Re: Some questions about protein synthesis...

Spencer,

Before starting, I would like to clarify some of the terms regarding mRNA: the "transcription start site" is the site on the DNA, at which RNA polymerase begins to make the RNA message; the "translation start site" or "start codon" is the AUG triplet on the mRNA, at which the ribosome begins to translate the RNA message into a peptide; the "ribosomal binding site" is the sequence upstream of the start codon, to which the ribosome initially binds prior to translation. In eukaryotes, there is a 5' cap consisting of a 5'-5' 7methylGuanidine that can act as the ribosomal binding site, while most prokaryotes have a conserved Shine-Dalgarno sequence that directs ribosomal binding. Also, both eukaryotes and prokaryotes use Internal Ribosomal Entry Sequences (IRES: very common in prokaryotes; very rare in eukaryotes) that can direct binding of ribosomes to the start codons of multiple cistrons (genes) on a single message.

So, "what happens if the tag is missing?" If there is no ribosomal binding site, the mRNA is never translated - this is almost impossible in eukaryotes, since the 5' cap is added to all messages as part of the post- transcriptional processing carried out in the nucleus before the mRNA's are allowed to exit to the cytoplasm. On the other hand, the Shine-Dalgarno sequence was defined by its requirement for ribosomal binding to cistrons, so a prokaryotic mRNA without ribosomal binding sites would simply not be recognized by ribosomes. Also, ribosomes can only read RNA in one direction, 5' to 3', so it would be impossible for a message to be "run through backwards," unless it was an "antisense" message.

Your second question was the subject of a Nobel Prize in 1968, and is summarized as "the Genetic Code:"

Basically, only two of the twenty common amino acids, methionine and tryptophan, are coded for by single codons; in most cases there are groups of two to six codons for each amino acid. One of the more interesting aspects of the Genetic Code is that most of the groupings of codons involve variability in the third base of the codon. This has lead to the "Wobble Hypothesis", that the code may have originally involved fewer amino acids coded by 16 doublet codons with single base spacers between them. The theory suggests that as other amino acids became common, the spacers were used to usurp some of the codons away from the older amino acids (this is supported to an extent by the biosynthetic pathways of related amino acids). If you look at the table above, you'll see three stop codons , UAG, UAA, and UGA. These triplets do not code for amino acids, but instead tell the ribosome to stop translating the message. Based on early studies of tRNA's, if there is no tRNA anticodon that recognizes a specific codon (i.e. the codon does not code for an amino acid), then that codon can act as a terminator.

Hope this answers your questions, and keep 'em coming!

Michael Onken, MadSci Moderator