Biological cells are wonderfully robust self-replicating machines that selfishly propagate their DNA until environmental factors such as nutrients limit them. Cells have mastered the use of nanoscale devices in a water environment to fabricate their progeny and perform many critical functions for survival. To understand how cellular machines work, we need to understand the identity and structure of molecular components as well as the network of interactions between these molecules. We also need to study the complex cell functions in which an orchestra of molecules interacts transiently in space and time to cause an observable cellular behavior. Such an integrated systems engineering view of the cell is currently far from our reach; however, there are sufficient tools and techniques in place to provide us with many useful insights into the complex functions of the wonderful machines that are cells.

In this book, we will mainly discuss eukaryotic cells and where possible the details of mouse embryo fibroblasts (3T3 cells) and a human cancer line (HeLa). Because there are over 300 different cell types with important specializations, we have chosen a relatively general cell type to describe what cells do. Many complex functions are missing in fibroblasts and there will be some necessary extrapolations at certain points. 3T3 and HeLa cells do not form multicellular tissues; cell–cell interactions and the higher-order functions of tissues will be discussed in later chapters. The level of integration and complexity needed for the control of multicellular complex functions is at least an order of magnitude greater than for single cell complex functions. We first focus on dissecting the individual complex functions in single cells, because it is then possible to analyze multicellular complex functions in a modular fashion.

In this chapter, we will define the biological cell that we wish to understand and discuss how evolution has made it more robust over the last two billion years (Huxley, 1958). A cutaway diagram of a cell in suspension (Figure 1.1) provides an illustration of the basic organelle compartments that are found in mammalian cells. Compartmentalization of functions is critical for a complex machine like a cell. Each compartment performs some basic function(s) and communicates bidirectionally with the rest of the cell. Often compartments, like the cell itself, are bounded by lipid bilayers, whose hydrophobic cores effectively prevent open movements of ions and charged materials into or out of the compartments.