 Now, in eukaryotes, you can also have regulation of transcription that's a little bit different than you'd find in bacteria. So we're going to talk about transcription factors and enhancers or silencers. So transcription factors are proteins that bind DNA and affect gene transcription. So the name kind of makes sense, transcription factors. And then these guys bind DNA that are either enhancers or silencers. So again, it's simply a region of DNA. But this DNA could be very close to a gene or it can be very far away from a gene. Now the DNA is very flexible and bendy. So the DNA can bend to bring the enhancers or silencers a lot closer to that promoter. And so you can see here, the DNA can simply bend over with those transcription factors and then interfere or enhance gene transcription. So again, when transcription factors are bound to the enhancers or silencers, they can either affect the gene and turn it off, or they can affect the gene by turning it on a little, turning it on a moderate amount, or turning it on full blast. Now another way that eukaryotic cells can modify their gene regulation is through RNA splicing. So in this particular case, you can have one gene, but it can make more than one protein product. Now when that first RNA message is made or that pre-MRNA, we've got what's called exons and introns. Now you guys know already that those introns are removed or cut out. And in this particular case, the gene has one, two, three, four exons. Now with RNA splicing, you can put those different exons together in different combinations. So here we've got one, two, three, four exons that we start off with. And when we splice them together, we only end up with exon one, exon two, or exon four. Or a different splice product that could take place is one, three, and four. And so when these guys are translated, they're going to make a different protein. Eukaryotic mRNAs, they can last in the cell for hours, or they can last in the cell for months. But eventually all of that mRNA is broken down. Now if an mRNA message is present, you can use it to make proteins. But if that mRNA message is degraded, you cannot use it to make a protein. So even at the mRNA level, you can affect gene regulation. Now another way that you can affect translation is through microRNA or MI RNA. So microRNA, kind of like the name sounds like, is small single-stranded RNA molecules. And these guys can bind that messenger RNA, that product that we've just made from the gene, and it can either inhibit translation or it can trigger its breakdown. So again that mRNA can bind the messenger RNA and either physically block the ribosome or it can trigger its breakdown. And then it kind of goes to the trash can or the recycling bin. And another step or another place where we can affect gene regulation is at the initiation of translation. Now there can be a lot of different inhibitory proteins, a lot of different inhibitory RNA. But again if you interfere with that messenger RNA, if you interfere with the ribosomes, or if you interfere with the enzymes or other factors in this process, again you can stop gene expression cold. And one of the last places that you can regulate gene expression is through protein activation. So some proteins require modifying chemical groups, maybe a phosphorylation, methylation or other things being added to the protein to make it active. Also other proteins require perhaps the initial protein to be cut before it's active. So a good example of this is digestive enzymes. So when a digestive enzyme is first made, you don't want it active. You don't want it starting to digest the cell. But instead once it's gotten to the right place, the right time and you're ready to use it, then you can cut that particular protein and now it's in its active form. And now it's useful in not harming the cell. And last but not least, you can go through the entire process. Make the messenger RNA, translate the messenger RNA, regulate its activity. You can also have proteins that break down other proteins or enzymes that chew up proteins. So again, if you get rid of the protein, you're going to be making amino acids, and if you have no protein product, it's as if the gene was never turned on. So again, there are many, many places where a gene can be turned off. Again if you stop it at transcription, stop it at translation, or break down any of those products, again you will never see the final product, you will never have its phenotype. Now another way that you can do gene regulation is you can have a group of genes affect another group of genes. So that's the case with homeotic genes. So homeotic genes are master genes that control groups of other genes during development. Now these guys are very important for the proper placement of body parts and organs. It determines that your head is up here and that your feet are down there. You've got two arms located right here on the shoulders and two legs on the bottom of your torso. Now if these homeotic genes are defective, such as mutations that might occur in fruit flies, you can end up with fruit flies that have double wings. Now initially that sounds really cool having two sets of wings if you're a fly, but that second set of wings is defective. So it actually inhibits the ability of that fly to get around. Now another thing that could take place with those fruit flies is that you can have feet on your head instead of a set of antennae. Again those feet are kind of in the way, not quite functional. And so you can get some very interesting changes if you mutate those homeotic genes. Now microarrays are one way that we can get a handle on which genes are active and which genes are silent. So in humans we've got 20,000 genes that might be on or might be off. How do we figure out which ones? So we can use a DNA microarray. We start off by isolating the messenger RNA from cells. We make cDNA that has a glowing tag. And then we put it on a microarray slide. Now wherever we've got a little glowing dot, that indicates that the messenger RNA is present and that gene is kind of turned on. Wherever it's completely dark or black, that indicates that there's no messenger RNA and that indicates that the gene is off. So why would we do DNA microarrays? Well if we wanted to compare cell types like liver cells to brain cells to heart cells, we could use a DNA microarray. We could also use a DNA microarray to compare disease tissue to healthy tissue, which genes are affected, which pathways are affected. And so hopefully it can develop a better treatment. Or we could use this to compare cells with and without a drug. So if we're using a new drug for the first time, we don't know if it's toxic. So we can do a DNA microarray with and without the drug, to compare which genes and pathways are affected. So again, we start off with 20, 21,000 genes and we can use those DNA microarrays to hopefully narrow down that list. But again, if you remember this lecture on gene regulation some of the earlier slides, it does not show if the protein is present, merely if that messenger RNA is made. Now one last topic is cell signaling. So cells can also communicate with each other. Rather than using cell phones like you or I might, cells release hormones and other chemicals. And those chemicals can affect neighboring cells or they could affect cells that are very far away in distant organs. So here's an example. We've got one cell that wants to send a signal to this target cell. And so it's going to secrete a chemical or secrete a hormone. And that hormone can travel all the way through the bloodstream to get to that target cell. Now if the target cell has a receptor for it, it can bind the hormone on its surface on a receptor protein. So here are these guys match up and so the signal is received. But if there is no receptor on that target cell, it will completely ignore the signal. So you could have a truck load, you could have a bucket load, you could have an immense amount of signal on the outside of that cell. But if it doesn't have that receptor protein, it will never receive that signal. Now the next step is signal transduction. So again, the hormone binds the receptor on the surface. But then that signal is passed into the cell. Not necessarily the hormone or chemical that was on the surface, but that signal is simply passed on into the cell. Then maybe a transcription factor might be activated and then that transcription factor can affect gene regulation. So again, we start off, that signal is bound to that receptor protein. And that hormone is going to stay on the outside of the cell. But instead the receptor protein is going to pass that signal inside. So it might affect this protein, it might affect this next protein. And then it might activate a transcription factor. And so that transcription factor when it becomes activated can then go into the nucleus and then affect gene regulation or gene expression. Now cell signaling, I was showing you a very simplified slide where you have one hormone affecting one pathway. But cell signaling in a cell can be very complicated. So you might have cytokines, survival factors, hormones, growth factors. Even extracellular matrix and all of these things are working in the cell to either turn genes on or turn genes off.