Sorry if I seem twisted in knots. Biology has always had that effect on me.
Let me recommend an excellent book that will propel you miles ahead in understanding all the molecular chemistry that you are curious about: "How LIfe Works", by Mahlon Hoagland. It is just 200 pages long, but 2/3 of that is large pictures and diagrams. It is an easy one day read that could be understood by (almost) any sixth grader. This is not meant to demean anyone's intelligence. It is just written the way any science book should be written, getting to the heart of each topic and revealing its true simplicity. Check it out on amazon.com, where it costs about $20, but any decent city library should have a copy.
An important point to remember about genomes, chromosomes, and DNA is how extremely 'sloppy' they are; or as biologists prefer to phrase it: they are very, very plastic. Your body has about 50 trillion cells and the genomes of no two are identical. Every time cells in your body divide to make new cells or replace dead cells, there are a couple of dozen random point mutations in the 6 billion nucleotides in your genome. Every gene in your genome also occurs in hundreds or even thousands of other species, but it is very rare for the nucleotide sequence of any gene or for the amino acid sequence of the protein it codes for to be identical between any two species. Its like a Chevy and a Ford sedan: they both have pistons, fenders, rear seats, etc., but there are slight differences between the two that make them non-interchangable, even though they have the same basic shape (morphology) and serve the same function (physiology). But this sloppiness or plasticity is exactly what is needed for adaptation and survival in rapidly changing environments.
As far as the preponderance of 'junk' DNA, in recent experiments, researches have removed DNA segments of several million nucleotides from mouse genomes with no apparent effect on the mice when examined over several generations. There appears to be very little cost to an organism (at least a complex one) to carrying around a lot of excess, unused DNA, just as there is very little burden to an architect to carry a bunch of old, unused drawings in his trunk. Remember, every cell in your body has the genes to produce insulin, although only a small number of beta cells in your pancreas actually do so.
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