In scope
Supplied College Board AP Biology CED (2025), printed pp. 76–78: 3.5.A.2–3 (coordinated reactions, electron transport, proton gradients, membrane folding, chemiosmosis and uncoupling); 3.5.B.2–5 (pyruvate transport, matrix reactions, CO₂, carriers and the ETC). Data analysis supports interpreting error bars and justifying conclusions from evidence.
No enzyme names, ETC complex names, intermediate structures or individual cycle steps are assessed. Acetyl-CoA and carbon counts provide explanatory context rather than extra memorization targets.
Read the simulations correctly
Stage models: net bookkeeping per pyruvate is 3 CO₂, 4 NADH, 1 FADH₂ and one ATP equivalent. Direct ATP is shown as ATP for simplicity. Newly entering acetyl carbons are not necessarily released in the same turn. The cycle regenerates its acceptor; it is not consumed.
Isolated membrane model: marker numbers, gradient strength and ATP formation events are qualitative teaching units, not molecular stoichiometry or a prediction of ATP per glucose. NADH and FADH₂ both donate electrons but FADH₂ enters downstream and contributes less modeled pumping; numerical pumping factors are illustrative. Oxygen and water are shown as endpoints, not balanced chemical equations. Each stage has its own finite preparation. Carbon stages do not recycle carriers internally; the membrane stage regenerates oxidized carriers. The transfer button copies the current reduced-carrier sample into a separate ETC trial with oxygen and ADP supplied. Selecting limited NAD⁺ starts a fresh trial. Other ETC controls can change during a run. The no-O₂ control makes the remaining oxygen unavailable; restoring control conditions makes that unconsumed oxygen available again. Reset replenishes the selected preparation. The separate mitochondrial views omit glycolysis and fermentation. The Whole-cell comparison includes both, with all non-tested supplies maintained and no incidental finite-carrier exhaustion; it has its own model-assumptions panel. H⁺ markers represent redistribution across the membrane, not creation of protons.
Controls represent complete blocks in an idealized model. ATP synthase blockade can restrict electron flow through gradient buildup; a leak dissipates the gradient and reduces coupling. Real rates, buffers, transport costs and other metabolic fuels are not modeled.
Data and uncertainty
The six 60-minute CO₂ means and SEM are supplied reference data, not simulated replicates. The source does not specify physical CO₂ units, sample size, raw observations or residual-signal causes. Animations explain possible mechanisms without fitting numerical outputs.
Default error bars are ±1 SEM. The optional ±2 SEM display is an illustrative expansion, not a calculated 95% confidence interval. Small samples require a larger t multiplier; sample size is unavailable here. Bar overlap alone does not prove equality or establish a statistical test result.