{"format":"molecular-machines.cards","version":1,"updated":"2026-10-01","decks":[{"machine":"hemoglobin","name":"Hemoglobin","count":28,"url":"/learn/cards/hemoglobin.json"}],"cards":[{"id":"hemoglobin-job","machine":"hemoglobin","kind":"qa","prompt":"What does hemoglobin carry, and from where to where?","answer":"Oxygen, from the lungs to the tissues.","explanation":"Hemoglobin loads oxygen in the lungs and unloads it where tissues need it, because it switches shape as a whole.","section":"summary","topic":"purpose","sources":["machine:summary","machine:tagline"],"tags":["oxygen","transport"],"difficulty":1,"url":"/machines/hemoglobin#summary","cites":[{"source":"machine:summary","machine":"hemoglobin","label":"Summary","section":"summary"},{"source":"machine:tagline","machine":"hemoglobin","label":"Summary","section":"summary"}]},{"id":"hemoglobin-no-fuel","machine":"hemoglobin","kind":"qa","prompt":"Hemoglobin spends no chemical fuel. What does the work of loading and unloading oxygen instead?","answer":"The oxygen gradient and the allosteric switch.","explanation":"SERCA also switches between two states, but it spends ATP to do so; hemoglobin spends nothing.","section":"summary","topic":"purpose","sources":["machine:energy","link:serca"],"tags":["energy","allostery"],"difficulty":2,"url":"/machines/hemoglobin#summary","cites":[{"source":"machine:energy","machine":"hemoglobin","label":"Summary","section":"summary"},{"source":"link:serca","machine":"hemoglobin","label":"Link to SERCA calcium pump","section":"story"}]},{"id":"hemoglobin-two-dimers","machine":"hemoglobin","kind":"cloze","prompt":"Human adult hemoglobin has two alpha and two beta chains, arranged as a pair of {{alpha-beta dimers}}.","answer":"alpha-beta dimers","explanation":"Each dimer changes little inside itself, so the T-to-R switch is one dimer moving against the other.","section":"summary","topic":"parts","sources":["stat:Chains in the working unit","evidence:human-hb-tetramer-two-dimers","ref:fermi1984"],"tags":["structure","subunits"],"difficulty":1,"url":"/machines/hemoglobin#summary","cites":[{"source":"stat:Chains in the working unit","machine":"hemoglobin","label":"Key number: Chains in the working unit","section":"summary"},{"source":"evidence:human-hb-tetramer-two-dimers","machine":"hemoglobin","label":"Subunit arrangement of the human hemoglobin tetramer (Takahashi K 2024)","section":"evidence","anchor":"ev-human-hb-tetramer-two-dimers"},{"source":"ref:fermi1984","machine":"hemoglobin","label":"Fermi et al.","section":"sources","anchor":"ref-fermi1984","href":"https://doi.org/10.1016/0022-2836(84)90472-8"}]},{"id":"hemoglobin-sigmoid-why","machine":"hemoglobin","kind":"qa","prompt":"Why is hemoglobin's oxygen binding curve sigmoid?","answer":"Its four sites are not independent: the tetramer switches from a low-affinity T state to a high-affinity R state.","explanation":"Early oxygens bind weakly to T; once the tetramer snaps to R, the remaining hemes bind with much higher affinity.","section":"summary","topic":"purpose","sources":["machine:summary","mechanism:The last oxygens bind","ref:monod1965"],"tags":["cooperativity","allostery"],"difficulty":2,"url":"/machines/hemoglobin#summary","cites":[{"source":"machine:summary","machine":"hemoglobin","label":"Summary","section":"summary"},{"source":"mechanism:The last oxygens bind","machine":"hemoglobin","label":"Step: The last oxygens bind","section":"mechanism"},{"source":"ref:monod1965","machine":"hemoglobin","label":"Monod et al.","section":"sources","anchor":"ref-monod1965","href":"https://doi.org/10.1016/S0022-2836(65)80285-6"}]},{"id":"hemoglobin-hill-value","machine":"hemoglobin","kind":"cloze","prompt":"Unmodified, stroma-free human hemoglobin at pH 7.40 and 37 °C has a Hill coefficient of {{2.8}}.","answer":"2.8","explanation":"A Hill coefficient of 1 would mean each site binds on its own, so 2.8 means the first oxygens to bind make the others bind more tightly. Phosphate buffer at 29 °C gives values near 3.1.","section":"summary","topic":"numbers","sources":["stat:Hill coefficient","evidence:hill-coefficient-unmodified-hb","ref:vanderplas1988"],"tags":["cooperativity","hill"],"difficulty":2,"url":"/machines/hemoglobin#summary","cites":[{"source":"stat:Hill coefficient","machine":"hemoglobin","label":"Key number: Hill coefficient","section":"summary"},{"source":"evidence:hill-coefficient-unmodified-hb","machine":"hemoglobin","label":"Hill coefficient of unmodified human hemoglobin in solution (van der Plas J 1988)","section":"evidence","anchor":"ev-hill-coefficient-unmodified-hb"},{"source":"ref:vanderplas1988","machine":"hemoglobin","label":"van der Plas et al.","section":"sources","anchor":"ref-vanderplas1988","href":"https://doi.org/10.1046/j.1537-2995.1988.28689059024.x"}]},{"id":"hemoglobin-fetal-gamma","machine":"hemoglobin","kind":"qa","prompt":"Why does fetal hemoglobin hold oxygen more tightly than adult hemoglobin?","answer":"Its gamma chains, which replace beta, bind 2,3-BPG only weakly.","explanation":"2,3-BPG lowers oxygen affinity, so weak binding moves the fetal curve left and fetal blood can take oxygen from maternal blood.","section":"summary","topic":"parts","sources":["component:gamma","species:Human fetal hemoglobin","ref:sankaran2013"],"tags":["fetal","2,3-bpg"],"difficulty":2,"url":"/machines/hemoglobin#summary","cites":[{"source":"component:gamma","machine":"hemoglobin","label":"Part: gamma","section":"summary"},{"source":"species:Human fetal hemoglobin","machine":"hemoglobin","label":"Human fetal hemoglobin","section":"summary"},{"source":"ref:sankaran2013","machine":"hemoglobin","label":"Sankaran and Orkin, Cold Spring Harb Perspect Med 2013","section":"sources","anchor":"ref-sankaran2013","href":"https://doi.org/10.1101/cshperspect.a011643"}]},{"id":"hemoglobin-global-allostery","machine":"hemoglobin","kind":"qa","prompt":"In the global allostery model of hemoglobin, what carries much of the affinity change and most of the Bohr effect?","answer":"Tertiary changes inside both the T and the R state.","explanation":"Broader oxygen-binding measurements support this model (status: demonstrated). The two-state model stays useful as a compact fit, not as the final mechanism.","section":"summary","topic":"debate","sources":["frontier:Beyond two states","ref:yonetani2003"],"tags":["allostery","models"],"difficulty":3,"url":"/machines/hemoglobin#summary","cites":[{"source":"frontier:Beyond two states","machine":"hemoglobin","label":"Open question: Beyond two states","section":"summary"},{"source":"ref:yonetani2003","machine":"hemoglobin","label":"Yonetani and Tsuneshige, C R Biol 2003","section":"sources","anchor":"ref-yonetani2003","href":"https://doi.org/10.1016/s1631-0691(03)00150-1"}]},{"id":"hemoglobin-designed-switch","machine":"hemoglobin","kind":"qa","prompt":"Hemoglobin shows the minimum parts for an allosteric switch. What are the three parts?","answer":"A rigid dimer, one interface with exactly two good arrangements, and a ligand site that senses which arrangement it occupies.","explanation":"Designed allosteric switches aim at the same set of parts; this is a proposal, not yet a result.","section":"summary","topic":"debate","sources":["frontier:Designed allosteric switches","ref:baldwin1979"],"tags":["design","allostery"],"difficulty":3,"url":"/machines/hemoglobin#summary","cites":[{"source":"frontier:Designed allosteric switches","machine":"hemoglobin","label":"Open question: Designed allosteric switches","section":"summary"},{"source":"ref:baldwin1979","machine":"hemoglobin","label":"Baldwin and Chothia, J Mol Biol 1979","section":"sources","anchor":"ref-baldwin1979","href":"https://doi.org/10.1016/0022-2836(79)90277-8"}]},{"id":"hemoglobin-iron-into-plane","machine":"hemoglobin","kind":"cloze","prompt":"When the first oxygen binds a hemoglobin heme, the iron moves {{into the heme plane}}.","answer":"into the heme plane","explanation":"In the T state without oxygen, the iron sits slightly out of the heme plane. Its move is the local trigger of the switch.","section":"mechanism","topic":"cycle","sources":["mechanism:The first oxygen binds","mechanism:The T state waits","ref:perutz1970"],"tags":["heme","iron"],"difficulty":1,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"mechanism:The first oxygen binds","machine":"hemoglobin","label":"Step: The first oxygen binds","section":"mechanism"},{"source":"mechanism:The T state waits","machine":"hemoglobin","label":"Step: The T state waits","section":"mechanism"},{"source":"ref:perutz1970","machine":"hemoglobin","label":"Perutz, Nature 1970","section":"sources","anchor":"ref-perutz1970","href":"https://doi.org/10.1038/228726a0"}]},{"id":"hemoglobin-proximal-histidine","machine":"hemoglobin","kind":"qa","prompt":"In hemoglobin, what links the heme iron to the protein, so that the iron's move pulls on a helix?","answer":"The proximal histidine.","explanation":"The iron binds oxygen on one side and the proximal histidine on the other. As the iron moves into the plane, it drags the histidine and its helix along: a tertiary change inside one subunit.","section":"mechanism","topic":"parts","sources":["mechanism:The first oxygen binds","component:heme","ref:perutz1970"],"tags":["heme","histidine"],"difficulty":2,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"mechanism:The first oxygen binds","machine":"hemoglobin","label":"Step: The first oxygen binds","section":"mechanism"},{"source":"component:heme","machine":"hemoglobin","label":"Part: heme","section":"summary"},{"source":"ref:perutz1970","machine":"hemoglobin","label":"Perutz, Nature 1970","section":"sources","anchor":"ref-perutz1970","href":"https://doi.org/10.1038/228726a0"}]},{"id":"hemoglobin-switch-contact","machine":"hemoglobin","kind":"cloze","prompt":"In hemoglobin, the {{alpha1-beta2}} contact is the switch point between the T and R quaternary states.","answer":"alpha1-beta2","explanation":"The helix shift from a bound heme travels to this contact, so local binding becomes a global signal.","section":"mechanism","topic":"cycle","sources":["mechanism:The change reaches the dimer interface","ref:baldwin1979"],"tags":["interface","allostery"],"difficulty":2,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"mechanism:The change reaches the dimer interface","machine":"hemoglobin","label":"Step: The change reaches the dimer interface","section":"mechanism"},{"source":"ref:baldwin1979","machine":"hemoglobin","label":"Baldwin and Chothia, J Mol Biol 1979","section":"sources","anchor":"ref-baldwin1979","href":"https://doi.org/10.1016/0022-2836(79)90277-8"}]},{"id":"hemoglobin-quaternary-turn","machine":"hemoglobin","kind":"cloze","prompt":"When hemoglobin snaps from T to R, one alpha-beta dimer rotates by about {{14 degrees}} against the other.","answer":"14 degrees","explanation":"The site measured 14.2 degrees from 2HHB to 2DN3; a published analysis gives 15.0 degrees. The turn comes with a small screw translation of about 1.4 A.","section":"mechanism","topic":"numbers","sources":["mechanism:The tetramer snaps to R","stat:Quaternary turn, T to R","ref:baldwin1979","ref:takahashi2024"],"tags":["quaternary","rotation"],"difficulty":2,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"mechanism:The tetramer snaps to R","machine":"hemoglobin","label":"Step: The tetramer snaps to R","section":"mechanism"},{"source":"stat:Quaternary turn, T to R","machine":"hemoglobin","label":"Key number: Quaternary turn, T to R","section":"summary"},{"source":"ref:baldwin1979","machine":"hemoglobin","label":"Baldwin and Chothia, J Mol Biol 1979","section":"sources","anchor":"ref-baldwin1979","href":"https://doi.org/10.1016/0022-2836(79)90277-8"},{"source":"ref:takahashi2024","machine":"hemoglobin","label":"Takahashi et al.","section":"sources","anchor":"ref-takahashi2024","href":"https://doi.org/10.1038/s41467-024-49947-x"}]},{"id":"hemoglobin-tissue-effectors","machine":"hemoglobin","kind":"qa","prompt":"Which three small molecules in working tissue push hemoglobin back toward the T state?","answer":"Protons, carbon dioxide and 2,3-BPG.","explanation":"They bind the T state better than the R state, so the equilibrium shifts back to T and oxygen comes off where it is needed.","section":"mechanism","topic":"cycle","sources":["mechanism:Tissues push the switch back","ref:benesch1967"],"tags":["effectors","bohr"],"difficulty":2,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"mechanism:Tissues push the switch back","machine":"hemoglobin","label":"Step: Tissues push the switch back","section":"mechanism"},{"source":"ref:benesch1967","machine":"hemoglobin","label":"Benesch and Benesch, Biochem Biophys Res Commun 1967","section":"sources","anchor":"ref-benesch1967","href":"https://doi.org/10.1016/0006-291x(67)90228-8"}]},{"id":"hemoglobin-bpg-favours-t","machine":"hemoglobin","kind":"qa","prompt":"Why does 2,3-BPG favour the T state of hemoglobin?","answer":"It binds the central cavity between the beta chains, which is wide enough only in the T state.","explanation":"The central cavity narrows when the tetramer snaps to R. By binding T better than R, 2,3-BPG lowers oxygen affinity.","section":"mechanism","topic":"cycle","sources":["evidence:dpg-binding-site-low-salt","mechanism:The tetramer snaps to R","ref:richard1993"],"tags":["2,3-bpg","cavity"],"difficulty":3,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"evidence:dpg-binding-site-low-salt","machine":"hemoglobin","label":"Contacts made by 2,3-diphosphoglycerate in the central cavity of deoxyhemoglobin (Richard V 1993)","section":"evidence","anchor":"ev-dpg-binding-site-low-salt"},{"source":"mechanism:The tetramer snaps to R","machine":"hemoglobin","label":"Step: The tetramer snaps to R","section":"mechanism"},{"source":"ref:richard1993","machine":"hemoglobin","label":"Richard et al.","section":"sources","anchor":"ref-richard1993","href":"https://doi.org/10.1006/jmbi.1993.1505"}]},{"id":"hemoglobin-myoglobin-no-switch","machine":"hemoglobin","kind":"qa","prompt":"Myoglobin has the same globin fold as hemoglobin. Why does myoglobin show no cooperativity?","answer":"It has one chain and one heme, so it has no dimer interface where a tertiary change could become a quaternary one.","explanation":"Myoglobin keeps the ancestral job of storing and buffering oxygen in muscle; it is the control case for cooperativity.","section":"mechanism","topic":"parts","sources":["evolution:Cooperativity after the monomer","species:Myoglobin","ref:hardison2012"],"tags":["myoglobin","evolution"],"difficulty":3,"url":"/machines/hemoglobin#mechanism","cites":[{"source":"evolution:Cooperativity after the monomer","machine":"hemoglobin","label":"Cooperativity after the monomer","section":"summary"},{"source":"species:Myoglobin","machine":"hemoglobin","label":"Myoglobin","section":"summary"},{"source":"ref:hardison2012","machine":"hemoglobin","label":"Hardison, Cold Spring Harb Perspect Med 2012","section":"sources","anchor":"ref-hardison2012","href":"https://doi.org/10.1101/cshperspect.a011627"}]},{"id":"hemoglobin-per-red-cell","machine":"hemoglobin","kind":"cloze","prompt":"One human red blood cell holds about {{270 million}} hemoglobin molecules.","answer":"270 million","explanation":"At 4 oxygen per hemoglobin, a full red cell carries about 1.1 x 10^9 oxygen molecules.","section":"story","topic":"numbers","sources":["fact:N8","stop:rbc","fact:N18","ref:bnid102740"],"tags":["red-cell","scale"],"difficulty":2,"url":"/machines/hemoglobin#story","cites":[{"source":"fact:N8","machine":"hemoglobin","label":"Hemoglobin molecules in one red cell: 2.7 × 10^8","section":"story"},{"source":"stop:rbc","machine":"hemoglobin","label":"Big picture: Red blood cell","section":"story"},{"source":"fact:N18","machine":"hemoglobin","label":"Oxygen molecules in one full red cell: 1.1 × 10^9 O2","section":"story"},{"source":"ref:bnid102740","machine":"hemoglobin","label":"BNID 102740","section":"sources","href":"https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102740"}]},{"id":"hemoglobin-rbc-no-burn","machine":"hemoglobin","kind":"qa","prompt":"Why does a red blood cell not burn the oxygen its hemoglobin carries?","answer":"It has no mitochondria.","explanation":"A mature red cell has thrown out its nucleus and mitochondria; it is little more than a bag of hemoglobin.","section":"story","topic":"purpose","sources":["fact:N9","stop:rbc","ref:openstax-ap2e-18-3"],"tags":["red-cell"],"difficulty":1,"url":"/machines/hemoglobin#story","cites":[{"source":"fact:N9","machine":"hemoglobin","label":"Nucleus and mitochondria in a mature red cell: None","section":"story"},{"source":"stop:rbc","machine":"hemoglobin","label":"Big picture: Red blood cell","section":"story"},{"source":"ref:openstax-ap2e-18-3","machine":"hemoglobin","label":"OpenStax A&P 18.3","section":"sources","href":"https://openstax.org/books/anatomy-and-physiology-2e"}]},{"id":"hemoglobin-share-of-blood-oxygen","machine":"hemoglobin","kind":"cloze","prompt":"Hemoglobin carries about {{98.5%}} of the oxygen in blood; the rest is dissolved.","answer":"98.5%","explanation":"Water holds only a little oxygen, so blood packs almost all of it into hemoglobin. This is a textbook value.","section":"story","topic":"purpose","sources":["fact:N2","stop:body","ref:openstax-bio2e-39-4"],"tags":["oxygen","blood"],"difficulty":2,"url":"/machines/hemoglobin#story","cites":[{"source":"fact:N2","machine":"hemoglobin","label":"Share of blood oxygen carried by hemoglobin: 98.5 %","section":"story"},{"source":"stop:body","machine":"hemoglobin","label":"Big picture: You, breathing","section":"story"},{"source":"ref:openstax-bio2e-39-4","machine":"hemoglobin","label":"OpenStax Biology 2e","section":"sources","href":"https://openstax.org/books/biology-2e"}]},{"id":"hemoglobin-rest-extraction","machine":"hemoglobin","kind":"qa","prompt":"At rest, roughly what share of the oxygen delivered by hemoglobin do the body's tissues take?","answer":"About a quarter.","explanation":"Blood returns to the lungs about 74% saturated (a calculation, not a measurement), which leaves a reserve for when you run.","section":"story","topic":"numbers","sources":["fact:N16","stop:muscle"],"tags":["reserve","exercise"],"difficulty":2,"url":"/machines/hemoglobin#story","cites":[{"source":"fact:N16","machine":"hemoglobin","label":"Oxygen saturation of blood that returns from the body at rest: 74 %","section":"story"},{"source":"stop:muscle","machine":"hemoglobin","label":"Big picture: Working muscle","section":"story"}]},{"id":"hemoglobin-van-analogy-breaks","machine":"hemoglobin","kind":"qa","prompt":"Hemoglobin is like a delivery van with four seats that loads and unloads as a team. Where does that analogy break?","answer":"The seats do not fill one by one; the whole molecule flips between T and R, and that shape sets the grip of all four seats at once.","explanation":"The analogy gets the teamwork right: once some seats fill, the rest fill more easily. There is also no driver and no fuel.","section":"story","topic":"purpose","sources":["analogy:A delivery van with four seats that loads and unloads as a team"],"tags":["analogy","allostery"],"difficulty":2,"url":"/machines/hemoglobin#story","cites":[{"source":"analogy:A delivery van with four seats that loads and unloads as a team","machine":"hemoglobin","label":"Analogy: A delivery van with four seats that loads and unloads as a team","section":"story"}]},{"id":"hemoglobin-cas9-fetal","machine":"hemoglobin","kind":"qa","prompt":"How does an approved Cas9 therapy use hemoglobin to treat sickle cell disease?","answer":"It edits a person's blood stem cells so their red cells make fetal hemoglobin.","explanation":"Turning gamma back on treats sickle cell disease and beta-thalassaemia while leaving the hemoglobin protein untouched.","section":"story","topic":"purpose","sources":["link:cas9","frontier:Re-induced fetal hemoglobin","ref:frangoul2021","ref:sankaran2013"],"tags":["cas9","sickle","fetal"],"difficulty":2,"url":"/machines/hemoglobin#story","cites":[{"source":"link:cas9","machine":"hemoglobin","label":"Link to Cas9","section":"story"},{"source":"frontier:Re-induced fetal hemoglobin","machine":"hemoglobin","label":"Open question: Re-induced fetal hemoglobin","section":"summary"},{"source":"ref:frangoul2021","machine":"hemoglobin","label":"Frangoul 2021","section":"sources","href":"https://doi.org/10.1056/NEJMoa2031054"},{"source":"ref:sankaran2013","machine":"hemoglobin","label":"Sankaran and Orkin, Cold Spring Harb Perspect Med 2013","section":"sources","anchor":"ref-sankaran2013","href":"https://doi.org/10.1101/cshperspect.a011643"}]},{"id":"hemoglobin-p50-standard","machine":"hemoglobin","kind":"cloze","prompt":"Human blood under standard conditions (pH 7.4, pCO2 40 mmHg, 37 °C) has a P50 of {{26.6 mmHg}}.","answer":"26.6 mmHg","explanation":"P50 is the oxygen pressure at which half the hemoglobin carries oxygen; a higher P50 means blood gives up oxygen more easily. Clerbaux and colleagues measured it (26.6 +/- 1.2 mmHg) from whole dissociation curves of fresh blood.","section":"evidence","topic":"numbers","sources":["evidence:p50-human-standard","stat:P50, standard conditions","ref:clerbaux1993"],"tags":["p50","affinity"],"difficulty":2,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:p50-human-standard","machine":"hemoglobin","label":"Oxygen pressure at half saturation of human blood under standard conditions (standard P50) (Clerbaux T 1993)","section":"evidence","anchor":"ev-p50-human-standard"},{"source":"stat:P50, standard conditions","machine":"hemoglobin","label":"Key number: P50, standard conditions","section":"summary"},{"source":"ref:clerbaux1993","machine":"hemoglobin","label":"Clerbaux et al.","section":"sources","anchor":"ref-clerbaux1993","href":"https://doi.org/10.1016/0300-9629(93)90382-e"}]},{"id":"hemoglobin-hill-steepness","machine":"hemoglobin","kind":"qa","prompt":"With a Hill coefficient of 2.8, by what factor must oxygen pressure rise to take hemoglobin from 10% to 90% saturation?","answer":"About 4.8-fold (against 81-fold with no cooperativity).","explanation":"Cooperativity makes the curve steep: the first oxygens to bind make the others bind more tightly. Van der Plas and colleagues measured n = 2.8 on purified human hemoglobin.","section":"evidence","topic":"numbers","sources":["evidence:hill-coefficient-unmodified-hb","ref:vanderplas1988"],"tags":["cooperativity","hill"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:hill-coefficient-unmodified-hb","machine":"hemoglobin","label":"Hill coefficient of unmodified human hemoglobin in solution (van der Plas J 1988)","section":"evidence","anchor":"ev-hill-coefficient-unmodified-hb"},{"source":"ref:vanderplas1988","machine":"hemoglobin","label":"van der Plas et al.","section":"sources","anchor":"ref-vanderplas1988","href":"https://doi.org/10.1046/j.1537-2995.1988.28689059024.x"}]},{"id":"hemoglobin-bohr-meaning","machine":"hemoglobin","kind":"qa","prompt":"Human hemoglobin has a Bohr coefficient of -0.29. What does a pH drop of 0.1 unit do to its P50?","answer":"Raises it by about 7 percent.","explanation":"Van der Plas and colleagues took the slope of log P50 against pH over pH 7.1 to 7.7. Acid from working muscle therefore makes hemoglobin release more oxygen.","section":"evidence","topic":"numbers","sources":["evidence:bohr-coefficient-unmodified-hb","stat:Bohr coefficient","ref:vanderplas1988"],"tags":["bohr","ph"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:bohr-coefficient-unmodified-hb","machine":"hemoglobin","label":"Proton Bohr factor of unmodified human hemoglobin (van der Plas J 1988)","section":"evidence","anchor":"ev-bohr-coefficient-unmodified-hb"},{"source":"stat:Bohr coefficient","machine":"hemoglobin","label":"Key number: Bohr coefficient","section":"summary"},{"source":"ref:vanderplas1988","machine":"hemoglobin","label":"van der Plas et al.","section":"sources","anchor":"ref-vanderplas1988","href":"https://doi.org/10.1046/j.1537-2995.1988.28689059024.x"}]},{"id":"hemoglobin-iron-out-of-plane","machine":"hemoglobin","kind":"qa","prompt":"In crystals of human deoxyhemoglobin, how far does the heme iron sit from the porphyrin plane?","answer":"About 0.4 A: 0.40 A in the alpha hemes, 0.36 A in the beta hemes.","explanation":"Fermi and colleagues measured this by X-ray crystallography at 1.74 A. In oxyhemoglobin the iron sits almost in the plane; that shift is the trigger the Perutz mechanism builds on.","section":"evidence","topic":"numbers","sources":["evidence:iron-out-of-plane-deoxy","fact:N13","ref:fermi1984"],"tags":["heme","iron","x-ray"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:iron-out-of-plane-deoxy","machine":"hemoglobin","label":"Displacement of the heme iron from the porphyrin nitrogen plane in deoxyhemoglobin (Fermi G 1984)","section":"evidence","anchor":"ev-iron-out-of-plane-deoxy"},{"source":"fact:N13","machine":"hemoglobin","label":"Distance of the iron from the heme plane without oxygen: 0.36–0.40 Å","section":"story"},{"source":"ref:fermi1984","machine":"hemoglobin","label":"Fermi et al.","section":"sources","anchor":"ref-fermi1984","href":"https://doi.org/10.1016/0022-2836(84)90472-8"}]},{"id":"hemoglobin-t-state-oxy-crystal","machine":"hemoglobin","kind":"qa","prompt":"When T-state hemoglobin crystals were oxygenated at all four hemes, what moved toward R while the tetramer stayed T?","answer":"The heme pockets and the alpha1-beta2 interface.","explanation":"The crystal lattice held the tetramer in T, separating the tertiary change from the quaternary switch. The hemes affect each other even inside the T state.","section":"evidence","topic":"cycle","sources":["evidence:four-hemes-bind-oxygen","ref:paoli1996"],"tags":["t-state","x-ray"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:four-hemes-bind-oxygen","machine":"hemoglobin","label":"Number of heme sites that bind oxygen in one tetramer, shown with the T quaternary structure kept (Paoli M 1996)","section":"evidence","anchor":"ev-four-hemes-bind-oxygen"},{"source":"ref:paoli1996","machine":"hemoglobin","label":"Paoli et al.","section":"sources","anchor":"ref-paoli1996","href":"https://doi.org/10.1006/jmbi.1996.0124"}]},{"id":"hemoglobin-effectors-in-r","machine":"hemoglobin","kind":"qa","prompt":"In R-state crystals of horse hemoglobin, what did the effector bezafibrate do to oxygen affinity?","answer":"Lowered it about threefold (P50 from 0.32 to 0.91 torr), with binding still non-cooperative.","explanation":"The lattice blocks the switch to T, so effectors can weaken the R state itself, not only shift the T-R balance as the two-state model assumes.","section":"evidence","topic":"debate","sources":["evidence:effectors-act-inside-the-r-state","frontier:Beyond two states","ref:shibayama2025"],"tags":["effectors","r-state","models"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:effectors-act-inside-the-r-state","machine":"hemoglobin","label":"Change in R-state oxygen affinity caused by allosteric effectors, with the quaternary structure held fixed (Shibayama N 2025)","section":"evidence","anchor":"ev-effectors-act-inside-the-r-state"},{"source":"frontier:Beyond two states","machine":"hemoglobin","label":"Open question: Beyond two states","section":"summary"},{"source":"ref:shibayama2025","machine":"hemoglobin","label":"Shibayama, Protein Sci 2025","section":"sources","anchor":"ref-shibayama2025","href":"https://doi.org/10.1002/pro.5232"}]},{"id":"hemoglobin-cryoem-r2","machine":"hemoglobin","kind":"cloze","prompt":"Cryo-EM puts liganded human hemoglobin, free of crystal contacts, closest to the {{R2}} quaternary arrangement.","answer":"R2","explanation":"Its dimers turn 22.1 degrees against deoxy hemoglobin, against 15.0 degrees for the R crystal form, so the single R state of the two-state picture is a simplification.","section":"evidence","topic":"debate","sources":["evidence:liganded-human-hb-closer-to-r2","frontier:Beyond two states","ref:takahashi2024"],"tags":["cryo-em","r2","models"],"difficulty":3,"url":"/machines/hemoglobin#evidence","cites":[{"source":"evidence:liganded-human-hb-closer-to-r2","machine":"hemoglobin","label":"Quaternary position of liganded human hemoglobin measured by cryo-EM in solution-like conditions (Takahashi K 2024)","section":"evidence","anchor":"ev-liganded-human-hb-closer-to-r2"},{"source":"frontier:Beyond two states","machine":"hemoglobin","label":"Open question: Beyond two states","section":"summary"},{"source":"ref:takahashi2024","machine":"hemoglobin","label":"Takahashi et al.","section":"sources","anchor":"ref-takahashi2024","href":"https://doi.org/10.1038/s41467-024-49947-x"}]}]}