all right Welcome to our second video for chapter 16 in this video we're looking at the lactose operon as well as epigenetic regulation of gene expression so in our previous video we talked about the tryptophan operon and negative Regulators now we're going to switch gears and look at the lactose operon and positive Regulators that turn genes on and activate their transcription so one example is the lactose operon again we're still looking at procaryotes because procaryotes remember their messenger RNA has multiple genes and they are organized into these structures called operons and we're going to look at the lactose operon in uh bacteria like eoli it turns out that most cells prefer glucose glucose is their main energy source but when you have little or no glucose when their levels fall eoli and other bacteria have the ability to use other sugars they can metabolize other sugars such as lactose for energy but they need different types of enzymes to break down uh these other sugars so we're going to look at the lactose operon and in the lactose operon we're going to see genes that are present to encode enzymes that will take in lactose into the cell and allow the processing or metabolism of lactose to produce energy for these positive Regulators we're going to look at cyclic and cap which stands for catabolite activator protein it turns out that when glucose levels are low so low glucose when glucose levels are low you're going to have greater levels of cyclicamp in the cell cyclicamp accumulates in the cell this is a signaling molecule that's involved in energy metabolism and when you have a lot of cyclicamp it's going to bind to catabolite activator protein and this complex together cyclicamp and cap is going to bind to the promoter region and what that does is it actually helps stabilize RNA RNA polymerase so that RNA polymerase has a greater transcription rate of these genes that are going to end up being used to catabolize or break down lactose for energy so when glucose levels are low and you have other sugars such as lactose available you're going to want to transcribe these genes that allow lactose to enter the cell and allow the cell to metabolize lactose for energy and how the suur occurs is for example shown down here this is the first step glucose levels become limited so glucose goes down and cyclicamp levels go up what happens next as I mentioned is cylic a binds to the cat protein and these are known as positive Regulators they're going to bind to that promoter region Upstream of where RNA polymerase binds and the cap Camp binding to the promoter stabilizes RNA polymerase so that it binds even well or even stronger to the promoter region and increases transcription increases transcription of these lactose catabolism genes interestingly the Lac operon or lactose operon is opposite of the tryptophan operon because it's an inducible operon what this means is the default state of this operon is off and this is because we usually do not break down lactose for energy we're usually breaking down glucose for energy that's our really primary or desired sugar source and you only use lactose when you have to so in the absence of lactose which is more common the common state the repressor protein is bound to the operator region and physically blocks RNA polymerase and this is because for this repressor the repressor of the lock opon the shape of the protein is naturally such that it naturally binds to the operator it's optimized to bind to the operator region and blocks RNA polymerase from transcribing these genes it's only when you have lactose so in the presence of lactose that lactose will bind to the repressor and change its shape so that it no longer binds to the operator and now AR PL race is free to transcribe the genes that will allow the intake and breakdown of lactose for energy so this is called an inducer lactose is the inducer because it binds to the repressor protein and makes it stop binding to the operator allowing transcription of the genes this is an inducible operon because of this and again this really depends on the needs of the cell much like the tryptophan operon when you have lactose then you want to transcribe the genes that allow the enzymes to met abize the breakdown of lactose notice however that if you just have lactose available and you don't know anything about whether glucose levels are high or low I don't see that cyclic amp or cap here this means that transcription will occur but it goes at a slow rate it's only when you have a high level of that cap Camp complex that transcription will occur at a greater rate and we see that scenario in this upper picture where lactose is available and I can tell that lactose is present at the moment because the repressor protein is not bound to the operator so RNA polymerase is free to move forward and transcribe these genes this is the presence of this picture indicates the presence of camp and cap which tells me that there's also low or no glucose currently available so in the presence of lactose and little or no glucose the transcript of the MRNA for these lactose metabolism genes will increase so in contrast to the low transcription rate we saw on the previous slide here we have a greater transcription rate notice though here down here even though we have cap and Camp if there is no lactose there will still be no transcription so if there's no lactose but also little glucose which is indicated by the the cyclic and cap complex there's still no transcription so you have to have both lactose present and the cap Camp if you want High rates of messenger RNA transcription of these lactose metabolism genes and underneath this figure in our textbook they POS the question in eoli the tryptophan operon is on by default while the lock operon is off why do you think this is the case so if we go back and think about the two operons remember that the tryptophan operon their purpose is to make tryptophan and tryptophan is an amino acid That's essential for proteins so we always need to have some tryptophan in the cell if there's too much trypan however it's wasteful to make more so we will repress the trip operon at that point in contrast lactose is a sugar that's not always available to to cells so it does not make sense to make the enzymes necessary to digest lactose unless it's available so the lock operon is only on when you have lactose that's present in the cell and our book provides a table that tells us the conditions where you will be transcribing the lock operon so for this last column you can think of it as is the operon on yes or no so if I look at the first row if glucose is available but cap does not bind and there is no lactose that means the repressor will be bound to the operator and you're not going to have transcription of the lactose operon genes so that makes sense if there's no lactose why would I make enzymes to metabolize lactose all right let's look at the second row I have glucose available so that means there's no cyclic so cap does not bind I do have lactose available when lactose is available it binds to the repressor protein so it doesn't bind to the operator so that means RNA polymerase is free to move forward and transcribe the genes so there's some remember there's a low rate of transcription because there's no cap protein with a cyclic bound to the promoter in the next case we have no glucose so the cap Camp finds but there's no lactose no lactose if there's no lactose again it would not make sense to make the enzymes to break down lactose and then let's look at the last one there's no glucose there is Cap bound to the promoter site there is lactose so this is when we have the highest rate of transcription of the operon of those lactose catabolism genes and I didn't talk about this cuz these were similar to to the above but remember that whenever lactose is available then the repressor would not be able to bind to the operator when lactose is not available then the repressor will be bound to the operator to prevent RNA polymerase from moving forward so for the operons so far we've been talking about procaryotes remember operons are present in procaryotic cells like bacteria and now we're going to switch gears let's talk about ukar ukots and we're going to talk about Gene regulation starting with epigenetics epigenetic Gene regulation remember that eukariotic gene expression is more complex because we have that nucleus so transcription happens in the nucleus translation's going to happen in the cytoplasm and remember regulation happens at many different levels rather than just the transcriptional level that we saw in procaryotes so the very first level of of control really starts with accessing the DNA are you even able to open up the DNA to read it and make messenger RNA that's the epigenetic regulation process and it occurs even before you can start transcription so there are two subcategories to epigenetic regulation one is chromatin Remodeling and this has to do with how DNA is associated with those histone proteins is it tightly bound to histone proteins or is the DNA Loosely wound around the histone proteins the second one it's not these are not the only two but the only two that we really talk about so far in this chapter the second one is DNA methylation and this is really associated with developmental changes that can occur as you age as well as gene silencing and we're going to see that if you methylate our DNA histone complex you're going to end up usually silent in genes so this usually is silencing like we see here later on in this chapter we're going to see that transcription factors are also important these are proteins that are going to regulate transcription of our genetic information if we look at how the human genome is regulated we can kind of see why epigenetics is so important to gene expression and the regulation of gene expression so our human genome encodes over 20,000 genes across those 46 chromosomes and 23 pairs of chromosomes so we have 23 I should say really pairs of chromosomes because we have 23 from Mom and 23 from Dad and within each chromosome there are thousands of genes we know from previous chapters that DNA is wound around histone proteins to compact it into chromatin and if we want to express these genes remember that means we were going to read DNA and make our messenger RNA then we have to unwind kind of loosen the way DNA is wrapped around those histone proteins so it's available to the polymerases and specifically remember these are RNA polymerases that Redna and make messenger RNA so it's very organized DNA the way it's organized in the nucleus has to be in a way that it's accessed accessible or the genes are accessible when they're needed by specific cell types we've seen the organization of DNA around histone protein several times already remember that this structure that looks like beads on a string is a nucleosome and under the electron microscope you can see tiny little circles everywhere and these are our nucleosomes these beads on a string DNA we remember is negatively charged overall because of the phosphate groups and then histone proteins are posit positively charged so there's usually a pretty strong interaction between the two if we think about adding methyl groups um or acetal groups we'll see later on as well these change the interaction between DNA and histone proteins to either tighten the interaction or loosen the interaction and in general methylation of these complexes will result in gene silencing and then adding acetal groups to these complexes will really uh result in gene expression or greater gene expression I should say and we see that here how nucleosomes are controlling the axis to DNA so when I say axis this is really axis from or by the RNA polymerases which need to access DNA in order to make messenger RNA oop sorry right there and I see the methylation over here methylation usually causes the packing tightly causes the nucleosomes to pack tightly together you can see there's no space and if I want to access this Gene right here it's not accessible so this means that genes are not expressed when the DNA and histone complexes are methylated so gene expression is turned off and this is General the general rule when it comes to methylation not always true in all species and all cell types but for our course we're going to say methylation silences genes again at the bot uh bottom picture I see histone acetalation acetalation results in loose packing of those nucleosomes you can see so much more space between the nucleosomes and here is my Gene of Interest now it's accessible and I can express these genes so when nucleosomes are far apart due to the addition of these acet groups hisone acetalation we're going to allow gene expression to occur so that will be our general rule the acetalation increases gene expression whereas methylation silences these genes so we call these additions these methyl or acetyl groups we call these chemical tags that are added to histones and DNA and they're not permanent they can be added or removed depending on the environment the diet and other factors these really act as signals to tell our histones if the regions of the chromosomes should be accessible or inaccessible so again this is known as epigenetic regulation which means above or around genetics these are temporary changes not always temporary some of them can be quite long lasting but they do not alter our nucleotide sequence they affect gene expression by again determining whether or not those genes are accessible to our RNA polymerases and how some of them work as I mentioned earlier for example acetyl groups will impact the charge the usual charge of DNA which is negatively charged binding to histone proteins which are positively charged if you add things like acetal groups the charge of the histone proteins becomes less positive than usual allowing that DNA to relax more around those histone proteins so we saw earlier that our nucleosomes can be methylated or other chemical tags can be added to loosen or tighten the wrapping of DNA around those histones and production of nucleosomes so that was here in fact DNA methylation can also occur directly so if the DNA itself is methylated this usually happens in specific regions we call cpg Islands these are called cpg Islands cuz in these regions of DNA we have a high frequency of our cytosine and guanine nucleotides and these are in the promoter region of our genes these are Upstream of the gene of interest just like adding methyl toogs to the nucleosomes methylated genes are also usually silenced and in fact genes that are silenced during the development of gametes um this is from a parent or the other or both this silencing can be transmitted to the spring and if this happens these are known as imprinted genes so what happens during your lifetime due to diet or do other environmental stressors can cause your genes to be methylated or silenced and you can pass that on to your Offspring if this is happening in gametes so again many different things can affect methylation patterns your diet the environmental conditions other stressors like those that we saw in the article and the film that we watched recently so we've seen epigenetic changes to chromatin can result from things like development can happen while you're still in the womb or during childhood due to exposure to chemicals or different drugs due to aging or even your diet and these changes can result in a variety of effects cancer autoimmune disease mental disorders diabetes and even more why does it matter if we have access to our DNA to our genes remember that in order to read DNA and make messenger RNA we need transcription factors to bind to the promoter region and other Upstream regions that enhance transcription and initiate transcription in the first place and this can only happen if our DNA is accessible twins studies are big in many biological Fields but also in epigenetics and a few years ago NASA published a study regarding these twin astronauts where Scott Kelly was the twin that um went into space whereas his brother stayed here and what they saw was that in Scott Kelly's uh genes there were so many changes while he was out there and those changes remain for a few months after he came back to Earth his tell got longer in space before they shrank back to normal or actually sometimes they even got shorter after he returned to Earth they also saw methylation changes compared to his twin and luckily most of the changes returned to normal um there are some changes that have not returned to normal but we're not sure if they're just different because of aging and time or if it was because of the mission and that takes us to the end of our second video in our third video we're going to look at eukariotic transcription and Gene regulation and the role of transcription Machinery in gene expression