hello bisque 130 this is the beginning of recorded lecture 33 and we are about to start on um chapter 12 and chapter 13 which are both about genetics so these are the titles of the chapters from the Open Stacks textbook that I'm using Mendel's experiments and heredity and modern understandings of inheritance kind of wordy um personally I think that the way the topics are organized in these two chapters is a is a little unintuitive uh so anyway what I'm going to do is I'm I'm scrapping this type of organization I'm lumping these two chapters together and I'm just calling this genetics so I apologize if you're trying to follow along closely with the textbook that this is going to be you know maybe a little bit out of order the way the textbook does it but I think the way that I've taken these topics uh and just put them in a different order is going to make more sense is going to be more intuitive is is just going to be easier to understand so these two chapters lumped together I'm just calling genetics okay so some some terminology to start off with chromosomes contain genes this is a concept I've introduced several times throughout this quarter but yeah the chromosomes we have have the instructions for making things um the term that I'm introducing though is the term genotype so all of these genes together are what we call the genotype of a cell or an organism the key terms Define genotype as the underlying genetic makeup of an organism genotype is describing your genes it's it's you know it's right there in the name uh all the genes you have contribute to your genotype now there's another term here most genes there will be some exceptions we'll see those in later chapters don't worry about that but for now most genes encode proteins they're a blueprint the instructions for how to build specific proteins proteins lead to what is called phenotype let me read the key terms definition for phenotype the key term say phenotype is the observable traits expressed by an organism so importantly this is you know what what you can see with your eyes this cat has uh short hair this cat has gray and black fur this cat has a a tabby patterning of of Stripes so phenotype is stuff that you can actually see you can't see genotype you can't look at you know a plant or a cat or another person and know the set of genes they have uh but you can look at a cat or a plant or whatever it is and and see these characteristics so importantly these are related to one another um because genes encode proteins and proteins lead to you know phenotype genotype leads to phenotype the set of genes that an individual has is going to result in what that individual looks like again there's some gene or genes that are related to having short hair and to having Tabby pattern and gray fur this cat has all these phenotypes because it has all these genes that lead to those phenotypes genotype leads to phenotype okay let's talk about inheritance now so how the how these things are are passed on what we're talking about is something called mandelian inheritance so this is called mandelian inheritance it's named after this Austrian monk named Gregor Mendel we're not really going to talk about his biography or much of his like exact experiments and stuff I'm just bringing him up because that's why this is called mendelian inheritance named after Gregor Mendel um it's also worth noting his groundbreaking experiments used the pea plant um it's not the most exciting organism out there uh but we're we're actually going to use the pea plant as an example of how mandelian inheritance works because even though it's not very exciting uh it actually uh makes for a very good example to understand basic genetics and yeah mandelian inheritance so the first principle here is the idea that there are different versions of genes that can exist so any given Gene can have different versions or different variations um these things are called alals very important term uh it's not in the key terms because an alil is just a different version or variation of a given Gene a fantastic example of this again using pea plants is the white alil for p flower color and the purple alil of the P flower color Gene so these two genes are actually the same gene this is the flower color gene on this chromosome purple and white are not two different genes they are two alals of the same gene this is the purple flower version of the flower color Jean this is The White Flower version or a of the flower color Gene again the terminology might be a little you know clunky here but it's very important to note Al are not different genes Al refer to different versions or different variations of the same gene as I've summarized here now the seem is pretty straightforward if you've got the purple flower Al you're going to have purple flowers if you have the white color Al you're going to have white flowers but um this gets a little complicated because PE Plants just like us are diploid diploid organisms have two copies of each chromosome you may remember this figure from an earlier chapter when I first defined diploid we've got two copies of every single chromosome which means for p plants they're going to have two copies of this chromosome which means they're going to have two copies of the flower color Gene so diploid organisms have two copies of each chromosome and two copies of each gene now there are several possibilities here for what an individual can have or a PE plant can have if we're continuing to use them as an example if this PE plant or whatever has two copies of the same alil the term for this is homozygous so if there's a pea plant out there on on one of its chromosomes it has the white flower alil and on the other chromosome because it's got two uh also has the alil for white flowers uh that's homozygous two of the same thing here's another way to have homozygous if you're a pea plant and you've got a purple flower Al on one of your chromosomes and also the purple flower Al on your other copy of that chromosome that's also homozygous two of the same thing means homozygous what phenotype are they going to have well that's it's pretty obvious if you've got two of The White Flower alil you're going to have white flowers and if you have two of the purple flower alil you're going to have purple flowers this much is pretty easy let me summarize this here so uh these homozygous individuals will have the phenotype of the AL version they have again they're either going to have purple flowers or white flowers depending on which Al they have two of but what if you have two different alals so an individual can have two different alals and the term for this is heterozygous and what's the Fe type going to be well yeah that that's that's a bit of a question mark here if you've got a purple Al and a white Al what is that going to lead to again genotype leads to phenotype what phenotype is going to come out of having one of each well the answer to this question actually depends on what these genes are doing so we're going to look deep at this exact example but again you you'll see in my summary that we're not memorizing all these details this is just to kind of walk through this particular example to understand in this way for flower color how genotype leads to phenotype so okay background flowers with purple because they have a pigment molecule called anthocyanin yeah here's a this is not a pea plant this is a cauliflower but yeah it's purple there are lots of things in nature that are purple uh vegetables in nature that are purple plants in nature that are purple they're all purple because they're making this class of pigment molecule called anthocyanins pigments should be a familiar concept to you we saw these in the photosynthesis chapter um here were you know Green pigments reflecting green to your eyes and absorbing everything else these things look purple to your eyes because this pigment reflects purple back to your eyes and absorbs all the other wavelengths of visible light so that's why these things are purple but where do these anthocyanin pigment molecules come from well we get anthocyan I keep saying we you know P plants pretend you're a PE plant for the next 10 minutes um we get these anthocyanins from oh one of these so do not memorize any of this but the basic structure of what we're looking at here should look familiar to you this is a metabolic pathway you know kind of like glycolysis was a metabolic pathway uh specifically this is one of those assembly lines this is an example of anabolism an anabolic pathway through a series of intermediates every single one with its own enzyme here uh these anthocyanin pigment molecules can be created uh by you know pretty simple starting materials that every cell is going to have so all right what does this have to do with the the purple Al Leo with the purple G remember genes encode proteins this purple flour Al in the DNA is the blueprint the instructions for building this protein what is this protein do well this protein doesn't build anthocyanin so remember there's like one two three four five there's a bunch of proteins in this pathway that contribute to building anthocyanins this protein acts as a switch for the entire pathway we'll talk more about switches and Gene regulation and the details of how things like this do their job in a later chapter but for now just know that this this protein turns on the pathway so if you have a purple flour Al that means you're making this switch protein you're turning the pathway on and you're building an the cyanin and your flowers are going to look purple in a homozygous purple flower you've got two of this alil so you're making double the copies of this protein of course the pathway is going to switched on be switched on and the flowers are going to look purple this is what we talked about earlier homozygous purple is going to have purple flowers but now we know why the genes make the proteins the proteins turn on the pathway the pathway builds pigments the pigments make it look purple so what if about the other Al this is what the purple version of this Gene does what about the white version well as it turns out the white Al for this flower color Gene encodes a defective protein it's sort of like a broken blueprint that doesn't build what it's supposed to build it doesn't really build anything at all so this white alil does not it encodes A protein that doesn't do anything um so so it's not going to switch on the pathway without the pathway switched on none of these chemical reactions are going to happen you're not going to build anthocyanins and so the flowers are not going to look purple they're going to look white which is sort of like the default color for most things if you're homozygous for this white alil you could imagine what happens you've got two defective genes making double the defective copies uh yeah it's still not going to work it's going to be turned turned off not it's not switched on uh none of these an thein are going to get made flowers are going to look white again this is what we said before if you have our homozygous white flowers are going to be white but now we understand the the order of events why this happens defective proteins pathway not switched on no pathway no purple white instead now I brought all of this up so that we could understand what happens in the heterozygous system situation so for this Gene for these alals what happens in a heterozygous situation well for heterozygous we have a purple flower alil this alil encodes this switch protein which could switch on the pathway and you know make purple but we also have the white flour alil the white flour alil encodes A non-functional protein that doesn't do anything this protein that doesn't do anything though doesn't get in the way of a functional copy it just doesn't do anything on its own so if you have a working copy of this switch and a dud the switch is going to get turned on it's going to get turned on just as much as it was turned on with two purple alals U and you're going to have activation of this pathway cells are going to build an thein flowers are going to look purple they're going to look just as purple as they they did with homozygous purple because you know either the pathway is on or it's not on it can't be like more on because there are more of this protein uh it's it's just as on as it was in either of these circumstances so whether you're homozygous purple or heterozygous the phenotype is going to be the same purple flowers and again the only reason we know that this is going to be purple is because we understand this pathway again it's important to appreciate that Al these these genes encode proteins and the proteins do stuff and the stuff that they do results in these phenotypes so there are a couple of terms here dominant and recessive so in the the relationship between the purple flower alil and the white flower alil we say that the purple alil is dominant and the white alil is recessive we say that because of this relationship when you put the two of them together the phenotype is purple white just kind of disappears here purple is sort of stronger than white in this you know matchup between the two of them that's why we declare that purple is dominant and white is recessive and again we know this because of all the biochemistry of what happens so again this is a lot of information but what's what's my take-home me Mage from this so here here's my summary of all all of this for any given Gene whether it's flower color or whatever one Al is dominant and the other Al is recessive if we want to look specifically at pea flowers purple is the dominant alil white is the recessive alil and we know why because of this heterozygous individuals will have the phenotype of the do Al so here's a heterozygous individual it's got one of each what is its phenotype going to be it's phenotype is going to correspond to whichever of these alals is the dominant alil in this case purple is dominant so the phenotype of a heterozygous individual is going to be purple uh example with PE Plants because purple is dominant heterozygous individuals are going to have purple flowers importantly there is no light purple there is no inet there is no blending here the heterozygous purple is just as purple as the purple of the homozygous uh you know again you don't take the average or anything like that uh it's either purple or white two options here the heterozygous individual looks exactly like the homozygous purple individual now we have some terminology um well we even more terminology there are three possible genotypes homozygous dominant homozygous recessive and heterozygous let me walk through these but again these should be familiar this is just we already defined homozygous now we're just throwing dominant and recessive into the mix a homozygous dominant individual is an individual that has two of the same thing that's what homozygous means and the thing that they have two of is the dominant alil homozygous recessive individuals have two of the same thing that's what homozygous means but the thing that they have two of is the recessive alil heterozygous individuals have one of each importantly there and I I will try to trick you on a multiple choice test I'm not really trick you but you know whatever there's no such thing as heterozygous dominant or heterozygous recessive just even thinking about that should just not make any sense at all heterozygous means you have one dominant and one recessive so heterozygous dominant just doesn't make any sense heterozygous recessive just doesn't make any sense it's just heterozygous one of each so when we're talking about genotypes of a specific Gene these are our only three options homozygous dominant two of the dominant homozygous recessive two of the recessive or heterozygous one of each and importantly all these genotypes lead to a specific phenotype the homozygous dominant genotype leads to the dominant phenotype purple in this case homozygous recessive genotype leads to white flowers whatever the recessive alal phenotype is and the heterozygous genotype leads to the dominant phenotype because you know we got two of them together the dominant is stronger than the recessive you end up with the dominant phenotype here's my summary slide three possible genotypes homozygous dominant has a dominant phenotype homozygous recessive has a recessive phenotype and heterozygous has the dominant phenotype I'm going to use these terms homozygous dominant homozygous recessive heterozygous I'm going to use these throughout this genetics chapter so you should really become familiar with these three terms used to describe genotype let's turn our attention now to inheritance to how these traits and these alals and genes are passed from parents to offspring so if we're talking about oops here we go um this should look familiar use this in an earlier chapter talking about reproduction so both parents again whether they're humans here or whether they're pea plants uh both parents are going to be diploid but when it comes time to making Offspring to making sperm or eggs as the case may be only one copy of each chromosome goes into the sperm only one copy of each chromosome goes into the egg so parents uh are both diploid but they only pass one of each chromosome to their offspring um back in the chapter when I used this slide I introduced this analogy of diploid meaning having two slightly different chairs and two slightly different tables and to slightly different nightstands and and so on uh so yeah when it comes time you know each parent is diploid but when it comes time to making eggs or sperm they make hloy cells they make haid rooms only one of each piece of furniture gets passed on to The Offspring and of course which one goes is chosen randomly we talked about all this in the meiosis chapter so which version of each chromosome that they put into any given egg or sperm is chosen randomly this results in many possible outcomes and again this increases genetic diversity that's really good for having diverse Offspring now there are many possible outcomes here but we can predict what these outcomes could be the way that we predict the outcomes is through things called punet squares these are diagrams that are used to predict the possible genetic outcomes of Offspring from parents this is usually done one gene at a time you could do bigger more complicated ones that track multiple genes but everything we're going to do in this class is just looking one gene at a time what do the parents have what combinations could The Offspring Have so there are some rules to building punet squares uh and you know we will draw some of the these I'll show these in in just a couple of minutes but let's let's outline the rules first so again we're tracking one trait one gene at a time the trait or the gene is assigned a letter so let's again keep looking a flower color by convention the letter that we choose is usually the letter associated with the dominant phenotype so for flower color as we've seen earlier the dominant phenotype is purple so by convention the letter we would choose is p we will see in just a minute why this is a bad idea but again by convention usually associated with a dominant phenotype individuals are diploid so they're going to have two of that letter so you know the parent each each one of these parents is going to have a p and another P how do we distinguish between dominant and recessive alals again P doesn't refer to any specific phen genotype p is just talking about flower color uh you know what what if there's a white alil do we use W no we don't use W never use W um we have to distinguish between dominant and recessive by doing capital and lowercase so the letter is capitalized if it is the dominant Alo and lower case if it's the recessive alal um again they're both P because they're both the same gene now you can see why p is a bad choice uh just be so dominant purple flowers capital P recessive white flowers lowercase p uh these are these look too close to one another these are easy to mix up with one another I don't recommend ever even if convention dictates you should use a letter associated with the dominant phenotype I don't recommend ever using letters where the lowercase and the uppercase are easy to mix up with one another I would use a a is an easy one Whatever font you're using uh capital a and lowercase a are are very easy to distinguish so you know just by default it doesn't matter what letter you use really uh a is a good choice so knowing that dominant is capital A and recessive is lower case a this gives us a very neat shorthand for describing those three genotypes that we defined earlier so homozygous dominant having two of the same thing and it's dominant that you have two of can very easily be um written out as capital a capital A homozygous recessive having two of the same thing and it's recessive you have two of is just lowercase a lowercase a very suin and of course heterozygous means one of each capital a lowercase a um I guess you could do lowercase a capital A the order doesn't technically matter uh by convention usually the heterozy uh is written like this with the capital letter and then the lowercase letter so yeah these are um important ways to sort of abbreviate these three genotypes using these conventions of capital and lowercase so where where's the actual Square this was just backstory so to do a punet square you start by drawing a square um and then drawing a couple of lines through it to create a 2X two grid so not really a punet square more of a punet grid but you know it is what it is we are going to write out the genotypes of the parents on the top of this grid and on the left side of this grid so we could do whatever parents we want uh as an example here um let's say one of the parents is homozygous dominant and let's say the other parent is homozygous recessive let's put some visual rules in here just to remind us what these things mean homozygous dominant means two of the purple alal and homozygous recessive means two of that white Al okay so how how are we going to fill this out well let's use our shorthand homozygous dominant means capital a capital A and we're going to put it up here just like this with one of these lined up with these two squares and the other letter lined up with these two homo IUS recessive means lowercase letter lowercase letter and we're going to put them over here on the left lined up with these squares just like this so this is just describing the parents the letters up here are describing one parent the letter the letters over here are describing the other parent this is supposed to look at The Offspring The Offspring are going to be in here these four boxes are going to describe what The Offspring could be B so to fill out the boxes in this grid we start by taking this letter and dragging it down to fill out this box it's a capital A so we're going to fill in this box with a capital A we're going to drag it down further to the other box fill out this one with another capital A now we're going to do the same thing with this a we're going to drag it down fill out this box it gets a capital a and this box gets another capital A so we filled out one of the parents now we have to do the same thing for the parent over here the lowercase a here gets pulled to the right and fills out this box it already had a capital A now we're adding a lowercase a going to drag it over to this box this box gets a lowercase a as well now we move down here pull this lowercase a into this box it gets lowercase a and pull it even further to this box now it gets a lowercase a as well so we've finished filling out this Square uh but what is it what does it mean well each one of these four boxes represents 25% of The Offspring because there are four of these 25% 25% 25% 25% it totals up to 100% again this is predicting what The Offspring could be each of the four boxes represents a 25% probability of possible Offspring now you might be wondering how I'm going to grade this on a multiple choice test yes all my tests are multiple choice I I'm not going to you know like handgrade your punet squares but what I could do is I could ask you a question like this in a crop cross a genetic cross between a homozygous dominant parent and a homozygous recessive parent what percentage of The Offspring will be heterozygous so this is heterozygous this is heterozygous this is heterozygous this is heterozygous the answer 25% plus 25% plus 25% plus 25% the answer is 100% 100% of The Offspring will be heterozygous CU each box is 25% I here's another I could say in a cross between homozygous dominant and homozygous recessive what percentage of The Offspring will be homozygous dominant the answer to that question would be zero none of these offspring are homozygous dominant so maybe you see where I'm going here the the questions will always what percentage of The Offspring will be you know so and so and you'll have to be able to draw and fill out this punet square and you know add up 25 25 25 25 to get whatever the percentage is let's do another one more more practice here so let's do a slightly more interesting cross Let's cross a heterozygous parent with another heterozygous parent visuals heterozygous means one of each each heterozygous means one of each capital A and lowercase a again it doesn't technically matter whether you put the the uppercase on the left or the right or whatever but by convention we always put them in this order with the the uppercase the the dominant Al on the left uh and the lower case on the right uppercase on the top lower case on the bottom so yeah we we filled this out just like we did before drag this a down drag it down further drag this Al down drag it down further we're halfway done now we're going to drag this Al to the right drag it further to the right to fill out this box again we had a lowercase a here we added an uppercase a by convention we always just put them in this order with the the uppercase on the left and the lower case on the right take this lowercase drag it over to fill out this Square take this lowercase drag it over to fill out this Square and there we go again I could these are the questions I could ask so yeah you do a cross between two heterozygous parents what percentage of The Offspring will be heterozygous the answer is 50% this box is heterozygous this box is heterozygous 25 plus 25 50% what percentage will be homozygous recessive the answer is 25% this one box is homozygous recessive oo I could get tricky I could ask what percentage of The Offspring will be purple you know what percentage of The Offspring will have the dominant phenotype here we have to think back this is going to be purple homozygous dominant has the dominant phenotype this is going to be purple heterozygous has the dominant phenotype heterozygous has the dominant phenotype this is going to be purple as well but this is going to have white flowers uh homozygous recessive does not have the dominant phenotype homozygous recessive has the recessive phenotype so if I asked you what percentage of The Offspring are going to have purple flowers the answer is 75% 25 plus 25 plus 25 so again these are the the sorts of questions that I could ask on an exam let's do one more and for this one I'm not I'm not going to do this one piece at a time for this one if you if you really want some practice if you got this down already that's great but if you really want some practice pause this video draw this out yourself on a piece of paper uh you know fill out the individual letters uh and then hit play on this video again I'll I'll give you the answer but yeah if you want some practice pause and do this on your own if you're coming back to this now your ponent Square should look like this so once again if I asked a test question you're doing a cross between a heterozygous parent and a homozygous recessive parent what percentage of The Offspring will be homozygous recessive the answer 50% homozygous recessive homozygous recessive 25 + 25 50% what percentage of The Offspring will have the dominant phenotype 50% heterozygous individuals have the dominant phenotype homozygous recessive individuals have the recessive phenotype so this is going to have the dominant phenotype this is going to have the dominant phenotype these this 50% is going to have the recessive phenotype so again lot of practice here but those are the sorts of questions that I could ask one more thing about this so when I write a test question I'm going to say a cross between a heterozygous parent and a homozygous recessive parent how do you know which one to put on top and which one to put on the left well it doesn't matter so if you put the heterozygous on top and the homozygous recessive on the left your Square would look like this if you put the homozygous recessive on top and the heterozygous on the left your Square would look like like this so technically the squares do look different depending on you know which parent you put on the left and which parent you put on the top but all the numbers all the results are exactly the same you know what percentage are going to be homozygous recessive it's still 50% what percentage are going to have the dominant phenotype it's still 50% so do do not worry about which one goes on the left and which one goes on the top it does not matter which parent goes on the left in which parent goes on the top you will get the same results either way now we've been talking a lot about PE Plants because again they're they're a convenient example and there's some historic reasons for this uh but I I do want to point out before you get too bored with all of this that there are a lot of human traits and human diseases um that follow everything that we've talked about um again don't memorize this table but it is an interesting one to look at um Hon's disease it is a dominant trait the AL for Huntington's is dominant the alil for uh you know normal um you know brain protein whatever uh is recessive if you've got one Huntington alil you will have Huntington's disease because it's dominant these are recessive things cystic fibrosis is recessive if you've got a cystic fibrosis alil if you've got just one of them you're going to be fine if you've got two of them you're going to have cystic fibrosis so um again just pea plants can be kind of boring I just wanted to point out in this single statement many human traits and human diseases follow what we've talked about follow mandelian inheritance patterns we use the same terminology of homozygous dominant homozygous recessive and things like that you can make Punit squares uh to track uh cystic fibrosis or Huntington's disease or fenal ketua or any of this stuff uh there's a lot of actually interesting human things uh that follow everything that we've talked about so far okay we are not done with the genetics chapter this is the genetics chapter it's it's a couple that have been lumped together we are not done talking about genetics uh but that is enough for this recorded lecture we will pick back up and do more genetics in the next one but this is the end of recorded lecture 33