In prokaryotes, regulatory proteins are often controlled by nutrient availability. This allows organisms such as bacteria to rapidly adjust their transcription patterns in response to environmental conditions. In addition, regulatory sites on prokaryotic DNA are typically located close to transcription promoter sites — and this plays an important part in gene expression.
For an example of how this works, imagine a bacterium with a surplus of amino acids that signal the turning “on” of some genes and the turning “off” of others. In this particular example, cells might want to turn “on” genes for proteins that metabolize amino acids and turn “off” genes for proteins that synthesize amino acids. Some of these amino acids would bind to positive regulatory proteins called activators. Activator proteins bind to regulatory sites on DNA nearby to promoter regions that act as on/off switches. This binding facilitates RNA polymerase activity and transcription of nearby genes. At the same time, however, other amino acids would bind to negative regulatory proteins called repressors, which in turn bind to regulatory sites in the DNA that effectively block RNA polymerase binding (Figure 3).
The control of gene expression in eukaryotes is more complex than that in prokaryotes. In general, a greater number of regulatory proteins are involved, and regulatory binding sites may be located quite far from transcription promoter sites. Also, eukaryotic gene expression is usually regulated by a combination of several regulatory proteins acting together, which allows for greater flexibility in the control of gene expression.
As previously mentioned, enhancer sequences are DNA sequences that are bound by an activator protein, and they can be located thousands of base pairs away from a promoter, either upstream or downstream from a gene. Activator protein binding is thought to cause DNA to loop out, bringing the activator protein into physical proximity with RNA polymerase and the other proteins in the complex that promote the initiation of transcription (Figure 4).
Different cell types express characteristic sets of transcriptional regulators. In fact, as multicellular organisms develop, different sets of cells within these organisms turn specific combinations of regulators on and off. Such developmental patterns are responsible for the variety of cell types present in the mature organism.
To live, cells must be able to respond to changes in their environment. Regulation of the two main steps of protein production — transcription and translation — is critical to this adaptability. Cells can control which genes get transcribed and which transcripts get translated; further, they can biochemically process transcripts and proteins in order to affect their activity. Regulation of transcription and translation occurs in both prokaryotes and eukaryotes, but it is far more complex in eukaryotes.