Biological Pathway: BioCyc:META_DENITRIFICATION-PWY
nitrate reduction I (denitrification) related metabolites
find 27 related metabolites which is associated with the biological pathway nitrate reduction I (denitrification)
this pathway object is a conserved pathway across multiple organism.
Water
Water is a chemical substance that is essential to all known forms of life. It appears colorless to the naked eye in small quantities, though it is actually slightly blue in color. It covers 71\\% of Earths surface. Current estimates suggest that there are 1.4 billion cubic kilometers (330 million m3) of it available on Earth, and it exists in many forms. It appears mostly in the oceans (saltwater) and polar ice caps, but it is also present as clouds, rain water, rivers, freshwater aquifers, lakes, and sea ice. Water in these bodies perpetually moves through a cycle of evaporation, precipitation, and runoff to the sea. Clean water is essential to human life. In many parts of the world, it is in short supply. From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the bodys solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Water is thus essential and central to these metabolic processes. Water is also central to photosynthesis and respiration. Photosynthetic cells use the suns energy to split off waters hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the suns energy and reform water and CO2 in the process (cellular respiration). Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH-) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7. Stomach acid (HCl) is useful to digestion. However, its corrosive effect on the esophagus during reflux can temporarily be neutralized by ingestion of a base such as aluminum hydroxide to produce the neutral molecules water and the salt aluminum chloride. Human biochemistry that involves enzymes usually performs optimally around a biologically neutral pH of 7.4. (Wikipedia). Water, also known as purified water or dihydrogen oxide, is a member of the class of compounds known as homogeneous other non-metal compounds. Homogeneous other non-metal compounds are inorganic non-metallic compounds in which the largest atom belongs to the class of other nonmetals. Water can be found in a number of food items such as caraway, oxheart cabbage, alaska wild rhubarb, and japanese walnut, which makes water a potential biomarker for the consumption of these food products. Water can be found primarily in most biofluids, including ascites Fluid, blood, cerebrospinal fluid (CSF), and lymph, as well as throughout all human tissues. Water exists in all living species, ranging from bacteria to humans. In humans, water is involved in several metabolic pathways, some of which include cardiolipin biosynthesis CL(20:4(5Z,8Z,11Z,14Z)/18:0/20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)), cardiolipin biosynthesis cl(i-13:0/i-15:0/i-20:0/i-24:0), cardiolipin biosynthesis CL(18:0/18:0/20:4(5Z,8Z,11Z,14Z)/22:5(7Z,10Z,13Z,16Z,19Z)), and cardiolipin biosynthesis cl(a-13:0/i-18:0/i-13:0/i-19:0). Water is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis tg(i-21:0/i-13:0/21:0), de novo triacylglycerol biosynthesis tg(22:0/20:0/i-20:0), de novo triacylglycerol biosynthesis tg(a-21:0/i-20:0/i-14:0), and de novo triacylglycerol biosynthesis tg(i-21:0/a-17:0/i-12:0). Water is a drug which is used for diluting or dissolving drugs for intravenous, intramuscular or subcutaneous injection, according to instructions of the manufacturer of the drug to be administered [fda label]. Water plays an important role in the world economy. Approximately 70\\% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a major source of food for many parts of the world. Much of long-distance trade of commodities (such as oil and natural gas) and manufactured products is transported by boats through seas, rivers, lakes, and canals. Large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a wide variety of chemical substances; as such it is widely used in industrial processes, and in cooking and washing. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, and diving .
Carbon monoxide
Carbon monoxide, with the chemical formula CO, is a colorless, odorless, and tasteless gas. It is the product of the incomplete combustion of carbon-containing compounds, notably in internal-combustion engines. It consists of one carbon atom covalently bonded to one oxygen atom. It is a gas at room temperature. Carbon monoxide is a significantly toxic gas and is the most common type of fatal poisoning in many countries. Exposures can lead to significant toxicity of the central nervous system and heart. Carbon monoxide has a higher diffusion coefficient compared to oxygen and the only enzyme in the human body that produces carbon monoxide is heme oxygenase which is located in all cells and breaks down heme. Because it has a higher diffusion coefficient than oxygen the body easily gets rid of any CO made. When CO is not ventilated it binds to hemoglobin, which is the principal oxygen-carrying compound in blood; this produces a compound known as carboxyhemoglobin. The traditional belief is that carbon monoxide toxicity arises from the formation of carboxyhemoglobin, which decreases the oxygen-carrying capacity of the blood and inhibits the transport, delivery, and utilization of oxygen by the body. The affinity between hemoglobin and carbon monoxide is approximately 230 times stronger than the affinity between hemoglobin and oxygen so hemoglobin binds to carbon monoxide in preference to oxygen. Following poisoning, long-term sequelae often occur. Carbon monoxide can also have severe effects on the fetus of a pregnant woman. Despite its serious toxicity, CO is extremely useful and underpins much modern technology, being a precursor to a myriad of useful - even life-saving - products. Carbon monoxide, though thought of as a pollutant today, has always been present in the atmosphere, chiefly as a product of volcanic activity. It occurs dissolved in molten volcanic rock at high pressures in the earths mantle. Carbon monoxide contents of volcanic gases vary from less than 0.01\\% to as much as 2\\% depending on the volcano. It also occurs naturally in bushfires. Because natural sources of carbon monoxide are so variable from year to year, it is extremely difficult to accurately measure natural emissions of the gas. (wikipedia). Carbon monoxide, with the chemical formula CO, is a colorless, odorless, and tasteless gas. It is the product of the incomplete combustion of carbon-containing compounds, notably in internal-combustion engines. It consists of one carbon atom covalently bonded to one oxygen atom. It is a gas at room temperature. D018377 - Neurotransmitter Agents > D064426 - Gasotransmitters D009676 - Noxae > D000963 - Antimetabolites V - Various > V04 - Diagnostic agents
Nitric oxide
The biologically active molecule nitric oxide (NO) is a simple, membrane-permeable gas with unique chemistry. It is formed by the conversion of L-arginine to L-citrulline, with the release of NO. The enzymatic oxidation of L-arginine to L-citrulline takes place in the presence of oxygen and NADPH using flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), heme, thiol, and tetrahydrobiopterin as cofactors. The enzyme responsible for the generation of NO is nitric oxide synthase (E.C. 1.7.99.7; NOS). Three NOS isoforms have been described and shown to be encoded on three distinct genes: neuronal NOS (nNOS, NOS type I), inducible NOS (NOS type II), and endothelial NOS (eNOS, NOS type III). Two of them are constitutively expressed and dependent on the presence of calcium ions and calmodulin to function (nNOS and eNOS), while iNOS is considered non-constitutive and calcium-independent. However, experience has shown that constitutive expression of nNOS and eNOS is not as rigid as previously thought (i.e. either present or absent), but can be dynamically controlled during development and in response to injury. Functionally, NO may act as a hormone, neurotransmitter, paracrine messenger, mediator, cytoprotective molecule, and cytotoxic molecule. NO has multiple cellular molecular targets. It influences the activity of transcription factors, modulates upstream signaling cascades, mRNA stability and translation, and processes the primary gene products. In the brain, many processes are linked to NO. NO activates its receptor, soluble guanylate cyclase by binding to it. The stimulation of this enzyme leads to increased synthesis of the second messenger, cGMP, which in turn activates cGMP-dependent kinases in target cells. NO exerts a strong influence on glutamatergic neurotransmission by directly interacting with the N-methyl-D-aspartate (NMDA) receptor. Neuronal NOS is connected to NMDA receptors (see below) and sharply increases NO production following activation of this receptor. Thus, the level of endogenously produced NO around NMDA synapses reflects the activity of glutamate-mediated neurotransmission. However, there is recent evidence showing that non-NMDA glutamate receptors (i.e. AMPA and type I metabotropic receptors) also contribute to NO generation. Besides its influence on glutamate, NO is known to have effects on the storage, uptake and/or release of most other neurotransmitters in the CNS (acetylcholine, dopamine, noradrenaline, GABA, taurine, and glycine) as well as of certain neuropeptides. Finally, since NO is a highly diffusible molecule, it may reach extrasynaptic receptors at target cell membranes that are some distance away from the place of NO synthesis. NO is thus capable of mediating both synaptic and nonsynaptic communication processes. NO is a potent vasodilator (a major endogenous regulator of vascular tone), and an important endothelium-dependent relaxing factor. NO is synthesized by NO synthases (NOS) and NOS are inhibited by asymmetrical dimethylarginine (ADMA). ADMA is metabolized by dimethylarginine dimethylaminohydrolase (DDAH) and excreted in the kidneys. Lower ADMA levels in pregnant women compared to non-pregnant controls suggest that ADMA has a role in vascular dilatation and blood pressure changes. Several studies show an increase in ADMA levels in pregnancies complicated with preeclampsia. Elevated ADMA levels in preeclampsia are seen before clinical symptoms have developed; these findings suggest that ADMA has a role in the pathogenesis of preeclampsia. In some pulmonary hypertensive states such as ARDS, the production of endogenous NO may be impaired. Nitric oxide inhalation selectively dilates the pulmonary circulation. Significant systemic vasodilation does not occur because NO is inactivated by rapidly binding to hemoglobin. In an injured lung with pulmonary hypertension, inhaled NO produces local vasodilation of well-ventilated lung units and may "steal" blood flow away from unventil... D002317 - Cardiovascular Agents > D014665 - Vasodilator Agents > D045462 - Endothelium-Dependent Relaxing Factors D019141 - Respiratory System Agents > D018927 - Anti-Asthmatic Agents > D001993 - Bronchodilator Agents D018373 - Peripheral Nervous System Agents > D001337 - Autonomic Agents D018377 - Neurotransmitter Agents > D064426 - Gasotransmitters D000975 - Antioxidants > D016166 - Free Radical Scavengers D020011 - Protective Agents > D000975 - Antioxidants R - Respiratory system
Nitrogen
Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78\\% by volume of Earths atmosphere. Nitrogen occurs in all living organisms. It is a constituent element of amino acids and therefore of proteins and nucleic acids (DNA and RNA). Nitrogen is found in the chemical structure of almost all neurotransmitters and is a key component of alkaloids. Specific bacteria (e.g. Rhizobium trifolium) possess nitrogenase enzymes which can fix atmospheric nitrogen into a form (ammonium ion) which is chemically useful to higher organisms. Animals use nitrogen-containing amino acids from plant sources, as starting materials for all nitrogen-compound animal biochemistry, including the manufacture of proteins and nucleic acids. Animal metabolism of NO (nitric oxide) results in production of nitrite. Animal metabolism of nitrogen in proteins generally results in excretion of urea, while animal metabolism of nucleic acids results in excretion of urea and uric acid. The characteristic odor of animal flesh decay is caused by nitrogen-containing long-chain amines, such as putrescine and cadaverine. Decay of organisms and their waste products may produce small amounts of nitrate, but most decay eventually returns nitrogen content to the atmosphere, as molecular nitrogen. The circulation of nitrogen from the atmosphere through organics and then back to the atmosphere is commonly referred to as the nitrogen cycle. Nitrogen can be measured in urine with the Kjeldahl method or by spectrophotometric methods (enzymic tests). Total urinary nitrogen is calculated based on urea urinary nitrogen quantified with these methods. V - Various > V03 - All other therapeutic products > V03A - All other therapeutic products > V03AN - Medical gases
Nitrous oxide
D002491 - Central Nervous System Agents > D002492 - Central Nervous System Depressants > D000777 - Anesthetics D018373 - Peripheral Nervous System Agents > D018689 - Sensory System Agents Aerosol propellant for foods. Nitrous oxide is a flavouring ingredien N - Nervous system > N01 - Anesthetics > N01A - Anesthetics, general C78272 - Agent Affecting Nervous System > C245 - Anesthetic Agent D002491 - Central Nervous System Agents > D000700 - Analgesics Aerosol propellant for foods. Flavouring ingredient [DFC]
Hydrogen cyanide
Hydrogen cyanide (with the historical common name of Prussic acid) is a chemical compound with chemical formula HCN. It is a colorless, extremely poisonous liquid that boils slightly above room temperature at 26 °C (79 °F). Hydrogen cyanide is a linear molecule, with a triple bond between carbon and nitrogen. A minor tautomer of HCN is HNC, hydrogen isocyanide. Hydrogen cyanide is weakly acidic with a pKa of 9.2. It partly ionizes in water solution to give the cyanide anion, CN. (Wikipedia) D009676 - Noxae > D011042 - Poisons > D002619 - Chemical Warfare Agents
Acetylene
Polyacetylene is also known as ethyne or ethin. Polyacetylene can be found in german camomile and roman camomile, which makes polyacetylene a potential biomarker for the consumption of these food products. Polyacetylene (IUPAC name: polyethyne) usually refers to an organic polymer with the repeating unit (C2H2)n. The name refers to its conceptual construction from polymerization of acetylene to give a chain with repeating olefin groups. This compound is conceptually important as the discovery of polyacetylene and its high conductivity upon doping helped to launch the field of organic conductive polymers. The high electrical conductivity discovered by Hideki Shirakawa, Alan Heeger, and Alan MacDiarmid for this polymer led to intense interest in the use of organic compounds in microelectronics (organic semiconductors). This discovery was recognized by the Nobel Prize in Chemistry in 2000. Early work in the field of polyacetylene research was aimed at using doped polymers as easily processable and lightweight "plastic metals". Despite the promise of this polymer in the field of conductive polymers, many of its properties such as instability to air and difficulty with processing have led to avoidance in commercial applications .
Hydrogen Ion
Hydrogen ion, also known as proton or h+, is a member of the class of compounds known as other non-metal hydrides. Other non-metal hydrides are inorganic compounds in which the heaviest atom bonded to a hydrogen atom is belongs to the class of other non-metals. Hydrogen ion can be found in a number of food items such as lowbush blueberry, groundcherry, parsley, and tarragon, which makes hydrogen ion a potential biomarker for the consumption of these food products. Hydrogen ion exists in all living organisms, ranging from bacteria to humans. In humans, hydrogen ion is involved in several metabolic pathways, some of which include cardiolipin biosynthesis cl(i-13:0/a-25:0/a-21:0/i-15:0), cardiolipin biosynthesis cl(a-13:0/a-17:0/i-13:0/a-25:0), cardiolipin biosynthesis cl(i-12:0/i-13:0/a-17:0/a-15:0), and cardiolipin biosynthesis CL(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)/18:1(11Z)/22:5(7Z,10Z,13Z,16Z,19Z)). Hydrogen ion is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis TG(20:3(8Z,11Z,14Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/22:5(7Z,10Z,13Z,16Z,19Z)), de novo triacylglycerol biosynthesis TG(18:2(9Z,12Z)/20:0/20:4(5Z,8Z,11Z,14Z)), de novo triacylglycerol biosynthesis TG(18:4(6Z,9Z,12Z,15Z)/18:3(9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)), and de novo triacylglycerol biosynthesis TG(24:0/20:5(5Z,8Z,11Z,14Z,17Z)/24:0). A hydrogen ion is created when a hydrogen atom loses or gains an electron. A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space. Due to its extremely high charge density of approximately 2×1010 times that of a sodium ion, the bare hydrogen ion cannot exist freely in solution as it readily hydrates, i.e., bonds quickly. The hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions . Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions. Under aqueous conditions found in biochemistry, hydrogen ions exist as the hydrated form hydronium, H3O+, but these are often still referred to as hydrogen ions or even protons by biochemists. [Wikipedia])
Nitrate
In inorganic chemistry, a nitrate is a salt of nitric acid. In organic chemistry the esters of nitric acid and various alcohols are called nitrates. The nitrate ion is a polyatomic anion with the empirical formula NO3- and a molecular mass of 62.01 daltons; it consists of one central nitrogen atom surrounded by three identical oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a negative one formal charge. Nitrates should not be confused with nitrites, the salts of nitrous acid. Organic compounds containing the nitro functional group (which has the same formula and structure as the nitrate ion save that one of the O2 atoms is replaced by the R group) are known as nitro compounds. Nitrate ions can be toxic. In particular, nitrate toxicosis in humans occurs through enterohepatic metabolism of nitrates to ammonia, with nitrite being an intermediate. Nitrites oxidize the iron atoms in hemoglobin from Ferrous Iron (2+) to Ferric Iron (3+), rendering it unable to carry oxygen. This condition is called methemoglobinemia and can lead to a lack of oxygen in tissues. Methemoglobinemia can be treated with methylene blue. -- Wikipedia. The nitrate ion is a polyatomic ion. Nitrates are mainly produced for use as fertilizers in agriculture because of their high solubility and biodegradability. The main nitrates are ammonium, sodium, potassium, and calcium salts. Several million kilograms are produced annually for this purpose. [Wikipedia]. Nitrate is found in many foods, some of which are canola, peach, spelt, and loquat.
water
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms
Cyclon
D009676 - Noxae > D011042 - Poisons > D002619 - Chemical Warfare Agents
nitric oxide
D002317 - Cardiovascular Agents > D014665 - Vasodilator Agents > D045462 - Endothelium-Dependent Relaxing Factors A nitrogen oxide which is a free radical, each molecule of which consists of one nitrogen and one oxygen atom. D019141 - Respiratory System Agents > D018927 - Anti-Asthmatic Agents > D001993 - Bronchodilator Agents D018373 - Peripheral Nervous System Agents > D001337 - Autonomic Agents D018377 - Neurotransmitter Agents > D064426 - Gasotransmitters D000975 - Antioxidants > D016166 - Free Radical Scavengers D020011 - Protective Agents > D000975 - Antioxidants R - Respiratory system It is used as a food additive .
Hydrogen cyanide
A one-carbon compound consisting of a methine group triple bonded to a nitrogen atom D009676 - Noxae > D011042 - Poisons > D002619 - Chemical Warfare Agents Hydrogen cyanide, also known as hydrocyanic acid or cyanide, is a member of the class of compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N. Hydrogen cyanide is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). Hydrogen cyanide can be found in a number of food items such as kiwi, java plum, yellow wax bean, and mamey sapote, which makes hydrogen cyanide a potential biomarker for the consumption of these food products. Hydrogen cyanide exists in all living organisms, ranging from bacteria to humans. Hydrogen cyanide is a non-carcinogenic (not listed by IARC) potentially toxic compound. Hydrogen cyanide (HCN), sometimes called prussic acid, is a chemical compound with the chemical formula HCN. It is a colorless, extremely poisonous and inflammable liquid that boils slightly above room temperature, at 25.6 °C (78.1 °F). HCN is produced on an industrial scale and is a highly valuable precursor to many chemical compounds ranging from polymers to pharmaceuticals . Antidotes to cyanide poisoning include hydroxocobalamin and sodium nitrite, which release the cyanide from the cytochrome system, and rhodanase, which is an enzyme occurring naturally in mammals that combines serum cyanide with thiosulfate, producing comparatively harmless thiocyanate. Oxygen therapy can also be administered (L97) (T3DB).
Carbon monoxide
A one-carbon compound in which the carbon is joined only to a single oxygen. It is a colourless, odourless, tasteless, toxic gas. D018377 - Neurotransmitter Agents > D064426 - Gasotransmitters D009676 - Noxae > D000963 - Antimetabolites V - Various > V04 - Diagnostic agents
nitrous oxide
D002491 - Central Nervous System Agents > D002492 - Central Nervous System Depressants > D000777 - Anesthetics D018373 - Peripheral Nervous System Agents > D018689 - Sensory System Agents N - Nervous system > N01 - Anesthetics > N01A - Anesthetics, general C78272 - Agent Affecting Nervous System > C245 - Anesthetic Agent D002491 - Central Nervous System Agents > D000700 - Analgesics