So I’ve got a few, step by step questions about this process of protein synthesis:
1. What sort of signal “prompts” the process of protein synthesis for a certain protein—say a cell needs some Protein X made, how does it “tell” the related parts to start the process of producing that protein?
2. What part of the cell is responsible for figuring out where, in all of the genes around it, to go in order to start the process of making a specific requested protein (Protein X, in this case)?
3. How does this part “know” which sequences correlate to which proteins are requested, and therefore “know” where to target in order to start the protein’s creation? For example is it able to “read” and decode gene sequences by itself (I want to say “mentally” even though that word wouldn’t really apply here, but basically “reading” DNA without having to do it as part of a translation process) until it finds a sequence that translates to the proper code for a protein? Or is it fully just pre-programmed targeting—and if that’s the case how does *that* work then?
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The “targeting” is not really as specific as you are imagining. A cell does not detect that it needs more Protein X and “put in an order” for more Protein X specifically.
What there is most similar to what you’re thinking (although not the only part), is [“transcription factors”](https://en.wikipedia.org/wiki/Transcription_factor) which are proteins with a “DNA binding domain”, which means they attach to certain sequences. Once attached they can increase or decrease the transcription of that protein, by making it more or less likely for RNA polymerase to bind to that part of the DNA.
So the process is more like:
1. Cell “detects” a lack of something (usually not the lack of protein directly, it’s probably more like, lack of calcium ions or some signaling molecule)
2. Some signal from step 1 activates (or deactivates) specific transcription factor proteins in the cell
3. They start (or stop) binding to semi-specific parts of DNA.
4. This might directly increase or decrease transcription, or it might cause acetylation or deacetylation of histone proteins, or it might cause other proteins to bind to the DNA to make something else happen.
5. Protein levels change, which causes some kind of negative feedback to step 1 that stabilizes everything.
There are *many* other possible options too, in terms of “how” a cell can respond, other than just changing transcription:
1. Increase or decrease protein degradation
2. Increase or decrease RNA degradation (RNA sticks around longer = more protein made from it)
Possibly the big misunderstanding in your post though is that things in a cell don’t “go looking” for stuff. Everything is sloshing around somewhat randomly (though sorted in “compartments”, ish), and the things modify the chances that stuff “sticks together” when they happen to bump into each other, or otherwise changes the chances that something happens.
RNA polymerase is “bumping into” DNA all over the place constantly. Huge numbers of different mechanisms and feedback loops control/adjust what happens when it does.
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