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I am not a biology expert but I have done some homework on understanding alleles, chromosomes, dna in the human genome. Still baffled by a question though:

As I understand it at a particular locus for e.g. if a human has a A on one chromosome and a G on another that individual is considered Heterozygous at that locus because of the difference in the nucleotides (A/G in this case).

However, my question is. What about an individual that has an A on the 3' -> 5' strand (and hence a complement T on the 5'-> 3' strand) on one chromosome but T on the 3'-> 5' (and its complement on the other strand) on the other chromosome. Is this individual considered heterozygos or homozygous?

Basically my question boils down to does the "directionality" of the A-T pairing matter on both chromosomes?

I was thinking it should as only one strand can code for genes which the other doesn't so it should matter whether the A is on the (3'-5') or on the other strand..

Any advice would be great!

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  • $\begingroup$ As @Nicolai's answer suggests, when you are thinking about coding genes, you should really just think about one strand at a time. Also note that zygosity is normally considered at the gene/allele level, as far as I know, people rarely talk about "zygosity" for a particular base pair, especially because single base changes don't always have an impact on the protein produced. (someone who does more genetics might disagree with me) $\endgroup$ – Bryan Krause Jul 22 '17 at 22:43
  • $\begingroup$ Thanks Bryan. I did accept @Nicolai's answer. However, I am not sure I understand what you mean by "Zygosity at a gene/allele level". Per my understanding a gene is just a certain sequence of nucloetides on a strand and allele's are just different "versions" of the same gene present on different chromosomes. So, I thought zygosity has to do with variances in nucleotides on different chromosomes. $\endgroup$ – HakunaMaData Jul 22 '17 at 23:13
  • $\begingroup$ crossposted on biostars.org: biostars.org/p/264076 $\endgroup$ – Pierre Jul 22 '17 at 23:14
  • $\begingroup$ @Shanbhag Yes, it does, I'm just saying that "allele" and zygosity has whole-gene connotations. If you are talking about alleles for just a single base pair, you are implying that there is no variation in any of the other base pairs. Also, alleles that are actually different at the base pair level but produce no phenotype in any combination might be grouped all as "wild type" alleles. It's just a different level of analysis in most contexts. $\endgroup$ – Bryan Krause Jul 22 '17 at 23:47
  • $\begingroup$ @BryanKrause When talking about SNPs zygosity or at least the terms homozygous/heterozygous are usually also used. I guess depending on ones background the connotation of zygosity with genes might differ $\endgroup$ – Nicolai Jul 23 '17 at 9:53
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The directionality of the strands matters, because genes can be encoded on both strands of a chromosome (each strand can be read in 3'-5' direction by RNA polymerase). Therefore someone with the A-T case you described is also heterozygous.

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