Operons and gene regulation in bacteria

So we're going to talk a little bit about DNA regulation. This is the general idea that if you look at an organism's genome, not all of the genes are being transcribed and translated at the same time. It could actually depend on the type of cell that DNA is inside of or it could depend on the environment for that organism.

For example, if you look at, say, a multicellular organism, maybe this is— and these are oversimplifications—maybe this is some type of immune cell, and let's say that this over here is a muscle cell. They're not necessarily, or not likely to be these perfect circles, but this is just for the idea. 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 eukaryotes. I'll draw the nuclear membrane there. Same DNA, but they have very different roles inside of this organism.

It doesn't make sense. In fact, in order for them to even have different structures, they're going to have to produce different proteins. They're going to have different enzyme proteins inside of their cytoplasm. 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?

Even if you think about a unicellular organism right here, we have a bacterium. 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—this is its 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. We will actually talk a little bit more in 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 high gear sometimes, 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 it 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 eukaryotic or a prokaryotic organism. What we’re going to do in this video is focus a little bit more, or a lot more, on the prokaryote side, especially we’re going to talk about this bacterium. When we talked about transcription in general in several videos ago, 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. We said, okay, that RNA polymerase needs to attach someplace. So that RNA polymerase needs to attach someplace, and we called that place that the RNA polymerase attaches—the promoter.

Then the promoter will transcribe the gene. 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.

This promoter here— a promoter is actually called a regulatory DNA sequence. Let me write this down. So the promoter—that’s this part right over here—that's the sequence that is a regulatory DNA sequence. Well, that's what the RNA polymerase—which I drew as this big blob, this protein here—this big blob will attach to, and then it will begin to transcribe all of these genes as a bundle.

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 and the genes, I’m talking about sequences of DNA—that combination is called an operon. This is called an operon. 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.

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. This should all be reviewed to produce the actual proteins that have functions within or even potentially outside of the cell.

We’re going to dig a little bit deeper into 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. This is an oversimplification for what it looks like, attaching to the regulatory DNA sequence, which we call the promoter. Then it will do the transcription, which will produce mRNA that 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 series of genes? Well then, we might—something in our environment might allow repressors to take action.

So what are we talking about with 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. 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 is called the operator.

So once again, the promoter was a regulatory sequence where the RNA polymerase can attach, and then the operator is a regulatory sequence where a repressor can attach and keep that RNA polymerase from actually being able to perform the actual transcription. This keeps the gene from continuing to transcribe and then translate these actual genes.

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—I should say this protein—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.

In that case, these smaller molecules are called co-repressors. Co-repressors. We’ll go into more detail when we talk about things like the trp operon of how tryptophan, an amino acid, can actually act as a co-repressor.

Now over here we have the other way around, where we want even more transcription. In that case, we would have something called an activator. This—let me shade it in—this DNA right over here would be the regulatory sequence where the activator binds. So this would be positive feedback. When you have more activators, you’re going to get more transcription.

This would be—and actually, I shouldn’t even call it feedback, because that implies that somehow these products produce the activator. These products produce the repressor. But that’s not necessarily the case. 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.

Just as we could have co-repressors, small molecules that you could think of as activating the repressor, you can also have small molecules that can turn the activator on. These small molecules that turn the activator on are called inducers. So this right over here—these are inducers. 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. 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, co-repressors, 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 feed-forward loops that might be going on, and that’s why the study—we could 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, these feedback and feed-forward loops, to understand how these things actually interact with each other.