Molecular and Cell Biology - Translation

Shine–Dalgarno sequence

A sequence in bacterial mRNA that base-pairs with rRNA in the small ribosomal subunit, positioning the start codon correctly.

Bacterial initiation sequence

The small subunit recognizes the Shine–Dalgarno sequence → the start codon is positioned → initiator fMet-tRNA enters the P site → the large subunit joins.

fMet

N-formylmethionine, the amino acid used by the initiator tRNA to begin bacterial protein synthesis. It distinguishes bacterial initiation from standard eukaryotic initiation.

Why is initiator tRNA placed in the P site?

The initiator tRNA is positioned directly at the start codon in the P site. The next aminoacyl-tRNA can enter the A site, allowing peptide-bond formation to begin in the correct order.

Eukaryotic initiation sequence

Initiation factors and the small ribosomal subunit recognize the 5′ cap; the small subunit scans along the mRNA to an appropriate AUG; initiator methionine-tRNA pairs with the start codon; the large subunit joins.

How does initiation differ?

Bacteria typically use Shine–Dalgarno base-pairing to position the ribosome near the start codon and use fMet-tRNA. Eukaryotes commonly recruit the small subunit to the 5′ cap and scan for AUG, using initiator Met-tRNA.