Step 1 · Biochemistry

Translation & the Genetic Code

Name: Translation & the Genetic Code
Creator: Veli Bakalov, MD

Codons, the A-P-E ribosome, and why antibiotics spare your ribosomes

Biochemistry·Molecular Biology·5 min read·9 high-yield points·Reviewed by Veli Bakalov, MD @HemeOncBuddy

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The genetic code is triplet, degenerate (many codons per amino acid), unambiguous (one amino acid per codon), commaless, nonoverlapping, and nearly universal.
AUG is the start codon and codes methionine (fMet in bacteria); UGA, UAA, and UAG are stop codons read by release factors, not tRNA.
Wobble at the third (3') codon base lets one tRNA read several codons and explains most degeneracy; third-base changes are often silent.
Eukaryotic ribosome 40S + 60S = 80S; prokaryotic 30S + 50S = 70S — the basis of antibiotic selectivity.
Aminoacyl-tRNA synthetase (ATP, attaches the amino acid to the 3' CCA end) is translation's fidelity checkpoint; peptidyl transferase is a large-subunit rRNA ribozyme; elongation uses GTP.
Buy AT 30 (aminoglycosides — bactericidal, misreading; tetracyclines — block A site); CCEL at 50 (chloramphenicol, clindamycin, erythromycin/macrolides, linezolid).
Mitochondrial ribosomes resemble bacterial ones, explaining linezolid myelosuppression and aminoglycoside ototoxicity.
Mutation severity: frameshift/nonsense usually worst, then missense (sickle cell), then silent; out-of-frame dystrophin deletion = Duchenne, in-frame = Becker.
Proinsulin is trimmed to insulin plus C-peptide, which marks endogenous insulin; γ-carboxylation of clotting factors is vitamin K–dependent.

The genetic code

Core features. The code is read in triplets (3 bases per codon) and is:

Degenerate/redundant — most amino acids are specified by more than one codon.
Unambiguous — each codon specifies only one amino acid.
Commaless and nonoverlapping — read continuously from a fixed start, each base used once.
Nearly universal — shared by almost all organisms.

Degenerate is not ambiguous: many codons can map to one amino acid, but each codon still means only one.

Start codon. AUG marks translation initiation and codes methionine — N-formylmethionine (fMet) in bacteria, plain methionine in eukaryotes. Memory aid: AUG in-AUG-urates protein synthesis.

Stop codons. UGA, UAA, and UAG terminate translation. They are recognized by release factors, not by any tRNA. Mnemonic: U Go Away, U Are Away, U Are Gone.

Wobble. The first two codon bases pair strictly with the anticodon, but the third (3') position pairs loosely, so one tRNA can read several codons. This is why most of the code's degeneracy sits in the third position — and why many third-base changes are silent (GAA and GAG both code glutamate).

Ribosomes, tRNA, and the steps of translation

Ribosome sizes. Eukaryotic ribosomes are 40S + 60S = 80S; prokaryotic ribosomes are 30S + 50S = 70S. Mnemonic: Even numbers (40, 60, 80) for Eukaryotes. This structural difference is the basis for antibiotic selectivity.

Charging tRNA — the fidelity checkpoint. Each aminoacyl-tRNA synthetase (one per amino acid) uses ATP to attach its amino acid to the 3' CCA end of the matching tRNA, proofreading the match. The ribosome checks only codon–anticodon pairing, not the amino acid, so a mischarged tRNA inserts the wrong residue; charging is therefore the accuracy checkpoint of translation.

A, P, and E sites. The A (aminoacyl) site receives the incoming charged tRNA, the P (peptidyl) site holds the tRNA carrying the growing chain, and the E site is where the uncharged tRNA exits. Peptidyl transferase — a ribozyme made of large-subunit rRNA, not protein — forms each peptide bond. Mnemonic: APE (Aminoacyl → Peptidyl → Exit).

ChargingSynthetase + ATP loads the amino acid onto tRNA
InitiationSmall subunit and initiator tRNA find AUG; large subunit joins (GTP)
A site entryIncoming aminoacyl-tRNA pairs with the next codon (GTP)
Peptide bondPeptidyl transferase (rRNA ribozyme) transfers the chain to the new amino acid
TranslocationRibosome shifts one codon toward the 3' end (GTP); tRNAs move A → P → E
TerminationRelease factor recognizes the stop codon; the polypeptide is released

Translation, start to finish

Direction and energy. mRNA is read 5'→3' and the protein grows from N-terminus to C-terminus. Charging uses ATP; aminoacyl-tRNA delivery and translocation during elongation use GTP.

Ribosome-targeting antibiotics

30S inhibitors. Aminoglycosides (e.g., gentamicin) block the initiation complex and cause misreading of mRNA; they are bactericidal. Tetracyclines block aminoacyl-tRNA from entering the A site and are bacteriostatic. Mnemonic: buy AT 30 (Aminoglycosides, Tetracyclines).

50S inhibitors. Macrolides such as erythromycin bind the 23S rRNA and block translocation; chloramphenicol blocks peptidyl transferase; clindamycin and linezolid also act on the 50S subunit. Mnemonic: CCEL at 50 (Chloramphenicol, Clindamycin, Erythromycin/macrolides, Linezolid). Most are bacteriostatic.

Protein-synthesis inhibitors

Drug class	Subunit	Mechanism	Classic toxicity
Aminoglycosides	30S	Block initiation, cause misreading (bactericidal)	Nephrotoxicity, ototoxicity, neuromuscular blockade
Tetracyclines	30S	Block aminoacyl-tRNA entry to A site	Tooth discoloration and impaired bone growth in children, photosensitivity
Macrolides	50S	Bind 23S rRNA, block translocation	GI dysmotility, QT prolongation
Chloramphenicol	50S	Blocks peptidyl transferase	Aplastic anemia, gray baby syndrome
Clindamycin	50S	Blocks peptide transfer (translocation)	C. difficile colitis
Linezolid	50S	Prevents initiation complex formation	Myelosuppression, serotonin syndrome

Aminoglycosides are bactericidal; the rest are mainly bacteriostatic (linezolid varies by organism).

Selective toxicity — and its limits. Bacterial 70S ribosomes differ from human 80S ribosomes, which is why these drugs spare our cytoplasmic protein synthesis. Human mitochondrial ribosomes, however, resemble bacterial ones, which helps explain linezolid myelosuppression and aminoglycoside ototoxicity.

Toxins that hit human translation. Diphtheria toxin and Pseudomonas exotoxin A inactivate elongation factor 2 (EF-2) by ADP-ribosylation; Shiga toxin and ricin inactivate the 60S subunit by damaging its rRNA.

Post-translational modification

Trimming. Proteolytic removal of segments activates many proteins; proinsulin is cleaved to insulin, releasing C-peptide. Because C-peptide is secreted only with endogenous insulin, it confirms endogenous production — high in insulinoma or sulfonylurea use, low after injected insulin.

Covalent additions. Phosphorylation, glycosylation (including the mannose-6-phosphate tag that routes enzymes to lysosomes), hydroxylation (proline and lysine residues of collagen, vitamin C–dependent), and vitamin K–dependent γ-carboxylation of clotting factors (II, VII, IX, X, protein C, protein S).

Ubiquitination. Attaching ubiquitin marks a protein for degradation by the proteasome. Chaperone proteins assist correct folding.

Mutation types

Point and frameshift mutations

Type	Change	Effect	Example
Silent	Base change, same amino acid	Usually none; often a third-base (wobble) change	GAA → GAG (both glutamate)
Missense	Base change, different amino acid	Variable; altered protein	Sickle cell (glutamate → valine in β-globin)
Nonsense	Base change creates a stop codon	Early stop, truncated protein	Some β⁰-thalassemia alleles
Frameshift	Insertion/deletion not a multiple of 3	All downstream codons garbled	Duchenne muscular dystrophy, Tay-Sachs

Severity is roughly frameshift/nonsense > missense > silent.

Duchenne vs Becker. An out-of-frame (frameshift) deletion in the dystrophin gene yields no functional dystrophin and severe Duchenne muscular dystrophy; an in-frame deletion (a multiple of 3) yields a shortened, partly functional protein and milder Becker muscular dystrophy.

A single-base insertion or deletion in a coding region is a frameshift until proven otherwise; an indel of 3 bases keeps the frame and removes or adds one amino acid (e.g., the CFTR ΔF508 deletion).