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Operons and gene regulation in bacteria

AP Bio: IST‑2 (EU), IST‑2.A (LO), IST‑2.A.1 (EK), IST‑2.A.3 (EK), IST‑2.B (LO), IST‑2.B.1 (EK), IST‑2.C (LO), IST‑2.C.1 (EK), IST‑2.C.2 (EK)

Video transcript

- [Voiceover] So we're gonna talk a little bit about DNA regulation. And this is the general idea that if you look at a organism's genome, that not all of the genes are being transcribed and translated at the same time. It could actually depend on the type of cell that that DNA is inside of, or it could depend on the environment for that organism. So for example, if you look at, say, a multicellular organism, this, maybe this is, and these are oversimplifications right over here, maybe this is type of immune cell, immune cell, and let's say that this over here is a muscle cell, and they're not necessarily, or not likely to be these perfect circles, but this is just for the idea. And they're going to have the exact same DNA. So the DNA in both of these is the same. So DNA is the same inside, and these are going to be, these are Eukaryotes, so I'll draw the nuclear membrane there, same DNA. But they have very different roles inside of this organism. So it doesn't make sense, in fact, in order for them to even have different structures, they're gonna have to produce different proteins. They're gonna have different enzyme proteins inside of their cytoplasm. And so DNA regulation, one way to think about it is, well if they have the exact same genome, how do they regulate which of those genes are being transcribed and then translated and which ones aren't? And even if you think about a unicellular organism. Right here we have a bacterium. And so it's just one cell, but even it will not want to transcribe and translate all of its genes at the same time. For example, this over here, so this is its, this is the bacterial chromosome. This right over here might be a gene involved in the digestion of a certain type of food, if that food is present. This type of, and actually it could even be several genes that are involved in that type of food, and we will actually talk, go into a little bit more detail about when you have several genes that are related and they tend to be transcribed all at once or not transcribed all at once. So maybe that's related to digesting or consuming some type of food. Maybe you have some genes over here that are related to some type of stress mechanism. Maybe it needs to go into hibernation some time. And so if it's not under stress, it does not have to express these genes, but if it is under stress, it does have to express these. Likewise, if that thing that needs to digest is around, it needs to transcribe these. If it's not around, it does not need to transcribe it. So that's how DNA regulation works, whether you're talking about a Eukaryote or a Prokaryotic organism. And so what we're gonna do in this video is focus a little bit more, or a lot more, on the Prokaryote side. Especially, we're gonna talk about this bacterium. When we talked about transcription in general, in several videos ago and in several videos, we talked about the idea of a promoter. That you have a gene that is a sequence of DNA that's part of the broader chromosome, and we said, "okay, that RNA polymerase needs to attach some place," so that RNA polymerase needs to attach some place, and we called that place that the RNA polymerase attaches, we call that the promoter, and then the polymerase will transcribe the gene. And when we first talked about the idea of a promoter, we said, and this is generally true in Eukaryotes, that each promoter is associated with a gene, or each gene has a promoter. But when we're talking about Prokaryotes, and in this case we're talking about this bacterium, it's actually typical to have multiple genes grouped together that have one promoter, so this promoter here, and a promoter is actually called a regulatory DNA sequence. Let me write this down. So the promoter, so that's this part right over here, that's the sequence. That is a regulatory, regulatory DNA sequence. Well that's what the RNA polymerase, which I drew as this big blob, it's protein here, this big blob, will attach to, and then it will begin to transcribe all of these genes as a bundle. And when you have a promoter associated with multiple genes, that combination of the promoter and the genes, and once again when I'm talking about the promoters of the genes I'm talking about sequences of DNA, that combination is called an operon. This is called an opeon. It's a combination of that regulatory DNA sequence which says, "Hey, RNA polymerase, bind here "so you can start transcribing," and the genes that it, essentially, promotes the transcription of. And then of course, that transcription process takes that genetic information in DNA, transcribes it into messenger RNA, which can then go with the ribosomes, and we have the whole translation process and this should all be review, to produce the actual proteins that have functions within, or even potentially, outside of the cell. And so what we're gonna dig a little bit deeper in is what can enhance this process, make this happen more frequently, or things that might inhibit this process in some way. So as I mentioned before, this is just what I had just drawn, we have our big RNA polymerase blob, and this is an oversimplification for what it looks like, attaching to the regulatory DNA sequence, which we call the promoter, and then it will do the transcription which will produce mRNA, which encodes the information in those genes. But what if we're in an environment where we don't want to transcribe this particular operon, this particular, or maybe I should say particular series of genes? Well then we might, something in our environment might allow repressors to take action. So what are we talking about a repressor? Well a repressor, a repressor right over here, you see it attaching to a sequence of DNA after the promoter, and so it blocks, it blocks the RNA polymerase from being able to do the transcription. And so this right over here, this is a protein that is called the repressor, it's literally repressing the transcription, and the regulatory DNA sequence where it attaches, that is called the operator. So once again, promoter was a regulatory sequence where the RNA polymerase can attach, and then operator is a regulatory sequence where a repressor can attach and keep that RNA polymerase from actually being able to perform the actual transcription. And so this keeps the gene from, continuing to transcribe and then translate these actual genes. And you might even have extra mechanisms, and you can even think of them as feedback mechanisms or ways to understand the environment where the repressor, this protein can only do its job, so let's say that's its repressor, where it can only do its job if it has other molecules that attach to it. So maybe this one can only do its job if it has another molecule attached to it, and in that case, these smaller molecules, these are called corepressors, co, co repressor. And we'll go into more detail when we talk about things like the trip operon of how tryptophan, an amino acid, can actually act as a corepressor. Now over here, we have the other way around where we want even more transcription, and in that case we would have something called, we would have an activator. And this, let me shade it in, this DNA right over here, this would be the regulatory sequence where the activator binds, and so this would be positive feedback. When you have more activators, you're gonna get more transcription, while this would be, and actually I shouldn't even call it feedback because that implies that somehow these products produce the activator, or this products produce the repressor, but that's not the necessarily the case. It could be, you could imagine that case, but it's not necessarily the case. I should just say that this is repressing and this is activating. It's going to make more of the transcription actually happen. And just as we could have corepressors, small molecules that you could think of as activating the repressor, you can also have small molecules that can turn the activator on, and these small molecules that turn the activator on, these are called inducers. So this right over here, these are inducers. So this protein right here couldn't activate that operon, but now that you have these inducers, and we'll study that a little bit more when we think about the lac operon, this could be a small sugar of some kind, well then it can turn on the activation. So this right over here is called an inducer. So that's just a high-level overview of DNA regulation. As you can imagine, this can get very, very interesting and complex, where you have your repressors and corepressors and activators and inducers that might be dependent on the environment that the cell is in, what's going on in its broader ecosystem. There's all sorts of feedback and feedforward loops that might be going on. And that's why the study, we can have the sequence, and in fact we do sequence entire genomes, but even once you have the sequence, it's incredibly complex to understand all of these loops of these feedback and feedforward loops to understand how these things actually interact with each other.