Protein Synthesis Simulator: Transcription and Translation
Equations in this simulation
| A, U, G, C | the four bases of RNA | A pairs with U (T in DNA) and G with C; RNA polymerase reads the template strand and builds mRNA from its 5′ end |
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With the current values:
| codon | three bases of mRNA, read in order from the start codon AUG | the anticodon of each tRNA pairs with one codon; most amino acids have several codons |
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With the current values:
| M | mass of the protein chain | the residues' average masses plus one water for the two ends |
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With the current values:
| mutation | Mutation | a substitution changes one codon at most; one base in or out shifts every codon after it |
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With the current values:
How to use the protein synthesis simulator
- Choose a gene or type your own DNA (the coding strand, 5′ to 3′). RNA polymerase opens the double helix and builds messenger RNA along it, the same sequence as the coding strand with U in place of T. Then a ribosome finds the first AUG and reads the mRNA three bases at a time; each transfer RNA brings the amino acid for its codon, and the chain grows until a stop codon.
- The results show the mRNA, the codons from the start codon, the protein in one- and three-letter code and its mass. Make a mutation: choose a substitution, an insertion or a deletion, its position and the new base. The simulation compares the two proteins and names the effect: silent, missense, nonsense, frameshift, a lost start or a lost stop. A substitution at base 20 to T in β-globin is the sickle-cell mutation.
- The chart plots the hydropathy of the original and the mutated protein, residue by residue; a frameshift scrambles everything after the mutation. Choose which gene to animate, original or mutated, and the speed. The Translate DNA to Protein and ORF Finder tools handle long sequences in all six reading frames.
Frequently asked questions
What are transcription and translation?
Transcription copies a gene's DNA into messenger RNA, made by RNA polymerase reading the template strand. Translation turns the mRNA into protein: a ribosome reads it codon by codon, three bases at a time, and transfer RNAs bring the matching amino acids. In bacteria both happen in the cytoplasm at once; in eukaryotes the mRNA is made and processed in the nucleus first.
How many codons are there?
Four bases taken three at a time give 4³ = 64 codons. Sixty-one code for the 20 amino acids, so most amino acids have several codons, and three (UAA, UAG, UGA) are stop codons. AUG codes for methionine and also marks where translation starts.
What is the difference between missense, nonsense and frameshift mutations?
A missense mutation changes one codon to another amino acid, as in sickle-cell disease, where GAG becomes GTG and glutamate becomes valine. A nonsense mutation turns a codon into a stop, cutting the protein short. A frameshift, from inserting or deleting a number of bases that is not a multiple of three, changes every codon after it. A silent mutation changes a codon to another for the same amino acid.
Why is the sickle-cell mutation called Glu6Val if it is codon 7?
By convention, positions in the hemoglobin protein are counted from the first amino acid of the finished chain, after the starting methionine has been removed. This simulation counts from the methionine, so the same change appears as E7V.
It says WebGL is turned off.
The 3D view needs WebGL, which every current browser has. It can be switched off by hardware acceleration being disabled in the browser settings, or by a very old graphics driver. Turn hardware acceleration on, or try another browser.
Is anything uploaded?
No. The simulation is drawn by your own browser with WebGL; nothing is sent anywhere, and it keeps working offline once the page has loaded.