Overview

This and the following two chapters are focused on analyzing and simulating chemical systems. These chapters will introduce basic concepts of thermodynamics and kinetics for application to biochemical systems, such as biochemical synthesis, cellular metabolism and signaling processes, and gene regulatory networks. Although we have seen examples of chemical kinetics in previous chapters, notably in Sections 2.3 and 2.4, in those examples we developed the expressions governing the chemistry more from intuition than from a physical theory. One of the primary goals here will be to develop a formal physical/chemical foundation for analyzing and simulating complex biochemical systems.

As is our practice throughout this book, these concepts will be applied to analyze real data (and understand the behavior of real systems) later in this chapter and elsewhere. Yet, because the rules governing the behavior of biochemical systems are grounded in thermodynamics, we must begin our investigation into chemical systems by establishing some fundamental concepts in chemical thermodynamics. The concept of free energy is particularly crucial to understanding thermodynamic driving forces in chemistry. We will see that both a physical definition and an intuitive understanding of free energy require physical definitions and intuitive understandings of temperature and entropy. All of this means that this chapter will begin with some abstract thought experiments and derivations of physical concepts.

Temperature, pressure, and entropy

Microstates and macrostates

All thermodynamic theory arises from the fact that physical systems composed of many atoms and/or molecules attain a large number (often a practically infinite number) of microstates under defined macroscopic conditions, such as temperature, pressure, and volume.