{"format":"molecular-machines.cards","version":1,"updated":"2026-10-12","decks":[{"machine":"rna-polymerase","name":"RNA polymerase II","count":10,"url":"/learn/cards/rna-polymerase.json"}],"cards":[{"id":"rna-polymerase-makes-mrna","machine":"rna-polymerase","kind":"cloze","prompt":"To use a gene, the cell first copies it. RNA polymerase II copies a DNA gene into {{messenger RNA}}, the molecule that ribosomes read.","answer":"messenger RNA","explanation":"The DNA stays in the nucleus. Only the copy goes out to the ribosomes.","section":"summary","topic":"purpose","sources":["machine:tagline","machine:summary","link:ribosome"],"difficulty":1,"url":"/machines/rna-polymerase#summary","cites":[{"source":"machine:tagline","machine":"rna-polymerase","label":"Summary","section":"summary"},{"source":"machine:summary","machine":"rna-polymerase","label":"Summary","section":"summary"},{"source":"link:ribosome","machine":"rna-polymerase","label":"Link to Ribosome","section":"story"}]},{"id":"rna-polymerase-same-genome-different-cells","machine":"rna-polymerase","kind":"qa","prompt":"A skin cell and a nerve cell carry the same full genome. What makes them different, in terms of what RNA polymerase II does?","answer":"They copy different genes.","explanation":"Like a scribe in a huge library, the cell copies only the pages it needs.","section":"story","topic":"purpose","sources":["stop:body","analogy:A scribe copying one page from a huge library"],"difficulty":1,"url":"/machines/rna-polymerase#story","cites":[{"source":"stop:body","machine":"rna-polymerase","label":"Big picture: You, a library","section":"story"},{"source":"analogy:A scribe copying one page from a huge library","machine":"rna-polymerase","label":"Analogy: A scribe copying one page from a huge library","section":"story"}]},{"id":"rna-polymerase-opens-dna","machine":"rna-polymerase","kind":"qa","prompt":"The letters RNA polymerase II must read are hidden inside the DNA double helix. What does it do to the DNA first?","answer":"It clamps onto it and opens a short bubble, about one turn.","explanation":"It then pairs RNA letters with one of the two DNA strands. Cas9 also opens DNA and reads one strand.","section":"summary","topic":"cycle","sources":["mechanism:Bubble formation","machine:summary","stop:machine"],"difficulty":1,"url":"/machines/rna-polymerase#summary","cites":[{"source":"mechanism:Bubble formation","machine":"rna-polymerase","label":"Step: Bubble formation","section":"mechanism"},{"source":"machine:summary","machine":"rna-polymerase","label":"Summary","section":"summary"},{"source":"stop:machine","machine":"rna-polymerase","label":"Big picture: Pol II at work","section":"story"}]},{"id":"rna-polymerase-energy-source","machine":"rna-polymerase","kind":"qa","prompt":"Many machines burn ATP as a separate fuel. What pays for each letter that RNA polymerase II adds to the RNA?","answer":"The incoming building block itself: the energy in its triphosphate.","explanation":"Each new letter arrives as a triphosphate. The release of pyrophosphate drives the chain forward.","section":"summary","topic":"purpose","sources":["machine:energy","step:The bond forms"],"difficulty":2,"url":"/machines/rna-polymerase#summary","cites":[{"source":"machine:energy","machine":"rna-polymerase","label":"Summary","section":"summary"},{"source":"step:The bond forms","machine":"rna-polymerase","label":"Step: The bond forms","section":"mechanism"}]},{"id":"rna-polymerase-brownian-ratchet","machine":"rna-polymerase","kind":"qa","prompt":"After each new letter, the polymerase must move one step along the DNA. How does it move forward?","answer":"It jiggles back and forth by thermal motion, and the next incoming building block catches it in the forward position.","explanation":"This is called a Brownian ratchet. Force data fit it better than a power stroke.","section":"evidence","topic":"debate","sources":["step:DNA and RNA move one base pair","mechanism:Translocation","evidence:brownian-ratchet-force-velocity"],"difficulty":2,"url":"/machines/rna-polymerase#evidence","cites":[{"source":"step:DNA and RNA move one base pair","machine":"rna-polymerase","label":"Step: DNA and RNA move one base pair","section":"mechanism"},{"source":"mechanism:Translocation","machine":"rna-polymerase","label":"Step: Translocation","section":"mechanism"},{"source":"evidence:brownian-ratchet-force-velocity","machine":"rna-polymerase","label":"Mechanism that fits the force-velocity data (Abbondanzieri EA 2005)","section":"evidence","anchor":"ev-brownian-ratchet-force-velocity"}]},{"id":"rna-polymerase-proofreading-backtrack","machine":"rna-polymerase","kind":"qa","prompt":"Now and then a wrong letter slips into the new RNA. How does the polymerase fix it?","answer":"It backs up one step and cuts off the RNA end that holds the error.","explanation":"The same active site that adds letters also cuts the wrong one off.","section":"mechanism","topic":"cycle","sources":["mechanism:Proofreading","stop:site","fact:s-backtrack"],"difficulty":1,"url":"/machines/rna-polymerase#mechanism","cites":[{"source":"mechanism:Proofreading","machine":"rna-polymerase","label":"Step: Proofreading","section":"mechanism"},{"source":"stop:site","machine":"rna-polymerase","label":"Big picture: Active site","section":"story"},{"source":"fact:s-backtrack","machine":"rna-polymerase","label":"How far the enzyme backs up to remove a wrong letter: 1 position","section":"story"}]},{"id":"rna-polymerase-error-rate","machine":"rna-polymerase","kind":"qa","prompt":"Even with proofreading, RNA polymerase II sometimes makes a mistake. Roughly how many mistakes does it make per million letters?","answer":"About four.","explanation":"This was measured across all the messenger RNAs of a worm.","section":"evidence","topic":"numbers","sources":["fact:V11","stat:Transcription error rate","evidence:transcription-error-rate"],"difficulty":2,"url":"/machines/rna-polymerase#evidence","cites":[{"source":"fact:V11","machine":"rna-polymerase","label":"Transcription errors: 4 × 10^-6 per letter","section":"story"},{"source":"stat:Transcription error rate","machine":"rna-polymerase","label":"Key number: Transcription error rate","section":"summary"},{"source":"evidence:transcription-error-rate","machine":"rna-polymerase","label":"Base-substitution error rate in mRNA in vivo (Gout JF 2013)","section":"evidence","anchor":"ev-transcription-error-rate"}]},{"id":"rna-polymerase-letters-per-second","machine":"rna-polymerase","kind":"qa","prompt":"RNA polymerase II writes RNA one letter at a time. Roughly how many letters does it add each second in human cells?","answer":"About 25 to 60.","explanation":"That is a few thousand letters a minute.","section":"story","topic":"numbers","sources":["fact:V10","stop:machine","stat:Elongation rate in human cells"],"difficulty":1,"url":"/machines/rna-polymerase#story","cites":[{"source":"fact:V10","machine":"rna-polymerase","label":"Speed of RNA polymerase II: 1.5–3.8 kb per minute","section":"story"},{"source":"stop:machine","machine":"rna-polymerase","label":"Big picture: Pol II at work","section":"story"},{"source":"stat:Elongation rate in human cells","machine":"rna-polymerase","label":"Key number: Elongation rate in human cells","section":"summary"}]},{"id":"rna-polymerase-dystrophin-time","machine":"rna-polymerase","kind":"qa","prompt":"Short genes take minutes to copy. Roughly how long does one polymerase take to copy the longest human gene, dystrophin?","answer":"Most of a day: about 16 hours.","explanation":"Dystrophin is over two million letters long.","section":"story","topic":"numbers","sources":["fact:V9","stop:gene"],"difficulty":2,"url":"/machines/rna-polymerase#story","cites":[{"source":"fact:V9","machine":"rna-polymerase","label":"Time to copy the dystrophin gene once: 16 h","section":"story"},{"source":"stop:gene","machine":"rna-polymerase","label":"Big picture: One long gene","section":"story"}]},{"id":"rna-polymerase-toxins","machine":"rna-polymerase","kind":"qa","prompt":"Some toxins and antibiotics kill by stopping RNA polymerase. How do they stop it?","answer":"They jam the moving parts next to the active site, so the enzyme slows or stops.","explanation":"The toxin alpha-amanitin binds next to the bridge helix. Other drugs hold the trigger loop away from the new letter.","section":"evidence","topic":"parts","sources":["frontier:Structure-guided inhibitor design","evidence:alpha-amanitin-binding-site"],"difficulty":2,"url":"/machines/rna-polymerase#evidence","cites":[{"source":"frontier:Structure-guided inhibitor design","machine":"rna-polymerase","label":"Open question: Structure-guided inhibitor design","section":"summary"},{"source":"evidence:alpha-amanitin-binding-site","machine":"rna-polymerase","label":"α-amanitin binding site on Pol II (Bushnell DA 2002)","section":"evidence","anchor":"ev-alpha-amanitin-binding-site"}]}]}