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Before anything else please pay attention of the double quotes on the "equal" in the title - I know they are not equal, but you will understand in a bit.

If I look at the DNA codon table here or in wikipedia, and at the RNA codon table here or in wikipedia, their only difference is that the former has thymine (T) whereas the latter has uridine (U). But I am not understanding how all other nucleotides are the same. Bear in mind that transcription reads DNA from 3'->5' and translation reads mRNA from 5'->3'.

Look at this example, focusing on the 3'-TAC-5' of the antisense strand.

enter image description here

The 3'-TAC-5' codes for Tyrosine according to the DNA codon table. However, it transcribes and translates 3'-TAC-5' -> 5'-AUG-3' -> Methionine.

Now focus on the corresponding codon in the sense strand, 5'-ATG-3', which codes for Valine according to the DNA table (it is read from 3' to 5'). This codon transcribes and translates 3'-GTA-5' -> 5'-CAU-3' -> Histidine, not Valine and not Methionine.

So my questions are:

  1. Why do DNA codon tables show the correspondence between codons and amino acids in the sense strands (5'-ATG-3'), if the only way to go from ATG to Met as in the figure is to consider the antisense strand?
  2. I can see that the AUG codon translates to Methionine, and it is translated by reading the 3'-TAC-5' codon in antisense strand, whose corresponding codon in sense strand is 5'-ATG-3'. But this last one is read from 3'->5', so it reads 3'-GTA-5' -> 5'-CAU-3' -> His.

I am guessing I'm getting many things wrongly in this... Maybe on the way that I'm reading the tables: I always take into account that transcription is read 3'->5' and this is the order I take to read DNA tables.

Thank you and sorry if I was confusing.

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  • $\begingroup$ Translation is done on the mRNA, not on the antisense strand, and it is done from 5' -> 3'. The first codon is AUG. This is a start code, and codes for methionine. Check this illustrated explanation out, too. $\endgroup$ – Jason C Nov 11 '14 at 13:12
  • $\begingroup$ Yes, I understand why AUG translates to Methionine. My question is on why do people refer to the ATG codon coding for Methionine if ATG -> UAC -> His. But I think the main message was that I was reading the tables as polimerase would, and this is not the right thing to do :) $\endgroup$ – Sosi Nov 11 '14 at 13:21
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    $\begingroup$ eh, now I understand that :) I was reading 5'-ATG-3' -> 3'-UAC-5' -> His because I was looking for the nucleotide order according to the transcription/translation order $\endgroup$ – Sosi Nov 11 '14 at 13:26
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I can understand your confusion but it all makes sense. The basic idea is that what we call the "antisense" strand is actually the one being transcribed. However, since that is in effect a mirror image, it is much simpler to think in terms of the sense strand.

To take a very simple example:

5' ATG 3' <-- sense strand
3' TAC 5' <-- antisense strand

The antisense strand will be read in a 3' to 5' direction:

3' TAC 5' <-- antisense strand
5' AUG 3' <-- mRNA

Since the mRNA is a mirror image, it has the sequence of the sense strand. It is this mRNA that is then translated and this is read in a 5' to 3' direction. So, AUG is translated as Met. To illustrate, have a look at this image from Wikipedia (click on it for a larger version),

                                                             protein translation animation

In the image above you can see the growing polypeptide (protein) chain snaking its way through the ribosome. The flying blue things are tRNA molecules and the black chain at the bottom is the mRNA being translated. You can't really see it very well in this image but if you look at the original you can clearly see it is moving from the right towards the left. The right hand side is the 5' end and the left is the 3'. Or, in a more static version (adapted from here):

       protein translation

So, the antisense strand is read, transcribed to RNA (which has the sequence of the sense strand but with T converted to U) and it is this mRNA which is read (in a 5' to 3' direction) to produce the protein.

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  • $\begingroup$ Thank you! But this raises another question in my mind. It seems kind of a "waste" to have the sense strand there if only the antisense is transcribed. Is the sense strand doing nothing more than stabilizing the DNA and wouldn't the same be achieved by having mRNA alone instead of DNA? $\endgroup$ – Sosi Nov 20 '14 at 10:15
  • $\begingroup$ @Sosi no, the double strands are essential for many things including i) DNA replication ii) error repair (the "right" sequence can be inferred from the opposite strand iii) most importantly, genes can be found on both strands. The sense/antisense is only with respect to a given gene. What is the sense strand for geneX can be the antisense for geneY. $\endgroup$ – terdon Nov 20 '14 at 13:11
  • $\begingroup$ Thank you! I see, I was misinterpreting and thinking that the sense strand was always the sense strand :) $\endgroup$ – Sosi Nov 20 '14 at 14:00
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Genetic code and codons are always used with reference to RNA. When talking about DNA, the the sense strand of a gene is considered its sequence. The anti-sense strand though is the template for mRNA synthesis, does not represent the gene.

DNA-codon table has simply U replaced by T. Apart from a wikipedia article, I don't find the term being popularly (not colloquially) used elsewhere.

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  • $\begingroup$ Maybe you'd like to add something about the reading of those tables not having to do with the reading direction of the polymerase? This seemed to have been my problem $\endgroup$ – Sosi Nov 11 '14 at 13:45
  • $\begingroup$ @Sosi The reading of those tables is directly related to the direction of the polymerase. The polymerase reads 5' to 3', translation happens in that direction too, and that is the direction the tables are read. $\endgroup$ – Jason C Nov 11 '14 at 13:49
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    $\begingroup$ @Sosi as I mentioned The anti-sense strand though is the template for mRNA synthesis, does not represent the gene. The direction of RNA polymerase movement is not a factor here. $\endgroup$ – WYSIWYG Nov 11 '14 at 13:54
  • $\begingroup$ @JasonC: Just for clarification — RNA polymerase reads 3'→ 5' but produces 5'→ 3'. $\endgroup$ – WYSIWYG Nov 11 '14 at 13:54
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    $\begingroup$ @Sosi.. No RNAP reads a 3'→ 5' strand (with 3'-…-TAC-…-5') and produces a 5'…-AUG-…-3' mRNA. And note that RNA synthesis does not start at ATG (it is the protein synthesis). $\endgroup$ – WYSIWYG Nov 11 '14 at 14:46

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