In bacterial (prokaryotic) mRNAs, the Shine–Dalgarno sequence serves what specific role during translation initiation?

Introduction / Context:
The Shine–Dalgarno (SD) sequence is a hallmark of prokaryotic translation initiation. Recognizing its function helps explain how ribosomes find the correct start codon, particularly in polycistronic mRNAs.

Given Data / Assumptions:

• Organism: bacteria (prokaryotes).
• Feature: SD sequence upstream of the start codon.
• We must identify its role in initiation.

Concept / Approach:

The SD sequence is a short, purine-rich stretch (often AGGAGG consensus) located a few nucleotides upstream of the AUG start codon. It base-pairs with the 3′ end of the 16S rRNA of the 30S subunit, positioning the start codon in the P site for accurate initiation with fMet-tRNA.

Step-by-Step Solution:

Verification / Alternative check:

Mutations weakening SD–rRNA pairing reduce initiation efficiency; strengthening it increases expression. Eukaryotes lack SD; they use 5′ cap-dependent scanning and Kozak consensus, underscoring the SD’s specific role in bacteria.

Why Other Options Are Wrong:

• Trailer sequence: refers to 3′ untranslated region, not the SD site.
• Stop codon: SD is not a termination signal.
• Reading frame definition: the start codon sets the frame; SD positions the ribosome but does not itself encode frame.

Common Pitfalls:

• Confusing SD with the Kozak sequence (eukaryotes).
• Thinking SD is at the 3′ end; it is upstream of the start codon near the 5′ coding region.

Final Answer:

It is a short purine-rich sequence that acts as a ribosomal binding site.