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I am trying to solve an exercise.

How many nucleotides does a gene contain if information about 287 amino acids is encoded in it? What is the molecular mass and length of this gene?

AFAIK, I have to consider two DNA chains to find molecular mass, and one DNA chain to find the length of the gene (am I right here?).

But I am stuck trying to find how many nucleotides are there in a gene. Should I consider both or only one DNA chain? I suppose that both (as for the molecular mass of the gene) but I am not totally sure.

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    $\begingroup$ This is a bad question from two perspectives. First, counting either one or two strands are equally correct or incorrect as there is nothing in the definition of a gene that specifies strandedness ( or even DNA). Second, the length of a gene is always longer than the DNA needed to encode the amino acids. All mRNAs have 3' and 5' non-coding regions of varying length, and, of course, there is always a stop codon. I approve of making students do calculations. I disapprove of questions that are biologically stupid. $\endgroup$
    – David
    Dec 14, 2020 at 16:46
  • $\begingroup$ @David, thank you very much for your reply. I agree with you. But this is exactly the question asked by my school teacher. Actually, these nuances are why I got stuck with this exercise. $\endgroup$
    – Demian Wolf
    Dec 14, 2020 at 16:57
  • $\begingroup$ Only your teacher can decide what the "right answer" is to their poorly thought out question. Either consult with them directly to find out what they want or give multiple answers and state clearly what assumptions you are making for each answer. Something like "If I assume that the gene only consists of an open reading frame and is single stranded then my answer is ###. However, if it is double stranded then my answer is #### etc." This has the advantage that you might be able to teach them ... $\endgroup$
    – tyersome
    Dec 14, 2020 at 18:46
  • $\begingroup$ @tyersome, thank you for the advice. I have written exactly that way) $\endgroup$
    – Demian Wolf
    Dec 14, 2020 at 19:13

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Counting both strands is admirably correct, but most people will multiply the number of amino acids by three, not six. For example, nucleotide positions in a reference sequence will increase by 3 for each amino acid in the presumptive coding sequence. Besides, if you want to be that pedantic, you should say zero, since the DNA contains nucleotide residues, not individual nucleotides, as they have undergone dehydration synthesis. I think in biology the right answer will almost never be marked correct by a machine. :)

The answer you come up with will also be influenced by whether you would like to include a stop codon (+3) to avoid nonsense-mediated degradation, and a transcriptional start site and polyadenylation sequence (in eukaryotes). The ''gene'' itself, in the genetic sense, will include enhancer elements over a much longer region of the chromosome and regulatory 3'-untranslated regions. And then there's alternative splicing to consider...

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  • $\begingroup$ Thank you very much. I understand now :) You've helped me a lot! $\endgroup$
    – Demian Wolf
    Dec 14, 2020 at 15:55
  • $\begingroup$ In fact, counting the nucleotides only one chain is mathematically the correct answer! The second chain does not contain any new information, since it is unambiguously determined by the first chain. On the other hand, the second chain does contain additional mass. $\endgroup$
    – Roger Vadim
    Dec 15, 2020 at 9:15
  • $\begingroup$ Well, you could have a mismatch. The mRNA produced will use the complement of the base on the template strand, unless mismatch repair alters it to match the coding strand. All six positions therefore may contain some information about the amino acid. $\endgroup$
    – Mike Serfas
    Dec 19, 2020 at 15:36

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