What it does
A protein is a chain of amino acids that folds into a precise shape, and its shape decides its job. Biologists describe that shape at four levels:
- Primary: the order of amino acids, joined by peptide bonds.
- Secondary: parts of the chain winding into an α-helix or lying side by side as a β-pleated sheet, held by hydrogen bonds in the backbone.
- Tertiary: the whole chain folding into a 3D shape, with water-fearing (hydrophobic) side chains tucked inside.
- Quaternary: two or more folded chains fitting together, as in haemoglobin.
Type any sequence in one-letter codes and switch between the four levels. The page counts the peptide bonds, the water released and the mass; draws your chain as a helix or a sheet with its size; folds it in a simple animation you can heat until it falls apart (denaturing); and shows haemoglobin’s four chains coming together.
It fits Class 11 Biology (biomolecules: proteins and their structure) and links to Class 12 (the molecular basis of inheritance, where the sequence comes from). See how a gene’s code becomes this sequence in central dogma lab, and how an enzyme’s folded shape makes it work in enzyme activity lab.
How to use it
- Type a sequence (or keep the made-up example MKLVAEFGSDLIKAWRVLEG). Only the 20 standard letters count; anything else is left out and the page says so.
- Pick a level: Primary, Secondary, Tertiary or Quaternary.
- At Secondary, switch between α-helix and β-pleated sheet.
- At Tertiary, watch the chain fold. Move Temperature above 60 °C to unfold it, back down to let it fold again, or press Stretch it out again.
- At Quaternary, press Separate the chains and Join the chains.
Worked example
The example has 20 amino acids, so it has 19 peptide bonds, and making them released 19 water molecules. Its mass is the sum of the 20 residue masses plus one water for the two ends: 2262.7 Da. There are 20²⁰ ≈ 1.05 × 10²⁶ possible sequences of this length, which is why proteins can be so varied.
As one α-helix it would make 20 ÷ 3.6 = 5.56 turns and be 20 × 0.15 = 3 nm long. Stretched out as a β-strand it would be about 20 × 0.33 = 6.6 nm.
At Tertiary, the 11 water-fearing beads (orange) drift together; after a few seconds the page reports most or all of them buried and the chain is compact. Raise the temperature to 80 °C and it opens up again.
Tips
- Heat, strong acids and alkalis break the weak bonds of the fold but not the peptide bonds, so a denatured protein keeps its primary structure.
- In a helix the side chains point outwards; the hydrogen bonds are between the backbone groups.
- Change one letter at the start of the sequence (for example a water-fearing one to a charged one) and refold: a single change can matter, as in sickle-cell haemoglobin.
FAQ
Is this how a real protein folds? Only in spirit. Real folding happens in 3D with many kinds of interactions. The bead model shows the main idea: the oily parts hide from water.
Why is the mass in daltons? One dalton (Da) is about the mass of a hydrogen atom. Proteins are usually thousands to hundreds of thousands of daltons.
Do all proteins have quaternary structure? No. Only proteins made of more than one chain, like haemoglobin, do.
Where the numbers come from
- Levels of protein structure, peptide bonds formed by condensation, α-helix (3.6 residues per turn, 0.15 nm rise per residue, 0.54 nm pitch) and β-strand (about 0.33 nm per residue) dimensions, and haemoglobin's four chains (2 α of 141 and 2 β of 146 amino acids, four haem groups, about 64,500 Da): general biochemistry, rounded.
- Masses come from each amino acid's formula and standard atomic weights, using fibub's peptide library (src/lib/sci/peptide.ts).
- The folding picture is fibub's own simple 2D hydrophobic-polar bead model (springs, attraction between water-fearing beads, random kicks for heat). It shows the idea only; it is not a prediction of any real protein's shape.
- Checked in the tests: GA = 146.146 Da and the example 20-residue chain = 2262.70 Da (sum of residue masses + water), 19 peptide bonds, 20^20 = 1.05 × 10²⁶ sequences, and the bead model folds at 25 °C and unfolds at 80 °C. Nothing you enter is stored or sent anywhere.
Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.
Last updated 2026-11-09.