Gene expression – transcription, translation and regulation
BiologyGeneticsAges 17–18
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Sign in to playPlace transcription factors, RNA polymerase, ribosomes and an mRNA-degrading enzyme on a stretch of DNA carrying three genes to make mRNA and then protein. Three screens: Expression (drag and drop through the whole chain transcription → translation → collect the protein of each gene), mRNA (the concentration and affinity of positive and negative transcription factors and of RNA polymerase set the rate of mRNA production) and Many Cells (protein levels fluctuate randomly from cell to cell around the expected value). Adapted from the "Gene Expression Essentials" simulation by PhET Interactive Simulations, University of Colorado Boulder (CC BY 4.0); rewritten.
Lesson: Gene expression and its regulation
What it shows
A simulation for the lesson on genes and gene expression in molecular genetics (ages 15–18): students assemble the molecules themselves to see the flow of information DNA → mRNA → protein and the role of the regulatory region.
How to use
On the Expression screen the DNA carries three genes, each with a regulatory region, a coding region and a terminator. Drag a positive transcription factor to the right site on the regulatory region, then drag RNA polymerase onto the promoter to transcribe: the mRNA strand grows and leaves the DNA. Drag a ribosome to the 5' end of the mRNA to translate it; the polypeptide chain grows and folds into a protein, and each gene gives its own kind of protein to drop into the collection box. A negative transcription factor blocks RNA polymerase, and the mRNA-degrading enzyme makes the mRNA disappear. On the mRNA screen the molecules diffuse randomly and the rate of mRNA production is measured against the concentration and affinity of the transcription factors and RNA polymerase. The Many Cells screen runs up to 90 cells with the same gene: the amount of protein differs between cells because molecular events are random, while the mean approaches the expected value set by the rates of making and degrading mRNA and protein. Qualitative model: the Many Cells screen uses the Gillespie algorithm with simplified rate constants, not measured data for a real gene.
Parameters you can change
- Starting screen Expression, mRNA, Many Cells
- Initial number of cells (Many Cells screen) 1–90 cells
- Draw the expected-value line on the protein graph
- Show the next-step hint (Expression screen)
Questions to explore
- Why can RNA polymerase not bind to the promoter when no positive transcription factor is present, or when a negative transcription factor is bound?
- How many proteins can one mRNA molecule make, and what stops it from making more?
- Do cells with the same gene under the same conditions contain the same amount of protein? How does the mean amount of protein change if you increase the protein degradation rate?
