If my understanding is correct, during interphase a normal human cell will have 46 chromosomes scattered about in the cell nucleus. These chromosomes can be thought of as pairs: there are two copies of "chromosome 1", one from mom and one from dad. Same goes for chromosome 2, chromosome 3, ... chromosome 22. Although we think of these as coming in pairs, are they actually attached or paired up in some way?

At some point, protein synthesis will take place via transcription. What I'm having trouble understanding is how and when the above pairing takes place. Does transcription occur independently for each of the 46 chromosomes? I don't think this is the case, because in my head I imagine that we will only get one set of proteins from the pair of each chromosome. Also, I'm unclear as to how dominant/recessive genes can come into play unless protein synthesis occurs as a function of both pairs of chromosomes.

I hope this is clear enough. Thanks.

  • $\begingroup$ This is actually a quite complex question. No, they are not paired up in the nucleus but rather just scattered around. The exact 3D location of each chromosome in the nucleus is not fully understood yet and is believed to be a dynamic process. Transcription does not occur, strictly speaking, independently because similar genes will use similar transcription factors. Now another factor impacting gene expression is the chromatin state at the location of the gene which is not guaranteed to be the same between chromosome copies (i.e. could be independent). $\endgroup$ May 15, 2016 at 15:09
  • $\begingroup$ For dominant/recessive genes, the effect is not necessarily linked to gene expression but rather to the function of the protein. A recessive mutation disrupting the protein simply means enough functional proteins are made to conserve the biological function and vice-versa, if the same mutation was dominant then having a decreased level of the functional protein leads to a complete disruption of the overall biological function. $\endgroup$ May 15, 2016 at 15:13

2 Answers 2


Although we think of these as coming in pairs, are they actually attached or paired up in some way?

Chromosomes only pair up during metaphase I of meiosis. And meiosis only occurs during the production of gametes (sperm and oocytes). Say Chr1 from mom pairs up with Chr1 from dad. http://media.web.britannica.com/eb-media/76/94976-004-7D0416E7.gif

Mitosis is what happens when somatic cells (say in your toes) replicate. Chromosome (inherited from your mom and dad) do not pair up in mitosis. Instead each chromosome is replicated

You are probably confusing chromosomes pairs (one copy from mom and another from dad) sitting side by side... undergoing chromatid crossover... with sister chromatids (ie the same chromosome which has been duplicated, so each daughter cell can have its own copy.) This forms the X shape that you think off when imagining a chromosome.

Transcription occurs on all 46 chromosomes. Aside from situations where the gene is controlled by parental epigenetics... both the paternal and maternal copy of the gene is active.

As for recessive/dominant allele... it has more to do with the function of the protein. If the protein is produced by one allele in sufficient to give a normal phenotype, then the allele is dominant. A dominant negative tends to occur when the mutant allele codes for a mutant protein that can interfere with the normal function of the protein that is encoded. A common example is that the protein works as a pair. And is one member of that pair is mutated, the entire complex is non-functional.


About the chromosomes.

The chromosomes are not paired physically in the cell but yes, there is 23 chromosones, that have two copies of each, one from the dad, one from the mom. The homologous chromosomes are physically paired during meiosis, where cross-over of DNA will happen but only for a littel time.

About protein synthesis.

These are two cases in a recessive/dominant allele combination.

  1. Both synthesize the protein, but the protein from the dominant gene will have the effect and the other just won't be able to.

  2. The recessive gene transcription is blocked. The dominant can be the reason by synthesizing an inhibiting protein, or it could be a physical change to it's DNA etc.

This is only a small example since there is a large numbers of regulations that exists from the DNA, methylation of DNA, mRNA, transcription inhibition etc.


There is a lot more cases and exceptions since this is an extremely complicated subject. To learn all of them you would need a genetic book or a complete review on this subject.


Genetics (Book)

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation

Chromatin regulation at the frontier of synthetic biology

RNA-mediated epigenetic regulation of gene expression


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