Animation of Protein Synthesis (Translation) in Prokaryotes.

Initiation of translation in prokaryotes:

The small ribosomal subunit is separated from the large subunit with the help of two initiation

factors: IF1 and IF3. This complex then binds a to purine-rich region -- the Shine-Dalgarno

sequence -- upstream of the AUG start codon on the mRNA. The Shine-Dalgarno sequence is

base-paired to a complementary sequence on the 16S rRNA - a component of the small subunit.

This alignment ensures that the start codon is in the right position within the ribosome.

Another initiation factor - IF2 - brings in the initiator tRNA charged with the initiator

amino acid N-formyl-methionine. The large ribosomal subunit joins the complex and all

initiation factors are released. The ribosome has three sites: the A-site is the entry site

for new tRNA charged with amino-acid or aminoacyl-tRNA; the P-site is occupied by peptidyl-tRNA - the

tRNA that carries the growing polypeptide chain; the E-site is the exit site for the

tRNA after it's done delivering the amino acid. The initiator tRNA is positioned in

the P-site. Elongation: A new tRNA carrying an amino acid

enters the A-site of the ribosome. On the ribosome, the anticodon of the incoming tRNA

is matched against the mRNA codon positioned in the A-site. During this proof-reading,

tRNA with incorrect anticodons are rejected and replaced by new tRNA that are again checked.

When the right aminoacyl-tRNA enters the A-site, a peptide bond is made between the two now-adjacent

amino-acids. As the peptide bond is formed, the tRNA in the P-site releases the amino-acids

onto the tRNA in the A-site and becomes empty. At the same time, the ribosome moves one triplet

forward on the mRNA. As a result, the empty tRNA is now in the E-site and the peptidyl

tRNA is in the P-site. The A-site is now unoccupied and is ready to accept a new tRNA. The cycle

is repeated for each codon on the mRNA. Termination: Termination happens when one

of the three stop codons is positioned in the A-site. No tRNA can fit in the A-site

at that point as there are no tRNA that match the sequence. Instead, these codons are recognized

by a protein, a release factor. Binding of the release factor catalyzes the cleavage

of the bond between the polypeptide and the tRNA. The polypeptide is released from the

ribosome. The ribosome is disassociated into subunits and is ready for a new round of translation.