The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.

Transcription of prokaryotic genes in an operon is regulated by two types of DNA binding proteins known as activators and repressors. Activators bind to the promoter, the site of transcription initiation, and aid in the binding of RNA polymerase, the key enzyme involved in transcription. Repressors bind to operators, short regulatory sequences in the operon between the promoter and the genes, and inhibit the binding of RNA polymerase to the promoter.

A structural pre-requisite for activators and promoters is that they should be able to exist in two alternate conformations, one where they can bind to the DNA and one where they cannot. Another characteristic feature specific to activators is that they have two binding surfaces to simultaneously bind to both RNA polymerase and DNA. This recruitment of the two molecules brings the polymerase closer to the promoter and aids in its binding. Activators have no catalytic role to play in transcription and their function is limited to facilitating the binding of the enzyme and DNA. In the absence of an activator, RNA polymerase can still bind to DNA and show low levels of expression. If a repressor is present in this system, then the basal expression of that gene is prevented.

Regulation of the expression of prokaryotic genes is largely dependent on the nutrient availability and requirements of the organisms. These nutrients control the binding of activators and repressors to the operon and ensure that only the required set of genes is expressed. For example, the presence of tryptophan in a cell leads to its binding to a repressor which prevents the transcription of the trp operon and subsequent production of tryptophan.