Reaction Process: Reactome:R-CEL-15869

Nucleotide metabolism related metabolites

find 48 related metabolites which is associated with chemical reaction(pathway) Nucleotide metabolism

Ade + PRPP ⟶ AMP + PPi

Thymidine

1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione

Deoxythymidine, also known as 2-deoxy-5-methyluridine or 5-methyl-2-deoxyuridine, is a member of the class of compounds known as pyrimidine 2-deoxyribonucleosides. Pyrimidine 2-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Deoxythymidine is soluble (in water) and a very weakly acidic compound (based on its pKa). Deoxythymidine can be synthesized from thymine. Deoxythymidine is also a parent compound for other transformation products, including but not limited to, tritiated thymidine, alpha-tritiated thymidine, and 5,6-dihydrothymidine. Deoxythymidine can be found in a number of food items such as butternut squash, mammee apple, catjang pea, and climbing bean, which makes deoxythymidine a potential biomarker for the consumption of these food products. Deoxythymidine can be found primarily in most biofluids, including blood, amniotic fluid, cerebrospinal fluid (CSF), and urine, as well as throughout most human tissues. Deoxythymidine exists in all living species, ranging from bacteria to humans. In humans, deoxythymidine is involved in the pyrimidine metabolism. Deoxythymidine is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). Moreover, deoxythymidine is found to be associated with canavan disease and degenerative disc disease. Thymidine (deoxythymidine; other names deoxyribosylthymine, thymine deoxyriboside) is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in G1/early S phase . Thymidine, also known as deoxythymidine or deoxyribosylthymine or thymine deoxyriboside, is a pyrimidine deoxynucleoside. It consists of the nucleobase thymine attached to deoxyribose through a beta N- glycosidic bond. Thymidine also belongs to the class of organic compounds known as pyrimidine 2-deoxyribonucleosides. Pyrimidine 2-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Deoxythymidine (or thymidine) is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. Therefore, thymidine is essential to all life. Indeed, thymidine exists in all living species, ranging from bacteria to plants to humans. Within humans, thymidine participates in a number of enzymatic reactions. In particular, thymidine can be biosynthesized from 5-thymidylic acid through its interaction with the enzyme cytosolic purine 5-nucleotidase. In addition, thymidine can be converted into 5-thymidylic acid; which is catalyzed by the enzyme thymidine kinase. Deoxythymidine can be phosphorylated with one, two or three phosphoric acid groups, creating dTMP (deoxythymidine monophosphate), dTDP, or dTTP (for the di- and tri- phosphates, respectively). dTMP can be incorporated into DNA via DNA polymerases. In cell biology, thymidine can be used to synchronize the cells in S phase. Derivatives of thymidine are used in a number of drugs, including Azidothymidine (AZT), which is used in the treatment of HIV infection. AZT inhibits the process of reverse transcription in the human immunodeficiency virus. Thymidine is a pyrimidine 2-deoxyribonucleoside having thymine as the nucleobase. It has a role as a metabolite, a human metabolite, an Escherichia coli metabolite and a mouse metabolite. It is functionally related to a thymine. It is an enantiomer of a telbivudine. Thymidine is a pyrimidine deoxynucleoside. Thymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in S phase. Thymidine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655). Thymidine is a natural product found in Fritillaria thunbergii, Saussurea medusa, and other organisms with data available. Thymidine is a pyrimidine nucleoside that is composed of the pyrimidine base thymine attached to the sugar deoxyribose. As a constituent of DNA, thymidine pairs with adenine in the DNA double helix. (NCI04) Thymidine is a metabolite found in or produced by Saccharomyces cerevisiae. A nucleoside in which THYMINE is linked to DEOXYRIBOSE. A pyrimidine 2-deoxyribonucleoside having thymine as the nucleobase. KEIO_ID T014; [MS2] KO009272 KEIO_ID T014 Thymidine, a specific precursor of deoxyribonucleic acid, is used as a cell synchronizing agent. Thymidine is a DNA synthesis inhibitor that can arrest cell at G1/S boundary, prior to DNA replication[1][2][3]. Thymidine, a specific precursor of deoxyribonucleic acid, is used as a cell synchronizing agent. Thymidine is a DNA synthesis inhibitor that can arrest cell at G1/S boundary, prior to DNA replication[1][2][3].

Adenine

7H-purin-6-amine

C5H5N5 (135.054493)

Adenine is the parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6. It has a role as a human metabolite, a Daphnia magna metabolite, a Saccharomyces cerevisiae metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a purine nucleobase and a member of 6-aminopurines. It derives from a hydride of a 9H-purine. A purine base and a fundamental unit of adenine nucleotides. Adenine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655). Adenine is a natural product found in Fritillaria cirrhosa, Annona purpurea, and other organisms with data available. Adenine is a purine nucleobase with an amine group attached to the carbon at position 6. Adenine is the precursor for adenosine and deoxyadenosine nucleosides. Adenine is a purine base. Adenine is found in both DNA and RNA. Adenine is a fundamental component of adenine nucleotides. Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose; it forms adenosine triphosphate (ATP), a nucleotide, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the basic methods of transferring chemical energy between chemical reactions. Purine inborn errors of metabolism (IEM) are serious hereditary disorders, which should be suspected in any case of neonatal fitting, failure to thrive, recurrent infections, neurological deficit, renal disease, self-mutilation and other manifestations. Investigation usually starts with uric acid (UA) determination in urine and plasma. (OMIM 300322, 229600, 603027, 232400, 232600, 232800, 201450, 220150, 232200, 162000, 164050, 278300). (A3372, A3373). Adenine is a metabolite found in or produced by Saccharomyces cerevisiae. A purine base and a fundamental unit of ADENINE NUCLEOTIDES. See also: adenine; dextrose, unspecified form (component of) ... View More ... Adenine is a purine base. Adenine is found in both DNA and RNA. Adenine is a fundamental component of adenine nucleotides. Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose; it forms adenosine triphosphate (ATP), a nucleotide, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the basic methods of transferring chemical energy between chemical reactions. Purine inborn errors of metabolism (IEM) are serious hereditary disorders, which should be suspected in any case of neonatal fitting, failure to thrive, recurrent infections, neurological deficit, renal disease, self-mutilation and other manifestations. Investigation usually starts with uric acid (UA) determination in urine and plasma. (OMIM 300322, 229600, 603027, 232400, 232600, 232800, 201450, 220150, 232200, 162000, 164050, 278300). (PMID: 17052198, 17520339). Widespread throughout animal and plant tissue, purine components of DNA, RNA, and coenzymes. Vitamin The parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6. Adenine (/ˈædɪnɪn/) (symbol A or Ade) is a purine nucleobase. It is one of the four nucleobases in the nucleic acids of DNA, the other three being guanine (G), cytosine (C), and thymine (T). Adenine derivatives have various roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD) and Coenzyme A. It also has functions in protein synthesis and as a chemical component of DNA and RNA.[2] The shape of adenine is complementary to either thymine in DNA or uracil in RNA. The adjacent image shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen (thereby removing the existing hydrogen atom). The remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose, as used in RNA and ATP; Deoxyadenosine is adenine attached to deoxyribose, as used to form DNA. Adenine forms several tautomers, compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i.e. in an inert gas matrix and in the gas phase, mainly the 9H-adenine tautomer is found.[3][4] Purine metabolism involves the formation of adenine and guanine. Both adenine and guanine are derived from the nucleotide inosine monophosphate (IMP), which in turn is synthesized from a pre-existing ribose phosphate through a complex pathway using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as the coenzyme tetrahydrofolate. Adenine (6-Aminopurine), a purine, is one of the four nucleobases in the nucleic acid of DNA. Adenine acts as a chemical component of DNA and RNA. Adenine also plays an important role in biochemistry involved in cellular respiration, the form of both ATP and the cofactors (NAD and FAD), and protein synthesis[1][2][3]. Adenine (6-Aminopurine), a purine, is one of the four nucleobases in the nucleic acid of DNA. Adenine acts as a chemical component of DNA and RNA. Adenine also plays an important role in biochemistry involved in cellular respiration, the form of both ATP and the cofactors (NAD and FAD), and protein synthesis[1][2][3]. Adenine (6-Aminopurine), a purine, is one of the four nucleobases in the nucleic acid of DNA. Adenine acts as a chemical component of DNA and RNA. Adenine also plays an important role in biochemistry involved in cellular respiration, the form of both ATP and the cofactors (NAD and FAD), and protein synthesis[1][2][3].

Guanine

Guanine, Pharmaceutical Secondary Standard; Certified Reference Material

C5H5N5O (151.049408)

Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA. Guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Being unsaturated, the bicyclic molecule is planar. The guanine nucleoside is called guanosine. The first isolation of guanine was reported in 1844 from the excreta of sea birds, known as guano, which was used as a source of fertilizer. High affinity binding of guanine nucleotides and the ability to hydrolyze bound GTP to GDP are characteristics of an extended family of intracellular proteins. Guanine nucleotide-binding regulatory proteins may be involved in the activation of phospholipases C and A2 by hormones and other ligands. The binding of hormones to receptors that activate phospholipase C is decreased by guanine nucleotides and these hormones also stimulate a high-affinity GTPase activity in cell membranes. Effects of hormones on phospholipase C activity in cell-free preparations are dependent on the presence of guanine nucleotides. Hypoxanthine-guanine phosphoribosyltransferase (HPRT, EC 2.4.2.8) is a purine salvage enzyme that catalyses the conversion of hypoxanthine and guanine to their respective mononucleotides. Partial deficiency of this enzyme can result in the overproduction of uric acid leading to a severe form of gout, whilst a virtual absence of HPRT activity causes the Lesch-Nyhan syndrome, an inborn error of metabolism, which is characterised by hyperuricaemia, mental retardation, choreoathetosis and compulsive self-mutilation. Peroxynitrite induces DNA base damage predominantly at guanine (G) and 8-oxoguanine (8-oxoG) nucleobases via oxidation reactions. G and 8-oxoG are the most reactive bases toward Peroxynitrite and possibly the major contributors to peroxynitrite-derived genotoxic and mutagenic lesions. The neutral G radical, reacts with NO2 to yield 8-nitroguanine and 5-nitro-4-guanidinohydantoin (PMID: 16352449, 2435586, 2838362, 1487231). Guanine is a 2-aminopurine carrying a 6-oxo substituent. It has a role as a human metabolite, an algal metabolite, a Saccharomyces cerevisiae metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a purine nucleobase, an oxopurine and a member of 2-aminopurines. It derives from a hydride of a 9H-purine. Guanine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655). Guanine is a natural product found in Fritillaria thunbergii, Isatis tinctoria, and other organisms with data available. Guanine is a purine base that is a constituent of nucleotides occurring in nucleic acids. Guanine is a mineral with formula of C5H3(NH2)N4O. The corresponding IMA (International Mineralogical Association) number is IMA1973-056. The IMA symbol is Gni. Guanine is a metabolite found in or produced by Saccharomyces cerevisiae. Occurs widely in animals and plants. Component of nucleic acids (CCD) A 2-aminopurine carrying a 6-oxo substituent. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS [Spectral] Guanine (exact mass = 151.04941) and 3,4-Dihydroxy-L-phenylalanine (exact mass = 197.06881) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. [Spectral] Guanine (exact mass = 151.04941) and D-Gluconic acid (exact mass = 196.0583) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. [Spectral] Guanine (exact mass = 151.04941) and L-Valine (exact mass = 117.07898) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. Acquisition and generation of the data is financially supported in part by CREST/JST. CONFIDENCE Reference Standard (Level 1); INTERNAL_ID 54 CONFIDENCE standard compound; ML_ID 43

Xanthine

2,3,6,7-tetrahydro-1H-purine-2,6-dione

C5H4N4O2 (152.0334244)

Xanthine, also known as 2,6-dioxopurine, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. Xanthine is also classified as an oxopurine. An oxopurine in which the purine ring is substituted by oxo groups at positions 2 and 6 and N-9 is protonated. Xanthine exists in all living species, ranging from bacteria to plants to humans. In plants, several stimulants can be derived from xanthine, including caffeine, theophylline, and theobromine. Derivatives of xanthine (known collectively as xanthines) are a group of alkaloids commonly used for their effects as mild stimulants and as bronchodilators, notably in the treatment of asthma or influenza symptoms. Within humans, xanthine participates in a number of enzymatic reactions. In particular, xanthine can be biosynthesized from guanine; which is mediated by the enzyme guanine deaminase. In addition, xanthine and ribose 1-phosphate can be biosynthesized from xanthosine through the action of the enzyme purine nucleoside phosphorylase. In humans and other primates, xanthine can be converted to uric acid by the action of the xanthine oxidase enzyme. People with rare genetic disorders, specifically xanthinuria and Lesch‚ÄìNyhan syndrome, lack sufficient xanthine oxidase and cannot convert xanthine to uric acid. Individuals with xanthinuria have unusually high concentrations of xanthine in their blood and urine, which can lead to health problems such as renal failure and xanthine kidney stones. Individuals with Lesch-Nyhan syndrome have a deficiency of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT). The HGPRT deficiency causes a build-up of uric acid in all body fluids. This results in both high levels of uric acid in the blood and urine, associated with severe gout and kidney problems. Neurological signs include poor muscle control and moderate intellectual disability. 9H-xanthine is an oxopurine in which the purine ring is substituted by oxo groups at positions 2 and 6 and N-9 is protonated. It has a role as a Saccharomyces cerevisiae metabolite. It is a tautomer of a 7H-xanthine. A purine base found in most body tissues and fluids, certain plants, and some urinary calculi. It is an intermediate in the degradation of adenosine monophosphate to uric acid, being formed by oxidation of hypoxanthine. The methylated xanthine compounds caffeine, theobromine, and theophylline and their derivatives are used in medicine for their bronchodilator effects. (Dorland, 28th ed) Xanthine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655). Xanthine is a natural product found in Beta vulgaris, Camellia sinensis var. assamica, and other organisms with data available. Xanthine is a purine base found in most body tissues and fluids, certain plants, and some urinary calculi. It is an intermediate in the degradation of adenosine monophosphate to uric acid, being formed by oxidation of hypoxanthine. The methylated xanthine compounds caffeine, theobromine, and theophylline and their derivatives are used in medicine for their bronchodilator effects. (Dorland, 28th ed.). Xanthine is a metabolite found in or produced by Saccharomyces cerevisiae. A purine base found in most body tissues and fluids, certain plants, and some urinary calculi. It is an intermediate in the degradation of adenosine monophosphate to uric acid, being formed by oxidation of hypoxanthine. The methylated xanthine compounds caffeine, theobromine, and theophylline and their derivatives are used in medicine for their bronchodilator effects. (Dorland, 28th ed) An oxopurine in which the purine ring is substituted by oxo groups at positions 2 and 6 and N-9 is protonated. Xanthine, a plant alkaloid found in tea, coffee, and cocoa, is a mild stimulant of the central nervous system. Xanthine also acts as an intermediate product on the pathway of purine degradation[1][2][3]. Xanthine, a plant alkaloid found in tea, coffee, and cocoa, is a mild stimulant of the central nervous system. Xanthine also acts as an intermediate product on the pathway of purine degradation[1][2][3]. Xanthine, a plant alkaloid found in tea, coffee, and cocoa, is a mild stimulant of the central nervous system. Xanthine also acts as an intermediate product on the pathway of purine degradation[1][2][3].

Pseudouridine

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

C9H12N2O6 (244.0695332)

Beta-pseudouridine, also known as p or 5-(b-D-ribofuranosyl)uracil, is a member of the class of compounds known as nucleoside and nucleotide analogues. Nucleoside and nucleotide analogues are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others. Beta-pseudouridine is soluble (in water) and a very weakly acidic compound (based on its pKa). Beta-pseudouridine can be found in a number of food items such as eggplant, wax gourd, asparagus, and garden cress, which makes beta-pseudouridine a potential biomarker for the consumption of these food products. Beta-pseudouridine can be found primarily in amniotic fluid, blood, feces, and urine. Beta-pseudouridine exists in all living species, ranging from bacteria to humans. Moreover, beta-pseudouridine is found to be associated with canavan disease. Pseudouridine, also known as psi-uridine or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides, such as phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides. Pseudouridine specifically has its uracil attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond to the ribofuranose. It is the most prevalent of the over one hundred different modified nucleosides found in RNA (PMID: 17113994). Pseudouridine is a solid that is soluble in water. Pseudouridine exists in all living species, ranging from bacteria to humans, and is in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA. Pseudouridine. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=1445-07-4 (retrieved 2024-07-01) (CAS RN: 1445-07-4). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0). Pseudouridine is an isomer of the nucleoside uridine, and the most abundant modified nucleoside in non-coding RNAs. Pseudouridine in rRNA and tRNA can fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation[1][2][3][4]. Pseudouridine is an isomer of the nucleoside uridine, and the most abundant modified nucleoside in non-coding RNAs. Pseudouridine in rRNA and tRNA can fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation[1][2][3][4].

5,6-Dihydrothymine

Dihydro-5-methyl-2,4(1H,3H)-pyrimidinedione

C5H8N2O2 (128.0585748)

Dihydrothymine (CAS: 696-04-8) is an intermediate breakdown product of thymine. Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine into 5,6-dihydrothymine; then dihydropyrimidinase hydrolyzes 5,6-dihydrothymine into N-carbamyl-beta-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-beta-alanine into beta-alanine. When present at abnormally high levels, dihydrothymine can be toxic, although the mechanism of toxicity is not clear. In particular, patients with dihydropyrimidinase deficiency exhibit highly increased concentrations of 5,6-dihydrouracil and 5,6-dihydrothymine; and moderately increased concentrations of uracil and thymine can be detected in urine. Dihydropyrimidinase deficiency is a disorder that can cause neurological and gastrointestinal problems in some affected individuals. The most common neurological abnormalities that occur are intellectual disability, seizures, weak muscle tone (hypotonia), abnormally small head size (microcephaly), and autistic behaviours that affect communication and social interaction. Gastrointestinal problems that occur in dihydropyrimidinase deficiency include the backflow of acidic stomach contents into the esophagus (gastroesophageal reflux) and recurrent episodes of vomiting. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS 5,6-Dihydro-5-methyluracil (Dihydrothymine), an intermediate breakdown product of thymine, comes from animal or plants. 5,6-Dihydro-5-methyluracil (Dihydrothymine) can be toxic when present at abnormally high levels[1].

Hypoxanthine

1,7-Dihydro-6H-purine-6-one

C5H4N4O (136.03850939999998)

Hypoxanthine, also known as purine-6-ol or Hyp, belongs to the class of organic compounds known as purines. Purines are a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring. Hypoxanthine is also classified as an oxopurine, Hypoxanthine is a naturally occurring purine derivative and a reaction intermediate in the metabolism of adenosine and in the formation of nucleic acids by the nucleotide salvage pathway. Hypoxanthine exists in all living species, ranging from bacteria to plants to humans. Hypoxanthine has been detected, but not quantified in, several different foods, such as radish (var.), mountain yams, welsh onions, greenthread tea, and common beets. Hypoxanthine is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. Biologically, hypoxanthine can be formed a number of ways. For instance, it is one of the products of the action of xanthine oxidase on xanthine. However, more frequently xanthine is formed from oxidation of hypoxanthine by xanthine oxidoreductase. The enzyme hypoxanthine-guanine phosphoribosyltransferase converts hypoxanthine into IMP in the nucleotide salvage pathway. Hypoxanthine is also a spontaneous deamination product of adenine. Under normal circumstances hypoxanthine is readily converted to uric acid. In this process, hypoxanthine is first oxidized to xanthine, which is further oxidized to uric acid by xanthine oxidase. Molecular oxygen, the oxidant in both reactions, is reduced to H2O2 and other reactive oxygen species. In humans, uric acid is the final product of purine degradation and is excreted in the urine. Within humans, hypoxanthine participates in a number of other enzymatic reactions. In particular, hypoxanthine and ribose 1-phosphate can be biosynthesized from inosine through its interaction with the enzyme purine nucleoside phosphorylase. Hypoxanthine is also involved in the metabolic disorder called the purine nucleoside phosphorylase deficiency. Purine nucleoside phosphorylase (PNP) deficiency is a disorder of the immune system (primary immunodeficiency) characterized by recurrent infections, neurologic symptoms, and autoimmune disorders. PNP deficiency causes a shortage of white blood cells, called T-cells, that help fight infection. Affected individuals develop neurologic symptoms, such as stiff or rigid muscles (spasticity), uncoordinated movements (ataxia), developmental delay, and intellectual disability. PNP deficiency is associated with an increased risk to develop autoimmune disorders, such as autoimmune hemolytic anemia, idiopathic thrombocytopenic purpura (ITP), autoimmune neutropenia, thyroiditis, and lupus. [Spectral] Hypoxanthine (exact mass = 136.03851) and Adenine (exact mass = 135.0545) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. Occurs widely in plant and animal tissue (CCD). Hypoxanthine is found in many foods, some of which are japanese chestnut, parsnip, okra, and horned melon. Hypoxanthine. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=68-94-0 (retrieved 2024-07-02) (CAS RN: 68-94-0). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0). Hypoxanthine, a purine derivative, is a potential free radical generator and could be used as an indicator of hypoxia. Hypoxanthine, a purine derivative, is a potential free radical generator and could be used as an indicator of hypoxia. Hypoxanthine, a purine derivative, is a potential free radical generator and could be used as an indicator of hypoxia.

Thymine

5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

C5H6N2O2 (126.04292559999999)

Thymine, also known as 5-methyluracil, belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves thymus glands, hence its name. Thymine is one of the 4 nuelcoebases found in DNA and is essential to all life. Thymine exists in all living species, ranging from bacteria to plants to humans. Thymine combined with deoxyribose creates the nucleoside deoxythymidine (also called thymidine) which when phosphorylated to dTDP can be incorporated into DNA via DNA polymerases. Thymidine can be phosphorylated with up to three phosphoric acid groups, producing dTMP (deoxythymidine monophosphate) dTDP and/or dTTP. In RNA thymine is replaced with uracil in most cases. In DNA, thymine binds to adenine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. Within humans, thymine participates in a number of enzymatic reactions. In particular, thymine and deoxyribose 1-phosphate can be biosynthesized from thymidine through its interaction with the enzyme thymidine phosphorylase. In addition, thymine can be converted into dihydrothymine; which is mediated by the enzyme dihydropyrimidine dehydrogenase [NADP(+)]. One of the pyrimidine bases of living matter. Derivation: Hydrolysis of deoxyribonucleic acid, from methylcyanoacetylurea by catalytic reduction. Use: Biochemical research. (Hawleys Condensed Chemical Dictionary) Acquisition and generation of the data is financially supported in part by CREST/JST. COVID info from COVID-19 Disease Map Corona-virus KEIO_ID T015 Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS Thymine is one of the four nucleobases in the nucleic acid of DNA and can be a target for actions of 5-fluorouracil (5-FU) in cancer treatment, with a Km of 2.3 μM. Thymine is one of the four nucleobases in the nucleic acid of DNA and can be a target for actions of 5-fluorouracil (5-FU) in cancer treatment, with a Km of 2.3 μM. Thymine is one of the four nucleobases in the nucleic acid of DNA and can be a target for actions of 5-fluorouracil (5-FU) in cancer treatment, with a Km of 2.3 μM.

Uric acid

2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione

C5H4N4O3 (168.0283394)

Uric acid is a heterocyclic purine derivative that is the final oxidation product of purine metabolism. It is a weak acid distributed throughout the extracellular fluid as sodium urate. Uric acid is produced by the enzyme xanthine oxidase, which oxidizes oxypurines such as xanthine into uric acid. In most mammals, except humans and higher primates, the enzyme uricase further oxidizes uric acid to allantoin. Interestingly, during the Miocene epoch (~15-20 million years ago), two distinct mutations in the primate genome occurred that led to a nonfunctioning uricase gene. Consequently, humans, apes, and certain New World monkeys have much higher uric acid levels (>120 μM) compared with other mammals (<<120 uM). The loss of uricase in higher primates parallels the similar loss of the ability to synthesize ascorbic acid vitamin C. This may be because in higher primates uric acid partially replaces ascorbic acid. Like ascorbic acid, uric acid is an antioxidant. In fact, in primates, uric acid is the major antioxidant in serum and is thought to be a major factor in lengthening life-span and decreasing age-specific cancer rates in humans and other primates (PMID: 6947260). Uric acid is also the end product of nitrogen metabolism in birds and reptiles. In these animal species, it is excreted in feces as a dry mass. In humans and other mammals, the amount of urate in the blood depends on the dietary intake of purines, the level of endogenous urate biosynthesis, and the rate of urate excretion. Several kidney urate transporters are involved in the regulation of plasma urate levels. These include the urate transporter 1 (URAT1), which controls the reabsorption of urate as well as a number of organic ion transporters (OAT), such as OAT1 and OAT3, and the ATP-dependent urate export transporter MRP4. URAT1 is believed to be most critical in the regulation of plasma urate levels. (PMID: 17890445) High levels of plasma uric acid lead to a condition called hyperuricemia while low levels are associated with a condition called hypouricemia. Hyperuricemia has been defined as a uric acid concentration greater than 380 μM, while hypouricemia is generally defined as a urate concentration of less than 120 μM. Hyperuricemia can arise from a number of factors, including both acute and chronic causes. Acute causes of hyperuricemia include the intake of large amounts of alcohol, tumor lysis syndrome and a diet that is rich in purines or proteins. Chronic hyperuricemia can arise from a reduction in the kidney’s glomerular filtration rate, a decrease in the excretion of urate or an increase in overall tubular absorption in the kidneys. Hyperuricemia has been linked to a number of diseases and conditions, including gout, hypertension, cardiovascular disease, myocardial infarction, stroke, and renal disease. Uric acid has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821). Many of the causes of hyperuricemia are correctable either with lifestyle changes or drugs. Lifestyle changes include reducing weight and reducing the consumption of protein, purines, and alcohol. There are two kinds of drugs that can be used to treat chronic hyperuricemia. Xanthine oxidase inhibitors, such as allopurinol, inhibit the production of urate by blocking urate synthesis. Alternately, uricosuric drugs, such as probenecid, sulfinpyrazone, and benzpromarone, are used to reduce the serum urate concentration through the inhibition of the URAT1 transporter. (PMID: 17890445). Uric acid (especially crystalline uric acid) is also thought to be an essential initiator and amplifier of allergic inflammation for asthma and peanut allergies (PMID: 21474346). Uric acid. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=69-93-2 (retrieved 2024-07-17) (CAS RN: 69-93-2). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0). Uric acid, scavenger of oxygen radical, is a very important antioxidant that help maintains the stability of blood pressure and antioxidant stress. Uric acid can remove reactive oxygen species (ROS) such as singlet oxygen and peroxynitrite, inhibiting lipid peroxidation[1][2]. Uric acid, scavenger of oxygen radical, is a very important antioxidant that help maintains the stability of blood pressure and antioxidant stress. Uric acid can remove reactive oxygen species (ROS) such as singlet oxygen and peroxynitrite, inhibiting lipid peroxidation[1][2].

Uracil

1,2,3,4-tetrahydropyrimidine-2,4-dione

C4H4N2O2 (112.0272764)

Uracil, also known as U, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Uracil is a common naturally occurring pyrimidine found in RNA. It base pairs with adenine and is replaced by thymine in DNA. Uracil is one of the four nucleobases in RNA that are represented by the letters A, G, C and U. Methylation of uracil produces thymine. The name "uracil" was coined in 1885 by the German chemist Robert Behrend, who was attempting to synthesize derivatives of uric acid. Originally discovered in 1900, uracil was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring sperm, and wheat germ. Uracil exists in all living species, ranging from bacteria to plants to humans. Uracils use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as an allosteric regulator and a coenzyme for many important biochemical reactions. Uracil (via the nucleoside uridine) can be phosphorylated by various kinases to produce UMP, UDP and UTP. UDP and UTP regulate carbamoyl phosphate synthetase II (CPSase II) activity in animals. Uracil is also involved in the biosynthesis of polysaccharides and in the transport of sugars containing aldehydes. Within humans, uracil participates in a number of enzymatic reactions. In particular, uracil and ribose 1-phosphate can be biosynthesized from uridine; which is mediated by the enzyme uridine phosphorylase 2. In addition, uracil can be converted into dihydrouracil through the action of the enzyme dihydropyrimidine dehydrogenase [NADP(+)]. Uracil is rarely found in DNA, and this may have been an evolutionary change to increase genetic stability. This is because cytosine can deaminate spontaneously to produce uracil through hydrolytic deamination. Therefore, if there were an organism that used uracil in its DNA, the deamination of cytosine (which undergoes base pairing with guanine) would lead to formation of uracil (which would base pair with adenine) during DNA synthesis. Uracil can be used for drug delivery and as a pharmaceutical. When elemental fluorine reacts with uracil, it produces 5-fluorouracil. 5-Fluorouracil is an anticancer drug (antimetabolite) that mimics uracil during the nucleic acid (i.e. RNA) synthesis and transcription process. Because 5-fluorouracil is similar in shape to, but does not undergo the same chemistry as, uracil, the drug inhibits RNA replication enzymes, thereby blocking RNA synthesis and stopping the growth of cancerous cells. Uracil is a common and naturally occurring pyrimidine derivative. Originally discovered in 1900, it was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring sperm, and wheat germ. It is a planar, unsaturated compound that has the ability to absorb light. Uracil. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=66-22-8 (retrieved 2024-07-01) (CAS RN: 66-22-8). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0). Uracil is a common and naturally occurring pyrimidine derivative and one of the four nucleobases in the nucleic acid of RNA. Uracil is a common and naturally occurring pyrimidine derivative and one of the four nucleobases in the nucleic acid of RNA. Uracil is a common and naturally occurring pyrimidine derivative and one of the four nucleobases in the nucleic acid of RNA.

5,6-dihydrouracil

5,6-Dihydro-2,4(1H,3H)-pyrimidinedione

C4H6N2O2 (114.0429256)

Dihydrouracil belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Dihydrouracil is an intermediate breakdown product of uracil. Dihydrouracil exists in all living organisms, ranging from bacteria to plants to humans. Within humans, dihydrouracil participates in a number of enzymatic reactions. In particular, dihydrouracil can be biosynthesized from uracil; which is mediated by the enzyme dihydropyrimidine dehydrogenase [NADP(+)]. The breakdown of uracil is a multistep reaction that leads to the production of beta-alanine. The reaction process begins with the enzyme known as dihydropyrimidine dehydrogenase (DHP), which catalyzes the reduction of uracil into dihydrouracil. Then the enzyme known as dihydropyrimidinase hydrolyzes dihydrouracil into N-carbamyl-beta-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-beta-alanine into beta-alanine. There is at least one metabolic disorder that is associated with altered levels of dihydrouracil. In particular, dihydropyrimidinase deficiency is an inborn metabolic disorder that leads to highly increased concentrations of dihydrouracil and 5,6-dihydrothymine, and moderately increased concentrations of uracil and thymine in urine. Dihydropyrimidinase deficiency can cause neurological and gastrointestinal problems in some affected individuals (OMIM: 222748). In particular, patients with dihydropyrimidinase deficiency exhibit a number of neurological abnormalities including intellectual disability, seizures, weak muscle tone (hypotonia), an abnormally small head size (microcephaly), and autistic behaviours that affect communication and social interaction. Gastrointestinal problems that occur in dihydropyrimidinase deficiency include backflow of acidic stomach contents into the esophagus (gastroesophageal reflux) and recurrent episodes of vomiting. 3,4-dihydrouracil, also known as 2,4-dioxotetrahydropyrimidine or 5,6-dihydro-2,4-dihydroxypyrimidine, is a member of the class of compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 3,4-dihydrouracil is soluble (in water) and a very weakly acidic compound (based on its pKa). 3,4-dihydrouracil can be found in a number of food items such as colorado pinyon, rocket salad (sspecies), wax gourd, and boysenberry, which makes 3,4-dihydrouracil a potential biomarker for the consumption of these food products. 3,4-dihydrouracil can be found primarily in blood, cerebrospinal fluid (CSF), saliva, and urine, as well as throughout most human tissues. 3,4-dihydrouracil exists in all living organisms, ranging from bacteria to humans. In humans, 3,4-dihydrouracil is involved in a couple of metabolic pathways, which include beta-alanine metabolism and pyrimidine metabolism. 3,4-dihydrouracil is also involved in several metabolic disorders, some of which include UMP synthase deficiency (orotic aciduria), dihydropyrimidinase deficiency, ureidopropionase deficiency, and carnosinuria, carnosinemia. Moreover, 3,4-dihydrouracil is found to be associated with dihydropyrimidine dehydrogenase deficiency and hypertension. Acquisition and generation of the data is financially supported in part by CREST/JST. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS Dihydrouracil (5,6-Dihydrouracil), a metabolite of Uracil, can be used as a marker for identification of dihydropyrimidine dehydrogenase (DPD)-deficient[1][2]. Dihydrouracil (5,6-Dihydrouracil), a metabolite of Uracil, can be used as a marker for identification of dihydropyrimidine dehydrogenase (DPD)-deficient[1][2].

Coenzyme Q10

2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

C59H90O4 (862.683874)

Coenzyme Q10 (ubiquinone) is a naturally occurring compound widely distributed in animal organisms and in humans. The primary compounds involved in the biosynthesis of ubiquinone are 4-hydroxybenzoate and the polyprenyl chain. An essential role of coenzyme Q10 is as an electron carrier in the mitochondrial respiratory chain. Moreover, coenzyme Q10 is one of the most important lipophilic antioxidants, preventing the generation of free radicals as well as oxidative modifications of proteins, lipids, and DNA, it and can also regenerate the other powerful lipophilic antioxidant, alpha-tocopherol. Antioxidant action is a property of the reduced form of coenzyme Q10, ubiquinol (CoQ10H2), and the ubisemiquinone radical (CoQ10H*). Paradoxically, independently of the known antioxidant properties of coenzyme Q10, the ubisemiquinone radical anion (CoQ10-) possesses prooxidative properties. Decreased levels of coenzyme Q10 in humans are observed in many pathologies (e.g. cardiac disorders, neurodegenerative diseases, AIDS, cancer) associated with intensive generation of free radicals and their action on cells and tissues. In these cases, treatment involves pharmaceutical supplementation or increased consumption of coenzyme Q10 with meals as well as treatment with suitable chemical compounds (i.e. folic acid or B-group vitamins) which significantly increase ubiquinone biosynthesis in the organism. Estimation of coenzyme Q10 deficiency and efficiency of its supplementation requires a determination of ubiquinone levels in the organism. Therefore, highly selective and sensitive methods must be applied, such as HPLC with UV or coulometric detection. For a number of years, coenzyme Q (CoQ10 in humans) was known for its key role in mitochondrial bioenergetics; later studies demonstrated its presence in other subcellular fractions and in plasma, and extensively investigated its antioxidant role. These two functions constitute the basis on which research supporting the clinical use of CoQ10 is founded. Also at the inner mitochondrial membrane level, coenzyme Q is recognized as an obligatory co-factor for the function of uncoupling proteins and a modulator of the transition pore. Furthermore, recent data reveal that CoQ10 affects expression of genes involved in human cell signalling, metabolism, and transport and some of the effects of exogenously administered CoQ10 may be due to this property. Coenzyme Q is the only lipid soluble antioxidant synthesized endogenously. In its reduced form, CoQH2, ubiquinol, inhibits protein and DNA oxidation but it is the effect on lipid peroxidation that has been most deeply studied. Ubiquinol inhibits the peroxidation of cell membrane lipids and also that of lipoprotein lipids present in the circulation. Dietary supplementation with CoQ10 results in increased levels of ubiquinol-10 within circulating lipoproteins and increased resistance of human low-density lipoproteins to the initiation of lipid peroxidation. Moreover, CoQ10 has a direct anti-atherogenic effect, which has been demonstrated in apolipoprotein E-deficient mice fed with a high-fat diet. (PMID: 15928598, 17914161). COVID info from clinicaltrial, clinicaltrials, clinical trial, clinical trials C - Cardiovascular system > C01 - Cardiac therapy C26170 - Protective Agent > C275 - Antioxidant D018977 - Micronutrients > D014815 - Vitamins Same as: D01065 Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS

Water

oxidane

H2O (18.0105642)

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 .

Oxygen

Molecular oxygen

O2 (31.98983)

Oxygen is the third most abundant element in the universe after hydrogen and helium and the most abundant element by mass in the Earths crust. Diatomic oxygen gas constitutes 20.9\\% of the volume of air. All major classes of structural molecules in living organisms, such as proteins, carbohydrates, and fats, contain oxygen, as do the major inorganic compounds that comprise animal shells, teeth, and bone. Oxygen in the form of O2 is produced from water by cyanobacteria, algae and plants during photosynthesis and is used in cellular respiration for all living organisms. Green algae and cyanobacteria in marine environments provide about 70\\% of the free oxygen produced on earth and the rest is produced by terrestrial plants. Oxygen is used in mitochondria to help generate adenosine triphosphate (ATP) during oxidative phosphorylation. For animals, a constant supply of oxygen is indispensable for cardiac viability and function. To meet this demand, an adult human, at rest, inhales 1.8 to 2.4 grams of oxygen per minute. This amounts to more than 6 billion tonnes of oxygen inhaled by humanity per year. At a resting pulse rate, the heart consumes approximately 8-15 ml O2/min/100 g tissue. This is significantly more than that consumed by the brain (approximately 3 ml O2/min/100 g tissue) and can increase to more than 70 ml O2/min/100 g myocardial tissue during vigorous exercise. As a general rule, mammalian heart muscle cannot produce enough energy under anaerobic conditions to maintain essential cellular processes; thus, a constant supply of oxygen is indispensable to sustain cardiac function and viability. However, the role of oxygen and oxygen-associated processes in living systems is complex, and they and can be either beneficial or contribute to cardiac dysfunction and death (through reactive oxygen species). Reactive oxygen species (ROS) are a family of oxygen-derived free radicals that are produced in mammalian cells under normal and pathologic conditions. Many ROS, such as the superoxide anion (O2-)and hydrogen peroxide (H2O2), act within blood vessels, altering mechanisms mediating mechanical signal transduction and autoregulation of cerebral blood flow. Reactive oxygen species are believed to be involved in cellular signaling in blood vessels in both normal and pathologic states. The major pathway for the production of ROS is by way of the one-electron reduction of molecular oxygen to form an oxygen radical, the superoxide anion (O2-). Within the vasculature there are several enzymatic sources of O2-, including xanthine oxidase, the mitochondrial electron transport chain, and nitric oxide (NO) synthases. Studies in recent years, however, suggest that the major contributor to O2- levels in vascular cells is the membrane-bound enzyme NADPH-oxidase. Produced O2- can react with other radicals, such as NO, or spontaneously dismutate to produce hydrogen peroxide (H2O2). In cells, the latter reaction is an important pathway for normal O2- breakdown and is usually catalyzed by the enzyme superoxide dismutase (SOD). Once formed, H2O2 can undergo various reactions, both enzymatic and nonenzymatic. The antioxidant enzymes catalase and glutathione peroxidase act to limit ROS accumulation within cells by breaking down H2O2 to H2O. Metabolism of H2O2 can also produce other, more damaging ROS. For example, the endogenous enzyme myeloperoxidase uses H2O2 as a substrate to form the highly reactive compound hypochlorous acid. Alternatively, H2O2 can undergo Fenton or Haber-Weiss chemistry, reacting with Fe2+/Fe3+ ions to form toxic hydroxyl radicals (-.OH). (PMID: 17027622, 15765131) [HMDB]. Oxygen is found in many foods, some of which are soy bean, watermelon, sweet basil, and spinach. Oxygen is the third most abundant element in the universe after hydrogen and helium and the most abundant element by mass in the Earths crust. Diatomic oxygen gas constitutes 20.9\\% of the volume of air. All major classes of structural molecules in living organisms, such as proteins, carbohydrates, and fats, contain oxygen, as do the major inorganic compounds that comprise animal shells, teeth, and bone. Oxygen in the form of O2 is produced from water by cyanobacteria, algae and plants during photosynthesis and is used in cellular respiration for all living organisms. Green algae and cyanobacteria in marine environments provide about 70\\% of the free oxygen produced on earth and the rest is produced by terrestrial plants. Oxygen is used in mitochondria to help generate adenosine triphosphate (ATP) during oxidative phosphorylation. For animals, a constant supply of oxygen is indispensable for cardiac viability and function. To meet this demand, an adult human, at rest, inhales 1.8 to 2.4 grams of oxygen per minute. This amounts to more than 6 billion tonnes of oxygen inhaled by humanity per year. At a resting pulse rate, the heart consumes approximately 8-15 ml O2/min/100 g tissue. This is significantly more than that consumed by the brain (approximately 3 ml O2/min/100 g tissue) and can increase to more than 70 ml O2/min/100 g myocardial tissue during vigorous exercise. As a general rule, mammalian heart muscle cannot produce enough energy under anaerobic conditions to maintain essential cellular processes; thus, a constant supply of oxygen is indispensable to sustain cardiac function and viability. However, the role of oxygen and oxygen-associated processes in living systems is complex, and they and can be either beneficial or contribute to cardiac dysfunction and death (through reactive oxygen species). Reactive oxygen species (ROS) are a family of oxygen-derived free radicals that are produced in mammalian cells under normal and pathologic conditions. Many ROS, such as the superoxide anion (O2-)and hydrogen peroxide (H2O2), act within blood vessels, altering mechanisms mediating mechanical signal transduction and autoregulation of cerebral blood flow. Reactive oxygen species are believed to be involved in cellular signaling in blood vessels in both normal and pathologic states. The major pathway for the production of ROS is by way of the one-electron reduction of molecular oxygen to form an oxygen radical, the superoxide anion (O2-). Within the vasculature there are several enzymatic sources of O2-, including xanthine oxidase, the mitochondrial electron transport chain, and nitric oxide (NO) synthases. Studies in recent years, however, suggest that the major contributor to O2- levels in vascular cells is the membrane-bound enzyme NADPH-oxidase. Produced O2- can react with other radicals, such as NO, or spontaneously dismutate to produce hydrogen peroxide (H2O2). In cells, the latter reaction is an important pathway for normal O2- breakdown and is usually catalyzed by the enzyme superoxide dismutase (SOD). Once formed, H2O2 can undergo various reactions, both enzymatic and nonenzymatic. The antioxidant enzymes catalase and glutathione peroxidase act to limit ROS accumulation within cells by breaking down H2O2 to H2O. Metabolism of H2O2 can also produce other, more damaging ROS. For example, the endogenous enzyme myeloperoxidase uses H2O2 as a substrate to form the highly reactive compound hypochlorous acid. Alternatively, H2O2 can undergo Fenton or Haber-Weiss chemistry, reacting with Fe2+/Fe3+ ions to form toxic hydroxyl radicals (-.OH). (PMID: 17027622, 15765131). V - Various > V03 - All other therapeutic products > V03A - All other therapeutic products > V03AN - Medical gases

Carbon dioxide

Carbonic acid anhydride

CO2 (43.98983)

Carbon dioxide is a colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals. Carbon dioxide is produced during respiration by all animals, fungi and microorganisms that depend on living and decaying plants for food, either directly or indirectly. It is, therefore, a major component of the carbon cycle. Additionally, carbon dioxide is used by plants during photosynthesis to make sugars which may either be consumed again in respiration or used as the raw material to produce polysaccharides such as starch and cellulose, proteins and the wide variety of other organic compounds required for plant growth and development. When inhaled at concentrations much higher than usual atmospheric levels, it can produce a sour taste in the mouth and a stinging sensation in the nose and throat. These effects result from the gas dissolving in the mucous membranes and saliva, forming a weak solution of carbonic acid. Carbon dioxide is used by the food industry, the oil industry, and the chemical industry. Carbon dioxide is used to produce carbonated soft drinks and soda water. Traditionally, the carbonation in beer and sparkling wine comes about through natural fermentation, but some manufacturers carbonate these drinks artificially. Leavening agent, propellant, aerating agent, preservative. Solvent for supercritical extraction e.g. of caffeine in manufacture of caffeine-free instant coffee. It is used in carbonation of beverages, in the frozen food industry and as a component of controlled atmosphere packaging (CAD) to inhibit bacterial growth. Especies effective against Gram-negative spoilage bacteria, e.g. Pseudomonas V - Various > V03 - All other therapeutic products > V03A - All other therapeutic products > V03AN - Medical gases

Hydrogen peroxide

Hydrogen peroxide (H2O2)

H2O2 (34.0054792)

Hydrogen peroxide (H2O2) is a very pale blue liquid that appears colourless in a dilute solution. H2O2 is slightly more viscous than water and is a weak acid. H2O2 is unstable and slowly decomposes in the presence of light. It has strong oxidizing properties and is, therefore, a powerful bleaching agent that is mostly used for bleaching paper. H2O2 has also found use as a disinfectant and as an oxidizer. H2O2 in the form of carbamide peroxide is widely used for tooth whitening (bleaching), both in professionally- and in self-administered products. H2O2 is a well-documented component of living cells and is a normal metabolite of oxygen in the aerobic metabolism of cells and tissues. A total of 31 human cellular H2O2 generating enzymes has been identified so far (PMID: 25843657). H2O2 plays important roles in host defence and oxidative biosynthetic reactions. At high levels (>100 nM) H2O2 is toxic to most cells due to its ability to non-specifically oxidize proteins, membranes and DNA, leading to general cellular damage and dysfunction. However, at low levels (<10 nM), H2O2 functions as a signalling agent, particularly in higher organisms. In plants, H2O2 plays a role in signalling to cause cell shape changes such as stomatal closure and root growth. As a messenger molecule in vertebrates, H2O2 diffuses through cells and tissues to initiate cell shape changes, to drive vascular remodelling, and to activate cell proliferation and recruitment of immune cells. H2O2 also plays a role in redox sensing, signalling, and redox regulation (PMID: 28110218). This is normally done through molecular redox “switches” such as thiol-containing proteins. The production and decomposition of H2O2 are tightly regulated (PMID: 17434122). In humans, H2O2 can be generated in response to various stimuli, including cytokines and growth factors. H2O2 is degraded by several enzymes including catalase and superoxide dismutase (SOD), both of which play important roles in keeping the amount of H2O2 in the body below toxic levels. H2O2 also appears to play a role in vitiligo. Vitiligo is a skin pigment disorder leading to patchy skin colour, especially among dark-skinned individuals. Patients with vitiligo have low catalase levels in their skin, leading to higher levels of H2O2. High levels of H2O2 damage the epidermal melanocytes, leading to a loss of pigment (PMID: 10393521). Accumulating evidence suggests that hydrogen peroxide H2O2 plays an important role in cancer development. Experimental data have shown that cancer cells produce high amounts of H2O2. An increase in the cellular levels of H2O2 has been linked to several key alterations in cancer, including DNA changes, cell proliferation, apoptosis resistance, metastasis, angiogenesis and hypoxia-inducible factor 1 (HIF-1) activation (PMID: 17150302, 17335854, 16677071, 16607324, 16514169). H2O2 is found in most cells, tissues, and biofluids. H2O2 levels in the urine can be significantly increased with the consumption of coffee and other polyphenolic-containing beverages (wine, tea) (PMID: 12419961). In particular, roasted coffee has high levels of 1,2,4-benzenetriol which can, on its own, lead to the production of H2O2. Normal levels of urinary H2O2 in non-coffee drinkers or fasted subjects are between 0.5-3 uM/mM creatinine whereas, for those who drink coffee, the levels are between 3-10 uM/mM creatinine (PMID: 12419961). It is thought that H2O2 in urine could act as an antibacterial agent and that H2O2 is involved in the regulation of glomerular function (PMID: 10766414). A - Alimentary tract and metabolism > A01 - Stomatological preparations > A01A - Stomatological preparations > A01AB - Antiinfectives and antiseptics for local oral treatment D - Dermatologicals > D08 - Antiseptics and disinfectants > D08A - Antiseptics and disinfectants S - Sensory organs > S02 - Otologicals > S02A - Antiinfectives > S02AA - Antiinfectives It is used in foods as a bleaching agent, antimicrobial agent and oxidising agent C254 - Anti-Infective Agent > C28394 - Topical Anti-Infective Agent D009676 - Noxae > D016877 - Oxidants > D010545 - Peroxides D000890 - Anti-Infective Agents

Bicarbonate ion

CHO3- (60.9925696)

D019995 - Laboratory Chemicals > D002021 - Buffers > D001639 - Bicarbonates

Pseudouridine 5'-phosphate

{[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

C9H13N2O9P (324.03586580000007)

Pseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a "fifth nucleoside" in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U-->psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant "rigidifying" influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context. PMID: 10902565 [HMDB]. Pseudouridine 5-phosphate is found in many foods, some of which are garland chrysanthemum, chives, broad bean, and green bell pepper. Pseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a "fifth nucleoside" in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U-->psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant "rigidifying" influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context. PMID: 10902565.

Ammonium

Ammonium compounds

H4N+ (18.0343724)

Ammonium, also known as ammonium(1+) or nh4+, 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. Ammonium can be found in a number of food items such as irish moss, sago palm, sorghum, and malabar spinach, which makes ammonium a potential biomarker for the consumption of these food products. Ammonium can be found primarily in blood and sweat. Ammonium exists in all living species, ranging from bacteria to humans. In humans, ammonium is involved in the the oncogenic action of 2-hydroxyglutarate. Ammonium is also involved in a couple of metabolic disorders, which include the oncogenic action of d-2-hydroxyglutarate in hydroxygluaricaciduria and the oncogenic action of l-2-hydroxyglutarate in hydroxygluaricaciduria. Moreover, ammonium is found to be associated with n-acetylglutamate synthetase deficiency. The ammonium cation is a positively charged polyatomic ion with the chemical formula NH+ 4. It is formed by the protonation of ammonia (NH3). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary ammonium cations (NR+ 4), where one or more hydrogen atoms are replaced by organic groups (indicated by R) . Ammonium is an important source of nitrogen for many plant species, especially those growing on hypoxic soils. However, it is also toxic to most crop species and is rarely applied as a sole nitrogen source. The ammonium (more obscurely: aminium) cation is a positively charged polyatomic cation with the chemical formula NH4+. It is formed by the protonation of ammonia (NH3). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary ammonium cations (NR4+), where one or more hydrogen atoms are replaced by organic radical groups (indicated by R). Ammonium is found to be associated with N-acetylglutamate synthetase deficiency, which is an inborn error of metabolism.

Hydrogen Ion

Hydrogen cation

H+ (1.0078246)

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])