involving nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; metabolism may be of either the oxidized form, NADP, or the reduced form, NADPH. [GOC:mah]


reduced nicotinamide adenine dinucleotide phosphate regeneration

A metabolic process that generates a pool of NADPH by the reduction of NADP+. [GOC:mah]


oxidized nicotinamide adenine dinucleotide metabolic process

oxidized nicotinamide adenine dinucleotide metabolism

The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. [GOC:jl, ISBN:0618254153]


NAD phosphorylation and dephosphorylation

OBSOLETE. The addition or removal of a phosphate group from nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. [GOC:jl, ISBN:0618254153]


nicotinamide nucleotide metabolic process

The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide. [ISBN:0198506732]


N-ribosylnicotinamide metabolic process
nicotinamide riboside metabolism

The chemical reactions and pathways involving nicotinamide riboside, the product of the formation of a glycosidic bond between ribose and nicotinamide. [ISBN:0198506732]


The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid, or niacin). [ISBN:0198506732]


Any process that generates a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base, from derivatives of them without de novo synthesis. [GOC:jl]


coenzyme Q metabolism
ubiquinone metabolism
coenzyme Q metabolic process

The chemical reactions and pathways involving ubiquinone, a lipid-soluble electron-transporting coenzyme. [GOC:mah]


The chemical reactions and pathways involving pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate. [GOC:curators]


Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis. [GOC:jl]


The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule. [GOC:jl, http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k]


phytonadione metabolism
vitamin K1 metabolism
phytylmenaquinone metabolism
vitamin K1 metabolic process
phytylmenaquinone metabolic process
phylloquinone metabolism
phytonadione metabolic process
phytomenadione metabolism
phytomenadione metabolic process

The chemical reactions and pathways involving phylloquinone, a quinone-derived compound synthesized by green plants. Phylloquinone has vitamin K activity and is known as vitamin K1. [GOC:jl, http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k]


The chemical reactions and pathways involving any of the menaquinones, quinone-derived compounds synthesized by intestinal bacteria. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones have vitamin K activity and are known as vitamin K2. [GOC:jl, http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k]


thiamine pyrophosphate metabolic process

The chemical reactions and pathways involving thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle. [GOC:jl, ISBN:0198506732]


TPP dephosphorylation
thiamin diphosphate dephosphorylation

The removal of one or more phosphate groups from thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle. [GOC:jl, ISBN:0198506732]


The chemical reactions and pathways involving corrin, C19H22N4, the fundamental heterocyclic skeleton of the corrinoids. It consists of four reduced pyrrole rings joined into a macrocyclic ring. Corrin is the core of the vitamin B12 molecule. [GOC:ai, ISBN:0198506732]


The chemical reactions and pathways involving chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment. [GOC:jl]


The chemical reactions and pathways involving a bacteriochlorophyll, any of the chlorophylls of photosynthetic bacteria. They differ structurally from the chlorophylls of higher plants. [GOC:mah, ISBN:0198506732]


haem metabolism
haem metabolic process
heme metabolism

The chemical reactions and pathways involving heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring. [GOC:jl, ISBN:0124325653]


heme a metabolism
haem a metabolism
haem a metabolic process

The chemical reactions and pathways involving heme a, a derivative of heme found in cytochrome aa3. [GOC:curators]


haem B metabolic process
haem B metabolism
protoheme metabolism
protoheme metabolic process
heme B metabolism

The chemical reactions and pathways involving heme b, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes. [GOC:yaf, PMID:29414780]


haem C metabolic process
haem C metabolism
heme C metabolism

The chemical reactions and pathways involving heme c, a derivative of heme found in cytochromes c, b4, and f. [GOC:curators]


sirohaem metabolic process
siroheme metabolism
sirohaem metabolism

The chemical reactions and pathways involving siroheme, a tetrahydroporphyrin with adjacent, reduced pyrrole rings. [ISBN:0198506732]


The chemical reactions and pathways involving protoporphyrinogen IX, the specific substrate for the enzyme ferrochelatase, which catalyzes the insertion of iron to form protoheme. It is probably also the substrate for chlorophyll formation. [ISBN:0198506732]


The chemical reactions and pathways involving uroporphyrinogen III, a precursor for synthesis of vitamin B12, chlorophyll, and heme in organisms that produce these compounds. [GOC:ai]


cobalamin metabolism
vitamin B12 metabolic process
vitamin B12 metabolism

The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. [GOC:go_curators]


The chemical reactions and pathways involving siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action. [ISBN:0198547684]


The chemical reactions and pathways involving rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti. [MetaCyc:PWY-761, PMID:11274118]


The chemical reactions and pathways involving vibriobactin, the major siderophore produced by Vibrio cholerae. [GOC:jl, PMID:11112537]


The chemical reactions and pathways involving tetrahydrocorphins, tetrapyrroles that combine the structural elements of both porphyrins and corrins. [Wikipedia:Morphine]


nickel-tetrapyrrole coenzyme metabolic process

The chemical reactions and pathways involving an enzyme cofactor consisting of a tetrapyrrole structure containing nickel, such as the F-430 cofactor found in methyl-coenzyme M reductase. [GOC:mah, Wikipedia:Cofactor_F430]


peptidyl-1-thioglycine anabolism from peptidyl-glycine

peptidyl-1-thioglycine synthesis from peptidyl-glycine

peptidyl-1-thioglycine formation from peptidyl-glycine

peptidyl-1-thioglycine biosynthetic process from peptidyl-glycine

The chemical reactions and pathways resulting in the formation of peptidyl-1-thioglycine from other compounds, including peptidyl-glycine. [http://www.uni-marburg.de/mpi/thauer/thauer_res.html, RESID:AA0265]


peptidyl-1-thioglycine biosynthetic process, carboxy-terminal

The chemical reactions and pathways resulting in the formation of carboxy-terminal peptidyl-1-thioglycine, which has a carboxy-terminal thiocarboxy-C(=O)-SH bond. [GOC:go_curators, http://www.uni-marburg.de/mpi/thauer/thauer_res.html, RESID:AA0265]


peptidyl-1-thioglycine biosynthetic process, internal

The chemical reactions and pathways resulting in the formation of internal peptidyl-1-thioglycine, which has an internal C=S bond, instead of an internal C=O bond, in the peptide. [GOC:go_curators, http://www.uni-marburg.de/mpi/thauer/thauer_res.html, RESID:AA0265]


OBSOLETE. (Was not defined before being made obsolete). [GOC:ai]


The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each. [ISBN:0198506732]


The process of transferring reducing equivalents from the cytosol into the mitochondria; NADH is used to synthesise glycerol 3-phosphate in the cytosol; this compound is then transported into the mitochondria where it is converted to dihydroxyacetone phosphate (DHAP) using FAD; DHAP then returns to the cytosol to complete the cycle. [GOC:jl, GOC:mtg_electron_transport, ISBN:0716720094, PMID:16368075]


oxidative phosphorylation, NADH to ubiquinone

mitochondrial electron transport, NADH to ubiquinone

The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation. [ISBN:0716731363]


oxidative phosphorylation, succinate to ubiquinone

mitochondrial electron transport, succinate to coenzyme Q

mitochondrial electron transport, succinate to ubiquinone

The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II. [ISBN:0716731363]


electron carrier, chlorophyll electron transport system

A process, occurring as part of photosynthesis, in which light provides the energy for a series of electron carriers to operate together to transfer electrons and generate a transmembrane electrochemical gradient. [GOC:mtg_electron_transport, ISBN:0198547684]


photosynthetic electron transport in cytochrome b6/f


photosynthetic electron transport in photosystem I

A photosynthetic electron transport chain in which electrons move from the primary electron acceptor (Quinone, X) through a chain of electron transport molecules in the thylakoid membrane until they reach ferredoxin which passes the electron to the ultimate electron acceptor; NADP. [GOC:jid, ISBN:0716731363, ISBN:0816017360]


photosynthetic electron transport in photosystem II

A photosynthetic electron transport chain in which electrons move from the primary electron acceptor (Quinone, Q) through a chain of electron transport molecules in the thylakoid membrane until they reach the ultimate electron acceptor of Photosystem II, which is plastocyanin (PC). The electron is then passed to the P700 chlorophyll a molecules of the reaction centre of photosystem I. [GOC:jid, ISBN:0716731363, ISBN:0816017360]


photosynthetic electron transport in plastocyanin


photosynthetic electron transport in plastoquinone


The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. [GOC:jl]

generation of precursor metabolites and energy


energy derivation by oxidation of organic compounds

The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. [GOC:mah]


aerobic respiration, using carbon monoxide as electron donor

The metabolic process in which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation. [PMID:18024677]


aerobic respiration, using ferrous ions as electron donor

The metabolic process in which ferrous ions (Fe2+) are oxidized to ferric ions (Fe3+) to generate energy, coupled to the reduction of carbon dioxide. [ISBN:3131084111]


aerobic respiration, using hydrogen as electron donor

The oxidation of hydrogen (H2) to water (H2O), using oxygen (O2) as the electron acceptor. A hydrogenase enzyme binds H2 and the hydrogen atoms are passed through an electron transfer chain to O2 to form water. [MetaCyc:P283-PWY]


aerobic respiration, using sulphur or sulphate as electron donor

aerobic respiration, using sulfur or sulfate as electron donor

An aerobic respiration process in which a sulfur-containing molecule (hydrogen sulfide, sulfur, sulfite, thiosulfate, and various polythionates) is oxidized. [PMID:11425697]


The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor. [GOC:das, GOC:jl, ISBN:0140513590]


The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. [GOC:mah]


The anaerobic chemical reactions and pathways resulting in the breakdown of acetate, yielding energy in the form of ATP. [GOC:jl, MetaCyc:P142-PWY]


The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids, yielding energy in the form of ATP. [GOC:curators, GOC:jl, MetaCyc:Fermentation]


anaerobic catabolism of pairs of amino acids

The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids; in these reactions, one amino acid is oxidised (acts as an electron donor) and a different amino acid is reduced (acts as an electron acceptor); oxidation of the electron-donating amino acid yields energy in the form of ATP. [GOC:mah, PMID:13140081]


glucose fermentation to butyrate
butyrate fermentation

The anaerobic chemical reactions and pathways resulting in the breakdown of glucose, with the production of acetic acid, butyric acid, carbon dioxide (CO2), and dihydrogen; effected by some saccharolytic species of Clostridium, e.g. C. butyricum. [ISBN:0198506732]


Fermentation that includes the anaerobic conversion of glucose to pyruvate via the glycolytic pathway. [GOC:curators]


glucose catabolic process to butanediol
butanediol fermentation
glucose fermentation to butanediol

The anaerobic chemical reactions and pathways resulting in the breakdown of glucose into butanediol; effected by some members of the Enterobacteriaceae, e.g. Enterobacter, Erwinia, Klebsiella, and Serratia. [GOC:dph, GOC:nr, ISBN:0198506732]


glucose fermentation to lactate via pyruvate

glucose catabolic process to lactate via pyruvate

The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, via canonical glycolysis, yielding energy in the form of adenosine triphosphate (ATP). [GOC:jl]


The anaerobic chemical reactions and pathways resulting in the breakdown of glucose into ethanol, lactate, formate, succinate, and acetate, yielding energy in the form of ATP. [ISBN:0716720094, MetaCyc:FERMENTATION-PWY]


acrylate pathway
nonrandomizing pathway
propionate fermentation

lactate fermentation to propionate and acetate

The anaerobic enzymatic conversion of lactate to propionate, concomitant with the oxidation of lactate to acetate and CO2 and yielding energy in the form of adenosine triphosphate (ATP). [GOC:jl, MetaCyc:PROPFERM-PWY]


lactate fermentation
glucose fermentation to lactate

The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, and possibly ethanol, yielding energy in the form of adenosine triphosphate (ATP). [GOC:jl]


glucose fermentation to D-lactate and ethanol

glucose catabolic process to D-lactate and ethanol

The anaerobic chemical reactions and pathways resulting in the enzymatic breakdown of D-glucose to D-lactate and ethanol, yielding energy in the form of adenosine triphosphate (ATP) at the rate of one ATP per glucose molecule. [GOC:jl, MetaCyc:P122-PWY]


The anaerobic chemical reactions and pathways resulting in the breakdown of a nitrogen-containing compound, yielding energy in the form of ATP. [GOC:mah]


Fermentation that does not include the anaerobic conversion of glucose to pyruvate via the glycolytic pathway. [GOC:jl, MetaCyc:Fermentation]


diacetyl fermentation
citrate fermentation to diacetyl

The anaerobic chemical reactions and pathways resulting in the breakdown of citrate to diacetyl, yielding energy in the form of ATP. [MetaCyc:P126-PWY]


ethanol-acetate fermentation to butyrate and caproate

The anaerobic chemical reactions and pathways resulting in the breakdown of ethanol and acetate to butyrate and caproate, yielding energy in the form of ATP. [MetaCyc:P127-PWY]


glucose catabolic process to lactate and acetate

glucose fermentation to lactate and acetate

The anaerobic chemical reactions and pathways resulting in the breakdown of glucose to lactate and acetate, yielding energy in the form of ATP. [MetaCyc:P124-PWY]


oxidation of galena
oxidation of lead sulfide
lead sulphide oxidation

The chemical reactions and pathways resulting in the conversion of lead sulfide to lead sulfate. [MetaCyc:P301-PWY]


The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I. [http://www.arabidopsis.org]


Absorption and transfer of the energy absorbed from light photons between photosystem reaction centers. [GOC:sm]


photosynthesis, light harvesting in photosystem I

After a photon of light is absorbed by one of the many chlorophyll molecules, in one of the light-harvesting complexes of an antenna on photosystem I, some of the absorbed energy is transferred to the pair of chlorophyll molecules in the reaction center. [GOC:jid, ISBN:0716731363, ISBN:0816017360]


photosynthesis, light harvesting in photosystem II

After a photon of light is absorbed by one of the many chlorophyll molecules, in one of the light-harvesting complexes of an antenna on photosystem II, some of the absorbed energy is transferred to the pair of chlorophyll molecules in the reaction center. [GOC:jid, ISBN:0716731363, ISBN:0816017360]


A photosynthetic phosphorylation process in which ATP synthesis is driven by a proton gradient generated across the thylakoid membrane. Involves only photosystem I. [ISBN:0198547684]


A photosynthetic phosphorylation process in which ATP synthesis is linked to the transport of electrons from water to NADP+ with the production of NADPH and dioxygen (O2). Involves photosystem I and photosystem II. [ISBN:0198547684]


regulation of photosynthesis, light reaction

Any process that modulates the frequency, rate or extent of the light-dependent reaction of photosynthesis. [GOC:jl]


The stabilization of the photosystem I protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis. [GOC:go_curators]


The stabilization of the photosystem II protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis. [GOC:go_curators]


The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol. [GOC:ai, ISBN:0198506732]


glyceride metabolism
glyceride metabolic process
acylglycerol metabolism

The chemical reactions and pathways involving acylglycerol, any mono-, di- or triester of glycerol with (one or more) fatty acids. [ISBN:0198506732]


diacylglycerol metabolism
diglyceride metabolism

The chemical reactions and pathways involving diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group. [PMID:11481335]


The chemical reactions and pathways involving CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate. It is a common intermediate in phospholipid biosynthesis. [PMID:24533860]


monoacylglycerol metabolism
monoglyceride metabolic process
monoglyceride metabolism

The chemical reactions and pathways involving monoacylglycerol, any ester of glycerol in which any one of its hydroxyl groups has been acylated with a fatty acid, the other being non-esterified. [ISBN:0198506732]


triacylglycerol metabolism
triacylglycerol metabolic process
triglyceride metabolism

The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins. [ISBN:0198506732]


The release of triglycerides, any triester of glycerol, from storage within cells or tissues, making them available for metabolism. [GOC:mah, PMID:11943743, PMID:15713625]


The chemical reactions and pathways involving ether lipids, lipids that contain (normally) one lipid alcohol in ether linkage to one of the carbon atoms (normally C-1) of glycerol. [ISBN:0198506732, PMID:15337120]


The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). [ISBN:0198506732]


vitamin B7 metabolism
biotin metabolism
vitamin B7 metabolic process
vitamin H metabolism
vitamin H metabolic process

The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions. [ISBN:0198506732]


The chemical reactions and pathways involving oxazole or thiazole, five-membered heterocyclic ring structures containing an oxygen and a sulfur, respectively, in the 1-position and a nitrogen in the 3-position. [GOC:curators]


The chemical reactions and pathways involving urate, the anion of uric acid, 2,6,8-trioxypurine, the end product of purine metabolism in certain mammals and the main excretory product in uricotelic animals. [ISBN:0198506732]


The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics. [ISBN:0198506732]


The chemical reactions and pathways involving auxins, a group of plant hormones that regulate aspects of plant growth. [GOC:lr]


The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones. [GOC:ai]


The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants. [GOC:jl, http://www.cogsci.princeton.edu/]


The chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids ubiquitous in insects and other arthropods, in which they initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females. [ISBN:0198506732]


The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development. [GOC:go_curators]


Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell. [GOC:go_curators]


down regulation of ecdysteroid secretion

down-regulation of ecdysteroid secretion

negative regulation of ecdysteroid secretion

Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid. [GOC:go_curators]


up-regulation of ecdysteroid secretion
upregulation of ecdysteroid secretion
up regulation of ecdysteroid secretion

positive regulation of ecdysteroid secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid. [GOC:go_curators]


regulation of ecdysteroid metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females. [ISBN:0198506732]


down-regulation of ecdysteroid metabolic process

down regulation of ecdysteroid metabolic process

negative regulation of ecdysteroid metabolism

downregulation of ecdysteroid metabolic process

negative regulation of ecdysteroid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids. [GOC:go_curators]


up-regulation of ecdysteroid metabolic process

upregulation of ecdysteroid metabolic process

up regulation of ecdysteroid metabolic process

positive regulation of ecdysteroid metabolism

positive regulation of ecdysteroid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids. [GOC:go_curators]


oestrogen metabolism
estrogen metabolic process
oestrogen metabolic process

The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants. [ISBN:0198506732]


glucocorticosteroid metabolism
glucocorticosteroid metabolic process
glucocorticoid metabolism

The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects. [ISBN:0198506732]


The chemical reactions and pathways involving juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis. [GOC:go_curators, ISBN:0198547684]


The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis. [GOC:go_curators, ISBN:0198547684]


regulation of juvenile hormone secretion

Any process that modulates the frequency, rate or extent of juvenile hormone secretion. [GOC:go_curators]


down-regulation of juvenile hormone secretion

downregulation of juvenile hormone secretion

down regulation of juvenile hormone secretion

negative regulation of juvenile hormone secretion

Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone. [GOC:go_curators]


up-regulation of juvenile hormone secretion

up regulation of juvenile hormone secretion

upregulation of juvenile hormone secretion

positive regulation of juvenile hormone secretion

Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone. [GOC:go_curators]


regulation of juvenile hormone metabolism

regulation of juvenile hormone metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone. [GOC:go_curators]


down-regulation of juvenile hormone metabolic process

down regulation of juvenile hormone metabolic process

downregulation of juvenile hormone metabolic process

negative regulation of juvenile hormone metabolism

negative regulation of juvenile hormone metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone. [GOC:go_curators]


upregulation of juvenile hormone metabolic process

up-regulation of juvenile hormone metabolic process

up regulation of juvenile hormone metabolic process

positive regulation of juvenile hormone metabolism

positive regulation of juvenile hormone metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone. [GOC:go_curators]


The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance. [ISBN:0198506732]


The generation of a mature peptide hormone by posttranslational processing of a prohormone. [GOC:mah]


The formation of mature insulin by proteolysis of the precursor preproinsulin. The signal sequence is first cleaved from preproinsulin to form proinsulin; proinsulin is then cleaved to release the C peptide, leaving the A and B chains of mature insulin linked by disulfide bridges. [ISBN:0198506732]


isopentenyl diphosphate metabolic process

isopentenyl pyrophosphate metabolic process

The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids. [ISBN:0198506732]


The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. [GOC:jl, ISBN:0787650153]


camphor metabolic process
(+)-camphor metabolism
camphor metabolism

The chemical reactions and pathways involving (+)-camphor, a bicyclic monoterpene ketone which is one of the major components in the leaves of common sage. Camphor exists in two enantiomers, but the (+)-isomer is more widely distributed. [UM-BBD_pathwayID:cam]


2-oxobutyrate metabolism
alpha-ketobutyrate metabolism
alpha-ketobutyrate metabolic process

The chemical reactions and pathways involving 2-oxobutyrate, the anion of the organic acid 2-oxobutyric acid, which contains a ketone group on carbon 2. [PMID:17034760]


The chemical reactions and pathways involving acetoin, 3-hydroxy-2-butanone, often as part of a fermentation pathway or for use as a carbon source. [GOC:mlg]


The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer. [ISBN:0198506732]


The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids. [GOC:mah, PMID:17979511]


The chemical reactions and pathways involving leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid. [GOC:ma]


The chemical reactions and pathways involving prostanoids, any compound based on or derived from the prostanoate structure. [ISBN:0198506732]


The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities. [ISBN:0198506732]


The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen. [ISBN:0198506732, MetaCyc:FAO-PWY]


A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway. [PMID:10198260]


A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively). [GOC:mah, ISBN:0198506732, MetaCyc:FAO-PWY]


Any process that modulates the frequency, rate or extent of fatty acid oxidation. [GOC:ai]


down-regulation of fatty acid oxidation
downregulation of fatty acid oxidation
down regulation of fatty acid oxidation

negative regulation of fatty acid oxidation

Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid oxidation. [GOC:ai]


up-regulation of fatty acid oxidation
upregulation of fatty acid oxidation
up regulation of fatty acid oxidation

positive regulation of fatty acid oxidation

Any process that activates or increases the frequency, rate or extent of fatty acid oxidation. [GOC:ai]


The chemical reactions and pathways involving jasmonic acid, a fatty acid derivative with the formula (1R-(1 alpha, 2 beta(Z)))-3-oxo-2-(2-pentenyl)cyclopentaneacetic acid. [ISBN:0387969845]


The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. [GOC:ajp]


regulation of fatty acid metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. [GOC:go_curators]


negative regulation of fatty acid metabolism

down regulation of fatty acid metabolic process

down-regulation of fatty acid metabolic process

downregulation of fatty acid metabolic process

negative regulation of fatty acid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. [GOC:go_curators]


up-regulation of fatty acid metabolic process

positive regulation of fatty acid metabolism

upregulation of fatty acid metabolic process

up regulation of fatty acid metabolic process

positive regulation of fatty acid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. [GOC:go_curators]


short-chain fatty acid metabolic process

The chemical reactions and pathways involving fatty acids with a chain length of less than C6. [Wikipedia:Fatty_acid_metabolism]


very long chain fatty acid metabolic process

very-long-chain fatty acid metabolic process

very long-chain fatty acid metabolic process

The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22. [GOC:hjd]


The chemical reactions and pathways involving glycerolipids, any lipid with a glycerol backbone. Diacylglycerol and phosphatidate are key lipid intermediates of glycerolipid biosynthesis. [GOC:ai, PMID:8906569]


The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. [ISBN:0198547684]


The chemical reactions and pathways involving farnesyl diphosphate, an intermediate in carotenoid, sesquiterpene, squalene and sterol biosynthesis, as well as a substrate in protein farnesylation. [GOC:go_curators]


polyterpene metabolism
polyterpene metabolic process


The chemical reactions and pathways involving terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure and including derivatives with various functional groups. [ISBN:0198506732]


The chemical reactions and pathways involving diterpenoid compounds, terpenoids with four isoprene units. [ISBN:0198547684]


gibberellin metabolism
gibberellic acid metabolism
gibberellic acid metabolic process

The chemical reactions and pathways involving gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators. [ISBN:0387969845]


The chemical reactions and pathways involving monoterpenoid compounds, terpenoids having a C10 skeleton. [ISBN:0198547684]


The chemical reactions and pathways involving polyterpenoid compounds, terpenoids with more than eight isoprene units. [ISBN:0198547684]


The chemical reactions and pathways involving sesquiterpenoid compounds, terpenoids with three isoprene units. [ISBN:0198547684]


The chemical reactions and pathways involving abscisic acid, 5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid. [ISBN:0387969845]


The chemical reactions and pathways involving tetraterpenoid compounds, terpenoids with eight isoprene units. [ISBN:0198547684]


The chemical reactions and pathways involving carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail. [ISBN:0198547684]


The chemical reactions and pathways involving carotenes, hydrocarbon carotenoids. [ISBN:0198547684]


The chemical reactions and pathways involving xanthophylls, oxygen-containing carotenoids. [ISBN:0198547684]


The chemical reactions and pathways involving triterpenoid compounds, terpenoids with six isoprene units. [ISBN:0198547684]


pentacyclic triterpenoid metabolic process

The chemical reactions and pathways involving pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings. [ISBN:0198506732]


The chemical reactions and pathways involving hopanoids, pentacyclic sterol-like compounds based on the hopane nucleus. [ISBN:0198547684]


The chemical reactions and pathways involving prenols, isoprenoids of general formula (H-CH2-C(CH3)=CH-CH2-)n-OH, any primary monohydroxy alcohol whose carbon skeleton consists of two or more isoprenoid residues linked head to tail. [ISBN:0198547684]


The chemical reactions and pathways involving polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans. [PMID:11108713]


The chemical reactions and pathways involving dolichols, any 2,3-dihydropolyprenol derived from four or more linked isoprene units. [ISBN:0198506732]


The chemical reactions and pathways involving dolichyl diphosphate, a diphosphorylated dolichol derivative. In eukaryotes, these function as carriers of mono- and oligosaccharide residues in the glycosylation of lipids and proteins within intracellular membranes. [ISBN:0198506732]


regulation of isoprenoid metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving isoprenoids. [GOC:go_curators]


negative regulation of isoprenoid metabolism

down-regulation of isoprenoid metabolic process

downregulation of isoprenoid metabolic process

down regulation of isoprenoid metabolic process

negative regulation of isoprenoid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. [GOC:go_curators]


up-regulation of isoprenoid metabolic process

upregulation of isoprenoid metabolic process

up regulation of isoprenoid metabolic process

positive regulation of isoprenoid metabolism

positive regulation of isoprenoid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. [GOC:go_curators]


The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity. [ISBN:0198506732]


The chemical reactions and pathways involving lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common. [ISBN:0198506732, PMID:20974832, PMID:22216004]


The covalent alteration of one or more fatty acids in a lipid, resulting in a change in the properties of the lipid. [GOC:mah]


Covalent attachment of a glycosyl residue to a lipid molecule. [GOC:mah]


The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane. [GOC:ai]


The chemical reactions and pathways involving glycolipids, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar group acylated by one or more fatty acids and the glycerol group may be absent. [ISBN:0198547684]


The chemical reactions and pathways involving galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine. [ISBN:0198506732]


The chemical reactions and pathways involving galactosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of galactose by a ceramide group. [GOC:ai]


The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide. [ISBN:0198547684]


The chemical reactions and pathways involving ceramide oligosaccharides carrying in addition to other sugar residues, one or more sialic acid residues. [ISBN:0198506732]


The chemical reactions and pathways involving globosides, globotetraosylceramides, ceramides containing a core structure of GalNAc-beta-(1->3)-Gal-alpha-(1->4)-Glc(I). Globosides are the major neutral glycosphingolipid in normal kidneys and erythrocytes. [ISBN:0198506732]


The chemical reactions and pathways involving glycosylsphingolipidinositol (GSI) anchors, which attach membrane proteins to the lipid bilayer of the cell membrane. [GOC:go_curators]


The chemical reactions and pathways involving glycosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of a monosaccharide (or derivative) by a ceramide group. [GOC:ai, ISBN:0198506732]


The chemical reactions and pathways involving glucosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of glucose by a ceramide group. They are neutral glycolipids containing equimolar amounts of fatty acid, glucose, and sphingosine or a sphingosine derivative. [ISBN:0198506732]


The chemical reactions and pathways involving lactosylceramides, Gal-beta-(1->4)-Glc-beta-(1->1') ceramides, any compound formed by the replacement of the glycosidic C1 hydroxyl group of lactose by a ceramide group. They are the precursors of both gangliosides and globosides. [ISBN:0198506732]


The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester. [ISBN:0198506732]


glycerophospholipid metabolism
phosphoglyceride metabolic process
phosphoglyceride metabolism

The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue. [ISBN:0198506732]


The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids. [ISBN:0198506732]


The chemical reactions and pathways involving phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline. They are important constituents of cell membranes. [ISBN:0198506732]


The chemical reactions and pathways involving phosphatidylglycerols, any of a class of phospholipids in which the phosphatidyl group is esterified to the hydroxyl group of glycerol. They are important constituents of cell membranes. [ISBN:0198506732]


The chemical reactions and pathways involving phosphatidylserines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of L-serine. They are important constituents of cell membranes. [ISBN:0198506732]


The chemical reactions and pathways involving glycosylphosphatidylinositol anchors, molecular mechanisms for attaching membrane proteins to the lipid bilayer of cell membranes. Structurally they consist of a molecule of phosphatidylinositol to which is linked, via the C-6 hydroxyl of the inositol, a carbohydrate chain. This chain is in turn linked to the protein through an ethanolamine phosphate group, the amino group of which is in amide linkage with the C-terminal carboxyl of the protein chain, the phosphate group being esterified to the C-6 hydroxyl of the terminal mannose of the core carbohydrate chain. [ISBN:0198506732]


The GPI anchor metabolic process that results in enzymatic cleavage of the anchor, releasing an anchored protein from the membrane. [GOC:mah, PMID:18811934]


phosphoinositide metabolic process
PtdIns metabolic process
phosphoinositide metabolism
PtdIns metabolism
phosphatidylinositol metabolism

The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol. [ISBN:0198506732]


inositol phosphorylceramide metabolic process

inositol phosphoceramide metabolic process

The chemical reactions and pathways involving inositol phosphoceramides, any lipid with a phosphodiester bridge between an inositol residue and the ceramide group. [PMID:19726565]


mannose-inositol-P-ceramide (MIPC) metabolic process

mannose inositol phosphoceramide metabolism

mannose inositol phosphoceramide metabolic process

mannosyl-inositol phosphorylceramide metabolic process

The chemical reactions and pathways involving mannosyl-inositol phosphorylceramide, any lipid with a phosphodiester bridge between an inositol residue and the ceramide group which contains a phosphoryl (-P(O)=) groups and a mannose derivative. [GOC:ai, MetaCyc:MIPC]


mannosyl diphosphorylinositol ceramide metabolism

mannosyl diphosphorylinositol ceramide metabolic process

The chemical reactions and pathways involving mannosyl diphosphorylinositol ceramide, any lipid with a phosphodiester bridge between an inositol residue and the ceramide group which contains two phosphoryl (-P(O)=) groups and a mannose derivative. [GOC:ai]


The transfer of a phospholipid from its site of synthesis to the plasma membrane. [GOC:go_curators]


PAF metabolism
PAF metabolic process
platelet activating factor metabolism

platelet activating factor metabolic process

The chemical reactions and pathways involving platelet activating factor, 1-O-alkyl-2-acetyl-sn-glycerol 3-phosphocholine, where alkyl = hexadecyl or octadecyl. Platelet activating factor is an inflammatory mediator released from a variety of cells in response to various stimuli. [ISBN:0198547684]


The chemical reactions and pathways involving sphingomyelin, N-acyl-4-sphingenyl-1-O-phosphorylcholine, any of a class of phospholipids in which the amino group of sphingosine is in amide linkage with one of several fatty acids, while the terminal hydroxyl group of sphingosine is esterified to phosphorylcholine. [ISBN:0198506732]


The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid). [GOC:mah, ISBN:0198506732]


sphingoid base metabolic process
sphingoid base metabolism
sphingoid metabolism

The chemical reactions and pathways involving sphingoids, any of a class of compounds comprising sphinganine and its homologues and stereoisomers, and derivatives of these compounds. [ISBN:0198506732]


The chemical reactions and pathways involving ceramides, any N-acylated sphingoid. [ISBN:0198547684]


The chemical reactions and pathways involving phytosphingosine, (2S,3S,4R)-2-aminooctadecane-1,3,4-triol, a constituent of many plant sphingolipids. [ISBN:0198506732]


dihydrosphingosine metabolic process
dihydrosphingosine metabolism
sphinganine metabolism

The chemical reactions and pathways involving sphinganine, D-erythro-2-amino-1,3-octadecanediol. [PMID:29165427]


The chemical reactions and pathways involving sphinganine-1-phosphate, the phosphorylated derivative of D-erythro-2-amino-1,3-octadecanediol. [GOC:ai]


The chemical reactions and pathways involving neutral lipids, lipids only soluble in solvents of very low polarity. [ISBN:0198547684]


Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. [GOC:go_curators]


down regulation of lipid metabolic process

down-regulation of lipid metabolic process

downregulation of lipid metabolic process

negative regulation of lipid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. [GOC:go_curators]


up regulation of lipid metabolic process

up-regulation of lipid metabolic process

positive regulation of lipid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. [GOC:go_curators]


bile acid 7alpha-dehydroxylation pathway


The chemical reactions and pathways involving phytosteroids, steroids of higher plants that differ from animal steroids in having substitutions at C24 and/or a double bond at C22. Phytosteroids are so named because they occur in higher plants; some, notably ergosterol, are also found in fungi. [GOC:mah, ISBN:0198547684]


The chemical reactions and pathways involving brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects. [ISBN:0192801023]


Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. [GOC:go_curators]


down-regulation of steroid metabolic process

negative regulation of steroid metabolism

downregulation of steroid metabolic process

down regulation of steroid metabolic process

negative regulation of steroid metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. [GOC:go_curators]


up-regulation of steroid metabolic process

upregulation of steroid metabolic process

positive regulation of steroid metabolism

up regulation of steroid metabolic process

positive regulation of steroid metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. [GOC:go_curators]


sulpholipid metabolic process
sulfolipid metabolism
sulpholipid metabolism

The chemical reactions and pathways involving sulfolipids, any compound containing a sulfonic acid residue joined by a carbon-sulfur bond to a lipid. [PMID:9751667]


The chemical reactions and pathways involving aldoximes, compounds derived by the reaction of an aldose with hydroxylamine, thus containing the aldoxime group -HC=NOH. [GOC:curators]


The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases). [GOC:lr, ISBN:0122146743]


The chemical reactions and pathways involving dipyrrins (pyrromethanes), compounds containing two pyrrole rings linked through a methine, -CH=, group. [http://www.chem.qmw.ac.uk/iupac/class/tetpy.html#03]


The chemical reactions and pathways involving nicotine, (S)(-)-3-(1-methyl-2-pyrrolidinyl)pyridine. [GOC:sm, ISBN:0198547684]


The chemical reactions and pathways involving purine alkaloids, compounds derived from purine and composed of an N-containing double ring structure. [GOC:ai]


terpenoid indole alkaloid metabolic process

The chemical reactions and pathways involving terpenoid indole alkaloids, compounds formed from the condensation of tryptamine (derived from tryptophan) and secologanin (derived from geranyl pyrophosphate). [GOC:ai, http://rycomusa.com/aspp2000/public/P29/0525.html]


The chemical reactions and pathways involving tropane alkaloids, compounds containing the 8-methyl-8-azabicyclo(3.2.1)octane ring system. [GOC:ai, ISBN:0198506732]


The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons. [GOC:mah, MetaCyc:AMMOXID-PWY, MetaCyc:P303-PWY, MetaCyc:PWY-2242]


The chemical reactions and pathways involving cyanate, NCO-, the anion of cyanic acid. [ISBN:0198506732]


The chemical reactions and pathways involving cyanide, NC-, the anion of hydrocyanic acid. Cyanide is a potent inhibitor of respiration, reacting with the ferric form of cytochrome aa3 and thus blocking the electron transport chain. [ISBN:0198506732]


The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen. [MetaCyc:DENITRIFICATION-PWY]


The chemical reactions and pathways involving nitrates, inorganic or organic salts and esters of nitric acid. [GOC:jl]


The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances. [GOC:das, GOC:mah, PMID:10542156, PMID:8122899]


The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water. [GOC:ai]


A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism. [GOC:mah, GOC:mlg]


Any process that modulates the frequency, rate or extent of nitrogen utilization. [GOC:go_curators]


down regulation of nitrogen utilization
down-regulation of nitrogen utilization
downregulation of nitrogen utilization

negative regulation of nitrogen utilization

Any process that stops, prevents, or reduces the frequency, rate or extent of nitrogen utilization. [GOC:go_curators]


up-regulation of nitrogen utilization
up regulation of nitrogen utilization
upregulation of nitrogen utilization

positive regulation of nitrogen utilization

Any process that activates or increases the frequency, rate or extent of nitrogen utilization. [GOC:go_curators]


The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate. [ISBN:0198506732]


The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2. [ISBN:0198506732]


cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism

cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

nucleobase-containing compound metabolic process

Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. [GOC:ai]


The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome. [GOC:mah]


The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. [GOC:jl, GOC:ma]


The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar. [GOC:ai]


The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar. [GOC:ai]


The covalent attachment of an ADP-ribosyl group to a residue in double-stranded DNA. [PMID:11592983, PMID:27471034, PMID:29361132, PMID:29520010]


The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis. [ISBN:0716735970]


The removal of an amino group from a nucleotide base in DNA. An example is the deamination of cytosine to produce uracil. [GOC:ai]


A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme. [GOC:jl, UniProtKB-KW:KW-0680]


DNA condensation
chromosome organization and biogenesis
chromosome organization
chromosome organisation

A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. [GOC:ai, GOC:dph, GOC:jl, GOC:mah]


The packing of viral DNA into a capsid. [ISBN:0781702534]


Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron. [PMID:10487208]


Lateral transfer of a group II intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron; group II introns are self-splicing introns with a conserved secondary structure. [GOC:mcc, ISBN:0716743663, PMID:10487208]


Lateral transfer of a group I intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron; group I introns are self-splicing introns that use guanosine as a cofactor in the splicing reaction. [GOC:mcc, ISBN:0716743663, PMID:10487208]


regulation of transposition, DNA-mediated

Any process that modulates the frequency, rate or extent of DNA transposition, the process of transposing (moving to a different location) a segment of a chromosome or a piece of a DNA molecule. [GOC:dph, GOC:krc]


negative regulation of DNA transposition

negative regulation of transposition, DNA-mediated

Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition. [GOC:dph, GOC:krc, GOC:tb]


positive regulation of DNA transposition

positive regulation of transposition, DNA-mediated

Any process that activates or increases the frequency, rate or extent of DNA transposition. [GOC:dph, GOC:krc]


The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous DNA region that occurs during mitotic cell cycles. [GOC:elh]


strand invasion involved in gene conversion at mating-type locus

The conversion of the mating-type locus from one allele to another resulting from the recombinational repair of a site-specific double-strand break at the mating-type locus with information from a silent donor sequence. There is no reciprocal exchange of information because the mating-type locus copies information from the donor sequence and the donor sequence remains unchanged. [GOC:elh, PMID:10716938, PMID:7646483, PMID:9928492]


The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA. [PMID:10357855]


The formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules. [GOC:elh, PMID:10357855]


The removal of nonhomologous sequences at the broken 3' single-strand DNA end before DNA repair synthesis can occur. [PMID:10357855]


recombination within ribosomal DNA repeats

Genetic recombination within the DNA of the genes coding for ribosomal RNA. [GOC:go_curators, ISBN:0198506732]


regulation of recombination within rDNA repeats

OBSOLETE. Any process that modulates the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA. [GOC:go_curators, ISBN:0198506732]


negative regulation of recombination within rDNA repeats

OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA. [GOC:go_curators, ISBN:0198506732]


positive regulation of recombination within rDNA repeats

OBSOLETE. Any process that activates or increases the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA. [GOC:go_curators, ISBN:0198506732]


A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region. [GOC:elh]


double-strand break repair via homologous recombination

The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule. [GOC:elh, PMID:10357855]


double-strand break repair via break-induced replication

The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome. [GOC:elh, PMID:10357855]


The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules. [PMID:10357855]


Any process that modulates the frequency, rate or extent of DNA recombination during mitosis. [GOC:go_curators]


down-regulation of mitotic recombination

down regulation of mitotic recombination

negative regulation of mitotic recombination

Any process that inhibits or decreases the rate of DNA recombination during mitosis. [GOC:go_curators, GOC:hjd]


up regulation of mitotic recombination
up-regulation of mitotic recombination
upregulation of mitotic recombination

positive regulation of mitotic recombination

Any process that activates or increases the frequency, rate or extent of DNA recombination during mitosis. [GOC:go_curators]


A process of DNA recombination occurring within a plasmid or between plasmids and other plasmids or DNA molecules. [GOC:mlg]


Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. [GOC:go_curators, ISBN:0198506732]


down regulation of DNA recombination
downregulation of DNA recombination
down-regulation of DNA recombination

negative regulation of DNA recombination

Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination. [GOC:go_curators]


upregulation of DNA recombination
up regulation of DNA recombination
up-regulation of DNA recombination

positive regulation of DNA recombination

Any process that activates or increases the frequency, rate or extent of DNA recombination. [GOC:go_curators]


The reverse transcription of an RNA molecule followed by recombination between the resultant cDNA and its homologous chromosomal allele. [GOC:jl, PMID:8380627]


Recombination occurring within or between DNA molecules in somatic cells. [GOC:ma]


somatic hypermutation of immunoglobulin genes

Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins. [GOC:add, ISBN:0781735149, PMID:11205330, PMID:11205333, PMID:14975236, PMID:7813007]


In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. [ISBN:0815316194]


The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired. [ISBN:0815316194]


The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair. [ISBN:1550091131]


Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template. [ISBN:1550091131]


The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide. [GOC:elh, GOC:vw, PMID:10535901]


The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT). [PMID:10946226]


The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix. [GOC:elh]


double-strand break repair via single-strand annealing

Repair of a DSB made between two repeated sequences oriented in the same direction occurs primarily by the single strand annealing pathway. The ends of the break are processed by a 5' to 3' exonuclease, exposing complementary single-strand regions of the direct repeats that can anneal, resulting in a deletion of the unique DNA between the direct repeats. [PMID:11606529]


double-strand break repair via single-strand annealing, removal of nonhomologous ends

During DSBR via single-strand annealing, the removal of nonhomologous sequences at the broken 3' single-strand DNA end before DNA repair synthesis can occur. [PMID:10357855]


nucleotide-excision repair, DNA damage recognition

The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix. [GOC:elh, PMID:10197977]


transcription-coupled nucleotide-excision repair, DNA damage recognition

The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway. [GOC:elh, PMID:10197977]


nucleotide-excision repair, DNA damage removal

The removal of the oligonucleotide that contains the DNA damage. The oligonucleotide is formed by dual incisions that flank the site of DNA damage. [GOC:elh, PMID:10197977]


nucleotide-excision repair, DNA duplex unwinding

The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage. [GOC:elh, PMID:10197977]


nucleotide-excision repair, DNA gap filling

Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes. [ISBN:0815316194]


nucleotide-excision repair, DNA incision, 3' to lesion

nucleotide-excision repair, DNA incision, 3'-to lesion

The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage. [GOC:elh, PMID:10197977]


nucleotide-excision repair, DNA incision, 5' to lesion

nucleotide-excision repair, DNA incision, 5'-to lesion

The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage. [GOC:elh, PMID:10197977]


nucleotide-excision repair, preincision complex formation

nucleotide-excision repair, preincision complex assembly

The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage. [GOC:elh, PMID:10197977]


nucleotide-excision repair, preincision complex stabilization

The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage. [GOC:elh, PMID:10197977]


pyrimidine dimer repair by nucleotide-excision repair

The repair of UV-induced T-T, C-T, and C-C dimers by the recognition and removal of the damaged DNA strand from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. [GOC:elh]


The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway. [PMID:10197977, PMID:11900249]


The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication. [GOC:elh]


The repair of UV-induced T-T, C-T and C-C dimers. [ISBN:0815316194]


The repair of UV-induced T-T, C-T and C-C dimers by directly reversing the damage to restore the original pyrimidines. [GOC:elh, PMID:10915863]


Any process that modulates the frequency, rate or extent of DNA repair. [GOC:go_curators]


downregulation of DNA repair
down regulation of DNA repair
down-regulation of DNA repair

Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair. [GOC:go_curators]


upregulation of DNA repair
up-regulation of DNA repair
up regulation of DNA repair

Any process that activates or increases the frequency, rate or extent of DNA repair. [GOC:go_curators]


The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair. [PMID:18626472]


The process of restoring viral DNA after damage or errors in replication. [ISBN:0781718325]


recruitment of helicase-primase complex to DNA lesions

The recruitment of the helicase-primase complex to viral DNA lesions during viral DNA repair. [ISBN:0781718325]


production of siRNA involved in post-transcriptional gene silencing by RNA

production of siRNA involved in chromatin silencing by small RNA

production of siRNA involved in RNA interference

chromatin silencing by small RNA, production of siRNA

RNA interference, production of guide RNAs

production of guide RNAs involved in RNA interference

chromatin silencing by small RNA, production of guide RNAs

production of guide RNAs involved in chromatin silencing by small RNA

A process leading to the generation of a functional small interfering RNA (siRNA). Includes the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides. May also include amplification of the siRNA by RNA-directed RNA polymerase. [GOC:mah, PMID:11524674, PMID:19239886, PMID:20687832]


The chemical reactions and pathways by which a purine nucleoside is synthesized from another purine nucleoside. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a purine deoxyribonucleoside is synthesized from another purine deoxyribonucleoside. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a purine nucleotide is synthesized from another purine nucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a purine deoxyribonucleotide is synthesized from another purine deoxyribonucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a purine ribonucleotide is synthesized from another purine ribonucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a pyrimidine nucleoside is synthesized from another pyrimidine nucleoside. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a pyrimidine deoxyribonucleoside is synthesized from another deoxyribopyrimidine nucleoside. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a pyrimidine nucleotide is synthesized from another pyrimidine nucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a pyrimidine deoxyribonucleotide is synthesized from another pyrimidine deoxyribonucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways by which a pyrimidine ribonucleotide is synthesized from another pyrimidine ribonucleotide. [GOC:mah, ISBN:0306444747, ISBN:0471394831]


The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine). [GOC:ma]


The chemical reactions and pathways involving any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside). [GOC:jl, ISBN:0140512713]


purine deoxyribonucleoside metabolic process

The chemical reactions and pathways involving any one of a family of organic molecules consisting of a purine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside). [GOC:ai]


The chemical reactions and pathways involving deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA. [GOC:go_curators]


The chemical reactions and pathways involving deoxyguanosine, a nucleoside consisting of the base guanine and the sugar deoxyribose. [GOC:jl]


pyrimidine deoxyribonucleoside metabolic process

The chemical reactions and pathways involving any one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside). [GOC:ai]


The chemical reactions and pathways involving deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA. [GOC:go_curators]


The chemical reactions and pathways involving deoxyinosine, hypoxanthine deoxyriboside. [GOC:go_curators]


The chemical reactions and pathways involving deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA. [GOC:go_curators]


deoxyribosylthymine metabolic process
deoxyribosylthymine metabolism
thymidine metabolism

The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA. [GOC:go_curators]


The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside). [GOC:jl, ISBN:0140512713]


The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine base is linked to a ribose (beta-D-ribofuranose) molecule. [GOC:ai]


The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes. [GOC:go_curators]


bis(5'-nucleosidyl) oligophosphate metabolic process

The chemical reactions and pathways involving a bis(5'-nucleosidyl) oligophosphate, a compound formed of two nucleosides joined together through their 5' carbons by a chain of phosphate molecules. [GOC:mah, PMID:10970777]


diadenosine polyphosphate metabolic process

The chemical reactions and pathways involving diadenosine polyphosphate, a derivative of the nucleoside adenosine with phosphate groups attached. [GOC:ai]


diadenosine tetraphosphate metabolic process

The chemical reactions and pathways involving diadenosine tetraphosphate, a derivative of the nucleoside adenosine with four phosphate groups attached. [GOC:ai]


diadenosine triphosphate metabolic process

The chemical reactions and pathways involving diadenosine triphosphate, a derivative of the nucleoside adenosine with three phosphate groups attached. [GOC:ai]


The chemical reactions and pathways involving guanine, guanine riboside, a nucleoside with a wide species distribution. [ISBN:0198506732]


The chemical reactions and pathways involving 7-methylguanosine, a modified nucleoside that forms a cap at the 5'-terminus of eukaryotic mRNA. [ISBN:0198506732]


The chemical reactions and pathways involving queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents. [ISBN:0198506732]


guanosine pentaphosphate (5'-pppGpp-3') metabolism

guanosine pentaphosphate (5'-pppGpp-3') metabolic process

guanosine pentaphosphate metabolic process

The chemical reactions and pathways involving guanine pentaphosphate (5'-pppGpp-3'), a derivative of guanine riboside with five phosphates. [GOC:ai]


guanosine tetraphosphate (5'-ppGpp-3') metabolic process

guanosine tetraphosphate (5'-ppGpp-3') metabolism

guanosine tetraphosphate metabolic process

The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates. [GOC:ai]


The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside). [GOC:jl, ISBN:0140512713]


pyrimidine ribonucleoside metabolic process

The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule. [GOC:ai]


The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside. [GOC:go_curators]


The chemical reactions and pathways involving inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs. [GOC:go_curators]


The chemical reactions and pathways involving uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids. [GOC:go_curators]


regulation of nucleoside metabolic process

Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides. [GOC:go_curators]


down regulation of nucleoside metabolic process

downregulation of nucleoside metabolic process

down-regulation of nucleoside metabolic process

negative regulation of nucleoside metabolism

negative regulation of nucleoside metabolic process

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleosides. [GOC:go_curators]


positive regulation of nucleoside metabolism

upregulation of nucleoside metabolic process

up-regulation of nucleoside metabolic process

up regulation of nucleoside metabolic process

positive regulation of nucleoside metabolic process

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleosides. [GOC:go_curators]


The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule. [GOC:jl]


The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue. [GOC:go_curators, ISBN:0198506732]


adenosine 3',5'-cyclophosphate metabolic process

The chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate). [GOC:go_curators]


The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate. [GOC:go_curators]