Department of Chemistry, Massachusetts Institute of Technology, Room 6-215, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
J Phys Chem B. 2010 Dec 30;114(51):17003-12. doi: 10.1021/jp107337g. Epub 2010 Nov 19.
Biochemical thermodynamics is based on the chemical thermodynamics of aqueous solutions, but it is quite different because pH is used as an independent variable. A transformed Gibbs energy G' is used, and that leads to transformed enthalpies H' and transformed entropies S'. Equilibrium constants for enzyme-catalyzed reactions are referred to as apparent equilibrium constants K' to indicate that they are functions of pH in addition to temperature and ionic strength. Despite this, the most useful way to store basic thermodynamic data on enzyme-catalyzed reactions is to give standard Gibbs energies of formation, standard enthalpies of formation, electric charges, and numbers of hydrogen atoms in species of biochemical reactants like ATP. This makes it possible to calculate standard transformed Gibbs energies of formation, standard transformed enthalpies of formation of reactants (sums of species), and apparent equilibrium constants at desired temperatures, pHs, and ionic strengths. These calculations are complicated, and therefore, a mathematical application in a computer is needed. Rapid-equilibrium enzyme kinetics is based on biochemical thermodynamics because all reactions in the mechanism prior to the rate-determining reaction are at equilibrium. The expression for the equilibrium concentration of the enzyme-substrate complex that yields products can be derived by applying Solve in a computer to the expressions for the equilibrium constants in the mechanism and the conservation equation for enzymatic sites. In 1979, Duggleby pointed out that the minimum number of velocities of enzyme-catalyzed reactions required to estimate the values of the kinetic parameters is equal to the number of kinetic parameters. Solve can be used to do this with steady-state rate equations as well as rapid-equilibrium rate equations, provided that the rate equation is a polynomial. Rapid-equilibrium rate equations can be derived for complicated mechanisms that involve several reactants and various types of inhibitors, activators, and moderators.
生物化学热力学基于水相溶液的化学热力学，但它有很大的不同，因为 pH 值被用作独立变量。使用的是转化后的 Gibbs 能量 G'，这导致了转化后的焓 H'和转化后的熵 S'。酶催化反应的平衡常数被称为表观平衡常数 K'，以表明它们是 pH 值、温度和离子强度的函数。尽管如此，存储酶催化反应基本热力学数据的最有用方法是给出形成的标准 Gibbs 能量、形成的标准焓、电荷和生物反应物（如 ATP）中物种的氢原子数。这使得可以计算所需温度、pH 值和离子强度下反应物（物种总和）的标准转化 Gibbs 能量、标准转化焓和表观平衡常数。这些计算很复杂，因此需要在计算机上进行数学应用。快速平衡酶动力学基于生物化学热力学，因为在决定速率的反应之前的机制中的所有反应都处于平衡状态。通过在计算机中应用 Solve 从机制中的平衡常数表达式和酶位守恒方程推导出产生产物的酶-底物复合物的平衡浓度表达式。1979 年，Duggleby 指出，估计动力学参数值所需的酶催化反应的最小速度数等于动力学参数数。Solve 可以用于稳态速率方程和快速平衡速率方程，只要速率方程是多项式。可以为涉及多个反应物和各种类型的抑制剂、激活剂和调节剂的复杂机制推导出快速平衡速率方程。
