Protein Synthesis Simulator — Transcribed message, Translated codons & Peptide residues Interactive

A nucleus-to-ribosome pathway transcribes a short DNA coding example, exports the mRNA and advances a ribosome through AUG GCU UUU GGA UAA.

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About this tool — how it works & FAQ

About the Protein Synthesis Simulator

A nucleus-to-ribosome pathway transcribes a short DNA coding example, exports the mRNA and advances a ribosome through AUG GCU UUU GGA UAA. tRNAs deliver amino acids and the chain stops at UAA.

What the simulator shows

• 3D scene parts: Nucleus and DNA template; mrna and nuclear pore; ribosome subunits; trna adaptors; nascent peptide. • Controls: Transcription duration (2–10 playback s); Translation dwell per codon (0.5–3 playback s); Block mRNA export. • Live readouts: Transcribed message (%); Translated codons; Peptide residues; Released peptide (0/1). • Guided experiments: Block nuclear export; Slower translation. • Four tabs (visual laboratory, curves and measurements, experiments, learn and assess), a model-verification run, a timestamped event log and a trial report.

The model equations

mRNA: 5′ AUG GCU UUU GGA UAA 3′ Peptide: Met–Ala–Phe–Gly UAA is a stop codon; it does not encode an amino acid.

Model limits and how to explore

Molecular geometry, organelle dimensions and animation time are enlarged and illustrative. Colors identify structures rather than natural tissue color. This is a conceptual teaching model, not a cell physiology predictor. Rates are playback times, not biochemical rates. Initiation, splicing, ribosomal A/P/E dynamics and peptide folding are represented conceptually. Try the preset experiments, then compare the live readouts with the equations.

Frequently asked questions

Does the animation show literal molecular dimensions and timing?

No. Geometry is enlarged and time is a teaching playback scale.

Does UAA add an amino acid?

No, it is a stop codon.

What does this simulator not model?

Molecular geometry, organelle dimensions and animation time are enlarged and illustrative. Colors identify structures rather than natural tissue color. This is a conceptual teaching model, not a cell physiology predictor. Rates are playback times, not biochemical rates. Initiation, splicing, ribosomal A/P/E dynamics and peptide folding are represented conceptually.

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