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I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA".

I'm just an interested layperson but I thought all combinations of three base pairs encoded one amino acid, with some amino acids being encoded by more than one combination of base pairs.

But if that were true then all of our DNA would encode something.

Or if only a tiny percentage of our DNA is "coding" that would mean that the vast majority of possible combinations of three base pairs don't represent any amino acid.

Or it could mean that there are a small number of "meaningless" combinations of three base pairs, but that those combinations are vastly overrepresented in our genome.

Which is correct? What am I missing?

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Would anyone like to add junk-dna and/or noncoding-dna (or should that be non-coding-dna tags? I barely have enough rep here to breathe (-: – hippietrail Sep 7 '12 at 10:42
Wikipedia has a well-written page on the genetic code with tables and pictures showing all the possible triplets and their meaning! – nico Sep 7 '12 at 11:06
@Hippietrail To the meta!!!! – bobthejoe Sep 7 '12 at 18:28
up vote 4 down vote accepted

You are correct in thinking that any sequence of bases corresponds, via the genetic code, to a sequence of amino acids. However not all stretches of DNA are actually transcribed into mRNA for translation into proteins. For this to happen the stretch of DNA requires (DNA-encoded) elements to promote and regulate the transcription and translation processes, and this, very broadly, is what defines a gene: a segment of DNA which has the required components to direct the synthesis of a protein (or in some cases an RNA that will not be translated into a protein). The segments of DNA that correspond to mRNA for proteins and to other RNA molecules are referred to as coding sequences.

Now, I've omitted lots of details here: some genes encode RNA molecules, such as ribosomal RNAs, which are not translated into proteins; eukaryotic genes include stretches of sequence (called introns) that are spliced out of the transcript before the mRNA>protein step. The original definition (if there ever was a definition) of "junk" DNA included these introns, as well as regions of DNA lying outside the coding sequences. We now know that there is useful information stored in much of this DNA, even though it doesn't code for anything directly via the genetic code.

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Hmm @DanielStandage 's answer got more votes but AlanBoyd your answer here answers my actual question. Both answers are full of interesting stuff but this is the one I'm accepting. – hippietrail Sep 7 '12 at 18:39

You bring up a good point. "Coding" is a term that obviously carries some historical baggage that is gradually becoming less and less relevant. "Coding DNA" has typically been used to refer to DNA that encodes one or more functional protein products, which are constructed from an mRNA intermediate. As we've been learning over the last several years (and as was confirmed by the recent release of 30+ coordinated, high-profile publications from the ENCODE project), DNA that is not "coding DNA" is not "junk" or "meaningless"--it simply does not, to our knowledge, encode a protein. There is still a lot to learn about what precisely the function and purpose of this DNA is, but we do know that a lot of it is transcribed into RNA and that a lot of it has been associated with human disease.

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Yes I put "junk" in scare quotes precisely because it's not really junk. So while I knew it wasn't junk I wanted to know a bit more deeply what non-coding DNA is. It seems that the terms "coding" etc are ambiguous if my understanding is right. – hippietrail Sep 7 '12 at 10:31
@hippietrail Agreed. A lot of what is sometimes called "non-coding DNA" indeed encodes something...just not a protein! We're definitely going to have to revisit our terminology as a community, but that is a slooooow process. Case in point: "junk DNA" is still commonly used. :-/ – Daniel Standage Sep 7 '12 at 10:36

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