The starting amino acid in eukaryote protein synthesis is methionine, while in prokaryotes it is N-formyl methionine. The tRNA molecule3 specific for these two amino acids are methionyl tRNA (tRNAmet) and N-formyl- methionyl IRNA (tRNAfmet) respectively.
These tRNAs are called initiator tRNAs, because they initiate protein synthesis. Initiator tRNAs have certain features which distinguish them from other tRNAs, and the initiator tRNAs of prokaryotes' and eukaryotes also differ.
In most prokaryotes the 5' terminal nucleoside is C. It has opposite it (i.e. in the fifth position from the 3' end) an A nucleotide. There is no Watson-Crick base pairing between the two. In the blue green 'alga' Anacystis nidulans, however, the fifth nucleotide from the 3' end is C. In eukaryotes there is an A.U base pair at the acceptor stem.
As noted previously, prokaryotes use tRNAf-met for initiation of protein synthesis, while eukaryotes use tRNAmet. The prokaryote Halo bacterium cutirubrum is, however, reported to initiate protein synthesis with tRNA met and has an A.U base pair at the end of the accept or stem. In these respects it resembles eukaryotes
The D loop of prokaryote initiator tRNAs contains an A11, U24 base pair. All other tRNAs have a Y11, R24 base pair. Eukaryotic cytoplasmic initiator tRNAs have AU or AU* instead of Tψ in the TψC loop. Also, in eukaryotes instead of a pyrimidine nucleotide (Y) there is A at the 3' end of the TψC loop.
In some eukaryotic cytoplasmic initiator tRNAs the anticodon sequence CAU is preceeded by C instead of U as in all other tRNAs.In prokaryotes the purine nucleotide following C in the TψC loop is A, while in eukaryotes it is G. In tRNA f-met the nucleotide adjacent to the 3' side of the anticodon triplet is adenosine while in tRNA met it is alkylated adenosine.
