What Darwin Never Knew: DNA

I just finished watching one of the best PBS NOVA episodes - "What Darwin Never Knew". It is exceptionally good. I was finally able to understand a little about DNA - the building blocks of all living creatures. In this episode they explain how evolution is happening and why there are so many species and why even animals from the same species look so different. How complex DNA is and what a gene is. It still did not answer all my questions but got pretty close. Here is one part I found on youtube, but please watch all parts. It is very good.



So now I know that DNA is a very large sequence and it contains genetic instructions to synthesize various parts of a living creature. In simple layman terms there are three kinds of genes identified so far

1. Genes that actually are used to create stuff. These are the sequences used to synthesize proteins and other things - the building blocks
2. Genes that simply act as switches which can be on or off. When on the "stuff" creating genes are used to create the stuff, when the switches are off the "stuff" is not created. The show provides an example of fruit flies. Why some of them have black spots on the wings while others don't. But have the same genes that makes the spots, but in some the switch is turned off
3. Genes that boss the switch genes. These are the ones that turn the switch genes on and off at various times. An example of this is the same bird species with same genes that creates the beak with the same switch genes, except the boss genes are different. So the switch genes are turned on at different times and the beaks of the birds are different (short and thick beak vs long and thin).

There is much more interesting stuff in there. However after seeing the show I still have a few questions. So the messenger RNA are created based on whether the switch is on or off. But how does that happen? Will the enzyme responsible for creating mRNA look at the switch? How does it "look"? Do the enzymes have sites that only lock on to the switch genes that are on? And then something happens from there on to make the enzyme use the genes to synthesize the mRNA or whatever? This means that the location of the switch genes should be close to the stuff making genes that they are controlling right?

Another question is how do the boss genes turn on and off the switches? What is the difference between an "on" gene and "off" gene? Probably the sequence. Then does it mean that the boss genes some how change the switch genes? I though a gene is an immutable entity. How can it change? Also how does the boss genes instruct the switch genes to change? Does it attract an enzyme of something to change the switch genes?

All these questions make me think I should probably study genetics or bio-engineering or something.