Gene Translation: RNA -> Protein

The problem: How does a particular sequence of nucleotides specify a particular sequence of amino acids?

The answer: by means of transfer RNA molecules, each specific for one amino acid and for a particular triplet of nucleotides in mRNA called a codon. The family of tRNA molecules enables the codons in a mRNA molecule to be translated into the sequence of amino acids in the protein.

This image shows the structure of alanine transfer RNA (tRNA^ala) from yeast. It consists of a single strand of 77 ribonucleotides. The chain is folded on itself, and many of the bases pair with each other forming four helical regions. Loops are formed in the unpaired regions of the chain. (The bases circled in blue have been chemically-modified following synthesis of the molecule.)

At least one kind of tRNA is present for each of the 20 amino acids used in protein synthesis. (Some amino acids employ the services of two or three different tRNAs, so most cells contain as many as 32 different kinds of tRNA.) The amino acid is attached to the appropriate tRNA by an activating enzyme (one of 20 aminoacyl-tRNA synthetases) specific for that amino acid as well as for the tRNA assigned to it.

      Anticodon:  3' CGA  5'
      Codon:      5' GCU  3'

The RNA Codons

Note:

• Most of the amino acids are encoded by synonymous codons that differ in the third position of the codon.
• In some cases, a single tRNA can recognize two or more of these synonymous codons.
• Example: phenylalanine tRNA with the anticodon 3' AAG 5' recognizes not only UUC but also UUU.
• The violation of the usual rules of base pairing at the third nucleotide of a codon is called "wobble"
• The codon AUG serves two related functions
  • It begins every message; that is, it signals the start of translation placing the amino acid methionine at the amino terminal of the polypeptide to be synthesized.
  • When it occurs within a message, it guides the incorporation of methionine.
• Three codons, UAA, UAG, and UGA, act as signals to terminate translation. They are called STOP codons.

The Steps of Translation

1. Initiation

• The small subunit of the ribosome binds to a site "upstream" (on the 5' side) of the start of the message.
• It proceeds downstream (5' -> 3') until it encounters the start codon AUG.
• Here it is joined by the large subunit and a special initiator tRNA.
• the initiator tRNA binds to the P site on the ribosome.
• In eukaryotes, initiator tRNA carries methionine (Met). (Bacteria use a modified methionine designated fMet.)

2. Elongation

• A tRNA able to base pair with the next codon on the mRNA arrives at the A site on the large subunit of the ribosome.
• The preceding amino acid (Met at the start of translation) is covalently linked to the incoming amino acid with a peptide bond (shown in red).
• The initiator tRNA is released from the P site.
• The ribosome moves one codon downstream.
• This shifts the more recently-arrived tRNA, with its attached peptide, to the P site and opens the A site for the arrival of a new tRNA.
• The last three steps are promoted by a protein elongation factor named EF2.

Note: the initiator tRNA is the only member of the tRNA family that can bind directly to the P site. The P site is so-named because, with the exception of initiator tRNA, it binds only to a peptidyl-tRNA molecule; that is, a tRNA with the growing peptide attached.

The A site is so-named because it binds only to the incoming aminoacyl-tRNA; that is the tRNA bringing the next amino acid. So, for example, the tRNA that brings Met into the interior of the polypeptide can bind only to the A site.

3. Termination

• The end of the message is marked by one or more STOP codons (UAA, UAG, UGG).
• No tRNA molecules have anticodons for STOP codons.
• However, a protein recognizes these codons.
• Binding of this protein releases the polypeptide from the ribosome.
• The ribosome splits into its subunits, which can later be reassembled for another round of protein synthesis.

Polysomes

Summary

• transcription of the information encoded in DNA into a molecule of RNA (discussed in Gene Expression: Transcription) and
• translation of the information encoded in the nucleotides of mRNA into a defined sequence of amino acids in a protein (discussed here).

In eukaryotes, the processes of transcription and translation are separated both spatially and in time. Transcription of DNA into mRNA occurs in the nucleus. Translation of mRNA into polypeptides occurs on polysomes in the cytoplasm.

In prokaryotes (which have no nucleus), both these steps of gene expression occur simultaneously: the nascent mRNA molecule begins to be translated even before its transcription from DNA is complete.