Objective IV

What are the three types of eukaryotic RNA Polymerases?

RNA Polymerase I, II, and III

RNA Polymerase I

transcribes rRNA (28S, 18S, 5.8S)

RNA Polymerase II

transcribes mRNA and some snRNA.

RNA Polymerase III

transcribes tRNA and 5S rRNA.

What is the structure of eukaryotic RNA Polymerase II (Pol II or RNA Pol B)?

A multi-subunit enzyme responsible for synthesizing precursor mRNA (hnRNA). It contains a Carboxyl-Terminal Domain (CTD) that is key for regulation and coordination of RNA processing.

What is the Carboxyl-Terminal Domain (CTD) and its function?

The CTD is a repetitive heptapeptide domain found on the largest subunit of RNA Polymerase II. It gets phosphorylated during transcription and plays a role in transitioning between initiation, elongation, and RNA processing.

What is the role of transcription factors in eukaryotic transcription?

Transcription factors help RNA Polymerase II bind to DNA, recognize the promoter, assemble the transcription initiation complex, and regulate transcription.

What is the core (basal) promoter in eukaryotes?

The minimal DNA sequence required for accurate transcription initiation. It includes the TATA box and the Initiator (Inr) element.

What is the TATA box?

A conserved sequence (TATAAA) located about 25–30 base pairs upstream of the transcription start site. It is recognized and bound by the TATA-Binding Protein (TBP), a component of TFIID.

What is the Initiator element (Inr)?

A core promoter element that overlaps the transcription start site (+1) and can function in transcription initiation, especially in TATA-less promoters.

What are enhancers in eukaryotic transcription?

DNA regulatory elements that increase transcription levels. They function at a distance by binding transcriptional activators and facilitating interaction with the transcription complex.

What are silencers?

Regulatory DNA elements that repress transcription when bound by repressor proteins.

What are response elements?

Specific DNA sequences that respond to external signals (like hormones or stress) by activating or repressing gene transcription through the binding of signal-responsive transcription factors.

What is the TATA-Binding Protein (TBP)?

TBP is a subunit of TFIID that specifically binds to the TATA box in the promoter, initiating the assembly of the transcription pre-initiation complex.

What are TBP-Associated Factors (TAFs)?

TAFs are proteins that associate with TBP in the TFIID complex. They help recognize other core promoter elements and aid in recruiting additional transcription machinery.

What is Transcription Factor IID (TFIID)?

TFIID is a multiprotein complex composed of TBP and TAFs. It binds to the core promoter and is the first general transcription factor to assemble on the DNA.

What is the function of Transcription Factor IIA (TFIIA)?

TFIIA stabilizes the interaction between TBP and the TATA box and assists in recruiting TFIIB to the promoter.

What is the function of Transcription Factor IIB (TFIIB)?

TFIIB binds both DNA and TBP, helps position RNA Polymerase II at the transcription start site, and assists in selecting the transcription start point.

What is the function of Transcription Factor IIE (TFIIE)?

TFIIE recruits TFIIH to the pre-initiation complex and regulates its helicase and kinase activities.

What is the function of Transcription Factor IIF (TFIIF)?

TFIIF binds to RNA Polymerase II and helps it associate with the promoter. It also aids in recruiting TFIIE and TFIIH.

What is the function of Transcription Factor IIH (TFIIH)?

TFIIH is a multifunctional factor with:

• Helicase activity to unwind DNA at the transcription start site.

• Kinase activity to phosphorylate the CTD (carboxyl-terminal domain) of RNA Polymerase II, enabling promoter clearance.

What happens during formation of the closed initiation complex?

General transcription factors and RNA Polymerase II assemble on the DNA promoter without DNA unwinding. TBP binds the TATA box, setting the stage for complex formation.

What happens during formation of the open initiation complex?

TFIIH unwinds the DNA at the transcription start site, creating the transcription bubble. RNA Pol II’s CTD is phosphorylated, triggering the start of transcription.

What is promoter escape?

After CTD phosphorylation, RNA Polymerase II leaves the promoter region, shedding most general transcription factors, and transitions into elongation.

What are elongation factors in eukaryotic transcription?

Elongation factors suppress the pausing or arrest of transcription at “pause sites”, G/C rich regions

What happens during the elongation phase of eukaryotic transcription?

RNA Polymerase II moves along the DNA template strand, synthesizing RNA in the 5′ to 3′ direction. Elongation factors ensure continuous RNA synthesis and help with mRNA processing.

How is eukaryotic transcription terminated?

Elongation factors dissociate, and the CTD is phosphorylated. Process facilitated by termination factors.