Document Detail


Levels of thermodynamic treatment of biochemical reaction systems.
MedLine Citation:
PMID:  8241405     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Equilibrium calculations on biochemical reaction systems can be made at three levels. Level 1 is the usual chemical calculation with species at specified temperature and pressure using standard Gibbs energies of formation of species or equilibrium constants K. Level 2 utilizes reactants such as ATP (a sum of species) at specified T, P, pH, and pMg with standard transformed Gibbs energies of formation of reactants or apparent equilibrium constants K'. Calculations at this level can also be made on the enzymatic mechanism for a biochemical reaction. Level 3 utilizes reactants at specified T, P, pH, and pMg, but the equilibrium concentrations of certain reactants are also specified. The fundamental equation of thermodynamics is derived here for Level 3. Equilibrium calculations at this level use standard transformed Gibbs energies of formation of reactants at specified concentrations of certain reactants or apparent equilibrium constants K". Level 3 is useful in calculating equilibrium concentrations of reactants that can be reached in a living cell when some of the reactants are available at steady-state concentrations. Calculations at all three levels are facilitated by the use of conservation matrices and stoichiometric number matrices for systems. Three cases involving glucokinase, glucose-6-phosphatase, and ATPase are discussed.
Authors:
R A Alberty
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Publication Detail:
Type:  In Vitro; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Biophysical journal     Volume:  65     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  1993 Sep 
Date Detail:
Created Date:  1994-01-03     Completed Date:  1994-01-03     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  1243-54     Citation Subset:  IM    
Affiliation:
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.
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MeSH Terms
Descriptor/Qualifier:
Adenosine Diphosphate / metabolism
Adenosine Triphosphatases / metabolism
Adenosine Triphosphate / metabolism
Biochemical Phenomena
Biochemistry*
Biophysical Phenomena
Biophysics
Glucokinase / metabolism
Glucose-6-Phosphatase / metabolism
Hydrogen-Ion Concentration
Kinetics
Magnesium / metabolism
Models, Chemical
Thermodynamics*
Chemical
Reg. No./Substance:
56-65-5/Adenosine Triphosphate; 58-64-0/Adenosine Diphosphate; 7439-95-4/Magnesium; EC 2.7.1.2/Glucokinase; EC 3.1.3.9/Glucose-6-Phosphatase; EC 3.6.1.-/Adenosine Triphosphatases
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