Protein Synthesis Simulator — Transcription and Translation

The Central Dogma of Molecular Biology

The central dogma describes how genetic information flows in living cells:

Exceptions exist: retroviruses use reverse transcriptase to copy RNA back into DNA, and some RNA molecules (ribozymes) act as catalysts — but for all standard proteins, the flow is always DNA → RNA → protein.

How to Use the Protein Synthesis Simulator

1. Open the Protein Synthesis Simulator
2. Enter a DNA template strand or use the pre-loaded sequence
3. Click Transcribe to see the complementary mRNA sequence generated
4. Click Translate to watch the ribosome read codons and build the amino acid chain
5. Step through the animation manually or use Auto Play for continuous translation
6. View the codon table to look up which amino acid each triplet codes for

Transcription in Detail

Initiation

RNA polymerase binds to a promoter sequence upstream of the gene. In eukaryotes, transcription factors must first bind the TATA box (a sequence ~25 base pairs upstream) before RNA polymerase II can attach. The double helix unwinds at the transcription bubble.

Elongation

RNA polymerase reads the template strand 3' to 5' and synthesises mRNA 5' to 3', adding complementary ribonucleotides (A pairs with U, not T; G pairs with C). The transcript is identical to the non-template (coding) strand, except U replaces T. RNA polymerase has no proofreading activity — error rate is ~1 per 10,000 bases.

Termination and RNA processing

In eukaryotes, the pre-mRNA is processed before it can be translated: a 5' cap (modified guanosine) and a 3' poly-A tail are added for stability and ribosome recognition. Introns (non-coding sequences) are spliced out by the spliceosome; exons are joined. The resulting mature mRNA exits through nuclear pores.

Translation in Detail

The genetic code

mRNA is read in triplets called codons. There are 64 possible codons (4³) encoding 20 amino acids plus 3 stop codons. The code is degenerate — most amino acids have multiple codons (synonyms). The code is nearly universal: the codon AUG (methionine) is the start codon in virtually all organisms.

Ribosome structure and function

Ribosomes have three binding sites: A (aminoacyl) accepts incoming tRNA carrying the next amino acid; P (peptidyl) holds the growing polypeptide; E (exit) releases spent tRNA. The ribosome moves codon by codon in the 5' to 3' direction, and a peptide bond forms between amino acids with each step — catalysed by rRNA (a ribozyme), not protein.

tRNA and anticodons

Transfer RNA molecules are the adapters that match codons to amino acids. Each tRNA has an anticodon loop that base-pairs with the mRNA codon, and an acceptor stem that carries the corresponding amino acid. Aminoacyl-tRNA synthetase enzymes "charge" tRNAs by attaching the correct amino acid — this is the critical step where the genetic code is physically enforced.

Mutations and Their Effects

Common Questions

Why is the genetic code nearly universal?

The code evolved very early in the history of life — before the divergence of major lineages. Because any change to a codon assignment would alter thousands of proteins simultaneously (almost certainly lethal), the code has been essentially frozen for ~3.5 billion years. Minor variations exist in mitochondrial genomes and a few microorganisms.

What are polyribosomes?

A polyribosome (polysome) is a chain of multiple ribosomes all translating the same mRNA simultaneously. As soon as one ribosome moves away from the start codon, another can begin. This massively amplifies protein output from a single mRNA — a single mRNA can be translated by 10–100 ribosomes at once.