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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“1. What sort of signal “prompts” the process of protein synthesis”
There are sensor proteins of whom only function is to monitor the presence (or too high level) or absence (or too low level) of certain chemicals. Such as presence of sugar, too low level of an amino acid, presence of a hormone etc.
The whole internal and external status of the cell is monitored this way, and the summary of all these signals tell the cell what it needs to do. We have sugar, we have all amino acids, we have growth hormone: ready to divide.
“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”
Aforementioned sensor proteins give their signal away to proteins called transcription factors (TF), or sometimes they are already TFs. So a TF is basically a secondary signal protein that gets activated (or inactivated) by the primary signal. But they are also summarizing/integrating primary signals. So everything that happens in the cell eventually goes down to the level of TFs.
A TF is capable of binding DNA and when bound they can recruit gene expression machinery. The trick is that the TF is not going to any random spot on the DNA, it can bind to only a specific spot, lets say a sequence of TTATGGCA. And it only binds when it’s activated first.
So every gene has parts to bind TFs. The gene can only start making the protein if the TF comes, because the TF is the only thing that can attract the gene synthesis machinery. So basically the logic is that every gene that is part of the same pathway (let’s say sugar catabolism), they all have a binding sequence for the involved TF.
So: sugar (primary signal) > sensor proteins > activating transcription factors > DNA binding > gene synthesis
“How does this part “know” which sequences correlate to which proteins”
As I mentioned before, the DNA has binding sequences for TFs. So if you imagine a piece of DNA, it has the genes on it. A gene is just a functional part on the DNA. But the gene does not only consist of the strict-sense protein coding part, in fact it always has to tell when and how much of the protein is needed, which is exactly done by TF binding sites.
This is how the cell knows which protein to express any given time.
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