DNA Translation

Translation begins with the binding of the small ribosomal subunit to a specific sequence on the mRNA chain. The small subunit binds via complementary base pairing between one of its internal subunits and the ribosome binding site, a sequence of about ten nucleotides on the mRNA located anywhere from 5 and 11 nucleotides from the initiating codon, AUG.

Once the small subunit has bound, a special tRNA molecule, called N-formyl methionine, or fMet, recognizes and binds to the initiator codon. Next, the large subunit binds, forming what is known as the initiation complex. With the formation of the initiation complex, the fMet-tRNA occupies the P site of the ribosome and the A site is left empty. This entire initiation process is facilitated by extra proteins, called initiation factors that help with the binding of ribosomal subunits and tRNA to the mRNA chain.

With the formation of the complex containing fMet-tRNA in the peptidyl site, an aminoacyl tRNA with the complementary anticodon sequence can bind to the mRNA passing through the acceptor site. This binding is aided by elongation factors that are dependent upon the energy from the hydrolysis of GTP. Elongation factors go through a cycle to regenerate GTP after its hydrolysis.

Now, with tRNA bearing a chain of amino acids in the p site and tRNA containing a single amino acid in the A site, the addition of a link to the chain can be made. This addition occurs through the formation of a peptide bond, the nitrogen-carbon bond that forms between amino acid subunits to form a polypeptide chain. This bond is catalyzed by the enzyme peptidyl transferase.

The peptide bond occurs between the carboxyl group on the lowest link in the peptide chain located at the p site and the amine group on the amino acid in the A group. As a result, the peptide chain shifts over to the A site, with the original amino acid on the A site as the lowest link in the chain. The tRNA in the A site becomes peptidyl RNA, and shifts over to the P site. Meanwhile, the ribosome engages in a process called translocation: spurred by elongation factors, the ribosome moves three nucleotides in the 3' prime direction along the mRNA. In other words, the ribosome moves so that a new mRNA codon is accessible in the A site. With the A site open again, the next appropriate aminoacyl tRNA can bind there and the same reaction takes place, yielding a three-amino acid peptide chain. This process repeats, creating a polypeptide chain in the P site of the ribosome. A single ribosome can translate 60 nucleotides per second. This speed can be vastly augmented when ribosomes link up to form polyribosomes.

Translation ends when one of three stop codons, UAA, UAG, or UGA, enters the A site of the ribosome. There are no aminoacyl tRNA molecules that recognize these sequences. Instead, release factors bind to the P site, catalyzing the release of the completed polypeptide chain and separating the ribosome into its original small and large subunits.

Remember that only eukaryotes, and not prokaryotes, underwent post- transcriptional RNA modifications. These modifications are responsible for one difference between prokaryotic and eukaryotic translation. Whereas prokaryotic initiation, which we have just covered, begins with the ribosomal recognition of the ribosome binding site on the mRNA, eukaryotic initiation begins with the ribosomal recognition of the 5' cap. Eukaryotic mRNA need not contain a ribosome binding cap because the post-transcriptionally added 5' cap suffices for recognition. Once the eukaryote ribosome binds to the mRNA, further differences appear. Whereas in prokaryotes the initiator codon can be either GUG or AUG, in eukaryotes the codon must be AUG. Additionally, the tRNA responsible for recognizing the initiator codon is not the special tRNA, fMet, but rather the normal met-tRNA.