I am reading Sean Carroll's "Endless forms most beautiful" and trying to understand genetic switches. I have trouble seeing the big picture of how it all works, tho the results are fairly clear.

It seems to me that homeoboxes are gene sequences (within genes) which express (I'm trying to use these terms correctly) protein domains which are transcription factors. The t-factors in turn bind to DNA regions which are genetic swtiches. Ok so far?

The switch then integrates the info from all the t-factors bound to it and returns a result of 0 or 1. (Aside: Can this be considered from an information perspective?)

Does the homeobox reside on the same gene it is regulating? I think not in general, but is it possible?

If the switch is far from the operon it is controlling, which it can be, at least according to all the bobby-pin-looking diagrams one sees on wikipedia, openstax, etc.. how does it "find" the operon it is controlling? And why is it so far away?

Why are the groups of homeobox genes in the same order as the body parts they control? Wouldn't it be easier just to have a separate hox gene for each part?

These are my first questions. I hope they show what it is I am trying to comprehend. If I can get the basics, I can probably figure out the rest.

Thanks in advance for your assistance.

P.S. I'm 75, so this is not a homework question. I was a physicist many years ago, so biology is quite new to me.

Hi,

A lot of your basic questions can be answered by having a read of the relevant Wiki articles.

Just want to comment on a few things, others might add to this:

Gene expression is never as simple as 0 or 1. Genes may be expressed at different levels or different times as well.

Protein-protein or protein-DNA interactions affect this and guide the right proteins to the right places for them to act.

In terms of why things are far away from each other unfortunately I don't have a straightforward answer but my guess would be that if there is DNA damage in one area  everything associated with a particular gene would be affected if everything was in the same area but because they're spread out there's a level of protection. Again others may have different perspectives.

a few points to note:
1. homeobox genes code for proteins that are transcription factors (TFs), each of which will bind to enhancer regions of other down-stream genes. each TF can therefore regulate the expression of multiple other genes - in terms of their levels, sites and timings. As said above this is not a binary on/off - the complete opposite is true and exquisite and subtle levels of regulation are possible between tissues, timings during development and differing genes.
2. the sequences in those downstream genes that are bound and thus regulated by the TFs can be within, up or downstream from those genes and in some cases may be hundreds of kilobases away - in other words long range regulation.
3. hox genes arose as a small number of primordial genes which were duplicated and then diverged. That is why often they are present as clusters rather than spread out over the whole genome. as above point 2 they can then regulate genes a long way away.