Learning Objective: By the end of this section, the learner will be able to compare prokaryotic and eukaryotic RNA polymerases—including their structure, function, locations, required factors, and inhibitors—and relate these differences to clinical pharmacology and disease.

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RNA polymerases synthesize RNA using DNA as a template. Unlike DNA polymerase, RNA polymerase does not require a primer and initiates transcription de novo.

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Prokaryotic RNA Polymerase

Structure

• A single RNA polymerase synthesizes all types of RNA (mRNA, tRNA, rRNA).
• Core enzyme: α₂ββ′
• Holoenzyme: Core + sigma (σ) factor

Function of Sigma Factor

• Recognizes promoter sequences (e.g., −10 Pribnow box, −35 region)
• Required only for initiation
• Released once elongation begins

Termination Factors

• Rho-independent termination: GC-rich hairpin + poly-U tail
• Rho-dependent termination: Requires rho (ρ) helicase

Pharmacologic Inhibition

• Rifampin: inhibits prokaryotic RNA polymerase → blocks initiation (TB treatment)
• Actinomycin D: binds DNA and prevents movement of RNA polymerase → inhibits transcription in both prokaryotes and eukaryotes

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Eukaryotic RNA Polymerases

Eukaryotes use three distinct RNA polymerases, each specialized for certain RNA types.

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RNA Polymerase I

Location: Nucleolus

Products:

• 28S rRNA
• 18S rRNA
• 5.8S rRNA

Note: Does NOT make 5S rRNA

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RNA Polymerase II

Location: Nucleoplasm

Products:

• hnRNA (pre-mRNA)
• mRNA
• Some snRNA

Initiation: Requires transcription factors (TFIID binds TATA box)

Inhibition:

• α-Amanitin (Amanita phalloides mushroom toxin) → severe hepatotoxicity
• Actinomycin D

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RNA Polymerase III

Location: Nucleoplasm

Products:

• tRNA
• 5S rRNA
• Some snRNA

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Comparison Table

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Activity