§ B-05 Gene Expression & Translation: Ribosomal mRNA Decoding & Polypeptide Elongation (Grade 10–11 · Genetic Code & Translation)
Central Dogma DNA → mRNA → Protein, Triplet Genetic Code, Ribosomal A–P–E Sites & tRNA Decoding. “Genetic information is read from mRNA in the 5′→3′ direction in non-overlapping nucleotide triplets (codons): within the ribosomal A, P, and E sites, aminoacyl-tRNA anticodons translate nucleotide sequences into polypeptides.”
Theory Summary & Scientific Mechanism
In the Central Dogma of Molecular Biology, genetic information flows from DNA via transcription into messenger RNA (mRNA) and via ribosomal translation into protein. The genetic code is triplet, non-overlapping, and degenerate: out of 4³ = 64 codons, 61 encode amino acids (starting at AUG for methionine) while 3 ( extUAA, UAG, UGA) serve as termination stop codons.
The ribosome (80S = 40S + 60S in eukaryotes; 70S = 30S + 50S in prokaryotes, stabilized by Mg²⁺) houses three tRNA-binding pockets: the A-site (aminoacyl entry delivered by EF-Tu·GTP), the P-site (peptidyl-tRNA holding the nascent chain), and the E-site (deacylated tRNA exit).
The rRNA ribozyme of the large subunit’s peptidyl transferase center catalyzes peptide bond formation (–CO–NH–), transferring the polypeptide onto the A-site residue. Elongation factor EF-G then hydrolyzes GTP to translocate the ribosome by exactly one codon (3 nt) along mRNA in the 5' → 3' direction, consuming ≈ 4 high-energy phosphate equivalents per amino acid.
Everyday Analogy
The ribosome is a molecular 3D printer reading an mRNA tape three letters at a time (a triplet codon). tRNA couriers match their anticodon to each triplet and add an amino acid until the ribosome hits a STOP codon (UAA, UAG, UGA), which adds no amino acid and releases the finished protein!
Interactive Question & Derivation
Each amino acid in a polypeptide chain is encoded by one mRNA triplet (codon) of 3 nucleotides, while the termination stop codon (UAA, UAG, or UGA) does not encode an amino acid. How many nucleotides are in the coding region of mature mRNA (including the AUG start codon and one stop codon), and how many high-energy ATP/GTP equivalents are consumed to synthesize a protein of Nₐa = 100 amino acids (4 equivalents per residue)?
- A: 100 mRNA nucleotides and 100 ATP molecules
- B: The coding mRNA region contains 3 Nₐa + 3 = 303 nucleotides (100 sense codons + 1 stop codon), and translation consumes ≈ 4 Nₐa = 400 high-energy ATP/GTP equivalents
- C: 300 mRNA nucleotides, because the stop codon also encodes tryptophan
- undefined: 900 mRNA nucleotides, because every nucleotide is read three times in overlapping frames
Study Hint: Encoding Nₐa amino acids plus one stop codon requires 3Nₐa+3 nucleotides (303 nt for 100 aa) and ≈ 4Nₐa = 400 ATP/GTP equivalents.
Proof & Explanation: The genetic code is triplet and non-overlapping: every 3 consecutive mRNA nucleotides specify one amino acid (starting with AUG for methionine). Translation termination is triggered by a stop codon (UAA, UAG, UGA) recognized by release factors (RF) rather than a tRNA. Thus, a polypeptide of Nₐa residues requires Nₙt = 3 Nₐa + 3 coding nucleotides (303 nt for 100 aa). Incorporating each residue consumes 2 high-energy bonds during aminoacyl-tRNA charging (ATP → AMP + PPᵢ) plus 2 GTP molecules on the ribosome (EF-Tu and EF-G), totaling 4 Nₐa = 400 ATP/GTP equivalents.
Key Equations & 3D Simulation Parameters
DNA xrightarrowtranscription mRNA xrightarrowribosome (A→P→E) Polypeptide (Nₐa)
- Ribosome translocation speed vᵣib (codons/s): 0.4 … 2.5 rel. (default: 1.2 rel.)
- Target polypeptide chain length Nₐa: 20 … 200 aa (default: 100 aa)
- Mg²⁺ concentration (40S+60S / 30S+50S subunit stabilization): 0.5 … 5 mM (default: 2.5 mM)
- Codon state in A-site (1=Wild-type UUC-Phe, 2=Silent UUU, 3=Missense UAC-Tyr): 1 … 3 (default: 1)