Prokaryotic Gene Expression

Transcriptional Control

The major mechanism for controlling protein production in the cell is determined by which genes are transcribed to encode a particular protein. This is important as the structure and function of the cell is determined by the proteins it contains. The cell regulates the proteins and speed of which they are produced by repressing and activating the gene in question.

repressing a gene: the corresponding mRNA is transcribed at a low rate (meaning little to nothing in the cell)

activating a gene: the corresponding mRNA is transcribed at a much higher rate (meaning up to 1000x or more RNA is transcribed)

Purpose of Transcriptional Control...

...in Single-Celled Organisms

Transcription of genes is regulated to adjust to changes in the nutritional and physical environment. The cell will produce only the proteins required for survival and will proliferate under the particular environmental conditions it experiences.

... in Multicellular Organisms

Transcription of genes is regulated to ensure coordination during embryonic development and tissue differentiation. Again, the level of organization is more complex.

Operons are Efficient for Control

Recall that operons are sequences that encode enzymes in a row that are involved in a particular metabolic pathway or proteins that interact to form a large multi-unit protein. This is characteristic of procaryotes, as eukaryotes have their proteins in different regions of the chromosome separated by large uncoded regions called introns. Point being, in E coli, half of the genes are clustered into such operons, with the trp operon coding for five enzymes needed in the biosynthesis of tryptophan, and the lac operon coding for three enzymes needed in the biosynthesis of lactose.

All genes on an operon are coordinately regulated, meaning that they are repressed and activated to the same extent, which is efficient and economic for controlling transcription regulation in bacteria. The regulation happens through RNA polymerase and specific repressor and activator proteins. To initate transcription, RNA polymerase must associate with a sigma factor, most commonly . These sigma factors are not conserved in eukaryotes.

Function of Sigma Factors

Sigma Factors recognize specific DNA sequences as promoters and recruit RNA polymerase which is a lot simpler sounding than that whole eukaryotic preinitiation complex razzmatazz. After transcription is initiated the sigma factor peaces out, or is released from the promoter upstream of the start site.  recognizes the sequence TTGACA (in the -30 region) ...15-17 bps... TATAAT (in the -10 region). On the other hand, recognizes a very difference sequence as it is involved with metabolizing nitrogen. Eg: the regions on the DNA which these sigma factors recognize are diverse.

The E coli Lac Operon Saga

The E coli lac operon exists in a repressed state.

The E coli Lac Operon encodes the three enzymes required to metabolize lactose in the cell. However, the cell much prefers to get its energy from glucose, so the enzymes will only be transcribed if there is a) high lactose and b) low glucose in the cell. Normally, this is not the case, so the lac repressor binds to the operator, blocking the start site, and the promoter is ready for polymerase to bind, no transcription occurs.

De-repressing the lac operon. 

However, when lactose enters the cell in high qualities, it binds to the lac repressor, causing a conformational change and for it to release from the operon. Then binds and recruits the polymerase to the promoter. Transcription occurs, until lactose levels are low once more in the cell, and then the lac repressor will again bind to the lac operator. It should be mentioned though, that transcription levels of the proteins are low for this scenario as glucose (the preferred metabolite) is still present in the cell.

Activating the lac operon. 

If both glucose levels are low in the cell, and lactose levels are high, then something else happens with the operon. cAMP is produced by the low glucose levels in the cell and then binds to CAP (catabolite activator protein) from there, the complex binds to a site upstream of the promoter called the CAP site. The lactose binds to the lac repressor, causing the conformational change and release from the operator, then the polymerase binds to the promoter complexed with . The cAMP and CAP complex greatly stimulate the rate of transcription.