🧱 Translation (Protein Synthesis)
Translation Overview
Translation is the process by which the mRNA sequence is decoded to synthesize a specific polypeptide (protein).
- Occurs at ribosomes in the cytoplasm (or on rough ER for secretory proteins).
- Direction: 5'→3' on mRNA; polypeptide grows from N-terminus → C-terminus.
- Requires: mRNA, tRNAs, ribosomes, amino acids, ATP/GTP, protein factors.
Ribosomes
Ribosomes are the molecular machines of translation. Composed of two subunits — each made of rRNA + proteins.
| Component | Prokaryotes | Eukaryotes |
|---|---|---|
| Whole ribosome | 70S | 80S |
| Large subunit | 50S (23S rRNA + 5S rRNA + ~31 proteins) | 60S (28S + 5.8S + 5S rRNA + ~49 proteins) |
| Small subunit | 30S (16S rRNA + ~21 proteins) | 40S (18S rRNA + ~33 proteins) |
NOTE
S = Svedberg unit (sedimentation coefficient); subunit S values are not additive because they reflect shape and density, not just mass.
Ribosome Sites (A, P, E)
| Site | Name | Function |
|---|---|---|
| A site | Aminoacyl site | Receives incoming aminoacyl-tRNA (aa-tRNA) |
| P site | Peptidyl site | Holds tRNA carrying the growing polypeptide chain |
| E site | Exit site | Holds deacylated (empty) tRNA before it exits the ribosome |
TIP
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Translation Overview
Translation is the process by which the mRNA sequence is decoded to synthesize a specific polypeptide (protein).
- Occurs at ribosomes in the cytoplasm (or on rough ER for secretory proteins).
- Direction: 5'→3' on mRNA; polypeptide grows from N-terminus → C-terminus.
- Requires: mRNA, tRNAs, ribosomes, amino acids, ATP/GTP, protein factors.
Ribosomes
Ribosomes are the molecular machines of translation. Composed of two subunits — each made of rRNA + proteins.
| Component | Prokaryotes | Eukaryotes |
|---|---|---|
| Whole ribosome | 70S | 80S |
| Large subunit | 50S (23S rRNA + 5S rRNA + ~31 proteins) | 60S (28S + 5.8S + 5S rRNA + ~49 proteins) |
| Small subunit | 30S (16S rRNA + ~21 proteins) | 40S (18S rRNA + ~33 proteins) |
NOTE
S = Svedberg unit (sedimentation coefficient); subunit S values are not additive because they reflect shape and density, not just mass.
Ribosome Sites (A, P, E)
| Site | Name | Function |
|---|---|---|
| A site | Aminoacyl site | Receives incoming aminoacyl-tRNA (aa-tRNA) |
| P site | Peptidyl site | Holds tRNA carrying the growing polypeptide chain |
| E site | Exit site | Holds deacylated (empty) tRNA before it exits the ribosome |
TIP
Think of translation as an assembly line: new amino acids enter at A, peptide transfers and chain grows at P, empty tRNA exits at E. Movement is always A→P→E.
Activation of Amino Acids (Aminoacylation)
Before translation can begin, each amino acid must be activated (attached to its cognate tRNA).
- Amino acid + ATP → aminoacyl-AMP + PPi (by aminoacyl-tRNA synthetase).
- Aminoacyl-AMP + tRNA → aminoacyl-tRNA (aa-tRNA) + AMP.
- Net: 2 ATP equivalents consumed per amino acid activation (ATP → AMP = 2 high-energy bonds).
- Each amino acid has its own specific aminoacyl-tRNA synthetase.
- These enzymes ensure fidelity of the genetic code (correct aa matched to correct tRNA).
Steps of Translation
1. Initiation
Prokaryotic initiation:
- Small subunit (30S) + initiation factors (IF-1, IF-2, IF-3) bind mRNA.
- Shine-Dalgarno sequence: purine-rich sequence (~AGGAGG) on mRNA, ~5-10 nt upstream of AUG start codon. Complementary to 3' end of 16S rRNA → positions ribosome at AUG.
- fMet-tRNAᶠᴹᵉᵗ (initiator tRNA; carries N-formyl methionine) binds directly to P site at AUG.
- IF-3 prevents premature association of large subunit.
- GTP hydrolysis → IFs released → 50S subunit joins → 70S initiation complex formed.
Eukaryotic initiation:
- Small subunit (40S) + eIFs (eukaryotic initiation factors) + Met-tRNAᵢᴹᵉᵗ form a pre-initiation complex.
- Complex scans mRNA from 5' cap until it finds AUG.
- Kozak sequence: GCCRCCAUGG (R = purine); context around AUG that determines initiation efficiency.
- 60S subunit joins → 80S initiation complex.
- Met (not fMet) initiates eukaryotic translation.
NOTE
In eukaryotes, the initiator Met is not formylated. In prokaryotes, initiation uses fMet (N-formyl methionine). The formyl group is often removed post-translationally.
2. Elongation
Elongation occurs in a cycle of 3 steps:
Step 1 — Aminoacyl-tRNA delivery (A-site entry):
- EF-Tu·GTP (prokaryotic) / eEF1A·GTP (eukaryotic) delivers aminoacyl-tRNA to A site.
- Codon-anticodon pairing → GTP hydrolysis → EF-Tu released → aa-tRNA accommodated into A site.
Step 2 — Peptide bond formation (Transpeptidation):
- The 23S rRNA (in 50S subunit) catalyzes peptide bond formation — rRNA acts as a ribozyme.
- Peptidyl transferase activity = ribozyme activity of 23S rRNA (proven by H.F. Noller, 1992).
- Polypeptide chain is transferred from P-site tRNA → A-site amino acid.
- P-site tRNA becomes deacylated; A-site tRNA now carries the extended polypeptide.
Step 3 — Translocation:
- EF-G·GTP (prokaryotic) / eEF2·GTP (eukaryotic) facilitates translocation.
- Ribosome moves 3 nucleotides (one codon) in the 5'→3' direction on mRNA.
- A-site tRNA (with polypeptide) → moves to P site.
- P-site tRNA (deacylated) → moves to E site → exits.
- A site is now empty → ready for next aa-tRNA.
- GTP hydrolysis drives translocation.
3. Termination
- Occurs when a stop codon (UAA, UAG, or UGA) enters the A site.
- No tRNA recognizes stop codons.
- Release factors (RF) recognize stop codons:
- RF1 — recognizes UAA and UAG.
- RF2 — recognizes UAA and UGA.
- RF3 — stimulates RF1/RF2 activity (GTPase).
- Eukaryotes have a single eRF1 (recognizes all 3 stop codons) + eRF3.
- RF binds A site → peptidyl transferase cleaves polypeptide from final P-site tRNA → polypeptide released.
- Ribosome dissociates into subunits (aided by RRF — ribosome recycling factor in prokaryotes).
Polysomes (Polyribosomes)
- Multiple ribosomes translating a single mRNA simultaneously.
- Increases efficiency — one mRNA → many polypeptide copies at once.
- In prokaryotes, transcription and translation are coupled (occur simultaneously in cytoplasm).
Post-Translational Modifications
After translation, polypeptides may undergo:
- Cleavage (e.g., removal of signal peptide, fMet, or pro-sequences).
- Glycosylation (addition of sugar groups).
- Phosphorylation, acetylation, ubiquitination.
- Folding assisted by chaperone proteins (e.g., Hsp70).
- Disulfide bond formation.
Antibiotics That Inhibit Translation
Antibiotic inhibition table
| Antibiotic | Target | Mechanism |
|---|---|---|
| Streptomycin | Prokaryotic 30S subunit | Causes misreading of mRNA; inhibits initiation |
| Tetracycline | Prokaryotic 30S subunit | Blocks aminoacyl-tRNA binding to A site |
| Chloramphenicol | Prokaryotic 50S subunit | Inhibits peptidyl transferase (blocks peptide bond formation) |
| Erythromycin | Prokaryotic 50S subunit | Blocks translocation; blocks exit tunnel |
| Linezolid | Prokaryotic 50S subunit | Inhibits initiation (binds 23S rRNA) |
| Cycloheximide | Eukaryotic 60S subunit | Inhibits peptidyl transferase in eukaryotes (NOT prokaryotes) |
| Rifampicin | Prokaryotic RNA polymerase | Inhibits transcription (not translation directly); blocks RNA synthesis |
| Fusidic acid | EF-G | Prevents EF-G dissociation after GTP hydrolysis; blocks translocation |
| Puromycin | Both prokaryotes & eukaryotes | tRNA analog; premature chain termination |
WARNING
Rifampicin acts on RNA polymerase (inhibits transcription), not translation directly — but is often grouped here because it indirectly prevents protein synthesis. Remember: antibiotics targeting 30S or 50S affect prokaryotes; cycloheximide specifically targets eukaryotic 60S.
Key Points to Remember
- Ribosomes: 70S in prokaryotes (30S + 50S); 80S in eukaryotes (40S + 60S). S units are not additive.
- Ribosome sites: A (incoming aa-tRNA), P (growing chain), E (exit).
- Activation: 2 ATP equivalents consumed; aminoacyl-tRNA synthetase ensures fidelity.
- Prokaryotic initiation: Shine-Dalgarno sequence + fMet + IF-1/2/3.
- Eukaryotic initiation: 5' cap scanning + Kozak sequence + Met (not fMet) + eIFs.
- Elongation: EF-Tu (aa-tRNA delivery) → peptide bond (ribozyme: 23S rRNA) → EF-G (translocation); each cycle = 2 GTP.
- Termination: RF1 (UAA/UAG), RF2 (UAA/UGA), RF3 (GTPase); eukaryotes = eRF1 + eRF3.
- Peptidyl transferase = 23S rRNA ribozyme (proven by Noller).
- Antibiotics: streptomycin/tetracycline → 30S; chloramphenicol/erythromycin → 50S; cycloheximide → eukaryotic 60S; rifampicin → RNA polymerase.
Summary Cheat Sheet
| Concept / Topic | Key Details / Explanation |
|---|---|
| Translation | mRNA decoded to synthesize polypeptide at ribosomes in cytoplasm |
| Direction | mRNA read 5'→3'; polypeptide grows N-terminus → C-terminus |
| Prokaryotic ribosome | 70S = 30S (16S rRNA) + 50S (23S + 5S rRNA) |
| Eukaryotic ribosome | 80S = 40S (18S rRNA) + 60S (28S + 5.8S + 5S rRNA) |
| S units | Not additive (reflect shape and density, not just mass) |
| Ribosome A site | Aminoacyl site — receives incoming charged tRNA |
| Ribosome P site | Peptidyl site — holds tRNA with growing polypeptide |
| Ribosome E site | Exit site — holds empty tRNA before release |
| Aminoacylation | Amino acid + ATP → aminoacyl-tRNA; costs 2 ATP equivalents; by aminoacyl-tRNA synthetase |
| Prokaryotic initiation | Shine-Dalgarno sequence (~AGGAGG) on mRNA; fMet-tRNA at P site; IF-1, IF-2, IF-3 |
| Eukaryotic initiation | 5' cap scanning; Kozak sequence (GCCRCCAUGG); Met (not fMet); eIFs |
| Elongation Step 1 | EF-Tu·GTP delivers aa-tRNA to A site (codon-anticodon matching) |
| Elongation Step 2 | Peptide bond formation by 23S rRNA (ribozyme = peptidyl transferase); proven by H.F. Noller (1992) |
| Elongation Step 3 | EF-G·GTP drives translocation — ribosome moves one codon (3 nt) on mRNA |
| Termination | Stop codon (UAA/UAG/UGA) enters A site; no tRNA recognizes it |
| Release factors (prokaryotic) | RF1 → UAA, UAG; RF2 → UAA, UGA; RF3 → GTPase |
| Release factors (eukaryotic) | eRF1 (all 3 stop codons) + eRF3 |
| Polysomes | Multiple ribosomes on single mRNA simultaneously; increases efficiency |
| Coupled transcription-translation | Only in prokaryotes (both in cytoplasm) |
| Post-translational modifications | Cleavage, glycosylation, phosphorylation, acetylation, ubiquitination, folding by chaperones |
| Streptomycin | Inhibits prokaryotic 30S; causes mRNA misreading |
| Tetracycline | Blocks aa-tRNA binding to A site (30S) |
| Chloramphenicol | Inhibits peptidyl transferase (50S) |
| Erythromycin | Blocks translocation (50S) |
| Cycloheximide | Inhibits peptidyl transferase in eukaryotic 60S only |
| Rifampicin | Inhibits prokaryotic RNA polymerase (transcription, not translation) |
| Puromycin | tRNA analog; causes premature chain termination; affects both pro- and eukaryotes |
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