SCOPE, STRUCTURES & LIMITS
Real biology. A readable model. × Designed for OCR A Biology H420 , photosynthesis (5.2.1): photoionisation, photolysis, electron transport, reduced NADP, proton gradients and chemiosmosis. Named carriers and protein architecture add explanatory detail. This is not the whole photosynthesis topic: cyclic photophosphorylation and the Calvin cycle are outside this lab.
The instant, offline view uses authored protein architecture. “Load real proteins” replaces it with experimental backbone and cofactor coordinates. A structure is marked as experimental only after its coordinates have loaded successfully. Internet access is needed for that first download; save an offline copy afterwards.
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What is measured — and what is drawn? Loaded protein backbones follow deposited Cα coordinates; selected non-protein cofactors retain their atomic positions. Major complexes are positioned and uniformly rescaled to make the teaching scene legible. Membrane orientation is taken from OPM where available, or estimated from structural landmarks. The arrangement combines representative structures, not a single measured membrane patch. Real thylakoids have spatially segregated complexes; the row shown here is deliberately unpacked.
The coloured electrons and protons are tracking symbols, greatly enlarged. Lines show the direction and sequence of transfer, not measured trajectories or exact cofactor-to-cofactor distances. Excitation energy transfer through antenna pigments is not an electron travelling between those pigments. Light-driven water oxidation is condensed from four PSII turnovers. The cytochrome b₆f Q cycle is shown as its net effect; its branching intermediates are omitted.
ATP synthase’s rotary overlay is illustrative; loaded experimental coordinates are not themselves a moving structure. Proton paths through the motor are representative, not atom-resolved half-channels. The ATP yield is not fixed to the number of NADPH molecules. In the experiment, a bounded, qualitative proton-gradient model links electron transport, proton leakage and ATP formation; it is not fitted to measurements. Electrical potential, buffering, detailed pH, photosystem damage and redox regulation in darkness are not simulated.
Small molecules ATP uses wwPDB CCD ideal heavy-atom coordinates. NADP⁺ (NAP ) and NADPH (NDP ) use RDKit-generated conformers from CCD stereochemical SMILES. Protonation of phosphates is simplified. Water uses an ideal bent geometry. Lipids, plastoquinone carrier symbols and offline chlorophyll sites are schematic.
PDB data: wwPDB / RCSB PDB, public-domain structural data. OPM: membrane orientation service. Native WebGL rendering; no account, analytics or third-party JavaScript libraries. Network requests are only for public protein coordinates. Cached structures are stored locally when the browser permits it.