To begin transcription, we have our target DNA which we wish to replicate. One of the two strands act a template strand, it can also be called the antisense strand. Thus, the other strand is the non-template strand or the sense strand. There is no reason as to why there are several names to describe the same thing.
Transcription begins when RNA polymerase attaches to the helix at the beginning of the gene where there is a start codon (a complementary triplet codon to the enzyme). RNA polymerase causes the hydrogen bonds between bases to break, breaking the helix so DNA uncoils. Thus, we have the template strand available. RNA polymerase then causes free floating RNA nucleotides to line up alongside the template strand. Remember, where we have adenine, rather than thymine being lined up, we have uracil. Once the RNA nucleotides have been paired up they join together so we begin to have a separated strand of RNA nucleotides (formation of messenger RNA). RNA polymerase continues to move down the template strand continuing the process of breaking apart hydrogen bonds, once the enzyme has passed, the hydrogen bonds begin to reform between the uncoiled parts of DNA. RNA continues to move down the DNA until it reaches the stop codon. The stop codon is like the start codon, but the stop codon causes RNA to detach itself from the stand. We now have messenger RNA which is ready to move out of the nucleus to the ribosomes to begin translation. However, transcription is more complicated than that, there is lots more detail to get into!
In prokaryotic transcription, there is no nucleus so transcription and translation can occur simultaneously and we have the operon. An operon is a group of related genes (structural genes, regulatory genes and control elements.) The control elements consist of a promoter region (where RNA polymerase binds) and an operator region (where repressor proteins bind to.) Multiple genes are transcribed as one transcript, this is called polycistronic RNA (another way to describe messenger RNA.)
There is a flow of genes, anything that moves to the right is described as downstream, anything to the left is upstream. At the upstream end, there is a 5’ promoter, this attracts and binds RNA polymerase. At the 3’ end there is the terminator (stop codon,) which signals the stop point for transcription. Bacterial RNA polymerase is composed of 2 alphas, beta, beta’ and omega subunits with a ratio of 2:1:1. An addition of a sigma subunit converts the enzyme to holoenzyme (a biochemically active compound formed by the combination of an enzyme with a coenzyme.) Core polymerase is when there is no sigma subunit present. Core polymerase binds to DNA non-specifically but as a sigma subunit binds to the core, this directs the polymerase holoenzyme to a gene promoter. In other words, the sigma subunit is required for specificity. If there was just one sigma subunit then all promoters would be occupied all the time, therefore there are multiple sigma units.