Introduction

This chapter deals with the complex network of biochemical reactions known as cellular metabolism. Understanding how the different components of this network coordinate their action towards generating coherent pipelines of chemical transformations, how the pipelines themselves are promptly assembled, disassembled and controlled as a function of changing environmental conditions, and how evolutionary adaptation shapes this whole system, constitute fundamental ongoing challenges. These questions are not only intellectually fascinating, but also practically important for many biomedical, engineering, and environmental problems. Because of the complexity of these networks, mathematical models and computer simulations are an essential component of this challenge. This chapter aims at providing a concise and elementary introduction to some basic concepts on mathematical modeling of metabolic networks, with a few examples of recent research applications. Those interested in serious background should refer to classical biochemistry textbooks and recent books on metabolic engineering and computational models of biological networks.

Cellular metabolism and its regulation

In the busy economy of a cell, the balance of resources is essential for survival and reproduction. The main currencies, free energy stored in chemical bonds, and molecular building blocks, can be used for a variety of purposes, from the synthesis of new molecules, to the maintenance of gradients across the membrane; from the capacity to move and find more food, to the production of all components necessary for self-reproduction. This economy involves several hundred to thousands of types of small molecules and biochemical reactions (Fig. 6.1).