{"format":"molecular-machines.cards","version":1,"updated":"2026-10-01","decks":[{"machine":"atp-synthase","name":"ATP synthase","count":28,"url":"/learn/cards/atp-synthase.json"}],"cards":[{"id":"atp-synthase-energy-source","machine":"atp-synthase","kind":"cloze","prompt":"ATP synthase in mitochondria is driven by the {{proton-motive force}} across the inner membrane.","answer":"proton-motive force","explanation":"Protons flow back down their gradient through the machine. Some bacteria use a sodium-motive force instead.","section":"summary","topic":"purpose","sources":["machine:energy","machine:where"],"tags":["energy","protons"],"difficulty":1,"url":"/machines/atp-synthase#summary","cites":[{"source":"machine:energy","machine":"atp-synthase","label":"Summary","section":"summary"},{"source":"machine:where","machine":"atp-synthase","label":"Summary","section":"summary"}]},{"id":"atp-synthase-ring-of-c-subunits","machine":"atp-synthase","kind":"cloze","prompt":"In ATP synthase, protons crossing the membrane spin a ring of {{c subunits}}.","answer":"c subunits","explanation":"Each c subunit carries one proton site on a conserved carboxylate, so the c-ring turns as sites load and unload.","section":"summary","topic":"parts","sources":["machine:summary","component:c-ring"],"tags":["c-ring","rotation"],"difficulty":1,"url":"/machines/atp-synthase#summary","cites":[{"source":"machine:summary","machine":"atp-synthase","label":"Summary","section":"summary"},{"source":"component:c-ring","machine":"atp-synthase","label":"Part: c-ring","section":"summary"}]},{"id":"atp-synthase-gamma-role","machine":"atp-synthase","kind":"qa","prompt":"Which ATP synthase subunit turns inside the α3β3 head and sets the state of each catalytic β subunit?","answer":"γ, the central stalk.","explanation":"The c-ring carries γ with it, so γ links the membrane rotor to the three catalytic sites in the head.","section":"summary","topic":"parts","sources":["component:γ","mechanism:The rotor turns the central stalk","ref:noji1997"],"tags":["gamma","rotation"],"difficulty":1,"url":"/machines/atp-synthase#summary","cites":[{"source":"component:γ","machine":"atp-synthase","label":"Part: γ","section":"summary"},{"source":"mechanism:The rotor turns the central stalk","machine":"atp-synthase","label":"Step: The rotor turns the central stalk","section":"mechanism"},{"source":"ref:noji1997","machine":"atp-synthase","label":"Noji et al.","section":"sources","anchor":"ref-noji1997","href":"https://doi.org/10.1038/386299a0"}]},{"id":"atp-synthase-atp-per-turn","machine":"atp-synthase","kind":"cloze","prompt":"One full turn of the ATP synthase rotor makes {{3}} ATP, one per β subunit.","answer":"3","explanation":"There are three catalytic β subunits, and each 120° turn of γ releases one ATP.","section":"summary","topic":"numbers","sources":["stat:ATP per full turn","ref:watt2010"],"tags":["atp","numbers"],"difficulty":1,"url":"/machines/atp-synthase#summary","cites":[{"source":"stat:ATP per full turn","machine":"atp-synthase","label":"Key number: ATP per full turn","section":"summary"},{"source":"ref:watt2010","machine":"atp-synthase","label":"Watt et al.","section":"sources","anchor":"ref-watt2010","href":"https://doi.org/10.1073/pnas.1011099107"}]},{"id":"atp-synthase-c-ring-range","machine":"atp-synthase","kind":"cloze","prompt":"Across species, the ATP synthase c-ring has {{8 to 15}} c subunits.","answer":"8 to 15","explanation":"It runs from c8 in animal mitochondria to c15 in Spirulina. A bigger ring costs more protons per ATP.","section":"summary","topic":"numbers","sources":["stat:c-ring size across species","evolution:Ring size as gear ratio","ref:watt2010"],"tags":["c-ring","species"],"difficulty":2,"url":"/machines/atp-synthase#summary","cites":[{"source":"stat:c-ring size across species","machine":"atp-synthase","label":"Key number: c-ring size across species","section":"summary"},{"source":"evolution:Ring size as gear ratio","machine":"atp-synthase","label":"Ring size as gear ratio","section":"summary"},{"source":"ref:watt2010","machine":"atp-synthase","label":"Watt et al.","section":"sources","anchor":"ref-watt2010","href":"https://doi.org/10.1073/pnas.1011099107"}]},{"id":"atp-synthase-bedaquiline","machine":"atp-synthase","kind":"qa","prompt":"How does the tuberculosis drug bedaquiline stop the mycobacterial ATP synthase?","answer":"It jams the c-ring, so the rotor stalls.","explanation":"It treats multidrug-resistant tuberculosis. Structures of the drug on the bacterial and human enzymes now guide safer analogs.","section":"summary","topic":"debate","sources":["frontier:Drugs that jam the rotor","species:Mycobacteria","ref:preiss2015","ref:andries2005"],"tags":["drug","c-ring"],"difficulty":2,"url":"/machines/atp-synthase#summary","cites":[{"source":"frontier:Drugs that jam the rotor","machine":"atp-synthase","label":"Open question: Drugs that jam the rotor","section":"summary"},{"source":"species:Mycobacteria","machine":"atp-synthase","label":"Mycobacteria","section":"summary"},{"source":"ref:preiss2015","machine":"atp-synthase","label":"Preiss et al.","section":"sources","anchor":"ref-preiss2015","href":"https://doi.org/10.1126/sciadv.1500106"},{"source":"ref:andries2005","machine":"atp-synthase","label":"Andries et al.","section":"sources","anchor":"ref-andries2005","href":"https://doi.org/10.1126/science.1106753"}]},{"id":"atp-synthase-custom-ratio-use","machine":"atp-synthase","kind":"qa","prompt":"Why would an engineered ATP synthase with a higher H+/ATP ratio (up to 5.8) be useful?","answer":"It could make ATP at proton gradients too weak for natural enzymes.","explanation":"Point mutations change the c-ring size, and extra peripheral stalks raise H+/ATP to 5.8. This work is still lab-scale.","section":"summary","topic":"debate","sources":["frontier:Custom proton-to-ATP ratios","ref:ueno2025","ref:pogoryelov2012"],"tags":["engineering","h-per-atp"],"difficulty":2,"url":"/machines/atp-synthase#summary","cites":[{"source":"frontier:Custom proton-to-ATP ratios","machine":"atp-synthase","label":"Open question: Custom proton-to-ATP ratios","section":"summary"},{"source":"ref:ueno2025","machine":"atp-synthase","label":"Ueno et al.","section":"sources","anchor":"ref-ueno2025","href":"https://doi.org/10.1038/s41467-025-61227-w"},{"source":"ref:pogoryelov2012","machine":"atp-synthase","label":"Pogoryelov et al.","section":"sources","anchor":"ref-pogoryelov2012","href":"https://doi.org/10.1073/pnas.1120027109"}]},{"id":"atp-synthase-arginine-barrier","machine":"atp-synthase","kind":"qa","prompt":"Why can a proton not slip straight across subunit a of ATP synthase?","answer":"The two half-channels in subunit a do not meet, and a conserved arginine sits between them.","explanation":"So the only way through is to ride on the c-ring almost a full turn, from one half-channel to the other.","section":"mechanism","topic":"cycle","sources":["step:Protons cross subunit a","mechanism:The proton leaves on the other side","ref:allegretti2015"],"tags":["subunit-a","protons"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"step:Protons cross subunit a","machine":"atp-synthase","label":"Step: Protons cross subunit a","section":"mechanism"},{"source":"mechanism:The proton leaves on the other side","machine":"atp-synthase","label":"Step: The proton leaves on the other side","section":"mechanism"},{"source":"ref:allegretti2015","machine":"atp-synthase","label":"Allegretti et al.","section":"sources","anchor":"ref-allegretti2015","href":"https://doi.org/10.1038/nature14185"}]},{"id":"atp-synthase-neutral-site-enters-lipid","machine":"atp-synthase","kind":"qa","prompt":"Why can only a protonated site on the ATP synthase c-ring turn into the membrane lipid?","answer":"A neutral carboxylate can enter the oily core of the membrane; a charged one cannot.","explanation":"Thermal motion jiggles the ring, and this charge rule lets only forward turns stick. The proton gradient pays for that bias.","section":"mechanism","topic":"cycle","sources":["step:The c-ring turns one step","mechanism:The c-ring glutamate takes the proton","ref:meier2005"],"tags":["c-ring","protons"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"step:The c-ring turns one step","machine":"atp-synthase","label":"Step: The c-ring turns one step","section":"mechanism"},{"source":"mechanism:The c-ring glutamate takes the proton","machine":"atp-synthase","label":"Step: The c-ring glutamate takes the proton","section":"mechanism"},{"source":"ref:meier2005","machine":"atp-synthase","label":"Meier et al.","section":"sources","anchor":"ref-meier2005","href":"https://doi.org/10.1126/science.1111199"}]},{"id":"atp-synthase-binding-change","machine":"atp-synthase","kind":"cloze","prompt":"In ATP synthase, each 120° turn of γ moves every β subunit {{one state along}}.","answer":"one state along","explanation":"At any moment one β is open and empty and two are closed. This is Boyer's binding-change mechanism.","section":"mechanism","topic":"cycle","sources":["step:Each β changes shape","mechanism:Each β cycles through three states","ref:boyer1997"],"tags":["beta","binding-change"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"step:Each β changes shape","machine":"atp-synthase","label":"Step: Each β changes shape","section":"mechanism"},{"source":"mechanism:Each β cycles through three states","machine":"atp-synthase","label":"Step: Each β cycles through three states","section":"mechanism"},{"source":"ref:boyer1997","machine":"atp-synthase","label":"Boyer, Annu Rev Biochem 1997","section":"sources","anchor":"ref-boyer1997","href":"https://doi.org/10.1146/annurev.biochem.66.1.717"}]},{"id":"atp-synthase-tight-site","machine":"atp-synthase","kind":"cloze","prompt":"In ATP synthase, a β site takes up ADP and phosphate while open, and ATP forms when the site closes {{tightly}}.","answer":"tightly","explanation":"Open, loose and tight follow each other as γ turns 120° at a time. The next opening releases the ATP.","section":"mechanism","topic":"cycle","sources":["step:ATP forms and leaves","mechanism:Each β cycles through three states","ref:boyer1997"],"tags":["beta","binding-change"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"step:ATP forms and leaves","machine":"atp-synthase","label":"Step: ATP forms and leaves","section":"mechanism"},{"source":"mechanism:Each β cycles through three states","machine":"atp-synthase","label":"Step: Each β cycles through three states","section":"mechanism"},{"source":"ref:boyer1997","machine":"atp-synthase","label":"Boyer, Annu Rev Biochem 1997","section":"sources","anchor":"ref-boyer1997","href":"https://doi.org/10.1146/annurev.biochem.66.1.717"}]},{"id":"atp-synthase-energy-goes-to-release","machine":"atp-synthase","kind":"qa","prompt":"In ATP synthase, which part of the catalytic cycle uses most of the proton energy?","answer":"Releasing the finished ATP from the site.","explanation":"The proton-motive force is used mainly to release ATP from the site, not to form it. The turning stalk pries the new ATP loose.","section":"mechanism","topic":"cycle","sources":["fact:A26","stop:site","ref:boyer1998"],"tags":["energy","binding-change"],"difficulty":3,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"fact:A26","machine":"atp-synthase","label":"Where the proton energy goes: Most into releasing ATP","section":"story"},{"source":"stop:site","machine":"atp-synthase","label":"Big picture: Catalytic site","section":"story"},{"source":"ref:boyer1998","machine":"atp-synthase","label":"Boyer 1998","section":"sources","href":"https://doi.org/10.1002/(SICI)1521-3773(19980918)37:17<2296::AID-ANIE2296>3.0.CO;2-W"}]},{"id":"atp-synthase-symmetry-mismatch","machine":"atp-synthase","kind":"qa","prompt":"How can an 8-subunit c-ring drive an ATP synthase head that works in three 120° steps?","answer":"The stalks and the head flex to absorb the mismatch.","explanation":"The rotor and stalk store elastic energy between proton steps. E. coli structures show the peripheral stalk bending and twisting as the rotor moves.","section":"mechanism","topic":"cycle","sources":["step:γ turns inside the head","mechanism:The rotor turns the central stalk","analogy:A loaded spring","ref:sobti2020"],"tags":["elastic","c-ring"],"difficulty":3,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"step:γ turns inside the head","machine":"atp-synthase","label":"Step: γ turns inside the head","section":"mechanism"},{"source":"mechanism:The rotor turns the central stalk","machine":"atp-synthase","label":"Step: The rotor turns the central stalk","section":"mechanism"},{"source":"analogy:A loaded spring","machine":"atp-synthase","label":"Analogy: A loaded spring","section":"story"},{"source":"ref:sobti2020","machine":"atp-synthase","label":"Sobti et al.","section":"sources","anchor":"ref-sobti2020","href":"https://doi.org/10.1038/s41467-020-16387-2"}]},{"id":"atp-synthase-reverse-mode","machine":"atp-synthase","kind":"qa","prompt":"What does ATP synthase do when ATP is present but the proton gradient is weak?","answer":"It runs backward: F1 drives the rotor the other way and Fo pumps protons.","explanation":"In mitochondria, the inhibitor protein IF1 blocks this reverse mode.","section":"mechanism","topic":"cycle","sources":["mechanism:The motor runs both ways","component:IF1","ref:noji1997","ref:diez2004"],"tags":["reverse","if1"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"mechanism:The motor runs both ways","machine":"atp-synthase","label":"Step: The motor runs both ways","section":"mechanism"},{"source":"component:IF1","machine":"atp-synthase","label":"Part: IF1","section":"summary"},{"source":"ref:noji1997","machine":"atp-synthase","label":"Noji et al.","section":"sources","anchor":"ref-noji1997","href":"https://doi.org/10.1038/386299a0"},{"source":"ref:diez2004","machine":"atp-synthase","label":"Diez et al.","section":"sources","anchor":"ref-diez2004","href":"https://doi.org/10.1038/nsmb718"}]},{"id":"atp-synthase-n-over-3","machine":"atp-synthase","kind":"qa","prompt":"Why does an ATP synthase with a c-ring of n subunits spend n/3 protons per ATP?","answer":"One full turn moves n protons, one per c subunit, and makes 3 ATP.","explanation":"So animals (c8) pay 2.7 protons per ATP, yeast (c10) 3.3 and chloroplasts (c14) 4.7.","section":"mechanism","topic":"cycle","sources":["mechanism:One turn costs n protons","ref:watt2010"],"tags":["h-per-atp","c-ring"],"difficulty":2,"url":"/machines/atp-synthase#mechanism","cites":[{"source":"mechanism:One turn costs n protons","machine":"atp-synthase","label":"Step: One turn costs n protons","section":"mechanism"},{"source":"ref:watt2010","machine":"atp-synthase","label":"Watt et al.","section":"sources","anchor":"ref-watt2010","href":"https://doi.org/10.1073/pnas.1011099107"}]},{"id":"atp-synthase-body-weight-per-day","machine":"atp-synthase","kind":"cloze","prompt":"A person remakes about {{their own body weight}} of ATP every day, most of it made by ATP synthase.","answer":"their own body weight","explanation":"An estimate from oxygen use: 54–68 kg a day for a college student.","section":"story","topic":"purpose","sources":["fact:A2","stop:body","story:summary","ref:bnid105606"],"tags":["atp","body"],"difficulty":1,"url":"/machines/atp-synthase#story","cites":[{"source":"fact:A2","machine":"atp-synthase","label":"ATP remade per day: 1 body weight","section":"story"},{"source":"stop:body","machine":"atp-synthase","label":"Big picture: You","section":"story"},{"source":"story:summary","machine":"atp-synthase","label":"Big picture","section":"story"},{"source":"ref:bnid105606","machine":"atp-synthase","label":"BNID 105606","section":"sources","href":"https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105606"}]},{"id":"atp-synthase-heart-stock","machine":"atp-synthase","kind":"qa","prompt":"Why must the ATP synthases of the heart make ATP as fast as the heart uses it?","answer":"The heart keeps only a few seconds' worth of ATP in stock.","explanation":"Yet the heart cycles about 6 kg of ATP a day, an estimate from a review.","section":"story","topic":"purpose","sources":["fact:A6","stop:heart","fact:A4","ref:grynberg1996"],"tags":["heart","atp"],"difficulty":1,"url":"/machines/atp-synthase#story","cites":[{"source":"fact:A6","machine":"atp-synthase","label":"The heart's ATP store: a few seconds of beating","section":"story"},{"source":"stop:heart","machine":"atp-synthase","label":"Big picture: Heart","section":"story"},{"source":"fact:A4","machine":"atp-synthase","label":"ATP cycled by the heart: 6 kg per day","section":"story"},{"source":"ref:grynberg1996","machine":"atp-synthase","label":"Grynberg 1996","section":"sources","href":"https://doi.org/10.1097/00005344-199600003-00003"}]},{"id":"atp-synthase-atp-per-second","machine":"atp-synthase","kind":"cloze","prompt":"One mitochondrial ATP synthase turning about 100 times per second makes about {{300}} ATP per second.","answer":"300","explanation":"3 ATP per turn × about 100 turns per second. The 100 turns per second is an estimate quoted from earlier work, not a direct measurement.","section":"story","topic":"numbers","sources":["fact:A22","fact:A14","stat:Turn rate in mitochondria","ref:watt2010"],"tags":["numbers","speed"],"difficulty":2,"url":"/machines/atp-synthase#story","cites":[{"source":"fact:A22","machine":"atp-synthase","label":"ATP per second, one synthase: 300 per second","section":"story"},{"source":"fact:A14","machine":"atp-synthase","label":"Turn rate in mitochondria: 100 turns per second","section":"story"},{"source":"stat:Turn rate in mitochondria","machine":"atp-synthase","label":"Key number: Turn rate in mitochondria","section":"summary"},{"source":"ref:watt2010","machine":"atp-synthase","label":"Watt et al.","section":"sources","anchor":"ref-watt2010","href":"https://doi.org/10.1073/pnas.1011099107"}]},{"id":"atp-synthase-turbine-breaks","machine":"atp-synthase","kind":"qa","prompt":"Where does the water-turbine analogy for ATP synthase break down?","answer":"Protons do not push on blades: each binds a site on the ring, rides almost a full turn and leaves.","explanation":"Thermal motion turns the ring, and binding and release set the direction. The \"turbine\" also runs backward as a pump.","section":"story","topic":"purpose","sources":["analogy:A water turbine below a dam","stop:machine"],"tags":["analogy","protons"],"difficulty":2,"url":"/machines/atp-synthase#story","cites":[{"source":"analogy:A water turbine below a dam","machine":"atp-synthase","label":"Analogy: A water turbine below a dam","section":"story"},{"source":"stop:machine","machine":"atp-synthase","label":"Big picture: The machine","section":"story"}]},{"id":"atp-synthase-flagellar-link","machine":"atp-synthase","kind":"qa","prompt":"How does the bacterial flagellar motor use a proton gradient differently from ATP synthase?","answer":"It turns the gradient straight into rotation, with no ATP in between.","explanation":"Both are ion-driven rotary motors, and the flagellar export ATPase FliI resembles the F1 α and β subunits.","section":"story","topic":"purpose","sources":["link:flagellar-motor","evolution:Shared parts with the flagellum","ref:imada2007"],"tags":["flagellum","rotation"],"difficulty":2,"url":"/machines/atp-synthase#story","cites":[{"source":"link:flagellar-motor","machine":"atp-synthase","label":"Link to Bacterial flagellar motor","section":"story"},{"source":"evolution:Shared parts with the flagellum","machine":"atp-synthase","label":"Shared parts with the flagellum","section":"summary"},{"source":"ref:imada2007","machine":"atp-synthase","label":"Imada et al.","section":"sources","anchor":"ref-imada2007","href":"https://doi.org/10.1073/pnas.0608090104"}]},{"id":"atp-synthase-first-rotation-method","machine":"atp-synthase","kind":"qa","prompt":"How did Noji and colleagues (1997) first see the γ rotor of F1 (the ATP synthase head) turn?","answer":"They fixed F1 to glass, attached a fluorescent actin filament to γ and filmed it spinning.","explanation":"The system was the α3β3γ part of thermophilic Bacillus PS3 F1, driven by ATP. From the drag on long filaments they set a lower limit of about 40 pN·nm on the torque.","section":"evidence","topic":"numbers","sources":["evidence:f1-rotation-torque","stat:Torque of F1","ref:noji1997"],"tags":["single-molecule","rotation"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:f1-rotation-torque","machine":"atp-synthase","label":"Torque of the F1 motor under high load (Noji H 1997)","section":"evidence","anchor":"ev-f1-rotation-torque"},{"source":"stat:Torque of F1","machine":"atp-synthase","label":"Key number: Torque of F1","section":"summary"},{"source":"ref:noji1997","machine":"atp-synthase","label":"Noji et al.","section":"sources","anchor":"ref-noji1997","href":"https://doi.org/10.1038/386299a0"}]},{"id":"atp-synthase-one-atp-per-step","machine":"atp-synthase","kind":"qa","prompt":"How did Yasuda and colleagues (1998) show that each 120° step of F1 in ATP synthase uses one ATP?","answer":"At low ATP, the rotation rate was about one third of the ATPase rate in solution.","explanation":"The waits between 120° steps also fit one ATP binding per step. So three ATP are used per turn.","section":"evidence","topic":"numbers","sources":["evidence:f1-steps-one-atp","stat:ATP per full turn","ref:yasuda1998"],"tags":["single-molecule","atp"],"difficulty":3,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:f1-steps-one-atp","machine":"atp-synthase","label":"ATP used per 120° step of γ (Yasuda R 1998)","section":"evidence","anchor":"ev-f1-steps-one-atp"},{"source":"stat:ATP per full turn","machine":"atp-synthase","label":"Key number: ATP per full turn","section":"summary"},{"source":"ref:yasuda1998","machine":"atp-synthase","label":"Yasuda et al.","section":"sources","anchor":"ref-yasuda1998","href":"https://doi.org/10.1016/s0092-8674(00)81456-7"}]},{"id":"atp-synthase-work-per-step","machine":"atp-synthase","kind":"qa","prompt":"In F1 of ATP synthase, how does the work done in one 120° step compare with the free energy of one ATP?","answer":"They are about equal: about 90 pN·nm against 80–110 pN·nm.","explanation":"So F1 turns nearly all the energy of an ATP into rotation. The authors note the scatter does not exclude efficiencies near 50%.","section":"evidence","topic":"numbers","sources":["evidence:f1-work-per-step","stat:Work per 120° step","ref:yasuda1998"],"tags":["efficiency","torque"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:f1-work-per-step","machine":"atp-synthase","label":"Mechanical work done in one 120° step (Yasuda R 1998)","section":"evidence","anchor":"ev-f1-work-per-step"},{"source":"stat:Work per 120° step","machine":"atp-synthase","label":"Key number: Work per 120° step","section":"summary"},{"source":"ref:yasuda1998","machine":"atp-synthase","label":"Yasuda et al.","section":"sources","anchor":"ref-yasuda1998","href":"https://doi.org/10.1016/s0092-8674(00)81456-7"}]},{"id":"atp-synthase-hand-cranked-synthesis","machine":"atp-synthase","kind":"qa","prompt":"What did Itoh and colleagues (2004) show by turning γ of isolated F1 with magnets in the synthesis direction?","answer":"ATP appeared, so turning the shaft alone is enough to make ATP.","explanation":"There was no proton gradient, and ATP appeared only when γ turned the right way. In the whole ATP synthase, the protons only supply the turning.","section":"evidence","topic":"numbers","sources":["evidence:f1-mechanical-synthesis","step:ATP forms and leaves","ref:itoh2004"],"tags":["rotation","synthesis"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:f1-mechanical-synthesis","machine":"atp-synthase","label":"ATP made by forcing γ to turn (Itoh H 2004)","section":"evidence","anchor":"ev-f1-mechanical-synthesis"},{"source":"step:ATP forms and leaves","machine":"atp-synthase","label":"Step: ATP forms and leaves","section":"mechanism"},{"source":"ref:itoh2004","machine":"atp-synthase","label":"Itoh et al.","section":"sources","anchor":"ref-itoh2004","href":"https://doi.org/10.1038/nature02212"}]},{"id":"atp-synthase-substeps","machine":"atp-synthase","kind":"cloze","prompt":"Each 120° step of the F1 rotor of ATP synthase splits into substeps of about {{80° and 40°}}.","answer":"80° and 40°","explanation":"They were first reported as about 90° and 30° (gold bead, high-speed camera); a slow β mutant later let the same group refine them to 81° and 39°.","section":"evidence","topic":"numbers","sources":["evidence:f1-substeps-80-40","evidence:f1-substeps-90-30","stat:Step size","ref:shimabukuro2003"],"tags":["substeps","rotation"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:f1-substeps-80-40","machine":"atp-synthase","label":"Refined substep angles (Shimabukuro K 2003)","section":"evidence","anchor":"ev-f1-substeps-80-40"},{"source":"evidence:f1-substeps-90-30","machine":"atp-synthase","label":"Substeps within each 120° step (Yasuda R 2001)","section":"evidence","anchor":"ev-f1-substeps-90-30"},{"source":"stat:Step size","machine":"atp-synthase","label":"Key number: Step size","section":"summary"},{"source":"ref:shimabukuro2003","machine":"atp-synthase","label":"Shimabukuro et al.","section":"sources","anchor":"ref-shimabukuro2003","href":"https://doi.org/10.1073/pnas.2434983100"}]},{"id":"atp-synthase-c8-method","machine":"atp-synthase","kind":"qa","prompt":"How did Watt and colleagues (2010) find that the animal ATP synthase c-ring has 8 subunits?","answer":"X-ray crystallography of the F1–c-ring complex from cow heart mitochondria.","explanation":"Eight protons and three ATP per turn give 2.7 H+/ATP. That is a ratio from structure, not a thermodynamic measurement.","section":"evidence","topic":"numbers","sources":["evidence:c8-ring-bovine","stat:H+ per ATP in animals","ref:watt2010"],"tags":["c-ring","x-ray"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:c8-ring-bovine","machine":"atp-synthase","label":"Number of c subunits in the mammalian c-ring (Watt IN 2010)","section":"evidence","anchor":"ev-c8-ring-bovine"},{"source":"stat:H+ per ATP in animals","machine":"atp-synthase","label":"Key number: H+ per ATP in animals","section":"summary"},{"source":"ref:watt2010","machine":"atp-synthase","label":"Watt et al.","section":"sources","anchor":"ref-watt2010","href":"https://doi.org/10.1073/pnas.1011099107"}]},{"id":"atp-synthase-equilibrium-method","machine":"atp-synthase","kind":"qa","prompt":"How did Petersen and colleagues (2012) measure the H+/ATP ratio of ATP synthase in lipid vesicles?","answer":"For several ATP/(ADP·phosphate) ratios, they found the proton gradient at which the enzyme neither made nor split ATP; the slope gives H+/ATP.","explanation":"This equilibrium method measures the thermodynamic ratio directly, rather than reading it off the c-ring size.","section":"evidence","topic":"numbers","sources":["evidence:h-per-atp-yeast-chloroplast","ref:petersen2012"],"tags":["h-per-atp","method"],"difficulty":3,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:h-per-atp-yeast-chloroplast","machine":"atp-synthase","label":"Thermodynamic H+/ATP ratio, yeast mitochondrial and chloroplast enzymes measured side by side (Petersen J 2012)","section":"evidence","anchor":"ev-h-per-atp-yeast-chloroplast"},{"source":"ref:petersen2012","machine":"atp-synthase","label":"Petersen et al.","section":"sources","anchor":"ref-petersen2012","href":"https://doi.org/10.1073/pnas.1202799109"}]},{"id":"atp-synthase-measured-vs-structural","machine":"atp-synthase","kind":"qa","prompt":"How do the measured H+/ATP ratios of yeast and chloroplast ATP synthase compare with the ratios from their c-ring sizes?","answer":"They are lower: 2.9 against 3.3 (yeast) and 3.9 against 4.7 (chloroplast).","explanation":"Pooled chloroplast data give 4.0 protons per ATP, 85% of the structural 4.7.","section":"evidence","topic":"debate","sources":["evidence:h-per-atp-yeast-chloroplast","evidence:dg-atp-synthesis-standard","mechanism:One turn costs n protons","ref:petersen2012","ref:turina2016"],"tags":["h-per-atp","contested"],"difficulty":2,"url":"/machines/atp-synthase#evidence","cites":[{"source":"evidence:h-per-atp-yeast-chloroplast","machine":"atp-synthase","label":"Thermodynamic H+/ATP ratio, yeast mitochondrial and chloroplast enzymes measured side by side (Petersen J 2012)","section":"evidence","anchor":"ev-h-per-atp-yeast-chloroplast"},{"source":"evidence:dg-atp-synthesis-standard","machine":"atp-synthase","label":"Standard free energy of ATP synthesis and pooled chloroplast H+/ATP (Turina P 2016)","section":"evidence","anchor":"ev-dg-atp-synthesis-standard"},{"source":"mechanism:One turn costs n protons","machine":"atp-synthase","label":"Step: One turn costs n protons","section":"mechanism"},{"source":"ref:petersen2012","machine":"atp-synthase","label":"Petersen et al.","section":"sources","anchor":"ref-petersen2012","href":"https://doi.org/10.1073/pnas.1202799109"},{"source":"ref:turina2016","machine":"atp-synthase","label":"Turina et al.","section":"sources","anchor":"ref-turina2016","href":"https://doi.org/10.1016/j.bbabio.2016.02.019"}]}]}