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dna-proteins-1 · content 1 · setup format 1
What supports the explanation?
Standard genetic code table 1 provides the 64-codon lookup used by the lesson.
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.
Peptide transfer and tRNA–mRNA translocation have distinct roles and ordered states.
Original 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.
PDB 4UG0 contains the source coordinates for this human ribosome inspection model.
Nature 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.
Synthetic intron-free coding region, 3–60 bases. Not a genome, natural gene, full mRNA or personal sequence report.
Standard genetic code table 1, initiation only at the annotated first AUG. No internal scanning, alternative initiation, code variants, splicing or RNA editing.
The event sequence preserves role and order; it does not solve molecular forces, reaction kinetics, error rates, charging, energy consumption, hybrid tRNA states or folding.
Displayed complementary anticodons omit wobble and modified bases. No stop-matching tRNA is introduced.
The source model uses all selected deposited atom centers grouped into RNA/protein components, with a declared smoothing and simplification process. It is not a solvent surface or an experimental EM density map.
The ribosome’s separation, colors and inspection controls are presentation changes. Removing a displayed group does not predict a biologically functional partial ribosome.
No medical, diagnostic, trait, enzyme-activity or pathogenicity prediction follows from these synthetic sequence changes.
The paper activity has not yet been classroom-trialed. Browser, accessibility, export and independent subject review remain pending.
Information is represented in different molecules: 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.
A codon has a direction: 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.
The standard code has 64 entries: 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.
One changed base does not have one universal effect: 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.
A static structure and an event model answer different questions: 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.
Know the missing biology: 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.
What has been checked
Analytical reference cases, conservation or transition invariants, finite drawing commands, bounded setup parsing, discovery and route integrity are checked automatically. These checks do not establish anatomical fidelity, learner outcomes or browser/device compatibility. Independent subject review, learner trials, comprehensive accessibility review and browser video encoding checks remain pending.
Each source supports the associated claim. Sources do not certify this implementation or its visuals.
About the cover illustration
The cover is an offline render of a simplified envelope derived from deposited PDB 4UG0 atom coordinates. The source is Khatter et al., Nature 2015; deposited archive data are CC0 1.0. It is not an experimental density map or a live molecular image. Colors, smoothing and mesh simplification are recorded in the lesson’s downloadable manifest.