Genetic code. Translation

Genetic code. Translation

How the four-letter code of mRNA is read three bases at a time into the twenty amino acids of a protein, by tRNAs, their synthetases and the ribosome.

Contents4 sections

At a glance

  1. The genetic code is read in triplets, codons. Of the 64, 61 specify amino acids and three, UAA, UAG and UGA, stop translation; AUG codes for methionine and starts it.
  2. The code is degenerate (most amino acids have several codons), unambiguous, read without gaps or overlaps from a fixed start, and nearly universal.
  3. Transfer RNAs are the adaptors: each carries an amino acid at its 3′ end and pairs its anticodon with a codon. Twenty aminoacyl-tRNA synthetases load the right amino acid onto each tRNA.
  4. The ribosome, of a small and a large subunit (70S in bacteria, 80S in our cytoplasm), holds the mRNA and three tRNA sites, A, P and E. Its rRNA makes the peptide bond.
  5. Translation runs in three stages, initiation, elongation and termination, and is powered by GTP. Drugs that tell bacterial ribosomes from ours are antibiotics.

The genetic code

Four bases cannot each stand for one of twenty amino acids, nor can pairs of them (sixteen); triplets give 64 combinations, more than enough. Each triplet in the mRNA is a codon. Marshall Nirenberg and Heinrich Matthaei found the first in 1961, when a synthetic RNA made only of uracil was translated into a chain of phenylalanine: UUU codes for phenylalanine. The whole code was worked out by 1966, and Nirenberg, Har Gobind Khorana and Robert Holley shared the 1968 Nobel Prize in Physiology or Medicine.

  • Degenerate. Most amino acids have two to six codons, which usually differ only in the third base. Methionine (AUG) and tryptophan (UGG) have one each.
  • Unambiguous. Each codon stands for one amino acid only.
  • Start and stop. AUG both codes for methionine and marks where translation starts; UAA, UAG and UGA code for no amino acid and end it.
  • A fixed reading frame. From the start codon, the mRNA is read three bases at a time, with no gaps and no overlaps. A sequence can be read in three frames, and only one gives the right protein: inserting or deleting a base shifts the frame and garbles everything after it.
  • Nearly universal. Bacteria, plants and people use the same code, which is why bacteria can make a human protein, such as insulin, from a DNA copy of its mRNA. The exceptions are few: in our mitochondria, for example, UGA codes for tryptophan rather than stop.
61 for amino acids, 3 for stop
64codons
one for each amino acid
20synthetases
put in wrongly, about
1 in 10,000amino acids
added by a bacterial ribosome, about
20amino acids a second

The adaptors: tRNA and its synthetase

A transfer RNA is about 80 nucleotides long. Drawn flat it is a cloverleaf of four short double helices; folded, it is an L. At one end of the L is the anticodon, three bases that pair with the codon, antiparallel; at the other is the 3′ end, CCA, to which the amino acid is attached.

Our cells have fewer kinds of tRNA than there are codons, because the first base of the anticodon pairs loosely with the third base of the codon: wobble. A G there can pair with U as well as C, for example, and inosine, a modified base found in some anticodons, can pair with U, C or A. So one tRNA can read several codons that differ only in their third base.

Each aminoacyl-tRNA synthetase recognises one amino acid and all the tRNAs for it, and joins the two, using ATP: the amino acid is first activated as aminoacyl-AMP, then moved onto the tRNA. The bond it makes between amino acid and tRNA holds the energy later used to make the peptide bond. Several synthetases also check their own work and remove a wrong amino acid. This step decides the meaning of the code: the ribosome checks only that codon and anticodon pair, never the amino acid.

The ribosome

BacteriaOur cytoplasm
Whole ribosome70S80S
Small subunit30S, with 16S rRNA40S, with 18S rRNA
Large subunit50S, with 23S and 5S rRNA60S, with 28S, 5.8S and 5S rRNA
First amino acidN-formylmethioninemethionine
Finding the startthe Shine–Dalgarno sequencethe 5′ cap, then scanning

The S values are rates of sedimentation in a centrifuge, which is why 30S and 50S make 70S, not 80S. The small subunit holds the mRNA and checks that codon and anticodon pair; the large one joins the amino acids. Between them lie three sites for tRNAs: the A site for the incoming aminoacyl-tRNA, the P site for the tRNA holding the growing chain, and the E site, from which empty tRNAs leave. The new chain leaves through a tunnel in the large subunit.

Initiation, elongation, termination

  1. 1

    Initiation

    In our cells, initiation factors bring the small subunit, already carrying the initiator methionine-tRNA (held by eIF2 with GTP), to the mRNA's 5′ cap, which eIF4E binds; it scans along the mRNA to the first AUG in a good context, the Kozak sequence. In bacteria the small subunit binds the Shine–Dalgarno sequence, a few bases before the AUG, which pairs with its 16S rRNA, and the initiator tRNA carries N-formylmethionine. Either way, the initiator tRNA sits in the P site and the large subunit joins.
  2. 2

    Elongation

    An elongation factor bound to GTP (EF-Tu in bacteria, eEF1A in ours) brings an aminoacyl-tRNA to the A site. If its anticodon pairs with the codon, the GTP is split and the factor leaves. The rRNA of the large subunit moves the growing chain from the tRNA in the P site onto the amino acid in the A site, making a peptide bond. Another factor with GTP (EF-G, or eEF2) then moves the ribosome one codon along: the tRNAs shift from A to P and from P to E.
  3. 3

    Termination

    When a stop codon reaches the A site, no tRNA matches it. A release factor, a protein shaped like a tRNA, binds instead, and the chain is cut from the last tRNA and released. The subunits separate and are used again.
Translation
A bacterial ribosome in section, reading a messenger RNA that runs across the picture: the small subunit below, holding the mRNA, with its E, P and A sites marked from left to right and the decoding centre under the A site, and the large subunit above, with the peptidyl transferase centre on its underside and an exit tunnel running up through it. First, the initiator tRNA stands on the start codon in the P site, holding the first amino acid, formylmethionine in bacteria; the A site is empty. Next, a second tRNA comes in from the right with its amino acid, held by EF-Tu, a pale green protein carrying an orange GTP: its anticodon pairs with the codon in the A site while its body still leans out. Then EF-Tu has gone and the methionine has been joined to the second amino acid: the short chain hangs from the tRNA in the A site, and both tRNAs lean to the left, their anticodons still on their codons. Next, EF-G, a deeper green protein with its GTP, by now split to GDP, stands in the A site; the tRNAs have moved on to the E and P sites, and the mRNA has moved one codon to the left. Then, many rounds later, a longer chain runs up the tunnel from a tRNA in the P site, and a release factor, a dark green protein shaped like a tRNA, sits in the A site on a stop codon. Last, the chain has been cut from the tRNA and is free. Step 1 of 6: Start. The small subunit and the initiator tRNA, carrying methionine (formylmethionine in bacteria), find the start codon, AUG, and the large subunit joins. The initiator tRNA sits in the P site; the A site is empty.EPA

Step 1 of 6Start. The small subunit and the initiator tRNA, carrying methionine (formylmethionine in bacteria), find the start codon, AUG, and the large subunit joins. The initiator tRNA sits in the P site; the A site is empty.

Point at a name or a part to light it.

A ribosome reads an mRNA one codon at a time: a tRNA brings each amino acid, the large subunit's rRNA joins it to the chain, and the tRNAs and the mRNA move on. At a stop codon a release factor frees the finished chain.

Simplified: a bacterial ribosome drawn; ours is larger and its factors have other names, but it works in much the same way; not to scale: the tRNAs and codons drawn as wide as each other, EF-Tu and EF-G as plain shapes, the release factor as a tRNA's outline; the mRNA drawn as a row of plain bases without letters, so the start and stop codons look like any other; the tRNAs drawn as flat cloverleaves, though each is folded in three dimensions; the tRNA's swing into the A site and the peptide bond drawn as one step; the two centres drawn as patches beside the tRNAs, though the tRNAs' ends and the release factor's tip reach into the peptidyl transferase centre, and the codon–anticodon pair sits in the decoding centre; initiation shown only by its result, the initiation factors left out; the mRNA drawn moving through the ribosome, rather than the ribosome along it; many rounds skipped before the stop codon, the mRNA moved on only one codon for them; the recycling factor, and the tRNA, mRNA and subunits coming apart, left out.

3 sources
  1. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell, 4th edition. Garland Science, 2002. From RNA to Protein.
  2. Cooper GM. The Cell: A Molecular Approach, 2nd edition. Sinauer Associates, 2000. Translation of mRNA.
  3. UniProt. P68104, Elongation factor 1-alpha 1 (human).

Each amino acid costs at least four high-energy bonds: two from the ATP used to load its tRNA and two GTPs during elongation. In a fast-growing bacterium, making proteins uses more of the cell's energy than anything else. Many ribosomes read one mRNA at a time, one behind the other, as a polysome; a bacterial ribosome adds about 20 amino acids a second, ours a few.

Check yourselfAnswer, then say how sure you were: a lucky guess still counts as a weak point.

1Of the 64 codons, how many specify an amino acid?

2A tRNA with the anticodon for cysteine is loaded with alanine by mistake. What happens at the ribosome?

3What catalyses the formation of the peptide bond on the ribosome?

4How does a human ribosome usually find the start codon of an mRNA?

5How does diphtheria toxin kill the cells of the throat and heart?

Linked topicsThe concepts this topic shares, and the topics they tie it to.

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Bacterial ribosome

How a ribosome reads mRNA into protein.