Glossary of important terms

• RNA polymerase: enzyme that catalyzes the synthesis of RNA strands based upon a DNA template.
• upstream: region of a nucleic acid lying in the direction of the 5’ end
• downstream: region of a nucleic acid lying in the direction of the 3’ end
• transcription start site (TSS): The first transcribed base on the DNA template after the promotor. This is the first base found in the transcribed RNA strand.
• Promotor: sequence of DNA, to which RNA polymerase and associated other proteins like transcription factors bind to initiate transcription. In bacteria such a Promotor usually contains a conserved element called the pribnow box (TATAAT) 10 base pairs upstream from the transcription start site.
• codon: A triplet of RNA base pairs, that corresponds to amino acids in the protein sequence the RNA is translated into.
• Protein coding sequence (CDS): Sequence of RNA, flanked by a start and stop codon, which can be translated into a protein sequence. Consists of codons. Also called the open reading frame (ORF). One RNA molecule can contain more than one coding sequence, in which case the structure is called an operon.
• Operon: Set of protein coding sequences transcribed together on one RNA molecule.
• UTR: Region of RNA downstream of a stop codon or upstream of a start codon in an operon. Not translated into a protein sequence.
• 5’ untranslated region (5’ UTR): Region of RNA upstream the start codon, which is not translated into a protein sequence. This region can contain regulatory structural elements, such as RNA thermometers, as well as binding sites like the ribosome binding site (RBS). In the case of an 5’ UTR existing, it contains the transcription start site.
• 3’ untranslated region (3’ UTR): Region of RNA downstream of the stop codon, which is not translated into a protein sequence. Contains the transcription stop site (TTS), at which transcription is stopped.

Transcription in prokaryotes

During Transcription, an RNA strand is synthesized by the protein complex RNA polymerase from 5’ to 3’ end. This process can be split into 3 main Phases.

Initiation

During this phase, the RNA polymerase complex is assembled at the promotor. After assembly the RNA polymerase escapes the promotor and begins forming a strand of complementary bases to the template DNA. The first base to be incorporated is called the transcription start site (TSS).

Elongation

In the second phase, the RNA polymerase complex moves along a single template DNA strand, adding bases complementary to the DNA template to the 3’ end of the existing RNA strand.

Termination

In the last phase, the RNA polymerase complex binding to the template DNA sequence gets destabilized, either by a protein complex, or by the synthesized RNA molecule, which causes the release of the synthesized RNA molecule and the end of transcription. Figure 1: Simplified schematic overview of prokaryotic operon and gene structure, with added phases of transcription