]> Dumontier Lab 2007-10-01 application/rdf+xml en Biochemical entities and processes. Michel Dumontier Biochemistry Ontology (primitive) 2.0 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. active site 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. adenine A purine base with the formula C5H5N5. adenosine A nucleoside comprised of adenine attached to a ribose ring via a β-N9-glycosidic bond. adenylate alanine aldopentose A pentose with an aldehyde functional group in position 1. 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. allosteric enzyme 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 interaction An interaction that permits a sensitive response to modulator concentration. allosteric protein A protein whose ability to bind a ligand at one site affects the binding properties of another site on the same protein. allosteric site The site on an allosteric protein that the modulator molecule binds to. alpha helix 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). amino acid An organic compound that contains both amine and carboxyl functional groups. amylopectin amylose arginine asparagine aspartic acid beta sheet A protein conformation consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. beta strand A conformation of proteins in which a stretch of amino acids typically 5–10 amino acids long have their peptide backbone almost fully extended. 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. cardiolipin A glycerophospholipid with a phosphatidyl-glycerol group. collagen A fibrous protein that contains a lot of glycine and proline. common protein amino acid An amino acid commonly found in proteins. competivite inhibition A reversible inhibition where binding of the inhibitor to the enzyme prevents binding of the substrate and vice versa. cooperative interaction An allosteric interaction in which the binding of one ligand affects the binding of any remaining unfilled binding sites. cysteine cytidine A nucleoside comprised of cytosine attached to a ribose ring via a β-N1-glycosidic bond. cytosine A pyrimidine base with the formula C4H5N3O. DNA deoxyribonucleic acid A nucleic acid composed of deoxyribonucleotides. dna cleavage The cleavage of bonds in dna molecules. Digital Object Identifier deoxyadenosine An adenosine attached to a deoxyribose ring. deoxycytidine A cytosine attached to a deoxyribose ring. deoxyguanine A guanine attached to a deoxyribose ring. deoxyribonucleoside A nucleoside that contains deoxyribose as its sugar component. deoxyribonucleotide A nucleotide that contains the sugar deoxyribose. deoxyribose An aldopentose with the formula C5H10O4. deoxythymidine A thymidine attached to a deoxyribose ring. 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. disaccharide A polysaccharide comprised of exactly two monosaccharides. domain One or more segments of protein that are evolutionary, structural or functional. elastin A fibrous protein conposed mostly of glycine, valine, alanine and proline. enzyme A protein that catalyses biochemical reactions. evolutionary domain A domain that is evolutionarily conserved. fatty acid A carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. fibrous protein A long filamentous protein molecule that are usually insoluable. fructose fucosylation A reaction in which an fucose group is transferred to a compound. functional domain A domain that provides a function. galactolipid A glycolipid with a glycosidic linkage to a galactose moiety. 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 glycolipid A lipid with 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part. glycoprotein An organic compound composed of a protein and a carbohydrate. glycosylation A reaction in which an sugar group is transferred to a compound. guanine A purine base with the formula C5H5ON5. guanosine A nucleoside comprised of a guanine attached to a ribose ring via a β-N9-glycosidic bond. heptose A monosaccharide with seven carbon atoms. heterocyclic aromatic organic compound An organic compound having a heterocyclic heterotropic interaction An interaction in which the normal ligand and the modulator are different. hexose A monosaccharide with six carbon atoms. histidine homotropic interaction An interaction in which the modulator and the normal ligand are identical. 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. inhibitor An agent that reduces the rate of reaction of some enzyme. irreversible inhibition An inhibition interaction that is irreversible. 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 lactose A disaccharide that contains a glucose and a galactose. leucine ligand Any kind of molecule that binds reversibly to a protein. 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. lipid An amphiphilic class of hydrocarbon-containing organic compounds. 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. molecular interaction An interaction between two molecules. molecular site monoglyceride A glyceride consisting of one fatty acid chain covalently bonded to a glycerol molecule through an ester linkage. monosaccharide A carbohydrate with the chemical formula (CH2O)n and the chemical structure H(CHOH)nC=O(CHOH)mH. nitrogenous base An organic compound with basic properties that is a result of having a lone pair of electrons on a nitrogen atom. noncompetitive inhibition 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. nucleic acid An organic polymer composed of nucleotides. nucleic acid base A nucleotide of a nucleic acid. nucleoprotein A protein having one or more nucleic acids as prosthetic groups. nucleoside An organic compound that only consists of a heterocyclic base and a sugar. nucleotide An organicl compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. 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) oligosaccharide A polysaccharide composed of 3 to 6 monosaccharides. 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. pentose A monosaccharide with five carbon atoms. 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 phi angle 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. phosphatidic acid A glycerophospholipid with a hydrogen. phosphatidylcholine A glycerophospholipid with a choline group. phosphatidylethanolamine A glycerophospholipid with a ethanolamine group. phosphatidylglycerol A glycerophospholipid with a glycerol group. phosphatidylinositol-4,5-biphosphate A glycerophospholipid with a myo-Inositol 4,5-bisphosphate group. phosphatidylserine A glycerophospholipid with a serine group. 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 protein 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 kinase A kinase that phosphorylates a protein. psi angle 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. purine A heterocyclic organic compound containing fused pyrimidine and imidazole rings. pyrimidine A heterocyclic organic compound containing nitrogen atoms at positions 1 and 3. ribonucleic acid RNA A nucleic acid composed of ribonucleotides. regulation interaction An interaction in which the functionality of some entity is regulated. regulator An agent that regulates (increases/decreases) the functionality of another molecule. regulatory enzyme An enzyme that exhibits increased or decreased catalytic activity in response to binding of a regulator compound. regulatory pathway A series of interactions leading to the regulation (activation/inhibition) of molecular entities. reversible inhibition An inhibition interaction in which an inhibitor binds to an enzyme with an affinity greater than the enzyme with its natural substrate. ribonucleoside A nucleoside that contains ribose as its sugar component. ribonucleotide A nucleotide that contains the sugar ribose. 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 sumoylation A reaction in which a sumo (small ubiquitin-related modifier) group is transferred to a compound. secondary structure The general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. selenocysteine Derived from serine, has selenium instead of cysteine. 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. sphingolipid 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). sphingomyelin A sphingolipid that contains phosphocholine or phosphoethanolamine as the polar head group. starch A polysaccharide that contains amylose and amylopectin. structural domain A domain that provides a structural role. 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. suicide inactivator An inhibitor that is converted to a very reactive compound which combines irreversibly with the enzyme. suicide inhibition An irreversible inhibition reaction in which a complex is formed between the two entities. sulfation A reaction in which a sulfate group is transferred to a compound. NCBI Taxonomy Identifier. tetrose A monosaccharide with four carbon atoms. threonine thymidine A molecule made when thymine is attached to a pentose ring. thymine A pyrimidine base with the formula C5H6N2O2. torsion angle The angle between 4 atoms. triglyceride A glyceride consisting of three fatty acid chain covalently bonded to a glycerol molecule through ester linkages. triose A monosaccharide with three carbon atoms. tryptophan tyrosine ubiquitination A reaction in which a ubiquitin group is transferred to a compound. uncommon amino acid uracil A pyrimidine base with the formula C4H4N2O2. uridine A nucleoside comprised of a uracil attached to a ribose ring via a β-N1-glycosidic bond. valine zymogen Inactive precursor to an enzyme. 4-hydroxy proline An imino acid found in plant cell wall proteins, collagen. 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