Regulation of Gene Activity in Prokaryotes

List differences between gene regulation in prokaryotes and eukaryotes.

In eukaryotes, genes can be switched "on" and "off." In prokaryotes, however, genes are rarely switched off completely- rather, they will transcribe at a low, basal level.

Another difference between prokaryotes and eukaryotes is that in prokaryotes, transcription and translation occur at the same time whereas in eukaryotes they occur separately. Also, prokaryotes have polycistronic mRNA- mRNA that code for multiple proteins- whereas eukaryotes only have monocistronic mRNA that code for one protein at a time. These have further implications in gene regulation, as we shall see.

Understand the effect of and reasons for gene regulation.

The reasons for gene regulation are simple: to make sure that cells have the proteins they need when they need them and don't have an excess of proteins that they don't need. Gene regulation helps to achieve this.

List four ways that a cell can control the proteins it makes.

Transcriptional control- controlling when and how much of a gene is transcribed.
RNA processing control- controlling the splicing and other modifications to the mRNA. I *think* this probably happens more in eukaryotes as transcription and translation do not occur simultaneously.
Translational control- controlling which mRNA get translated.
Post-translational control- controlling the activity of a protein that has already been translated. This can be done by adding phosphate groups etc.

Describe the basic principles of coordinate regulation, catabolic vs. anabolic pathways, and positive vs. negative regulation.

Coordinate regulation refers to the simultaneous transcription of all of the proteins needed for a particular pathway. For example, let's say that degradation of a particular molecule requires enzymes A, B and C. Since all of them are needed or not needed at the same time, you are likely to find polycistronic mRNA in prokaryotic cells that encodes all three enzymes.

Catabolic pathways are those in which larger molecules are broken down into smaller ones, and anabolic pathways are those in which smaller molecules are combined to form larger ones. In catabolic pathways, often the availability of the larger molecule to be degraded determines whether or not the enzymes needed are synthesised. In anabolic pathways, the reverse happens: the final product tends to regulate the synthesis of the enzymes. I think the final product here also tends to decrease the synthesis of anabolic enzymes- after all if you already have a lot of final product, you probably don't need too much more.

Positive and negative regulation depends on whether activators or repressors are used. In positive regulation, an activator binds to the DNA, increasing the transcription of the gene. This may be by making the promoter site more susceptible to binding by DNA polymerase. In negative regulation, a repressor binds to the DNA, decreasing the transcription of the gene.

Describe the tryptophan operon of E. coli and its negative regulation.

The tryptophan operon codes for the synthesis of enzymes that produce tryptophan. This is an example of an anabolic pathway, since tryptophan is being produced by smaller molecules. Like many anabolic pathways, the end product (tryptophan) controls the synthesis of enzymes- in this case, it decreases the synthesis of enzymes so as to prevent over-production of tryptophan.

The regulation of the tryptophan operon is also an example of negative regulation. The tryptophan repressor, TrpR, can bind to the DNA in order to stop the transcription of enzymes that produce tryptophan. TrpR binds to the DNA when tryptophan is bound to it. In this case, tryptophan is known as a corepressor, as it causes the repressor to bind to the DNA. (There are also inducers, which stop repressors from binding to DNA. I'll talk about one of these in a later post.)

Define the terms operon, promoter, operator, repressor and polycistronic mRNA.

I'm not really sure how to define "operon," but it seems to be a section of DNA that has a promoter, an operator and several genes that usually code for enzymes in the same pathway. Operons tend to produce polycistronic mRNA- mRNA that can code for multiple different proteins.

A promoter is the place where the RNA polymerase binds to during the transcription of mRNA.

An operator is the place where repressors or activators bind in order to prevent or induce transcription of a gene.

A repressor is a molecule that prevents the transcription of DNA when it is bound.