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.