Mitochondrial electron transport and oxidative phosphorylation. The respiratory chain redrawn so that each node carries its quantum chemistry and the evidence behind it. Solid heavy borders mark entities where a magnetic-field effect has been demonstrated (T1); solid light, where it has been shown for the containing process (T2); dashed, where a physical route exists but no field measurement has been made (T3); hairline, structural context with no quantum claim (T4). The map is almost entirely dashed, and that is the finding: the Arabidopsis near-null-field literature is developmental and nutritional, and has not yet measured a respiratory complex directly. Alternative oxidase and the type II NAD(P)H dehydrogenases are drawn because they are the confounders — a plant can route electrons around a lesion in complex I or complex IV, so respiration rate alone cannot test the hypothesis and cytochrome-versus-alternative flux must be partitioned. Derived from: Figures 1A and 4 of Porterfield & Barker, "Plant Responses to Near-Null Magnetic Fields" — expanded to gene level and bound to Arabidopsis loci structural_context CHEBI:57945 CHEBI:57540 C00004 C00003 structural_context CHEBI:30031 C00042 structural_context CHEBI:15379 C00007 flavin_semiquinone iron_sulfur_4Fe4S iron_sulfur_2Fe2S ros_leak_site 1H 14N 57Fe 33S CHEBI:58210 AT5G37510 AT5G08530 AT4G02580 AT5G11770 GO:0005747 7.1.1.2 The FMN site forms a flavin semiquinone during turnover and is a known superoxide-producing leak site, and the Fe/S chain performs sequential one-electron transfers — both of the physical routes the radical-pair and hyperfine arguments require. No published experiment has applied a near-null field and measured plant complex I activity, so this is a hypothesis with a mechanism, not a result. Electron transfer along the Fe/S chain is fast relative to plausible singlet-triplet mixing times, so a coherent radical-pair effect here is harder to argue than at the flavin. Treat the flavin and the cluster chain as separate hypotheses rather than one. flavin_semiquinone radical_pair_acceptor ros_leak_site 1H 14N CHEBI:58210 CHEBI:58210 AT5G08530 A one-electron-reduced flavin is the best-characterised magnetosensitive species in biology; the same chemistry underlies the cryptochrome radical-pair model. The review's argument is precisely that this chemistry is not confined to photoreceptors. flavin_semiquinone iron_sulfur_2Fe2S iron_sulfur_4Fe4S iron_sulfur_3Fe4S ros_leak_site 1H 14N 57Fe 33S CHEBI:57692 AT5G66760 AT3G27380 AT5G40650 AT5G09600 AT2G46505 GO:0005749 1.3.5.1 Carries all three cluster types plus a covalent flavin, and sits at the junction the review nominates as the bottleneck — a change here propagates into both TCA flux and respiratory electron flow. flavin_semiquinone 1H 14N CHEBI:57692 AT1G07180 AT2G29990 AT4G28220 AT4G05020 AT2G20800 FAD-dependent, so the same flavin semiquinone chemistry applies. Included mainly as the second confounder alongside AOX — a plant can route around a complex I lesion, which blunts any phenotype and must be controlled for. structural_context CHEBI:16389 C00399 semiquinone_radical radical_pair_donor ros_leak_site 1H CHEBI:16389 A free-radical intermediate held in a protein pocket. If any respiratory species supports spin-correlated chemistry, this is the leading candidate. structural_context AT3G22370 AT3G22360 AT3G27620 AT1G32350 AT5G64210 GO:0005739 rieske_2Fe2S semiquinone_radical ros_leak_site 57Fe 33S 1H AT5G13430 AT5G13440 GO:0005750 The Qo site generates a kinetically stabilised ubisemiquinone — a genuine, comparatively long-lived organic radical in a defined protein pocket, which is the most favourable setting for a field-dependent branching effect anywhere in the respiratory chain. Qo-site semiquinone is short-lived and its occupancy is debated; a field effect here would be easier to argue if lifetime were measured under the relevant conditions. heme_electron_carrier 57Fe 1H AT1G22840 AT4G10040 GO:0005758 Cytochrome c and the transcription factor ABI4 link mitochondrial status to ABA-dependent seed germination. A one-electron heme carrier, paramagnetic in the ferric state. Included because Racca et al. place cytochrome c on the path from mitochondrial state to germination timing, which is the developmental window the review argues matters most. heme_copper_binuclear cu_a_binuclear heme_electron_carrier 57Fe 1H GO:0005751 7.1.1.9 The review names cytochrome oxidase explicitly as a candidate direct metabolic target. The heme a3/CuB centre passes through paramagnetic oxygen intermediates (P, F, oxoferryl) whose spin states are, in principle, field-addressable. Strongly exchange-coupled metal centres relax very fast, which argues against coherent spin effects. This is a mechanistically attractive but physically demanding hypothesis, and is labelled T3 for that reason. structural_context GO:0005753 7.1.2.2 ros_leak_site CHEBI:18421 CHEBI:16240 AT3G10920 Near-null magnetic field exposure alters ROS-associated transcriptomic and metabolomic programmes in Arabidopsis. Reactive oxygen species and mitochondria jointly regulate seed germination, establishing the route from mitochondrial ROS to a developmental outcome. Not a magnetosensitive mechanism itself — it is the amplifier. A field effect too small to measure as a rate change can still register here, because ROS signalling is threshold-like. iron_sulfur_4Fe4S 57Fe 33S AT4G35830 AT4G26970 AT2G05710 4.2.1.3 The review nominates aconitase as the sentinel of Fe/S integrity, and the biochemistry supports it: the exposed cluster iron makes aconitase the first TCA activity to fall under oxidative stress, so it reports cluster damage before anything else does. Precisely because aconitase responds to any oxidative insult, a change under NNMF would NOT by itself implicate a magnetic mechanism. It is a sensitive readout and a poor discriminator; it needs a paired ROS-independent control. iron_sulfur_4Fe4S radical_pair_donor 57Fe 33S 1H AT2G20860 2.8.1.8 A radical-SAM enzyme generating a 5'-deoxyadenosyl radical from a [4Fe-4S] cluster — genuine organic radical chemistry on an iron-sulfur centre, which is the tightest coupling of the review's two proposed mechanisms found anywhere in primary metabolism. Its product lipoylates pyruvate dehydrogenase and the 2-oxoglutarate dehydrogenase complex, so a defect propagates straight into TCA flux. The radical is generated inside the active site and quenched within one turnover; whether a spin-correlated pair with a long enough lifetime to be field-sensitive ever forms is untested. electron_transfer electron_transfer cofactor_insertion electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer electron_transfer energy_feedback energy_feedback energy_feedback direct_influence direct_influence redox_feedback redox_feedback indirect_influence indirect_influence