Systems Biology Ontology, OWL export generated by SBO Browser (http://www.ebi.ac.uk/sbo/) 23:01:2012 16:29 Generated: 09:02:2012 07:00 Entity defined by the absence of any actual object. An empty set is often used to represent the source of a creation process or the result of a degradation process. empty set Synonym: potential of hydrogen pH Et kcats Et kcats Synonym: Vmaxr reverse maximal velocity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to three reactant quantities. mass action rate law for third order irreversible reactions Synonym: ribonucleic acid enzyme ribozyme substrate Inhibitor V Ks n L Ki V substrate Ks substrate n 1 L Ks 1 Inhibitor Ki n Ks substrate n Enzymatic rate law which follows from the allosteric concerted model (symmetry model or MWC model).This states that enzyme subunits can assume one of two conformational states (relaxed or tense), and that the state of one subunit is shared or enforced on the others. The binding of a ligand to a site other than that bound by the substrate (active site) can shift the conformation from one state to the other. L represents the equilibrium constant between active and inactive states of the enzyme, and n represents the number of binding sites for the substrate and inhibitor. enzymatic rate law for irreversible allosteric inhibition Ratio of the dissociation constant of an inhibitor from the complex enzyme-substrate on the dissociation constant of an inhibitor from the free enzyme. relative inhibition constant kf kr R1 R2 kf R1 R1 R2 kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme Measure of the degree to which an object opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. electrical resistance kf kr R1 R2 P kf R1 R2 kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. mass action rate law for zeroth order reversible reactions A protein that catalyzes a chemical reaction. The word comes from en ("at" or "in") and simo ("leaven" or "yeast"). enzyme Time during which some action is awaited. delay kf kr R P1 P2 P3 kf R R R kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme Constant with the dimension of a powered concentration. It is determined at half-saturation, half-activity etc. equilibrium or steady-state constant kf kr R1 R2 R3 P1 P2 P3 kf R1 R2 R3 kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, three products, continuous scheme Non-covalent association between several macromolecules multimer of macromolecules Addition of an acetyl group (-COCH3) to a chemical entity. acetylation kcat Et S Ks kcat Et S Ks S Kinetics of enzymes that react only with one substance, their substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting unireactant enzymes kf kr R1 R2 P kf R1 R1 R2 kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, first order reverse, reversible reactions, two reactants, continuous scheme Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. The models take into account the distribution of the entities and describe the spatial fluxes. spatial continuous framework Synonym: miRNA microRNA kcat Et S I Ks Ki a kcat Et S S 1 I a Ki Ks 1 I Ki Synonym: simple intersecting linear mixed-type competitive inhibition enzymatic rate law for simple mixed-type inhibition of irreversible unireactant enzymes k R1 R2 k R1 R2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the product of two reactant quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order irreversible reactions, two reactants, continuous scheme substrate product Inhibitor Kms Kmp Vf Vr Kis Kic Vf substrate Kms Vr product Kmp 1 Inhibitor Kis substrate Kms product Kmp 1 Inhibitor Kic Reversible inhibition of a unireactant enzyme by inhibitors that can bind to the enzyme-substrate complex and to the free enzyme with the same equilibrium constant. The inhibitor is noncompetitive with the substrate. enzymatic rate law for mixed-type inhibition of reversible enzymes by mutually exclusive inhibitors Kinetics of enzymes that react only with one substance, their substrate, and are not modulated by other compounds. enzymatic rate law for non-modulated unireactant enzymes Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. forward trimolecular rate constant, discrete case Parameter characterising a physical system or the environment, and independent of life's influence. physical characteristic Synonym: chemical potential biochemical potential Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of two products. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants Covalent linkage to the protein ubiquitin. ubiquitination Molecule which is acted upon by an enzyme. The substrate binds with the enzyme's active site, and the enzyme catalyzes a chemical reaction involving the substrate. substrate kcat Et S Ks kcat Et S Ks S First general rate equation for reactions involving enzymes, it was presented in "Victor Henri. Lois Générales de l'Action des Diastases. Paris, Hermann, 1903.". The reaction is assumed to be made of a reversible of the binding of the substrate to the enzyme, followed by the breakdown of the complex generating the product. Ten years after Henri, Michaelis and Menten presented a variant of his equation, based on the hypothesis that the dissociation rate of the substrate was much larger than the rate of the product generation. Leonor Michaelis, Maud Menten (1913). Die Kinetik der Invertinwirkung, Biochem. Z. 49:333-369. Henri-Michaelis-Menten rate law Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of two reactants. mass action rate law for second order irreversible reactions, two reactants Non-covalent association between several simple chemicals multimer of simple chemicals Vmax R K h n Vmax R h K n R h Empirical equation created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). Hill-type rate law, generalised form Addition of a methyl group (-CH3) to a chemical entity. methylation kcat Et S I Ks Ki kcat Et S S 1 I Ki Ks 1 I Ki Inhibition of a unireactant enzyme by one inhibitor that can bind to the complex enzyme-substrate and the free enzyme with the same equilibrium constant, and totally prevent the catalysis. enzymatic rate law for simple irreversible non-competitive inhibition of unireactant enzymes k R k R R R Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the cube of one reactant quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order irreversible reactions, one reactant, continuous scheme Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. The models do not take into account the distribution of the entities and describe only the temporal fluxes. non-spatial continuous framework Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of two products. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants kcat Km kcat Km Constant representing the actual efficiency of an enzyme, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. catalytic efficiency Synonym: tRNA transfer RNA Naturally occurring macromolecule formed by the repetition of amino-acid residues linked by peptidic bonds. A polypeptide chain is synthesized by the ribosome. CHEBI:16541 polypeptide chain Chemical entity having a net electric charge. non-macromolecular ion Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. forward bimolecular rate constant, discrete case Synonym: DNA deoxyribonucleic acid A mathematical expression that describes a steady state situation steady state expression kf kr R1 R2 R3 P kf R1 R2 R3 kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, one product, continuous scheme Numerical parameter that quantifies the velocity of a chemical reaction involving only one reactant. unimolecular rate constant Biochemical reaction that does not result in the modification of covalent bonds of reactants, but rather modifies the conformation of some reactants, that is the relative position of their atoms in space. conformational transition none new term name Empirical constant created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). Different from a microscopic dissociation constant, it has the dimension of concentration to the power of the Hill coefficient. Hill constant Removal of a proton (hydrogen ion H+) from a chemical entity. deprotonation The mass of an entity expressed with reference to another dimension, such as unit length, area or volume. mass density of an entity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. mass action rate law for second order forward, reversible reactions, two reactants kf kr R P1 P2 kf R R kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the cube of one reactant quantity. mass action rate law for third order irreversible reactions, one reactant Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic. The models take into account the distribution of the entities and describe the spatial fluxes. spatial discrete framework kcat Et S I Ks Ki n kcat Et S S Ks 1 I Ki n Synonym: multiple competitive inhibition by one inhibitor of unireactant enzymes enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by one inhibitor kf kr R1 R2 P kf R1 R1 R2 kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme Vmax Km Vmax Km Constant representing the actual efficiency of an enzyme at a given concentration, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. NB. The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). total catalytic efficiency Entity composed of several independant components that are not linked by covalent bonds. non-covalent complex kf kr R1 R2 kf R1 R2 kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme Synonym: rRNA ribosomal RNA Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. It is to be used in a reaction modelled using a discrete framework. forward unimolecular rate constant, discrete case chemical entity possessing an unpaired electron. non-macromolecular radical Numerical parameter that quantifies the velocity of a chemical reaction involving two reactants. bimolecular rate constant Transformation of a non-covalent complex that results in the formation of several independent biochemical entities dissociation A quantitative measure of an amount or property of an entity expressed in terms of another dimension, such as unit length, area or volume. density of an entity pool Synonym: binary switch boolean switch Synonym: Michaelis-Menten constant Michaelis constant Addition of a proton (H+) to a chemical entity. protonation Empirical parameter created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). Hill coefficient kf kr R1 R2 R3 P1 P2 kf R1 R2 R3 kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, two products, continuous scheme kf kr R P1 P2 P3 kf R R kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme Kinetics of enzymes that react with one substance, and whose activity may be positively or negatively modulated. enzymatic rate law for modulated unireactant enzymes Synonym: TSS transcription start site Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. reverse unimolecular rate constant, continuous case Chemical process during which a molecular entity loses electrons. oxidation The simultaneous binding modular rate law makes the assumption that substrates and products can be bound simultaneously, and in any combination. simultaneous binding modular rate law Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of three products. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants k R1 R2 k R1 R1 R2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order irreversible reactions, two reactants, continuous scheme kf kr R1 R2 P1 P2 kf R1 R1 R2 kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme substrate product Activator Kms Kmp Vf Vr Kas Kac Vf substrate Kms Vr product Kmp Activator Kas Activator substrate Kms product Kmp Kac Activator Enzymatic rate law where the activator enhances the rate of reaction through specific and catalytic effects, which increase the apparent limiting rate and decrease apparent Michaelis constant. The activator can bind reversibly both the free enzyme and enzyme-substrate complex, while the substrate can bind only to enzyme-activator complex. Catalytic activity is seen only when enzyme, substrate and activator are complexed. enzymatic rate law for reversible mixed activation Synonym: snoRNA small nucleolar RNA Vmax R* h Vmax R* h 1 R* h Hill equation rewritten by replacing the concentration of reactant with its reduced form, that is the concentration divide by a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. Hill-type rate law, reduced form Quantitative parameter that characterises a biochemical equilibrium. equilibrium or steady-state characteristic kf kr R P kf R R kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme The Gibbs free energy change observed in a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). The standard unit of measure is kJ/mol. symbol: ΔG˚ standard Gibbs energy of reaction Covalent reaction that results in the removal of a chemical group from a molecule. removal of a chemical group kf kr R P1 P2 kf R R R kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, two products, continuous scheme Numerical parameter that quantifies the velocity of a chemical reaction involving three reactants. trimolecular rate constant Rate with which two components associate into a complex. bimolecular association rate constant kf kr R kf R kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, zeroth order reverse, reversible reactions, continuous scheme Mass of an entity per unit length. linear density of an entity Synonym: Keq equilibrium constant Synonym: kinact inactivation rate constant Process through which a DNA sequence is copied to produce a complementary RNA. transcription kf kr R1 R2 R3 P1 P2 kf R1 R2 R3 kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, two products, continuous scheme Synonym: isoprenylation prenylation Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. reverse bimolecular rate constant, continuous case substrate product Keq Vf Ks Kp h Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 substrate Ks product Kp h Reversible equivalent of Hill kinetics, where substrate and product bind co-operatively to the enzyme. A Hill coefficient (h) of greater than 1 indicates positive co-operativity between substrate and product, while h values below 1 indicate negative co-operativity. unmodulated reversible Hill-type rate law Chemical process in which atoms have their oxidation number (oxidation state) changed. redox reaction Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of three products. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants kf kr R1 R2 P kf R1 R2 kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme A real thing that is defined by its physico-chemical structure. material entity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. mass action rate law for third order irreversible reactions, two reactants substrate V Ksc Ksa V substrate Ksa 2 1 substrate Ksc substrate Ksa substrate Ksa 2 This enzymatic rate law is available only for irreversible reactions, with one substrate and one product. There is a second binding site for the enzyme which, when occupied, activates the enzyme. Substrate binding at either site can occur at random. enzymatic rate law for irreversible substrate activation Ka Ka Synonym: potential of acid pKa Concentration of an object divided by the value of another parameter having the dimension of a concentration. specific concentration of an entity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of three products. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant Synonym: [X] concentration of an entity pool A duration of time after which a phase shift occurs. temporal offset kcat Et S I Ks Ki kcat Et S Ks 1 I Ki S Synonym: simple intersecting linear competitive inhibition of unireactant enzymes enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by one inhibitor Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of three products. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant Covalent reaction that results in the addition of a chemical group on a molecule. addition of a chemical group A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure. functional entity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. mass action rate law for first order reversible reactions Substance that changes the velocity of a chemical reaction without itself being consumed or transformed by the reaction. modifier Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities. occurring entity representation koff Kon koff Kon Synonym: Kd dissociation constant Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of three products. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants Synonym: sulphation sulfation Synonym: RNA ribonucleic acid Biochemical reaction that results in the modification of some covalent bonds. conversion kf kr R1 R2 P kf R1 R1 R2 kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme kf kr R1 R2 P kf R1 R2 kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme A B KmA KmB KiA Et kcat Et kcat A B KiA KmB KmB A KmA B A B Enzymatic rate law for an irreversible reaction involving two substrates and one product. irreversible Michaelis Menten rate law for two substrates Et kcat Et kcat Synonym: Vmax maximal velocity Reaction in which a reactant gives birth to two products identical to itself. duplication kf kr R P1 P2 kf R R kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, second order reverse, reversible reactions, two products, continuous scheme Synonym: siRNA small interfering RNA substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp 1 Inhibitor Ki Reversible inhibition of a unireactant enzyme by one inhibitor that can bind to the enzyme-substrate complex and to the free enzyme with the same equilibrium constant. The inhibitor is noncompetitive with the substrate. enzymatic rate law for simple reversible non-competitive inhibition of unireactant enzymes K K Synonym: dissociation potential pK A component that allows another component to pass through itself, possibly connecting different compartments. channel koff Kon kon Koff Synonym: Ka association constant Synonym: Ki inhibitory constant Vmax R K h Vmax R h K h R h Hill equation rewritten by creating a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. Hill-type rate law, microscopic form kf kr R P kf R R R kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme The total length of time over which a model is simulated, where the time scale is indicated within the model simulation. simulation duration Movement of a physical entity without modification of the structure of the entity. transport reaction Addition of a geranylgeranyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity. geranylgeranylation Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of two products. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants kf kr R1 R2 P1 P2 kf R1 R2 kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme Sa Sb Pp Pq Keq Vf Vr Kma Kmb Kmp Kmq Kia Kib Kip Vf Sa Sb Pp Pq Keq Sa Sb 1 Pp Kip Kma Sb Kmb Sa Kia Vf Vr Keq Kmq Pp 1 Sa Kia Pq Kmp 1 Kma Sb Kia Kmb Pp 1 Sb Kib Enzymatic rate law for a reaction involving two substrates and two products. The products P and then Q are released strictly in order, while the substrates are bound strictly in the order A and then B. Ordered Bi-Bi mechanism rate law kf kr R1 R2 P1 P2 kf R1 R1 R2 kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme Chemical process in which a molecular entity gain electrons. reduction Ratio of an equilibrium constant in a given condition by the same equilibrium constant is not fullfilled. relative equilibrium constant Synonym: snRNA small nuclear RNA kf kr R P kf R R kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme Synonym: specific activation enzymatic rate law for reversible essential activation Negative logarithm (base 10) of the activity of hydroxyde in a solution. In a diluted solution, this activity is equal to the concentration of ions HO-. pOH Specific location of space, that can be bounded or not. A physical compartment can have 1, 2 or 3 dimensions. physical compartment kcat Et S I Ks Ki n kcat Et S Ks 1 i 1 n I i Ki i S Inhibition of a unireactant enzyme by inhibitors that bind to the free enzyme on the same binding site than the substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by exclusive inhibitors Synonym: kd dissociation rate constant A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions. Sequence Ontology SO:0000704 gene A conceptualisation of time which is intrinsic to a mathematical model, and which can be used to describe other variables or parameters of the model. model time kf kr R P1 P2 kf R R R kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme Dissociation constant equivalent to an intrinsic microscopic dissociation constant, but obtained from an averaging process, for instance by extracting the root of a Hill constant. pseudo-dissociation constant kcat Et S I Ks Ki kcat Et S S 1 I Ki Ks Synonym: simple linear uncompetitive inhibition enzymatic rate law for simple uncompetitive inhibition of irreversible unireactant enzymes Process in which a polypeptide chain is produced from a messenger RNA. translation In biochemistry, a ligand is an effector, a physical entity that binds to a site on a receptor's surface by intermolecular forces. ligand Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity. farnesylation kf kr R1 R2 R3 P kf R1 R2 R3 kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, one product, continuous scheme Modification of the velocity of a reaction by lowering the energy of the transition state. catalysis substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp 1 Inhibitor Ki Reversible inhibition of a unireactant enzyme by one inhibitor, which binds to the enzyme-substrate complex. The inhibitor is uncompetitive with the substrate. enzymatic rate law for simple uncompetitive inhibition of reversible unireactant enzymes kf kr R1 R2 R3 kf R1 R2 R3 kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, zeroth order reverse, reversible reactions, three reactants, continuous scheme Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of "genes" that control each other. logical framework Change in enthalpy observed in the constituents of a thermodynamic system when undergoing a transformation or chemical reaction. This is the preferred way of expressing the energy changes to a system at constant pressure, since enthalpy itself cannot be directly measured. The enthalpy change is positive in endothermic reactions, negative in exothermic reactions, and is defined as the difference between the final and initial enthalpy of the system under study: ΔH = Hf - Hi. The standard unit of measure is J. Symbol: ΔH enthalpy change kf kr R kf R R R kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme Participating entity that binds to a specific physical entity and initiates the response to that physical entity.The original concept of the receptor was introduced independently at the end of the 19th century by John Newport Langley (1852-1925) and Paul Ehrlich (1854-1915). Langley JN.On the reaction of cells and of nerve-endings to certain poisons, chiefly as regards the reaction of striated muscle to nicotine and to curari. J Physiol. 1905 Dec 30;33(4-5):374-413. receptor substrate product Activator Kms Kmp Vf Vr Ka Vf substrate Kms Vr product Kmp Activator Ka 1 substrate Kms product Kmp Activator Enzymatic rate law for one substrate, one product and one modifier which acts as an activator. The activator enhances the rate of reaction by decreasing the apparent Michaelis constant. The activator reversibly binds to the enzyme before the enzyme can bind the substrate. enzymatic rate law for reversible specific activation Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. mass action rate law for third order forward, reversible reactions, one reactant Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of two products. mass action rate law for second order forward, second order reverse, reversible reactions, one reactant An annotation which directs one to information contained within a published body of knowledge, usually a book or scientific journal. bibliographical reference Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. forward zeroth order rate constant, continuous case Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. reverse trimolecular rate constant k A k A Reaction scheme in which the reaction velocity is direct proportional to the activity or concentration of a single molecular species. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of the stimulator. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order irreversible reactions, single essential stimulator, continuous scheme Synonym: activator stimulator All the preceding events or participating entities are necessary to perform the control. and kf kr R1 R2 R3 P kf R1 R2 R3 kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, first order reverse, reversible reactions, three reactants, continuous scheme Entity that affects or is affected by an event. participant Synonym: activator potentiator Molecular entity mainly built-up by the repetition of pseudo-identical units. CHEBI:33839 macromolecule kf kr R P kf R R R kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, first order reverse, reversible reactions, one reactant, continuous scheme The enthalpy change observed in a constituent of a thermodynamic system when one mole of a compound, in its standard state, is formed from its elementary antecedents, in their standard state(s), under standard conditions (1 bar). The standard unit of measure is kJ/mol. Symbol: DeltaHf0, DeltafH0 standard enthalpy of formation substrate Activator Kms V Ka V substrate Activator Kms substrate Ka Activator Enzymatic rate law where an activator enhances the rate of reaction by increasing the apparent limiting rate; The activator binding to the enzyme-substrate complex (irreversibly) is required for enzyme catalytic activity (to generate the product). enzymatic rate law for irreversible catalytic activation with one activator kf kr R P kf R R kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, first order reverse, reversible reactions, one reactant, continuous scheme Synonym: db xref database cross reference k R k R Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order irreversible reactions, continuous scheme Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction. inhibitor A ratio that represents the quantity of a defined constituent entity over the total number of all constituent entities present. fraction of an entity pool Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. It is to be used in a reaction modelled using a continuous framework. forward unimolecular rate constant, continuous case Positive modulation of the execution of a process. stimulation substrate Activator Kms V Kas Kac V substrate Activator Kms Kas Activator substrate Kac Activator Enzymatic rate law where the activator enhances the rate of reaction through specific and catalytic effects, which increase the apparent limiting rate and decrease apparent Michaelis constant. The activator can bind irreversibly both free enzyme and enzyme-substrate complex, while the substrate can bind only to enzyme-activator complex. Catalytic activity is seen only when enzyme, substrate and activator are complexed. enzymatic rate law for irrreversible mixed activation A phenomenon that takes place and which may be observable, or may be determined to have occurred as the result of an action or process. obsolete event c A c A Reaction scheme in which the reaction velocity is direct proportional to the activity or quantity of a single molecular species. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of the stimulator. It is to be used in a reaction modelled using a discrete framework. mass action rate law for first order irreversible reactions, single essential stimulator, discrete scheme Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of two products. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. forward non-integral order rate constant Parameters used in the study of thermodynamics, a physical science that pertains to the relationship between heat and other forms of energy such as 'work done' in material bodies. thermodynamic parameter Macromolecule whose sequence is encoded in the genome of living organisms. information macromolecule Synonym: Gibbs function Gibbs free energy The use of an abbreviated name, taken from a controlled vocabulary of terms, which is used to represent some information about the entity to which it is attached. controlled short label R T F z X x R T z F X x Synonym: reversal potential Nernst potential Numerical parameter that quantifies the velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. zeroth order rate constant kf kr R kf R R kr Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme The number of moles of a constituent entity, divided by the total number of all constituent entities present in a system. mole fraction Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. forward bimolecular rate constant, continuous case Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. mass action rate law for third order forward, reversible reactions, three reactants Synonym: trigger necessary stimulation Addition of an hydroxyl group (-OH) to a chemical entity. hydroxylation Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator activities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator substrate product Activator Kms Kmp Vf Vr Ka Vf substrate Kms Vr product Kmp Activator 1 substrate Kms product Kmp Ka Activator Enzymatic rate law where an activator enhances the rate of reaction by increasing the apparent limiting rate; The reversible binding of the activator to the enzyme-substrate complex is required for enzyme catalytic activity (to generate the product). enzymatic rate law for reversible catalytic activation with one activator Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. reverse non-integral order rate constant A thermodynamic potential whose natural variables are entropy (S) and pressure (p). The enthalpy of a system, measured in Joules (J), is defined as H = U + pV (where H is enthalpy, U is the internal energy, p is the pressure at the system boundary, and V is the system volume). symbol: H enthalpy kf kr R P kf R R R kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme The change in Gibbs free energy associated with the formation of 1 mole of substance from elements in their standard states under standard conditions (1 bar). The standard unit of measure is kJ/mol. symbol: DeltafG(degree) standard Gibbs energy of formation Simple, non-repetitive chemical entity. simple chemical k k Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order irreversible reactions, continuous scheme Additional information that supplements existing data, usually in a document, by providing a link to more detailed information, which is held externally, or elsewhere. reference annotation Quantitative parameter that characterises a dissociation. dissociation characteristic The increase or decrease of the Gibbs free energy of a system. During a reaction, this is equal to the change in enthalpy of the system minus the change in the product of the temperature times the entropy of the system: DeltaG = DeltaH - T DeltaS A negative value indicates that the reaction will be favoured and will release energy. The magnitude of the value indicates how far the reaction is from equilibrium, where there will be no free energy change. The standard unit of measure is kJ/mol. symbol: DeltaG Gibbs free energy change Synonym: R0 basic reproductive ratio Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. forward trimolecular rate constant, continuous case The preceding event or participating entity cannot participate to the control. not Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. forward trimolecular rate constant The increase or decrease of the entropy of a system. For values greater than zero, there is an implied increase in the disorder of a system, for example during a reaction, and decreased disorder where the values are less than zero. The entropy change of a process is defined as the initial system entropy value minus the final entropy value: DeltaS = Sf - Si. The standard unit of measure is J/K. symbol: DeltaS entropy change Macromolecule whose sequence is not directly encoded in the genome. chemical macromolecule k R A k R A Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator activities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. It is to be used in a reaction modelled using a continuous framework. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator, continuous scheme Substance consumed by a chemical reaction. Reactants react with each other to form the products of a chemical reaction. In a chemical equation the Reactants are the elements or compounds on the left hand side of the reaction equation. A reactant can be consumed and produced by the same reaction, its global quantity remaining unchanged. reactant Measure of the amount of electric charge stored (or separated) for a given electric potential. The unit of capacitance id the Farad. capacitance Enzyme kinetics is the study of the rates of chemical reactions that are catalysed by enzymes, how this rate is controlled, and how drugs and poisons can inhibit its activity. enzymatic rate law Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. mass action rate law for first order irreversible reactions The entropy change observed in a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). The standard unit of measure is kJ/(mol K). This can be calculated using the entropies for products and reactants: DeltaS(reaction)=sum DeltaS (products) - sum DeltaS reactants. The standard unit of measure is kJ/(mol K). symbol: DeltaSro standard entropy of reaction Regulation of the influence of a reaction participant by binding an effector to a binding site of the participant different of the site of the participant conveying the influence. allosteric control Synonym: turnover number catalytic rate constant kcat Et S Ks kcat Et S Ks S Rate-law presented in "Donald D. Van Slyke and Glenn E. Cullen. The mode of action of urease and of enzymes in general. J. Biol. Chem., Oct 1914; 19: 141-180". It assumes that the enzymatic reaction occurs as two irreversible steps.E+S -> ES -> E+P. Although of the same form than the Henri-Michaelis-Menten equation, it is semantically different since K now represents the ratio between the production rate and the association rate of the enzyme and the substrate. Van Slyke-Cullen rate law Substance that is produced in a reaction. In a chemical equation the Products are the elements or compounds on the right hand side of the reaction equation. A product can be produced and consumed by the same reaction, its global quantity remaining unchanged. product c R A c R A Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator quantities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. It is to be used in a reaction modelled using a discrete framework. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator, discrete scheme Macromolecule consisting of a large number of monosaccharide residues linked by glycosidic bonds. CHEBI:18154 polysaccharide Synonym: electrical potential difference voltage Kinetics of enzymes that catalyse the transformation of only one substrate. enzymatic rate law for unireactant enzymes Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to two reactant quantity. mass action rate law for second order irreversible reactions Supplementary information that does not modify the semantics of the presented information. annotation Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. mass action rate law for irreversible reactions The enthalpy change observed in a constituent of a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). The standard unit of measure is kJ/mol. Symbol: DeltaHr0, DeltarH0 standard enthalpy of reaction Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. forward unimolecular rate constant The Law of Mass Action, first expressed by Waage and Guldberg in 1864 (Waage, P.; Guldberg, C. M. Forhandlinger: Videnskabs-Selskabet i Christiana 1864, 35) states that the speed of a chemical reaction is proportional to the quantity of the reacting substances. More formally, the change of a product quantity is proportional to the product of reactant activities. In the case of a reaction occurring in a gas phase, the activities are equal to the partial pressures. In the case of a well-stirred aqueous medium, the activities are equal to the concentrations. In the case of discrete kinetic description, the quantity are expressed in number of molecules and the relevant volume are implicitely embedded in the kinetic constant. mass action rate law Synonym: new synonym physical entity representation A physical constant that is required in the calculation of a system parameter. systems description constant kcat Et S Km kcat Et S Km S The Briggs-Haldane rate law is a general rate equation that does not require the restriction of equilibrium of Henri-Michaelis-Menten or irreversible reactions of Van Slyke, but instead make the hypothesis that the complex enzyme-substrate is in quasi-steady-state. Although of the same form than the Henri-Michaelis-Menten equation, it is semantically different since Km now represents a pseudo-equilibrium constant, and is equal to the ratio between the rate of consumption of the complex (sum of dissociation of substrate and generation of product) and the association rate of the enzyme and the substrate. Briggs-Haldane rate law Parameter that depends on the biochemical properties of a system. biochemical parameter Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. reverse unimolecular rate constant Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. mass action rate law for reversible reactions A thermodynamic property which acts as a measure of the state of disorder of a system. Its natural variables are the internal energy (U) and the volume (V). It is defined by dS = (1/T)dU + (p/T)dV. The second law of thermodynamics states that in an isolated system, natural processes tend to increase in disorder or entropy. The standard unit of measure is Joules per Kelvin (J/K). symbol: S entropy Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. forward bimolecular rate constant Combining the influence of several entities or events in a unique influence. logical combination Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed. This effect is achieved by lowering the free energy of the transition state. catalyst The permeability of an ion through a channel or membrane expressed in relation to the reference ion, which is given the value 1. For example, if a membrane is most permeable to K+, then that is assigned the reference permeability value of 1, and the value for Na+ may be 0.05. relative permeability Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. reverse bimolecular rate constant Measure of how easily electricity flows along a certain path through an electrical element. The SI derived unit of conductance is the Siemens. conductance Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. mass action rate law for third order forward, reversible reactions, two reactants Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. mass action rate law for zeroth order irreversible reactions Synonym: regulation control Substance that, when bound, decreases enzymatic activity to a lower, nonzero value, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. The enzyme-inhibitor complex does retain some basal level of activity. partial inhibitor The direct binding modular rate law makes the assumption that both substrates and products bind simultaneously and in a single step, hence the total binding states possible enumerate to 3; nothing bound, substrates bound, and products bound. Substrates and products cannot be bound at the same time. direct binding modular rate law The amount of a specific entity pool substrate present per unit of volume. The participant role 'substrate' is defined in SBO:0000015. concentration of substrate A reaction in which the principal reactant and principal product are isomers of each other isomerisation Rate with which three components associate into a complex. trimolecular association rate constant substrate product Inhibitor Vf Vr Kms Kmp n Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp Inhibitor Ki n Enzymatic rate law where the reversible binding of one ligand decreases the affinity for substrate at other active sites. The ligand does not bind the same site as the substrate on the enzyme. This is an empirical equation, where n represents the Hill coefficient. enzymatic rate law for reversible empirical allosteric inhibition by one inhibitor Annotation which does not comply with, or is not restricted by, any rules in its construction. Examples would include free text annotations. uncontrolled annotation Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. forward rate constant, continuous case Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. reverse trimolecular rate constant, continuous case The amount of a specific entity pool reactant present per unit of volume. The participant role 'reactant' is defined in SBO:0000010. concentration of reactant Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a discrete framework. reverse non-integral order rate constant, discrete case Synonym: standard chemical potential standard biochemical potential Synonym: diffusivity diffusion coefficient An essential activator that affects the apparent value of the Michaelis constant(s). binding activator An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants. biochemical or transport reaction Extension of the Boolean logical framework which allows intermediate or undetermined values for the logical variables. fuzzy logical framework kf kr R P kf R kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme The amount, expressed as a mass, of a specific substrate entity pool. The participant role 'substrate' is defined in SBO:0000015. mass of substrate Et kp n S1 S2 S3 K1 K2 K3 Et kp S1 K1 S2 K2 S3 K3 1 S1 K1 1 S2 K2 1 S3 K3 Kinetics of enzymes that react with three substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting trireactant enzymes Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. forward rate constant R T F P p C c A a R T F A p c P a p C P Synonym: Goldman-Hodgkin-Katz voltage equation Goldman equation Annotation which complies with the full set of defined rules in its construction. controlled annotation kcat Et S Sa Ks Ksa n kcat Et S Ks 1 i 1 n Sa i Ksa i S Inhibition of a unireactant enzyme by competing substrates (Sa) that bind to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. enzymatic rate law for inhibition of irreversible unireactant enzymes by competing substrates substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp Inhibitor Ki This enzymatic rate law involves one substrate, one product and one modifier. The modifier acts as a competitive inhibitor with the substrate at the enzyme binding site; The modifier (inhibitor) reversibly bound to the enzyme blocks access to the substrate. The inhibitor has the effect of increasing the apparent Km. enzymatic rate law for reversible competitive inhibition by one inhibitor Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. reverse non-integral order rate constant, continuous case An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity. non-essential activator Amplitude is the magnitude of change in the oscillating variable, with each oscillation, within an oscillating system. amplitude Synonym: membrane permeability ionic permeability c R c R Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. It is to be used in a reaction modelled using a discrete framework. mass action rate law for first order irreversible reactions, discrete scheme Modular rate laws are a set of rate laws that provide a means to parameterise a system in a manner that is a compromise between mathematical abstraction and biochemical detail. They share the same common form: v = u f (T/(D + Dreg)) The individual numerator and denominator terms can substituted with alternative forms, depending on reaction details and model formulation, to generate specific modular rate laws. The terms represented are; v, reaction rate; u, enzyme amount; T, modular term derived from stoichiometries, metabolite concentrations and reactant constants; D, modular term for polynomial of scaled concentrations; Dreg, competitive regulation binding states term; f, modular term for regulation factor. modular rate law Et kp n S1 S2 K1 K2 Et kp S1 K1 S2 K2 1 S1 K1 1 S2 K2 Kinetics of enzymes that react with two substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting bireactant enzymes Kms x n i 1 x Kms i n i The product of the substrate Michaelis constants, to the power of their respective stoichiometric coefficients. powered product of substrate Michaelis constants Extension of the boolean logical framework which associates a defined number of possible integer values (states) with the variables. multi-valued logical framework The amount, expressed as a number, of a specific modifier comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'modifier' is defined in SBO:0000019. number of a modifier mathematical description that relates quantities of reactants to the reaction velocity. rate law kcat Et S I1 I2 a Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 I1 I2 a Ki1 Ki2 S Inhibition of a unireactant enzyme by two inhibitors that can bind once to the free enzyme and preclude the binding of the substrate. Binding of one inhibitor may affect binding of the other, or not. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive inhibitors Named after Michael Faraday, it is the magnitude of electric charge per mole of electrons. It has the value 96,485.3365 C/mol (Coulombs per Mole), and the symbol F. Faraday constant substrate product Inhibitor Kms Kmp Vf Vr Ki n Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp i 1 n I i Ki i This enzymatic rate law involves one substrate, one product and one or more modifiers. The modifiers act as competitive inhibitors of the substrate at the enzyme binding site; The modifiers (inhibitors) reversibly bound to the enzyme block access to the substrate. The inhibitors have the effect of increasing the apparent Km, and bind exclusively to the enzymes. enzymatic rate law for reversible reactions with competitive inhibition Numerical parameter that quantifies the reverse velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. reverse zeroth order rate constant c R c R R 1 2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the square of one reactant quantity. It is to be used in a reaction modelled using a discrete framework. mass action rate law for second order irreversible reactions, one reactant, discrete scheme The mass of an entity per unit of surface area. area density of an entity Amount, expressed as a number, of a specific enzyme comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'enzymatic catalyst' is defined in SBO:0000460. number of an enzyme A measure of enzyme activity under standard conditions, at a specific substrate concentration (usually saturation), expressed as the amount of product formed per unit time, per amount of enzyme. This is often expressed as micromol per min per mg, rather than the less practical official unit, Katal (1 mol per second). specific activity The measurable dimensions of an object which are minimally required to define the space that an object occupies. spatial measure Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.It is to be used in a reaction modelled using a continuous framework. forward non-integral order rate constant, continuous case The common modular rate law is a generalised form of reversible Michaelis Menten kinetics, using a denominator where each binding state of the enzyme is represented. It is assumed that substrates and products bind independently and randomly, and that substrates and products cannot be bound at the same time. common modular rate law Substance that, when bound, completely negates enzymatic activity, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. The inhibitor binds to all enzyme species independently and with the same affinity, completely inhibiting any enzymatic activity. complete inhibitor Negative modulation of the execution of a process. inhibition The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. forward reaction velocity c c Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. It is to be used in a reaction modelled using a discrete framework. mass action rate law for zeroth order irreversible reactions, discrete scheme Et kp n S K Et kp i 1 n S i K i i 1 n 1 S i K i Kinetics of enzymes that react with one or several substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting reactant enzymes Complete disappearance of a physical entity. degradation Km x n i 1 x Km i n i The product of the Michaelis constants, to the power of their respective stoichiometric coefficients, for either substrates or products. powered product of Michaelis constant Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' denoting false and true values, respectively. boolean logical framework The amount of a specific modifier entity pool present per unit of volume. The participant role 'modifier' is defined in SBO:0000019. concentration of modifier Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network. systems biology representation substrate Activator Kms V Ka V substrate Activator Kms Ka Kms substrate Activator Enzymatic rate law for one substrate, one product and one modifier which acts as an activator. The activator enhances the rate of reaction by decreasing the apparent Michaelis constant. The activator must bind to the enzyme before the enzyme can bind the substrate. enzymatic rate law for irreversible specific activation Annotation that directly incorporates information into the body of a document. embedded annotation Number of molecules which are generated by an enzyme. number of products The amount, expressed as a number, of a specific reactant comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'reactant' is defined in SBO:0000010. number of a reactant Mass of an entity per unit volume. volume density of an entity Assignment of a state or a value to a state variable, characteristic or property, of a biological entity. state variable assignment Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. forward non-integral order rate constant, discrete case Synonym: molar gas constant universal gas constant The amount, expressed as a mass, of a specific modifier entity pool. The participant role 'modifier' is defined in SBO:0000019. mass of modifier Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities. cleavage A non-numerical value that defines certain characteristics of systems or system functions. qualitative systems description parameter Modular rate law where the D term is given by the square root of the product of terms (c/KM)^m where c, KM, and m denote the concentrations, Michaelis constants, and molecularities, respectively, and the product is taken over all reactants and products involved in the reaction. force-dependent modular rate law Synonym: temporal offset phase shift A transmembrane domain is any three-dimensional protein structure which is thermodynamically stable in a membrane. This may be a single alpha helix, a stable complex of several transmembrane alpha helices, a transmembrane beta barrel, a beta-helix of gramicidin A, or any other structure. transmembrane domain Function which ranges from 0 to 1, to describe the relative activation or inhibition of a reaction or process, actual or conceptual. relative activity function k R k i 1 2 R i Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to two reactant quantity. It is to be used in a reaction modelled using a continuous framework. second order irreversible mass action kinetics, continuous scheme k n mu R k i 0 n R i mu i Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. It is to be used in a reaction modelled using a continuous framework. mass action rate law for irreversible reactions, continuous scheme Amount of enzyme present per unit of volume. The participant role 'enzymatic catalyst' is defined in SBO:0000460. concentration of enzyme Control that precludes the execution of a process. absolute inhibition The area of an object is a quantity expressing its two-dimensional size, usually part or all of its surface. area c R c R R 1 R 2 6 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the cube of one reactant quantity. It is to be used in a reaction modelled using a discrete framework. mass action rate law for third order irreversible reactions, one reactant, discrete scheme substrate Modifier Km V Kd a b V substrate 1 b Modifier a Kd Km 1 Modifier Kd substrate 1 Modifier a Kd Enzymatic rate law where the modifier can act as an activator or inhibitor, depending upon the values of the kinetic constants. The modifier can bind irreversibly to all forms of the enzyme and all enzyme-substrate complexes are reactive. 'a' represents the ratio of dissociation constant of the elementary step Enzyme-Substrate complex + Modifier = Enzyme-Substrate-Modifier complex) over that of Enzyme + Modifier = Enzyme-Modifier complex. 'b' represents ratio of the rate constant of elementary step Enzyme-Substrate-Modifier complex -> Enzyme-Modifier complex + Product over that of Enzyme-Substrate complex -> Enzyme + Product. enzymatic rate law for irreversible unireactant enzyme with a single hyperbolic modulator The order of a reaction with respect to a certain reactant is defined as the power to which its concentration term in the rate equation is raised. order of a reaction with respect to a reactant For the power-law rate law, the denominator is set to be a constant, and the rate law does not saturate. power-law modular rate law Interaction between several biochemical entities that results in the formation of a non-covalent complex non-covalent binding The period is the duration of one cycle in a repeating event. [wikipedia] period A parameter that has three discrete values which may be alternated between. ternary switch b vmax b vmax The ratio of the basal activity to the maximal velocity of a reaction. The values range between 0 and 1. relative basal rate constant A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation. systems description parameter The length of an object is the longest measurable distance between its extremities. length Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. forward zeroth order rate constant c R1 R2 c R1 R2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of two reactants. It is to be used in a reaction modelled using a discrete framework. mass action rate law for second order irreversible reactions, two reactants, discrete scheme Amount, expressed as a mass, of an enzyme. The participant role 'enzymatic catalyst' is defined in SBO:0000460. mass of enzyme An entity that can be measured quantitatively observable A measure of the amount of active enzyme present, expressed under specified conditions. This is often expressed as micromol per min (also known as enzyme unit, U), rather than the less practical official SI unit, Katal (1 mol per second). Enzyme activity normally refers to the natural substrate for the enzyme, but can also be given for standardised substrates such as gelatin, where it is then referred to as GDU (Gelatin Digesting Units). enzyme activity Number of different substances consumed by a chemical reaction. number of reactants substrate product Modifier Kms Kmp Vf Vr Kd a b Vf substrate Kms Vr product Kmp 1 b Modifier a Kd 1 Modifier Kd substrate Kms product Kmp 1 Modifier a Kd Enzymatic rate law where the modifier can act as an activator or inhibitor, depending upon the values of the kinetic constants. The modifier can bind reversibly to all forms of the enzyme and all enzyme-substrate complexes are reactive. 'a' represents the ratio of dissociation constant of the elementary step Enzyme-Substrate complex + Modifier = Enzyme-Substrate-Modifier complex over that of Enzyme + Modifier = Enzyme-Modifier complex. 'b' represents ratio of the rate constant of elementary step Enzyme-Substrate-Modifier complex -> Enzyme-Modifier complex + Product over that of Enzyme-Substrate complex -> Enzyme + Product. enzymatic rate law for reversible unireactant enzyme with a single hyperbolic modulator time Theta0 Theta1 Phi Tp Tc Tw Theta0 0.5 Theta1 1 time Phi Tc time Phi Tc Tw 1 time Phi Tc time Phi Tc Tp Tw 1 time Phi Tc time Phi Tc Tc Tw Synonym: input signal step function periodic forcing function An essential activator that affects the apparent value of the catalytic constant. catalytic activator An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants. biochemical reaction Supplementary information relating to a primary item of data, traditionally termed 'data about data'. It can describe, for example, the location or type of the data, or its relationship to other data. metadata representation c n mu R c i 0 n R i R i mu i mu i Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. It is to be used in a reaction modelled using a discrete framework. mass action rate law for irreversible reactions, discrete scheme A parameter value taken by a switch, which has a discrete set of values which can be alternated or switched between. switch value Function which ranges from 0 to 1, to describe the relative inhibition of a reaction or process, actual or conceptual. relative inhibition function A specific domain of a spatio-temporal entity to which another spatio-temporal entity is able to bind, forming chemical bonds. binding site A spatial region of an entity that confers a function functional domain Region of a gene that is involved in the modulation of the expression of the gene. gene regulatory region Entity that results from the interaction between other entities. interaction outcome The numerical quantification of an entity pool. This may be expressed as, for example, the number of molecules or the number of moles of identical entities of which an specific entity pool is comprised. number of entity pool constituents c R1 R2 R3 c R1 R2 R3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of three reactants. It is to be used in a reaction modelled using a discrete framework. mass action rate law for third order irreversible reactions, three reactants, discrete scheme Non-covalent association between portions of macromolecules that carry genetic information multimer of informational molecule segment Synonym: inclusion containment substrate Km V Ki V substrate Km substrate Km substrate Ki 2 Enzymatic rate law where the substrate for an enzyme also acts as an irreversible inhibitor. This may entail a second (non-active) binding site for the enzyme. The inhibition constant is then the dissociation constant for the substrate from this second site. enzymatic rate law for irreversible substrate inhibition Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. reverse rate constant Synonym: exclusive or xor An essential activator that affects the apparent value of the specificity constant. Mechanistically, the activator would need to be bound before reactant and product binding can take place. specific activator Mathematical function commonly used in biological modeling, which enable simplification of more complex expressions convenience function k R k i 1 3 R i Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to three reactant quantities. It is to be used in a reaction modelled using a continuous framework. third order irreversible mass action kinetics, continuous scheme A nonspecific coalescence of misfolded proteins which may or may not form a precipitate, depending upon particle size. protein aggregate Function which ranges from 0 to 1, to describe the relative activation of a reaction or process, actual or conceptual. relative activation function A catalytic site is the region which confers specificity of a substrate for the binding entity, and where specific reactions take place in the conversion of the substrate to the product. catalytic site c R1 R2 c R1 R2 R2 1 2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. It is to be used in a reaction modelled using a discrete framework. mass action rate law for third order irreversible reactions, two reactants, discrete scheme A quantity representing the three-dimensional space occupied by all or part of an object. volume Effect of a biological entity on biological structures or processes. biological activity The mass that comprises an entity pool. mass of an entity pool substrate product Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp substrate Ki 2 Enzymatic rate law where the substrate for an enzyme also acts as a reversible inhibitor. This may entail a second (non-active) binding site for the enzyme. The inhibition constant is then the dissociation constant for the substrate from this second site. enzymatic rate law for reversible substrate inhibition Non-covalent association between several independant complexes multimer of complexes Any of the preceding events or participating entities are necessary to perform the control. or Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. forward rate constant, discrete case One of the two values possible from a boolean switch, which equates to '0', 'off' or 'no input'. false Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to two reactant quantities. mass action rate law for second order reversible reactions Genetic enhancement is said to have occurred when the phenotypic effect of an initial mutation in a gene is made increasingly severe by a subsequent mutation. genetic enhancement A biochemical network can generate phenotypes or affects biological processes. Such processes can take place at different levels and are independent of the biochemical network itself. phenotype Number of entities that inhibit a reaction. number of inhibitors k n n i 1 n k i The geometric mean turnover rate of an enzyme in either forward or backward direction for a reaction, measured per second. geometric mean rate constant l 1 l Synonym: mean lifetime exponential time constant Quantity resulting from the difference between two thermodynamic temperatures. A difference or interval of temperature may be expressed in Kelvins or in degrees Celsius. temperature difference The 'kind' of entity involved in some process, action or reaction in the system. This may be enzyme, simple chemical, etc. obsolete participant type The transfer of an amino group between two molecules. Commonly in biology this is restricted to reactions between an amino acid and an alpha-keto carbonic acid, whereby the reacting amino acid is converted into an alpha-keto acid, and the alpha-keto acid reactant into an amino acid. transamination kcat Et S P Ks Kp kcat Et S Ks 1 P Kp S Inhibition of a unireactant enzyme by a competing product (P) that binds to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. enzymatic rate law for competitive inhibition of irreversible unireactant enzyme by product kf n n i 1 n kf i The geometric mean turnover rate of an enzyme in the forward direction for a reaction, measured per second. forward geometric mean rate constant kf kr P1 P2 kf kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, second order reverse, reversible reactions, two products, continuous scheme Removal of a phosphate group (-H2PO4) from a chemical entity. dephosphorylation Concentration of an active compound at which 50% of its maximal effect is observed. The EC50 is not a pure characteristic of the compound but depends on the conditions or the measurement. EC50 In reversible reactions this is the concentration of product that is required to achieve half activation or inhibition in Hill-type kinetics, in the absence of the substrate. pseudo-dissociation constant for product Term to signify where a material or conceptual entity is represented or denoted by a symbol or by some other abbreviated form. denotement Synonym: kcatp product catalytic rate constant kf kr R1 R2 P1 P2 P3 kf R1 R2 kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme substrate product Kms Kmp Kii Vf Keq Vf substrate product Keq substrate 1 product Kii Kms 1 product Kmp Enzyme catalysed reaction involving one substrate and one product. Unlike the reversible uni-uni mechanism (SBO:0000326), the mechanism assumes an enzyme intermediate. Therefore, the free enzyme generated after the release of product from enzyme-product complex is not the same form as that which bind the substrate to form enzyme-substrate complex. Some permeases are thought to follow this mechanism, such that isomerization in the membrane may be accomplished through re-orientation in the membrane. reversible Iso Uni-Uni The amount of a specific inhibitor entity pool present per unit of volume. The participant role 'inhibitor' is defined in SBO:0000020. concentration of inhibitor Vmax S Ks Vmax S Ks S Version of Henri-Michaelis-Menten equation where kp*[E]t is replaced by the maximal velocity, Vmax, reached when all the enzyme is active. Henri-Michaelis-Menten equation, Vmax form One or more processes that are not represented in certain representations or interpretations of a model. omitted process A numerical value that represents the amount of some entity, process or mathematical function of the system. obsolete parameter Covalent reaction that results in the transfer of a chemical group from one molecule to another. transfer of a chemical group One of the two values possible from a boolean switch, which equates to '1', 'on' or 'input'. true Molality denotes the number of moles of solute per kilogram of solvent (not solution). The term molal solution is used as a shorthand for a "one molal solution", i.e. a solution which contains one mole of the solute per kilogram of the solvent. The SI unit for molality is mol/kg. molal concentration of an entity Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of three reactants. mass action rate law for third order irreversible reactions, three reactants Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. mass action rate law for second order forward, reversible reactions, one reactant Amount of time during which an event persists. duration kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 S Inhibition of a unireactant enzyme by two inhibitors that bind to the free enzyme on the same binding site than the substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by two exclusive inhibitors The stoichiometric coefficient represents the degree to which a chemical species participates in a reaction. It corresponds to the number of molecules of a reactant that are consumed or produced with each occurrence of a reaction event. stoichiometric coefficient Synthetic lethality is said to have occurred where gene mutations, each of which map to a separate locus, fail to complement in an offspring to correct a phenotype, as would be expected. synthetic lethality Biochemical networks can be affected by external influences. Those influences can be well-defined physical perturbations, such as a light pulse, or a change in temperature but also more complex of not well defined phenomena, for instance a biological process, an experimental setup, or a mutation. biological effect of a perturbation Temperature is the physical property of a system which underlies the common notions of "hot" and "cold"; the material with the higher temperature is said to be hotter. Temperature is a quantity related to the average kinetic energy of the particles in a substance. The 10th Conference Generale des Poids et Mesures decided to define the thermodynamic temperature scale by choosing the triple point of water as the fundamental fixed point, and assigning to it the temperature 273,16 degrees Kelvin, exactly (0.01 degree Celsius). thermodynamic temperature Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to three product quantities. mass action rate law for zeroth order forward, third order reverse, reversible reactions, continuous scheme kcat Et S Sa Ks Ksa Kp Kpa P Pa n kcat Et S Ks 1 Sa Ksa P Kpa Pa Kpa S Inhibition of a unireactant enzyme by a competing substrate (Sa) that binds to the free enzyme on the same binding site, and competitive inhibition by a product (P) and an alternative product (Pa). The enzyme does not catalyse the reactions in both directions. enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate with product inhibition Sa Sb Pp Pq Keq Vf Vr Kma Kmb Kmp Kmq Kia Kiq Vf Sa Sb Pp Pq Keq Sa Sb Kmb Sa Kma Sb 1 Pq Kiq Vf Vr Keq Kmq Pp 1 Sa Kia Pq Kmp Pp Enzymatic rate law for a reaction involving two substrates and two products. The first product (P) is released after the first substrate (A) has been bound. The second product (Q) is released after the second substrate (B) has been bound. Ping Pong Bi-Bi mechanism rate law Non-covalent association of identical, or pseudo-identical, entities. By pseudo-identical entities, we mean biochemical elements that differ chemically, although remaining globally identical in structure and/or function. Examples are homologous subunits in an hetero-oligomeric receptor. multimer Inhibitory constant for the binding of a given ligand with an isomeric form of an enzyme. isoinhibition constant kf kr R1 R2 P1 P2 kf R1 R2 kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme Molarity, or molar concentration, denotes the number of moles of a given substance per litre of solution. The unit of measure of molarity is mol/L, molar, or the capital letter M as an abbreviated form. molar concentration of an entity The amount, expressed as a mass, of a specific inhibitor entity pool. The participant role 'inhibitor' is defined in SBO:0000020. mass of inhibitor A number of objects of the same type, identical or different, involved in a biochemical event. number of biochemical items Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves. logical relationship Participating entity that facilitates the movement of another physical entity from a defined subset of the physical environment (for instance a cellular compartment) to another. transporter Fundamental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. temporal measure Chemical reaction where a proton is given by a compound, the acid, to another one, the base (Brønsted-Lowry definition). An alternative, more general, definition is a reaction where a compound, the base, gives a pair of electrons to another, the acid (Lewis definition). acid-base reaction For a given substance, A, its mass fraction (x A) is defined as the ratio of its mass (m A) to the total mass (m total) in which it is present, where the sum of all mass fractions is equal to 1. This provides a means to express concentration in a dimensionless size. mass fraction Positional relationship between entities on different sides, or strands trans A material entity that is responsible for a perturbing effect perturbing agent Synonym: reaction rate constant kinetic constant kf kr P1 P2 kf kr P1 P2 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, third order reverse, reversible reactions, two products, continuous scheme Value which ranges from 0 to 1, to describe the relative activity of a process or reaction. relative activity l 2 l Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2. half-life of an exponential decay substrate productp productq Kms Kmq Kmp Kip Keq Vf Vr Vf substrate productp productq Keq Kms substrate 1 productp Kip Vf Vr Keq Kmq productp Kmp productq productp productq Enzymatic rate law for a reaction with one substrate and two products. The products P and then Q are released in the strict order P and then Q. Ordered Uni-Bi mechanism rate law Reversible Hill-type kinetics represents the situation where a single substrate and product bind cooperatively and reversibly to the enzyme. Co-operativity is seen if the Hill coefficient (h) is greater than 1, indicating that the binding of one substrate (or product) molecule facilitates the binding of the next. The opposite effect is evident with a coefficient less than 1. reversible Hill-type enzymatic rate law The minimal velocity observed under defined conditions, which may or may not include the presence of an effector. For example in an inhibitory system, this would be the residual velocity observed under full inhibition. In non-essential activation, this would be the velocity in the absence of any activator. basal rate constant kf kr P kf kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, third order reverse, reversible reactions, one product, continuous scheme kcat Et S I Ks Ki a n kcat Et S Ks 1 i 1 n I i Ki i S 1 i 1 n I i a i Ki i Inhibition of a unireactant enzyme by inhibitors that can bind to the complex enzyme-substrate and the free enzyme, possibly with different equilibrium constants, and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for mixed-type inhibition of irreversible enzymes by mutually exclusive inhibitors The coefficient that describes the proportional change of Ks or Ki when inhibitor or substrate is bound, respectively, to the enzyme. biochemical cooperative inhibitor substrate coefficient kcat S Ks kcat S Ks S Kinetics of enzymes that react only with one substance, their substrate. The total enzyme concentration is considered to be equal to 1, therefore the maximal velocity equals the catalytic constant. normalised enzymatic rate law for unireactant enzymes Number of regions on a reactant to which specific other reactants, in this context collectively called ligands, form a chemical bond. number of binding sites Material entity whose nature is unknown or irrelevant. material entity of unspecified nature kf kr R P kf R kr P P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, third order reverse, reversible reactions, one product, continuous scheme Michaelis constant derived or experimentally measured under non-equilibrium conditions. Michaelis constant in non-equilibrium situation A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide. decarboxylation Numerical parameter that quantifies the velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. non-integral order rate constant Genetic suppression is said to have occurred when the phenotypic effect of an initial mutation in a gene is less severe, or entirely negated, by a subsequent mutation. genetic suppression a n S i 0 n a i S i A chemical moiety that exists under different forms but is not created nor destroyed in a biochemical system. In any given system such a conserved moiety is characterized by a finite number of particles that exist in the system and is invariant. mass conservation law Fundmental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. time Synonym: Ka acid dissociation constant kf kr R P1 P2 P3 kf R kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, third order reverse, reversible reactions, three products, continuous scheme Positional relationship between entities on the same strand (e.g. in DNA), or on the same side. cis Ionization is the physical process of converting an atom or molecule into an ion by changing the difference between the number of protons and electrons. ionisation Functional entity associated with or derived from a unit of inheritance. unit of genetic information Basic assumptions that underlie a mathematical model. obsolete modelling framework Number of molecules which are acted upon by an enzyme. number of substrates kf kr P1 P2 P3 kf kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, third order reverse, reversible reactions, three products, continuous scheme kcat Et S I Ks Ki n m kcat Et S Ks i 1 n 1 I i Ki i m i S Inhibition of a unireactant enzyme by inhibitors that bind independently to the free enzyme and preclude the binding of the substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by non-exclusive non-cooperative inhibitors kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 I1 I2 Ki1 Ki2 S Inhibition of a unireactant enzyme by two inhibitors that can bind independently once to the free enzyme and preclude the binding of the substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive, non-cooperative inhibitors Sa Sb P Kma Kmb Kmp Kia Keq Vf Vr Vf Sa Sb P Keq Sa Sb Kma Sb Kmb Sa Vf Vr Keq Kmp P 1 Sa Kia Enzymatic rate for a reaction involving two substrates and one product. The substrates A and then B are bound strictly in order. Ordered Bi-Uni mechanism rate law Time interval over which a quantified entity is reduced to half its original value. half-life A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone. Genetic interaction between perturbed genes is usually expected to generate a 'defective' phenotype. The level of defectiveness is often used to sub-classify this phenomenon. genetic interaction kr n n i 1 n kr i The geometric mean turnover rate of an enzyme in the reverse direction for a reaction, measured per second. reverse geometric mean rate constant The amount, expressed as a mass, of a specific reactant entity pool. The participant role 'reactant' is defined in SBO:0000010. mass of reactant kcat Et S Sa Ks Ksa n kcat Et S Ks 1 Sa Ksa S Inhibition of a unireactant enzyme by a competing substrate (Sa) that binds to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate The amount, expressed as a number, of a specific inhibitor comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'inhibitor' is defined in SBO:0000020. number of an inhibitor Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of a reactant quantity. mass action rate law for third order reversible reactions kf kr R P1 P2 kf R kr P1 P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, third order reverse, reversible reactions, two products, continuous scheme In reversible reactions this is the concentration of substrate that is required to achieve half activation or inhibition in Hill-type kinetics, in the absence of the product. pseudo-dissociation constant for substrate Michaelis constant derived using a steady-state assumption for enzyme-substrate and enzyme-product intermediates. For example see Briggs-Haldane equation (SBO:0000031). Michaelis constant in quasi-steady state situation Addition of a phosphate group (-H2PO4) to a chemical entity. phosphorylation Synonym: Kx activation constant Fragment of a macromolecule that carries genetic information. informational molecule segment The connectedness between entities as related by their position positional relationship number used as an exponential factor for quantities, expressions or functions biochemical exponential coefficient Macromolecular complex containing one or more polypeptide chains possibly associated with simple chemicals. CHEBI:36080 protein complex The function of a physical entity, that is its role, in the execution of an event. participant role Term to signify those material or conceptual entities that are identical in some respect within a frame of reference equivalence Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic. discrete framework Relationship between molecular entities, based on contacts, direct or indirect. molecular interaction Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, by stericaly hindering the interaction between reactants. competitive inhibitor Michaelis constant as determined in a reaction where the formation of the enzyme-substrate complex occurs at a much faster rate than subsequent steps, and so are assumed to be in a quasi-equilibrium situation. K is equivalent to an equilibrium constant. For example see Henri-Michaelis-Menten equation (SBO:0000029). Michaelis constant in fast equilibrium situation kf kr R P1 P2 kf R kr P1 P2 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, second order reverse, reversible reactions, two products, continuous scheme Michaelis constant derived assuming enzyme-substrate and enzyme-product intermediates are formed in consecutive irreversible reactions. The constant K is the ratio of the forward rate constants. For example see Van Slyke-Cullen equation (SBO:0000030). Michaelis constant in irreversible situation Synonym: Precursor mRNA heterogeneous nuclear RNA Et kcatp Et kcatp Synonym: Vmaxf forward maximal velocity The amount, expressed as a mass, of a specific activator entity pool. The participant role 'activator' is defined in SBO:0000459. mass of activator The amount, expressed as a number, of a specific product comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'product' is defined in SBO:0000011. number of a product RNA molecule that is not translated into a protein. Sequence Ontology SO:0000655 non-coding RNA kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S S 1 I1 Ki1 I2 Ki2 Ks 1 I1 Ki1 I2 Ki2 Inhibition of unireactant enzymes by two inhibitors that can bind to the complex enzyme-substrate and the free enzyme with the same equilibrium constant and totally prevent the catalysis. enzymatic rate law for non-competitive inhibition of irreversible unireactant enzymes by two exclusively binding inhibitors substrate product Modifier Keq Vf Ks Kp h Mhalf alpha Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 Modifier Mhalf h 1 alpha Modifier Mhalf h substrate Ks product Kp h The modifier can be either an activator or inhibitor depending on the value of alpha (activator for values larger than 1, inhibitor for values smaller than 1; no effect if exactly 1). This reflects the effect of the presence of substrate and product on the binding of the modifier. The equation, derived by Hofmeyr and Cornish-Bowden (Comput. Appl. Biosci. 13, 377 - 385 (1997) modulated reversible Hill-type rate law with one modifier Addition of a saccharide group to a chemical entity. glycosylation Number of monomers composing a multimeric entity. multimer cardinality Non-covalent complex of one or more macromolecules and zero or more simple chemicals. macromolecular complex The potential action that a biological entity has on other entities. Example are enzymatic activity, binding activity etc. biological activity The coefficient used to quantify the effect on inhibition constants of multiple inhibitors binding non-exclusively to the enzyme. biochemical cooperative inhibition coefficient Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the square of one reactant quantity. mass action rate law for second order irreversible reactions, one reactant The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. reverse reaction velocity Formal representation of a calculus linking parameters and variables of a model. mathematical expression A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone. Genetic interaction between perturbed genes is usually expected to generate a 'defective' phenotype. The level of defectiveness is often used to sub-classify this phenomenon. genetic interaction A process that leads to the generation of a material or conceptual entity. production connectedness between entities and/or interactions representing their relatedness or influence. relationship A numerical value that defines certain characteristics of systems or system functions. It may be part of a calculation, but its value is not determined by the form of the equation itself, and may be arbitrarily assigned. quantitative systems description parameter The change in entropy associated with the formation of one mole of a substance from its elements in their standard states under standard conditions (1 bar). The standard unit of measure is kJ/(mol K). symbol: DeltaSfo standard entropy of formation Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. non-competitive inhibitor Completely processed single strand of messenger ribonucleic acid (mRNA), synthesized from a DNA template in the nucleus of a cell by transcription and containing copies of only the exons of a gene. mature messenger RNA Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to three product quantities. mass action rate law for first order forward, third order reverse, reversible reactions Synonym: Kmp Michaelis constant for product Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a discrete framework. forward zeroth order rate constant, discrete case The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000297). protein complex formation Coefficient that quantifies the effect on inhibition constants of either binding of multiple substrates or inhibitors. biochemical inhibitory proportionality coefficient l R R l Monotonic decrease of a quantity proportionally to its value. monoexponential decay rate law The amount of a specific entity pool product present per unit of volume. The participant role 'product' is defined in SBO:0000011. concentration of product kf kr P kf kr P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, first order reverse, reversible reactions, continuous scheme Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic.The models do not take into account the distribution of the entities and describe only the temporal fluxes. non-spatial discrete framework A quantitative parameter that represents a probability value, assigned to a specific event. probabilistic parameter Reversible Hill-type kinetics in the presence of at least one modifier whose binding is affected by the presence of the substrate or product. modulated reversible Hill-type rate law kcat Et S I1 I2 Ks Ki1 Ki2 a b kcat Et S S 1 I1 a Ki1 I2 b Ki2 Ks 1 I1 Ki1 I2 Ki2 Inhibition of unireactant enzymes by two inhibitors that can bind to the complex enzyme-substrate and the free enzyme, possibly with different equilibrium constant, and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for mixed-type inhibition of irreversible unireactant enzymes by two inhibitors Synonym: necessary stimulator essential activator Substance produced by metabolism or by a metabolic process. metabolite new term name Control that always triggers the controlled process. absolute stimulation number used as a multiplicative or exponential factor for quantities, expressions or functions biochemical coefficient Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity. palmitoylation Process in which a DNA duplex is transformed into two identical DNA duplexes. dna replication Km x n i 1 x Km i n i The product of the product Michaelis constants, to the power of their respective stoichiometric coefficients. powered product of product Michaelis constants t 1 t Kinetic constant characterising a mono-exponential decay. It is the inverse of the mean lifetime of the continuant being decayed. Its unit is "per time". decay constant A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner. process Removal of an amine group from a molecule, often under the addition of water deamination A process that consumes a material or conceptual entity. consumption k R1 R2 R3 k R1 R2 R3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the product of three reactant quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order irreversible reactions, three reactants, continuous scheme Mutual or reciprocal action or influence between molecular entities. molecular or genetic interaction The description of a system in mathematical terms. obsolete mathematical expression The amount, expressed as a mass, of a specific product entity pool. The participant role 'product' is defined in SBO:0000011. mass of product An aggregation of interactions and entities into a single process. encapsulating process Synonym: Kms Michaelis constant for substrate The amount, expressed as a number, of a specific activator comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'activator' is defined in SBO:0000459. number of an activator Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to two product quantities. mass action rate law for first order forward, second order reverse, reversible reactions Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into. A compartment can have any number of dimensions, including 0, and be of any size including null. functional compartment substrate product Kms Kmp Vf Keq Vf substrate product Keq substrate Kms 1 product Kmp Synonym: Uni-Uni Uni-Uni Reversible using Haldane relationship The enumeration of co-localised, identical biochemical entities of a specific state, which constitute a pool. The form of enumeration may be purely numerical, or may be given in relation to another dimension such as length or volume. quantity of an entity pool Entity participating in a physical or functional interaction. interactor A substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed, by lowering the free energy of the transition state. The substance acting as a catalyst is an enzyme. enzymatic catalyst Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional totwo product quantities. mass action rate law for zeroth order forward, second order reverse, reversible reactions, continuous scheme Pressure (symbol: p) is the force per unit area applied on a surface in a direction perpendicular to that surface. The unit of pressure is the Pascal (Pa), that is equal to 1 Newton per square meter. pressure Kinetics of enzyme-catalysed reactions with 2 or more substrates or products enzymatic rate law for multireactant enzymes A compartment whose existence is inferred due to the presence of known material entities which must be bounded, allowing the creation of material entity pools. implicit compartment A multiplicative factor for quantities, expressions or functions biochemical proportionality coefficient k R k R R Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the square of one reactant quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for second order irreversible reactions, one reactant, continuous scheme kf kr R1 R2 P1 P2 P3 kf R1 R1 R2 kr P1 P2 P3 Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme Chemical entity that is engineered by a human-designed process ex-vivo rather than a produced by a living entity. synthetic chemical compound Mathematical expression stating that a quantity is conserved in a system, whatever happens within the boundaries of that system. conservation law a n S i 0 n a i S i If all forms of a moiety exist in a single compartment and the size of that compartment is fixed then the Mass Conservation is also a Concentration Conservation. concentration conservation law Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity. myristoylation Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions. composite biochemical process Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products hydrolysis Rate with which components associate into a complex. association rate constant Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide decarbonylation Set of assumptions that underlay a mathematical description. modelling framework Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. continuous framework kf kr R P kf R kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order forward, second order reverse, reversible reactions, one product, continuous scheme An equivocal or conjectural process, whose existence is assumed but not proven. uncertain process Quantitative parameter that characterises an acid-base reaction. acid dissociation characteristic The amount, expressed as a number, of a specific substrate comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'substrate' is defined in SBO:0000015. number of a substrate Also called half maximal inhibitory concentration, it represents the concentration of an inhibitor substance that is required to suppress 50% of an effect. IC50 substrate product Kms Kmp Et kcatp kcats Et kcatp substrate Kms kcats product Kmp 1 substrate Kms product Kmp Synonym: Uni-Uni Reversible Simple Michaelis-Menten reversible Uni-Uni Synonym: kcats substrate catalytic rate constant Synonym: Et total concentration of enzyme substrate product ModifierA ModifierB Keq Vf Shalve Phalve h MAhalf alphaA MBhalf alphaB alphaAB Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 ModifierA MAhalf h ModifierB MBhalf h 1 alphaA ModifierA MAhalf h alphaB ModifierB MBhalf h alphaA alphaB alphaAB ModifierA MAhalf h ModifierB MBhalf h substrate Ks product Kp h The modifiers can be either activators or inhibitors depending on the values of and alpha (activators for values larger than 1, inhibitors for values smaller than 1; no effect if exactly 1). The assumption is that the binding of one modifier affects the binding of the second. Modifiers are assumed to bind at different sites. The synergetic effects of the two modifiers depend on the parameter alpha (if unity then they are independent; if zero they compete for the same binding site). and reflect the effect of the presence of substrate and product on the binding of modifier A or modifier B. alphaA and alphaB factors account for the effect of substrate and product binding on the binding of modifier A and modifier B respectively. alphaAB accounts for the interaction of the modifiers on each others binding. (if < 1 Ma is inhibitor, if > 1 activator) alpha_2 : factor accounting for the effect of S and P on the binding of Mb (if < 1 Mb is inhibitor, if > 1 activator) alpha_3 : factor accounting for interaction of Ma to Mb binding to the enzyme (and v. v.). modulated reversible Hill-type rate law with two modifiers kf kr P kf kr P P Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. mass action rate law for zeroth order forward, second order reverse, reversible reactions, one product, continuous scheme A numerical measure of the quantity, or of some property, of the entities that constitute the entity pool. amount of an entity pool Synonym: mRNA messenger RNA The amount of a specific activator entity pool present per unit of volume. The participant role 'activator' is defined in SBO:0000459. concentration of activator Portion of DNA or RNA that is transcribed into another RNA, such as a messenger RNA or a non-coding RNA (for instance a transfert RNA or a ribosomal RNA). gene coding region part of