Protein Synthesis Simulator — Transcription and Translation

Protein Synthesis Stage by Stage

How to Use the Protein Synthesis Simulator

1. Open the protein synthesis simulator.
2. Enter a DNA template strand (3′→5′ direction) or use the provided example sequence.
3. Click Transcribe to see RNA polymerase read the template and produce the complementary mRNA sequence (5′→3′).
4. Click Translate to see ribosomes move along the mRNA. Each codon (3 bases) pairs with a tRNA anticodon carrying its amino acid — the amino acid chain grows step by step.
5. The simulator shows each codon, the corresponding tRNA anticodon, and the amino acid added — until a stop codon is reached.
6. Use the Mutate option to introduce base substitutions or insertions and see how the protein product changes.

The Genetic Code

The genetic code translates the four-base language of DNA/RNA (A, T/U, G, C) into the 20-amino-acid language of proteins. The code is read in triplets called codons — three mRNA bases specify one amino acid. Key properties:

• Degenerate (redundant): Multiple codons can code for the same amino acid. There are 64 possible codons (4³) but only 20 amino acids — most amino acids have 2, 4, or 6 synonymous codons.
• Non-overlapping: Each base is read as part of exactly one codon — they do not overlap.
• Comma-less: There is no "punctuation" between codons — the reading frame is set by the start codon (AUG) and maintained by ribosome translocation.
• Universal: The same genetic code is used by nearly all living organisms — with minor exceptions in mitochondria and some protists — demonstrating the common ancestry of life.

The start codon is AUG (codes for methionine). The three stop codons — UAA ("ochre"), UAG ("amber"), UGA ("opal") — do not code for any amino acid; they terminate translation.

Transcription in Detail

RNA polymerase (in eukaryotes: RNA Pol II for mRNA) binds to the promoter — a specific DNA sequence upstream of the gene. In humans, key promoter elements include the TATA box (approximately 25–30 bases upstream of the transcription start site) and other regulatory elements.

RNA polymerase reads the template strand 3′→5′ and synthesises mRNA complementary to it, 5′→3′. Base pairing rules during transcription:

• DNA A → mRNA U
• DNA T → mRNA A
• DNA G → mRNA C
• DNA C → mRNA G

The mRNA sequence is identical to the coding (sense) strand of DNA — except T is replaced by U. The coding strand is also called the "non-template" strand or "sense strand." The template strand is read; the coding strand shows what the mRNA will say.

mRNA Processing (Eukaryotes)

In eukaryotes (including humans), the primary RNA transcript (pre-mRNA) requires processing before it can be translated:

• 5′ cap: A modified guanosine (7-methylguanosine) is added to the 5′ end. Protects mRNA from degradation; required for ribosome recognition during translation initiation.
• 3′ poly-A tail: A string of approximately 200 adenosine residues is added to the 3′ end. Increases mRNA stability; assists export from nucleus; required for efficient translation.
• Splicing: Introns (intervening sequences — non-coding regions) are removed by the spliceosome (a complex of snRNA and proteins). Exons (expressed sequences) are joined together. Alternative splicing allows one gene to produce multiple protein isoforms by joining different combinations of exons.

Prokaryotes (bacteria) lack nuclei and do not perform mRNA splicing — ribosomes can begin translating mRNA before transcription is complete.

Translation in Detail

Translation occurs at the ribosome — a complex of ribosomal RNA (rRNA) and proteins. The ribosome has three sites:

• A site (Aminoacyl): Where incoming aminoacyl-tRNAs bind. Each tRNA carries one amino acid and has an anticodon complementary to the mRNA codon in the A site.
• P site (Peptidyl): Where the growing polypeptide chain is held. The tRNA here carries the chain built so far.
• E site (Exit): Where uncharged tRNAs exit the ribosome after their amino acid has been added to the chain.

Each elongation cycle: an aminoacyl-tRNA enters the A site → peptide bond forms between the A site amino acid and the growing chain in the P site → ribosome translocates one codon (A→P→E shift) → next codon in A site. This cycle repeats hundreds of times per second.

Mutations and Their Effects on Protein Synthesis

Common Questions

What is the difference between the coding strand and the template strand?

The DNA double helix has two strands. The template strand (antisense strand) is the one RNA polymerase reads to make mRNA — it is complementary to the mRNA. The coding strand (sense strand, non-template strand) has the same sequence as the mRNA (with T instead of U) and represents the gene as it appears in databases. When a gene sequence is written, it is conventionally written as the coding strand 5′→3′.

How many amino acids are there and how many codons code for each?

There are 20 standard amino acids. With 64 codons (4 bases × 4 × 4 = 64 combinations) and 3 stop codons, 61 codons encode the 20 amino acids. The degeneracy varies: methionine (Met) and tryptophan (Trp) each have only 1 codon. Serine (Ser), leucine (Leu), and arginine (Arg) each have 6. Alanine, threonine, glycine, proline, and valine each have 4. The "wobble position" (third base of codon) allows more flexibility — changes at position 3 often code for the same amino acid.

What happens to a protein after translation?

Post-translational modifications (PTMs) alter protein function, localisation, stability, and interactions. Common PTMs: phosphorylation (adds phosphate group — switches protein on/off); glycosylation (adds sugar chains — important for membrane proteins and antibodies); ubiquitination (tags protein for degradation by the proteasome); cleavage (signal peptides removed; propeptides processed — e.g., insulin is made as proinsulin, then cleaved to active form); disulphide bond formation (in secreted and membrane proteins — provides structural stability).