Bacterial and Eukaryotic Transcription Introduction

Vocabulary terms based on the transcription process in bacteria, including promoter regions, polymerase subunits, and termination mechanisms.

Promoter

A DNA sequence located upstream of the RNA coding region that identifies the beginning of a gene and sets the directionality of transcription, though it is not itself transcribed.

$+1$ site

The start site of transcription identifying the first base used to produce the RNA transcript.

RNA coding region

The region of DNA that is literally converted into an RNA molecule during the transcription process.

Terminator region

A sequence that signals the stopping of transcription and the release of the RNA produced.

Core polymerase

The bacterial RNA polymerase complex consists of two $\alpha$, two $\beta$, and an $\omega$ subunit, which is responsible for the actual building of the RNA molecule.

Sigma factor ($\sigma$)

A subunit of the bacterial RNA polymerase holoenzyme responsible for promoter recognition, binding to specific regions, and orienting the machinery at the correct strand.

Initiation

The first step of transcription involving the recognition of the promoter and the assembly of RNA polymerase machinery at the correct location.

$-10$ consensus sequence

A promoter region typically containing the sequence $TATAAT$, which is essential for sigma factor binding.

Pribnow box

Another name for the bacterial $-10$ consensus sequence that allows RNA polymerase to face the correct way during binding.

Upstream elements

DNA sequences located approximately $-40$ to $-60$ nucleotides away from the transcription start site in bacteria that play a role in regulating transcription rate.

De novo

A term describing the ability of RNA polymerase to start the synthesis of an RNA transcript without a primer.

Triphosphate form

The chemical state of the very first nucleotide at the beginning of every RNA transcript, which retains all three phosphate groups.

Elongation

The phase of transcription where the core enzyme adds nucleotides at a rate of about $40$ nucleotides per second while unwinding and rewinding the DNA helix.

Intrinsic termination

Also known as Rho-independent termination, this process occurs when the RNA molecule's own sequence triggers cleavage and termination through physical strain.

Inverted repeat sequence

A DNA sequence near the end of a gene that, when transcribed, forms a complementary stem-loop structure in the RNA molecule.

Hairpin structure

A physically rigid stem-loop formed by the RNA transcript that destabilizes the DNA-RNA hybrid to cause the termination of transcription.

Rho-dependent termination

A termination mechanism requiring a specific protein factor to bind to the RNA and separate the RNA-DNA hybrid.

Rho protein ($\rho$)

A helicase protein that binds to the RNA transcript at the rut site and travels toward the polymerase to denature the RNA-DNA hybrid.

Rut site

Standing for Rho utilization site, this is the sequence in the RNA molecule that the Rho protein identifies and binds to.