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.
So, the problem here is you’re thinking these things are “decided” when, really, it’s always happening and when things are “needed” they’re used and when they’re not they’re recycled.
It’s all just a question if electrochemical gradients and different concentrations of molecules.
For example, let’s say I have a system for sorting different size balls into hoppers where I take a slanted surface and punch holes in it of different sizes. Up near the top are 1″ holes, in the middle are 3″ holes, and near the bottom are 6″ holes. I then pour a continuous stream of mixed balls of those sizes down the ramp. The 1″ balls fall in first, then the 3″ balls, then the 6″ balls.
Eventually, the hoppers fill up to the point they’re clogging the holes and then no more balls fall so all the balls just keep running to the bottom of the ramp where they’re caught and recycled.
So then someone empties the 1″ hopper and the 1″ balls can start to fall again.
Physiological processes work in much the same way. Cells are just a bunch of assembly lines that interact with each other to create complex systems. One system might make the 1″ balls, another the 3″, etc. Then another system moves the bin from one to the next to collect them all. Then another system pours them down the ramp, and another system detects when the hoppers are full and moves them to pass on to another system that uses that size ball.
Those systems just work at the same thing all the time and if the system is super saturated there might be a system in place to trigger production to slow or stop. If it’s under saturated to speed up. If it’s chronically undersaturated it might trigger a system to build more of the systems that produce the balls. That can cause problems if levels later return to normal but you have developed these systems to overproduce things and it might take too long for them to be reversed and you could die before that’s possible unless you get more of what was needed and slowly taper off. That’s why quitting some drugs cold turkey can be dangerous, for example.
Sorry I didn’t answer your points one by one but it wouldn’t let me copy the text on my phone and I didn’t want to figure out a way to flip back and forth, so I thought it better to just address the underlying misconception/lack of information that was at the root of these questions.
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.
“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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