RNA Polymerases and General Transcription Factors

What are the three main processes of the central dogma of molecular biology?

Replication (DNA copying), Transcription (DNA to RNA), Translation (RNA to protein).

What enzyme catalyzes transcription?

RNA Polymerase.

What is the function of a gene’s promoter region?

It specifies where transcription begins by providing a recognition site for RNA polymerase.

What are the -10 and -35 consensus sequences in a prokaryotic promoter?

-35 region: TTGACA; -10 region (Pribnow box): TATAAT.

What determines promoter strength in prokaryotes?

The closer the promoter sequence matches the consensus (-10 and -35) and correct spacing (17 bp), the stronger the promoter.

Which DNA strand serves as the transcription template?

The noncoding (template) strand.

In what direction is RNA synthesized?

5′ → 3′ direction.

What are the three main stages of transcription?

Initiation, Elongation, Termination.

What happens during transcription initiation?

RNA polymerase and transcription factors bind to the promoter; DNA unwinds to form the open promoter complex.

What happens during transcription elongation?

RNA polymerase moves along the template strand, adding ribonucleotides to synthesize RNA.

What causes transcription termination?

A termination signal causes RNA polymerase to dissociate from DNA.

What are the subunits of E. coli RNA polymerase?

α (2): binds regulatory sequences; β: forms phosphodiester bonds; β′: binds DNA; σ⁷⁰: recognizes promoter and initiates synthesis.

Where does transcription occur in eukaryotes, and where does translation occur?

Transcription: nucleus; Translation: cytoplasm.

What are the main eukaryotic promoter elements?

-25 TATA box (TATAAAA), -75 CAAT box, and upstream enhancers (-50 to -500).

Which transcription factor binds to the TATA box?

TATA-binding protein (TBP), a component of TFIID.

Which transcription factor bridges TBP and RNA polymerase II?

TFIIB.

Which transcription factor has helicase activity to open the DNA double helix?

TFIIH.

What is the function of the kinase subunit (TFIIK) of TFIIH?

It phosphorylates the carboxyl-terminal domain (CTD) of RNA Pol II, enabling promoter clearance.

Which transcription factors remain bound at the promoter after initiation?

TFIID and TFIIA stay at the TATA box; others dissociate after promoter clearance.

List the roles of general transcription factors for RNA Pol II.

TFIID – DNA binding; TFIIA – anti-repression; TFIIB – bridge between TBP and Pol II; TFIIF – recruits RNA Pol II; TFIIE – opens DNA; TFIIH – helicase & CTD kinase.

What are enhancers?

DNA elements that increase gene expression, act at variable distances (5′, intronic, or 3′) and orientations, often cell-type specific.

How do enhancers differ from promoters?

Promoters define transcription start; enhancers boost expression and can act far from the promoter in either direction.

What are the three eukaryotic RNA polymerases and their products?

RNA Pol I – rRNA (28S, 18S, 5.8S); RNA Pol II – mRNA, snRNA; RNA Pol III – tRNA, 5S rRNA.

What are the promoter characteristics of RNA Pol I and Pol III?

Pol I: CG-rich upstream elements; Pol III: internal promoters within transcribed region.

How does prokaryotic RNA polymerase differ from eukaryotic RNA polymerase?

Prokaryotes: single polymerase + σ factor; Eukaryotes: 3 polymerases, each with ~12 subunits and specific transcription factors.

Which antibiotic inhibits bacterial RNA polymerase β-subunit?

Rifampin – used to treat tuberculosis and meningitis.

Which toxin inhibits RNA polymerase II?

α-Amanitin from Amanita phalloides (death cap mushroom) – halts mRNA synthesis.

Which antibiotic intercalates DNA and prevents elongation by RNA polymerase?

Actinomycin D – used to treat some pediatric cancers like Wilms tumor and sarcoma.