STEPTRACKERBIOCHEMISTRY + PHARMACOLOGY + MICROBIOLOGY | MOLECULAR BIOLOGY | HIGH-YIELD REVIEW

Genetic Code & Translation

mRNA → protein on the ribosome: tRNA charging, the A-P-E sites, the energy cost — and where antibiotics jam the machine.

FOCUS ON
The code is unambiguous (one codon → one amino acid), degenerate (most amino acids have several codons; Met and Trp have one), commaless and nearly universal. Start = AUG (Met; fMet in bacteria). Stops = UAA, UAG, UGA. Ribosomes: eukaryotic 80S (60S + 40S), prokaryotic 70S (50S + 30S). tRNA enters A site, peptide grows on P, empty tRNA leaves from E.
STEP · PART
WHAT HAPPENS
ENERGY · FACTORS
CLUE · ANTIBIOTIC
tRNA charging
Aminoacyl-tRNA synthetase attaches the correct amino acid to the 3′ CCA end; proofreads
1 ATP (→ AMP, 2 high-energy bonds)
Synthetase is the real "decoder"; mupirocin inhibits Ile-tRNA synthetase
Wobble
Third codon base pairs loosely with the anticodon
—
Explains degeneracy; silent mutations at position 3
Initiation
Small subunit + initiator Met-tRNA find AUG (Shine-Dalgarno in bacteria; 5′ cap scanning in eukaryotes); large subunit joins
GTP; initiation factors (eIFs)
Aminoglycosides (30S) cause misreading and block initiation
Elongation — A site
Charged tRNA enters the aminoacyl (A) site
GTP; EF-Tu (bacteria) / eEF1
Tetracyclines block tRNA binding at the A site (30S)
Peptide bond formation
Peptidyl transferase (a ribozyme — rRNA of the large subunit) links the chain to the new amino acid
No extra energy
Chloramphenicol (50S) blocks peptidyl transferase
Translocation
Ribosome moves 3 nucleotides; tRNA shifts A → P → E
GTP; EF-G / eEF2
Macrolides, clindamycin, linezolid (50S) · diphtheria and Pseudomonas exotoxin A inactivate eEF2
Termination
Stop codon in A site → release factor frees the polypeptide
GTP
No tRNA for stop codons
Ribosome sizes
Eukaryotes 80S (60S + 40S) · prokaryotes 70S (50S + 30S)
—
Mitochondria have 70S-like ribosomes → linezolid, chloramphenicol toxicity
Polysomes & location
Free ribosomes make cytosolic proteins; RER ribosomes make secretory, membrane and lysosomal proteins
Signal recognition particle
Plasma cells, pancreatic acinar cells → lots of RER
Ricin & Shiga toxin
Remove an adenine from 28S rRNA of the 60S subunit
—
Shiga/Shiga-like → HUS · ricin from castor beans

Mechanism — one elongation cycle

Charged tRNA → A siteGTP, EF-Tu
→
Peptidyl transferaseChain moves onto A-site tRNA
→
TranslocationGTP, EF-G/eEF2
→
Empty tRNA exits EA site free again

Cost per amino acid ≈ 4 high-energy bonds: 2 for charging (ATP → AMP) + 2 GTP for elongation.

Antibiotics by subunit — "buy AT 30, CCEL at 50"

SUBUNIT
DRUG
BLOCKS
30S
Aminoglycosides
Initiation; misreading (bactericidal)
30S
Tetracyclines
tRNA binding at A site
50S
Chloramphenicol, clindamycin
Peptidyl transferase / translocation
50S
Erythromycin (macrolides)
Translocation
50S
Linezolid
Initiation complex formation

How it's tested

COMMON CONFUSIONThe ribozyme that forms the peptide bond is rRNA, not a protein. tRNA charging uses ATP; ribosome steps use GTP.
THE TRAPA toxin that ADP-ribosylates eEF2 (diphtheria, Pseudomonas exotoxin A) stops translocation in human cells — a host, not bacterial, target.
YOUR APPROACHPin the step (charge, start, A site, bond, move, stop) → factor or site → drug or toxin acting there.

If you see… think…

Start codon → AUG (methionine; fMet in bacteria)
Stop codons → UAA, UAG, UGA
Amino acids with a single codon → Met and Trp
Enzyme that matches amino acid to tRNA → aminoacyl-tRNA synthetase
Peptide bond made by rRNA → peptidyl transferase (ribozyme)
Toxin inactivating eEF2 → diphtheria / Pseudomonas exotoxin A
Toxin cleaving 28S rRNA → Shiga toxin, ricin
Antibiotic causing mRNA misreading → aminoglycoside (30S)
Gray baby syndrome drug → chloramphenicol (50S)
Topical antibiotic blocking isoleucyl-tRNA synthetase → mupirocin