Translation (biology) Study Guide

📖 Core Concepts Translation – cellular process that reads mRNA codons to polymerize a specific amino‑acid chain (protein). Codon – three‑nucleotide mRNA sequence that specifies one amino acid; the mapping is the genetic code (largely universal). Ribosome – two‑subunit machine (eukaryotic 40S + 60S) that positions mRNA, tRNAs, and catalyzes peptide‑bond formation. tRNA – adaptor RNA (70–93 nt) with a 3′‑terminal amino‑acid attachment site and an anticodon that pairs with a codon. Aminoacyl‑tRNA synthetase – enzyme that “charges” tRNA by forming an ester bond between the amino‑acid carboxyl and the tRNA 3′‑OH. Initiation factors (eIFs) – proteins that assemble the 43S pre‑initiation complex, bind the 5′ cap, unwind structure, and deliver the Met‑tRNA\({i}^{Met}\). Elongation factors (eEF1A, eEF2) – bring charged tRNAs to the A‑site and use GTP to translocate the ribosome by one codon. Release factors (eRF1, eRF3) – recognize stop codons, catalyze peptide release, and promote ribosome disassembly. Energy cost – each added residue uses 1 ATP (tRNA charging) + 1 GTP (eEF1A) + 1 GTP (eEF2) ≈ $4n‑1$ high‑energy phosphate bonds for a protein of n amino acids. 📌 Must Remember Start codon: AUG (Met) – most common; UUG & CUG can serve as alternatives in some organisms. Stop codons: UAA, UAG, UGA – recognized by eRF1. Cap‑dependent initiation: eIF4E binds 5′ cap → eIF4G scaffold → eIF4A helicase → 43S complex scans to AUG. Cap‑independent initiation: internal ribosome entry site (IRES) bypasses scanning; used during stress. Translation speed: prokaryotes ≈ 21 aa · s⁻¹; eukaryotes ≈ 6–9 aa · s⁻¹. Error rates: 1 error per 10⁵–10³ codons; mischarging is a rare but possible source of mistranslation. eIF2α phosphorylation → ↓ Met‑tRNA delivery → global translation inhibition (e.g., amino‑acid starvation). 4EBP binds eIF4E → blocks cap‑dependent initiation; phosphorylation of 4EBP releases eIF4E. 🔄 Key Processes Initiation (cap‑dependent) Cap recognition – eIF4E binds 5′ m⁷G cap. Scaffold formation – eIF4G bridges eIF4E, eIF4A, and the 40S subunit. Helicase activity – eIF4A (ATP‑dependent) unwinds secondary structure. Pre‑initiation complex (43S) – 40S + eIF2·GTP·Met‑tRNA\(i^{Met}\) + other eIFs. Scanning – 43S moves 5′→3′ until AUG is in the P‑site. GTP hydrolysis (eIF2) – releases initiation factors; 60S joins → 80S ribosome ready for elongation. Elongation A‑site delivery – eEF1A·GTP brings charged tRNA to the amino‑acyl (A) site. Peptide bond formation – peptidyl‑transferase center (large subunit rRNA) links nascent peptide to the A‑site amino acid. Translocation – eEF2·GTP moves ribosome one codon downstream; A‑site becomes P‑site, P‑site becomes E‑site. E‑site exit – deacylated tRNA leaves the ribosome. Termination & Recycling Stop‑codon entry – eRF1 recognizes UAA/UAG/UGA in the A‑site. Peptide release – eRF1 + eRF3·GTP hydrolysis cleave the ester bond, freeing the polypeptide. Ribosome recycling – ribosome recycling factors split 60S and 40S for new rounds. 🔍 Key Comparisons Cap‑dependent vs. Cap‑independent initiation Cap‑dependent: requires eIF4E, scanning from 5′ end, majority of mRNAs. Cap‑independent: uses IRES, no scanning, favored under stress or viral infection. eIF2·GTP vs. eEF2·GTP eIF2·GTP: delivers Met‑tRNA\(i^{Met}\) to the P‑site (initiation). eEF2·GTP: drives ribosomal translocation after each peptide bond (elongation). Prokaryotic vs. Eukaryotic ribosome speed Prokaryote: 21 aa · s⁻¹ (high throughput). Eukaryote: 6–9 aa · s⁻¹ (more regulation, quality control). ⚠️ Common Misunderstandings “All stop codons are the same.” They differ in context; eRF1 treats them identically, but some antibiotics preferentially block specific stop‑codon recognition. “Only the start codon matters.” The Kozak consensus (eukaryotes) surrounding AUG strongly influences initiation efficiency. “tRNA charging is error‑free.” Aminoacyl‑tRNA synthetases can mischarge; proofreading domains reduce but do not eliminate errors. “Translation stops as soon as a stop codon appears.” Release factors must bind and hydrolyze GTP; the process takes 0.1–0.2 s, allowing a brief pause. 🧠 Mental Models / Intuition “Conveyor‑belt ribosome” – Think of the ribosome as a moving platform: mRNA is the belt, tRNAs are cargo trucks delivering amino acids, and the large subunit is the glue that welds each new truck to the growing chain. “Energy budget per amino acid = 4 high‑energy bonds” – Visualize each residue as costing a “four‑coin” toll (1 ATP + 2 GTP + 1 GTP for recycling). “Scanning as a searchlight” – The 43S complex shines forward from the cap, moving one nucleotide at a time until the light hits the AUG “target.” 🚩 Exceptions & Edge Cases Alternative start codons (UUG, CUG) can initiate translation in certain organisms or viral mRNAs. Mitochondrial genetic code reassigns several codons (e.g., UGA codes for Trp instead of STOP). Antibiotics: chloramphenicol blocks the peptidyl‑transferase center in bacteria; cycloheximide blocks eukaryotic translocation. Internal ribosome entry sites bypass the cap requirement, but not all IRES elements function equally across species. 📍 When to Use Which Choose cap‑dependent initiation when the mRNA has a 5′ m⁷G cap and a strong Kozak sequence. Choose IRES‑mediated initiation for viral RNAs, stress‑responsive transcripts, or when eIF4E is limited. Use eIF2α phosphorylation status as a read‑out for global translation repression (e.g., amino‑acid starvation). Apply antibiotics: chloramphenicol for bacterial studies; cycloheximide to freeze eukaryotic ribosomes in profiling experiments. 👀 Patterns to Recognize “GTP‑hydrolysis → factor release” – every major step (eIF2, eEF2, eRF3) couples GTP hydrolysis to a conformational change and factor dissociation. “Codon‑anticodon perfect match → high fidelity” – mismatches usually trigger proofreading or abortive termination. “High ribosome density → slower elongation” – queueing effects appear in kinetic models and ribosome‑profiling heatmaps. “Stress → selective translation” – look for upstream open reading frames (uORFs) or IRES elements in mRNAs that stay active under eIF2α phosphorylation. 🗂️ Exam Traps Trap: “Only ATP is used in translation.” Why tempting: ATP is needed for tRNA charging. Why wrong: GTP is also hydrolyzed by eIF2, eEF1A, eEF2, eRF3; total cost = $4n‑1$ high‑energy bonds. Trap: “All organisms use the same genetic code.” Why tempting: The code is called “universal.” Why wrong: Mitochondrial and some protozoan genomes have reassigned codons. Trap: “Stop codons never appear in coding regions.” Why tempting: Stop signals termination. Why wrong: Programmed frameshifts and selenocysteine insertion use UGA in a specific context. Trap: “Higher ribosome speed always means more protein.” Why tempting: Faster assembly seems beneficial. Why wrong: Speed can reduce fidelity; eukaryotes balance speed (6–9 aa/s) with quality control. Trap: “Phosphorylation of eIF4E activates translation.” Why tempting: eIF4E is a “starter” factor. Why wrong: It is 4EBP that binds eIF4E; phosphorylation of 4EBP releases eIF4E, not phosphorylation of eIF4E itself.