Understanding the physical principles and mechanisms underlying biochemical reactions allows to create mechanistic mathematical models of complex biological processes, such as those occurring during neuronal signal transduction. In this chapter we introduce basic concepts of chemical and enzyme kinetics, and reaction thermodynamics. Furthermore we show, how the temporal evolution of a reaction system can be described by ordinary differential equations, that can numerically solved on a computer. Finally we give a short overview of different approaches to modelling cooperative binding to, and allosteric control of, receptors and ion channels.