Read the diagram first
The main loop shows carbon fixation by Rubisco, reduction of GP to TP, and regeneration of RuBP. Rubisco is a catalyst: it stays at the fixation step and is not consumed. ATP and reduced NADP come from the light-dependent reactions.
Simple keeps just the pathway and its inputs. Carbon counting adds the quantities for three CO₂: six GP form, six TP form, five TP regenerate three RuBP, and one TP is the net gain. Molecular opens the 3D viewer without changing the cycle layout.
What is simplified?
Arrows represent a sequence of chemical reactions, not a physical track. Moving markers indicate reaction order, not individual atoms. Carbon dots count atoms within molecules; their arrangement is not a bond diagram or an isotope-tracing result. Successive stages do not represent simultaneous molecule stocks.
Water, H⁺ and inorganic phosphate are omitted from the overview. It is a pathway map and carbon/energy budget, not a fully balanced chemical equation. Net TP withdrawal need not mean transport out of the chloroplast. TP supplies carbon for other molecules through further reactions.
The molecular shapes are calculated conformers, not experimentally measured structures or reaction dynamics. Neutral acid forms are used for consistent drawings; many groups are ionised in the stroma. Glyceraldehyde 3-phosphate is the TP shown; GP is glycerate 3-phosphate, a different compound.
The experiment is a qualitative, carbon-conserving model. Pool levels are normalised to their own initial values. Rates, temperature responses and time units are illustrative, not measured plant data. Stomata, photorespiration and light-dependent enzyme activation are not modelled.