Cells and organisms are crowded and complicated (Figure 5-1). Although the macromolecular structures within cells must be self-assembling, they perform this self-assembly following elaborate temporal expression and spatial localization of their individual constituents. The highly energy-requiring events of a living cell require the synthesis of large macromolecules and their specific localization against concentration gradients and through crowded solutions. The flux of energy that moves through the system allows the reactions to be held away from equilibrium, and this is an essential characteristic of living systems. Understanding these processes requires an appreciation of nonequilibrium thermodynamics, a situation that can be sustained when energy is constantly added, as it is during life.
In chemistry one of the most powerful, unifying concepts is equilibrium thermodynamics, the principle that allows a prediction with confidence that ice left at room temperature will melt and that water put in a freezer will become ice. Under any given set of conditions, a chemical system will tend to change its properties, including temperature, pressure, and concentration of reactive chemical species, toward a particular stable state called “equilibrium.” If the system is perturbed slightly away from its equilibrium state, it will robustly return to equilibrium. If the system is left alone, it will remain at equilibrium indefinitely. There are excellent, accurate mathematical formalisms for calculating and predicting equilibrium states of even