Transcription: RNA Synthesis

Transcription Overview - Blueprinting Life's Code

• Core Process: Selective synthesis of RNA from a DNA template strand.
• Key Enzyme: DNA-dependent RNA Polymerase (RNAP); no primer needed.
• Synthesis Direction: New RNA chain grows exclusively 5' → 3'.
• DNA Template Strand: Antisense strand, read by RNAP in the 3' → 5' direction.
• DNA Coding Strand: Sense strand; its sequence matches RNA (Uracil replaces Thymine).
• Fundamental Stages: Initiation at promoter, Elongation, Termination at signal.

  ⭐ Transcription is the primary regulatory point for gene expression. oka

Prokaryotic Transcription - Bacterial RNA Show

• Enzyme: DNA-dependent RNA Polymerase (RNAP).
  • Holoenzyme: $\alpha_2\beta\beta'\omega\sigma$ (sigma for initiation).
  • Core enzyme: $\alpha_2\beta\beta'\omega$ (for elongation).
• Promoter Elements: Recognized by $\sigma$ factor.
  • -10 sequence (Pribnow box: TATAAT).
  • -35 sequence (TTGACA).
• Process: No primer needed.

• Inhibitor: Rifampicin (binds $\beta$ subunit). 📌 RNA Pol inhibited by Rifampicin.

⭐ The $\sigma$ factor is crucial for promoter specificity in prokaryotic transcription, dissociating after initiation.

Eukaryotic Transcription - Complex RNA Symphony

• RNA Polymerases (RNAPs) & Location:
  • RNAP I: rRNA (28S, 18S, 5.8S) - Nucleolus.
  • RNAP II: mRNA, snRNA, miRNA - Nucleoplasm. Highly sensitive to α-amanitin.
  • RNAP III: tRNA, 5S rRNA, U6 snRNA - Nucleoplasm.
• Promoter Elements: Core (TATA box, Inr, DPE, BRE) & Proximal (CAAT box, GC box).
• General Transcription Factors (GTFs): e.g., TFIID (contains TATA-Binding Protein - TBP), TFIIH (helicase & kinase activity).
• Regulatory Elements: Enhancers & Silencers (distal, position/orientation-independent).
• Chromatin Remodeling: Histone modifications (e.g., acetylation, methylation) essential for access.
• RNA Processing (Co-transcriptional): 5' capping (7-methylguanosine), 3' polyadenylation (poly-A tail), Splicing (introns removed by spliceosome).

⭐ α-Amanitin, a toxin from Amanita phalloides (death cap mushroom), potently inhibits RNA Polymerase II, halting mRNA synthesis. At higher concentrations, it also inhibits RNA Pol III.

RNA Processing - Post-Transcriptional Tailoring

• Eukaryotic hnRNA (pre-mRNA) tailored to mature mRNA.
• 5' Capping: 7-methylguanosine (7-mG) added; 5'-5' triphosphate linkage.
  • Protects, aids ribosome binding.
• Splicing: Introns removed, exons joined by spliceosome (snRNPs: U1, U2, U4, U5, U6).
  • Consensus sites: GU (5' splice), AG (3' splice).
  • Alternative splicing ↑ protein diversity.
• 3' Polyadenylation: Poly(A) tail (~200-250 A's) by poly(A) polymerase.
  • Signal: AAUAAA.
  • Enhances stability, export, translation.

⭐ Systemic Lupus Erythematosus (SLE) patients often have autoantibodies against spliceosomal snRNPs (e.g., anti-Sm, anti-RNP).

Transcription Inhibitors - Silencing the Message

• Rifampicin: Binds prokaryotic RNA Pol (β-subunit), blocks initiation. For TB. 📌 "R for Rifampicin, R for RNA Pol".
• Actinomycin D: Intercalates DNA, stalls RNA Pol (prokaryotes & eukaryotes). Anticancer.
• α-Amanitin: Inhibits eukaryotic RNA Pol II (mRNA synthesis). From Amanita phalloides.

  ⭐ α-Amanitin specifically inhibits RNA Polymerase II, halting mRNA synthesis and leading to severe hepatotoxicity.

• Fidaxomicin: Inhibits bacterial RNA Pol; treats C. difficile infection.

High‑Yield Points - ⚡ Biggest Takeaways

• Eukaryotic RNA Polymerases: Pol I (major rRNAs), Pol II (mRNA, snRNA), Pol III (tRNA, 5S rRNA).
• Single Prokaryotic RNA Polymerase needs sigma (σ) factor for promoter recognition.
• Key promoter elements: Pribnow box (prokaryotes, -10), TATA box (eukaryotes, -25).
• Transcription is 5' → 3', reads template 3' → 5'; no primer is needed.
• Key inhibitors: Rifampicin (prokaryotic RNA Pol), α-amanitin (eukaryotic RNA Pol II).
• mRNA sequence matches coding strand (U for T), complementary to the template DNA strand.