{"format":"molecular-machines.cards","version":1,"updated":"2026-10-01","decks":[{"machine":"ribosome","name":"Ribosome","count":28,"url":"/learn/cards/ribosome.json"}],"cards":[{"id":"ribosome-purpose","machine":"ribosome","kind":"qa","prompt":"What does the ribosome do in a cell?","answer":"It reads an mRNA and builds the matching protein chain.","explanation":"It turns a nucleic acid sequence into a protein sequence. Every protein in your body comes off a ribosome.","section":"summary","topic":"purpose","sources":["machine:tagline","machine:summary","story:summary"],"tags":["translation"],"difficulty":1,"url":"/machines/ribosome#summary","cites":[{"source":"machine:tagline","machine":"ribosome","label":"Summary","section":"summary"},{"source":"machine:summary","machine":"ribosome","label":"Summary","section":"summary"},{"source":"story:summary","machine":"ribosome","label":"Big picture","section":"story"}]},{"id":"ribosome-small-subunit-role","machine":"ribosome","kind":"cloze","prompt":"The ribosome's {{small subunit}} checks each codon against the anticodon of the incoming tRNA.","answer":"small subunit","explanation":"In bacteria its core, 16S rRNA, reads the codon and holds the mRNA channel. The large subunit joins the amino acids.","section":"summary","topic":"parts","sources":["machine:summary","component:16S rRNA"],"tags":["decoding","subunits"],"difficulty":1,"url":"/machines/ribosome#summary","cites":[{"source":"machine:summary","machine":"ribosome","label":"Summary","section":"summary"},{"source":"component:16S rRNA","machine":"ribosome","label":"Part: 16S rRNA","section":"summary"}]},{"id":"ribosome-rna-catalyst","machine":"ribosome","kind":"cloze","prompt":"In the bacterial ribosome, the peptide bond is made by {{23S rRNA}} of the large subunit, not by protein.","answer":"23S rRNA","explanation":"Only 23S rRNA lines the catalytic centre, so the ribosome is a ribozyme: an enzyme made of RNA.","section":"summary","topic":"parts","sources":["component:23S rRNA","mechanism:Peptide bond formation","ref:nissen2000"],"tags":["ribozyme","rrna"],"difficulty":1,"url":"/machines/ribosome#summary","cites":[{"source":"component:23S rRNA","machine":"ribosome","label":"Part: 23S rRNA","section":"summary"},{"source":"mechanism:Peptide bond formation","machine":"ribosome","label":"Step: Peptide bond formation","section":"mechanism"},{"source":"ref:nissen2000","machine":"ribosome","label":"Nissen et al.","section":"sources","anchor":"ref-nissen2000","href":"https://doi.org/10.1126/science.289.5481.920"}]},{"id":"ribosome-protein-role","machine":"ribosome","kind":"qa","prompt":"No ribosomal protein sits in the catalytic centre. What job do the ribosomal proteins do instead?","answer":"They sit on the surface and stabilise the rRNA folds.","explanation":"The catalytic centre is all RNA, with proteins on the outside. That fits an RNA-first origin of the ribosome.","section":"summary","topic":"parts","sources":["evolution:RNA came first","component:30S proteins S2-S21","component:50S proteins L2-L36","ref:nissen2000","ref:ban2000"],"tags":["evolution","rrna"],"difficulty":2,"url":"/machines/ribosome#summary","cites":[{"source":"evolution:RNA came first","machine":"ribosome","label":"RNA came first","section":"summary"},{"source":"component:30S proteins S2-S21","machine":"ribosome","label":"Part: 30S proteins S2-S21","section":"summary"},{"source":"component:50S proteins L2-L36","machine":"ribosome","label":"Part: 50S proteins L2-L36","section":"summary"},{"source":"ref:nissen2000","machine":"ribosome","label":"Nissen et al.","section":"sources","anchor":"ref-nissen2000","href":"https://doi.org/10.1126/science.289.5481.920"},{"source":"ref:ban2000","machine":"ribosome","label":"Ban et al.","section":"sources","anchor":"ref-ban2000","href":"https://doi.org/10.1126/science.289.5481.905"}]},{"id":"ribosome-three-sites","machine":"ribosome","kind":"cloze","prompt":"A tRNA passes through the ribosome's three binding sites in the order {{A, P, E}}.","answer":"A, P, E","explanation":"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.","section":"summary","topic":"parts","sources":["stat:tRNA binding sites","step:The A site is open","ref:rheinberger1981"],"tags":["trna","sites"],"difficulty":1,"url":"/machines/ribosome#summary","cites":[{"source":"stat:tRNA binding sites","machine":"ribosome","label":"Key number: tRNA binding sites","section":"summary"},{"source":"step:The A site is open","machine":"ribosome","label":"Step: The A site is open","section":"mechanism"},{"source":"ref:rheinberger1981","machine":"ribosome","label":"Rheinberger, Sternbach and Nierhaus, PNAS 1981","section":"sources","anchor":"ref-rheinberger1981","href":"https://doi.org/10.1073/pnas.78.9.5310"}]},{"id":"ribosome-ecoli-rate","machine":"ribosome","kind":"qa","prompt":"How many amino acids per second does a ribosome add in E. coli, from slow to fast growth?","answer":"About 12 to 17.","explanation":"12 at slow growth and 17 at fast growth, measured by pulse labelling. At 17 per second, one full cycle takes about 60 ms.","section":"summary","topic":"numbers","sources":["stat:Elongation rate in E. coli","step:The A site is open","ref:young1976"],"tags":["speed"],"difficulty":2,"url":"/machines/ribosome#summary","cites":[{"source":"stat:Elongation rate in E. coli","machine":"ribosome","label":"Key number: Elongation rate in E. coli","section":"summary"},{"source":"step:The A site is open","machine":"ribosome","label":"Step: The A site is open","section":"mechanism"},{"source":"ref:young1976","machine":"ribosome","label":"Young and Bremer, Biochemical Journal 1976","section":"sources","anchor":"ref-young1976","href":"https://doi.org/10.1042/bj1600185"}]},{"id":"ribosome-error-rate","machine":"ribosome","kind":"cloze","prompt":"The ribosome's error rate is about {{10^-3 to 10^-5}} per elongation step.","answer":"10^-3 to 10^-5","explanation":"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.","section":"summary","topic":"numbers","sources":["stat:Error rate per step","evidence:manickam2014-misreading-floor","ref:rundlet2021"],"tags":["accuracy"],"difficulty":2,"url":"/machines/ribosome#summary","cites":[{"source":"stat:Error rate per step","machine":"ribosome","label":"Key number: Error rate per step","section":"summary"},{"source":"evidence:manickam2014-misreading-floor","machine":"ribosome","label":"Lowest missense error frequencies measured in vivo (Manickam N 2014)","section":"evidence","anchor":"ev-manickam2014-misreading-floor"},{"source":"ref:rundlet2021","machine":"ribosome","label":"Rundlet et al.","section":"sources","anchor":"ref-rundlet2021","href":"https://doi.org/10.1038/s41586-021-03713-x"}]},{"id":"ribosome-ribo-t","machine":"ribosome","kind":"qa","prompt":"What did tethering the two ribosomal subunits into one molecule (Ribo-T) show?","answer":"The subunits need not exchange: Ribo-T keeps E. coli alive without wild-type ribosomes.","explanation":"Short RNA linkers join small- and large-subunit rRNA. The tethered ribosome still makes protein, both in vitro and in cells.","section":"summary","topic":"debate","sources":["frontier:Tethered subunits","ref:orelle2015"],"tags":["engineering","subunits"],"difficulty":2,"url":"/machines/ribosome#summary","cites":[{"source":"frontier:Tethered subunits","machine":"ribosome","label":"Open question: Tethered subunits","section":"summary"},{"source":"ref:orelle2015","machine":"ribosome","label":"Orelle et al.","section":"sources","anchor":"ref-orelle2015","href":"https://doi.org/10.1038/nature14862"}]},{"id":"ribosome-non-natural-polymers","machine":"ribosome","kind":"qa","prompt":"What is the status of using ribosomes to make polymers that are not proteins?","answer":"Proposed: no such polymer chemistry yet runs on a ribosome at scale.","explanation":"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.","section":"summary","topic":"debate","sources":["frontier:Ribosomes for non-natural polymers","frontier:Tethered subunits","frontier:Private translation channels","frontier:Expanded genetic codes","ref:orelle2015","ref:rackham2005","ref:neumann2010"],"tags":["engineering","frontier"],"difficulty":2,"url":"/machines/ribosome#summary","cites":[{"source":"frontier:Ribosomes for non-natural polymers","machine":"ribosome","label":"Open question: Ribosomes for non-natural polymers","section":"summary"},{"source":"frontier:Tethered subunits","machine":"ribosome","label":"Open question: Tethered subunits","section":"summary"},{"source":"frontier:Private translation channels","machine":"ribosome","label":"Open question: Private translation channels","section":"summary"},{"source":"frontier:Expanded genetic codes","machine":"ribosome","label":"Open question: Expanded genetic codes","section":"summary"},{"source":"ref:orelle2015","machine":"ribosome","label":"Orelle et al.","section":"sources","anchor":"ref-orelle2015","href":"https://doi.org/10.1038/nature14862"},{"source":"ref:rackham2005","machine":"ribosome","label":"Rackham and Chin, Nature Chemical Biology 2005","section":"sources","anchor":"ref-rackham2005","href":"https://doi.org/10.1038/nchembio719"},{"source":"ref:neumann2010","machine":"ribosome","label":"Neumann et al.","section":"sources","anchor":"ref-neumann2010","href":"https://doi.org/10.1038/nature08817"}]},{"id":"ribosome-eftu-holds-end","machine":"ribosome","kind":"qa","prompt":"Why does EF-Tu hold the amino-acid end of an incoming tRNA while the anticodon reaches down to the codon?","answer":"To keep the amino acid away from the catalytic centre until the codon has been checked.","explanation":"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.","section":"mechanism","topic":"cycle","sources":["step:EF-Tu brings an aminoacyl-tRNA","mechanism:Delivery","ref:pape1998"],"tags":["ef-tu","decoding"],"difficulty":2,"url":"/machines/ribosome#mechanism","cites":[{"source":"step:EF-Tu brings an aminoacyl-tRNA","machine":"ribosome","label":"Step: EF-Tu brings an aminoacyl-tRNA","section":"mechanism"},{"source":"mechanism:Delivery","machine":"ribosome","label":"Step: Delivery","section":"mechanism"},{"source":"ref:pape1998","machine":"ribosome","label":"Pape, Wintermeyer and Rodnina, EMBO J 1998","section":"sources","href":"https://doi.org/10.1093/emboj/17.24.7490"}]},{"id":"ribosome-decoding-trigger","machine":"ribosome","kind":"qa","prompt":"On the ribosome, what does a correct codon–anticodon pair switch on?","answer":"GTP hydrolysis by EF-Tu, which then releases the tRNA into the A site.","explanation":"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.","section":"mechanism","topic":"cycle","sources":["step:The codon is checked","mechanism:Decoding","ref:voorhees2010","ref:pape1998"],"tags":["decoding","ef-tu","gtp"],"difficulty":2,"url":"/machines/ribosome#mechanism","cites":[{"source":"step:The codon is checked","machine":"ribosome","label":"Step: The codon is checked","section":"mechanism"},{"source":"mechanism:Decoding","machine":"ribosome","label":"Step: Decoding","section":"mechanism"},{"source":"ref:voorhees2010","machine":"ribosome","label":"Voorhees et al.","section":"sources","anchor":"ref-voorhees2010","href":"https://doi.org/10.1126/science.1194460"},{"source":"ref:pape1998","machine":"ribosome","label":"Pape, Wintermeyer and Rodnina, EMBO J 1998","section":"sources","href":"https://doi.org/10.1093/emboj/17.24.7490"}]},{"id":"ribosome-hybrid-states","machine":"ribosome","kind":"cloze","prompt":"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.","answer":"acceptor ends","explanation":"Translocation happens in two moves, so the acceptor ends and then the anticodons shift one at a time.","section":"mechanism","topic":"cycle","sources":["mechanism:Hybrid states","step:The subunits ratchet","evidence:moazed1989-hybrid-states","ref:moazed1989"],"tags":["translocation","trna"],"difficulty":2,"url":"/machines/ribosome#mechanism","cites":[{"source":"mechanism:Hybrid states","machine":"ribosome","label":"Step: Hybrid states","section":"mechanism"},{"source":"step:The subunits ratchet","machine":"ribosome","label":"Step: The subunits ratchet","section":"mechanism"},{"source":"evidence:moazed1989-hybrid-states","machine":"ribosome","label":"Number of discrete steps in tRNA translocation (Moazed D 1989)","section":"evidence","anchor":"ev-moazed1989-hybrid-states"},{"source":"ref:moazed1989","machine":"ribosome","label":"Moazed and Noller, Nature 1989","section":"sources","anchor":"ref-moazed1989","href":"https://doi.org/10.1038/342142a0"}]},{"id":"ribosome-ratchet-driver","machine":"ribosome","kind":"qa","prompt":"What carries the ribosome's small subunit into its rotated (ratcheted) state after the peptide bond forms?","answer":"Thermal motion: the move happens on its own, without EF-G or GTP.","explanation":"The small subunit turns about 10° against the large subunit. The move is spontaneous and reversible.","section":"mechanism","topic":"cycle","sources":["step:The subunits ratchet","ref:rundlet2021"],"tags":["translocation","rotation"],"difficulty":3,"url":"/machines/ribosome#mechanism","cites":[{"source":"step:The subunits ratchet","machine":"ribosome","label":"Step: The subunits ratchet","section":"mechanism"},{"source":"ref:rundlet2021","machine":"ribosome","label":"Rundlet et al.","section":"sources","anchor":"ref-rundlet2021","href":"https://doi.org/10.1038/s41586-021-03713-x"}]},{"id":"ribosome-efg-catches","machine":"ribosome","kind":"qa","prompt":"What does EF-G·GTP do when it first binds the ribosome after the subunits have rotated?","answer":"It catches and holds the rotated state, which the ribosome reaches on its own, and starts to unlock the small subunit.","explanation":"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.","section":"mechanism","topic":"cycle","sources":["step:EF-G binds with GTP","mechanism:Ratchet and translocation","ref:rundlet2021"],"tags":["ef-g","gtp","translocation"],"difficulty":3,"url":"/machines/ribosome#mechanism","cites":[{"source":"step:EF-G binds with GTP","machine":"ribosome","label":"Step: EF-G binds with GTP","section":"mechanism"},{"source":"mechanism:Ratchet and translocation","machine":"ribosome","label":"Step: Ratchet and translocation","section":"mechanism"},{"source":"ref:rundlet2021","machine":"ribosome","label":"Rundlet et al.","section":"sources","anchor":"ref-rundlet2021","href":"https://doi.org/10.1038/s41586-021-03713-x"}]},{"id":"ribosome-reading-frame","machine":"ribosome","kind":"qa","prompt":"Why must the ribosome move the mRNA by exactly three nucleotides in each cycle?","answer":"To keep the reading frame.","explanation":"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.","section":"mechanism","topic":"cycle","sources":["step:EF-G moves the tRNAs one codon","step:EF-G leaves","ref:wen2008","ref:selmer2006"],"tags":["translocation","mrna"],"difficulty":1,"url":"/machines/ribosome#mechanism","cites":[{"source":"step:EF-G moves the tRNAs one codon","machine":"ribosome","label":"Step: EF-G moves the tRNAs one codon","section":"mechanism"},{"source":"step:EF-G leaves","machine":"ribosome","label":"Step: EF-G leaves","section":"mechanism"},{"source":"ref:wen2008","machine":"ribosome","label":"Wen et al.","section":"sources","href":"https://doi.org/10.1038/nature06716"},{"source":"ref:selmer2006","machine":"ribosome","label":"Selmer et al.","section":"sources","anchor":"ref-selmer2006","href":"https://doi.org/10.1126/science.1131127"}]},{"id":"ribosome-exit-tunnel","machine":"ribosome","kind":"qa","prompt":"Why can't a new protein chain fold into domains inside the ribosome's exit tunnel?","answer":"The tunnel is too narrow for any fold larger than an alpha-helix.","explanation":"The chain runs from the catalytic centre through the large subunit to the surface. Chains that cannot fold alone are then caught by GroEL.","section":"mechanism","topic":"cycle","sources":["mechanism:The chain leaves through the tunnel","evidence:voss2006-tunnel-width","link:groel","ref:voss2006"],"tags":["tunnel","folding"],"difficulty":2,"url":"/machines/ribosome#mechanism","cites":[{"source":"mechanism:The chain leaves through the tunnel","machine":"ribosome","label":"Step: The chain leaves through the tunnel","section":"mechanism"},{"source":"evidence:voss2006-tunnel-width","machine":"ribosome","label":"Width of the polypeptide exit tunnel (Voss NR 2006)","section":"evidence","anchor":"ev-voss2006-tunnel-width"},{"source":"link:groel","machine":"ribosome","label":"Link to GroEL–GroES","section":"story"},{"source":"ref:voss2006","machine":"ribosome","label":"Voss et al.","section":"sources","anchor":"ref-voss2006","href":"https://doi.org/10.1016/j.jmb.2006.05.023"}]},{"id":"ribosome-human-cell-count","machine":"ribosome","kind":"cloze","prompt":"One human HeLa cell holds about {{3.3–9.5 million}} ribosomes.","answer":"3.3–9.5 million","explanation":"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.","section":"story","topic":"numbers","sources":["fact:R4","stop:cell","fact:R6","ref:bnid107552","ref:bnid107347"],"tags":["scale","copies"],"difficulty":2,"url":"/machines/ribosome#story","cites":[{"source":"fact:R4","machine":"ribosome","label":"Ribosomes in one human cell (HeLa): 3.3–9.5 × 10^6","section":"story"},{"source":"stop:cell","machine":"ribosome","label":"Big picture: One cell","section":"story"},{"source":"fact:R6","machine":"ribosome","label":"Share of the protein mass of a HeLa cell that is ribosomes: 6 %","section":"story"},{"source":"ref:bnid107552","machine":"ribosome","label":"BNID 107552","section":"sources","href":"https://bionumbers.hms.harvard.edu/bionumber.aspx?id=107552"},{"source":"ref:bnid107347","machine":"ribosome","label":"BNID 107347","section":"sources","href":"https://bionumbers.hms.harvard.edu/bionumber.aspx?id=107347"}]},{"id":"ribosome-body-protein","machine":"ribosome","kind":"qa","prompt":"About how much protein does a human body build each day?","answer":"A few hundred grams (estimates run from about 175 to 400 g).","explanation":"All of it comes off ribosomes. Protein turnover takes about 20% of resting energy in an average healthy young adult.","section":"story","topic":"purpose","sources":["fact:R2","fact:R1","fact:R3","stop:body","ref:schutz2011","ref:norton1981","ref:welle1990"],"tags":["scale","body"],"difficulty":2,"url":"/machines/ribosome#story","cites":[{"source":"fact:R2","machine":"ribosome","label":"Protein turnover in the whole body: 300–400 g per day","section":"story"},{"source":"fact:R1","machine":"ribosome","label":"Protein made by the whole body per day, small study: 175 g per day","section":"story"},{"source":"fact:R3","machine":"ribosome","label":"Share of resting energy spent on protein turnover: 20 %","section":"story"},{"source":"stop:body","machine":"ribosome","label":"Big picture: You, building","section":"story"},{"source":"ref:schutz2011","machine":"ribosome","label":"Schutz 2011","section":"sources","href":"https://doi.org/10.1024/0300-9831/a000064"},{"source":"ref:norton1981","machine":"ribosome","label":"Norton 1981","section":"sources","href":"https://doi.org/10.1097/00000658-198108000-00001"},{"source":"ref:welle1990","machine":"ribosome","label":"Welle 1990","section":"sources","href":"https://doi.org/10.1152/ajpendo.1990.258.6.e990"}]},{"id":"ribosome-titin-time","machine":"ribosome","kind":"qa","prompt":"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)?","answer":"About 1.7 hours.","explanation":"34,350 ÷ 5.6 ≈ 6,130 s. A typical 400-residue protein takes about 71 s. Both are calculations, not measured times.","section":"story","topic":"numbers","sources":["fact:R11","fact:R9","ref:uniprot-titin","ref:ingolia2011"],"tags":["speed","scale"],"difficulty":2,"url":"/machines/ribosome#story","cites":[{"source":"fact:R11","machine":"ribosome","label":"Time to build a typical protein: 71 s","section":"story"},{"source":"fact:R9","machine":"ribosome","label":"Speed of a ribosome in mammal cells: 5.6 amino acids per second","section":"story"},{"source":"ref:uniprot-titin","machine":"ribosome","label":"UniProt Q8WZ42","section":"sources","href":"https://rest.uniprot.org/uniprotkb/Q8WZ42"},{"source":"ref:ingolia2011","machine":"ribosome","label":"Ingolia 2011","section":"sources","href":"https://doi.org/10.1016/j.cell.2011.10.002"}]},{"id":"ribosome-printer-analogy","machine":"ribosome","kind":"qa","prompt":"Where does the analogy of the ribosome as 'a 3D printer that reads a tape' break down?","answer":"The ribosome does not place units by position: tRNA adapters bring each one, and it only checks that the adapter pairs with the code.","explanation":"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.","section":"story","topic":"purpose","sources":["analogy:A 3D printer that reads a tape"],"tags":["analogy","trna"],"difficulty":2,"url":"/machines/ribosome#story","cites":[{"source":"analogy:A 3D printer that reads a tape","machine":"ribosome","label":"Analogy: A 3D printer that reads a tape","section":"story"}]},{"id":"ribosome-factory-line-analogy","machine":"ribosome","kind":"qa","prompt":"Many ribosomes read one mRNA at once. Why is 'a factory line' a misleading picture of this?","answer":"All the ribosomes on the message make the same product: they are copies, not stations with different jobs.","explanation":"Each ribosome further along the message carries a longer chain. The first such ribosome clusters ever seen were making hemoglobin.","section":"story","topic":"purpose","sources":["analogy:A factory line","stop:polysome","fact:R7","link:hemoglobin","ref:warner1962"],"tags":["analogy","polysome"],"difficulty":2,"url":"/machines/ribosome#story","cites":[{"source":"analogy:A factory line","machine":"ribosome","label":"Analogy: A factory line","section":"story"},{"source":"stop:polysome","machine":"ribosome","label":"Big picture: String of ribosomes","section":"story"},{"source":"fact:R7","machine":"ribosome","label":"Protein made by the first ribosome clusters ever seen: Hemoglobin","section":"story"},{"source":"link:hemoglobin","machine":"ribosome","label":"Link to Hemoglobin","section":"story"},{"source":"ref:warner1962","machine":"ribosome","label":"Warner 1962","section":"sources","href":"https://doi.org/10.1126/science.138.3548.1399"}]},{"id":"ribosome-proteasome-balance","machine":"ribosome","kind":"qa","prompt":"In mouse L929 cells, how does the number of proteins the proteasome destroys per minute compare with the number ribosomes make?","answer":"About half as many.","explanation":"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.","section":"story","topic":"numbers","sources":["link:proteasome","fact:R5","ref:princiotta2003"],"tags":["proteasome","turnover"],"difficulty":3,"url":"/machines/ribosome#story","cites":[{"source":"link:proteasome","machine":"ribosome","label":"Link to Proteasome","section":"story"},{"source":"fact:R5","machine":"ribosome","label":"Proteins made per minute in one mouse cell: 4 × 10^6 per minute","section":"story"},{"source":"ref:princiotta2003","machine":"ribosome","label":"Princiotta 2003","section":"sources","href":"https://doi.org/10.1016/s1074-7613(03)00051-7"}]},{"id":"ribosome-young-method","machine":"ribosome","kind":"qa","prompt":"How did Young and Bremer (1976) measure the ribosome's elongation rate in E. coli?","answer":"By pulse labelling: they timed how long proteins of each size took to become fully labelled with a pulse of radioactive leucine.","explanation":"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.","section":"evidence","topic":"numbers","sources":["evidence:young1976-elongation-rate","ref:young1976"],"tags":["speed","method"],"difficulty":2,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:young1976-elongation-rate","machine":"ribosome","label":"Peptide-chain elongation rate in E. coli at three growth rates (Young R 1976)","section":"evidence","anchor":"ev-young1976-elongation-rate"},{"source":"ref:young1976","machine":"ribosome","label":"Young and Bremer, Biochemical Journal 1976","section":"sources","anchor":"ref-young1976","href":"https://doi.org/10.1042/bj1600185"}]},{"id":"ribosome-ingolia-method","machine":"ribosome","kind":"qa","prompt":"How did Ingolia and colleagues (2011) measure the elongation rate in mouse embryonic stem cells?","answer":"They blocked new initiation with harringtonine, then used ribosome profiling to track how fast the front of the ribosome-free zone moved along genes.","explanation":"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.","section":"evidence","topic":"numbers","sources":["evidence:ingolia2011-mammalian-elongation","ref:ingolia2011"],"tags":["speed","method"],"difficulty":3,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:ingolia2011-mammalian-elongation","machine":"ribosome","label":"Translation elongation rate in mouse embryonic stem cells (Ingolia NT 2011)","section":"evidence","anchor":"ev-ingolia2011-mammalian-elongation"},{"source":"ref:ingolia2011","machine":"ribosome","label":"Ingolia 2011","section":"sources","href":"https://doi.org/10.1016/j.cell.2011.10.002"}]},{"id":"ribosome-wen-step","machine":"ribosome","kind":"cloze","prompt":"Held in optical tweezers, a single E. coli ribosome advanced along an mRNA hairpin by {{about 3 nucleotides}} per step.","answer":"about 3 nucleotides","explanation":"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.","section":"evidence","topic":"numbers","sources":["evidence:wen2008-codon-step","step:EF-G moves the tRNAs one codon","ref:wen2008"],"tags":["translocation","single-molecule"],"difficulty":2,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:wen2008-codon-step","machine":"ribosome","label":"Translocation step of a single ribosome (Wen JD 2008)","section":"evidence","anchor":"ev-wen2008-codon-step"},{"source":"step:EF-G moves the tRNAs one codon","machine":"ribosome","label":"Step: EF-G moves the tRNAs one codon","section":"mechanism"},{"source":"ref:wen2008","machine":"ribosome","label":"Wen et al.","section":"sources","href":"https://doi.org/10.1038/nature06716"}]},{"id":"ribosome-pape-slow-steps","machine":"ribosome","kind":"qa","prompt":"In Pape and colleagues' (1998) kinetics of tRNA selection on E. coli ribosomes, which two steps were slowest?","answer":"Accommodation (the tRNA swinging into the A site, about 8 per s) and EF-Tu·GDP release (about 4 per s).","explanation":"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.","section":"evidence","topic":"numbers","sources":["evidence:pape1998-decoding-kinetics","step:The tRNA swings into the A site","ref:pape1998"],"tags":["kinetics","ef-tu"],"difficulty":3,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:pape1998-decoding-kinetics","machine":"ribosome","label":"Rate constants of EF-Tu-dependent aminoacyl-tRNA binding to the A site (Pape T 1998)","section":"evidence","anchor":"ev-pape1998-decoding-kinetics"},{"source":"step:The tRNA swings into the A site","machine":"ribosome","label":"Step: The tRNA swings into the A site","section":"mechanism"},{"source":"ref:pape1998","machine":"ribosome","label":"Pape, Wintermeyer and Rodnina, EMBO J 1998","section":"sources","href":"https://doi.org/10.1093/emboj/17.24.7490"}]},{"id":"ribosome-nissen-distance","machine":"ribosome","kind":"cloze","prompt":"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.","answer":"about 18 Å","explanation":"Only conserved 23S rRNA touched the substrates, so the catalyst is RNA: the ribosome is a ribozyme.","section":"evidence","topic":"numbers","sources":["evidence:nissen2000-rna-catalyst","stat:Protein near the new peptide bond","ref:nissen2000"],"tags":["ribozyme","structure"],"difficulty":2,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:nissen2000-rna-catalyst","machine":"ribosome","label":"Distance from the forming peptide bond to the nearest protein (Nissen P 2000)","section":"evidence","anchor":"ev-nissen2000-rna-catalyst"},{"source":"stat:Protein near the new peptide bond","machine":"ribosome","label":"Key number: Protein near the new peptide bond","section":"summary"},{"source":"ref:nissen2000","machine":"ribosome","label":"Nissen et al.","section":"sources","anchor":"ref-nissen2000","href":"https://doi.org/10.1126/science.289.5481.920"}]},{"id":"ribosome-error-floor","machine":"ribosome","kind":"qa","prompt":"Using a sensitive β-galactosidase reporter in E. coli, how low were most missense error rates that Manickam et al. (2014) measured?","answer":"About 2.3 × 10^-6 per codon (10 of 14 codons tested).","explanation":"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.","section":"evidence","topic":"debate","sources":["evidence:manickam2014-misreading-floor","evidence:kramer2007-missense-rates","stat:Error rate per step","ref:manickam2014"],"tags":["accuracy","contested"],"difficulty":3,"url":"/machines/ribosome#evidence","cites":[{"source":"evidence:manickam2014-misreading-floor","machine":"ribosome","label":"Lowest missense error frequencies measured in vivo (Manickam N 2014)","section":"evidence","anchor":"ev-manickam2014-misreading-floor"},{"source":"evidence:kramer2007-missense-rates","machine":"ribosome","label":"Missense error frequency of tRNALys at near-cognate codons in vivo (Kramer EB 2007)","section":"evidence","anchor":"ev-kramer2007-missense-rates"},{"source":"stat:Error rate per step","machine":"ribosome","label":"Key number: Error rate per step","section":"summary"},{"source":"ref:manickam2014","machine":"ribosome","label":"Manickam et al.","section":"sources","href":"https://doi.org/10.1261/rna.039792.113"}]}]}