KPrime#
- class biopax-explorer.biopax.kprime.KPrime(*args, **kwargs)[source]#
Bases:
UtilityClassClass KPrime
Definition: The apparent equilibrium constant, K’, and associated values.
Usage: Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K’ = [ADP][P<sub>i</sub>]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K’ T I pH pMg). This property may have multiple values, representing different measurements for K’ obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc) See http://www.chem.qmul.ac.uk/iubmb/thermod/ for a thermodynamics tutorial.
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
get_comment()Attribute _comment getter
Attribute _ionicStrength getter
Attribute _kPrime getter
get_pMg()Attribute _pMg getter
get_ph()Attribute _ph getter
Attribute _temperature getter
attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_ionicStrength
set_kPrime
set_pMg
set_ph
set_temperature
set_uri_string
to_json
type_attributes
Methods Summary
Attribute _ionicStrength getter
Attribute _kPrime getter
get_pMg()Attribute _pMg getter
get_ph()Attribute _ph getter
Attribute _temperature getter
set_ionicStrength(value)set_kPrime(value)set_pMg(value)set_ph(value)set_temperature(value)set_uri_string(uristr)to_json()Methods Documentation
- get_ionicStrength()[source]#
- Attribute _ionicStrength getter
The ionic strength is defined as half of the total sum of the concentration (ci)
of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M
- get_kPrime()[source]#
- Attribute _kPrime getter
The apparent equilibrium constant K’. Concentrations in the equilibrium constant
equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K’ = [ADP][P<sub>i</sub>]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). (Definition from EcoCyc)
- get_pMg()[source]#
- Attribute _pMg getter
A measure of the concentration of magnesium (Mg) in solution. (pMg =
-log<sub>10</sub>[Mg<sup>2+</sup>])
- get_ph()[source]#
- Attribute _ph getter
A measure of acidity and alkalinity of a solution that is a number on a scale on
which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution. (Definition from Merriam-Webster Dictionary)