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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Say someone takes some testosterone, which goes into a cell and makes its way into a nucleus. It binds to a testosterone receptor protein that is bound to certain sites on DNA near genes for proteins that are controlled by testosterone. The testosterone receptor only binds specific DNA sequences. How does the receptor bind only specific DNA sequences? It is folded in just the right shape to interlock with only those unique DNA sequences. The receptor changes shape when it binds testosterone, which allows it to bind other proteins that make chemical changes to the tightly wound inactive form of DNA that contains the gene of interest. These modifications of the chromatin will in turn be recognized by enzymes that will unwind the DNA and make it accessible to complexes that will transcribe the gene into mRNA (which will then be translated to protein).
That’s a feel for how it would work in one case. A lot comes down to the idea of proteins (called transcription factors) that – like you said – bind specific sequences of DNA that control the expression of specific genes. But there can also be effects at the mRNA level, like degradation of mRNA by certain proteins that target certain sequences of mRNA. Almost every step in the overall process of gene transcription is subject to some kind of regulation.
There are general trends but it can be tweaked in many ways. In some sense everything in biology converges on regulation of gene expression, understanding all the nuances involved in the expression for just one protein is enough for a lifetime of study.
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