Take apart a human ribosome, follow a message three letters at a time, then change a DNA base and discover what the peptide does.
Enable JavaScript to change the conditions and run the interactive experiment.
A cell can copy information from DNA into RNA. A ribosome reads the RNA in three-base codons, and transfer RNAs connect those codons to amino acids. A changed DNA base can leave the amino-acid sequence unchanged, alter it, or introduce an earlier stop.
Change coding DNA GCT to GCC. Must the peptide’s amino-acid sequence change?
The RNA letter changes, but both codons encode alanine in the standard table. This is synonymous at the amino-acid-sequence level; it does not prove that every other biological effect is absent.
In the human-cell context used here, DNA stays in the nucleus. RNA polymerase uses one DNA strand as a template, reading it 3′ to 5′ while extending RNA at its 3′ end. The new RNA grows 5′ to 3′. Coding DNA resembles that RNA except that DNA uses T where RNA uses U. The coding strand is the editor’s input convention; it is not the strand directly read by polymerase.
A eukaryotic RNA normally undergoes processing, and a mature mRNA can leave the nucleus for translation in the cytoplasm. Our invented coding region has no introns. Caps, untranslated regions and the poly(A) tail provide biological context but lie outside the editable sequence. The small sequence is not a complete gene or a whole transcript.
A human initiation complex selects a start site and positions initiator methionine-tRNA in the P site. The large ribosomal subunit joins. We annotate the first triplet as the candidate start and require AUG there. Actual start recognition depends on additional factors and sequence context; this model does not search for an internal start.
The next codon is read at the A site, where a matching charged tRNA brings an amino acid. A peptide bond forms and the growing chain transfers from the P-site tRNA to the amino acid at A. During translocation, the tRNAs move A to P and P to E relative to the ribosome, while the mRNA moves by one codon. The uncharged tRNA can exit and be reused.
In the standard code, UAA, UAG and UGA are stop signals. A release factor helps free the peptide from the P-site tRNA. A stop does not bring a final amino acid, and there is no stop-matching tRNA in this explanation. Later RNA bases can remain in the message without being translated in this frame. A stop codon ends translation of the coding region, not transcription of the complete RNA.
DNA and RNA are nucleic acids. A peptide is an amino-acid chain. RNA is not physically turned into a protein: its sequence is read while separate amino acids are joined. Many RNAs also have jobs that do not encode proteins. The ribosome itself includes ribosomal RNA as well as proteins.
Read an RNA codon 5′ to 3′. For AUG, an ideal complementary anticodon aligned beneath it reads 3′-UAC-5′; the same anticodon written alone 5′ to 3′ is CAU. Confusing those representations changes what the written letters mean. Real tRNA pairing also involves wobble and modified bases, omitted here.
Four RNA bases in three positions make 4³ = 64 codons. Standard genetic code table 1 assigns 61 to amino acids and three to stops. Multiple codons can specify the same amino acid. AUG specifies methionine internally as well as serving as the annotated start in this simplified example. Other biological contexts use variant codes and initiation rules.
GCU and GCC both encode alanine, so that change is synonymous at the amino-acid-sequence level. UUU to UCU changes phenylalanine to serine: a missense change. CAA to UAA introduces a stop: a nonsense change. These terms classify sequence consequences. Synonymous does not guarantee no biological effect, and missense does not automatically mean disease.
PDB 4UG0 preserves an experimentally determined human 80S ribosome conformation with an E-site tRNA. Our lightweight envelope shows the spatial arrangement of deposited components. The separate event workbench explains causal order using enlarged tokens. It does not interpolate arbitrary shapes and call them measured molecular trajectories.
Peptides may fold, be processed, combine with partners or be modified before functioning. The six-residue reference is invented for decoding practice. We do not predict folding, expression amount, protein activity, pathogenicity or a person’s traits. An absent stop in the supplied region is reported as an incomplete context rather than repaired automatically.
Coding-strand direction, reading frame and reference context matter before interpreting a letter change. The workbench practices those distinctions using an invented sequence; it is not a personal genetic interpretation tool.
Structural biologists use methods such as cryo-electron microscopy to investigate molecular machines. A deposited coordinate model is a research result with its own resolution, preparation and conformation. The model can be inspected without pretending it is a live-cell movie.
Muscles, enzymes and many cellular structures depend on proteins. Understanding the message-reading step connects molecular information to later lessons on cells, immunity and biological function. It does not imply that every trait has a simple one-gene explanation.
Write 5′-ATG GCT TTT CAA GGA TGG TAA-3′ on a strip. Mark a candidate start at the first triplet. This is an invented coding region, not a complete gene. Leave room beneath it for the template and RNA rows.
Write the aligned template 3′-TAC CGA AAA GTT CCT ACC ATT-5′. Copy that template into RNA: 5′-AUG GCU UUU CAA GGA UGG UAA-3′. Point to the paired letters and explain why RNA resembles coding DNA even though polymerase reads the template.
Fold a paper window around one codon. Move it in three-base steps. Write cards for methionine, alanine, phenylalanine, glutamine, glycine and tryptophan in that order. At UAA, stop without adding another amino acid. Explain why the letters remain in the RNA.
First change DNA position 6 from T to C. Update RNA and check the codon table: the peptide stays MAFQGW. Then restore the reference and change position 10 from C to T. RNA CAA becomes UAA; the peptide ends after MAF. Record the difference between a sequence result and a claim about health or protein function.
Can you change the message without changing its amino-acid sequence—and then make it stop earlier?
Paper and synthetic sequences only. No biological samples, genetic testing or wet-lab procedure. Peptide cards teach information order, not the size, fold or activity of a real protein.
The complementary template strand It reads the template 3′ → 5′ and extends RNA 5′ → 3′. Coding DNA is the convenient sequence convention in our editor.
3′-UAC-5′ The strands pair antiparallel. Written alone 5′ → 3′, this same ideal anticodon is CAU.
An assembly containing ribosomal RNA and proteins Its RNA is structurally and functionally central. The source inspection can reveal RNA and protein components separately.
The P site Initiator tRNA occupies P. The next charged tRNA brings its amino acid to A; initiation is different from an ordinary elongation step.
From the P-site tRNA to the amino acid on the A-site tRNA The chain transfers to A as a peptide bond forms. Translocation then brings that tRNA from A to P.
Nothing; a release factor helps release the chain Stop is a signal, not an amino acid. The message can retain later bases without translating them in this frame.
Both codons specify alanine in the standard code This particular pair is synonymous. The third base can matter for other codons; the model does not repair the RNA.
A peptide prefix and the missing termination context It decodes the complete codons supplied and reports what is missing. It does not invent a stop, a fold or a biological outcome.
The amino-acid row is distinguished from start annotations. NCBI uses T by convention; the public RNA chart replaces it with U. Variant codes and alternative starts are not erased from the biological explanation.
NCBI · The Genetic CodesSupports template copying, mRNA, tRNA, codons and the existence of noncoding RNAs. Figures are not reproduced.
NHGRI · RNA fact sheetUsed to check the coding-input convention and the aligned versus standalone template display.
UCSC · Strand directionOriginal structural study. Our first-AUG rule is an explicit model boundary, not a universal claim about initiation.
Yi et al. 2022 · Human initiation complexOriginal mammalian ribosome study supports A/P/E relationships and the role of eEF2. The lesson’s teaching-token motion is not a measured trajectory from these complexes.
Flis et al. 2018 · Ribosomal translocationPrimary publication and deposited isolated eRF1 structure. No eRF1 coordinates are copied into the workbench; its token is schematic.
Song et al. 2000 · Human release factorSupports the term and the explicit separation between a sequence consequence and a health prediction.
NHGRI · Missense mutationSupports the earlier-stop comparison. Changing an existing stop into an amino-acid codon is treated separately.
NHGRI · Nonsense mutationNature 520, 640–645; doi:10.1038/nature14427. Deposited coordinate atom centers span approximately 28 × 30 × 28 nm; the 3.6 Å experimental resolution is not that physical size.
Khatter et al. 2015 · Human 80S structureThe coordinate data license is recorded in the downloadable manifest. We do not apply it to unrelated website articles or illustrations.
RCSB PDB · Data usage policyIndependent subject review is pending.
Read the sources and model assumptions
Interactive explorationOpen a leaf, explore a chloroplast, and supply a tiny carbon-building recipe. Discover what comes from air, what comes from water, and what light contributes.
Move a load closer to an elbow on a transparent teaching arm. See the force change, then explore how muscles can work without visible movement.
Interactive explorationFollow a meal through the gut, then zoom into its lining. Choose starch, protein or long-chain fat and discover why their next routes differ.