Controllable genes behave like analogue computers

In this chapter we have presented a lot of new information and several new technical terms, so a summary might be useful at this point.

  • A gene is a segment of DNA that codes for a protein. The protein is made when the gene is expressed.
  • The first (and crucial) step in expressing a gene is to transcribe it, i.e. to make an RNA replica or "photocopy" (a messenger).
  • Transcription is carried out by an enzyme called RNA polymerase II ("polymerase" for short).
  • Transcription begins when the polymerase is placed on the DNA at the gene's promoter and ends when the polymerase reaches the gene's termination site.
  • Promoters and termination sites are DNA sequences that bind specific groups of proteins.
  • The proteins that bind at the promoter are collectively called the initiation complex. It is the initiation complex that launches the polymerase on to the gene; that is, it initiates transcription.
  • One way of switching off a gene (preventing expression) is to modify the DNA chemically so that the polymerase cannot function.


Initiation complex


Initiation complex gene

Such modification is often irreversible. The modified DNA is usually very compact.

  • Another way of switching off a gene is to introduce a repressor protein that binds to the DNA near the promoter and prevents initiation of transcription. This way of suppressing genes, common in prokaryotes, can be reversed under the right circumstances.
  • A third way of switching off a gene is to alter the components of the initiation complex so that the complex cannot form. This means that transcription cannot be initiated. Again, this form of suppression is reversible.
  • If a gene is not switched off in any of these three ways, then it is expressed. However, transcription usually proceeds at a constant slow rate unless it is accelerated.
  • Acceleration is achieved by the interaction of transcription factors with the initiation complex. There are often several transcription factors for any one gene. Some of them inhibit transcription but most stimulate it. Their effects are additive.
  • Transcription factors are presented to the initiation complex when they bind to DNA regions called enhancers, which in terms of linear measurement might be very distant from the gene.

A controllable gene, expressed at a rate that can vary from zero (when the gene is switched off) to a high maximum (when all the transcription factors are acting in concert), is rather like an analogue computer. Think of the transcription rate, i.e. the rate of production of messenger RNA, as the output. It is continuously variable. Think of the transcription factors as the inputs. Think of the initiation complex as the integrator, summing the inputs and modulating the output accordingly. A eukaryotic cell contains numerous controllable genes - a bank of analogue computers. This analogy might help some readers to picture the control of gene expression more vividly. We shall not develop it further at present, but we shall return to it in the final chapter.

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