Upstream of a gene (a DNA sequence that is transcribed) is a region called the promoter. Its sequence is recognized and bound specifically by a protein (in bacteria: sigma factors; in eukaryotes: TATA-box binding protein and transcription factors) that also binds to the RNA polymerase complex and brings it to the transcription start site.
The bacterial promoter consists of two parts, one located 35 nucleotides upstream of the transcription start site (referred to as the -35 region) and one 10 nucleotides upstream (-10 region, also called the TATA box). There are different sigma factors, which are expressed under different growth conditions and recognize different promoter sequences. This is a way of regulating the transcription of genes that are needed under certain growth conditions. There is, for example, a specific sigma factor recognizing promoters upstream of genes that need to be transcribed when the temperature is higher than normal (heat-shock genes).
Eukaryotes, instead of having several sigma factors, use different RNA polymerases to transcribe different types of genes (rRNA, mRNA etc.).
In bacteria, several genes are often transcribed together from one promoter; this arrangement is called an operon. In eukaryotes, on the other hand, each gene is usually transcribed from its own promoter.
2. Why is it so important for organisms to be able to regulate the expression of their genes? Take as examples: i) a multicellular organism, ii) your favorite bacterium - and discuss the different challenges they face.
i) All cells in a multicellular organism have the same set of genetic material (DNA). However, they are specialized in different functions, e.g. different organs, and have to express the right amounts of different proteins in the right places. Furthermore, different proteins are needed during the different stages in the cell cycle, for example when cells are dividing or replicating their DNA.
ii) Bacteria do not differentiate into different cell types, but they need to adjust to their environment, depending on which food source is available (e.g. different kinds of sugar), starvation, temperature etc. Like eukaryotes, they also need to regulate the expression of certain genes during different cell cycle stages.
3. Describe different ways bacteria use to regulate gene transcription, taking the lactose (lac) operon as an example.
Regulation of transcription can be negative, i.e. RNA is transcribed all the time unless repressed by a repressor, or positive, i.e. no RNA is transcribed unless activation occurs by an activator. The E. coli lac operon provide good examples of both these mechanisms (see figure).
