Cycles, cooperativity, and molecular machines (Chapter 8)

Molecular machines such as transporters, motors, and genome processors underpin much of cell biology, and these in turn must be understood using biochemical cycles. This chapter lays out the basic biophysics of cycles, from rate constants to free energies, and illustrates how cycles are driven to perform biologically useful functions. Starting from simple conformational and binding cycles, the chapter builds up to a simple description of secondary active transport, in which free energy stored in one chemical species is used "pump" another. The phenomenon of "coupling" (or cooperativity), in which one step of a process affects another, plays a key role in the function of molecular machines and can be understood on both a kinetic and free energy basis.