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#columns:id	Front	Back	Explanation	Machine	Tags
atp-synthase-energy-source	ATP synthase in mitochondria is driven by the […] across the inner membrane.	ATP synthase in mitochondria is driven by the proton-motive force across the inner membrane.	Protons flow back down their gradient through the machine. Some bacteria use a sodium-motive force instead.	atp-synthase	mm::atp-synthase mm::purpose energy protons
atp-synthase-ring-of-c-subunits	In ATP synthase, protons crossing the membrane spin a ring of […].	In ATP synthase, protons crossing the membrane spin a ring of c subunits.	Each c subunit carries one proton site on a conserved carboxylate, so the c-ring turns as sites load and unload.	atp-synthase	mm::atp-synthase mm::parts c-ring rotation
atp-synthase-gamma-role	Which ATP synthase subunit turns inside the α3β3 head and sets the state of each catalytic β subunit?	γ, the central stalk.	The c-ring carries γ with it, so γ links the membrane rotor to the three catalytic sites in the head.	atp-synthase	mm::atp-synthase mm::parts gamma rotation
atp-synthase-atp-per-turn	One full turn of the ATP synthase rotor makes […] ATP, one per β subunit.	One full turn of the ATP synthase rotor makes 3 ATP, one per β subunit.	There are three catalytic β subunits, and each 120° turn of γ releases one ATP.	atp-synthase	mm::atp-synthase mm::numbers atp numbers
atp-synthase-c-ring-range	Across species, the ATP synthase c-ring has […] c subunits.	Across species, the ATP synthase c-ring has 8 to 15 c subunits.	It runs from c8 in animal mitochondria to c15 in Spirulina. A bigger ring costs more protons per ATP.	atp-synthase	mm::atp-synthase mm::numbers c-ring species
atp-synthase-bedaquiline	How does the tuberculosis drug bedaquiline stop the mycobacterial ATP synthase?	It jams the c-ring, so the rotor stalls.	It treats multidrug-resistant tuberculosis. Structures of the drug on the bacterial and human enzymes now guide safer analogs.	atp-synthase	mm::atp-synthase mm::debate drug c-ring
atp-synthase-custom-ratio-use	Why would an engineered ATP synthase with a higher H+/ATP ratio (up to 5.8) be useful?	It could make ATP at proton gradients too weak for natural enzymes.	Point mutations change the c-ring size, and extra peripheral stalks raise H+/ATP to 5.8. This work is still lab-scale.	atp-synthase	mm::atp-synthase mm::debate engineering h-per-atp
atp-synthase-arginine-barrier	Why can a proton not slip straight across subunit a of ATP synthase?	The two half-channels in subunit a do not meet, and a conserved arginine sits between them.	So the only way through is to ride on the c-ring almost a full turn, from one half-channel to the other.	atp-synthase	mm::atp-synthase mm::cycle subunit-a protons
atp-synthase-neutral-site-enters-lipid	Why can only a protonated site on the ATP synthase c-ring turn into the membrane lipid?	A neutral carboxylate can enter the oily core of the membrane; a charged one cannot.	Thermal motion jiggles the ring, and this charge rule lets only forward turns stick. The proton gradient pays for that bias.	atp-synthase	mm::atp-synthase mm::cycle c-ring protons
atp-synthase-binding-change	In ATP synthase, each 120° turn of γ moves every β subunit […].	In ATP synthase, each 120° turn of γ moves every β subunit one state along.	At any moment one β is open and empty and two are closed. This is Boyer's binding-change mechanism.	atp-synthase	mm::atp-synthase mm::cycle beta binding-change
atp-synthase-tight-site	In ATP synthase, a β site takes up ADP and phosphate while open, and ATP forms when the site closes […].	In ATP synthase, a β site takes up ADP and phosphate while open, and ATP forms when the site closes tightly.	Open, loose and tight follow each other as γ turns 120° at a time. The next opening releases the ATP.	atp-synthase	mm::atp-synthase mm::cycle beta binding-change
atp-synthase-energy-goes-to-release	In ATP synthase, which part of the catalytic cycle uses most of the proton energy?	Releasing the finished ATP from the site.	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.	atp-synthase	mm::atp-synthase mm::cycle energy binding-change
atp-synthase-symmetry-mismatch	How can an 8-subunit c-ring drive an ATP synthase head that works in three 120° steps?	The stalks and the head flex to absorb the mismatch.	The rotor and stalk store elastic energy between proton steps. E. coli structures show the peripheral stalk bending and twisting as the rotor moves.	atp-synthase	mm::atp-synthase mm::cycle elastic c-ring
atp-synthase-reverse-mode	What does ATP synthase do when ATP is present but the proton gradient is weak?	It runs backward: F1 drives the rotor the other way and Fo pumps protons.	In mitochondria, the inhibitor protein IF1 blocks this reverse mode.	atp-synthase	mm::atp-synthase mm::cycle reverse if1
atp-synthase-n-over-3	Why does an ATP synthase with a c-ring of n subunits spend n/3 protons per ATP?	One full turn moves n protons, one per c subunit, and makes 3 ATP.	So animals (c8) pay 2.7 protons per ATP, yeast (c10) 3.3 and chloroplasts (c14) 4.7.	atp-synthase	mm::atp-synthase mm::cycle h-per-atp c-ring
atp-synthase-body-weight-per-day	A person remakes about […] of ATP every day, most of it made by ATP synthase.	A person remakes about their own body weight of ATP every day, most of it made by ATP synthase.	An estimate from oxygen use: 54–68 kg a day for a college student.	atp-synthase	mm::atp-synthase mm::purpose atp body
atp-synthase-heart-stock	Why must the ATP synthases of the heart make ATP as fast as the heart uses it?	The heart keeps only a few seconds' worth of ATP in stock.	Yet the heart cycles about 6 kg of ATP a day, an estimate from a review.	atp-synthase	mm::atp-synthase mm::purpose heart atp
atp-synthase-atp-per-second	One mitochondrial ATP synthase turning about 100 times per second makes about […] ATP per second.	One mitochondrial ATP synthase turning about 100 times per second makes about 300 ATP per second.	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.	atp-synthase	mm::atp-synthase mm::numbers numbers speed
atp-synthase-turbine-breaks	Where does the water-turbine analogy for ATP synthase break down?	Protons do not push on blades: each binds a site on the ring, rides almost a full turn and leaves.	Thermal motion turns the ring, and binding and release set the direction. The "turbine" also runs backward as a pump.	atp-synthase	mm::atp-synthase mm::purpose analogy protons
atp-synthase-flagellar-link	How does the bacterial flagellar motor use a proton gradient differently from ATP synthase?	It turns the gradient straight into rotation, with no ATP in between.	Both are ion-driven rotary motors, and the flagellar export ATPase FliI resembles the F1 α and β subunits.	atp-synthase	mm::atp-synthase mm::purpose flagellum rotation
atp-synthase-first-rotation-method	How did Noji and colleagues (1997) first see the γ rotor of F1 (the ATP synthase head) turn?	They fixed F1 to glass, attached a fluorescent actin filament to γ and filmed it spinning.	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.	atp-synthase	mm::atp-synthase mm::numbers single-molecule rotation
atp-synthase-one-atp-per-step	How did Yasuda and colleagues (1998) show that each 120° step of F1 in ATP synthase uses one ATP?	At low ATP, the rotation rate was about one third of the ATPase rate in solution.	The waits between 120° steps also fit one ATP binding per step. So three ATP are used per turn.	atp-synthase	mm::atp-synthase mm::numbers single-molecule atp
atp-synthase-work-per-step	In F1 of ATP synthase, how does the work done in one 120° step compare with the free energy of one ATP?	They are about equal: about 90 pN·nm against 80–110 pN·nm.	So F1 turns nearly all the energy of an ATP into rotation. The authors note the scatter does not exclude efficiencies near 50%.	atp-synthase	mm::atp-synthase mm::numbers efficiency torque
atp-synthase-hand-cranked-synthesis	What did Itoh and colleagues (2004) show by turning γ of isolated F1 with magnets in the synthesis direction?	ATP appeared, so turning the shaft alone is enough to make ATP.	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.	atp-synthase	mm::atp-synthase mm::numbers rotation synthesis
atp-synthase-substeps	Each 120° step of the F1 rotor of ATP synthase splits into substeps of about […].	Each 120° step of the F1 rotor of ATP synthase splits into substeps of about 80° and 40°.	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°.	atp-synthase	mm::atp-synthase mm::numbers substeps rotation
atp-synthase-c8-method	How did Watt and colleagues (2010) find that the animal ATP synthase c-ring has 8 subunits?	X-ray crystallography of the F1–c-ring complex from cow heart mitochondria.	Eight protons and three ATP per turn give 2.7 H+/ATP. That is a ratio from structure, not a thermodynamic measurement.	atp-synthase	mm::atp-synthase mm::numbers c-ring x-ray
atp-synthase-equilibrium-method	How did Petersen and colleagues (2012) measure the H+/ATP ratio of ATP synthase in lipid vesicles?	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.	This equilibrium method measures the thermodynamic ratio directly, rather than reading it off the c-ring size.	atp-synthase	mm::atp-synthase mm::numbers h-per-atp method
atp-synthase-measured-vs-structural	How do the measured H+/ATP ratios of yeast and chloroplast ATP synthase compare with the ratios from their c-ring sizes?	They are lower: 2.9 against 3.3 (yeast) and 3.9 against 4.7 (chloroplast).	Pooled chloroplast data give 4.0 protons per ATP, 85% of the structural 4.7.	atp-synthase	mm::atp-synthase mm::debate h-per-atp contested
flagellar-motor-what-it-turns	What does the bacterial flagellar motor turn?	A long helical filament (the flagellum).	The motor sits in the cell envelope; the turning filament works as the cell's propeller.	flagellar-motor	mm::flagellar-motor mm::purpose rotation swimming
flagellar-motor-why-reverse	Why does a bacterium need its flagellar motor to reverse?	Switching between runs and tumbles steers the cell toward food.	Counterclockwise rotation gives runs; a short spell of clockwise rotation gives a tumble and a new direction.	flagellar-motor	mm::flagellar-motor mm::purpose chemotaxis switch
flagellar-motor-fuel-by-species	The E. coli flagellar motor runs on an inward flow of protons; the Vibrio polar flagellar motor runs on an inward flow of […].	The E. coli flagellar motor runs on an inward flow of protons; the Vibrio polar flagellar motor runs on an inward flow of sodium ions.	Both ions flow into the cell across the inner membrane. Vibrio uses PomA/PomB stator units instead of MotA/MotB.	flagellar-motor	mm::flagellar-motor mm::purpose ions energy
flagellar-motor-stator-build	What subunits make one stator unit of the flagellar motor, and how are they arranged?	A ring of five MotA around two MotB (MotA5B2).	Deme and colleagues found the same 5:2 build in stator units from Vibrio, Clostridium and Bacillus.	flagellar-motor	mm::flagellar-motor mm::parts stator structure
flagellar-motor-motb-role	In the flagellar motor stator unit, what two jobs does MotB do?	It anchors the stator unit to the cell wall (peptidoglycan) and carries the aspartate that binds the ion.	Because MotB is held fixed by its anchor, the MotA ring can turn around it.	flagellar-motor	mm::flagellar-motor mm::parts stator parts
flagellar-motor-chey-site	Phosphorylated CheY reverses the flagellar motor by binding the N-terminus of […] on the C-ring.	Phosphorylated CheY reverses the flagellar motor by binding the N-terminus of FliM on the C-ring.	FliM is the middle ring of the C-ring; in the clockwise structure all 34 FliM carry a CheY.	flagellar-motor	mm::flagellar-motor mm::parts switch chemotaxis
flagellar-motor-stall-torque	About how much torque does a fully induced E. coli flagellar motor give at high load?	About 1,260 pN·nm.	Measured with 1 µm beads at about 63 Hz, close to stall. One stator unit gives about 146 pN·nm.	flagellar-motor	mm::flagellar-motor mm::numbers torque
flagellar-motor-steps-vs-flig	The flagellar rotor takes 26 steps per turn at low driving force. Why can those steps no longer be read as one step per FliG?	A Salmonella C-ring has 34 FliG subunits, not 26.	Sowa and colleagues linked 26 to the FliG ring; later cryo-EM (Tan et al. 2024) counted 34 FliG, so the two counts differ.	flagellar-motor	mm::flagellar-motor mm::debate steps c-ring
flagellar-motor-wider-ring-proposal	What proposed (not yet done) way could build a stronger flagellar motor, copying how nature raises torque?	Transplant scaffold rings that hold more stator units at a wider radius.	High-torque motors such as those of Vibrio and Campylobacter use scaffolds to place more stator units further out. The idea's status is "proposed".	flagellar-motor	mm::flagellar-motor mm::debate torque frontier
flagellar-motor-proton-site	In the E. coli flagellar stator unit, which residue takes up the incoming proton?	MotB Asp32 (a conserved aspartate on MotB).	The proton enters a channel between MotA and MotB; Asp32 sits inside a ring of five MotA Thr209.	flagellar-motor	mm::flagellar-motor mm::cycle stator ions
flagellar-motor-36-degrees	In the proposed model of the flagellar stator, each ion turns the MotA ring about 36°, so […] ions turn MotA once.	In the proposed model of the flagellar stator, each ion turns the MotA ring about 36°, so ten ions turn MotA once.	This is a model built from the lopsided 5:2 structures; the MotA step has not been seen directly.	flagellar-motor	mm::flagellar-motor mm::cycle stator rotation
flagellar-motor-ratchet-direction	In the Deme model of the flagellar stator, why do ions always push the MotA ring the same way?	The 5:2 ring is lopsided, so the two MotB aspartates sit in different surroundings; binding at one while the other lets go acts like a ratchet.	Ions bind and leave the two MotB helices in turn, and MotB stays fixed by its cell-wall anchor.	flagellar-motor	mm::flagellar-motor mm::cycle stator ratchet
flagellar-motor-torque-per-unit	Torque is force times lever. What force and lever radius give each enteric flagellar stator unit its torque of about 146 pN·nm?	About 7 pN at about 20 nm from the axis.	The 7.3 pN is derived (146 pN·nm ÷ 20 nm), not measured directly. A full set of units gives the 1,260 pN·nm of an E. coli motor.	flagellar-motor	mm::flagellar-motor mm::cycle torque lever
flagellar-motor-drive-train	In the flagellar motor, what part does the rod spin inside as it passes through the cell wall and outer membrane?	The LP-ring, a bushing that does not turn.	Torque goes C-ring → MS-ring → rod → hook → filament; the LP-ring (FlgH, FlgI) is anchored and lets the rod spin.	flagellar-motor	mm::flagellar-motor mm::cycle rotor bearing
flagellar-motor-switch-flig-flip	When CheY-P binds the flagellar C-ring, how do the FliG domains move, and what does that change for the stator units?	They turn by 180°, so the stator units meet FliG from the inside of the ring instead of the outside.	The ring keeps its 34-fold symmetry; only the contact side changes.	flagellar-motor	mm::flagellar-motor mm::cycle switch c-ring
flagellar-motor-gear-reversal	MotA keeps turning clockwise in both states of the flagellar motor. Why does moving its contact from the outer to the inner face of the FliG ring reverse the rotor?	Gears that touch on their outer faces turn opposite ways; a gear driving the inside of a ring turns it the same way.	So the rotor turns counterclockwise with outside contact and clockwise with inside contact, without reversing the ion flow.	flagellar-motor	mm::flagellar-motor mm::cycle switch gear
flagellar-motor-catch-bond	Why do more stator units bind the flagellar motor when the load rises?	The MotB anchor forms a catch bond that holds longer under force.	Stator units bind and leave all the time; under high load each bound unit stays longer, so more gather and torque rises.	flagellar-motor	mm::flagellar-motor mm::cycle stator load
flagellar-motor-coast-distance	About how far does a swimming bacterium coast after its flagellar motors stop?	About 0.1 Å, less than an atom's width.	At this size water feels like thick syrup (Reynolds number about 3 × 10^-5), so drag stops the cell almost at once. Purcell's order-of-magnitude estimate.	flagellar-motor	mm::flagellar-motor mm::numbers low-reynolds swimming
flagellar-motor-reverse-gear-analogy	The flagellar motor is like a car with a reverse gear. Where does that analogy break?	Reversing does not drive the cell backward; it breaks up the bundle and the cell tumbles to a new heading.		flagellar-motor	mm::flagellar-motor mm::purpose analogy switch
flagellar-motor-protons-per-turn	About how many protons pass through the flagellar motor of Streptococcus per rotor turn?	About 1,240 (± 240).	Measured in Streptococcus, not E. coli, so it should not be multiplied by E. coli motor speeds. Proton flux rises in direct proportion to speed.	flagellar-motor	mm::flagellar-motor mm::numbers protons energy
flagellar-motor-atp-synthase-link	Which part of the flagellar motor resembles the F1 α and β subunits of ATP synthase?	The export ATPase FliI.	FliJ also looks like the γ coiled-coil, so the flagellar export machine and the rotary ATPases likely share an ancestor.	flagellar-motor	mm::flagellar-motor mm::parts evolution atp-synthase
flagellar-motor-how-torque-measured	How did Reid and colleagues measure the torque of single E. coli flagellar motors?	They tracked a 1 µm bead on a flagellar stub by laser interferometry and took torque = speed × bead drag coefficient.	At these low speeds torque sits near its stall value, so a fully induced motor gives the motor's maximum, about 1,260 pN·nm.	flagellar-motor	mm::flagellar-motor mm::numbers bead-assay torque
flagellar-motor-resurrection-count	In "resurrection" experiments on paralysed E. coli flagellar motors, how was the number of stator units counted?	By counting the discrete jumps in bead speed as new stator units joined the motor.	Reid and colleagues counted at least 11 levels, beating the older estimate of eight; the jumps got smaller at high numbers.	flagellar-motor	mm::flagellar-motor mm::numbers stator resurrection
flagellar-motor-zero-load-one-unit	Near zero load, how does the speed of the E. coli flagellar motor depend on the number of stator units?	It does not: one unit gives the same speed as many (about 300 Hz at 23 °C).	Yuan and Berg used 60 nm gold spheres on hooks with no filament; a sphere jumped from rest to full speed when the first unit arrived.	flagellar-motor	mm::flagellar-motor mm::numbers speed load
flagellar-motor-torque-speed-knee	At 23 °C the torque of the E. coli flagellar motor stays roughly constant up to a knee near […], then falls to zero near 350 Hz.	At 23 °C the torque of the E. coli flagellar motor stays roughly constant up to a knee near 200 Hz, then falls to zero near 350 Hz.	Chen and Berg varied the load with Ficoll. Later work puts the knee at 170–175 Hz.	flagellar-motor	mm::flagellar-motor mm::numbers torque-speed
flagellar-motor-backward-steps	What did the occasional backward steps of the slowed flagellar motor (Sowa et al. 2005) show about each step?	Each step uses little energy, close to that of one ion crossing.	They slowed a Na+-driven chimeric motor in E. coli with low sodium-motive force and few stator units to see 26 steps per turn.	flagellar-motor	mm::flagellar-motor mm::cycle steps energy
flagellar-motor-hill-disagreement	Cluzel et al. found a Hill coefficient of about 10 for the flagellar switch; Yuan and Berg found 16.5–20.7. Why the difference?	Yuan and Berg changed CheY-P faster than motors could change their FliM content; the earlier curve pooled motors that had adapted their FliM.	With a fixed make-up the switch is about twice as steep.	flagellar-motor	mm::flagellar-motor mm::debate switch ultrasensitivity
kinesin-direction	Which way along a microtubule does kinesin-1 carry its cargo?	Toward the plus end.	Its two heads take turns: the rear head swings past the bound head and lands 16 nm ahead.	kinesin	mm::kinesin mm::purpose direction transport
kinesin-neck-linker-role	Which part of kinesin-1 docks onto the head when ATP binds and pulls the partner head forward?	The neck linker.	It is a short segment of about 13-15 residues after helix α6; papers draw its boundaries differently.	kinesin	mm::kinesin mm::parts neck-linker parts
kinesin-direction-from-neck	Plus-end and minus-end kinesins have nearly identical cores. Which part of a kinesin sets the direction it walks?	The neck next to the core.	Swapping necks or domain order reverses motion, so the core alone does not set direction.	kinesin	mm::kinesin mm::parts direction evolution
kinesin-step-size	Kinesin-1's centre of mass moves […] per step, the length of one tubulin dimer.	Kinesin-1's centre of mass moves 8 nm per step, the length of one tubulin dimer.	Each head moves about twice as far (17.3 ± 3.3 nm), because the heads pass each other.	kinesin	mm::kinesin mm::numbers step numbers
kinesin-steps-per-run	About how many steps does a single kinesin-1 take before it lets go of the microtubule?	About 100 (a run of about 1 µm).	The fitted run length at zero load is 1.12 µm, which is more than 100 steps per encounter with the microtubule.	kinesin	mm::kinesin mm::numbers processivity numbers
kinesin-turnover-time	With no load, kinesin-1 walks at about 800 nm/s, so one turnover takes about […].	With no load, kinesin-1 walks at about 800 nm/s, so one turnover takes about 10 ms.	At 8 nm per step, 800 nm/s is about 100 steps per second.	kinesin	mm::kinesin mm::numbers speed numbers
kinesin-molecular-shuttle	In a kinesin 'molecular shuttle', what does the kinesin do?	It is fixed on a surface and pushes microtubules that carry cargo.	Surface patterns steer the microtubules, and the ATP supply sets their speed. This use is demonstrated.	kinesin	mm::kinesin mm::debate frontier engineering
kinesin-designed-motor	Unlike kinesin, how does a designed protein motor (a protease-coated hub) move across a peptide lawn?	By cutting the path behind it.	It reaches up to 80 nm/s. Designed protein motors are now possible at lab scale, but they are simpler than kinesin.	kinesin	mm::kinesin mm::debate frontier design
kinesin-atp-docks-linker	In kinesin-1, […] to the bound head makes its neck linker zip onto the head.	In kinesin-1, ATP binding to the bound head makes its neck linker zip onto the head.	This docking is the power stroke: the neck linker ends up pointing to the plus end.	kinesin	mm::kinesin mm::cycle neck-linker atp power-stroke
kinesin-why-docking-needs-atp	Why do ATP binding and neck-linker docking go together in a kinesin-1 head?	Only the closed, ATP-bound head offers the groove the neck linker docks into.	Closing the nucleotide pocket turns two parts of the head (by about 22° and 11°), and that opens a groove along the head.	kinesin	mm::kinesin mm::cycle neck-linker atp
kinesin-diffusion-search	In a kinesin-1 step, […] carries the free head forward; neck-linker docking only sets the direction.	In a kinesin-1 step, diffusion carries the free head forward; neck-linker docking only sets the direction.	The docked neck linker of the bound head holds the tethered head near the forward site, and it lands about 16 nm ahead.	kinesin	mm::kinesin mm::cycle diffusion stepping
kinesin-adp-release-trigger	What makes a kinesin-1 head release its ADP?	Binding the microtubule, which opens the nucleotide cleft.	A dimer that lands on a microtubule releases only one of its two ADPs, so one head binds the track and the other stays free.	kinesin	mm::kinesin mm::cycle adp microtubule
kinesin-adp-weak-binding	A kinesin-1 head holding […] binds the track only weakly, so it can search or let go.	A kinesin-1 head holding ADP binds the track only weakly, so it can search or let go.	A head with an empty pocket grips the track tightly, so the new front head anchors the motor before the rear head lets go.	kinesin	mm::kinesin mm::cycle adp gating
kinesin-phosphate-gate	Why does kinesin-1 stay on the track for about 100 steps instead of falling off after one?	The rear head lets go only after phosphate leaves, and by then the front head is bound.	This order keeps one head on the track at all times.	kinesin	mm::kinesin mm::cycle processivity gating phosphate
kinesin-hydrolysis-timing-debate	When kinesin-1 splits its ATP is still argued. What does tracking single heads at 1,000 frames per second suggest?	The bound head must split its ATP before the free head can land.	The animation in the notes shows the split after the front head lands instead.	kinesin	mm::kinesin mm::debate hydrolysis debate
kinesin-back-step-cause	Under a heavy opposing load, why does kinesin-1's free head land behind its partner instead of ahead?	The pull on the stalk cancels the small forward bias from neck-linker docking.	The landing site is set by where the head is when it touches down. The chemistry is the same as a forward step, one ATP per step.	kinesin	mm::kinesin mm::cycle load back-steps
kinesin-drift-time	If proteins made near the spine just drifted down a 1 m nerve cell, they would need about […] to reach the foot.	If proteins made near the spine just drifted down a 1 m nerve cell, they would need about 300 years to reach the foot.	Diffusion time grows with the square of distance: about two weeks for 1 cm becomes about 300 years for 1 m. Kinesin motors make the trip in a few days.	kinesin	mm::kinesin mm::purpose axon diffusion
kinesin-fast-transport-time	About how long does fast outward transport take to carry cargo 1 m along a nerve cell?	About 2.5-5 days.	Fast outward transport runs at 200-400 mm per day (2-5 µm/s).	kinesin	mm::kinesin mm::numbers axon transport
kinesin-teams-of-motors	A single kinesin falls off after about 1 µm. How does cargo still finish a 1 m trip down an axon?	Teams of motors grab on again and again.	One motor would let go about 10^6 times on the way; this is where the delivery-truck analogy breaks.	kinesin	mm::kinesin mm::purpose analogy processivity
kinesin-walker-analogy	The 'walker with two feet' picture of kinesin gets hand-over-hand stepping right. What does it get wrong about the free foot?	It does not swing by muscle: it jiggles by heat, and the zipped neck linker only biases where it lands.	Diffusion does the travel; docking sets the direction.	kinesin	mm::kinesin mm::purpose analogy diffusion
kinesin-dynein-tug	On a cargo vesicle in an axon, which motor pulls against kinesin, back toward the cell body?	Dynein.	Vesicles from mouse brain carry 1-4 kinesins and 1-5 dyneins, and the cargo moves in fits and starts.	kinesin	mm::kinesin mm::purpose dynein axon cargo
kinesin-svoboda-method	How did Svoboda and colleagues (1993) first see kinesin's 8 nm steps?	With optical trapping interferometry: they tracked a bead carried by one kinesin.	The bead moved in discrete 8 nm steps, the length of one tubulin dimer, the repeat of the track.	kinesin	mm::kinesin mm::numbers method optical-trap step
kinesin-hand-over-hand-proof	Yildiz and colleagues put one dye on one head of kinesin. What pattern of dye movement showed that kinesin walks hand over hand?	The dye jumped about 17 nm, then not at all, in turn.	Meanwhile the motor as a whole moved 8.3 nm per step, so the heads must swap places.	kinesin	mm::kinesin mm::numbers method fluorescence hand-over-hand
kinesin-one-atp-method	How did Coy and colleagues (1999) show that kinesin takes one step per ATP?	They divided the bead speed by an 8.1 nm step, then by the ATP turnover of the same beads.	Every preparation gave close to one: 1.08 ± 0.09 steps per ATP pooled.	kinesin	mm::kinesin mm::numbers method atp coupling
kinesin-backstep-stall	In Carter and Cross's optical trap, kinesin-1 took as many back steps as forward steps near […] of opposing load.	In Carter and Cross's optical trap, kinesin-1 took as many back steps as forward steps near 7 pN of opposing load.	That is the stall force; above it kinesin walked backward. It is higher than the 5.4 pN measured against a glass fibre.	kinesin	mm::kinesin mm::debate stall-force back-steps load
kinesin-stall-vs-atp	Visscher and colleagues (1999) measured kinesin's stall force at different ATP levels. What did they find?	The stall force rises with ATP concentration.	So the stall force is not one fixed number. Against a glass fibre, Meyhöfer and Howard found about the same force at high and low ATP.	kinesin	mm::kinesin mm::debate stall-force atp
kinesin-neck-charge	Why does extra positive charge on kinesin's neck coiled coil make its runs longer?	The positive neck holds on to the negatively charged tails of tubulin.	Runs grew about four-fold with speed unchanged. Salt, or removing the tubulin tails, cancelled the gain.	kinesin	mm::kinesin mm::numbers processivity engineering
kinesin-phosphate-evidence	In Milic and colleagues' force-clamp runs, what effect of added phosphate showed that kinesin's processivity is gated by phosphate release?	Added phosphate made the runs longer.	Under forward load, runs became up to about twice as long: the rear head lets go only after it releases phosphate.	kinesin	mm::kinesin mm::numbers processivity phosphate method
myosin-class-differences	Myosin classes share the same head. Name the three things that differ between them.	Lever length, direction, and time spent bound to actin.	Across isoforms the motor-domain states are nearly invariant; the lever position differs.	myosin	mm::myosin mm::purpose classes lever
myosin-converter-lever-role	In a myosin head, what does the long lever-arm helix do with the rotation of the converter?	It amplifies the rotation into a stroke.	The converter turns with the motor state; the lever turns that small turn into a large stroke, so lever length sets the stroke.	myosin	mm::myosin mm::parts lever converter
myosin-tail-role	What does the coiled-coil tail of myosin do?	It joins the two heavy chains and builds thick filaments or binds cargo.	The head does the work on actin; the tail decides what the pull is applied to.	myosin	mm::myosin mm::parts tail cargo
myosin-duty-ratio-definition	What is the duty ratio of a myosin head?	The fraction of the cycle it spends strongly bound to actin.	Myosin-5 has a duty ratio of about 0.7; muscle myosin spends only a small fraction of its cycle bound.	myosin	mm::myosin mm::numbers duty-ratio
myosin-muscle-low-duty	Muscle myosin spends only a small fraction of its cycle bound to actin. How does muscle still pull steadily?	Its heads work in large ensembles.	Each thick filament carries about 300 myosins. Only a few hold on at any moment; each pulls, lets go and grabs again.	myosin	mm::myosin mm::numbers duty-ratio muscle
myosin-cardiac-drugs-pocket	Omecamtiv mecarbil activates cardiac myosin and mavacamten inhibits it. What do the two drugs have in common at the structure level?	They bind the same pocket.	Structures of this shared pocket support rational design of the next cardiac myosin drugs.	myosin	mm::myosin mm::debate drugs heart
myosin-cardiac-drug-approved	Both cardiac myosin drugs completed phase 3 trials, and regulators have approved […].	Both cardiac myosin drugs completed phase 3 trials, and regulators have approved mavacamten.	Mavacamten, first reported as MYK-461, lowers the ATPase of cardiac myosin.	myosin	mm::myosin mm::debate drugs heart
myosin-cleft-gates-phosphate	When a primed myosin head first docks on actin, why can phosphate not leave yet?	The actin-binding cleft is still open.	Contacts with the actin N-terminus rotate the upper 50-kDa subdomain and close the cleft; only then can phosphate leave and the head bind strongly.	myosin	mm::myosin mm::cycle phosphate cleft
myosin-power-stroke-angle	In the myosin power stroke, the converter rotates and the lever swings through about […], mostly along the filament.	In the myosin power stroke, the converter rotates and the lever swings through about 93 degrees, mostly along the filament.	Measured for myosin-5 on actin by time-resolved cryo-EM. Because the swing runs along the filament, nearly all of it moves the load forward.	myosin	mm::myosin mm::cycle power-stroke lever
myosin-atp-releases-why	Why does ATP binding make a myosin head let go of actin?	A head cannot hold both ATP and actin tightly, so the actin-binding cleft opens.	Pospich and colleagues call ATP binding and actin binding reciprocal. The transducer links the pocket to the cleft.	myosin	mm::myosin mm::cycle atp cleft
myosin-recovery-stroke	What does a myosin head do during the recovery stroke, off actin?	It swings its lever back and hydrolyses ATP, holding ADP and phosphate in the primed state.	This re-cocks the lever, so the head is ready for its next power stroke.	myosin	mm::myosin mm::cycle recovery-stroke atp
myosin-myosin5-pace-step	Which step sets the walking pace of myosin-5?	ADP release from the rear head.	ADP leaves at 11.7 per second, close to the whole ATPase rate of 12–15 per second.	myosin	mm::myosin mm::cycle adp myosin-5 kinetics
myosin-myosin5-why-bound	Why does a single myosin-5 head spend about 70% of its cycle strongly bound to actin?	Its slowest step, ADP release, happens while it is strongly bound.	A high duty ratio lets a two-headed myosin-5 keep one head on actin while the other steps.	myosin	mm::myosin mm::cycle duty-ratio myosin-5
myosin-myosin5-13-subunits	Why do the two heads of myosin-5 bind actin 13 subunits apart?	A site 13 subunits on faces the same way, so the motor walks straight.	Actin repeats its pattern about every 36 nm; 13 subunits at about 2.75 nm each is about 36 nm, the step of myosin-5.	myosin	mm::myosin mm::cycle actin myosin-5 step
myosin-myosin5-lead-held	In a two-headed myosin-5 on actin, what holds the lead head's lever in the primed position after it releases phosphate?	The pull from the rear head.	The lead head waits with ADP until the rear head lets go; then nothing holds its lever back and it swings.	myosin	mm::myosin mm::cycle myosin-5 strain
myosin-muscle-layout	In muscle, how do myosins add their forces, and how do sarcomeres add their shortening?	Myosins sit side by side, so forces add; sarcomeres sit end to end, so shortenings add.	This layout turns strokes of a few nanometres into movements of centimetres.	myosin	mm::myosin mm::purpose muscle sarcomere
myosin-train-analogy-breaks	Muscle is like train carriages coupled in a row. What does this analogy get wrong about the sarcomere?	Nothing in a sarcomere shrinks; the filaments slide past each other.	The analogy is right that units in series add their travel and units side by side add their force.	myosin	mm::myosin mm::purpose analogy sarcomere
myosin-rowing-analogy-breaks	Myosin heads are like a rowing crew. Where does this analogy break down?	Rowers pull in time; each myosin head works on its own clock.	Each head also lets go of actin for most of its cycle, so only a few hold on at any moment.	myosin	mm::myosin mm::purpose analogy duty-ratio
myosin-gain-to-hand	From the phosphate in a myosin head to the hand, movement grows about […] times.	From the phosphate in a myosin head to the hand, movement grows about 30 million times.	About 0.5 nm at the active site becomes about 15 mm at the hand, through the lever, many heads, sarcomeres in a row and the arm (human biceps estimate).	myosin	mm::myosin mm::numbers scale gain
myosin-link-serca	Calcium switches myosin on. How does SERCA switch it off?	By pumping the calcium away.	Calcium is the on switch for myosin, so removing it switches myosin off.	myosin	mm::myosin mm::purpose serca calcium
myosin-kinesin-shared-core	Myosin and kinesin share almost no sequence identity. What do they share?	The same fold of the catalytic core.	The two motor families probably evolved from a common ancestor; kinesin walks on microtubules, myosin on actin.	myosin	mm::myosin mm::purpose kinesin evolution
myosin-finer-method	How did Finer, Simmons and Spudich (1994) measure the step of a single myosin molecule?	With a laser trap holding one actin filament against a single myosin molecule.	Each time the myosin bound, the filament jumped forward in a discrete step, averaging 11 nm at low load.	myosin	mm::myosin mm::numbers optical-trap stroke
myosin-stroke-dispute	Finer 1994 found a stroke of about 11 nm for muscle myosin. What stroke did Molloy 1995 find for a single head (S1)?	About 4 nm.	The single-head estimate depends on how the broad spread of displacements is analysed, so the stroke size is disputed.	myosin	mm::myosin mm::debate stroke disputed
myosin-yildiz-hand-over-hand	Yildiz and colleagues tracked one dye on the lever of myosin-5. What step pattern showed that it walks hand over hand?	Long and short steps in turn (37 + 2x and 37 − 2x nm).	If the same head always led, as in an inchworm, every step would be the same size. The centre of mass moves about 37 nm per ATP.	myosin	mm::myosin mm::numbers myosin-5 stepping
myosin-uyeda-lever-test	What did Uyeda, Abramson and Spudich (1996) find when they changed the neck length of Dictyostelium myosin?	Gliding speed rose linearly with lever length.	Speed fell on a line that reached zero near a fulcrum in the motor domain, so the neck acts as a lever arm.	myosin	mm::myosin mm::numbers lever motility
myosin-delacruz-method	How did De La Cruz and colleagues measure how much of the cycle a myosin-5 head stays strongly bound?	With pyrene-labelled actin, whose glow is quenched by strongly bound myosin, in stopped flow.	Most heads stayed strongly bound for most of each cycle: a duty ratio of about 0.7.	myosin	mm::myosin mm::numbers duty-ratio stopped-flow
myosin-rief-adp-gates	In single-molecule stepping of myosin-5 (Rief 2000), what showed that ADP release gates each step?	Adding ADP slowed the stepping rate, from 12.5 to 6.4 per second.	The rate matches ADP release measured in solution by De La Cruz and colleagues.	myosin	mm::myosin mm::numbers adp optical-trap
myosin-klebl-method	How did Klebl and colleagues (2025) see myosin-5 both before and after its stroke on actin?	They mixed myosin-ADP-Pi with actin and froze it 10 or 120 ms later (time-resolved cryo-EM).	Primed motors fell from 62% at 10 ms to 36% at 120 ms, so both shapes could be compared on the same filament.	myosin	mm::myosin mm::numbers cryo-em power-stroke
dynein-direction	Cytoplasmic dynein carries cargo along microtubules toward the […].	Cytoplasmic dynein carries cargo along microtubules toward the minus end.	Kinesin walks the same microtubule tracks the other way, so the two motors pull cargo in a tug of war.	dynein	mm::dynein mm::purpose direction transport
dynein-activators	Alone, human dynein-1 is mostly inactive. Which two partners switch it on?	Dynactin and a cargo adaptor (such as BICD2).	Together they turn dynein into an ultraprocessive motor. The adaptor also links dynein and dynactin to the cargo.	dynein	mm::dynein mm::parts regulation dynactin
dynein-ring	What forms the ring at the core of each dynein motor domain?	Six AAA+ domains (AAA1 to AAA6).	The AAA+ fold is an ATP-binding module found in many cellular machines. In dynein, all six come in tandem from one heavy chain.	dynein	mm::dynein mm::parts aaa structure
dynein-main-atp-site	Which of dynein's six AAA+ domains is the main site that splits ATP?	AAA1	AAA2 to AAA4 also bind nucleotide, but they tune the cycle rather than drive it.	dynein	mm::dynein mm::parts atp aaa
dynein-stalk	Dynein's ATPase ring reaches the microtubule through a coiled-coil […] about 15 nm long, with the microtubule-binding foot (MTBD) at its tip.	Dynein's ATPase ring reaches the microtubule through a coiled-coil stalk about 15 nm long, with the microtubule-binding foot (MTBD) at its tip.	Ring and foot are 15 nm apart, so signals between them must travel along this rod.	dynein	mm::dynein mm::parts stalk structure
dynein-step-size	The most frequent step of yeast dynein is […], close to the spacing of tubulin dimers.	The most frequent step of yeast dynein is 8 nm, close to the spacing of tubulin dimers.	Steps vary from 4 to 24 nm, and side and backward steps also occur.	dynein	mm::dynein mm::numbers stepping
dynein-reverse-direction	How did Can and colleagues make yeast dynein walk toward the plus end?	They changed the angle and the length of its stalk.	So stalk geometry sets dynein's direction. All natural dyneins studied so far walk toward the minus end.	dynein	mm::dynein mm::debate direction engineering
dynein-atp-closes-ring	When ATP binds AAA1, dynein's ring of six AAA+ domains […].	When ATP binds AAA1, dynein's ring of six AAA+ domains closes.	ATP binding pulls AAA1 and AAA2 together. Because the six domains form one ring, the closure spreads all the way around it.	dynein	mm::dynein mm::cycle atp ring
dynein-helix-sliding	Dynein's stalk carries the signal from the ring to the foot by helix […], not by bending.	Dynein's stalk carries the signal from the ring to the foot by helix sliding, not by bending.	As the ring closes, the buttress drags helix CC2 past CC1 by about one turn of helix, and the foot lets go of the microtubule.	dynein	mm::dynein mm::cycle stalk signalling
dynein-registry-affinity	In dynein's stalk, what does the registry (the alignment) of the two helices CC1 and CC2 control?	How tightly the foot (MTBD) binds the microtubule.	With AAA1 empty, the ring holds the alpha registry and the foot binds tightly. Locking the registry with disulfides traps strong or weak binding.	dynein	mm::dynein mm::cycle stalk affinity
dynein-why-linker-bends	After ATP binds, why is dynein's linker forced into a bent, primed shape?	The closed ring clashes with the straight linker; there is no room for it.	The bent linker's free end swings across the ring toward AAA2, ready for the next power stroke.	dynein	mm::dynein mm::cycle linker priming
dynein-power-stroke	When dynein's primed head rebinds the microtubule, phosphate leaves and the linker […]: this is the power stroke.	When dynein's primed head rebinds the microtubule, phosphate leaves and the linker straightens: this is the power stroke.	The energy stored in the primed linker is released while the foot holds the track, so the tail and its cargo move toward the minus end.	dynein	mm::dynein mm::cycle linker power-stroke
dynein-slow-step	Which step of the dynein cycle appears to be the slow one?	ADP release from AAA1.	Among active human dynein-1 motors off microtubules, most held ADP in an open AAA1 pocket. Microtubule binding opens the pocket wide and speeds ADP release.	dynein	mm::dynein mm::cycle adp kinetics
dynein-tension-coordination	Dynein's two heads step mostly independently, but they show coordination when far apart. What kind of mechanism does that point to?	A tension-based mechanism.	There is no tight gate between the heads: either head can step, whether it is in front or behind.	dynein	mm::dynein mm::cycle stepping coordination
dynein-stroke-order	In the classic dynein cycle, the head rebinds the microtubule before its linker straightens. What did Chai and colleagues see that does not fit this order?	The linker straightened even in motors that were not bound to microtubules.	They propose instead that the cargo moves as the docked linker shifts from AAA4 to AAA5.	dynein	mm::dynein mm::debate linker power-stroke
dynein-mucus-escalator	Dynein-driven cilia line your airways. What do they push up toward your throat?	A thin layer of mucus that traps dust and germs.	This mucus escalator moves about 5.5 mm per minute and keeps the lungs clean without you noticing.	dynein	mm::dynein mm::purpose cilia lungs
dynein-lung-cilia-count	An adult human lung holds an estimated […] motile cilia, each driven by dynein.	An adult human lung holds an estimated three trillion motile cilia, each driven by dynein.	Each cilium beats 10 to 20 times a second, which adds up to 0.9 to 1.7 million beats a day.	dynein	mm::dynein mm::numbers cilia scale
dynein-sliding-to-bending	Dynein arms try to slide one rail of a cilium's axoneme past the next. Why does the cilium bend instead?	The rails are tied together at the base, so they cannot slide far.	Without the base links the rails would just slide apart; tied together, the sliding turns into a bend.	dynein	mm::dynein mm::purpose cilia bending
dynein-pcd	In primary ciliary dyskinesia, airway cilia lack their dynein arms. What happens to the mucus?	The cilia cannot move, so the mucus does not clear.	The disease affects about 1 in 15,000 births, and about half of the people affected have mirrored organs.	dynein	mm::dynein mm::purpose disease cilia
dynein-bimetal-breaks	A cilium is like a bimetal strip: two tied layers turn a change in length into a bend. Where does that analogy break down?	In a cilium, motors actively slide one rail along the next; in a bimetal strip, heat changes the length.	The geometry fits, but the cause differs: the dynein arms on one rail walk along the next rail.	dynein	mm::dynein mm::purpose analogy cilia
dynein-arms-per-cilium	By calculation, about how many outer dynein arms does one airway cilium hold?	About 2,000 to 2,600.	Four outer arms sit in each 96 nm repeat along nine doublets, over 5.5 to 7 µm of length. It is a calculation, not a measured count.	dynein	mm::dynein mm::numbers cilia scale
dynein-step-method	How did Reck-Peterson and colleagues measure the 8 nm step of yeast dynein?	They tracked a quantum dot on the dynein tail to a few nanometres (FIONA, TIRF microscopy) at low ATP.	Low ATP (4 µM) slowed stepping so single steps could be found: 1342 steps from 27 molecules.	dynein	mm::dynein mm::numbers method stepping
dynein-head-vs-tail-step	A label on one head of yeast dynein moved about 16 to 18 nm per step, twice as far as the tail's 8 nm. Why?	The two heads take turns stepping.	Each head moves about two tubulin dimers each time it steps, while the tail between them advances one dimer per step.	dynein	mm::dynein mm::numbers stepping heads
dynein-superstall	Pulled backward with more than its stall force, yeast dynein walks […].	Pulled backward with more than its stall force, yeast dynein walks toward the plus end.	In an optical trap at 10 pN it moved about 15 nm/s toward the plus end at any ATP level, and it stepped even with no ATP.	dynein	mm::dynein mm::numbers force optical-trap
dynein-stall-disagreement	Reported stall forces for full-length yeast dynein differ about […]: 7 pN (Gennerich 2007) versus 3.6 pN (Belyy 2016).	Reported stall forces for full-length yeast dynein differ about twofold: 7 pN (Gennerich 2007) versus 3.6 pN (Belyy 2016).	Both values are for full-length yeast dynein. Human dynein-1 alone stalled lower still, at about 2.0 pN.	dynein	mm::dynein mm::debate force contested
dynein-ddb-trap-method	How did Belyy and colleagues make their optical trap pull only on complete dynein–dynactin–BICD2 complexes?	They attached the bead through a GFP tag on the adaptor, BICD2N.	These complexes stalled at 4.3 pN, about twice the 2.0 pN of human dynein alone.	dynein	mm::dynein mm::numbers method force optical-trap
dynein-tug-of-war	One dynein–dynactin–BICD2 complex was linked to one kinesin-1. How did the pair move?	The pairs crawled (median 26 nm/s), and about one in five moved toward the minus end.	Without dynactin and BICD2N the pairs ran almost as fast as kinesin alone. One activated dynein can hold its own against one kinesin.	dynein	mm::dynein mm::numbers kinesin force
dynein-two-dyneins	Why do dynein complexes built with the adaptors BICDR1 or HOOK3 pull harder and move faster than those built with BICD2?	They mostly recruit two dyneins per dynactin.	Complexes with one active dynein and one tail that cannot walk were as slow as BICD2 complexes. With BICDR1 the stall force (6.5 pN) beat kinesin-1 (5.7 pN).	dynein	mm::dynein mm::numbers dynactin force speed
ribosome-purpose	What does the ribosome do in a cell?	It reads an mRNA and builds the matching protein chain.	It turns a nucleic acid sequence into a protein sequence. Every protein in your body comes off a ribosome.	ribosome	mm::ribosome mm::purpose translation
ribosome-small-subunit-role	The ribosome's […] checks each codon against the anticodon of the incoming tRNA.	The ribosome's small subunit checks each codon against the anticodon of the incoming tRNA.	In bacteria its core, 16S rRNA, reads the codon and holds the mRNA channel. The large subunit joins the amino acids.	ribosome	mm::ribosome mm::parts decoding subunits
ribosome-rna-catalyst	In the bacterial ribosome, the peptide bond is made by […] of the large subunit, not by protein.	In the bacterial ribosome, the peptide bond is made by 23S rRNA of the large subunit, not by protein.	Only 23S rRNA lines the catalytic centre, so the ribosome is a ribozyme: an enzyme made of RNA.	ribosome	mm::ribosome mm::parts ribozyme rrna
ribosome-protein-role	No ribosomal protein sits in the catalytic centre. What job do the ribosomal proteins do instead?	They sit on the surface and stabilise the rRNA folds.	The catalytic centre is all RNA, with proteins on the outside. That fits an RNA-first origin of the ribosome.	ribosome	mm::ribosome mm::parts evolution rrna
ribosome-three-sites	A tRNA passes through the ribosome's three binding sites in the order […].	A tRNA passes through the ribosome's three binding sites in the order A, P, E.	The A site takes in the new aminoacyl-tRNA, the P site holds the tRNA that carries the chain, and the E site holds the empty tRNA until it leaves.	ribosome	mm::ribosome mm::parts trna sites
ribosome-ecoli-rate	How many amino acids per second does a ribosome add in E. coli, from slow to fast growth?	About 12 to 17.	12 at slow growth and 17 at fast growth, measured by pulse labelling. At 17 per second, one full cycle takes about 60 ms.	ribosome	mm::ribosome mm::numbers speed
ribosome-error-rate	The ribosome's error rate is about […] per elongation step.	The ribosome's error rate is about 10^-3 to 10^-5 per elongation step.	It holds this accuracy over thousands of cycles. The range is quoted from a review; measurements in E. coli span about 10^-6 to 10^-3 per codon.	ribosome	mm::ribosome mm::numbers accuracy
ribosome-ribo-t	What did tethering the two ribosomal subunits into one molecule (Ribo-T) show?	The subunits need not exchange: Ribo-T keeps E. coli alive without wild-type ribosomes.	Short RNA linkers join small- and large-subunit rRNA. The tethered ribosome still makes protein, both in vitro and in cells.	ribosome	mm::ribosome mm::debate engineering subunits
ribosome-non-natural-polymers	What is the status of using ribosomes to make polymers that are not proteins?	Proposed: no such polymer chemistry yet runs on a ribosome at scale.	The proposed starting point is a dedicated ribosome that is tethered and orthogonal (it reads only its own mRNA). Those parts, and ribosomes that read four-base codons, are each already demonstrated.	ribosome	mm::ribosome mm::debate engineering frontier
ribosome-eftu-holds-end	Why does EF-Tu hold the amino-acid end of an incoming tRNA while the anticodon reaches down to the codon?	To keep the amino acid away from the catalytic centre until the codon has been checked.	This is the A/T state. EF-Tu complexes also bind and fall off fast, so the ribosome can try and reject many wrong tRNAs at little cost.	ribosome	mm::ribosome mm::cycle ef-tu decoding
ribosome-decoding-trigger	On the ribosome, what does a correct codon–anticodon pair switch on?	GTP hydrolysis by EF-Tu, which then releases the tRNA into the A site.	16S rRNA bases, among them A1492 and A1493, recognise the correct pair, and the small subunit closes around the tRNA. The GTPase rate differs most between right and wrong tRNAs, so it largely decides which tRNA is accepted.	ribosome	mm::ribosome mm::cycle decoding ef-tu gtp
ribosome-hybrid-states	After the ribosome forms a peptide bond, the tRNA […] move on the large subunit while the anticodons stay put, giving hybrid A/P and P/E states.	After the ribosome forms a peptide bond, the tRNA acceptor ends move on the large subunit while the anticodons stay put, giving hybrid A/P and P/E states.	Translocation happens in two moves, so the acceptor ends and then the anticodons shift one at a time.	ribosome	mm::ribosome mm::cycle translocation trna
ribosome-ratchet-driver	What carries the ribosome's small subunit into its rotated (ratcheted) state after the peptide bond forms?	Thermal motion: the move happens on its own, without EF-G or GTP.	The small subunit turns about 10° against the large subunit. The move is spontaneous and reversible.	ribosome	mm::ribosome mm::cycle translocation rotation
ribosome-efg-catches	What does EF-G·GTP do when it first binds the ribosome after the subunits have rotated?	It catches and holds the rotated state, which the ribosome reaches on its own, and starts to unlock the small subunit.	In the structures of Rundlet and colleagues, EF-G still carries unsplit GTP at this point. So the energy of GTP is spent later in translocation than once thought.	ribosome	mm::ribosome mm::cycle ef-g gtp translocation
ribosome-reading-frame	Why must the ribosome move the mRNA by exactly three nucleotides in each cycle?	To keep the reading frame.	EF-G splits its GTP and the small-subunit head swivels, and the tRNA anticodons move with the mRNA by one codon. A kink in the mRNA, held by a metal ion, may also stop it from slipping out of frame.	ribosome	mm::ribosome mm::cycle translocation mrna
ribosome-exit-tunnel	Why can't a new protein chain fold into domains inside the ribosome's exit tunnel?	The tunnel is too narrow for any fold larger than an alpha-helix.	The chain runs from the catalytic centre through the large subunit to the surface. Chains that cannot fold alone are then caught by GroEL.	ribosome	mm::ribosome mm::cycle tunnel folding
ribosome-human-cell-count	One human HeLa cell holds about […] ribosomes.	One human HeLa cell holds about 3.3–9.5 million ribosomes.	3.3 million comes from the mass of 28S rRNA, 9.5 million from the total RNA per cell. Ribosomes make up about 6% of a HeLa cell's protein mass.	ribosome	mm::ribosome mm::numbers scale copies
ribosome-body-protein	About how much protein does a human body build each day?	A few hundred grams (estimates run from about 175 to 400 g).	All of it comes off ribosomes. Protein turnover takes about 20% of resting energy in an average healthy young adult.	ribosome	mm::ribosome mm::purpose scale body
ribosome-titin-time	At the mouse stem-cell rate of 5.6 amino acids per second, about how long would one ribosome take to build titin (34,350 amino acids)?	About 1.7 hours.	34,350 ÷ 5.6 ≈ 6,130 s. A typical 400-residue protein takes about 71 s. Both are calculations, not measured times.	ribosome	mm::ribosome mm::numbers speed scale
ribosome-printer-analogy	Where does the analogy of the ribosome as 'a 3D printer that reads a tape' break down?	The ribosome does not place units by position: tRNA adapters bring each one, and it only checks that the adapter pairs with the code.	The chain also folds itself into shape afterwards. What the analogy gets right: it reads a coded tape and builds a chain one unit at a time.	ribosome	mm::ribosome mm::purpose analogy trna
ribosome-factory-line-analogy	Many ribosomes read one mRNA at once. Why is 'a factory line' a misleading picture of this?	All the ribosomes on the message make the same product: they are copies, not stations with different jobs.	Each ribosome further along the message carries a longer chain. The first such ribosome clusters ever seen were making hemoglobin.	ribosome	mm::ribosome mm::purpose analogy polysome
ribosome-proteasome-balance	In mouse L929 cells, how does the number of proteins the proteasome destroys per minute compare with the number ribosomes make?	About half as many.	The ribosomes in one such cell make about 4 million proteins a minute. The proteasome destroys what the ribosome makes, which sets each protein's lifetime.	ribosome	mm::ribosome mm::numbers proteasome turnover
ribosome-young-method	How did Young and Bremer (1976) measure the ribosome's elongation rate in E. coli?	By pulse labelling: they timed how long proteins of each size took to become fully labelled with a pulse of radioactive leucine.	The delay grows with protein size, and the slope gives the chain speed: 17 amino acids per second at fast growth and 12 at slow growth, at 37 °C.	ribosome	mm::ribosome mm::numbers speed method
ribosome-ingolia-method	How did Ingolia and colleagues (2011) measure the elongation rate in mouse embryonic stem cells?	They blocked new initiation with harringtonine, then used ribosome profiling to track how fast the front of the ribosome-free zone moved along genes.	The front moved at 5.6 ± 0.5 codons per second, averaged over thousands of genes: slower than the 12–17 per second of E. coli.	ribosome	mm::ribosome mm::numbers speed method
ribosome-wen-step	Held in optical tweezers, a single E. coli ribosome advanced along an mRNA hairpin by […] per step.	Held in optical tweezers, a single E. coli ribosome advanced along an mRNA hairpin by about 3 nucleotides per step.	The measured step was 2.94 ± 0.72 nucleotides, one codon, taken in about 0.078 s. The pauses between steps (median 2.8 s) took far longer than the steps.	ribosome	mm::ribosome mm::numbers translocation single-molecule
ribosome-pape-slow-steps	In Pape and colleagues' (1998) kinetics of tRNA selection on E. coli ribosomes, which two steps were slowest?	Accommodation (the tRNA swinging into the A site, about 8 per s) and EF-Tu·GDP release (about 4 per s).	Codon reading (about 100 per s) and GTPase activation (about 500 per s) are fast. Measured at 20 °C; the peptide bond does not wait for EF-Tu·GDP to leave.	ribosome	mm::ribosome mm::numbers kinetics ef-tu
ribosome-nissen-distance	In the Haloarcula 50S crystal structure with substrate analogues bound, no protein side-chain atom came closer than […] to the forming peptide bond.	In the Haloarcula 50S crystal structure with substrate analogues bound, no protein side-chain atom came closer than about 18 Å to the forming peptide bond.	Only conserved 23S rRNA touched the substrates, so the catalyst is RNA: the ribosome is a ribozyme.	ribosome	mm::ribosome mm::numbers ribozyme structure
ribosome-error-floor	Using a sensitive β-galactosidase reporter in E. coli, how low were most missense error rates that Manickam et al. (2014) measured?	About 2.3 × 10^-6 per codon (10 of 14 codons tested).	Four error-prone codons were about 100-fold higher. With Kramer and Farabaugh 2007, per-codon errors span about 10^-6 to 10^-3, while the page range of 10^-3 to 10^-5 is quoted from a review.	ribosome	mm::ribosome mm::debate accuracy contested
rna-polymerase-makes-mrna	RNA polymerase II copies a DNA gene into […], the molecule that ribosomes read.	RNA polymerase II copies a DNA gene into messenger RNA, the molecule that ribosomes read.	It works one base at a time: it pairs the template strand with a growing RNA chain.	rna-polymerase	mm::rna-polymerase mm::purpose purpose mrna
rna-polymerase-energy-source	What pays for each nucleotide that RNA polymerase II adds to the RNA?	The incoming nucleoside triphosphate itself: the energy of its triphosphate.	The new bond takes the energy of the triphosphate, and pyrophosphate is split off and leaves.	rna-polymerase	mm::rna-polymerase mm::purpose energy ntp
rna-polymerase-cleft-subunits	In RNA polymerase II, the two largest subunits, […], build the DNA cleft and the active site.	In RNA polymerase II, the two largest subunits, Rpb1 and Rpb2, build the DNA cleft and the active site.	Rpb1 also carries the bridge helix, the trigger loop, the clamp core and metal A; Rpb2 forms the second wall of the cleft.	rna-polymerase	mm::rna-polymerase mm::parts subunits active-site
rna-polymerase-rpb4-rpb7-role	Which part of RNA polymerase II sits next to the RNA exit groove and binds the emerging transcript?	The Rpb4-Rpb7 stalk.	Crystal structures also show Rpb7 wedging between the clamp and the linker to the tail domain, which locks the clamp closed.	rna-polymerase	mm::rna-polymerase mm::parts subunits rna-exit
rna-polymerase-subunit-count	Complete RNA polymerase II has […] subunits: a ten-subunit core plus the Rpb4-Rpb7 pair.	Complete RNA polymerase II has 12 subunits: a ten-subunit core plus the Rpb4-Rpb7 pair.	Bushnell and Kornberg tagged Rpb4 so every purified enzyme carried the pair, then solved the whole complex at 4.1 Å.	rna-polymerase	mm::rna-polymerase mm::numbers subunits
rna-polymerase-hybrid-length	Inside transcribing RNA polymerase II, the DNA-RNA hybrid is […] base pairs long.	Inside transcribing RNA polymerase II, the DNA-RNA hybrid is 9 base pairs long.	The hybrid runs from the active site at nearly a right angle to the entering DNA (yeast Pol II crystal structure, 3.3 Å).	rna-polymerase	mm::rna-polymerase mm::numbers hybrid structure
rna-polymerase-antibiotic-target	Which state of RNA polymerase is an explicit target for new antibiotics, according to structures with streptolydigin?	The preinsertion state: the NTP held before the trigger loop folds over it.	Streptolydigin holds the trigger loop away, so the nucleotide stays in an inactive preinsertion position. This inhibitor-design idea is lab-scale.	rna-polymerase	mm::rna-polymerase mm::debate trigger-loop drugs
rna-polymerase-t7-private-channel	Why does phage T7 RNA polymerase give a private expression channel in an E. coli cell?	It transcribes only T7 promoters, so it copies only the chosen gene.	One subunit does the whole job and needs no factors. It is still the standard tool for recombinant protein work.	rna-polymerase	mm::rna-polymerase mm::debate t7 biotech
rna-polymerase-post-translocation	In which translocation state can an NTP pair in the addition site of RNA polymerase II?	The post-translocation state, with template base i+1 facing the empty addition site.	Until an NTP binds and holds it forward, the enzyme can still slide back to the pre-translocation state by thermal motion.	rna-polymerase	mm::rna-polymerase mm::cycle translocation ntp
rna-polymerase-trigger-loop-folds	What does the trigger loop of RNA polymerase II do when a matching NTP pairs in the addition site?	It folds into a hairpin under the NTP, touches its base, sugar and phosphates, and seals the active site.	Leu1081 touches the base, Gln1078 reaches the 3′-OH through Asn479, and His1085 binds the β-phosphate.	rna-polymerase	mm::rna-polymerase mm::cycle trigger-loop
rna-polymerase-trigger-loop-coupling	Why does the trigger loop link NTP recognition to catalysis in RNA polymerase II?	The same loop that checks the NTP places His1085 where it may trigger the reaction.	The loop closes over a correct NTP, so recognising the NTP and catalysis are coupled.	rna-polymerase	mm::rna-polymerase mm::cycle trigger-loop fidelity
rna-polymerase-two-metals-roles	Of the two Mg2+ ions in the active site of RNA polymerase II, which stays and which comes and goes each cycle?	Metal A stays bound to Rpb1 aspartates; metal B comes in with the NTP and leaves with the pyrophosphate.	Metal A sits by the RNA 3′-OH and metal B holds the triphosphate, about 4 Å apart.	rna-polymerase	mm::rna-polymerase mm::cycle metals catalysis
rna-polymerase-loop-opens-before-ppi	Why must the trigger loop of RNA polymerase II open before pyrophosphate can leave?	The closed loop blocks the way out and holds the pyrophosphate through His1085.	Only the fully open loop lets pyrophosphate move back to the entry site and out through the pore (Yi et al. 2026 preprint; Li et al. 2026 agrees).	rna-polymerase	mm::rna-polymerase mm::cycle trigger-loop pyrophosphate
rna-polymerase-brownian-ratchet	In the Brownian ratchet model, RNA polymerase slides back and forth along the DNA by thermal motion, and […] catches it in the forward position.	In the Brownian ratchet model, RNA polymerase slides back and forth along the DNA by thermal motion, and an incoming NTP catches it in the forward position.	Each cycle moves the DNA and RNA one base pair; the trigger loop swings between open, wedged and closed positions as part of this motion.	rna-polymerase	mm::rna-polymerase mm::cycle translocation ratchet
rna-polymerase-proofreading-backtrack	How does RNA polymerase II remove a wrong base it has just added?	It backtracks one position, and the same active site cuts off the RNA end that holds the error.	The wrong base first frays away from the template and the enzyme pauses. DNA polymerases, in contrast, use a separate nuclease site.	rna-polymerase	mm::rna-polymerase mm::cycle proofreading fidelity
rna-polymerase-tfiis-rescue	The factor […] rescues backtracked RNA polymerase II by helping it cut its RNA.	The factor TFIIS rescues backtracked RNA polymerase II by helping it cut its RNA.	In a backtracked enzyme the RNA end runs into the pore and traps the trigger loop; TFIIS reaches into the active site, pushes the RNA out and helps cut it.	rna-polymerase	mm::rna-polymerase mm::parts backtracking proofreading
rna-polymerase-same-genome-different-cells	A skin cell and a nerve cell carry the same genome. What makes them differ, in terms of what RNA polymerase II copies?	Which genes (pages) they read.	Every cell with a nucleus holds the full set of instructions; RNA polymerase II copies only the genes that cell needs.	rna-polymerase	mm::rna-polymerase mm::purpose purpose genome
rna-polymerase-dystrophin-time	One RNA polymerase II takes about […] to copy the human dystrophin gene once.	One RNA polymerase II takes about 16 hours to copy the human dystrophin gene once.	Dystrophin is at least 2,300 kb long; muscle cell cultures copied about 1,770 kb in about 12 h (about 2.4 kb per minute), and the authors extrapolated.	rna-polymerase	mm::rna-polymerase mm::numbers speed genes
rna-polymerase-copies-per-hela	About how many RNA polymerase II molecules does one HeLa cell hold?	About 320,000.	About 65,000 (roughly 20%) copy a gene at one time, but the source cites that share from earlier work rather than measuring it.	rna-polymerase	mm::rna-polymerase mm::numbers copy-number
rna-polymerase-ribosome-link	In a fast-growing yeast cell, […] of all RNA polymerase II transcription serves the genes for ribosomal proteins.	In a fast-growing yeast cell, half of all RNA polymerase II transcription serves the genes for ribosomal proteins.	Ribosomes read the messenger RNA that RNA polymerase II writes.	rna-polymerase	mm::rna-polymerase mm::purpose ribosome links
rna-polymerase-train-analogy-breaks	Where does the "train on a track" analogy for RNA polymerase II break down?	Pol II pauses, backs up to fix errors, and speeds up and slows down along a gene.	The analogy gets one thing right: Pol II runs along the gene in one direction.	rna-polymerase	mm::rna-polymerase mm::cycle analogy speed
rna-polymerase-rate-long-genes	Over long human genes, RNA polymerase II copies about […], about 63 nucleotides per second.	Over long human genes, RNA polymerase II copies about 3.8 kb per minute, about 63 nucleotides per second.	Measured in human Tet-21 cells: 3.79 ± 0.26 kb per minute over 15 gene regions. That is about 16 ms per nucleotide.	rna-polymerase	mm::rna-polymerase mm::numbers speed
rna-polymerase-rate-method	How did Singh and Padgett measure the speed of RNA polymerase II over long human genes?	They blocked new transcription with DRB, washed it out, and timed when new pre-mRNA reached exon-intron junctions far apart in the same gene.	The delay between two junctions, read by RT-PCR, gives the speed; it was about the same over long introns and exon-rich stretches.	rna-polymerase	mm::rna-polymerase mm::numbers speed method
rna-polymerase-error-rate	About what transcription error rate per base was measured across all mRNA of the worm Caenorhabditis elegans?	About 4 x 10^-6 per base.	That is about four mistakes per million letters (4.1 × 10^-6 pooled over three strains).	rna-polymerase	mm::rna-polymerase mm::numbers fidelity
rna-polymerase-error-rate-method	How did Gout and colleagues tell real transcription errors apart from errors made while copying and sequencing the RNA?	They tagged each RNA fragment, copied it three times, and counted a change only if every copy carried it.	Requiring the change in every copy removes errors made during copying and sequencing.	rna-polymerase	mm::rna-polymerase mm::numbers fidelity method
rna-polymerase-mismatch-slows-next	According to Thomas and colleagues, what delay, more than the slow addition of the wrong base itself, lets RNA polymerase II tell right from wrong?	The next nucleotide is added at least 15- to 20-fold more slowly after a mismatched RNA end.	The pause gives the enzyme time to back up and cut out the error. Measured with Pol II complexes from human nuclear extract.	rna-polymerase	mm::rna-polymerase mm::cycle fidelity proofreading
rna-polymerase-deoxy-ntp-chemistry	How did Wang and colleagues show that RNA polymerase II rejects 2′-deoxy NTPs mainly at the chemical step, not at binding?	Deoxy NTPs were added at least 400-fold more slowly, while their KM values were much closer to normal.	A deoxy NTP still binds the addition site, so binding alone cannot tell it from an RNA building block; trigger-loop closure and the chemistry do.	rna-polymerase	mm::rna-polymerase mm::cycle fidelity ntp
rna-polymerase-ppi-power-stroke-debate	Which model of RNA polymerase movement did optical-trap force-velocity data favour over a power stroke tied to pyrophosphate release?	A Brownian ratchet with a second NTP site.	The power stroke fitted poorly (reduced χ² 6.03), measured on E. coli RNA polymerase. The machine notes still say pyrophosphate release drives the chain forward.	rna-polymerase	mm::rna-polymerase mm::debate ratchet pyrophosphate
groel-what-it-does	What does GroEL do for a protein that has not folded?	It closes the protein in a chamber where it folds alone, safe from aggregation.	Hydrophobic surfaces in one ring catch the protein; ATP and the lid GroES then close the chamber around it.	groel	mm::groel mm::purpose folding aggregation
groel-equatorial-domain-role	Which GroEL domain binds ATP and holds the two rings together?	The equatorial domain.	Each GroEL subunit has three domains: equatorial (ATP, ring contacts), intermediate (the hinge) and apical (binds substrate and GroES).	groel	mm::groel mm::parts domains atp
groel-apical-helices-h-i	Through which helices does the GroEL apical domain bind both the unfolded substrate and GroES?	Helices H and I.	The same sites hold the client first and GroES later, so GroES binding takes the sites away from the client.	groel	mm::groel mm::parts domains binding
groel-thermosome-built-in-lid	Why does the archaeal thermosome, a group II chaperonin, need no GroES lid?	Its own apical domains form a built-in lid.	Group I chaperonins such as GroEL, in bacteria and organelles, use a separate GroES lid. The thermosome also has eight subunits per ring, not seven.	groel	mm::groel mm::parts evolution lid
groel-seven-per-ring	GroEL is a cylinder of two stacked rings, each made of […] subunits.	GroEL is a cylinder of two stacked rings, each made of seven subunits.	That gives 14 GroEL subunits, capped by one GroES ring of 7 subunits (X-ray structure, Braig et al. 1994).	groel	mm::groel mm::numbers structure
groel-size-limit	The closed GroEL–GroES chamber can hold unfolded proteins up to about […].	The closed GroEL–GroES chamber can hold unfolded proteins up to about 60 kDa.	Denatured proteins smaller than the 57 kDa GroEL subunit stay inside; an 82 kDa protein binds GroEL but never enters.	groel	mm::groel mm::numbers chamber size
groel-atp-per-cycle	How many ATP does one GroEL ring bind and hydrolyse in each folding cycle?	7	One ATP per subunit of the ring. Each turn of the alternating-ring cycle uses one ringful of ATP (Rye et al. 1999).	groel	mm::groel mm::numbers atp
groel-evolved-specialist-cost	What did GroEL/GroES variants evolved to fold green fluorescent protein lose in return?	General folding ability.	The best variant made cells 8-fold brighter with GFP but cut lambda phage plaque formation about 1000-fold. A specialist cage trades away the generalist one.	groel	mm::groel mm::debate evolution engineering
groel-capture-hydrophobic	What does an unfolded protein expose that lets the open GroEL ring catch it?	Water-repelling (hydrophobic) stretches.	These stretches bind a water-repelling collar formed by helices H and I of all seven subunits, with several contacts at once.	groel	mm::groel mm::cycle capture hydrophobic
groel-ring-anticooperativity	In GroEL, ATP binding is cooperative within a ring but […] between the two rings.	In GroEL, ATP binding is cooperative within a ring but strongly anti-cooperative between the two rings.	Yifrach and Horovitz fitted an inter-ring Hill coefficient of 0.003. So a ring binds its seven ATP together, and the two rings do not do so at the same time.	groel	mm::groel mm::cycle atp allostery
groel-apical-rise-stretches	As the GroEL apical domains rise after ATP binds, they stretch the bound protein, which can […].	As the GroEL apical domains rise after ATP binds, they stretch the bound protein, which can pull misfolded parts apart.	The apical domains rise and move outwards, so the protein is pulled between its contact points.	groel	mm::groel mm::cycle apical unfolding
groel-what-opens-old-chamber	In GroEL, what makes the closed chamber on one ring open and release GroES?	ATP (with a new client) binding to the opposite ring.	The signal crosses the ring contact through the equatorial domains. The old ring lets go of GroES and its protein, folded or not, so the two rings alternate.	groel	mm::groel mm::cycle alternation release
groel-power-stroke-twist	When GroES docks on GroEL, what does the final twist of about 100° of the apical domains do to the bound client?	It peels the water-repelling sites off the client and drops it into the chamber.	Clare and colleagues call this twist the power stroke of GroEL. It buries the sites against GroES and doubles the chamber volume.	groel	mm::groel mm::cycle power-stroke apical
groel-why-no-aggregation-inside	Why can a protein folding inside the closed GroEL chamber not aggregate?	The chamber holds only that one protein, so it meets no other chains.	The chamber lining is also water-loving, so the folding protein finds nothing sticky.	groel	mm::groel mm::cycle chamber aggregation
groel-hydrolysis-timer	In GroEL, […] in the closed ring sets how long the chamber stays shut.	In GroEL, ATP hydrolysis in the closed ring sets how long the chamber stays shut.	The ADP state holds GroES less tightly (Rye et al. 1997), and only after hydrolysis can the opposite ring take up a client and GroES (Rye et al. 1999).	groel	mm::groel mm::cycle atp timer
groel-stuck-chains-clump	In E. coli, why is a new protein chain that gets stuck half-folded a problem for the cell?	Its sticky patches can stick to other stuck chains and form a useless clump.	Such clumps are useless and can be toxic. GroEL catches stuck chains so they get another chance to fold.	groel	mm::groel mm::purpose aggregation cell
groel-share-of-proteins	In E. coli during normal growth, about […] of cytoplasmic protein passes through GroEL.	In E. coli during normal growth, about 10–15% of cytoplasmic protein passes through GroEL.	Under heat stress the share rises to 30% or more. Most proteins leave GroEL within 10–30 s.	groel	mm::groel mm::numbers cell flux
groel-essential-for-growth	How well does E. coli grow without GroEL and GroES?	Not at all: it cannot grow at any temperature tested.	About 85 E. coli proteins need GroEL to fold, and 13 of those are essential to the cell.	groel	mm::groel mm::purpose essential cell
groel-human-hsp60	What is the GroEL relative in human mitochondria called?	Hsp60	Mitochondria descend from bacteria and kept this folding chamber. Human Hsp60 with its lid, Hsp10, lets E. coli grow without its own GroEL and GroES.	groel	mm::groel mm::parts mitochondria evolution
groel-quiet-room-open-question	The GroEL chamber is often pictured as "a quiet room for one". What does that picture leave open?	Whether the chamber actively helps the fold, beyond keeping other chains out.	This is debated (Hayer-Hartl et al. 2016; Horwich et al. 2009). The room also changes: its walls are sticky while catching the chain and water-loving once the lid closes.	groel	mm::groel mm::debate analogy debate
groel-second-chance-by-chance	How does a chain that GroEL releases still unfolded get another round of folding?	It simply binds GroEL again by chance; GroEL does not check the result.	Of about 300 new proteins that bind GroEL strongly, about one third are unstable and return to it again and again.	groel	mm::groel mm::cycle analogy rebinding
groel-size-limit-method	How did Sakikawa and colleagues (1999) find which unfolded E. coli proteins fit inside the closed GroEL–GroES cage?	They closed GroES over the captured proteins and digested everything outside with protease; only proteins inside survived.	Only proteins smaller than one 57 kDa GroEL subunit survived. An 82 kDa GFP trimer bound GroEL but was always digested, so it never entered.	groel	mm::groel mm::numbers method size
groel-hydrolysis-rates-differ	ATP hydrolysis in the closed GroEL ring was measured at 0.12 s^-1 per subunit (Burston et al. 1995) and as a burst at 0.518 s^-1 (Ye and Lorimer 2013). Why do the two rates differ?	The studies used different methods and salt conditions.	Burston and colleagues used transient kinetics after GroES binding; Ye and Lorimer followed phosphate release by stopped-flow at 0.2 M K+.	groel	mm::groel mm::debate atp kinetics
groel-groes-stay-no-substrate	Without substrate protein, about how long does the GroES lid stay on E. coli GroEL?	About 24 s.	In trapping experiments GroES left at 0.042 s^-1 per subunit, the same as the steady-state ATPase rate; 24 s is 1 divided by that rate. Without substrate, GroES release is the slowest step.	groel	mm::groel mm::numbers groes kinetics
groel-substrate-speeds-release	In stopped-flow FRET experiments, unfolded substrate protein sped up GroES release from GroEL […].	In stopped-flow FRET experiments, unfolded substrate protein sped up GroES release from GroEL 20- to 50-fold.	The fast route grew with denatured Rubisco. Unfolded protein binds the open ring first and speeds release of the old cage, so GroEL spends its time folding rather than waiting.	groel	mm::groel mm::numbers groes kinetics fret
groel-cage-volume-method	How did Tang and colleagues (2006) change the volume of the GroEL cavity?	By deleting or extending the C-terminal Gly-Gly-Met repeats that hang into it.	Shrinking the cavity by 1.9–4.4% sped folding of 33 kDa rhodanese and MetF, while any change slowed 41 kDa MBP and 50 kDa RuBisCo. The natural cage size suits fast folding, not just shelter.	groel	mm::groel mm::parts method chamber
groel-sr1-folds-inside	Rhodanese trapped under GroES in single-ring GroEL (SR1), which never opens, still became active. What does this show?	The protein folds inside the closed cage, not only after release.	The trapped rhodanese reached native activity with a half-time of about 7 min while still bound to SR1.	groel	mm::groel mm::cycle sr1 chamber
groel-one-or-two-lids-in-cells	In living E. coli cells, […] of GroEL carried one GroES lid and the rest carried two.	In living E. coli cells, 55 to 70% of GroEL carried one GroES lid and the rest carried two.	With client protein in vitro, Ye and Lorimer found most complexes carry GroES on both rings ("footballs"), so the simple one-lid alternating cycle is not the whole story.	groel	mm::groel mm::debate football in-cell
proteasome-tag-signal	What mark does the cell put on a protein to send it to the 26S proteasome?	A chain of ubiquitin.	Ubiquitin receptors in the proteasome bind this chain, so the proteasome picks marked proteins out of thousands of others.	proteasome	mm::proteasome mm::purpose ubiquitin recognition
proteasome-sealed-barrel-why	Why does the proteasome keep its cutting sites inside a sealed barrel?	So that only a chain fed through the gate meets them, which keeps the cell's other proteins safe.	All six active sites face the inner chamber, and the gate into it is shut until the ATPase ring opens it.	proteasome	mm::proteasome mm::purpose core-particle safety
proteasome-atpase-ring-role	Which part of the 26S proteasome grips, unfolds and pulls the tagged protein into the barrel?	The ring of six AAA+ ATPases, Rpt1 to Rpt6.	The same ring also opens the gate into the core particle.	proteasome	mm::proteasome mm::parts atpase motor
proteasome-rpn11-role	What does Rpn11, a zinc enzyme of the proteasome lid, do to the substrate?	It cuts the ubiquitin chain off the substrate at the pore entrance.	Rpn11 is a deubiquitinase. It removes the tag in the same cycle that pulls the protein in.	proteasome	mm::proteasome mm::parts rpn11 ubiquitin
proteasome-active-beta-subunits	Which three beta subunits of the proteasome core particle carry the active sites?	beta1, beta2 and beta5.	They cut after acidic, basic and bulky water-repelling residues: caspase-like, trypsin-like and chymotrypsin-like. The other four beta types are structural.	proteasome	mm::proteasome mm::parts core-particle active-site
proteasome-core-subunits	The proteasome core particle has 28 subunits in […]: (alpha1-7 beta1-7)2.	The proteasome core particle has 28 subunits in four rings of seven: (alpha1-7 beta1-7)2.	Two outer alpha rings form the gate; two inner beta rings hold the active sites, three per ring, so six sites per core.	proteasome	mm::proteasome mm::numbers core-particle structure
proteasome-hbyx-older	Why is the proteasome's HbYX gate signal thought to be older than the 26S particle itself?	Archaea use the simpler PAN ATPase with the same HbYX gate signal as the eukaryotic Rpt subunits.	Free HbYX peptides of 7 to 10 residues open the gate of the archaeal core on their own (Smith et al. 2007).	proteasome	mm::proteasome mm::parts evolution gate
proteasome-protac	How does a PROTAC get the proteasome to destroy a chosen protein?	It ties the protein to an E3 ligase, which marks it with ubiquitin.	The two-headed molecule supplies the address; the proteasome does the rest. dBET1 removed BET proteins in cells and in mice (status: demonstrated).	proteasome	mm::proteasome mm::debate protac drugs
proteasome-commitment	Ubiquitin binding alone does not commit a protein to the proteasome. What does?	The pore loops of the ATPase ring gripping the protein's unstructured tail.	Ubiquitin chains bind and leave quickly. Only a substrate whose tail engages the motor triggers the switch to the working shape and goes on to be degraded.	proteasome	mm::proteasome mm::cycle engagement tail
proteasome-pull-speeds-cut	Rpn11 cuts the ubiquitin chain off faster when […].	Rpn11 cuts the ubiquitin chain off faster when the motor pulls on the substrate.	This couples tag removal to translocation: the tag comes off as the protein moves into the pore.	proteasome	mm::proteasome mm::cycle rpn11 coupling
proteasome-gate-opening	How do the proteasome's ATPases open the gate into the core particle?	Their C-terminal HbYX tails dock in pockets between alpha subunits, which rotates the alpha subunits and opens the gate.	The tails work like a key in a lock. Closed, the N-terminal tails of the alpha subunits fill the entrance.	proteasome	mm::proteasome mm::cycle gate hbyx
proteasome-staircase-one-way	The six proteasome ATPases stand in a spiral staircase. Why does the substrate chain move one way only?	ATP hydrolysis passes around the ring in order, so each subunit grips the chain in turn.	The gripping subunits move down together and carry the chain with them, hand over hand.	proteasome	mm::proteasome mm::cycle atpase translocation
proteasome-seam-subunit	In the proteasome's ATPase staircase, what does the subunit at the bottom do next?	It lets go of the chain and climbs to the top.	This 'seam' subunit then binds ATP and grips the chain again at the top, so the ring keeps cycling.	proteasome	mm::proteasome mm::cycle atpase translocation
proteasome-hinge	In each proteasome ATPase, a […] driven by ATP hydrolysis sets when that subunit holds or releases the chain.	In each proteasome ATPase, a hinge motion driven by ATP hydrolysis sets when that subunit holds or releases the chain.	Bound nucleotide locks the large and small AAA+ subdomains into one rigid body; release lets them hinge by 20–25°.	proteasome	mm::proteasome mm::cycle atpase unfolding
proteasome-thr1	Which residue in the proteasome's active beta subunits attacks the peptide bond?	The N-terminal threonine (Thr1).	It sits on beta1, beta2 and beta5. Deleting Thr1 or changing it to alanine stops the enzyme.	proteasome	mm::proteasome mm::cycle active-site threonine
proteasome-release	What decides when peptides leave the proteasome barrel, according to Kisselev and colleagues' proposal?	Cutting goes on until a piece is short enough to diffuse out.	Product length hardly changed when one type of active site was blocked. The products are 3 to 22 residues long.	proteasome	mm::proteasome mm::cycle peptides release
proteasome-body-turnover	An adult human breaks down and rebuilds about […] of body protein a day, but eats only 50–80 g.	An adult human breaks down and rebuilds about 300–400 g of body protein a day, but eats only 50–80 g.	Most of the parts are recycled, and most of that breakdown happens in the proteasome. The figure is a review estimate.	proteasome	mm::proteasome mm::purpose body turnover
proteasome-pieces-fate	Most proteasome peptides become amino acids for new proteins. What happens to a few of them?	They go to the cell surface on MHC class I, where immune cells check them.	The display is a sample of what the cell is making, so immune cells can spot an infected cell.	proteasome	mm::proteasome mm::purpose immune mhc
proteasome-vs-ribosome-rate	In mouse L929 cells, how does the number of proteins the proteasomes destroy per minute compare with the number the ribosomes make?	About half: 2 × 10^6 destroyed versus 4 × 10^6 made per minute.	It is a calculation: 8 × 10^5 proteasomes × 2.5 proteins per minute each. Together the two machines set protein levels.	proteasome	mm::proteasome mm::numbers cell ribosome
proteasome-shredder-breaks	Where does the analogy 'the proteasome is a paper shredder' break down about how input gets in?	A shredder is fed; the proteasome pulls and unfolds its input itself, with six ATP motors.	It also takes off the ubiquitin tag and returns it for reuse. The analogy gets right that the enclosed blades hurt nothing else.	proteasome	mm::proteasome mm::purpose analogy
proteasome-healthy-proteins	Unlike a recycling plant, the proteasome also destroys healthy proteins on schedule. What does that let the cell do?	Turn signals off.	For example, the proteasome destroys transcription factors, so it helps decide when genes switch on.	proteasome	mm::proteasome mm::purpose analogy signalling
proteasome-time-per-protein	One mouse 26S proteasome needs about […] to degrade one ubiquitinated DHFR molecule (Ub5-DHFR).	One mouse 26S proteasome needs about 13 s to degrade one ubiquitinated DHFR molecule (Ub5-DHFR).	A longer ubiquitinated protein, Sic1, took about twice as long (26 s), so time depends on the substrate.	proteasome	mm::proteasome mm::numbers rate dhfr
proteasome-time-method	How did Peth and colleagues get the 13 s a proteasome needs per Ub5-DHFR molecule?	From the maximal degradation rate (Vmax) at rising substrate levels: time per molecule = 1/Vmax.	They followed 32P-labelled substrate turning into acid-soluble peptides with purified mouse 26S proteasomes; the maximum was about 4.7 molecules per minute per particle.	proteasome	mm::proteasome mm::numbers method kinetics
proteasome-atp-cost	Mouse 26S proteasomes spend […] ATP to destroy one Ub5-DHFR molecule.	Mouse 26S proteasomes spend 50–80 ATP to destroy one Ub5-DHFR molecule.	Peth and colleagues combined the maximal degradation rate with ATP hydrolysis measured by a malachite green phosphate assay.	proteasome	mm::proteasome mm::numbers atp cost
proteasome-folate-meaning	Folic acid stabilises the DHFR fold. What happened to proteasome ATP use per minute and to degradation time when it was bound?	ATP use per minute stayed the same, but degradation slowed from 13 s to 23 s per molecule.	So each molecule cost more, 90–140 ATP instead of 50–80: unfolding is a slow and costly step for a stable protein.	proteasome	mm::proteasome mm::numbers unfolding atp
proteasome-single-rpt-mutant	Blocking ATP binding in one yeast proteasome ATPase (Rpt3, Rpt5 or Rpt6) cut basal ATP use by about 66%, not the 16% expected. What does that show?	The six ATPases run in an ordered cycle, so one stalled subunit holds up the others.	If the subunits worked on their own, losing one of six would cost only about one sixth of the activity.	proteasome	mm::proteasome mm::cycle atpase coordination
proteasome-step-size	In cryo-EM of working yeast 26S proteasomes, how far does the substrate move per ATP?	About 6 Å, read as two amino acids per ATP.	De la Peña and colleagues saw the engaged pore-1 loop tyrosines move down by that distance between consecutive motor states.	proteasome	mm::proteasome mm::numbers translocation cryo-em
proteasome-mass-not-measured	The human 26S proteasome is often given as 2.5 MDa, citing Dong et al. 2019. What is the problem with that source?	Dong et al. state the mass but do not measure it; a primary measurement still has to be found.	Their paper is a cryo-EM structure study, and its own results are the seven structures, not a mass.	proteasome	mm::proteasome mm::debate mass provenance
serca-job	What job does SERCA do in a muscle cell after each contraction?	It clears calcium from the cytoplasm, pumping it back into the sarcoplasmic reticulum.	Calcium switches muscle on, so the muscle can only relax and fire again once SERCA has taken the calcium away.	serca	mm::serca mm::purpose calcium muscle
serca-ca-per-atp	SERCA burns one ATP to push […] calcium ions out of the cytoplasm.	SERCA burns one ATP to push two calcium ions out of the cytoplasm.	The crystal structure shows two calcium sites side by side inside the membrane domain, which fits this ratio.	serca	mm::serca mm::numbers stoichiometry atp
serca-p-domain	Which SERCA domain holds the aspartate that accepts the phosphoryl group from ATP?	The P (phosphorylation) domain.	The P domain has the same fold as haloacid dehalogenase, a general phosphotransfer scaffold.	serca	mm::serca mm::parts domains phosphorylation
serca-n-domain	What part of ATP does SERCA's N domain bind?	The adenosine part.	When nucleotide binds, the N domain swings onto the P domain, which holds the aspartate that takes the phosphate.	serca	mm::serca mm::parts domains atp
serca-a-domain	What does SERCA's A (actuator) domain drive when it tilts against the membrane helices?	Gating and dephosphorylation.	Release of ADP opens the lumenal gate and release of phosphate closes it, mainly through movements of the A domain.	serca	mm::serca mm::parts domains gating
serca-phospholamban-role	How does phospholamban change the cardiac SERCA pump?	It raises the calcium level the pump needs to cycle.	Phospholamban is an inhibitory membrane micropeptide of cardiac muscle: the same pump rate then needs more calcium.	serca	mm::serca mm::parts regulation heart
serca-dworf-safer	Why is the activator DWORF seen as a safer way to boost SERCA than removing phospholamban?	Complete loss of phospholamban is lethal in humans; DWORF instead raises turnover and competes phospholamban off its site.	This is a lab-scale idea: DWORF is the only known activator in the regulin family.	serca	mm::serca mm::debate heart-failure regulation
serca-gene-transfer-status	What is the state of SERCA2a gene transfer as a treatment for heart failure?	It restored contractile function in failing heart muscle, but clinical results have been inconsistent.	SR calcium cycling and SERCA2a activity fall in heart failure. The approach is still rated lab-scale.	serca	mm::serca mm::debate heart-failure
serca-e1-magnesium	In SERCA's calcium-free E1 state, one Mg2+ sits in a calcium site. What does it block until calcium arrives?	Phosphorylation.	Calcium is the trigger: once the two high-affinity sites fill, phosphorylation can go ahead. In skeletal muscle, sarcolipin stabilises this E1 state with magnesium.	serca	mm::serca mm::cycle e1 magnesium
serca-atp-bridges	What does ATP binding do to SERCA's N and P domains?	It bridges them, pulling the widely separated domains together.	The A domain then tilts and one membrane helix moves to lock the cytoplasmic gate, occluding the two calcium ions.	serca	mm::serca mm::cycle atp domains
serca-no-backflow	When SERCA phosphorylates itself, what stops the bound calcium from flowing back to the cytoplasm?	Helices M1 and M2 shift and close the cytosolic entrance.	The same movement that transfers the phosphate to the aspartate shuts the entry door, so the ions are trapped before the exit opens.	serca	mm::serca mm::cycle gating phosphorylation
serca-lumenal-gate-trigger	In SERCA, the change from E1P to E2P after […] opens the exit path for calcium to the lumen.	In SERCA, the change from E1P to E2P after phosphorylation opens the exit path for calcium to the lumen.	Helices M1 to M6 open the path, and a shift of M4 exposes Glu 309, Glu 771 and Asn 796 to the lumen, where calcium leaves.	serca	mm::serca mm::cycle gating e2p
serca-protons-empty-sites	After SERCA releases its two calcium ions to the lumen, what binds the empty sites?	Protons, which become occluded.	The pump carries protons back the other way; then the phosphoenzyme is hydrolysed and the cycle can reset.	serca	mm::serca mm::cycle protons counter-transport
serca-tges-motif	SERCA's phosphoenzyme is hydrolysed through the conserved […] motif, by the same associative chemistry as the forward transfer.	SERCA's phosphoenzyme is hydrolysed through the conserved Thr-Gly-Glu-Ser motif, by the same associative chemistry as the forward transfer.	This motif (TGES) lets water attack the phosphate while the counter-transported protons stay occluded.	serca	mm::serca mm::cycle dephosphorylation
serca-e2-headpiece	In SERCA's calcium-free E2 state, the three cytoplasmic domains gather into […].	In SERCA's calcium-free E2 state, the three cytoplasmic domains gather into one compact headpiece.	Without nucleotide in E1 they sit far apart; between the states, six of the ten membrane helices rearrange.	serca	mm::serca mm::cycle e2 domains
serca-gradient-size	At rest, the SERCA pumps hold about […] times more free calcium inside the sarcoplasmic reticulum than in the muscle cytosol.	At rest, the SERCA pumps hold about 4,000 times more free calcium inside the sarcoplasmic reticulum than in the muscle cytosol.	Calculated from free Ca2+ of about 390 µM in the SR and about 100 nM in the cytosol of mouse fibres. The often-quoted 10,000-fold is outside the cell versus the cytosol.	serca	mm::serca mm::numbers gradient calcium
serca-atp-pays	Why is one ATP enough to pay for SERCA pushing two calcium ions up the SR gradient?	The push costs about 43 kJ/mol, and one ATP supplies 57–64 kJ/mol in the cell.	The 43 kJ/mol is 2 × RT × ln(3,900) at 37 °C; it leaves out any voltage across the SR membrane.	serca	mm::serca mm::numbers energy atp
serca-resting-oxygen	In resting mouse muscle, SERCA accounts for about […] of the muscle's oxygen use.	In resting mouse muscle, SERCA accounts for about 40–50% of the muscle's oxygen use.	Measured in isolated mouse muscles at 30 °C. The authors scale this to 12–15% of whole-body resting oxygen use, an estimate.	serca	mm::serca mm::numbers energy metabolism
serca-heart-share	In mouse heart muscle cells, SERCA removes about […] of each beat's calcium.	In mouse heart muscle cells, SERCA removes about 90% of each beat's calcium.	The sodium-calcium exchanger removes most of the rest (9%), so SERCA sets how fast the heart relaxes.	serca	mm::serca mm::numbers heart calcium
serca-airlock-breaks	SERCA is often compared to an airlock whose two doors never open together. Where does that analogy break?	An airlock is passive; the energy of ATP drives SERCA's doors.	The analogy gets the gating right: because the two gates never open at once, the store cannot leak back.	serca	mm::serca mm::purpose analogy gating
serca-myosin-link	How does SERCA switch myosin off at the end of a contraction?	It takes away the calcium that switched myosin on.	SERCA is the off switch for the calcium signal that myosin, the consumer, responds to.	serca	mm::serca mm::purpose myosin contraction
serca-ratio-method	How did Yu and Inesi (1995) measure SERCA's calcium-per-ATP ratio?	By following 45Ca2+ uptake and Ca2+-dependent phosphate release side by side in native rabbit SR vesicles.	At the start of pumping, close to two calcium ions went in for each ATP split, and the ratio was never seen above 2.	serca	mm::serca mm::numbers stoichiometry method
serca-ratio-best-case	Why is two calcium ions per ATP the best case for SERCA rather than a fixed rule?	The ratio falls as calcium builds up inside the vesicles.	With oxalate clamping lumenal calcium, the steady ratio was about 1.5.	serca	mm::serca mm::numbers stoichiometry coupling
serca-plateau-not-leak	After SERCA's calcium uptake into vesicles levelled off, ATP splitting went on. Thapsigargin stopped it, and no calcium leaked out. What did this show?	The extra ATP went to pumps cycling without moving calcium, not to re-pumping leaked calcium.	Lumenal calcium slows the pump itself, so back-inhibition, not leak, limits the gradient SERCA can build.	serca	mm::serca mm::numbers coupling gradient
serca-proton-ratio	In reconstituted proteoliposomes, SERCA moved […] H+ out of the lumen for each Ca2+ moved in.	In reconstituted proteoliposomes, SERCA moved 1 H+ out of the lumen for each Ca2+ moved in.	Yu and colleagues (1993) read calcium with murexide and lumenal pH with trapped pyranine; the two traces ran in parallel for 10 minutes. Earlier studies gave 1.0–1.5.	serca	mm::serca mm::numbers protons counter-transport
serca-pln-max-rate	When purified phospholamban was added to SERCA, how did it change the pump's ATP splitting?	It shifted the calcium curve to higher calcium (KCa 0.26 to 0.62 µM) without lowering the maximal rate.	Phospholamban is a brake on calcium affinity, not on top speed; the superinhibitory mutant PLB4 shifted KCa further, to 1.38 µM.	serca	mm::serca mm::numbers phospholamban regulation
serca-thapsigargin-tool	Why did thapsigargin become a standard tool for blocking SERCA?	It inhibits SERCA's calcium uptake at sub-nanomolar doses but leaves calcium release channels and the plasma-membrane calcium pump unaffected.	Free thapsigargin at 0.1 nM already inhibits uptake in SR vesicles; it binds the calcium-free pump and blocks calcium binding.	serca	mm::serca mm::numbers thapsigargin inhibitor
serca-monomer-method	How did Heegaard and colleagues show that a single SERCA chain can pump calcium on its own?	In lipid-rich vesicles that still pumped, freeze-fracture EM counted one membrane particle per chain, and cross-linking found no pump pairs.	So one polypeptide is the working unit; regulators such as phospholamban bind from the membrane.	serca	mm::serca mm::parts monomer method
hemoglobin-job	What does hemoglobin carry, and from where to where?	Oxygen, from the lungs to the tissues.	Hemoglobin loads oxygen in the lungs and unloads it where tissues need it, because it switches shape as a whole.	hemoglobin	mm::hemoglobin mm::purpose oxygen transport
hemoglobin-no-fuel	Hemoglobin spends no chemical fuel. What does the work of loading and unloading oxygen instead?	The oxygen gradient and the allosteric switch.	SERCA also switches between two states, but it spends ATP to do so; hemoglobin spends nothing.	hemoglobin	mm::hemoglobin mm::purpose energy allostery
hemoglobin-two-dimers	Human adult hemoglobin has two alpha and two beta chains, arranged as a pair of […].	Human adult hemoglobin has two alpha and two beta chains, arranged as a pair of alpha-beta dimers.	Each dimer changes little inside itself, so the T-to-R switch is one dimer moving against the other.	hemoglobin	mm::hemoglobin mm::parts structure subunits
hemoglobin-sigmoid-why	Why is hemoglobin's oxygen binding curve sigmoid?	Its four sites are not independent: the tetramer switches from a low-affinity T state to a high-affinity R state.	Early oxygens bind weakly to T; once the tetramer snaps to R, the remaining hemes bind with much higher affinity.	hemoglobin	mm::hemoglobin mm::purpose cooperativity allostery
hemoglobin-hill-value	Unmodified, stroma-free human hemoglobin at pH 7.40 and 37 °C has a Hill coefficient of […].	Unmodified, stroma-free human hemoglobin at pH 7.40 and 37 °C has a Hill coefficient of 2.8.	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.	hemoglobin	mm::hemoglobin mm::numbers cooperativity hill
hemoglobin-fetal-gamma	Why does fetal hemoglobin hold oxygen more tightly than adult hemoglobin?	Its gamma chains, which replace beta, bind 2,3-BPG only weakly.	2,3-BPG lowers oxygen affinity, so weak binding moves the fetal curve left and fetal blood can take oxygen from maternal blood.	hemoglobin	mm::hemoglobin mm::parts fetal 2,3-bpg
hemoglobin-global-allostery	In the global allostery model of hemoglobin, what carries much of the affinity change and most of the Bohr effect?	Tertiary changes inside both the T and the R state.	Broader oxygen-binding measurements support this model (status: demonstrated). The two-state model stays useful as a compact fit, not as the final mechanism.	hemoglobin	mm::hemoglobin mm::debate allostery models
hemoglobin-designed-switch	Hemoglobin shows the minimum parts for an allosteric switch. What are the three parts?	A rigid dimer, one interface with exactly two good arrangements, and a ligand site that senses which arrangement it occupies.	Designed allosteric switches aim at the same set of parts; this is a proposal, not yet a result.	hemoglobin	mm::hemoglobin mm::debate design allostery
hemoglobin-iron-into-plane	When the first oxygen binds a hemoglobin heme, the iron moves […].	When the first oxygen binds a hemoglobin heme, the iron moves into the heme plane.	In the T state without oxygen, the iron sits slightly out of the heme plane. Its move is the local trigger of the switch.	hemoglobin	mm::hemoglobin mm::cycle heme iron
hemoglobin-proximal-histidine	In hemoglobin, what links the heme iron to the protein, so that the iron's move pulls on a helix?	The proximal histidine.	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.	hemoglobin	mm::hemoglobin mm::parts heme histidine
hemoglobin-switch-contact	In hemoglobin, the […] contact is the switch point between the T and R quaternary states.	In hemoglobin, the alpha1-beta2 contact is the switch point between the T and R quaternary states.	The helix shift from a bound heme travels to this contact, so local binding becomes a global signal.	hemoglobin	mm::hemoglobin mm::cycle interface allostery
hemoglobin-quaternary-turn	When hemoglobin snaps from T to R, one alpha-beta dimer rotates by about […] against the other.	When hemoglobin snaps from T to R, one alpha-beta dimer rotates by about 14 degrees against the other.	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.	hemoglobin	mm::hemoglobin mm::numbers quaternary rotation
hemoglobin-tissue-effectors	Which three small molecules in working tissue push hemoglobin back toward the T state?	Protons, carbon dioxide and 2,3-BPG.	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.	hemoglobin	mm::hemoglobin mm::cycle effectors bohr
hemoglobin-bpg-favours-t	Why does 2,3-BPG favour the T state of hemoglobin?	It binds the central cavity between the beta chains, which is wide enough only in the T state.	The central cavity narrows when the tetramer snaps to R. By binding T better than R, 2,3-BPG lowers oxygen affinity.	hemoglobin	mm::hemoglobin mm::cycle 2,3-bpg cavity
hemoglobin-myoglobin-no-switch	Myoglobin has the same globin fold as hemoglobin. Why does myoglobin show no cooperativity?	It has one chain and one heme, so it has no dimer interface where a tertiary change could become a quaternary one.	Myoglobin keeps the ancestral job of storing and buffering oxygen in muscle; it is the control case for cooperativity.	hemoglobin	mm::hemoglobin mm::parts myoglobin evolution
hemoglobin-per-red-cell	One human red blood cell holds about […] hemoglobin molecules.	One human red blood cell holds about 270 million hemoglobin molecules.	At 4 oxygen per hemoglobin, a full red cell carries about 1.1 x 10^9 oxygen molecules.	hemoglobin	mm::hemoglobin mm::numbers red-cell scale
hemoglobin-rbc-no-burn	Why does a red blood cell not burn the oxygen its hemoglobin carries?	It has no mitochondria.	A mature red cell has thrown out its nucleus and mitochondria; it is little more than a bag of hemoglobin.	hemoglobin	mm::hemoglobin mm::purpose red-cell
hemoglobin-share-of-blood-oxygen	Hemoglobin carries about […] of the oxygen in blood; the rest is dissolved.	Hemoglobin carries about 98.5% of the oxygen in blood; the rest is dissolved.	Water holds only a little oxygen, so blood packs almost all of it into hemoglobin. This is a textbook value.	hemoglobin	mm::hemoglobin mm::purpose oxygen blood
hemoglobin-rest-extraction	At rest, roughly what share of the oxygen delivered by hemoglobin do the body's tissues take?	About a quarter.	Blood returns to the lungs about 74% saturated (a calculation, not a measurement), which leaves a reserve for when you run.	hemoglobin	mm::hemoglobin mm::numbers reserve exercise
hemoglobin-van-analogy-breaks	Hemoglobin is like a delivery van with four seats that loads and unloads as a team. Where does that analogy break?	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.	The analogy gets the teamwork right: once some seats fill, the rest fill more easily. There is also no driver and no fuel.	hemoglobin	mm::hemoglobin mm::purpose analogy allostery
hemoglobin-cas9-fetal	How does an approved Cas9 therapy use hemoglobin to treat sickle cell disease?	It edits a person's blood stem cells so their red cells make fetal hemoglobin.	Turning gamma back on treats sickle cell disease and beta-thalassaemia while leaving the hemoglobin protein untouched.	hemoglobin	mm::hemoglobin mm::purpose cas9 sickle fetal
hemoglobin-p50-standard	Human blood under standard conditions (pH 7.4, pCO2 40 mmHg, 37 °C) has a P50 of […].	Human blood under standard conditions (pH 7.4, pCO2 40 mmHg, 37 °C) has a P50 of 26.6 mmHg.	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.	hemoglobin	mm::hemoglobin mm::numbers p50 affinity
hemoglobin-hill-steepness	With a Hill coefficient of 2.8, by what factor must oxygen pressure rise to take hemoglobin from 10% to 90% saturation?	About 4.8-fold (against 81-fold with no cooperativity).	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.	hemoglobin	mm::hemoglobin mm::numbers cooperativity hill
hemoglobin-bohr-meaning	Human hemoglobin has a Bohr coefficient of -0.29. What does a pH drop of 0.1 unit do to its P50?	Raises it by about 7 percent.	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.	hemoglobin	mm::hemoglobin mm::numbers bohr ph
hemoglobin-iron-out-of-plane	In crystals of human deoxyhemoglobin, how far does the heme iron sit from the porphyrin plane?	About 0.4 A: 0.40 A in the alpha hemes, 0.36 A in the beta hemes.	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.	hemoglobin	mm::hemoglobin mm::numbers heme iron x-ray
hemoglobin-t-state-oxy-crystal	When T-state hemoglobin crystals were oxygenated at all four hemes, what moved toward R while the tetramer stayed T?	The heme pockets and the alpha1-beta2 interface.	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.	hemoglobin	mm::hemoglobin mm::cycle t-state x-ray
hemoglobin-effectors-in-r	In R-state crystals of horse hemoglobin, what did the effector bezafibrate do to oxygen affinity?	Lowered it about threefold (P50 from 0.32 to 0.91 torr), with binding still non-cooperative.	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.	hemoglobin	mm::hemoglobin mm::debate effectors r-state models
hemoglobin-cryoem-r2	Cryo-EM puts liganded human hemoglobin, free of crystal contacts, closest to the […] quaternary arrangement.	Cryo-EM puts liganded human hemoglobin, free of crystal contacts, closest to the R2 quaternary arrangement.	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.	hemoglobin	mm::hemoglobin mm::debate cryo-em r2 models
cas9-job	What does Cas9 do for the bacterium that carries it?	It destroys invading DNA.	Cas9 is a bacterial immune protein. It cuts the DNA of an invader, so the cell survives the attack.	cas9	mm::cas9 mm::purpose immunity dna
cas9-address-in-rna	In Cas9, what part of the machine holds the address of the target?	The guide RNA, not the protein.	Because the address sits in the RNA, one enzyme reaches any sequence: a new guide gives a new target.	cas9	mm::cas9 mm::purpose guide-rna targeting
cas9-energy	Cas9 spends no ATP on targeting; cleavage needs […] and the free energy of RNA-DNA base pairing.	Cas9 spends no ATP on targeting; cleavage needs Mg2+ and the free energy of RNA-DNA base pairing.	Nothing in the search or the cut is paid for with ATP. The metal serves the two nuclease sites.	cas9	mm::cas9 mm::purpose energy magnesium
cas9-hnh-strand	Which DNA strand does the HNH domain of Cas9 cut?	The target strand, the one that base pairs with the guide.	HNH, residues 770-921, carries His840 as its proton acceptor. Its position, not its chemistry, decides whether cleavage happens.	cas9	mm::cas9 mm::parts hnh domains
cas9-ruvc-strand	Which DNA strand does the RuvC domain of Cas9 cut?	The non-target strand, the displaced strand that carries the PAM.	RuvC is built from three segments of the chain (1-62, 718-765 and 925-1102) and uses Asp10 as its catalytic residue.	cas9	mm::cas9 mm::parts ruvc domains
cas9-catalytic-residues	The two catalytic residues of SpCas9 are […].	The two catalytic residues of SpCas9 are D10 and H840.	Asp10 serves the RuvC-like site and His840 is the proton acceptor of the HNH site, so changing both removes all cutting.	cas9	mm::cas9 mm::numbers active-site residues
cas9-pam-arginines	Which two Cas9 residues read the two guanines of the NGG PAM?	Arg1333 and Arg1335.	The PAM is the protospacer adjacent motif. Reading it limits which sites the enzyme can reach.	cas9	mm::cas9 mm::parts pam residues
cas9-prime-editing-scope	What share of known disease-associated genetic variants do the prime editing authors estimate it could in principle correct?	Up to 89 percent.	Prime editing installs insertions, deletions and every point mutation class without double-strand breaks. The 89 percent is an author estimate of scope, not a measured correction rate.	cas9	mm::cas9 mm::debate prime-editing frontier
cas9-open-frontier	Which goal on the Cas9 frontier list is still only proposed rather than demonstrated?	Reliable in-place writing of whole genes or chromosomes.	Today's editors change a few bases or insert short cassettes. Programmable writing of long sequences is still ahead.	cas9	mm::cas9 mm::debate frontier editing
cas9-guide-arms-protein	What has to happen before Cas9 can accept DNA at all?	The guide RNA must bind and turn the two lobes toward each other, forming the central channel.	Apo Cas9 has no channel for DNA. Most of the rearrangement happens before any DNA arrives.	cas9	mm::cas9 mm::cycle guide-rna conformation
cas9-skips-matches-without-pam	Why does Cas9 pass over a perfect sequence match that has no nearby PAM?	Binding and cleavage both need a short PAM next to the target.	During the search, affinity for non-target DNA scales with PAM density, so the PAM is what the enzyme checks first.	cas9	mm::cas9 mm::cycle pam search
cas9-rloop-growth	Strand separation in Cas9 starts at the […], and the RNA-DNA heteroduplex then grows away from there toward the far end of the target.	Strand separation in Cas9 starts at the PAM, and the RNA-DNA heteroduplex then grows away from there toward the far end of the target.	That directional growth of base pairing builds the R-loop.	cas9	mm::cas9 mm::cycle r-loop pam
cas9-first-checkpoint	What is the first checkpoint in the Cas9 cycle, the one that allows catalysis?	PAM recognition: PAM contacts trigger catalytic activity.	Checking the PAM first means Cas9 wastes little time on sites it cannot cut.	cas9	mm::cas9 mm::cycle pam checkpoint
cas9-final-checkpoint	Which step is the final specificity checkpoint of Cas9?	HNH docking into its activated conformation.	Cleavage rate tracks how much HNH samples that conformation, and DNA binding is far less selective than cleavage.	cas9	mm::cas9 mm::cycle hnh specificity
cas9-concerted-cut	What makes the two nuclease domains of Cas9 fire together instead of one at a time?	Allosteric communication between them.	HNH cuts the complementary strand and RuvC cuts the other, so the product is a double-strand break.	cas9	mm::cas9 mm::cycle allostery cleavage
cas9-ocean-infections	How many virus infections start in the ocean every second, the pressure that CRISPR immunity answers?	About 10^23 per second.	Viruses that infect bacteria are the most numerous biological things on Earth, so bacteria have had to defend themselves for billions of years.	cas9	mm::cas9 mm::numbers phage scale
cas9-search-time	How long does one Cas9 need to find its target in E. coli?	About six hours.	Measured by tracking one labelled dCas9. Because one copy is so slow, a cell keeps many copies searching.	cas9	mm::cas9 mm::numbers search kinetics
cas9-pam-spacing	In random DNA an NGG PAM turns up about once every […] base pairs, counting both strands.	In random DNA an NGG PAM turns up about once every 8 base pairs, counting both strands.	That is why the search has so many stops: about 10^6 PAM sites sit in one E. coli cell. In phage lambda DNA the spacing measured one PAM per 8.5 base pairs.	cas9	mm::cas9 mm::numbers pam search
cas9-therapy-target	What does the approved Cas9 therapy cut in a patient's own blood stem cells?	The red-cell enhancer of the BCL11A gene.	The red cells those stem cells make then produce fetal hemoglobin, which treats sickle cell disease and transfusion-dependent beta-thalassaemia.	cas9	mm::cas9 mm::purpose medicine hemoglobin
cas9-scissors-analogy-breaks	Calling Cas9 search-and-cut scissors gets one tool and one target right. What does it get wrong?	Scissors are aimed; Cas9 is not. It bumps into DNA at random, checks for a PAM and moves on.	That random search is why finding one target takes hours.	cas9	mm::cas9 mm::purpose analogy search
cas9-immune-memory-analogy-breaks	How is the bacterial CRISPR memory unlike our own immune memory?	It is written into the genome, so daughter cells inherit it.	Both remember past infections and respond faster, but our antibody memory is not passed to our children.	cas9	mm::cas9 mm::purpose analogy immunity
cas9-residues-crystallised	The ternary complex structure crystallised a full-length SpCas9 chain of […] residues.	The ternary complex structure crystallised a full-length SpCas9 chain of 1368 residues.	X-ray crystallography at 2.5 A, with a 98-nucleotide single-guide RNA and a 23-nucleotide target DNA, anchors the sequence length in a primary structure study.	cas9	mm::cas9 mm::numbers structure size
cas9-single-mutant-nicks	What does a Cas9 carrying only one of the two active-site mutations do to DNA?	It nicks one strand instead of cutting both.	Point mutants assayed on paired target sites offset by 4 base pairs showed which residue serves which strand: D10 for RuvC, H840 for HNH.	cas9	mm::cas9 mm::numbers nickase active-site
cas9-binding-vs-cleavage-kd	Gel binding assays gave dCas9 a Kd of 0.80 nM on target. What was the Kd with 8 PAM-distal mismatches?	20 nM.	A 25-fold spread in affinity sits beside cleavage that drops to undetectable, which is why binding is called far less selective than cleavage.	cas9	mm::cas9 mm::numbers affinity specificity
cas9-hnh-fret-method	How was the link between HNH conformation and cleavage rate in Cas9 measured?	Intramolecular FRET between dyes on REC1 and HNH, compared with cleavage rate constants on the same substrates.	With enough PAM-distal mismatches the domain stays undocked and no cleavage is detected, which makes the conformational step the checkpoint.	cas9	mm::cas9 mm::numbers fret method
cas9-hnh-swing-distance	Cryo-EM of the active Cas9 complex with magnesium shows the HNH domain travelling about […] A to reach the target-strand scissile bond.	Cryo-EM of the active Cas9 complex with magnesium shows the HNH domain travelling about 34 A to reach the target-strand scissile bond.	Three states were resolved at about 3.3 A: pre-catalytic, post-catalytic and product. The motion is a translation with a rotation about a central axis.	cas9	mm::cas9 mm::numbers cryo-em hnh
cas9-cut-position	Where does Cas9 cut the target strand, relative to the PAM?	Between the third and fourth nucleotide upstream of the PAM.	Read from cryo-EM density across the cleavage site in the pre-catalytic, post-catalytic and product states.	cas9	mm::cas9 mm::numbers cleavage cryo-em
cas9-search-mode-dispute	Single-molecule imaging on DNA curtains found Cas9 reaching targets only by three-dimensional collisions. How did later FRET work qualify that?	It saw facilitated lateral diffusion carrying Cas9 from one PAM to a neighbouring one.	Over short distances lateral diffusion competes with three-dimensional diffusion; no rate for it is confirmed from the abstract that is available.	cas9	mm::cas9 mm::debate search single-molecule
shared-rotary-ion-motors	Which two machines in the atlas are rotary motors driven by ions flowing across a membrane?	ATP synthase and the bacterial flagellar motor	Both turn an inward flow of protons (or sodium ions) into rotation. Kinesin, dynein and myosin are walkers instead: they step along a filament and burn ATP.	shared	mm::shared mm::purpose rotary ion-gradient compare
shared-flagellum-skips-atp	ATP synthase and the flagellar motor both run on a proton gradient. What does the flagellar motor do differently with that energy?	It turns the proton flow straight into rotation, with no ATP in between.	ATP synthase uses the same kind of gradient to make ATP, which other machines then spend.	shared	mm::shared mm::purpose energy ion-gradient rotary
shared-sodium-motors	Besides protons, the polar flagellar motor of Vibrio and the ATP synthase of some bacteria run on a flow of […].	Besides protons, the polar flagellar motor of Vibrio and the ATP synthase of some bacteria run on a flow of sodium ions.	Ion-driven rotary motors are not tied to protons. The fastest flagellar motor in the atlas, at 1,700 turns per second, is the Na+-driven motor of Vibrio alginolyticus.	shared	mm::shared mm::purpose energy sodium ion-gradient
shared-ribosome-gtp	The motors in the atlas burn ATP. Which nucleotide do the ribosome's helpers EF-Tu and EF-G hydrolyse instead?	GTP	The cell recharges GTP with a phosphate from ATP, using the enzyme nucleoside diphosphate kinase.	shared	mm::shared mm::purpose energy gtp
shared-no-fuel-machines	Which two machines in the atlas spend no chemical fuel at all?	Cas9 and hemoglobin	Cas9 relies on Mg2+ and the free energy of RNA-DNA base pairing. Hemoglobin relies on the oxygen gradient and its allosteric switch.	shared	mm::shared mm::purpose energy compare
shared-serca-reverse-trade	ATP synthase uses an ion gradient to make ATP. What is the opposite trade that SERCA makes?	SERCA spends ATP to build an ion (calcium) gradient.	SERCA burns one ATP to push two calcium ions out of the cytoplasm. ATP synthase can also run this way: with ATP and no gradient, it runs backward and pumps ions.	shared	mm::shared mm::purpose energy ion-gradient pump
shared-power-stroke-trigger	In both myosin and dynein, which nucleotide event, after the head binds its track, comes with the power stroke?	Phosphate release	Myosin binds actin, releases phosphate and swings its lever; dynein rebinds the microtubule, phosphate leaves and the linker straightens. In kinesin, by contrast, ATP binding docks the neck linker, and that docking is the power stroke.	shared	mm::shared mm::cycle power-stroke motors compare
shared-dynein-lever-unrelated	Kinesin shares its catalytic fold with myosin. Which atlas motor also pulls with a lever-like part but belongs to an unrelated family?	Dynein (an AAA+ ring with a lever-like linker)	Kinesin and myosin share almost no sequence, yet their cores share one fold and probably a common ancestor. Dynein's ring is built from six AAA+ modules instead.	shared	mm::shared mm::parts evolution motors power-stroke
shared-flii-f1-relative	Which part of the bacterial flagellum looks like the α and β subunits of the F1 head of ATP synthase?	The export ATPase FliI	FliJ also looks like the coiled-coil of γ. This points to a common ancestor of the flagellar export machine and the rotary ATPases.	shared	mm::shared mm::parts evolution rotary
shared-aaa-rings	Dynein's motor ring and the proteasome's substrate-pulling ring are both made of six […] ATPase units.	Dynein's motor ring and the proteasome's substrate-pulling ring are both made of six AAA+ ATPase units.	In dynein the six AAA+ modules sit in one heavy chain; in the proteasome they are six subunits, Rpt1 to Rpt6. The AAA+ fold forms active arrays in many cellular machines.	shared	mm::shared mm::parts evolution aaa atp
shared-xray-rna-catalyst	How did Nissen and colleagues use X-ray crystallography to show that the ribosome's catalyst is RNA?	They soaked substrate mimics into crystals of the large subunit and found no protein within about 18 Å of the forming bond.	The method needs crystals: the mimics were soaked into crystals of the archaeal 50S subunit. Only 23S rRNA touched the substrate analogues, so the ribosome is a ribozyme.	shared	mm::shared mm::numbers x-ray methods ribosome
shared-cryoem-crystal-contacts	Cryo-EM showed liganded human hemoglobin turning further (about 22°) than the classic R crystal structure (15.0°). What did the cryo-EM molecules lack that crystal models have?	Crystal contacts	Cryo-EM images single molecules in solution-like conditions. Free of crystal contacts, the liganded tetramer sat almost on top of the R2 crystal form, so a single R state is a simplification.	shared	mm::shared mm::debate cryo-em x-ray methods
shared-cryoem-sorting-states	Cryo-EM studies of the proteasome, dynein and GroEL each found several cycle states in one sample. How?	They froze the machines while they worked and sorted the particle images into separate classes (states).	Dong and colleagues sorted about 3.6 million proteasome images into seven states; Chai and colleagues found eight major dynein states.	shared	mm::shared mm::cycle cryo-em methods
shared-time-resolved-myosin	How did Klebl and colleagues use cryo-EM to catch myosin-5 both before and after its power stroke?	They mixed myosin-ADP-Pi with actin and plunge-froze the mix 10 or 120 ms later (time-resolved cryo-EM).	The frozen sample held primed and post-stroke motors on the same filament. The lever swung about 93°, mostly along the actin axis.	shared	mm::shared mm::cycle cryo-em power-stroke methods
shared-c8-proton-cost	The X-ray structure of the bovine F1–c-ring showed 8 c subunits, so animal ATP synthase spends about […] protons per ATP.	The X-ray structure of the bovine F1–c-ring showed 8 c subunits, so animal ATP synthase spends about 2.7 protons per ATP.	Eight protons turn the ring once and one turn makes three ATP: 8/3 ≈ 2.7. Larger c-rings (up to c15) cost more protons per ATP.	shared	mm::shared mm::numbers x-ray energy rotary
shared-step-sizes	Kinesin-1 steps 8 nm and yeast dynein most often steps 8 nm. About how far does myosin-5 step per ATP on actin?	About 37 nm	The myosin-5 step matches the 36 nm pseudo-repeat of actin. Kinesin's 8 nm is the length of one tubulin dimer.	shared	mm::shared mm::numbers scale motors walkers
shared-fastest-rotor	Which motor is the fastest rotary motor in the atlas, at about 1,700 turns per second, and what ion drives it?	The flagellar motor of Vibrio alginolyticus, driven by sodium ions	For comparison, E. coli flagellar motors reach about 300–350 turns per second with no load, and ATP synthase in mitochondria is estimated at about 100 turns per second.	shared	mm::shared mm::numbers scale rotary sodium
shared-largest-mass	Which machine in the atlas has the largest listed mass?	The flagellar motor (Salmonella motor–hook model, about 14,881 kDa)	That model has no stator units and only the proximal hook. The human 26S proteasome is about 2.5 MDa and the E. coli 70S ribosome about 2.2 MDa; hemoglobin is 64.5 kDa.	shared	mm::shared mm::numbers scale size compare
shared-make-vs-destroy	In one mouse L929 cell, how does the proteasome's rate of destroying proteins compare with the ribosomes' rate of making them?	About half: 2 × 10^6 destroyed per minute against 4 × 10^6 made per minute	Together the two machines set protein levels, and the recycled amino acids feed the ribosome.	shared	mm::shared mm::numbers scale counts compare
shared-atp-body-weight	Every ATP-burning machine in the atlas draws on ATP synthase, and a human body remakes about […] of ATP per day.	Every ATP-burning machine in the atlas draws on ATP synthase, and a human body remakes about one body weight of ATP per day.	An upper estimate from oxygen use: 54–68 kg per day for a college student. The links show kinesin, myosin, dynein, SERCA, GroEL and the proteasome all spending this ATP.	shared	mm::shared mm::numbers scale atp energy