Transcription & Translation
A boards-focused walkthrough of the central dogma — eukaryotic RNA polymerases, mRNA processing, and translation — anchored to the toxins and antibiotics that inhibit each step (α-amanitin/RNA Pol II, rifampin/rpoB, diphtheria & Pseudomonas EF-2, 30S/50S ribosomal antibiotics). Includes two classic vignettes and high-yield mnemonics.
The Central Dogma & Why Boards Test It
DNA → (transcription) → RNA → (translation) → protein. Transcription occurs in the nucleus (eukaryotes): RNA polymerase reads the template (antisense) strand 3'→5' and synthesizes mRNA 5'→3', which is identical to the coding (sense) strand except U replaces T. RNA polymerases have no proofreading. Translation occurs on ribosomes in the cytoplasm, decoding mRNA codons into amino acids.
Step 1 rarely asks the pathway for its own sake — it tests it through inhibitors: toxins (α-amanitin, diphtheria toxin) and antibiotics (rifampin, aminoglycosides, macrolides) that each strike one specific enzyme or ribosomal site. The winning strategy is to memorize which step each agent blocks, plus RNA processing and the genetic code.
- Eukaryotic RNA polymerases: Pol I → rRNA (in nucleolus, most abundant); Pol II → mRNA (+ snRNA, miRNA); Pol III → tRNA + 5S rRNA
- α-amanitin (from Amanita phalloides, death cap) inhibits RNA Pol II → blocks mRNA → hepatotoxicity
- Actinomycin D (dactinomycin) intercalates DNA, blocks transcription; also chemo for Wilms, Ewing, rhabdomyosarcoma
- Prokaryotes: a single RNA polymerase makes all RNA; σ (sigma) factor directs it to the promoter to initiate; transcription & translation are coupled (no nucleus)
- Rifampin inhibits bacterial DNA-dependent RNA polymerase (rpoB β-subunit) → TB & meningococcal prophylaxis; resistance = rpoB mutation; turns secretions red-orange
- Promoter elements: TATA and CAAT boxes (upstream); enhancers/silencers can act at a distance
RNA Polymerases at a Glance
| Polymerase | Makes | Key point / inhibitor |
|---|---|---|
| RNA Pol I | rRNA (most abundant) | In nucleolus |
| RNA Pol II | mRNA, snRNA, miRNA | α-amanitin (death cap) → hepatotoxicity |
| RNA Pol III | tRNA, 5S rRNA | Smallest RNAs |
| Prokaryotic (single) | all RNA | Rifampin (rpoB); σ factor initiates |
Primary transcript (hnRNA / pre-mRNA) is processed before export:
- 5' cap: 7-methylguanosine added to the 5' end → ribosome binding + stability
- 3' poly-A tail: added after cleavage at the AAUAAA signal → stability + nuclear export
- Splicing: introns removed, exons joined by the spliceosome (snRNPs) via a lariat intermediate
- Anti-Smith (anti-Sm, highly specific for SLE) and anti-U1 RNP (MCTD) antibodies target these snRNPs
- Alternative splicing → multiple proteins from one gene (e.g., membrane vs secreted antibody)
- Only mature mRNA (capped, tailed, spliced) is exported to the cytoplasm for translation
- Start codon AUG = methionine (fMet in prokaryotes/mitochondria); "AUG inAUGurates"
- Stop codons UGA, UAA, UAG — no tRNA; recognized by release factors
- Ribosomes: eukaryotic 40S + 60S = 80S; prokaryotic 30S + 50S = 70S
- tRNA sites: A (incoming aminoacyl-tRNA), P (peptidyl/growing chain), E (exit)
- Aminoacyl-tRNA synthetase charges tRNA using ATP → AMP + PPi, and proofreads; wobble occurs at the 3rd codon position
- Peptidyl transferase (large-subunit rRNA = a ribozyme) forms the peptide bond
- Cost = 4 high-energy phosphates per peptide bond (2 to charge tRNA + 2 GTP for elongation)
- Diphtheria toxin & Pseudomonas exotoxin A ADP-ribosylate EF-2 → halt eukaryotic elongation
A family develops severe watery diarrhea, vomiting, and abdominal cramps ~10 hours after eating wild-foraged mushrooms. Symptoms briefly improve, then 2–3 days later one member develops jaundice, coagulopathy, and markedly elevated transaminases — fulminant hepatic failure.
- Diagnosis: Amanita phalloides (death cap) poisoning; toxin = α-amanitin
- Mechanism: inhibits RNA polymerase II → no mRNA → hepatocyte (and renal tubular) death
- Classic clue: delayed, biphasic course (GI phase → apparent recovery → hepatic failure)
- Next best step: aggressive IV fluids/supportive care, activated charcoal, adjunctive silibinin / high-dose penicillin G and N-acetylcysteine; evaluate early for liver transplant if fulminant failure
An unvaccinated child presents with sore throat, low-grade fever, and a gray pseudomembrane over the tonsils/pharynx that bleeds when scraped, plus bull-neck lymphadenopathy. Days later he develops myocarditis and a soft-palate palsy.
- Diagnosis: Diphtheria (Corynebacterium diphtheriae)
- Mechanism: diphtheria toxin ADP-ribosylates EF-2 → blocks eukaryotic translation (elongation) → cardiac/neural cell death; toxin gene is β-prophage (lysogen) encoded
- Same EF-2 target: Pseudomonas exotoxin A
- Next best step: give diphtheria antitoxin immediately (do not wait for cultures) plus antibiotics (penicillin or erythromycin) and supportive care; isolate and update immunization
- Stop codons: UGA = "U Go Away," UAA = "U Are Away," UAG = "U Are Gone"
- Start codon: AUG "inAUGurates" protein synthesis (= Met)
- RNA Pol products: I, II, III → r, m, t RNA (in order of use)
- Ribosome-targeting antibiotics — "Buy AT 30, CCEL at 50":
- 30S: Aminoglycosides (bactericidal), Tetracyclines (static)
- 50S: Chloramphenicol, Clindamycin, Erythromycin/macrolides, Linezolid (+ streptogramins)
- tRNA sites in order: A → P → E ("APE": Aminoacyl, Peptidyl, Exit)
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