Transcription

 
Transcription is the process where a gene (DNA) is copied into single-stranded RNA. The enzyme responsible for this process is called RNA polymerase. (DNA polymerase is the enzyme that copies DNA during DNA replication. They are very different enzymes even though they carry out similar reactions.)

Transcription can be divided into three steps: initiation, elongation, and termination. It's easiest to describe the process in bacteria because it's simpler than eukaryotic transcription. The basics are the same in all species.

The bacterial enzyme is called the RNA polymerase holoenzyme because it's actually a complex of RNA polymerase and an activator protein. The initiation step involves assembling a transcription initiation complex at the beginning of the gene. The site of initiation is called the promoter.

The first thing that happens is that RNA polymerase binds to any old sequence of DNA then it slides along the DNA looking for a promoter sequence. The non-specific binding of E. coli RNA polymerase holoenzyme is weak and it dissociates after about three seconds. However, during that time it can slide about 2000 base pairs looking for a promoter sequence. This one-dimensional search allows it to find the start of a gene and initiate transcription much more quickly than if it had to bind directly to a promoter.

Promoters have specific DNA sequences that are recognized by the activator protein. Recall that the activator protein is part of the hololenzyme complex. In E. coli the bound activators are called σ (sigma) factors. Different σ factors recognize different promoters. In other species the activator proteins may bind to the promoter first and the RNA polymerase will encounter it when it slides along DNA. The net effect is the same whether the activator binds first to DNA or to the promoter: a transcription initiation complex assembles at the promoter.
The actual initiation event requires opening the double-stranded DNA to make a transcription bubble. Then the first few nucleotides of RNA are synthesized by copying one of the strands of DNA.

At this point the activator protein releases the RNA polymerase, which is now tightly bound to the transcription bubble. Various elongation factors join the complex and transcription proceeds along the gene copying one of the strands into RNA. As the complex moves the RNA unwinds behind the RNA polymerase and the DNA reforms a double helix. The transcription bubble moves along the gene. In the example shown below the major elongation factor (NusA) is binding to RNA polymerase as the σ factor is ejected.

Note that the shift from initiation complex to elongation complex is a crucial step in initiation. The activation protein is tightly bound to the promoter and the complex would not be able to leave the promoter if it didn't dissociate from the activator protein (σ factor, in the case of E. coli).

At the end of the gene, the elongation complex encounters a specific termination signal where specific termination factors catalyze the dissociation of RNA polymerase from DNA and the completed RNA is released.

Whether or not a gene is transcribed depends on the promoter sequence. If there's an activator protein in the cell that binds to that promoter then the gene will be transcribed. The rate of transcription will depend on how much of the activator protein is present because the more activator there is the more quickly it will find and bind to the promoter.

The rate of transcription will also depend on the strength of the promoter. If the promoter sequence is a perfect match to the ideal binding site of the activator then the gene will be transcribed often. On the other hand, if the promoter sequence is similar to the ideal binding site but not a perfect match then it will be transcribed less often because the activator won't bind as tightly. Selection will favor the appropriate promoter strength—not all promoters are ideal binding sites because not all genes need to be transcribed at maximum rate.