Biological molecular systems work inside living cells. As a cell prototype we consider the prokaryote Escherichia coli. This may be viewed as a small bag of DNA, RNA and proteins, surrounded by a membrane. The bag has a volume of about 1 μm3. This volume varies as the cell grows and divides, and also varies in response to external conditions such as osmotic pressure. The interior of the cell is a very crowded environment, with about 30% to 40% of its weight in proteins and other macromolecules, and only about 60% as water. Further, the water contains a number of salts, in particular K+, Cl- and Mg2+, each of which influences the stability of different molecular complexes.

The dry weight of E. coli consists of 3% DNA, 15% RNA and 80% proteins. The genome of E. coli is a singleDNAmolecule with 4.6 × 106 base pairs (total length of about 1.5 mm). It codes for 4226 different proteins and a number of RNA molecules. However, the information content of the genome is larger than that corresponding to the structure of the coded macromolecules. Important information is hidden and resides in the regulation mechanisms that appear when these proteins interact with the DNA and with each other. Some proteins, called transcription factors, regulate the production of other proteins by turning on or off their genes. Figure 7.1 shows two ways by which a transcription factor can regulate the transcription of a gene. The figure also shows a specific example of a regulatory protein bound to the DNA: the CAP protein.