A major theme of molecular genetics is the central dogma, which states that genetic information flows from DNA to RNA to proteins (see Figure 8.14). Although the central dogma provided a molecular basis for the connection between genotype and phenotype, it failed to address a critical question: How is the flow of information along the molecular pathway regulated?

Consider E. coli, a bacterium that resides in your large intestine. Your eating habits completely determine the nutrients available to this bacterium: it can neither seek out nourishment when nutrients are scarce nor move away when confronted with an unfavorable environment. But E. coli makes up for its inability to alter the external environment by being internally flexible. For example, if glucose is present, E. coli uses it to generate ATP; if there’s no glucose, it uses lactose, arabinose, maltose, xylose, or any of a number of other sugars. When amino acids are available, E. coli uses them to synthesize proteins; if a particular amino acid is absent, E. coli produces the enzymes needed to synthesize that amino acid. Thus, E. coli responds to environmental changes by rapidly altering its biochemistry. This biochemical flexibility, however, has a high price. Constantly producing all the enzymes necessary for every environmental condition would be energetically expensive. So how does E. coli maintain biochemical flexibility while optimizing energy efficiency?

The answer is gene regulation. Bacteria carry the genetic information for synthesizing many proteins, but only a subset of that genetic information is expressed at any time. When the environment changes, new genes are expressed, and proteins appropriate for the new environment are synthesized. For example, if a carbon source appears in the environment, genes encoding enzymes that take up and metabolize that carbon source are quickly transcribed and translated. When that carbon source disappears, the genes that encode the enzymes are shut off.

Multicellular eukaryotic organisms face a different challenge. Individual cells in a multicellular organism are specialized for particular tasks. The proteins produced by a nerve cell, for example, are quite different from those produced by a white blood cell. But although they differ in shape and function, a nerve cell and a blood cell still carry the same genetic instructions. A multicellular organism’s challenge is to bring about the specialization of different cell types that have a common set of genetic instructions (the process of development). This challenge is met through gene regulation: all of an organism’s cells carry the same genetic information, but only a subset of genes are expressed in each cell type. Genes needed for other cell types are not expressed. Gene regulation is therefore the key to both unicellular flexibility and multicellular specialization, and it is critical to the success of all living organisms.

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The mechanisms of gene regulation were first investigated in bacterial cells, in which the availability of mutants and the ease of laboratory manipulation made it possible to unravel those mechanisms. When the study of gene regulation mechanisms in eukaryotic cells began, eukaryotic gene regulation seemed very different from bacterial gene regulation. However, as more and more information has accumulated about gene regulation, a number of common themes have emerged. Today, many aspects of gene regulation in bacterial and eukaryotic cells are recognized to be similar. Before examining specific elements of bacterial and eukaryotic gene regulation, we will briefly consider some themes of gene regulation common to all organisms.