]> Dumontier Lab application/rdf+xml Michel Dumontier Biochemistry Ontology (primitive) An ontology of biochemical entities and processes. 2007-07-01 en 1.0 acetylation A reaction in which an acetyl functional group is transferred to a compound. activation interaction An interaction in which the functionality of an entity becomes activated. activator An effector that increases the rate of reaction of some enzyme. A small pocket on an enzyme that contains residues responsible for the substrate specificity (charge, hydrophobicity, steric hindrance) and catalytic residues which often act as proton donors or acceptors or are responsible for binding a cofactor. active site adenine A purine base with the formula C5H5N5. A nucleoside comprised of adenine attached to a ribose ring via a β-N9-glycosidic bond. adenosine adenylate alanine A pentose with an aldehyde functional group in position 1. aldopentose aklylation A reaction in which an alkyl functional group is transferred to a compound. allosteric activiation An allosteric interaction that results in the activation of a participant entity. An enzyme whose function is regulated by reversible, noncovalent binding of regulatory compounds called allosteric modulators or allosteric effectors, which are generally small metabolites or cofactors. allosteric enzyme An interaction that permits a sensitive response to modulator concentration. allosteric interaction allosteric protein A protein whose ability to bind a ligand at one site affects the binding properties of another site on the same protein. The site on an allosteric protein that the modulator molecule binds to. allosteric site A right-handed coiled conformation of a protein in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier (i+4 -> i hydrogen bonding). alpha helix amino acid An organic compound that contains both amine and carboxyl functional groups. amylopectin amylose arginine asparagine aspartic acid A protein conformation consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. beta sheet A conformation of proteins in which a stretch of amino acids typically 5–10 amino acids long have their peptide backbone almost fully extended. beta strand binding site A site on a protein that is required for binding. biochemical cleavage The breaking of chemical bonds. biochemical modification A chemical modification to a biomolecule. biotinylation A reaction in which an biotin group is transferred to a compound. carbohydrate An organic compound comprised of aldehydes or ketones and hydroxyl groups. A glycerophospholipid with a phosphatidyl-glycerol group. cardiolipin A fibrous protein that contains a lot of glycine and proline. collagen An amino acid commonly found in proteins. common protein amino acid competivite inhibition A reversible inhibition where binding of the inhibitor to the enzyme prevents binding of the substrate and vice versa. An allosteric interaction in which the binding of one ligand affects the binding of any remaining unfilled binding sites. cooperative interaction cysteine A nucleoside comprised of cytosine attached to a ribose ring via a β-N1-glycosidic bond. cytidine cytosine A pyrimidine base with the formula C4H5N3O. deoxyribonucleic acid A nucleic acid composed of deoxyribonucleotides. DNA The cleavage of bonds in dna molecules. dna cleavage Digital Object Identifier An adenosine attached to a deoxyribose ring. deoxyadenosine A cytosine attached to a deoxyribose ring. deoxycytidine A guanine attached to a deoxyribose ring. deoxyguanine A nucleoside that contains deoxyribose as its sugar component. deoxyribonucleoside deoxyribonucleotide A nucleotide that contains the sugar deoxyribose. deoxyribose An aldopentose with the formula C5H10O4. A thymidine attached to a deoxyribose ring. deoxythymidine desmosine An amino acid found in elastin. diglyceride a glyceride consisting of two fatty acid chain covalently bonded to a glycerol molecule through ester linkages. A polysaccharide comprised of exactly two monosaccharides. disaccharide domain One or more segments of protein that are evolutionary, structural or functional. A fibrous protein conposed mostly of glycine, valine, alanine and proline. elastin enzyme A protein that catalyses biochemical reactions. evolutionary domain A domain that is evolutionarily conserved. A carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. fatty acid fibrous protein A long filamentous protein molecule that are usually insoluable. fructose A reaction in which an fucose group is transferred to a compound. fucosylation functional domain A domain that provides a function. A glycolipid with a glycosidic linkage to a galactose moiety. galactolipid galactose glucose glutamate glutamine glutamylation A reaction in which an glutamyl functional group is transferred to a compound. glyceride A lipid composed of esters of glycerol (propane-1,2,3-triol) with fatty acids. glycerol A sugar alcohol that has three hydrophilic alcoholic hydroxyl groups and has the formula C3H5(OH)3. glycerophospholipid A diacylglycerol that links alcohols to the head-group through a phosphodiester bond. glycine A lipid with 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part. glycolipid An organic compound composed of a protein and a carbohydrate. glycoprotein A reaction in which an sugar group is transferred to a compound. glycosylation A purine base with the formula C5H5ON5. guanine A nucleoside comprised of a guanine attached to a ribose ring via a β-N9-glycosidic bond. guanosine A monosaccharide with seven carbon atoms. heptose An organic compound having a heterocyclic heterocyclic aromatic organic compound An interaction in which the normal ligand and the modulator are different. heterotropic interaction A monosaccharide with six carbon atoms. hexose histidine An interaction in which the modulator and the normal ligand are identical. homotropic interaction hydrolase hydroxylation A reaction in which an hydroxyl functional group is transferred to a compound. imino acid inhibition interaction An interaction in which the functionality of an entity becomes inhibited. An agent that reduces the rate of reaction of some enzyme. inhibitor An inhibition interaction that is irreversible. irreversible inhibition isoleucine isoprenylation A reaction in which an isoprenyl functional group is transferred to a compound. keratin A fibrous protein that contains a lot of cysteine and are stabilized by disulfide bridges ketopentose A pentose with an ketone functional group in position 2. kinase An enzyme capable of phosphorylating an organic molecule. LifeScienceIdentifier A disaccharide that contains a glucose and a galactose. lactose leucine Any kind of molecule that binds reversibly to a protein. ligand ligand interaction An interaction between two chemical entities in which one shares electron through a (coordinate) covalent bond. ligase lipase An enzyme that catalyzes the hydrolysis of triacylglycerols. An amphiphilic class of hydrocarbon-containing organic compounds. lipid A reaction in which an lipoyl functional group is transferred to a compound. lipoylation lysine Mature messenger RNA metabolic pathway A series of chemical reactions that are catalyzed by enzymes. methionine A reversible inhibition where competitive inhibition and uncompetitive inhibition may occur such that the inhibitor can bind to either the free enzyme or the enzyme-substrate complex. In mixed inhibition, the inhibitor binds to a site different from the active site where the substrate binds. An interaction between two molecules. molecular interaction molecular site monoglyceride A glyceride consisting of one fatty acid chain covalently bonded to a glycerol molecule through an ester linkage. A carbohydrate with the chemical formula (CH2O)n and the chemical structure H(CHOH)nC=O(CHOH)mH. monosaccharide nitrogenous base An organic compound with basic properties that is a result of having a lone pair of electrons on a nitrogen atom. A reversible inhibition where the inhibition that reduces the maximum rate of a chemical reaction (Vmax) without changing the apparent binding affinity of the catalyst for the substrate. noncompetitive inhibition nucleic acid An organic polymer composed of nucleotides. nucleic acid base A nucleotide of a nucleic acid. A protein having one or more nucleic acids as prosthetic groups. nucleoprotein An organic compound that only consists of a heterocyclic base and a sugar. nucleoside An organicl compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. nucleotide A nucleotide that contains exactly 2 phosphates (as well as the base and sugar). A nucleotide that contains one phosphate (as well as the base and sugar). A nucleotide that contains exactly 3 phosphates (as well as the base and sugar) A polysaccharide composed of 3 to 6 monosaccharides. oligosaccharide omega angle The bond angle resulting from a rotation involving the backbone atoms Cα − C' − N − Cα. A molecule that participates in biologically relevant processes. A monosaccharide with five carbon atoms. pentose peptide angle peptide bond A chemical bond between the carboxyl groups and amino groups, usually uniting a peptide. peptide cleavage The cleavage of peptide bonds. phenylalanine The bond angle resulting from rotations at Calpha of the NOC bond. phi is defined as 180degrees when the polypeptide is in its fully extended conformation and all peptide groups are in the same plane. phi angle phosphatidic acid A glycerophospholipid with a hydrogen. phosphatidylcholine A glycerophospholipid with a choline group. A glycerophospholipid with a ethanolamine group. phosphatidylethanolamine A glycerophospholipid with a glycerol group. phosphatidylglycerol phosphatidylinositol-4,5-biphosphate A glycerophospholipid with a myo-Inositol 4,5-bisphosphate group. A glycerophospholipid with a serine group. phosphatidylserine phospholipid A lipid with a phosphate moiety as the polar head group. phosphopantetheinylation A reaction in which an phosphopantetheinyl functional group is transferred to a compound. phosphorylase An enzyme that removes a phosphate group from another organic molecule. phosphorylation A reaction in which a phosphoryl group is transferred to a compound. polypeptide An organic molecule consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain. Are polymers made up of many monosaccharides joined together by glycosidic links with the chemical formula Cn(H2O)n-1. Pre-messenger RNA proline An imino acid protease An enzyme that cleaves a protein at a specific peptide bond A large organic compound made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. protein protein kinase A kinase that phosphorylates a protein. The bond angle resulting from rotations for the Calpha-OC bond. psi is defined as 180degrees when the ppolypeptide is in its fully extended conformation and all peptide groups are in the same plane. psi angle purine A heterocyclic organic compound containing fused pyrimidine and imidazole rings. A heterocyclic organic compound containing nitrogen atoms at positions 1 and 3. pyrimidine A nucleic acid composed of ribonucleotides. ribonucleic acid RNA An interaction in which the functionality of some entity is regulated. regulation interaction regulator An agent that regulates (increases/decreases) the functionality of another molecule. An enzyme that exhibits increased or decreased catalytic activity in response to binding of a regulator compound. regulatory enzyme regulatory pathway A series of interactions leading to the regulation (activation/inhibition) of molecular entities. An inhibition interaction in which an inhibitor binds to an enzyme with an affinity greater than the enzyme with its natural substrate. reversible inhibition ribonucleoside A nucleoside that contains ribose as its sugar component. A nucleotide that contains the sugar ribose. ribonucleotide ribose An aldopentose with the formula C5H10O5. s-nitrosylation A reaction in which a s-nitro group is transferred to a compound. Sacchromyces Genome Database Identifier A reaction in which a sumo (small ubiquitin-related modifier) group is transferred to a compound. sumoylation The general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. secondary structure Derived from serine, has selenium instead of cysteine. selenocysteine serine signaling pathway A series of molecular interactions that converts one kind of signal or stimulus into another. soluble protein A protein that is generally soluble in aqueous solution. A lipid composed of a polar head group and two nonpolar tails, one of which is a amino alcohol sphingosine or one of its derivates, the other a long chain fatty acid (excluding glycerol). sphingolipid sphingomyelin A sphingolipid that contains phosphocholine or phosphoethanolamine as the polar head group. A polysaccharide that contains amylose and amylopectin. starch A domain that provides a structural role. structural domain sucrose A disaccharide that contains a glucose and a fructose. A hydrogenated form of saccharide, whose carbonyl group has been reduced to a primary or secondary hydroxyl group. An inhibitor that is converted to a very reactive compound which combines irreversibly with the enzyme. suicide inactivator An irreversible inhibition reaction in which a complex is formed between the two entities. suicide inhibition A reaction in which a sulfate group is transferred to a compound. sulfation NCBI Taxonomy Identifier. A monosaccharide with four carbon atoms. tetrose threonine thymidine A molecule made when thymine is attached to a pentose ring. thymine A pyrimidine base with the formula C5H6N2O2. The angle between 4 atoms. torsion angle A glyceride consisting of three fatty acid chain covalently bonded to a glycerol molecule through ester linkages. triglyceride A monosaccharide with three carbon atoms. triose tryptophan tyrosine A reaction in which a ubiquitin group is transferred to a compound. ubiquitination uncommon amino acid A pyrimidine base with the formula C4H4N2O2. uracil uridine A nucleoside comprised of a uracil attached to a ribose ring via a β-N1-glycosidic bond. valine Inactive precursor to an enzyme. zymogen An imino acid found in plant cell wall proteins, collagen. 4-hydroxy proline 5-hydroxylysine Found in collagen. 6-N-Methyl lysine Messenger RNA Non coding RNA Ribosomal RNA Rybosomal RNA Small cytoplasmic RNA Small interfering RNA Small nuclear RNA Transfer RNA