hello bisque 130 this is the beginning of recorded lecture 43 uh continuing on with the chapter on regulating gene expression we began this in the last recorded lecture just to introduce some terminology like transcription factors activators repressors uh but now I'm going to get uh deep into a specific example that will hopefully make those Concepts make a little bit more sense so uh this extended example which is going to take most of this recorded lecture to be honest is talking about something called the lack operon so there are two parts to this what the heck does lack stand for and what is an operon um let's go after operon first uh the Lac operon is an operon so okay so what is an operon uh well the key terms defined an operon as a collection of related genes that are transcribed together as a single mRNA we should visualize this so in the last chapter when we were looking at transcription and translation you know we have the promoter and the transcription start site and then we have a Terminator that tells transcription you know where to end and we transcribe an mRNA and then that mRNA gets translated into protein with a start code on and a stop code on in an operon there are multiple genes in this case three but it's not always three in and operon there are multiple genes that are transcribed together back to back as part of one big long messenger RNA so you have a single transcription start site a single promoter a single Terminator here and you end up with this massive messenger RNA that contains several genes each one has their own start code on stop code on start code on stop code on start code on stop code on um this is just a way of organizing things uh it's useful if you have multiple genes that are all related to one another if they're doing kind of the same job if they're involved in the same metabolic pathway or process so yeah this is a convenient way to to lump things together like this importantly this is procaryote only we do not have operons ukar nots we do not organize our genes like this we have you know one gene one mRNA one protein it's only procaryotes that will lump them together like this so This example we're going through is going to be a a procaryote example so that explains the operon part of this title here what about Lac well the Lac stands for lactose so this operon contains three genes that in code proteins that are involved in breaking down lactose you may remember lactose from any many chapters ago it is a disaccharide in order to do anything with this um we have to break apart this glycosidic Bond uh and create monosaccharides and you know obviously we break down lactose as as humans uh milk unless you're lactose intolerant and these pills will help you uh but again we have these genes we just don't organize them in an operon this operon we're talking about is procaryote only so the reason I'm bringing up this operon is because it's controlled we're talking about transcription factors here and this is kind of a two for one because there are two transcription factors involved in controlling the lack operon so let's start with the the the simpler one and let's look at the logic here because there there is a mechanism there's a protein there's a thing that's physically going on but there's also a logic behind why this is the way it is bacteria really want to be as efficient as possible I don't want to waste any energy they're living in highly competitive environments surrounded by other bacteria and fungi and microorganisms whatever they don't want to waste energy so it takes a lot of energy to express a gene or an operon transcription takes a lot of energy and raw materials and translating this mRNA into protein that also takes a lot of energy a lot of raw materials amino acids a lot of ATP it costs a lot of energy to go from Gene to Mr na protein these bacteria don't want to waste energy so they only want to express the lack operon again gene expression means uh you Gene to mRNA a protein to do and stuff they only want to express this lack operon if lactose is actually around them if lactose is actually available um this logically this should make a lot of sense and my my dumb analogy here is if you were a potato farmer and you were surrounded by potatoes and you had fields and Fields of potatoes would you go to the store and buy a fancy expensive wheat processing machine no that would be a massive waste of money don't buy this if you don't have any Wheat to process so yeah don't do this operon unless there's actually lactose around for you to deal with that's the logic here it's wasteful to make useless proteins now how is this accomplished well this is accomplished through again I I numbered this one because like I said there are going to be two transcription factors controlling this process this uh logic gate uh is controlled by a transcription Factor called the lack repressor protein sometimes just called Lac repressor but Lac repressor protein is going to be used to make this happen oh side note I'm not going to be a stickler for this on my exam questions but in case you're curious um you're supposed to put genes in italics that's why every time I say Lac operon I have the little italics there uh it's not italics here because I'm not talking about a gene in this phrase I'm talking about a protein so anyway I'm not a stickler for that if you're wondering why these things are italics uh by convention biologists put Gene names in italics okay so what is this Lac repressor proteins so the Lac repressor protein can do one of two things depending on whether there's lactose around or not let's start with the if lactose is absent so if there is no lactose around this Lac repressor protein will bind to something called the operator so operator is in the key terms but let me show this so here's our slide from before uh there's you know our operon here's the transcription start site right there the plus one and here's the operator so we can see that it's before the genes actually start in the DNA but it's after you know it's right after the transcription starts right after where RNA a polymerase would bind so how do the key terms define this the key terms say an operator is a region of DNA outside of the promoter region that is bound by activators or repressors so this part of the DNA exists only for transcription factors to bind to uh let's zoom in a little bit on this region there we go there's promoter there's RNA polymerase these are our three important genes in the operon there's the operator and here is the repressor protein like I said repressor protein binds to this operator so what is this going to do well this is going to shut the whole thing down remember what RNA polymerase is supposed to do when it binds to the promot it's supposed to create a transcription bubble it's unzip the DNA locally and sort of move along if there is a big old protein stuck in the way uh this is a this is a roadblock this is uh this is something that's going to prevent RNA polymerase from actually moving its little transcription bubble onto these genes that's going to shut down transcription so Lac repressor binds to the operator this is sequence specific so again there there is a sequence here that we are obviously not memorizing but this repressor protein does not just bind randomly to the chromosome it's got some specific g g a TCC a whatever sequence that it specifically recognizes and binds to so it represses just this thing not random genes across the chromosome so the repressor protein binds to the operator sequence specific and yeah this one's straightforward it physically blocks RNA polymerase from transcrip describing expression of the Lac operon is going to be repressed or off so for this scenario you should understand the mechanism it's off because repressor gets in the way you should also understand the logic it is off because there's not any lactose around don't don't make weight don't make useless proteins it should be off if lactose is absent what about the other scenario what if there is lactose around well if lactose is present lactose like the actual sugar itself binds to the Lac repressor protein and you know we we've seen this before and I think we'll see this again when you bind things to proteins when you attach uh I guess we saw phosphorilation in an earlier chapter we saw activators and repressors in earlier chapters and anytime you add something to a protein that's going to change its shape so when lactose binds to the Lac repressor protein it causes a shape change and as it turns out this Lac repressor protein with lactose attached to it is no longer able to bind to DNA here's our visual on this uh there's promoter operator genes and yeah here's the repressor not repressing it has lactose attached to it it's not not bound to the operator it can't bind to DNA in this scenario so there is no repression happening uh so RNA Paul can now transcribe the Lac operon freely Lac operon is going to be on but it's going to be low so I'll explain this in just a second but it is it is going to be slightly on and logically that should make sense yep there's lactose around you should be going for it it's worth it to spend all the energy to do transcription and translation because there's actually lactose around so why is it low uh and what do I mean by low well we talked about promoters in an earlier chapter and how this is a very specific sequence that this RNA polymeris is supposed to bind to so it knows where it is supposed to start as it turns out not all promoters are equal not all promoters have exactly the correct ideal sequence some promoters for some genes or operons are what we call weak promoters their sequence is just not quite right uh and so what that means is RNA polymerase is going to bind to these kind of weak promoters and you know maybe start transcription but it's going to be so uncertain as to whether this is a real promoter or not that more often than not the RNA polymer is just going to detach and not actually do anything in the first place so the promoter for this Lac operon is one of those weak promoters its exact sequence here is just not quite right so even if there's no roadblock at all you're still only going to have low expression levels because the promoter is just not recognized by RNA polymerase that well so yeah in this scenario we have low expression levels because the promoter is quote unquote weak which means it's not easily Bound by RNA polymerase so how do we how do we actually get strong expression how do we get lots and lots of expression well to understand that we have to look at our second transcription Factor again all of this was the action of the lack repressor protein either repressing and getting in the way in the absence of lactose or not repressing not getting in the way in the presence of lactose so what's the other one all right again let's do the logic first then the mechanism there are a ton of sugars out there and lactose is kind of a pain in the butt to deal with it kind of takes you know a bunch of extra genes and processing steps to make this usable form if you're trying to be as efficient as possible you don't want to touch this stuff if there's a better sugar around so our second mechanism takes this logic into account these bacterial cells only want to express the Lac operon if a better sugar source is not available it takes some energy to deal with lactose it is more efficient to use glucose if it is available glucose you know goes straight into the cellular respiration pathway it's the simplest easiest sugar to deal with and yeah if you've got both of these available the cells will not even want to deal with lactose they would rather use glucose instead I've got another analogy for you let's pretend that you are trying to be as lazy as possible you're trying to be as efficient with your energy as possible on uh you know a slow Sunday afternoon uh but you're hungry you need some food and so you get up and go to the kitchen and uh in this scenario you're kind of a weirdo because in this scenario there are only two items sitting there in your fridge there's a carton of blueberries and there is an entire pineapple now if you are trying to be as lazy as possible as efficient with your energy as possible the pineapple is delicious but man you got to cut off the top and trim off the sides and cut the you know the fruit away from the core and then then you should wash your knife wash your cutting board you know put all that stuff away then you can eat your pineapple it's nutritious and delicious and good but it takes a lot of energy to deal with the blueberries you just eat those uh there's not even any stems or seeds or cutting involved at all you just eat them hopefully they're already washed and you don't even have to do that you can just eat these so in this scenario you would always go after the EAS easier food source if it's if it's available uh if there were no blueberries and the only food was pineapple sure yeah don't starve to death eat your pineapple but you always want to go for the easy one first here these cells always want to go after glucose first only lactose if they've run out of glucose so in order to achieve this logic in order to achieve this uh the cells are going to use a transcription Factor called catabolite activator protein abbreviated cap or capap this one is not a repressor like the last protein was this is as the name implies this is an activator the exact opposite before we talk about how cap works we have to talk about something called cyclic am now cyclic is something I brought up in an earlier chapter if this slide looks slightly familiar this was an example of something that I called a second messenger several chapters ago so why is this coming up now well this whole whole logic here for our second mechanism has to do with glucose but we are not going to directly involve glucose instead these mechanisms are going to involve cyclicamp so how does cyclic relate to glucose well like this if there are high levels of glucose in the cell that means there will be low levels of cyclic amp you can say Camp you could pay you could say CM you could say cyclic all of those refer to the same the same molecule high glucose means low cyclic this is a small signaling molecule and conversely if there are low levels of glucose there are going to be high levels of cyclicamp so glucose and cyclic are inversely related and it's very important to remember the relationship between these CU we're actually we're not going to directly involve glucose we're going to involve cyclic in this regulation process so we've got our catabolite activator protein and here's where it devolves into alphabet soup and try to follow me with this cap needs Camp to activate this catabolite activator protein it's an activator it turns up transcription levels it cannot function on its own it needs this small signaling molecule in order to activate in other words it needs low glucose to activate because low glucose is the only scenario where you would have lots of cyclicamp side note these are easy to mix up cap and Camp my dumb way of remembering which one is which is cap is a big protein proteins are very large compared to you know things like this uh cap is all capital letters It's all big letters the C is a big letter this is a big protein in contrast Camp is a lowercase C it's a little C there at the beginning uh that helps me remember that camp is the small signaling molecule whereas cap is the big protein anyway just a side note but don't get which them confused which one is which protein small signaling molecule so okay how does this actually work well just like we had for the last control mechanism there are going to be two scenarios if glucose is around and if glucose is not around so if glucose is not around that means we can go back to this low glucose levels or no glucose levels means high levels of cyclic am that means cap is going to have its partner and yeah here we go the the cap Camp complex uh the uh activator protein with its little partner and what this activator protein does is it binds close to the promoter uh and it binds to RNA polymerase remember RNA polymerase does not have a very strong hold on this promoter this is a weak promoter because of its sequence but with this activator bound right next to it oops sorry skipped to the wrong one with this activator bound right next to it that is going to stabilize RNA polymerase at the promoter and help it get started and yeah it'll create its little transcription bubble move past the operator start transcribing these genes remember this is an activator it's supposed to help things work which is exactly what we're seeing here so in summary if glucose is low or absent there's going to be plenty of Camp cap binds Camp then it binds close to the promoter once again in a sequence specific fashion we don't want this binding willy-nilly all over the chromosome random sequences it's specific for some sequence here near the promoter the cap Camp complex uh stabilizes RNA polymerase and helps start transcription expression is going to be on and it's going to be strong you should understand the mechanism for why the expression is going to be activated and turned on and you should understand the logic for what for this this was if glucose is low or absent this was the if you have run out of easy food yes you should go ahead and start doing the you know pain in the butt more difficult food because you don't want to starve to death so yes you should understand the mechanism you should understand the logic what about the other scenario if glucose is around if glucose levels are high or if glucose is present you know around the cell well high levels of glucose mean if I can return to this slide low levels of cyclic Am low levels of cyclic means cap does not have its partner and so it's not going to do any of the stuff that I just showed without cyclic cap can't bind to near the promoter and then bind to RNA polymerase so without that there's just no activation Happening Here uh this is a weak promoter so without any activation you're just going to get lower weak expression levels in summary if glucose is high or present cap has no camp Camp levels are going to be low uh cap cannot bind to DNA without its cyclic partner that means there's going to be no stabilization of RNA polymerase expression is on uh but again because this is a weak promoter and there's no activator helping out expression levels are going to be low now the fun part of this both of these transcription Factor mechanisms are working together the presence or absence of lactose and and the presence or absence of glucose are both at work in determining whether this operon is transcribed or not let's walk through this because there are four possible scenarios here with regards to lactose and glucose four possible combinations so let's start out with and this is no new information you know I got all all four of these scenarios here this is nothing new uh this is everything we've already talked about this is just kind of recapping or summarizing what these look like together so let's look at this one low glucose lactose available so lactose available means the repressor is not going to be repressing lactose is going to be bound to that repressor the repressor protein is going to be floating off somewhere not bound to the operator that's what happens when lactose is around so no repressor here low glucose means High Cy and look at that cap has its cyclic partner it's bound near the promoter it's stabilizing RNA polymerase genes are going to be strongly expressed there is no repressor and there is an activator doing its thing genes are going to strongly be on that's the mechanism double check with the logic we've run out of easy sugar we have lactose available of course we want to make these genes so we could metabolize lactose let's look at the next one high levels of glucose lactose unavailable well lactose unavailable means the repressor protein is going to be doing its thing it's going to be Road blocking it's going to get be bound to the operator it's going to get in the way high glucose means low cyclicamp which means the activator protein is not able to do its thing so not only is there no activation but there's a repressor in the way these genes are definitely not going to be expressed and again this makes sense there's no lactose around there is glucose just use glucose you don't want to be expressing this now we have low glucose and lactose unavailable no lactose means the repressor is repressing low glucose means High cyclic amp which means cap will have its partner it will be activating it will be helping get things started but it doesn't matter how good of a job cap does it's stabilizing RNA polymerase and helping it begin transcription if there is a repressor in the way you're not going to get transcription it's going to stop the whole thing so in this scenario yeah operon is off and again this makes sense there's no lactose around don't make genes for metabolizing lactose finally we have high glucose lactose available so lactose available means there's going to be no repressor here it's not bound to the operator it's going to be floating off somewhere with lactose bound to it high glucose means low cyclic am which means cap is not going to have its partner it's not going to be bound to the The Binding site next to the promoter it's not going to be stabilizing RNA polymerase so even though there is no roadblock here there's also no activator so expression levels they'll be on but because this is a weak promoter and there's no Act activator helping things out there's going to be very low levels of this the genes in this operon being expressed um so I'm not going to be you know writing down any of these you could try to memorize what happens in all four of these scenarios but honestly if you understand how cap functions when it activates when it doesn't activate how lack repressor protein functions when it represses when it doesn't repress press you could you know logic through and and figure out what would happen in any of these four combinations of scenarios so yeah I really like this figure as a good summary of things but I'm not going to write down all this we we've already kind of talked about what happens in all these scenarios this is just putting all of them together the one last thing I do want to note is the only you know as as we as we saw here the only scenario in which this lack lack operon is expressed strongly is if lactose is present and there are low levels of glucose and again this should make sense mechanistically and this should make sense logically there's lactose around there's not a better sugar green light game on okay now there are there are a bunch of other sections in this chapter all of which I'm sort of cutting for time and uh Andor for complexity uh so yeah this this takes us to the end of the regulating genus expression chapter but not to the end of this recorded lecture I do briefly want to begin the next couple of chapters the next two chapters chapter 18 and 19 both deal with Evolution evolution in the Origin of Species and the evolution of populations just like I did for the two genetics chapters I just don't I I I I like the textbook and I like what it has I just don't necessarily like the way things are organized so I'm sorry if you're following along with the textbook but I'm going to Mush these two together and just call this topic Evolution covering topics from both chapter 18 uh and chapter 19 so okay before we get into Evolution at all there are a few terms that I really want to outline these are the terms hypothesis Theory and law so let's start with hypothesis hypothesis is defined in the key terms as a suggested explanation for an observation which one can test so you see something going on in the world you know whether it's biology or astronomy or chemistry or physics or you know whatever you see something happening in the natural world and you come up with a a a guess maybe an educated guess maybe a reasonable guess maybe a logical guess but you you come up with something like oh maybe this is happening for this reason this is the ground floor this is how we understand the world around us we formulate a hypothesis and yeah maybe there's very little evidence to support it maybe there's no evidence to support it but this is the reason why we make careful observations and we do experiments in the first place to test this hypothesis and see whether our experiments or observations will support this observation or this uh this explanation or whether they don't support this explanation this is sort of the the ground floor close to the ground floor of things if you're taking the bisque 131 lab I know as part of that lab you'll formulate a lot of hypotheses and test a lot of hypotheses so uh this might be familiar to you if you are taking or have taken that lab already the other term that I want to bring up is Theory or scientific theory scientific theory is defined in the key terms as a tested and confirmed explanation for observations or phenomenon theories or scientific theories are based on reproducible experiments and reproducible observations so you may start with a hypothesis you may do a bunch of careful experiments on observations you see the same things every time different research groups see the same things over and over and over again once there has been a lot of support for whatever this explanation is we could start calling this a theory this is this is very weird because in our everyday English language the word theory is not a very strong word in our everyday English language the word theory is is is usually means a guess like yeah my car is making a clunking sound yeah I got a theory about what's doing that like in in the English language uh theory is like a hypothesis it's a guess it's where we start but what I want to impress upon you is whether it's biology or chemistry or physics or whatever in a scientific field when something is called a theory that is not not a guess that is not a like Baseline explanation if we call something a theory there's a ton of support for it let me give you an example of something that's kind of a no duh uh these days and that's something called germ Theory a germ theory states many diseases are caused by microorganisms and again this is a no duh we've got bacteria we've got viruses we have these these microbes uh that are responsible for causing infectious diseases don't memorize this table but yeah I think most people know bacteria can cause disease and there is a ton of support for this for for all of these things uh causing various diseases this is germ Theory uh not because it's a guess there's an overwhelming amount of support for you know diseases being caused by bacteria and other microorganisms the reason why it is a theory is because of its scope so not only are theories based on reproducible experimentation and or observation uh theories are always things that are Broad in scope they explain the how and the why how uh you know Anthrax produces toxins that you know trigger the immune response whatever and why it does that and you things like that theories are always Broad in how they explain things now we can contrast this with our third term here so we got a hypothesis Theory or scientific theory and law or scientific law a law is to read from the key terms a tested and confirmed explanation for observations or phenomena wait a second that that sounds familiar a tested so scientific law was a tested and confirmed explanation for observations or phenomena uh theory was a tested and conf confirmed explanation for observations or phenomena oh those definitions are the same so uh theories and laws hold the same amount of weight and I even wrote the same thing here just like a scientific theory a scientific law is based on reproducible experimentation and or observation you only start calling some explanation a law after there is a lot of support for it once again this is at odds with just our English language in the English language the word law is very strong you follow the law you can't break the law they're they're they're written down in stone or whatever uh and so yeah law sounds very strong Theory sounds very weak like a gas or whatever but in the field of physics chemistry biology in science theory is very strong law is very strong the only difference between the two is not one of strength or support it is one of scope theories as we saw were very Broad in scope laws are very narrow in scope often just explaining the you know what's going on not talking about why or how just what is observed there's a great example of this we've already talked about laws earlier in the quarter maybe you remember the first law of thermodynamics energy cannot be created or destroyed that doesn't explain how energy you know behaves or why it can't be destroyed all this law is saying is that you can't destroy energy or create energy just the the what of you know energy behaving the rules of energy and the reason why this is a law of thermodynamics and not a theory of thermodynamics is because it's very narrow in scope in the same way the reason why this is germ Theory and not germ law is because this explanation about diseases and microorganisms is very Broad in scope it's not narrow in scope this will never be germ law uh it will always be germ Theory uh because of because of its scope and what it's trying to explain so a very important Point here and again I'm making a I'm making a big point of this cuz this is this is unintuitive for how our English language Works a law is not a better supported Theory they hold equal weight to one another theories and laws whether some well supported observation of the natural world counts as a you know is classified as a theory or a law is simply one of scope okay now that we've outlined these terms we can talk about the theory of evolution so evolution is going to be a theory there's going to be a lot of support for it and this is is going to be a very broad scoped explanation but actually before we get to the theory of evolution I actually just want to Define what evolution is so this is not in the key terms because I I wanted to write out this definition and sort of unpack this because there are three important parts to this simple definition that I want to talk about in more detail we can define evolution as change in the genetic makeup of a population over time and hopefully I drill this short little sentence into your head cuz I'm going to use this phrase changing the genetic makeup of a population over time many many times over the next couple of uh recorded lectures so one part of this that I want to explore is population evolution is change in a population that means Evolution occurs not at the individual level but at the population level so I defined population I think on the first day of class I think in the first chapter but you know it's been a while so it's it's in the key terms for this chapter as well population is defined as all of the individuals of a single species living within a specific area so these changes that we are going to observe are not going to be one Little Critter changing the changes that we're going to see are changes within a group of Critters uh I like Pokémon as much as the next person but yeah the idea that one individual is going to morph into a different kind of thing is not what we observe in nature uh individuals do not evolve it's changes in the group level again this is kind of an odd with art like everyday English you know we'll talk about Evolution oh yeah my taste in music has evolved a lot since middle school or you know something like that um individuals do not evolve uh we're talking about changes within a group another important part to this phrase change in the genetic makeup of a population over time is genetic makeup and yeah recently we had a bunch of chapters talking about genes and genetic makeup so when I say genetic makeup I mean AAL frequency we're talking about which alals are within the population so AAL frequency itself is defined in the key terms let me read that the rate at which a specific alil appears within a population so the changes that we are seeing are changes in genotype you know which Al are common which Al are not common and again this has to be on the population level uh your alals are not going to change over your lifetime uh but you know within a big group of people you could have you know individuals being born individuals dying you know that can change in a big group it's not going to change within an individual so we're talking about changes in simply the frequency of Al which alal are common with which are less common the third part of this definition is the term overtime so when I say overtime I don't mean you know in the next five minutes or whatever uh I don't even necessarily mean in the next year when we say the phrase over time what we're talking about is Generations so in order for us to observe these sorts of changes we have to see individuals in the population being born or created and dying we have to see that kind of turnover and yeah it's going to take generations for that turnover to happen so exactly how long this takes depends on what population you're looking at bacteria you know that can reproduce in 30 minutes to an hour uh yeah you're going to be able to see meaningful changes in a Le frequency in those bacterial populations overnight but if you're talking about organism Ms that have generation times of years it's going to take much longer to observe changes in the genetic makeup of these populations so yeah over time we mean Generations that's what it's going to take to be able to observe these changes so this is our definition of what evolution is changing the genetic makeup of a population over time but how and why how do these Chang happen why do these changes happen if the theory of evolution is a theory it should explain these things and there should be a ton of support for it we this will happen we will talk about how these changes happen why these changes happen and the you know overwhelming support we have for this we will do that starting in the next recorded lecture so yeah I just briefly wanted to start on on Evolution here to Define these terms get us ready we will really get into this ch chapter or I suppose these chapters in the next one but this is the end of recorded lecture 43