Protein Synthesis Simulator: Transcription and Translation in 3D
Follow one gene from DNA to protein: RNA polymerase reads the template strand, the RNA is capped, spliced and given a tail, and ribosomes read it codon by codon. Compare a bacterium with a human cell, then break a step with a mutation or an antibiotic.
Pick a mutation, then press ▶. Each one breaks a different step.
Add one to the cell. Some stop bacteria but not human cells: that is how antibiotics can kill bacteria without harming you.
What the cell makes
Lab notebook
Every run you finish is written here: the gene, what you changed, what happened and the protein. Export a CSV, or turn the session into a PDF lab report.
| # | Gene | Change | Result | Protein |
|---|
Concept library
Click "New problem" to begin.
Click "Start quiz" for 5 questions on transcription, RNA processing, translation, bacteria vs eukaryotes, and mutations and antibiotics.
1 Overview
Simulate follows one gene from DNA to protein. The big view on the left is the cell; the camera goes where the action is (Follow), or pick Gene, RNA, Cell or Ribosome yourself. The view on the right lines up the gene's sequences, maps the steps, or times every step on a timeline. Experiment has five labs that end in a PDF lab report, and Quiz has a practice quiz with worked solutions and a 5-question quiz.
2 Playing the story
- Press ▶ (or Space). › jumps to the next step. The bar under the caption shows how far the gene has got.
- Teach gives every step time on screen; Fast is ten times real time; Real runs at the speed of a real cell (RNA polymerase II about 40 bases a second, a human ribosome about 6 amino acids a second). The Status panel always shows the real time in the cell.
- Choose the gene in the top bar or the Gene panel: an example human gene with one intron, an example bacterial gene, or the real human insulin gene.
3 What you see
- Gene: the coding strand on top, the template strand underneath, coloured by the bases. RNA polymerase opens a bubble and builds RNA on the template strand; the band under the DNA marks the promoter, untranslated regions, exons and introns.
- RNA: the pre-mRNA drawn by its parts while the cap is added, the spliceosome cuts the introns out as lariats and the poly(A) tail grows.
- Cell: the mRNA leaving the nucleus through a pore (or, in a bacterium, the nucleoid with no nucleus at all).
- Ribosome: the codons of the mRNA, the E, P and A sites, tRNAs with their anticodons, peptide bonds, translocation, and the release factor at the stop codon. Tick Polysome to zoom out and see every ribosome on the mRNA.
4 Mutations and drugs
Mutate lists mutations that each break one step: the promoter, a splice site, the poly(A) signal, the Shine–Dalgarno box (bacteria), and silent, missense, nonsense and frameshift mutations in the coding sequence. Drugs adds an antibiotic or toxin; each stops one step, and only in the kinds of cell it acts on. What the cell makes says what came out: no mRNA, an unstable mRNA, no protein, a shorter or changed protein, or the normal one.
5 The right-hand view
Sequence lines up the DNA, the pre-mRNA, the mature mRNA and the protein, with the part being worked on lit up. Steps is a map of the whole process (nucleus, pore, cytoplasm) with the current step lit and any blocked step crossed out. Timeline draws every step in real seconds, so you can see that splicing starts before transcription has finished and that a bacterium translates while it transcribes.
6 2D and 3D
The 2D | 3D switch at the top changes how the stage is drawn; both show the same moment of the same model. In 3D drag to turn, hold Ctrl or ⌘ and scroll to zoom (a plain scroll scrolls the page). The page opens in 3D on computers and tablets and in 2D on phones; your choice is remembered.
7 Experiment mode and the lab report
Five labs: transcribe and translate by hand, splicing (how long is the mature mRNA?), antibiotics that stop bacteria but not you, how long translation takes (a graph of time against protein length), and bacterium vs human cell. Each shows its aim, what you need and a real-lab note; the method ticks off as you work, a conclusion question checks your result, and Create lab report builds a PDF.
8 Quiz, units and keyboard
- The practice quiz covers transcription, RNA processing, translation, counting bases and amino acids, bacteria vs eukaryotes, and mutations and antibiotics, each with a worked solution; Take the quiz gives five mixed questions and a star rating.
- The SI (m) | US (ft) switch changes everyday lengths only; molecules stay in nanometers and bases.
- Space plays or pauses, → jumps a step, 1–4 pick a view, 0 follows the story, S opens Status. Right-click a view to save it as an image.
Protein synthesis: how a gene becomes a protein
Every protein in a cell is built from instructions in its DNA, and protein synthesis is how the cell reads them. The gene is first copied into messenger RNA (transcription), and the mRNA is then read by ribosomes to join amino acids in the right order (translation). This free protein synthesis simulator runs both, one molecule at a time, in 3D or 2D. One model, timed in real seconds, drives every view, so a mutation or an antibiotic changes the picture, the timeline and the protein together.
The steps of protein synthesis
- Initiation of transcription. Transcription factors bind the promoter (in human cells the TATA box, about 30 bases before the start), and RNA polymerase II joins them.
- Elongation. RNA polymerase unwinds about 14 base pairs at a time and moves along the template strand 3′ → 5′, building RNA 5′ → 3′ at about 40 bases a second. The RNA has the same sequence as the coding strand, with U in place of T.
- RNA processing (eukaryotes only). The pre-mRNA gets a 5′ cap, its introns are spliced out and a poly(A) tail of about 200 A is added.
- Export. The mature mRNA leaves the nucleus through a nuclear pore.
- Translation. A ribosome finds the start codon AUG, reads the mRNA codon by codon with the help of tRNAs and releases the finished polypeptide at a stop codon.
Transcription and translation compared
| Transcription | Translation | |
|---|---|---|
| Template | DNA (template strand) | mRNA |
| Product | RNA (pre-mRNA, then mRNA) | A polypeptide |
| Done by | RNA polymerase | Ribosomes, tRNAs |
| Building blocks | Nucleotides (A, U, G, C) | Amino acids |
| Where (eukaryotes) | Nucleus | Cytoplasm, free ribosomes or rough ER |
| Speed (human cell) | About 40 bases a second | About 6 amino acids a second |
RNA processing: cap, splicing and tail
A eukaryotic gene is longer than its mRNA. Its coding parts, the exons, are interrupted by introns. A spliceosome recognises each intron by the GU at its start, the AG at its end and an A branch point near its end, loops the intron into a lariat and joins the exons. The human insulin gene is a good example: its 1,428-base pre-mRNA loses introns of 179 and 786 bases, leaving a mature mRNA of 463 bases (plus the tail) that codes for 110 amino acids. The 5′ cap and poly(A) tail protect the mRNA, help it out of the nucleus and help the ribosome find it.
Translation: the ribosome, tRNA and the A, P and E sites
The small ribosomal subunit binds the mRNA (at the cap in eukaryotes, at the Shine–Dalgarno sequence in bacteria) with the initiator tRNA carrying methionine, and finds AUG. The large subunit then joins. Each tRNA's anticodon pairs with a codon in the A site. The chain held by the tRNA in the P site is joined to the new amino acid by a peptide bond, made by the ribosome's RNA. The ribosome then moves one codon on, and the empty tRNA leaves from the E site. Each amino acid costs four high-energy phosphate bonds: two to charge the tRNA and two GTPs. At a stop codon a release factor frees the chain. Many ribosomes read one mRNA at once, forming a polysome.
Protein synthesis in prokaryotes vs eukaryotes
A bacterium has no nucleus, so its ribosomes start translating an mRNA while RNA polymerase is still making it (coupled transcription and translation). Bacterial genes have no introns, their mRNA has no cap or tail, and translation runs at about 15 amino acids a second. In the simulator the bacterial gene gives its first protein within seconds of transcription starting. The human-style gene takes about 45 seconds, most of it spent processing and exporting the RNA.
Mutations and antibiotics that stop protein synthesis
A mutation outside the coding sequence can be as harmful as one inside it. A damaged promoter means almost no mRNA, a damaged splice site keeps an intron in the mRNA, and a missing poly(A) signal means the RNA is destroyed. A nonsense mutation early in a gene with introns triggers nonsense-mediated decay, which destroys the mRNA. Many antibiotics work because bacterial ribosomes and RNA polymerase differ from ours. Rifampicin, tetracycline, streptomycin and chloramphenicol stop bacteria but not human cells, while α-amanitin and cycloheximide act only on eukaryotes. For the genetic code itself, use the Interactive Codon Chart & DNA to Protein Translator.
Experiments and course links
The five labs match AP Biology Unit 6 (6.3 transcription and RNA processing, 6.4 translation, 6.7 mutations), NGSS HS-LS1-1, AQA GCSE 4.6.1.6, AQA A-level 3.4.2 and IB D1.2. This is an educational model, not medical advice.
Frequently asked questions
What are the steps of protein synthesis?
Protein synthesis has two stages. In transcription, RNA polymerase binds the promoter of a gene, unwinds the DNA and builds a strand of mRNA that is complementary to the template strand. In eukaryotes the pre-mRNA is then processed in the nucleus (a 5′ cap is added, introns are spliced out and a poly(A) tail is added) and leaves through a nuclear pore. In translation, a ribosome binds the mRNA, finds the start codon AUG and reads the mRNA codon by codon; tRNAs bring the matching amino acids, which are joined by peptide bonds, until a stop codon is reached and the finished polypeptide is released.
What is the difference between transcription and translation?
Transcription copies a gene from DNA into mRNA; translation reads that mRNA to build a protein. Transcription is done by RNA polymerase, uses DNA as the template and makes RNA from nucleotides; in eukaryotes it happens in the nucleus. Translation is done by ribosomes with the help of tRNAs, uses mRNA as the template and makes a chain of amino acids; it happens in the cytoplasm, on free ribosomes or on the rough endoplasmic reticulum. In bacteria, which have no nucleus, the two happen at the same time.
What do mRNA, tRNA and rRNA do in protein synthesis?
Messenger RNA (mRNA) carries the gene's code from the DNA to the ribosome as a sequence of three-base codons. Transfer RNA (tRNA) is an adapter: each tRNA carries one amino acid and has an anticodon that pairs with the matching codon on the mRNA. Ribosomal RNA (rRNA), together with proteins, makes up the ribosome; it holds the mRNA and tRNAs in the A, P and E sites and its RNA catalyses the peptide bond between amino acids.
Explore related simulators
Read any codon, translate a sequence of your own and classify mutations with the Interactive Codon Chart & DNA to Protein Translator. See the double helix that RNA polymerase opens, base pair by base pair, in the DNA Structure 3D Model. Follow insulin from the rough ER through the Golgi and out of the cell in the Virtual Living Cell. See a cell with no nucleus, and antibiotics at work, in the Virtual Bacteria Simulator. Watch a virus take over a cell's ribosomes in the Virus Virtual Lab.
Sources: OpenStax Biology 2e, chapter 15 (Genes and Proteins); Urry et al., Campbell Biology 12th edition, chapter 17; Alberts et al., Molecular Biology of the Cell 7th edition, chapter 6; Milo and Phillips, Cell Biology by the Numbers (2015); Bell et al., Nature 284 (1980), the human insulin gene; NCBI RefSeq NM_000207.3; College Board, AP Biology Course and Exam Description, Unit 6. Rates and times are typical values; the example genes are made up and the insulin introns are shown with their real lengths but stand-in sequences. Everything is an educational model, and nothing here is medical advice.
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