Protein Synthesis Simulator

What protein synthesis is

Protein synthesis is how a cell makes a protein from a gene, in two stages. In transcription, RNA polymerase copies the gene’s template strand into messenger RNA; in translation, a ribosome reads that mRNA three bases at a time, from the start codon AUG to a stop codon, and joins one amino acid for every codon before the stop.

Three rules do all the work, and the tool applies them to whatever you type:

• mRNA = coding strand with U in place of T, because each mRNA base pairs with the template base opposite it: A with U, T with A, G with C and C with G.
• amino acids = (bases from the A of AUG to the last base of the stop codon) ÷ 3 − 1, because the stop codon adds none.
• anticodon = the complement of the codon, read the other way, because tRNA and mRNA pair antiparallel: under 5′-AUG-3′ sits 3′-UAC-5′.

The equation above, t = L ÷ v, is the one thing timed: the length made divided by the elongation rate, which gives the readouts that say how long a real cell would take.

How to use it

Type or paste a DNA or mRNA sequence, or choose an example, then say which strand it is. The coding strand reads like the mRNA; the template strand is the one RNA polymerase reads, and it can be typed written either way round, 3′ to 5′ or 5′ to 3′. Choose a eukaryotic cell to see the mRNA capped, tailed and exported from the nucleus, or a bacterium, which has no nucleus.

Press Play to watch the whole process, or Next to go one event at a time: each base the polymerase adds, each tRNA that arrives, each peptide bond and each move of the ribosome. The caption under the scene says what the current step does, and the codon table lists every codon, its anticodon and its amino acid; choose a codon’s number to jump to the moment its tRNA arrives. Edit a base while paused on a codon and the scene stays on that codon, showing the new tRNA.

Worked example: from a template strand to a protein

Take the template strand 3′-TAC GGT CTT AAG ATT-5′ and find the mRNA, the anticodons and the protein. Written 3′ to 5′, the template already runs alongside the mRNA it makes, so each base is simply paired: 5′-AUG CCA GAA UUC UAA-3′.

The protein is Met-Pro-Glu-Phe. The 15 bases run from the A of AUG to the last base of UAA, so the count is 15 ÷ 3 − 1 = 4 amino acids. In a human cell the release factor at UAA is eRF1; in a bacterium it would be RF1 or RF2. At the rates in the readouts, transcribing the 15 bases takes 15 ÷ 100 = 0.15 s to 15 ÷ 50 = 0.3 s, and joining the 4 amino acids takes 4 ÷ 6 = 0.67 s.

Choose Template strand exercise in the Example list and press Next to go through it: the tool shows it in 35 steps, from the closed double helix to the finished chain.

Transcription, step by step

RNA polymerase binds at a promoter and unwinds a short stretch of the helix, the transcription bubble. It reads the template strand 3′ to 5′ and builds the RNA 5′ to 3′, adding each new base to the RNA’s 3′ end, and the newest 8 or 9 bases stay paired with the template inside the enzyme, the RNA and DNA hybrid Nudler and colleagues measured in E. coli in 1997. The RNA made before them leaves through an exit channel and the DNA closes up behind.

In a eukaryote the RNA is processed on the way. A cap of 7-methylguanosine goes on its 5′ end early, mostly while the transcript is 20 to 30 bases long, as Rasmussen and Lis found on fruit fly heat shock genes in 1993. The RNA is cut a short way past a poly(A) signal, AAUAAA, and poly(A) polymerase adds a tail of about 200 adenines that no template spells out. Introns are spliced out, and the finished mRNA leaves through a nuclear pore 5′ end first, which is how Mehlin, Daneholt and Skoglund saw a particle of RNA and protein cross in the salivary gland cells of a midge in 1992. A bacterium does none of this and has no nucleus, so its ribosomes can start on an mRNA while it is still being made.

Translation, step by step

Initiation. In a bacterium the small ribosomal subunit, 30S, is placed by pairing with a Shine-Dalgarno sequence just before the start codon, and the initiator tRNA brings formylmethionine. In a eukaryote the small subunit, 40S, already carrying the initiator tRNA with methionine, binds the 5′ cap and scans along the mRNA to the first AUG. The large subunit then joins, 50S to make a 70S ribosome or 60S to make an 80S one, with the initiator tRNA in the P site.

Elongation, one codon at a time. A tRNA whose anticodon pairs with the codon in the A site arrives with its amino acid. The ribosome’s own RNA catalyses a peptide bond that moves the whole chain onto that amino acid. Then the ribosome moves one codon towards the 3′ end, so each tRNA shifts from the A site to the P site to the E site, from which the empty one leaves.

Termination. Normally no tRNA pairs with UAA, UAG or UGA. A release factor fills the A site instead: RF1 reads UAA and UAG, RF2 reads UAA and UGA, and in eukaryotes eRF1 reads all three. The ribosome adds water to the bond holding the chain to the last tRNA, the chain leaves through the exit tunnel N-terminus first, and the subunits part.

Mutations you can watch happen

• One base changed. In the beta-globin example, base 70 is an A; the sickle cell example makes it a T. Codon 7 becomes GUG instead of GAG, the tRNA that arrives has the anticodon 3′-CAC-5′ instead of 3′-CUC-5′, and valine goes in where glutamic acid belongs. Every other codon, and the other 146 amino acids, are unchanged. Textbooks call this change Glu6Val, because they number the finished chain, which has lost its first methionine; counted from the start codon, as the tool counts, it is codon 7.
• One base deleted. Sarcolipin with its tenth base removed keeps its first three codons and then reads a different message: Met-Gly-Ile-Thr-Pro-Gly-Ser-Cys-Phe-Ser-Thr-Ser-Leu-Leu-Ser, stopped by UGA at codon 16. The chain is 15 amino acids long instead of 31, and 11 of the 12 after the third are different ones; the ninth, phenylalanine, matches only by chance.
• No stop codon. With its last three bases gone, sarcolipin’s mRNA ends before any stop codon, and the ribosome reaches the end with nothing to fill the A site. It stalls with the chain still attached, which cells treat as damage to be cleared up.

Why the anticodons here are exact complements

The anticodon the tool shows pairs with its codon base for base. A cell often does something looser. The third base of a codon can pair with the first base of an anticodon in more than one way, which Crick called wobble in 1966, so one tRNA can read several codons. In human cells both phenylalanine codons, UUU and UUC, are read by tRNAs with the anticodon GAA, written 5′ to 3′: it pairs with UUC exactly and with UUU through a G and U pair at the third position. The Genomic tRNA Database’s high-confidence set for the human genome has no tRNA gene with the anticodon AAA.

How long it takes in a real cell

The readouts divide the length made by the elongation rates Milo and Phillips collect in Cell Biology by the Numbers: RNA polymerase at 40 to 80 bases a second in E. coli and 50 to 100 in mammalian cells, and ribosomes at about 20 amino acids a second in E. coli and about 6 in mammalian cells, measured in mouse embryonic stem cells. For human beta-globin that is 628 ÷ 100 = 6.28 s to 628 ÷ 50 = 12.56 s to transcribe its mRNA, shown as 6.3 to 13 s, and 147 ÷ 6 = 24.5 s to join its chain, shown as 25 s. In a cell the polymerase also copies the gene’s two introns, which splicing then removes, so real transcription takes longer than the mRNA’s length suggests. For the E. coli trpL leader peptide, 14 amino acids at 20 a second take 0.7 s.

Those are elongation times only. Starting a gene, pausing, splicing, which Milo and Phillips put at 5 to 10 minutes on average, and export all take longer, and the animation’s own pace is set for watching, not for timing.

What this does not cover

• Promoters, transcription factors and terminators. Transcription starts at the first base you type and stops at the last, as though a promoter sat just before the sequence.
• Introns. What you type is treated as exons only; the beta-globin example is the spliced mRNA, with the gene’s two introns already gone.
• How a bacterial ribosome finds its start. The tool takes the first AUG, where a real ribosome is placed by a Shine-Dalgarno sequence and can pass an earlier AUG; some bacterial genes also start at GUG or UUG, which NCBI translation table 11 allows.
• The Kozak context that makes a eukaryotic ribosome stop at one AUG rather than another, and upstream open reading frames.
• Many ribosomes at once. A real mRNA is read by several ribosomes spaced along it, a polysome; here one ribosome reads it, and in a bacterium transcription and translation are shown one after the other, not overlapping.
• The elongation factors and GTP that drive each step, the enzymes that load each tRNA with its amino acid, wobble pairing, and modified bases.
• Selenocysteine. In a few human proteins a special tRNA reads UGA as selenocysteine instead of stop; the tool reads every UGA as a stop, as the standard code does.
• Folding, and changes made to the chain afterwards, such as removing the first methionine.
• Sizes. Nothing is drawn to scale: the ribosome, the tRNAs and the polymerase are schematic shapes, drawn small enough to sit beside the bases they work on.

For a whole sequence at once, in all six reading frames, use the DNA to Protein Translator. To see why the two strands of a gene run in opposite directions, turn the helix in the DNA Double Helix Explorer. The Cell Structure Explorer shows where the nucleus and the ribosomes sit in a whole cell. Many of the proteins a cell makes are enzymes, and the Enzyme Kinetics Simulator shows how fast one works. Two of the four chains of adult haemoglobin are beta-globin, and the Oxygen Dissociation Curve Simulator plots how that haemoglobin binds oxygen.

Common mistakes

• Writing the mRNA as the complement of the coding strand. The mRNA is the complement of the template strand, so it reads like the coding strand, with U for T.
• Forgetting to reverse a template written 5′ to 3′. Pair every base and reverse the result, or the mRNA is written backwards.
• Starting at the first base instead of the first AUG. The ribosome starts at AUG, and every codon after it is counted from there.
• Counting the stop codon as an amino acid. It is read by a release factor, not a tRNA, and adds nothing to the chain.
• Reading an anticodon the wrong way round. Lined up under AUG it reads 3′-UAC-5′; written 5′ to 3′, the way tRNAs are named, it is CAU.
• Putting U in DNA or T in RNA. DNA uses T and RNA uses U; both pair with A.