Transcription in Prokaryotes: E. Coli RNA Polymerase

14 Questions

Which feature is characteristic of a Rho-independent terminator?

G-C rich stem

What is the role of the Rho factor during transcription termination?

Binding to RNA and separating RNA-DNA

What directly stops the chain elongation of RNA during transcription?

Transcription-termination signal

In the hot pursuit model, where does the Rho factor initially bind?

RNA tail

What is a common feature between Rho-independent and Rho-dependent termination?

Dissociation of the RNA-DNA hybrid

During which stages does RNA synthesis occur?

Initiation, elongation, and termination

What is the function of the β subunit in the E. coli RNA polymerase?

ribonucleoside triphosphate binding site

Which part of the promoter is known as the Pribnow box?

-10 sequence

What is the designation for bases immediately following the transcript initiation site?

downstream sequences

Which protein is released after RNA polymerase undergoes a conformational change during transcription initiation?

σ factor

What is the role of rho (ρ) in transcription termination in E. coli?

terminate transcription

Which component of the RNA polymerase holoenzyme is specifically required for the initiation of transcription?

σ factor

Which of these sequences is found at the -35 region of a promoter in E. coli?

-35 sequence

What is a common feature of many terminators that signals the end of transcription?

Hairpin forming sequences

Study Notes

E.Coli RNA Polymerase

The core enzyme consists of α, β, β', and ω subunits.
The holoenzyme is composed of α2, β, β', ω, and σ subunits.

Functions of RNA Polymerase Subunits

α subunit is responsible for assembling the tetrameric core.
β subunit has a ribonucleoside triphosphate binding site.
β' subunit is the DNA template binding region.
σ subunit initiates transcription.

Promoters

E.coli promoters must be at least 12 bp to avoid random occurrence.
Promoters have limited sequence conservation.
Four main regions of promoters are:
- Startpoint
- -10 sequence (Pribnow box)
- -35 sequence
- 17 nucleotide spacer sequence between -10 and -35 sequences

Transcription Unit Numbering

The transcript initiation site is denoted as +1.
Bases preceding the initiation site have minus (-) prefixes and are referred to as upstream sequences.
Bases following the initiation site have plus (+) prefixes and are referred to as downstream sequences.

Starting Transcription

RNA polymerase holoenzyme binds to a promoter region in DNA.
Localized unwinding of DNA strands occurs around the -10 region.
Phosphodiester bonds form between the first few ribonucleotides in the nascent RNA chain.
A conformational change in the enzyme occurs, and the promoter is cleared.
Sigma factor is released, and Nus A protein binds to form an "antitermination complex" for elongation.

Terminating Transcription

Transcription stops when RNA polymerase encounters a terminator.
The RNA product dissociates from the DNA template.
Many terminators are hairpin-forming sequences.
Two types of terminators exist in E.coli:
- Rho-dependent terminators
- Rho-independent terminators

Rho-Independent Termination

Rho-independent terminators have a G-C rich stem and a 7-9 base U-run after the loop.
U-DNA pairing is very weak, allowing dissociation.

Rho-Dependent Termination

The Rho factor is a 46-kD protein that functions as a hexamer.
Rho binds to RNA and has helicase activity.
The Rho-dependent termination process involves the "hot pursuit model":
- Rho binds to the RNA tail and moves along the transcript until it catches the polymerase.
- Rho's helicase activity causes RNA-DNA separation.

Key Points

RNA synthesis occurs in three stages: initiation, elongation, and termination.
RNA polymerases are complex multimeric proteins.
Covalent extension of RNA chains occurs within locally unwound segments of DNA.
Chain elongation stops when RNA polymerase encounters a transcription-termination signal.
Transcription, translation, and degradation of mRNA molecules often occur simultaneously in prokaryotes.