RNA for Dummies

So in coli, the ribosome binds to a Shine-Dalgarno sequence 4 to 7 nucleotides upstream from a start codon (AUG). The rRNA interacts directly with the SD sequence and positions the ribosome over the start codon for translation start. So, yes, if this were longer, it would interfere. Also, remember bacterial messages are polycistronic (many genes per mRNA), meaning that the ribosomes have to be able to tell different open reading frames apart. They depend on consensus sequence at the start site in order to do so.

In eukaryotes, it is similar, but the 40S subunit can scan before assembling with the 60S subunit in order to begin translation. A good example of how this works occurs in the GCN4 transcript of S. cerevisiae, but I won’t go into that because it is irrelevant.

Thanks, edwino about TRH, I suspected as much. But it makes me wonder if any polypetide chain is synthesized which is shorter than the length of the exit channel of the ribosome. If such polypeptide chains exist, how do they move through the ribosome?

All the short ORFs I know about are involved in regulation of gene translation. Basically, they act as a starvation sensor in the yeast GCN4 transcript and elsewhere. I will look up the lengths of these.