is_a
systems biology representation
Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network.
rate law
mathematical description that relates quantities of reactants to the reaction velocity.
quantitative systems description parameter
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.
participant role
The function of a physical entity, that is its role, in the execution of an event.
modelling framework
Set of assumptions that underlay a mathematical description.
obsolete mathematical expression
The description of a system in mathematical terms.
obsolete parameter
A numerical value that represents the amount of some entity, process or mathematical function of the system.
obsolete participant type
The 'kind' of entity involved in some process, action or reaction in the system. This may be enzyme, simple chemical, etc.
obsolete modelling framework
Basic assumptions that underlie a mathematical model.
kinetic constant
Numerical parameter that quantifies the velocity of a chemical reaction.
reaction rate constant
reactant
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.
product
Substance that is produced in a reaction. In a chemicalnequation the Products are the elements or compounds on the right hand sidenof the reaction equation. A product can be produced and consumed by thensame reaction, its global quantity remaining unchanged.
mass action rate law
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.
catalyst
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.
enzyme
A protein that catalyzes a chemical reaction. The word comes from en ("at" or "in") and simo ("leaven" or "yeast").
substrate
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.
unimolecular rate constant
Numerical parameter that quantifies the velocity of a chemical reaction involving only one reactant.n
bimolecular rate constant
Numerical parameter that quantifies the velocity of a chemical reaction involving two reactants.
trimolecular rate constant
Numerical parameter that quantifies the velocity of a chemical reaction involving three reactants.n
modifier
Substance that changes the velocity of a chemical reaction withoutnitself being consumed or transformed by the reaction.
inhibitor
Substance that decreases the probability of a chemical reaction withoutnitself being consumed or transformed by the reaction.
potentiator
activator
Substance that increases the probability of a chemical reaction withoutnitself being consumed or transformed by the reaction. This effect is achieved by increasing the difference of free energy between the reactant(s) and the product(s)
forward unimolecular rate constant
Numerical parameter that quantifies the forward velocity of a chemicalnreaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant.
forward bimolecular rate constant
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 trimolecular rate constant
Numerical parameter that quantifies the forward velocity of a chemicalnreaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.
catalytic rate constant
Numerical parameter that quantifies the velocity of an enzymatic reaction.
kcat
turnover number
new term name
none
Michaelis constant
Substrate concentration at which the velocity of reaction is half its maximum. Michaelis constant is an experimental parameter. According to the underlying molecular mechanism it can be interpreted differently in terms of microscopic constants.
Michaelis-Menten constant
enzymatic rate law for irreversible non-modulated non-interacting unireactant enzymes
Kinetics of enzymes that react only with one substance, their substrate. The enzymes do not catalyse the reactions in both directions. n n n kcat n Et n S n Ks n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n Ks n S n n n n n
Henri-Michaelis-Menten rate law
First general rate equation for reactions involving enzymes, it was presented in "Victor Henri. Lois GC)nC)rales 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. n n n kcat n Et n S n Ks n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n Ks n S n n n n n
Van Slyke-Cullen rate law
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. n n n kcat n Et n S n Ks n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n Ks n S n n n n n
Briggs-Haldane rate law
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. n n n kcat n Et n S n Km n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n Km n S n n n n n
reverse unimolecular rate constant
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
reverse trimolecular rate constant
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.
forward unimolecular rate constant, continuous case
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 bimolecular rate constant, continuous case
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 trimolecular rate constant, continuous case
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.
reverse unimolecular rate constant, continuous case
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
reverse trimolecular 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.
mass action rate law for irreversible reactions
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 reversible reactions
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 zeroth order irreversible reactions
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 first order irreversible reactions
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 second order irreversible reactions
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.
zeroth order rate constant
Numerical parameter that quantifies the velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity.
mass action rate law for zeroth order irreversible reactions, 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 constant. It is to be used in a reaction modelled using a continuous framework. n n n k n n k n n n n
forward zeroth order rate constant, continuous case
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.
mass action rate law for first order irreversible reactions, 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 quantity of one reactant. It is to be used in a reaction modelled using a continuous framework. n n n k n R n n <times/>n k n R n n n n
mass action rate law for second order irreversible 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 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, 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 square of one reactant quantity. It is to be used in a reaction modelled using a continuous framework. n n n k n R n n <times/>n k n R n R n n n n
mass action rate law for second order irreversible 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 proportional to the quantity of two reactants.
mass action rate law for second order irreversible 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 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. n n n k n R1 n R2 n n <times/>n k n R1 n R2 n n n n
mass action rate law for third order irreversible reactions
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, 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 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, 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, 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. n n n k n R n n <times/>n k n R n R n R n n n n
mass action rate law for third order irreversible 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 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, 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 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. n n n k n R1 n R2 n n <times/>n k n R1 n R1 n R2 n n n n
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 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, 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, 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. n n n k n R1 n R2 n R3 n n <times/>n k n R1 n R2 n R3 n n n n
continuous 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.
discrete framework
Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic.
mathematical expression
Formal representation of a calculus linking parameters and variables of a model.
forward zeroth order rate constant, discrete case
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 unimolecular rate constant, discrete case
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. n
forward bimolecular rate constant, discrete case
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 trimolecular rate constant, discrete case
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.
mass action rate law for zeroth order reversible reactions
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 forward, first order reverse, reversible reactions, 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. 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. n n n kf n kr n P n n <minus/>n kf n n <times/>n kr n P n n n n n
mass action rate law for zeroth order forward, second order reverse, reversible reactions, 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. The rate of the reverse process is proportional totwo product quantities.
mass action rate law for zeroth order forward, second order reverse, reversible reactions, one product, 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. 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.nn n n n kf n kr n P n n <minus/>n kf n n <times/>n kr n P n P n n n n n
mass action rate law for zeroth order forward, second order reverse, reversible reactions, 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 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.n n n n kf n kr n P1 n P2 n n <minus/>n kf n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for zeroth order forward, third order reverse, reversible reactions, 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. 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, one product, 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. 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. n n n kf n kr n P n n <minus/>n kf n n <times/>n kr n P n P n P n n n n n nn
mass action rate law for zeroth order forward, third order reverse, reversible reactions, 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 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. n n n kf n kr n P1 n P2 n n <minus/>n kf n n <times/>n kr n P1 n P2 n P2 n n n n n nn
mass action rate law for zeroth order forward, third order reverse, reversible reactions, three 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 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. n n n kf n kr n P1 n P2 n P3 n n <minus/>n kf n n <times/>n kr n P1 n P2 n P3 n n n n n n
mass action rate law for first order reversible reactions
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 forward, zeroth order reverse, reversible reactions, 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 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. n n n kf n kr n R n n <minus/>n n <times/>n kf n R n n kr n n n n
mass action rate law for first order forward, first order reverse, reversible reactions, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P n n n n n
mass action rate law for first order forward, second order reverse, reversible reactions
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, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P n P n n n n n
mass action rate law for first order forward, second order reverse, reversible reactions, 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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for first order forward, third order reverse, reversible reactions
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, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P n P n P n n n n n
mass action rate law for first order forward, third order reverse, reversible reactions, 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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for first order forward, third order reverse, reversible reactions, three 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 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. n n n kf n kr n R n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R n n n <times/>n kr n P1 n P2 n P3 n n n n n
mass action rate law for second order reversible reactions
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 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.
mass action rate law for second order forward, zeroth order reverse, reversible reactions, one reactant, 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 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. n n n kf n kr n R n n <minus/>n n <times/>n kf n R n R n n kr n n n n
mass action rate law for second order forward, first order reverse, reversible reactions, one reactant, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P n n n n n
mass action rate law for second order forward, second order reverse, 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, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P n P n n n n n
mass action rate law for second order forward, second order reverse, reversible reactions, 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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for second order forward, third order reverse, 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 three products.
mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P n P n P n n n n n
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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, three 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 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. n n n kf n kr n R n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R n R n n n <times/>n kr n P1 n P2 n P3 n n n n n
mass action rate law for second 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 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, zeroth 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 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. n n n kf n kr n R1 n R2 n n <minus/>n n <times/>n kf n R1 n R2 n n kr n n n n
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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P n n n n n
mass action rate law for second order forward, second order reverse, 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P n P n n n n n
mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for second order forward, third order reverse, 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P n P n P n n n n n
mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, three 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R1 n R2 n n n <times/>n kr n P1 n P2 n P3 n n n n n
mass action rate law for third order reversible reactions
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 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 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, zeroth 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 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. n n n kf n kr n R1 n R2 n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n kr n n n n
mass action rate law for third 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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P n n n n n
mass action rate law for third order forward, second order reverse, 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P n P n n n n n
mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n P n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P n P n P n n n n n
mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, three 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 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. n n n kf n kr n R1 n R2 n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R1 n R1 n R2 n n n <times/>n kr n P1 n P2 n P3 n n n n n
mass action rate law for third order forward, reversible 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 product of three reactant quantities.
mass action rate law for third order forward, zeroth order reverse, reversible reactions, three 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 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. n n n kf n kr n R1 n R2 n R3 n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n kr n n n n
mass action rate law for third order forward, first order reverse, reversible reactions, three 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 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. n n n kf n kr n R1 n R2 n R3 n P n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P n n n n n
mass action rate law for third order forward, second order reverse, reversible 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n R3 n P n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P n P n n n n n
mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, 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 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. n n n kf n kr n R1 n R2 n R3 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, reversible 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 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, one product, 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 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. n n n kf n kr n R1 n R2 n R3 n P n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P n P n P n n n n n
mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, 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 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. n n n kf n kr n R1 n R2 n R3 n P1 n P2 n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, three 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 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. n n n kf n kr n R1 n R2 n R3 n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R1 n R2 n R3 n n n <times/>n kr n P1 n P2 n P3 n n n n n
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 cube of one reactant quantity.
mass action rate law for third order forward, zeroth order reverse, reversible reactions, one reactant, 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 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. n n n kf n kr n R n n <minus/>n n <times/>n kf n R n R n R n n kr n n n n
mass action rate law for third order forward, first order reverse, reversible reactions, one reactant, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P n n n n n
mass action rate law for third order forward, second order reverse, 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 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, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P n P n n n n n
mass action rate law for third order forward, second 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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, 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 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, one product, 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 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. n n n kf n kr n R n P n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P n P n P n n n n n
mass action rate law for third 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 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. n n n kf n kr n R n P1 n P2 n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P1 n P1 n P2 n n n n n
mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, three 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 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. n n n kf n kr n R n P1 n P2 n P3 n n <minus/>n n <times/>n kf n R n R n R n n n <times/>n kr n P1 n P2 n P3 n n n n n n
mass action rate law for zeroth order irreversible reactions, 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 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. n n n c n n c n n n n
mass action rate law for first order irreversible reactions, 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 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. n n n c n R n n <times/>n c n R n n n n
mass action rate law for second order irreversible reactions, one reactant, 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 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. n n n c n R n n <times/>n c n n <divide/>n n <times/>n R n n <minus/>n R n 1 n n n 2 n n n n n nn
mass action rate law for second order irreversible reactions, two reactants, 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 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. n n n c n R1 n R2 n n <times/>n c n R1 n R2 n n n n
mass action rate law for third order irreversible reactions, one reactant, 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 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. n n n c n R n n <times/>n c n n <divide/>n n <times/>n R n n <minus/>n R n 1 n n n <minus/>n R n 2 n n n 6 n n n n n
mass action rate law for third order irreversible reactions, two reactants, 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 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. n n n c n R1 n R2 n n <times/>n c n R1 n n <divide/>n n <times/>n R2 n n <minus/>n R2 n 1 n n n 2 n n n n n
mass action rate law for third order irreversible reactions, three reactants, 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 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. n n n c n R1 n R2 n R3 n n <times/>n c n R1 n R2 n R3 n n n n
thermodynamic temperature
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).
temperature difference
Quantity resulting from the difference between two thermodynamic temperatures. A difference or interval of temperature may be expressed in Kelvins or in degrees Celsius.n
number of substrates
Number of molecules which are acted upon by an enzyme.
enzymatic rate law for irreversible non-modulated non-interacting reactant enzymes
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. n n n Et n kp n n n S n K n n <divide/>n n <times/>n Et n kp n n <product/>n i n 1 n n n n <divide/>n n <selector/>n S n i n n n <selector/>n K n i n n n n n n <product/>n i n n 1 n n n n n n n <plus/>n 1 n n <divide/>n n <selector/>n S n i n n n <selector/>n K n i n n n n n n n n
enzymatic rate law for irreversible non-modulated non-interacting bireactant enzymes
Kinetics of enzymes that react with two substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. n n n Et n kp n n n S1 n S2 n K1 n K2 n n <divide/>n n <times/>n Et n kp n n <times/>n n <divide/>n S1 n K1 n n n <divide/>n S2 n K2 n n n n n <times/>n n <plus/>n 1 n n <divide/>n S1 n K1 n n n n <plus/>n 1 n n <divide/>n S2 n K2 n n n n n n n
enzymatic rate law for irreversible non-modulated non-interacting trireactant enzymes
Kinetics of enzymes that react with three substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. n n n Et n kp n n n S1 n S2 n S3 n K1 n K2 n K3 n n <divide/>n n <times/>n Et n kp n n <times/>n n <divide/>n S1 n K1 n n n <divide/>n S2 n K2 n n n <divide/>n S3 n K3 n n n n n <times/>n n <plus/>n 1 n n <divide/>n S1 n K1 n n n n <plus/>n 1 n n <divide/>n S2 n K2 n n n n <plus/>n 1 n n <divide/>n S3 n K3 n n n n n n n n
forward rate constant
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, continuous case
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, discrete case
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.
reverse rate constant
number of reactants
Number of different substances consumed by a chemical reaction.
order of a reaction with respect to a reactant
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.
non-integral order rate constant
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.
forward non-integral order rate constant
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.
reverse non-integral order rate constant
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.
forward zeroth order rate constant
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.
mass action rate law for irreversible reactions, 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. It is to be used in a reaction modelled using a continuous framework. n n n k n n n mu n R n n <times/>n k n n <product/>n i n 0 n n n n <power/>n n <selector/>n R n i n n n <selector/>n mu n i n n n n n n n n
second order irreversible mass action kinetics, 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 two reactant quantity. It is to be used in a reaction modelled using a continuous framework. n n n k n R n n <times/>n k n n <product/>n i n 1 n 2 n n <selector/>n R n i n n n n n n
third order irreversible mass action kinetics, 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 three reactant quantities. It is to be used in a reaction modelled using a continuous framework. n n n k n R n n <times/>n k n n <product/>n i n 1 n 3 n n <selector/>n R n i n n n n n n
mass action rate law for irreversible reactions, 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 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. n n n c n n n mu n R n n <times/>n c n n <product/>n i n 0 n n n n <divide/>n n <factorial/>n n <selector/>n R n i n n n n <times/>n n <factorial/>n n <minus/> n n <selector/>n R n i n n n <selector/>n mu n i n n n n n <factorial/>n n <selector/>n mu n i n n n n n n n n n
biochemical or transport reaction
An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants.
control
regulation
Modification of the execution of an event or a process.
modulation
inhibition
Negative modulation of the execution of a process.
stimulation
Positive modulation of the execution of a process.
necessary stimulation
Control that is necessary to the execution of a process.
absolute stimulation
trigger
catalysis
Modification of the velocity of a reaction by lowering the energy of the transition state.
and
All the preceding events or participating entities are necessary to perform the control.
Any of the preceding events or participating entities are necessary to perform the control.
xor
exclusive or
Only one of the preceding events or participating entities can perform the control at one time.
biochemical reaction
An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.n
non-covalent binding
Interaction between several biochemical entities that results in the formation of a non-covalent complex
cleavage
Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities.
degradation
Complete disappearance of a physical entity.
dissociation
Transformation of a non-covalent complex that results in the formation of several independent biochemical entities
conformational transition
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.
conversion
Biochemical reaction that results in the modification of some covalent bonds.
transcription
Process through which a DNA sequence is copied to produce a complementary RNA.
translation
Process in which a polypeptide chain is produced from a messenger RNA.
transport reaction
Movement of a physical entity without modification of the structure of the entity.
maximal velocity
Limiting maximal velocity of an enzymatic reaction, reached when the substrate is in large excess and all the enzyme is complexed. n n Et n kcat n n <times/>n Et n kcat n n n
Vmax
Henri-Michaelis-Menten equation, Vmax form
Version of Henri-Michaelis-Menten equation where kp*[E]t is replaced by the maximal velocity, Vmax, reached when all the enzyme is active. n n n Vmax n S n Ks n n <divide/>n n <times/>n Vmax n S n n n <plus/>n Ks n S n n n n n
number of biochemical items
A number of objects of the same type, identical or different, involved in a biochemical event.
number of binding sites
Number of regions on a reactant to which specific other reactants, in this context collectively called ligands, form a chemical bond.
Hill coefficient
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 constant
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-type rate law, generalised form
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). n n n Vmax n R n K n h n n n n <divide/>n n <times/>n Vmax n n <power/>n R n h n n n n <plus/>n n <power/>n K n n n n n <power/>n R n h n n n n n n
equilibrium or steady-state constant
Constant with the dimension of a powered concentration. It is determined at half-saturation, half-activity etc.
pseudo-dissociation constant
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.
Hill-type rate law, microscopic form
Hill equation rewritten by creating a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. n n n Vmax n R n K n h n n <divide/>n n <times/>n Vmax n n <power/>n R n h n n n n <plus/>n n <power/>n K n h n n n <power/>n R n h n n n n n n
concentration of an entity pool
[X]
The amount of an entity per unit of volume.
specific concentration of an entity
Concentration of an object divided by the value of another parameter having the dimension of a concentration.
Hill-type rate law, reduced form
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. n n n Vmax n R* n h n n <divide/>n n <times/>n Vmax n n <power/>n R* n h n n n n <plus/>n 1 n n <power/>n R* n h n n n n n n
normalised enzymatic rate law for unireactant enzymes
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. n n n kcat n S n Ks n n <divide/>n n <times/>n kcat n S n n n <plus/>n Ks n S n n n n n
redox reaction
Chemical process in which atoms have their oxidation number (oxidation state) changed.
oxidation
Chemical process during which a molecular entity loses electrons.
reduction
Chemical process in which a molecular entity gain electrons.
duplication
Reaction in which a reactant gives birth to two products identical to itself.
dna replication
Process in which a DNA duplex is transformed into two identical DNA duplexes.
composite biochemical process
Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions.
competitive inhibitor
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.
non-competitive inhibitor
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.
acid-base reaction
Chemical reaction where a proton is given by a compound, the acid, to another one, the base (BrC8nsted-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).
ionisation
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.
addition of a chemical group
Covalent reaction that results in the addition of a chemical group on a molecule.
removal of a chemical group
Covalent reaction that results in the removal of a chemical group from a molecule.
protonation
Addition of a proton (H+) to a chemical entity.
deprotonation
Removal of a proton (hydrogen ion H+) from a chemical entity.
methylation
Addition of a methyl group (-CH3) to a chemical entity.
acetylation
Addition of an acetyl group (-COCH3) to a chemical entity.
phosphorylation
Addition of a phosphate group (-H2PO4) to a chemical entity.
glycosylation
Addition of a saccharide group to a chemical entity.
palmitoylation
Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity.
myristoylation
Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity.
sulfation
Addition of a sulfate group (SO4--) to a chemical entity.
sulphation
prenylation
Addition of a prenyl group (generic sense) to a chemical entity.
isoprenylation
farnesylation
Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity.
geranylgeranylation
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.
ubiquitination
Covalent linkage to the protein ubiquitin.
delay
Time during which some action is awaited.
density of an entity pool
A quantitative measure of an amount or property of an entity expressed in terms of another dimension, such as unit length, area or volume.
mass density of an entity
The mass of an entity expressed with reference to another dimension, such as unit length, area or volume.
volume density of an entity
Mass of an entity per unit volume.
area density of an entity
The mass of an entity per unit of surface area.
linear density of an entity
Mass of an entity per unit length.
occurring entity representation
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.
obsolete event
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.
hydroxylation
Addition of an hydroxyl group (-OH) to a chemical entity.
logical framework
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.
participant
Entity that affects or is affected by an event.
physical entity representation
new synonym
Representation of an entity that may participate in an interaction, a process or relationship of significance.n
logical combination
Combining the influence of several entities or events in a unique influence.
not
The preceding event or participating entity cannot participate to the control.
allosteric control
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.
material entity
A real thing that is defined by its physico-chemical structure.n
functional entity
A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure.
channel
A component that allows another component to pass through itself, possibly connecting different compartments.
gene
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.nnSequence Ontology SO:0000704
receptor
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).nnLangley 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.
macromolecule
Molecular entity mainly built-up by the repetition of pseudo-identical units.nnCHEBI:33839
information macromolecule
Macromolecule whose sequence is encoded in the genome of living organisms.
simple chemical
Simple, non-repetitive chemical entity.
chemical macromolecule
Macromolecule whose sequence is not directly encoded in the genome.
polysaccharide
Macromolecule consisting of a large number of monosaccharide residues linked by glycosidic bonds.nnCHEBI:18154
ribonucleic acid
RNA
Macromolecule formed by a repetition of ribonucleosides linked by phosphodiester bonds.nnCHEBI:33697
deoxyribonucleic acid
Polymer composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.nnCHEBI:16991
DNA
polypeptide chain
Naturally occurring macromolecule formed by the repetition of amino-acid residues linked by peptidic bonds. A polypeptide chain is synthesized by the ribosome.nnCHEBI:16541
non-covalent complex
Entity composed of several independant components that are not linked by covalent bonds.
electrical resistance
Measure of the degree to which an object opposes the passage of an electric current. The SI unit of electrical resistance is the ohm.
physical characteristic
Parameter characterising a physical system or the environment, and independent of life's influence.
biochemical parameter
Parameter that depends on the biochemical properties of a system.
conductance
Measure of how easily electricity flows along a certain path through an electrical element. The SI derived unit of conductance is the Siemens.
capacitance
Measure of the amount of electric charge stored (or separated) for a given electric potential. The unit of capacitance id the Farad.
voltage
Difference of electrical potential between two points of an electrical network, expressed in volts.
electrical potential difference
enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by one inhibitor
simple intersecting linear competitive inhibition of unireactant enzymes
Inhibition of a unireactant enzyme by one inhibitor that binds once to the free enzyme and prevents the binding of the substrate. The enzymes do not catalyse the reactions in both directions. n n n kcat n Et n S n I n Ks n Ki n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I n Ki n n n n S n n n n n
inhibitory constant
inhibition constant
Dissociation constant of a compound from a target of which it inhibits the function.
enzymatic rate law for simple uncompetitive inhibition of irreversible unireactant enzymes
Inhibition of a unireactant enzyme by one inhibitor that binds only to the complex enzyme-substrate and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. n n n kcat n Et n S n I n Ks n Ki n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n S n n <plus/>n 1 n n <divide/>n I n Ki n n n n Ks n n n n n
simple linear uncompetitive inhibition
relative equilibrium constant
Ratio of an equilibrium constant in a given condition by the same equilibrium constant is not fullfilled.
relative inhibition constant
Ratio of the dissociation constant of an inhibitor from the complex enzyme-substrate on the dissociation constant of an inhibitor from the free enzyme.
enzymatic rate law for simple mixed-type inhibition of irreversible unireactant enzymes
simple intersecting linear mixed-type competitive inhibition
Inhibition of a unireactant enzyme by one inhibitor 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. n n n kcat n Et n S n I n Ks n Ki n a n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n S n n <plus/>n 1 n n <divide/>n I n n <times/>n a n Ki n n n n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I n Ki n n n n n n n n
enzymatic rate law for simple irreversible non-competitive inhibition of unireactant enzymes
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. n n n kcat n Et n S n I n Ks n Ki n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n S n n <plus/>n 1 n n <divide/>n I n Ki n n n n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I n Ki n n n n n n n n
enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by one inhibitor
multiple competitive inhibition by one inhibitor of unireactant enzymes
Inhibition of a unireactant enzyme by one inhibitor that can bind one or several times to the free enzyme, and prevent the binding of the substrate. The enzymes do not catalyse the reactions in both directions.nn n n n kcat n Et n S n I n Ks n Ki n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n S n n <times/>n Ks n n <power/>n n <plus/>n 1 n n <divide/>n I n Ki n n n n n n n n n n n
enzymatic rate law
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 for unireactant enzymes
Kinetics of enzymes that catalyse the transformation of only one substrate.
enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by exclusive inhibitors
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. n n n kcat n Et n S n I n Ks n Ki n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <sum/>n i n 1 n n n n <divide/>n n <selector/>n I n i n n n <selector/>n Ki n i n n n n n n S n n n n n n
enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by two exclusive inhibitors
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. n n n kcat n Et n S n I1 n I2 n Ks n Ki1 n Ki2 n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n n S n n n n n
number of inhibitors
Number of entities that inhibit a reaction.
enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by non-exclusive non-cooperative inhibitors
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. n n n kcat n Et n S n I n Ks n Ki n n n m n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <product/>n i n 1 n n n n <power/>n n <plus/>n 1 n n <divide/>n n <selector/>n I n i n n n <selector/>n Ki n i n n n n n <selector/>n m n i n n n n n S n n n n n n
enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive, non-cooperative inhibitors
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. n n n kcat n Et n S n I1 n I2 n Ks n Ki1 n Ki2 n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n <divide/>n n <times/>n I1 n I2 n n n <times/>n Ki1 n Ki2 n n n n n S n n n n n
enzymatic rate law for mixed-type inhibition of irreversible enzymes by mutually exclusive inhibitors
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. n n n kcat n Et n S n I n Ks n Ki n a n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <sum/>n i n 1 n n n n <divide/>n n <selector/>n I n i n n n <selector/>n Ki n i n n n n n n n <times/>n S n n <plus/>n 1 n n <sum/>n i n 1 n n n n <divide/>n n <selector/>n I n i n n n <times/>n n <selector/>n a n i n n n <selector/>n Ki n i n n n n n n n n n n n
enzymatic rate law for mixed-type inhibition of irreversible unireactant enzymes by two inhibitors
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. n n n kcat n Et n S n I1 n I2 n Ks n Ki1 n Ki2 n a n b n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n S n n <plus/>n 1 n n <divide/>n I1 n n <times/>n a n Ki1 n n n n <divide/>n I2 n n <times/>n b n Ki2 n n n n n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n n n n n n
enzymatic rate law for non-competitive inhibition of irreversible unireactant enzymes by two exclusively binding inhibitors
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. n n n kcat n Et n S n I1 n I2 n Ks n Ki1 n Ki2 n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n S n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n n n n n n
messenger RNA
A messenger RNA is a ribonucleic acid synthesized during the transcription of a gene, and that carries the information to encode one or several proteins.
mRNA
pressure
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.
ligand
In biochemistry, a ligand is an effector, a physical entity that binds to a site on a receptor's surface by intermolecular forces.
equilibrium constant
Keq
Quantity characterizing a chemical equilibrium in a chemical reaction, which is a useful tool to determine the concentration of various reactants or products in a system where chemical equilibrium occurs.
dissociation constant
Equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions. The dissociation constant is usually denoted Kd and is the inverse of the affinity constant. n n koff n Kon n n <divide/>n koff n Kon n n n n
acid dissociation constant
Equilibrium constant that indicates the extent of dissociation of hydrogen ions from an acid. The equilibrium is that of a proton transfer from an acid, HA, to water, H2O. The term for the concentration of water, [H2O], is omitted from the general equilibrium constant expression. Ka=([H3O+]*[A-])/(HA)
transporter
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.
material entity of unspecified nature
Material entity whose nature is unknown or irrelevant.
multimer
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.
EC50
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.
IC50
Also called half maximal inhibitory concentration, it represents the concentration of an inhibitor substance that is required to suppress 50% of an effect.
functional compartment
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.
physical compartment
Specific location of space, that can be bounded or not. A physical compartment can have 1, 2 or 3 dimensions.
empty set
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.
spatial continuous 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. The models take into account the distribution of the entities and describe the spatial fluxes.
non-spatial continuous 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. The models do not take into account the distribution of the entities and describe only the temporal fluxes.
spatial discrete framework
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.
non-spatial discrete framework
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. n
macromolecular complex
Non-covalent complex of one or more macromolecules and zero or more simple chemicals.
protein complex
Macromolecular complex containing one or more polypeptide chains possibly associated with simple chemicals.nnCHEBI:36080
synthetic chemical compound
Chemical entity that is engineered by a human-designed process ex-vivo rather than a produced by a living entity.
metabolite
Substance produced by metabolism or by a metabolic process.
total concentration of enzyme
Total amount of enzyme catalysing a reaction, divided by the volume of reaction.
total catalytic efficiency
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.nnNB. 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). n n Vmax n Km n n <divide/>n Vmax n Km n n n n
catalytic efficiency
Constant representing the actual efficiency of an enzyme, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. n n kcat n Km n n <divide/>n kcat n Km n n n
biochemical potential
Derivative of a biochemical energy per a substance.
chemical potential
Negative logarithm (base 10) of the activity of hydrogen in a solution. Ina diluted solution, this activity is equal to the concentration of protons (in fact of ions H3O+). The pH is proportional to the chemical potential of hydrogen, by the relation: pH = -B5H C7 2.3RT. (with B5H=-RTln[H+]).
potential of hydrogen
pOH
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-.
negative logarithm (base 10) of a dissociation constant. n n K n n <minus/>n n <log/>n K n n n n
dissociation potential
pKa
negative logarithm (base 10) of an acid dissociation constant. n n Ka n n <minus/>n n <log/>n Ka n n n n
potential of acid
equilibrium or steady-state characteristic
Quantitative parameter that characterises a biochemical equilibrium.
dissociation characteristic
Quantitative parameter that characterises a dissociation.
acid dissociation characteristic
Quantitative parameter that characterises an acid-base reaction.
heterogeneous nuclear RNA
Incompletely 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 the introns and exons of a gene.
pre-mRNA
Precursor mRNA
mature messenger RNA
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.
transfer RNA
tRNA
Small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a site for amino acid attachment and a three-base region called the anticodon that recognizes the corresponding three-base codon region on mRNA via complementary base pairing. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code is degenerate - that is, it contains multiple codons that specify the same amino acid - multiple types of tRNA molecules bearing different anticodons may carry the same amino acid.
ribosomal RNA
Type of RNA that is the central component of the ribosome, the protein manufacturing machinery of all living cells.
rRNA
ribozyme
ribonucleic acid enzyme
RNA molecule that catalyzes a chemical reaction.
microRNA
miRNA
Single-stranded RNA molecules thought to regulate the expression of other genes. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA).
small interfering RNA
siRNA
siRNA are 20-25 nucleotide-long double-stranded RNA molecules involved in the regulation of the expression of specific genes, antiviral mechanisms, shaping the chromatin structure of a genome etc.
small nuclear RNA
snRNA
Small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns from heterogeneous nuclear RNA), regulation of transcription factors or RNA polymerase II and maintaining the telomeres. They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP).
small nucleolar RNA
snoRNA
Small RNA molecules that guide chemical modifications (methylation or pseudouridylation) of ribosomal RNAs (rRNAs) and other RNA genes. They are frequently encoded in the introns of ribosomal proteins and are synthesized by RNA polymerase II, but can also be transcribed as independent (sometimes polycistronic) transcriptional units. snoRNAs are a component in the small nucleolar ribonucleoprotein (snoRNP), which contains snoRNA and proteins.
product catalytic rate constant
Numerical parameter that quantifies the velocity of product creation by a reversible enzymatic reaction. n
kcatp
substrate catalytic rate constant
kcats
Numerical parameter that quantifies the velocity of substrate creation by a reversible enzymatic reaction.
Michaelis constant for substrate
Substrate concentration at which the velocity of product production by the forward activity of a reversible enzyme is half its maximum.
Kms
Michaelis constant for product
Product concentration at which the velocity of substrate production by the reverse activity of a reversible enzyme is half its maximum.
Kmp
forward maximal velocity
Limiting maximal velocity of the forward reaction of a reversible enzyme, reached when the substrate is in large excess and all the enzyme is complexed. n n Et n kcatp n n <times/>n Et n kcatp n n n
Vmaxf
reverse maximal velocity
Limiting maximal velocity of the reverse reaction of a reversible enzyme, reached when the product is in large excess and all the enzyme is complexed. n n Et n kcats n n <times/>n Et n kcats n n n
Vmaxr
enzymatic rate law for non-modulated unireactant enzymes
Kinetics of enzymes that react only with one substance, their substrate, and are not modulated by other compounds.
non-macromolecular ion
Chemical entity having a net electric charge.
non-macromolecular radical
chemical entity possessing an unpaired electron.
transcription start site
TSS
First nucleotide of a gene that is copied in the transcribed RNA.nnSequence Ontology SO:0000315
dephosphorylation
Removal of a phosphate group (-H2PO4) from a chemical entity.
half-life
Time interval over which a quantified entity is reduced to half its original value.
half-life of an exponential decay
Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2. n n l n n <divide/>n n <ln/> n 2 n n l n n n n
monoexponential decay rate law
Monotonic decrease of a quantity proportionally to its value. n n n l n R n n <divide/>n R n l n n n n
non-coding RNA
RNA molecule that is not translated into a protein. nnSequence Ontology SO:0000655
gene coding region
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).
interactor
Entity participating in a physical or functional interaction.
association constant
affinity constant
Equilibrium constant that measures the propensity of two objects to assemble (associate) reversibly into a larger component. The association constant is usually denoted Ka and is the inverse of the dissociation constant. n n koff n Kon n n <divide/>n kon n Koff n n n n
dissociation rate constant
Rate with which a complex dissociates into its components.
bimolecular association rate constant
Rate with which two components associate into a complex.
trimolecular association rate constant
Rate with which three components associate into a complex.
association rate constant
Rate with which components associate into a complex.
molecular or genetic interaction
Mutual or reciprocal action or influence between molecular entities.
genetic interaction
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.n
molecular interaction
Relationship between molecular entities, based on contacts, direct or indirect.
time
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 ofn9,192,631,770 periods of the radiation corresponding to the transitionnbetween the two hyperfine levels of the ground state of the caesium 133natom.
temporal measure
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.
duration
Amount of time during which an event persists.
exponential time constant
mean lifetime
Time that it takes for an exponential decay to reach 1/e (about 37%) of the original value. This characterises the frequency response of a first-order, linear time-invariant system. This is also the average lifetime of an element in the decaying set. It is the inverse of the exponential decay constant. n n l n n <divide/>n 1 n l n n n n
inactivation rate constant
kinact
Kinetic constant describing the rate of an irreversible enzyme inactivationnby decay of the active enzyme into its inactive form.
forward reaction velocity
The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme.
reverse zeroth order rate constant
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 reaction velocity
informational molecule segment
Fragment of a macromolecule that carries genetic information.
conservation law
Mathematical expression stating that a quantity is conserved in a system, whatever happens within the boundaries of that system.
decay constant
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". n n t n n <divide/>n 1 n t n n n n
biological effect of a perturbation
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.
phenotype
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.n
mass conservation law
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.n n n a n n n S n n <sum/>n i n 0 n n n n <times/>n n <selector/>n a n i n n n <selector/>n S n i n n n n n n
quantity of an entity pool
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.
amount of an entity pool
A numerical measure of the quantity, or of some property, of the entities that constitute the entity pool. n
concentration conservation law
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.nn n n a n n n S n n <sum/>n i n 0 n n n n <times/>n n <selector/>n a n i n n n <selector/>n S n i n n n n n n
activation constant
Dissociation constant of a potentiator (activator) from a target (e.g. annenzyme) of which it activates the function.
multimer cardinality
Number of monomers composing a multimeric entity.
forward non-integral order rate constant, continuous case
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, discrete case
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.
reverse non-integral order rate constant, discrete case
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.n
reverse non-integral order rate constant, continuous case
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.
gene regulatory region
Region of a gene that is involved in the modulation of the expression of the gene.
Michaelis constant in non-equilibrium situation
Michaelis constant derived or experimentally measured under non-equilibrium conditions.
Michaelis constant in quasi-steady state situation
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 irreversible situation
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 fast equilibrium situation
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).
relationship
connectedness between entities and/or interactions representing their relatedness or influence.
process
A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner.
hydrolysis
Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products
isomerisation
A reaction in which the principal reactant and principal product are isomers of each other
enzymatic rate law for inhibition of irreversible unireactant enzymes by competing substrates
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.nnnnn n n n kcat n Et n S n Sa n Ks n Ksa n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <sum/>n i n 1 n n n n <divide/>n n <selector/>n Sa n i n n n <selector/>n Ksa n i n n n n n n S n n n n n nn
enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive inhibitors
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. n n n kcat n Et n S n I1 n I2 n a n Ks n Ki1 n Ki2 n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n I1 n Ki1 n n n <divide/>n I2 n Ki2 n n n <divide/>n n <times/>n I1 n I2 n n n <times/>n a n Ki1 n Ki2 n n n n n S n n n n n
biochemical coefficient
number used as a multiplicative or exponential factor for quantities, expressions or functions
biochemical proportionality coefficient
A multiplicative factor for quantities, expressions or functions
biochemical exponential coefficient
number used as an exponential factor for quantities, expressions or functions
biochemical cooperative inhibition coefficient
The coefficient used to quantify the effect on inhibition constants of multiple inhibitors binding non-exclusively to the enzyme.
biochemical inhibitory proportionality coefficient
Coefficient that quantifies the effect on inhibition constants of either binding of multiple substrates or inhibitors.
biochemical cooperative inhibitor substrate coefficient
The coefficient that describes the proportional change of Ks or Ki when inhibitor or substrate is bound, respectively, to the enzyme.
enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate
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. n n n kcat n Et n S n Sa n Ks n Ksa n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n Sa n Ksa n n n n S n n n n n n
enzymatic rate law for competitive inhibition of irreversible unireactant enzyme by product
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.n n n n kcat n Et n S n P n Ks n Kp n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n P n Kp n n n n S n n n n n nn
enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate with product inhibition
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.n n n n kcat n Et n S n Sa n Ks n Ksa n Kp n Kpa n P n Pa n n n n <divide/>n n <times/>n kcat n Et n S n n n <plus/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n Sa n Ksa n n n <divide/>n P n Kpa n n n <divide/>n Pa n Kpa n n n n S n n n n n n
switch value
A parameter value taken by a switch, which has a discrete set of values which can be alternated or switched between.
boolean switch
binary switch
A parameter that has precisely two discrete values which may be switched between. Usually for the boolean parameter these are indicated as '0 or 1' or 'True or False'.
steady state expression
A mathematical expression that describes a steady state situation
equivalence
Term to signify those material or conceptual entities that are identical in some respect within a frame of reference
production
Generation of a material or conceptual entity.
consumption
Decrease in amount of a material or conceptual entity.
encapsulating process
An aggregation of interactions and entities into a single process.
uncertain process
An equivocal or conjectural process, whose existence is assumed but not proven.
omitted process
One or more processes that are not represented in certain representations or interpretations of a model.
logical relationship
Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves.
decarboxylation
A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide.
decarbonylation
Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide
deamination
Removal of an amine group from a molecule, often under the addition of water
transfer of a chemical group
Covalent reaction that results in the transfer of a chemical group from one molecule to another.
transamination
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.
unit of genetic information
Functional entity associated with or derived from a unit of inheritance.
perturbing agent
A material entity that is responsible for a perturbing effect
observable
An entity that can be measured quantitatively
absolute inhibition
Control that precludes the execution of a process.
biological activity
Effect of a biological entity on biological structures or processes.
interaction outcome
Entity that results from the interaction between other entities.
implicit compartment
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.
Control that always triggers the controlled process.
The potential action that a biological entity has on other entities. Example are enzymatic activity, binding activity etc.
positional relationship
The connectedness between entities as related by their positionn
cis
Positional relationship between entities on the same strand (e.g. in DNA), or on the same side.n
trans
Positional relationship between entities on different sides, or strands
One of the two values possible from a boolean switch, which equates to '1', 'on' or 'input'.
One of the two values possible from a boolean switch, which equates to '0', 'off' or 'no input'.
multimer of complexes
Non-covalent association between several independant complexes
multimer of informational molecule segment
Non-covalent association between portions of macromolecules that carry genetic information
multimer of macromolecules
Non-covalent association between several macromolecules
multimer of simple chemicals
Non-covalent association between several simple chemicals
isoinhibition constant
Inhibitory constant for the binding of a given ligand with an isomeric form of an enzyme.n
pseudo-dissociation constant for product
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 substrate
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.
reversible Hill-type enzymatic 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.
modulated reversible Hill-type rate law
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 with one modifier
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) n n n n substraten n n n productn n n n Modifiern n n n Keqn n n n Vfn n n n Ksn n n n Kpn n n n hn n n n Mhalfn n n n alphan n n n <divide/>n n <times/>n n <divide/>n n <times/>n Vf n substrate n n Ks n n n <minus/>n 1 n n <divide/>n product n n <times/>n substrate n Keq n n n n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n n <minus/>n h n 1 n n n n n <plus/>n n <divide/>n n <plus/>n 1 n n <power/>n n <divide/>n Modifier n Mhalf n n h n n n n <plus/>n 1 n n <times/>n alpha n n <power/>n n <divide/>n Modifier n Mhalf n n h n n n n n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n h n n n n n n n
modulated reversible Hill-type rate law with two modifiers
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.n (if < 1 Ma is inhibitor, if > 1 activator)nalpha_2 t: factor accounting for the effect of S and P on the binding of Mbn (if < 1 Mb is inhibitor, if > 1 activator)nalpha_3 t: factor accounting for interaction of Ma to Mb binding to the enzyme (and v. v.). n n n n substrate n n n product n n n ModifierA n n n ModifierB n n n Keq n n n Vf n n n Shalve n n n Phalve n n n h n n n MAhalf n n n alphaA n n n MBhalf n n n alphaB n n n alphaAB n n n <divide/>n n <times/>n n <divide/>n n <times/>n Vf n substrate n n Ks n n n <minus/>n 1 n n <divide/>n product n n <times/>n substrate n Keq n n n n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n n <minus/>n h n 1 n n n n n <plus/>n n <divide/>n n <plus/>n 1 n n <power/>n n <divide/>n ModifierA n MAhalf n n h n n n <power/>n n <divide/>n ModifierB n MBhalf n n h n n n n <plus/>n 1 n n <times/>n alphaA n n <power/>n n <divide/>n ModifierA n MAhalf n n h n n n n <times/>n alphaB n n <power/>n n <divide/>n ModifierB n MBhalf n n h n n n n <times/>n alphaA n alphaB n alphaAB n n <power/>n n <divide/>n ModifierA n MAhalf n n h n n n <power/>n n <divide/>n ModifierB n MBhalf n n h n n n n n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n h n n n n n n
enzymatic rate law for multireactant enzymes
Kinetics of enzyme-catalysed reactions with 2 or more substrates or productsn
enzymatic rate law for modulated unireactant enzymes
Kinetics of enzymes that react with one substance, and whose activity may be positively or negatively modulated.
unmodulated reversible Hill-type rate law
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. n n n n n substraten n n n productn n n n Keqn n n n Vfn n n n Ksn n n n Kpn n n n hn n n n <divide/>n n <times/>n n <divide/>n n <times/>n Vf n substrate n n Ks n n n <minus/>n 1 n n <divide/>n product n n <times/>n substrate n Keq n n n n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n n <minus/>n h n 1 n n n n n <plus/>n 1 n n <power/>n n <plus/>n n <divide/>n substrate n Ks n n n <divide/>n product n Kp n n n h n n n n n n
irreversible Michaelis Menten rate law for two substrates
Enzymatic rate law for an irreversible reaction involving two substrates and one product. nt n n n A n n n B n n n KmA n n n KmB n n n KiA n n n Et n n n kcat n nt nt <divide/>nt ntt<times/>ntt Et ntt kcat ntt A ntt B nt nt ntt<plus/>ntt ntt <times/>ntt KiA ntt KmB ntt ntt ntt <times/>ntt KmB ntt A ntt ntt ntt <times/>ntt KmA ntt B ntt ntt ntt <times/>ntt A ntt B ntt nt nt n nt n
Ordered Bi-Bi mechanism rate law
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. n n n n Sa n n n Sb n n n Pp n n n Pq n n n Keq n n n Vf n n n Vr n n n Kma n n n Kmb n n n Kmp n n n Kmq n n n Kia n n n Kib n n n Kip n n n <divide/>n n <times/>n Vf n n <minus/>n n <times/>n Sa n Sb n n n <divide/>n n <times/>n Pp n Pq n n Keq n n n n n <plus/>n n <times/>n Sa n Sb n n <plus/>n 1 n n <divide/>n Pp n Kip n n n n n <times/>n Kma n Sb n n n <times/>n Kmb n n <plus/>n Sa n Kia n n n n <times/>n n <divide/>n Vf n n <times/>n Vr n Keq n n n n <plus/>n n <times/>n Kmq n Pp n n <plus/>n 1 n n <divide/>n Sa n Kia n n n n n <times/>n Pq n n <plus/>n n <times/>n Kmp n n <plus/>n 1 n n <divide/>n n <times/>n Kma n Sb n n n <times/>n Kia n Kmb n n n n n n <times/>n Pp n n <plus/>n 1 n n <divide/>n Sb n Kib n n n n n n n n n n n n
Ordered Bi-Uni mechanism rate law
Enzymatic rate for a reaction involving two substrates and one product. The substrates A and then B are bound strictly in order. n tn n n Sa n n n Sb n n n P n n n Kma n n n Kmb n n n Kmp n n n Kia n n n Keq n n n Vf n n n Vr n n n <divide/>n n <times/>n Vf n n <minus/>n n <times/>n Sa n Sb n n n <divide/>n P n Keq n n n n n <plus/>n n <times/>n Sa n Sb n n n <times/>n Kma n Sb n n n <times/>n Kmb n Sa n n n <times/>n n <divide/>n Vf n n <times/>n Vr n Keq n n n n <plus/>n Kmp n n <times/>n P n n <plus/>n 1 n n <divide/>n Sa n Kia n n n n n n n n n n
Ordered Uni-Bi mechanism rate law
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. n n n n substrate n n n productp n n n productq n n n Kms n n n Kmq n n n Kmp n n n Kip n n n Keq n n n Vf n n n Vr n n n <divide/>n n <times/>n Vf n n <minus/>n substrate n n <divide/>n n <times/>n productp n productq n n Keq n n n n n <plus/>n Kms n n <times/>n substrate n n <plus/>n 1 n n <divide/>n productp n Kip n n n n n <times/>n n <divide/>n Vf n n <times/>n Vr n Keq n n n n <plus/>n n <times/>n Kmq n productp n n n <times/>n Kmp n productq n n n <times/>n productp n productq n n n n n n n n
Ping Pong Bi-Bi mechanism rate law
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. n n n n Sa n n n Sb n n n Pp n n n Pq n n n Keq n n n Vf n n n Vr n n n Kma n n n Kmb n n n Kmp n n n Kmq n n n Kia n n n Kiq n n n <divide/>n n <times/>n Vf n n <minus/>n n <times/>n Sa n Sb n n n <divide/>n n <times/>n Pp n Pq n n Keq n n n n n <plus/>n n <times/>n Sa n Sb n n n <times/>n Kmb n Sa n n n <times/>n Kma n Sb n n <plus/>n 1 n n <divide/>n Pq n Kiq n n n n n <times/>n n <divide/>n Vf n n <times/>n Vr n Keq n n n n <plus/>n n <times/>n Kmq n Pp n n <plus/>n 1 n n <divide/>n Sa n Kia n n n n n <times/>n Pq n n <plus/>n Kmp n Pp n n n n n n n n n
reversible Iso Uni-Uni
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. n n n n substraten n n n productn n n n Kmsn n n n Kmpn n n n Kiin n n n Vfn n n n Keqn n n n <divide/>n n <times/>n Vf n n <minus/>n substrate n n <divide/>n product n Keq n n n n n <plus/>n n <times/>n substrate n n <plus/>n 1 n n <divide/>n product n Kii n n n n n <times/>n Kms n n <plus/>n 1 n n <divide/>n product n Kmp n n n n n n n n
reversible Uni-Uni
Uni-Uni Reversible Simple Michaelis-Menten
Reversible Michaelis Menten
The reversible equivalent of the Henri-Michaelis-Menten rate law (SBO:0000029). n n n n substrate n n n product n n n Kms n n n Kmp n n n Et n n n kcatp n n n kcats n n n <divide/>n n <times/>n Et n n <minus/>n n <divide/>n n <times/>n kcatp n substrate n n Kms n n n <divide/>n n <times/>n kcats n product n n Kmp n n n n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n n n
Uni-Uni Reversible using Haldane relationship
Uni-Uni
Enzyme catalysed reaction involving one substrate and one product. It is a modification of SBO:0000326 that directly incorporates the equilibrium constant in the rate law.n nt n n n substrate n n n product n n n Kms n n n Kmp n n n Vf n n n Keq n n n <divide/>n n <times/>n Vf n n <minus/>n substrate n n <divide/>n product n Keq n n n n n <plus/>n substrate n n <times/>n Kms n n <plus/>n 1 n n <divide/>n product n Kmp n n n n n n nt n
enzymatic rate law for irreversible allosteric inhibition
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. n n n n substrate n n n Inhibitor n n n V n n n Ks n n n n n n n L n n n Ki n n n <divide/>n n <times/>n V n substrate n n <power/>n n <plus/>n Ks n substrate n n n <minus/>n n n 1 n n n n n <plus/>n n <times/>n L n n <power/>n n <times/>n Ks n n <plus/>n 1 n n <divide/>n Inhibitor n Ki n n n n n n n n n <power/>n n <plus/>n Ks n substrate n n n n n n n n n
enzymatic rate law for mixed-type inhibition of reversible enzymes by mutually exclusive inhibitors
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. n n n n substrate n n n product n n n Inhibitor n n n Kms n n n Kmp n n n Vf n n n Vr n n n Kis n n n Kic n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n Inhibitor n Kis n n n <times/>n n <plus/>n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n 1 n n <divide/>n Inhibitor n Kic n n n n n n n n
enzymatic rate law for simple reversible non-competitive inhibition of unireactant enzymes
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.n n n n n substrate n n n product n n n Inhibitor n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ki n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <times/>n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n 1 n n <divide/>n Inhibitor n Ki n n n n n n n
enzymatic rate law for reversible essential activation
specific activation
Enzymatic rate law where the free enzyme, in the absence of the activator, is unable to bind substrate and has no activity.
compulsory activation
enzymatic rate law for reversible mixed activation
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. n n n n substrate n n n product n n n Activator n n n Kms n n n Kmp n n n Vf n n n Vr n n n Kas n n n Kac n n n <divide/>n n <times/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n Activator n n n <plus/>n Kas n Activator n n <times/>n n <plus/>n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n Kac n Activator n n n n n n n
enzymatic rate law for irreversible substrate activation
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.n n n n n substrate n n n V n n n Ksc n n n Ksa n n n <divide/>n n <times/>n V n n <power/>n n <divide/>n substrate n Ksa n n 2 n n n n <plus/>n 1 n n <divide/>n substrate n Ksc n n n <divide/>n substrate n Ksa n n n <power/>n n <divide/>n substrate n Ksa n n 2 n n n n n n
enzymatic rate law for irrreversible mixed activation
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. n n n n substrate n n n Activator n n n Kms n n n V n n n Kas n n n Kac n n n <divide/>n n <times/>n V n substrate n Activator n n n <plus/>n n <times/>n Kms n n <plus/>n Kas n Activator n n n n <times/>n substrate n n <plus/>n Kac n Activator n n n n n n n
enzymatic rate law for reversible catalytic activation with one 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). n n n n n substrate n n n product n n n Activator n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ka n n n <divide/>n n <times/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n Activator n n n <times/>n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n Ka n Activator n n n n n n
enzymatic rate law for reversible specific activation
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. n n n n substrate n n n product n n n Activator n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ka n n n <divide/>n n <times/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n Activator n n n <plus/>n Ka n n <times/>n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n Activator n n n n n n
enzymatic rate law for irreversible catalytic activation with one 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). n n n n substrate n n n Activator n n n Kms n n n V n n n Ka n n n <divide/>n n <times/>n V n substrate n Activator n n n <times/>n n <plus/>n Kms n substrate n n n <plus/>n Ka n Activator n n n n n n
enzymatic rate law for irreversible specific activation
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. n n n n substrate n n n Activator n n n Kms n n n V n n n Ka n n n <divide/>n n <times/>n V n substrate n Activator n n n <plus/>n n <times/>n Kms n Ka n n n <times/>n n <plus/>n Kms n substrate n n Activator n n n n n n
enzymatic rate law for reversible reactions with competitive inhibition
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. n n n n substrate n n n product n n n Inhibitor n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ki n n n n n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n <sum/>n n i n n n 1 n n n n n n n <divide/>n n <selector/>n I n i n n n <selector/>n Ki n i n n n n n n n n
enzymatic rate law for reversible competitive inhibition by one inhibitor
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. n n n n substrate n n n product n n n Inhibitor n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ki n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n <divide/>n Inhibitor n Ki n n n n n n
enzymatic rate law for reversible empirical allosteric inhibition by one inhibitor
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. n n n n substrate n n n product n n n Inhibitor n n n Vf n n n Vr n n n Kms n n n Kmp n n n n n n n Ki n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n <power/>n n <divide/>n Inhibitor n Ki n n n n n n n n n
enzymatic rate law for reversible substrate inhibition
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. n n n n substrate n n n product n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ki n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n <power/>n n <divide/>n substrate n Ki n n 2 n n n n n n
enzymatic rate law for irreversible substrate inhibition
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.n n n n n substrate n n n Km n n n V n n n Ki n n n <divide/>n n <times/>n V n substrate n n n <plus/>n Km n substrate n n <times/>n Km n n <power/>n n <divide/>n substrate n Ki n n 2 n n n n n n n
enzymatic rate law for reversible unireactant enzyme with a single hyperbolic modulator
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. n'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.n'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.n n n n n substrate n n n product n n n Modifier n n n Kms n n n Kmp n n n Vf n n n Vr n n n Kd n n n a n n n b n n n <divide/>n n <times/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <divide/>n n <times/>n b n Modifier n n n <times/>n a n Kd n n n n n n <plus/>n 1 n n <divide/>n Modifier n Kd n n n <times/>n n <plus/>n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n 1 n n <divide/>n Modifier n n <times/>n a n Kd n n n n n n n n n
enzymatic rate law for irreversible unireactant enzyme with a single hyperbolic modulator
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. n'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.n'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.n n n n n substrate n n n Modifier n n n Km n n n V n n n Kd n n n a n n n b n n n <divide/>n n <times/>n V n substrate n n <plus/>n 1 n n <divide/>n n <times/>n b n Modifier n n n <times/>n a n Kd n n n n n n <plus/>n n <times/>n Km n n <plus/>n 1 n n <divide/>n Modifier n Kd n n n n n <times/>n substrate n n <plus/>n 1 n n <divide/>n Modifier n n <times/>n a n Kd n n n n n n n n n
enzymatic rate law for simple uncompetitive inhibition of reversible unireactant enzymes
Reversible inhibition of a unireactant enzyme by one inhibitor, which binds to the enzyme-substrate complex. The inhibitor is uncompetitive with the substrate.n n n n n substrate n n n product n n n Inhibitor n n n Kms n n n Kmp n n n Vf n n n Vr n n n Ki n n n <divide/>n n <minus/>n n <divide/>n n <times/>n Vf n substrate n n Kms n n n <divide/>n n <times/>n Vr n product n n Kmp n n n n <plus/>n 1 n n <times/>n n <plus/>n n <divide/>n substrate n Kms n n n <divide/>n product n Kmp n n n n <plus/>n 1 n n <divide/>n Inhibitor n Ki n n n n n n n n
stimulator
Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed.
enzymatic catalyst
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.
essential activator
necessary stimulator
A substance that is absolutely required for occurrence and stimulation of a reaction.
non-essential activator
An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity.
standard biochemical potential
The biochemical potential of a substance measured at standard concentrations and under standard conditions.
standard chemical potential
state variable assignment
Assignment of a state or a value to a state variable, characteristic or property, of a biological entity.
spatial measure
The measurable dimensions of an object which are minimally required to define the space that an object occupies.
length
The length of an object is the longest measurable distance between its extremities.
area
The area of an object is a quantity expressing its two-dimensional size, usually part or all of its surface.
volume
A quantity representing the three-dimensional space occupied by all or part of an object.
containment
An entity that is a subset of another entity or object.
inclusion
mass fraction
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.
molal concentration of an entity
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.
molar concentration of an entity
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.
denotement
Term to signify where a material or conceptual entity is represented or denoted by a symbol or by some other abbreviated form.
convenience function
Mathematical function commonly used in biological modeling, which enable simplification of more complex expressions
periodic forcing function
input signal step function
Function that enables the modeling of cyclic inputs with on and off phases, such as the light and dark phases in circadian rhythm. It includes parameters for the 'on' period (Tp), the cycle period (Tc), and the time taken to move or 'ramp' between 'on' and 'off' stages (Tw). Theta0 and Theta1 represent the minimal offset and maximal values of 'on' stage, respectively. Small values of Tw result in step-like changes. Phi is the time of the phase shift offset. In the case of light forcing, Tp represents 'light' period, Tc the cycle period, and Tw the 'twilight' timescale. Theta0 is the light value at the off state, and Theta1 the additional value at the on phase. n n n time n Theta0 n Theta1 n Phi n Tp n Tc n Tw n n <plus/>n Theta0 n n <times/>n 0.5 n Theta1 n n <plus/>n n <minus/>n n <plus/>n 1 n n <tanh/>n n <divide/>n n <minus/>n n <plus/>n time n Phi n n n <times/>n Tc n n <floor/>n n <divide/>n n <plus/>n time n Phi n n Tc n n n n n Tw n n n n n <plus/>n 1 n n <tanh/>n n <divide/>n n <minus/>n n <minus/>n n <plus/>n time n Phi n n n <times/>n Tc n n <floor/>n n <divide/>n n <plus/>n time n Phi n n Tc n n n n n Tp n n Tw n n n n n 1 n n <tanh/>n n <divide/>n n <minus/>n n <minus/>n n <plus/>n time n Phi n n n <times/>n Tc n n <floor/>n n <divide/>n n <plus/>n time n Phi n n Tc n n n n n Tc n n Tw n n n n n n n n
period
The period is the duration of one cycle in a repeating event. [wikipedia]
phase shift
The measurable amount of time by which a periodic or cyclic is shifted or offset from defined reference point.
temporal offset
powered product of Michaelis constant
The product of the Michaelis constants, to the power of their respective stoichiometric coefficients, for either substrates or products. n n Km n x n n n n <product/>n i n 1 n x n nt<power/>nt nt <selector/>nt Km nt i nt nt nt <selector/>nt n nt i nt n n n n
powered product of substrate Michaelis constants
The product of the substrate Michaelis constants, to the power of their respective stoichiometric coefficients. n n Kms n x n n n n <product/>n i n 1 n x n nt<power/>nt nt <selector/>nt Kms nt i nt nt nt <selector/>nt n nt i nt n n n n n
powered product of product Michaelis constants
The product of the product Michaelis constants, to the power of their respective stoichiometric coefficients. n n Km n x n n n n <product/>n i n 1 n x n nt<power/>nt nt <selector/>nt Km nt i nt nt nt <selector/>nt n nt i nt n n n n
stoichiometric coefficient
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.
geometric mean rate constant
The geometric mean turnover rate of an enzyme in either forward or backward direction for a reaction, measured per second. n n k n n n n <root/>n n n n nt<product/>nt i nt 1 nt n nt nt <selector/>nt k nt i nt n n n n
forward geometric mean rate constant
The geometric mean turnover rate of an enzyme in the forward direction for a reaction, measured per second. n n kf n n n n <root/>n n n n nt<product/>nt i nt 1 nt n nt nt <selector/>nt kf nt i nt n n n n
reverse geometric mean rate constant
The geometric mean turnover rate of an enzyme in the reverse direction for a reaction, measured per second. n n kr n n n n <root/>n n n n nt<product/>nt i nt 1 nt n nt nt <selector/>nt kr nt i nt n n n n
basal rate constant
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.
relative basal rate constant
The ratio of the basal activity to the maximal velocity of a reaction. The values range between 0 and 1. n n b n vmax n n <divide/>n b n vmax n n n
relative activity function
Function which ranges from 0 to 1, to describe the relative activation or inhibition of a reaction or process, actual or conceptual.
relative activation function
Function which ranges from 0 to 1, to describe the relative activation of a reaction or process, actual or conceptual.
relative inhibition function
Function which ranges from 0 to 1, to describe the relative inhibition of a reaction or process, actual or conceptual.
number of products
Number of molecules which are generated by an enzyme.
diffusion coefficient
diffusivity
A proportionality constant representing the amount of substance diffusing across a unit area through a unit concentration gradient in unit time. The higher the diffusion coefficient (of one substance with respect to another), the faster they diffuse into each other. This coefficient has an SI unit of mB2/s (lengthB2/time).
amplitude
Amplitude is the magnitude of change in the oscillating variable, with each oscillation, within an oscillating system.
functional domain
A spatial region of an entity that confers a function
binding site
A specific domain of a spatio-temporal entity to which another spatio-temporal entity is able to bind, forming chemical bonds.
catalytic site
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.
transmembrane domain
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.nn
ternary switch
A parameter that has three discrete values which may be alternated between.
relative activity
Value which ranges from 0 to 1, to describe the relative activity of a process or reaction.
genetic suppression
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. n
genetic enhancement
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.
synthetic lethality
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.nn
number of entity pool constituents
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.
mass of an entity pool
The mass that comprises an entity pool.
concentration of enzyme
Amount of enzyme present per unit of volume. The participant role 'enzymatic catalyst' is defined in SBO:0000460.
mass of enzyme
Amount, expressed as a mass, of an enzyme. The participant role 'enzymatic catalyst' is defined in SBO:0000460.
number of an enzyme
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 a reactant
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.
concentration of reactant
The amount of a specific entity pool reactant present per unit of volume. The participant role 'reactant' is defined in SBO:0000010.n
mass of reactant
The amount, expressed as a mass, of a specific reactant entity pool. The participant role 'reactant' is defined in SBO:0000010.
number of a product
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.
concentration of product
The amount of a specific entity pool product present per unit of volume. The participant role 'product' is defined in SBO:0000011.
mass of product
The amount, expressed as a mass, of a specific product entity pool. The participant role 'product' is defined in SBO:0000011.
number of a substrate
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.
concentration of substrate
The amount of a specific entity pool substrate present per unit of volume. The participant role 'substrate' is defined in SBO:0000015.
mass of substrate
The amount, expressed as a mass, of a specific substrate entity pool. The participant role 'substrate' is defined in SBO:0000015.
number of a modifier
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.
concentration of modifier
The amount of a specific modifier entity pool present per unit of volume. The participant role 'modifier' is defined in SBO:0000019.
mass of modifier
The amount, expressed as a mass, of a specific modifier entity pool. The participant role 'modifier' is defined in SBO:0000019.
number of an inhibitor
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.
concentration of inhibitor
The amount of a specific inhibitor entity pool present per unit of volume. The participant role 'inhibitor' is defined in SBO:0000020.n
mass of inhibitor
The amount, expressed as a mass, of a specific inhibitor entity pool. The participant role 'inhibitor' is defined in SBO:0000020.
number of an activator
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.
concentration of activator
The amount of a specific activator entity pool present per unit of volume. The participant role 'activator' is defined in SBO:0000459.
mass of activator
The amount, expressed as a mass, of a specific activator entity pool. The participant role 'activator' is defined in SBO:0000459.
protein complex formation
The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000297).
modular rate law
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:nnv = u f (T/(D + Dreg))nnThe 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,nv, reaction rate,nu, enzyme amount,nT, modular term derived from stoichiometries, metabolite concentrations and reactant constants,nD, modular term for polynomial of scaled concentrations,nDreg, competitive regulation binding states term,nf, modular term for regulation factor.
common modular rate law
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.
direct binding modular rate law
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.
simultaneous binding modular rate law
The simultaneous binding modular rate law makes the assumption that substrates and products can be bound simultaneously, and in any combination.
power-law modular rate law
For the power-law rate law, the denominator is set to be a constant, and the rate law does not saturate.
force-dependent modular rate law
Modular rate law where the D term is given by the square root of the product ofnterms (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.
specific activator
An essential activator that affects the apparent value of the specificitynconstant. Mechanistically, the activator would need to be bound beforenreactant and product binding can take place.
catalytic activator
An essential activator that affects the apparent value of the catalyticnconstant.
binding activator
An essential activator that affects the apparent value of the Michaelisnconstant(s).
partial inhibitor
Substance that, when bound, decreases enzymatic activity to a lower,nnonzero value, without itself being consumed or transformed by thenreaction, and without sterically hindering the interaction betweennreactants. The enzyme-inhibitor complex does retain some basal level of activity.
complete inhibitor
Substance that, when bound, completely negates enzymatic activity, withoutnitself being consumed or transformed by the reaction, and withoutnsterically hindering the interaction between reactants. The inhibitornbinds to all enzyme species independently and with the same affinity,ncompletely inhibiting any enzymatic activity.
ionic permeability
membrane permeability
A parameter that represents the permeability of an ion channel with respect to a particular ion.
probabilistic parameter
A quantitative parameter that represents a probability value, assigned to a specific event.
fraction of an entity pool
A ratio that represents the quantity of a defined constituent entity over the total number of all constituent entities present.
mole fraction
The number of moles of a constituent entity, divided by the total number of all constituent entities present in a system.
basic reproductive ratio
basic reproductive rate
basic reproduction number
An epidemiological term representing the mean number of secondary cases which result from a single infection, where the population under consideration has no immunity, and no intervention is performed.
protein aggregate
A nonspecific coalescence of misfolded proteins which may or may not form a precipitate, depending upon particle size.
metadata representation
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.
systems description parameter
A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation.
qualitative systems description parameter
A non-numerical value that defines certain characteristics of systems or system functions.
boolean logical framework
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.
multi-valued logical framework
Extension of the boolean logical framework which associates a defined number of possible integer values (states) with the variables.
fuzzy logical framework
Extension of the Boolean logical framework which allows intermediate or undetermined values for the logical variables.
annotation
Supplementary information that does not modify the semantics of the presented information.
controlled short label
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.
reference annotation
Additional information that supplements existing data, usually in a document, by providing a link to more detailed information, which is held externally, or elsewhere.
bibliographical reference
An annotation which directs one to information contained within a published body of knowledge, usually a book or scientific journal.
database cross reference
An annotation which directs one to information contained within a database.
db xref
database cross-reference
controlled annotation
Annotation which complies with the full set of defined rules in its construction.
uncontrolled annotation
Annotation which does not comply with, or is not restricted by, any rules in its construction. Examples would include free text annotations.
embedded annotation
Annotation that directly incorporates information into the body of a document.
specific activity
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).
enzyme activity
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).
mass action rate law for first order irreversible reactions, single essential stimulator, continuous scheme
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. n n n k n A n n <times/>n k n A n n n n
mass action rate law for first order irreversible reactions, single essential stimulator, discrete scheme
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. n n n c n A n n <times/>n c n A n n n n
mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator
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, continuous scheme
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. n n n k n R n A n n <times/>n k n R n A n n n n
mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator, discrete scheme
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. n n n c n R n A n n <times/>n c n R n A n n n n
systems description constant
A physical constant that is required in the calculation of a system parameter.
relative permeability
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.
universal gas constant
molar gas constant
ideal gas constant
gas constant
A physical constant featured in many fundamental equations in the physical sciences. It is equivalent to the Boltzmann constant, but expressed in units of energy per temperature increment per mole (rather than energy per temperature increment per particle). It has the value 8.314 J.K-1.mol-1 and is denoted by the symbol R.
Faraday constant
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.
Goldman equation
Goldman-Hodgkin-Katz voltage equation
Expression to determine the equilibrium potential (membrane potential) across a cellular membrane, taking into consideration all the ions on either side of the membrane, and their permeability through the membrane. Permeability values are often recorded as relative permeability, with the most permeable ion being given a reference value of 1. The unit of measure for membrane potential is Volts, though values are typically reported as millivolts (mV).nnThe given formula represents the voltage equation for 'C' monovalent cations, and 'A' monovalent anions, assuming that C is the most permeable, and thereby reporting all other permeabilities as a proportion of the reference value, of 1. 'P' represents the membrane permeability of C (assumed reference molecule, value 1), 'p', the relative permeability of each non-reference molecule, 'C', the external monovalent cation, 'c', the internal monovalent cation concentration, 'A', the external monovalent anion, 'a', the internal monovalent anion concentration, 'R', the universal gas constant, 'T', the temperature in Kelvin, 'F' the Faraday constant. n n n R n n n T n n n F n n n P n n n p n n n C n n n c n n n A n n n a n n n n <divide/>n n n <times/>n R n T n n n F n n n <ln/>n n <divide/>n n <plus/>n n <sum/>n n <times/>n A n p n n n n <sum/>n n <times/>n c n P n n n n n n <plus/>n n <sum/>n n <times/>n a n p n n n n <sum/>n n <times/>n C n P n n n n n n n n n
Nernst potential
reversal potential
The membrane potential at which there is no net flow of an ions across a biological membrane. In a single ion system, this is equal to the equilibrium potential and can be calculated from the Nernst equation. It takes into consideration the charge, z, of the ion, as well as its concentration inside (x) and outside (X) the membrane. n n n R n n n T n n n F n n n z n n n X n n n x n n n n <divide />n n <times />n R n T n n n <times />n z n F n n n n <ln />n n <divide />n n X n n x n n n n n
thermodynamic parameter
Parameters used in the study of thermodynamics, a physical science thatnpertains to the relationship between heat and other forms of energy suchnas 'work done' in material bodies.
enthalpy
A thermodynamic potential whose natural variables are entropy (S) andnpressure (p). The enthalpy of a system, measured in Joules (J), is definednas H = U + pV (where H is enthalpy, U is the internal energy, p is thenpressure at the system boundary, and V is the system volume).nsymbol: H
enthalpy change
Change in enthalpy observed in the constituents of a thermodynamic systemnwhen undergoing a transformation or chemical reaction. This is thenpreferred way of expressing the energy changes to a system at constantnpressure, since enthalpy itself cannot be directly measured. The enthalpynchange is positive in endothermic reactions, negative in exothermicnreactions, and is defined as the difference between the final and initial enthalpy of the system under study: NH = Hf - Hi. The standard unit of measure is J. Symbol: NH
standard enthalpy of formation
The enthalpy change observed in a constituent of a thermodynamic systemnwhen one mole of a compound, in its standard state, is formed from itsnelementary antecedents, in their standard state(s), under standardnconditions (1 bar). The standard unit of measure is kJ/mol.nSymbol: DeltaHf0, DeltafH0
standard enthalpy of reaction
The enthalpy change observed in a constituent of a thermodynamic systemnwhen one mole of substance reacts completely, under standard conditions (1nbar). The standard unit of measure is kJ/mol.nSymbol: DeltaHr0, DeltarH0
entropy
A thermodynamic property which acts as a measure of the state of disordernof a system. Its natural variables are the internal energy (U) and thenvolume (V). It is defined by dS = (1/T)dU + (p/T)dV. The second law ofnthermodynamics states that in an isolated system, natural processes tendnto increase in disorder or entropy. The standard unit of measure is Joulesnper Kelvin (J/K).nsymbol: S
entropy change
The increase or decrease of the entropy of a system. For values greaternthan zero, there is an implied increase in the disorder of a system, fornexample during a reaction, and decreased disorder where the values arenless than zero. The entropy change of a process is defined as the initialnsystem entropy value minus the final entropy value: DeltaS = Sf - Si. Thenstandard unit of measure is J/K.nsymbol: DeltaS
standard entropy of reaction
The entropy change observed in a thermodynamic system when one mole ofnsubstance reacts completely, under standard conditions (1 bar). Thenstandard unit of measure is kJ/(mol K). This can be calculated using thenentropies for products and reactants: DeltaS(reaction)=sum DeltaS (products) - sum DeltaS reactants. The standard unit of measure is kJ/(mol K).nsymbol: DeltaSro
standard entropy of formation
The change in entropy associated with the formation of one mole of ansubstance from its elements in their standard states under standardnconditions (1 bar). The standard unit of measure is kJ/(mol K).nsymbol: DeltaSfo
Gibbs free energy
A thermodynamic potential that measures the useful work obtainable from anthermodynamic system at constant pressure and temperature. Its naturalnvariables are pressure (p) and temperature (T) and the definition is: G =nH - TS. Gibbs free energy is minimised when a system reaches equilibriumnat constant pressure and temperature. The standard unit of measure isnkJ/mol.nsymbol: G
free enthalpy
Gibbs energy
Gibbs function
Gibbs free energy change
The increase or decrease of the Gibbs free energy of a system. During anreaction, this is equal to the change in enthalpy of the system minus thenchange in the product of the temperature times the entropy of the system: nDeltaG = DeltaH - T DeltaSnA negative value indicates that the reaction will be favoured and willnrelease energy. The magnitude of the value indicates how far the reactionnis from equilibrium, where there will be no free energy change. Thenstandard unit of measure is kJ/mol.nsymbol: DeltaG
standard Gibbs energy of formation
The change in Gibbs free energy associated with the formation of 1 mole ofnsubstance from elements in their standard states under standard conditionsn(1 bar). The standard unit of measure is kJ/mol.nsymbol: DeltafG(degree)
standard Gibbs energy of reaction
The Gibbs free energy change observed in a thermodynamic system when onenmole of substance reacts completely, under standard conditions (1 bar).nThe standard unit of measure is kJ/mol.nsymbol: NGK
A duration of time after which a phase shift occurs.
simulation duration
The total length of time over which a model is simulated, where the time scale is indicated within the model simulation.
model time
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.
transcellular membrane influx reaction
A transport reaction which results in the entry of the transported entity, into the cell.
transcellular membrane efflux reaction
A transport reaction which results in the removal of the transported entity from the cell.