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The process of translation starts with the initiator tRNA identifying the codon coding for methionine (AUG). However, my textbook also says that there are various untranslated regions present on the mRNA. It was then that this question had occurred to me. How does the tRNA actually differentiate between the regions that are ought to be coded and that are not? One may say that translation always start with the methionine, but my question is different. For example, if the code is

5'...GUAUGCAUGAUC...3'

then when the tRNA arrives, it reads from which of them? Does it leave the first two nucleotides and read it as AUG CAU GAU and so on or does it leave out the first six nucleotides and read it as AUG AUC and so on?

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    $\begingroup$ I suggest you read further in your text book or consult a better textbook if necessary (look at NCBI Bookshelf on line) before posting here. Be advised that the answer is different in prokaryotes and eukaryotes. $\endgroup$
    – David
    Feb 9, 2017 at 19:47

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There are different processes for recognising the initiator site in prokaryotes and eukaryotes.

In prokaryotes the process relies upon the Shine-Dalgarno sequence, this is a well conserved sequence throughout prokaryotes found upstream of the start codon. It interacts with the 16s ribosomal RNA to place the initiator codon in the A site of the ribosome.

In eukaryotes the process is somewhat more complex and relies upon a large protein complex which assembles on the 5' cap of mRNAs. This complex mediates an interaction between the mRNA and the ribosome, the ribosome then scans (using GTP for energy) 5' to 3' to detect the start codon.

One final process which is unusual but does occur is cap independent initiation mediated by internal ribosome entry sites (IRES). These are sequences which form structured loops which can mimic the interactions usually formed by the cap complex. These sequences appear in viral mRNAs allowing viruses to bipass anitviral mechanisms in cells.

You will need to do some reasonably extensive reading if you want to uderstand fully these processes and how they may be manipulated by cells to alter expression.

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    $\begingroup$ To explain this to a beginner, rather than encouraging him to do some more reading, I would leave out IRES and instead correct your description of eukaryotic initiation, which does not involve placing the AUG in the correct position but involves scanning from the cap to the first AUG in a suitable context. $\endgroup$
    – David
    Feb 9, 2017 at 21:38
  • $\begingroup$ @david I have adjusted as suggested I felt that introducing scanning left the obvious question, how does the ribosome know when it has reached the start codon? However upon your advice I have altered the answer. I have included IRES as these are important in viral infection and will point the reader to literature which could help understand the regulation of eukaryote initiation. $\endgroup$
    – Jakob45
    Feb 9, 2017 at 22:04

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