Translation Molecular Lab

Build the complex. Read the message. Grow the peptide.

01 Initiation02 Elongation03 Termination

v005 · 80S model

5′ → 3′ mRNA reading direction
Assemble at the start codon

Cytosolic workbench · procedural 3D

Grab & move is activeDrag a molecule by its surface or name. Release near the glowing target.

40S subunit60S subunit PTC (rRNA) mRNARelease factor

GRAB · drag to dock

Initiation · action 1

Bind the small subunit

P site · peptide holder—

A site · incoming—

Your first moveDock the blue 40S subunit at the highlighted AUG region.

Translation field notes

Decode the message

Align the anticodon antiparallel to the mRNA codon. Here every anticodon is written 3′ → 5′, while each mRNA codon is written 5′ → 3′.

Codon 5′→3′	Anticodon 3′→5′	Meaning
AUG	UAC	Met · start
UUU	AAA	Phe
GGC	CCG	Gly
UAC	AUG	Tyr
UAA	None	Stop · release factor
UAG / UGA	None	Other standard stops
CUU	GAA	Leu · pool distractor
AAA	UUU	Lys · pool distractor

This is the reference for the codons used in this model, rather than a full 64-codon table. A pairs with U; G pairs with C. Wobble pairing and synonymous codons are not simulated.

Finding the start codon

The mRNA carries a 5′ UTR before the start codon and a 3′ UTR after the stop codon. Neither is translated. The reading frame is not set by the 5′ end: it is set when the start codon AUG sits in the 40S P site and pairs with the initiator tRNA (3′–UAC–5′). From there the ribosome reads non-overlapping triplets until a stop codon reaches the A site. That is why the nucleotides in the sequence bar are not grouped into codons until initiation.

In cells, the 40S subunit (already carrying the initiator tRNA and initiation factors) loads near the 5′ cap and scans 5′→3′, usually starting at the first AUG in a favorable sequence context, such as the ACCAUG used here. In this lab you do the scanning: slide the 40S along the mRNA and watch its gold P-site window.

The three sites

A: accepts the next charged tRNA. P: holds the tRNA carrying the nascent peptide. E: holds a deacylated tRNA before it exits. The initiator tRNA enters the P site directly.

Large-subunit landmarks

The 60S subunit is drawn as a rounded body of rRNA resting on the mRNA, with three pockets along its lower half for the E, P and A sites. The lower half is nearly transparent so you can watch codon–anticodon pairing. (In real ribosomes the mRNA runs through the 40S, and the 60S sits on the 40S with the tRNAs between them.) The peptidyl transferase center (the glowing point) is made of rRNA, which makes the ribosome a ribozyme. The growing peptide threads through the exit tunnel and emerges at the top.

What each action represents

Peptidyl transferase activity in the large subunit’s rRNA catalyzes the peptide bond. The peptide’s C terminus transfers from the P-site tRNA to the amino acid on the A-site tRNA. Afterward, translocation moves the ribosome by three nucleotides toward the mRNA’s 3′ end.

A release factor is a protein, with no anticodon or attached amino acid. At a stop codon it promotes hydrolysis of the linkage between the peptide and the P-site tRNA. Recycling then separates the subunits.

Model scope

Default: eukaryotic cytosolic translation (40S + 60S → 80S), with an initiator Met-tRNA. Bacterial translation instead uses 30S + 50S → 70S and an initiator fMet-tRNA. S values describe sedimentation behavior and are not additive.

Cap-dependent scanning (here you slide the 40S yourself), initiation/elongation/recycling factors, aminoacyl-tRNA synthetases, and nucleotide cofactors are omitted; the 5′ cap and poly(A) tail appear only as landmarks. In cells, tRNA delivery and translocation involve factors and GTP; recycling is factor-dependent. E-site exit is paused here so you can manipulate it.

All structures are procedural schematics, not atomic structures. Site spacing, molecular shapes, and tunnel length are expanded or compressed for visibility, and the UTRs are far shorter than typical cellular UTRs. The four-residue peptide is deliberately enlarged; a real peptide this short would normally remain within the exit tunnel. The tube/ribbon tRNA depicts its folded L shape, rather than an atomic backbone.

Controls

Grab: drag a molecule to its glowing target and release. Grabbing projects it onto a camera-facing plane through the active site. Camera: drag to orbit; scroll to zoom; right-drag to pan. On touch screens, use one finger to grab or orbit and two fingers to zoom in Camera mode.

Space: switch modes. Arrow keys: move a selected molecule in the camera plane; hold Shift for larger moves. Enter: attempt docking at the selected molecule’s current position. Escape: cancel a drag or close this drawer. Overview: restore the full workbench. Ribosome: zoom in on the ribosome.

Labels: Smart shows the key labels and reveals details for the molecule you hover over or hold; Detailed shows every label; Minimal keeps only sequences and sites. Where labels would overlap, the less important one steps aside. On the mRNA, ←/→ slide a selected 40S one nucleotide (Shift: three).

Scientific references

The Cell: Translation of mRNA
Translation Phases in Eukaryotes
Molecular Biology of the Cell: From RNA to Protein
Cotranslational Folding of Proteins on the Ribosome

Translation Molecular Lab⁠‌‍‌‍‌‌‍‍‌‍‍‍‌‍‌‌‌‍‍‌‌‌‌‍‌‍‍‍‌‌‍‌‌‍‌‌‌‍‍‌‌‍‍‌‍‌‌‍‌‍‍‌‌‍‌‍‌‍‍‌‍‍‌‌‌‍‍‌‌‍‌‌‌‌‍‌‌‌‌‌‌‍‌‌‌‌‍‌‌‍‍‌‍‌‌‍‌‍‍‌‌‍‍‍‌‍‌‍‌‍‌‌‌‍‍‍‌‌‍‌‌‍‍‌‌‍‌‍‌‍‍‌‌‍‌‍⁠ · Created by StarField BigTree · v005

The 3D workbench could not load