Genetics and Molecular Biology Exam Prep

we're in module 10. so if you've looked at the uh syllabus we we're almost there right um exam Three is coming up and it's going to cover chapters 10 through 17. so I did a review last week it's it's going to be there if you didn't watch it please watch it because the exam is coming up so you need to have time to practice those genetics problems as we went over them a monohybrid in complete dominance sex-linked blood type and there will be a dihybrid question about phenotype uh ratio so that's chapters 12 and 13 looking at those types of problems for chapter 14 this was replication so we worked on that last week as far as sharkov's rule a to T C to G so it should be a fairly easy short answer question for that one you flip the ends and you use those base pairing rules and that should be pretty straightforward and then transcription and translation I introduced as a lab concept so if you watch the lab video from last week in module nine I covered it that comes from this week's lecture in chapter 15. so we're going to go over that in more detail but there will be one transcription question one translation question on the short answer portion so the bulk of your short answer problems are genetics one replication one transcription one translation and those are things that you have to practice it's not just I'm going to memorize a fact and regurgitate it you're going to have to actually work something and so that's why I'm saying practice that the test is coming up these things require you to look at them a couple of times so just to give you an example let's just do two genetics problems real quick let's do a blood type um let's say uh mom has blood type O and dad has blood type B on the test I'm going to ask you what are the genotypic and phenotypic ratios possible for The Offspring and then probably a probability question okay so I'm going to tell you mom has blood type O dad has blood type B give me the genotypic and phenotypic ratios that are possible from this cross and so you just get the blood type you have to know what the genotype is for that so remember with blood type O it can only be one way it looks like this you do those two little recessive alleles for blood type B while there are two ways to be blood type B I told you just to remember the heterozygote version for both B and for a so you would just write that down that way you never miss a possibility in doing that cross and so then I really need a finer tip stylus that door will never be open just so you know um so then this is what the the cross ends up looking like and genotypically you write what you see so you can just make a list two that look like this and two that look like that that's genotypic you're showing me the genetic makeup so that's what I want to see for the genotypic ratios phenotypically you would have two blood type B possibilities two blood type O possibilities and then I'll ask that probability question so if I had asked what's the probability they'll have a child with blood type B it's two out of four one half or 50 percent and again I give you all those options not because you have to put that on the short answer portion of the test but because the multiple choice you will see sometimes it's a fraction response sometimes it's a percentage and I want you to know it's all coming from the same cross it's just giving it to you in a different version so on the short answer portion you just have to give me one answer but just know that when we work across it could be any of those so guaranteed one blood type question on your exam it's a short answer question you'll have to give me genotypic and phenotypic ratios and then I'll ask a probability as always with my exams you get partial credit so even if you only can give me one part you're going to earn something as opposed to just leaving it blank okay and again you'll get to use a scratch sheet of paper I know you need to work this out so you'll just show that blank sheet of paper both sides to the camera that way you have something to work this on um and I I turned off the flag setting so it won't flag you for lifting your head and not looking directly at the screen the whole time a Sex Link problem um let's do one of those just real quick before we add on um sex linked I could say mom's a carrier for red green color blindness if I say she's a carrier she looks like this males are Hemi zygous they cannot be heterozygous which means they can never be a carrier so let's say Dad has red green color blindness he's gonna look like this all of our sex link crosses for this class are going to be x-linked recessive conditions when you get to genetics you'll see that's not the only the genetics course uh not not the topic uh you'll see that's not the only type of x-linked or sex-linked problem that can occur there are y-linked problems there are dominant genes that uh get carried by the X chromosome but I like consistency for the first time I introduce something so I'm only going to give you x-linked recessive because that's what the book highlights and that's all the problems that we've done so just know that on your test it's going to be a problem that we've seen for a disease that we have seen or at least talked about so for sex linked it looks kind of like wood types because you are tracking the allele that's raised to the chromosome that's representing where it's being carried so you have to use the sex chromosomes for this you always keep that dominant allele first and then when you analyze the results it's gender specific so if I say what are the odds that you're going to have a son that's affected it's not one out of four it's one out of two so it's a 50 chance that you're going to have a male that's affected so gender uh specific questions or sex-linked questions you just look at the two males and you assess those if I ask a male question if I ask a female question you look at it that way as well so these questions are both on your lab exam and this lecture exam so the lecture exam I have the dates on the board your lab practical exam is at the end of the the same month end of April okay and you'll see this problem so I'm asking you an x-linked cross problem on the lab practical and questions a b c d will be that you just list the genotypes for that cross so as you're studying for this test just know that you're helping yourself out by preparing for that lab exam as well because blood type will be on the lab practical as will sex linked so you want to get it now because it'll help boost your grade if you get right on both both problems so genotypically you just list everything that you see in the cross so that's genotypic phenotypic you'd have one daughter who's a carrier one daughter who is affected one unaffected male and one effective male and since this is red green color blindness that's we're looking at affected by red green color blindness and then I could ask that probability question and again you just look at it based on which gender I'm asking for so questions on blood type or sex linked and then again you'll have a dihybrid question and so um remember with dihybrid we're looking at the law of segregation and the Law of Independent Assortment just in gamete formation so what you learned about in meiosis which was chapter 11 we are seeing applied in genetics so the the order of the book may seem random and you think we're jumping around but it's setting the Precedence for why these things happen and why we see things skip Generations or recombine Etc so for gamete formation here you can only have one R and one y in each of The Offspring That's the Law of segregation you're separating them out and the Law of Independent Assortment says you've got to look at all the possible combinations between these two genes so this is dihybrid looking at two different traits so I told you you could use foil or I said you could take the first set of genes write them out once like that and then take the second set of genes and write them once for each letter that you just separated before so the Y goes here and then you do the same thing for this that gives you all four possible gametes right so you won't miss a combination because you'll catch them all so on the exam that you have coming up I'm going to ask you a dihybrid question but just about the phenotypic ratios so I'm just going to make this easy so I can actually get started with new materials so let's say we cross the same setup and this is Mendel's ratios um where we can put them together and again this makes it more apparent why you keep dominant alleles first and you keep same genes together because that will make it easier to read rather than if you just start scrambling R's and y's and then it doesn't matter where you start because that rule of keeping the dominant Gene first and similar letters together will make it easy to interpret no matter where you start it at I shouldn't have picked the why that makes it hard here and I gave myself very little room ah I don't know what I hit writing on this screen is uh new experience for me okay so then we track them and so remember with Mendel's ratios the first thing he looked for was dominant for both traits so a dominant r a dominant y once you use it towards that end you cannot use it again so you just need one of each and then that means you've counted it for dominant for both particular um areas so if you count all of those one two three four five six seven eight nine Mendel's ratios told us that first number for two heterozygous being dominant for both having a Big R and A Big Y he gave us this 9331 ratio so I'm just showing you where it came from once you've counted it towards something you can't use it again so your number should always add up to 16 every time you do a cross second trait that you track should be dominant just for that first Gene so you're just looking for the dominant R so we have one here two three and so that's what we're looking at here second one would just be dominant for the Y the one two three and then that last one is going to be recessive for both and there's just one so nine plus three plus three plus one adds up to your sixteen we've accounted for all of them this is a phenotypic ratio so the short answer question is not going to be two heterozygous cross but the approach is the same you're just going to set up the gametes for both parents put them at the top and the side and then fill those in and then just count how many are dominant for the verse for both dominant for the first dominant for second and recessive for both and you're just giving me those numbers you don't have to write all the genotypes you don't have to do anything crazy if you present it in this order that's all I'm asking you for for that question okay so again I'm always recording these so you can go back and and watch them and I gave you lots of practice problems in the genetics uh module um which I think was like module eight seven or eight somewhere around there um we had a lab so you had lots of PDFs that I did not take for grades just so you'd have something to try it on and then you could come back to me with hey I don't know this problem or hey can you verify I did this right however you want to approach it you can even send me a picture and say can you look at this and tell me if I did it correctly and that way you know you're on the right track so you've got some time but these are the kinds of things that I'm saying you need to practice you can't just put this in your head and then regurgitate it on a test this is this is very much going to require some practice oh last last week we were talking about DNA we've talked about the structure we know it's a double helix we know it's anti-parallel we know the monomer form is a nucleotide so we have a five carbon sugar we have a phosphate group and we have a nitrogenous base and we talked about schargov's rules the Ada T C to G I also introduced you to all the enzymes and I made a list last week in the recording so you can go back and track those those enzymes and so the short answer question I'm going to ask you about on replication on your exam is not about these enzymes those are going to be on the multiple choice where you're what what enzyme does this or what what uh protein does this um problem instead what I'm going to do is I'm going to ask you to replicate a given strand so if I tell you that this is the parent strand I'm just going to make it short that's what you're going to see typed on the test I'm going to say replicate this strip what direction does replication go does anyone remember right so the ends are going to flip and it always goes five to three but on a tight test I can't tell if you start on this end so replication goes 5 Prime to 3 Prime because of the orientation of the phosphate group on that five Prime end but you do have to flip the ends you're typing this so you're gonna you know on this end you would type a three on the other end you're going to type a five in a Cell it's going to start at that five Prime in and work to the three prime Direction but on the test I'm looking for did you flip the ends that shows me you know it's anti-parallel we can't have two five Prime ends on the same side they would repel each other because they're both negative charges and then I'm looking for chargoff's rule for replication that is going to be a to T and C to G so for this strand what would the daughter strand be it's it's that easy the short answer question is going to be that easy what enzyme makes DNA I'm going to ask you that on the test and remember there's multiple different DNA polymerases I'm only having you know two DNA polymerase 3 and DNA polymerase one Paul one is the proofreader it removes the okazaki fragments the the little primers that are RNA it removes those and then puts in DNA but actually synthesizing DNA is DNA polymerase 3 and again it works in the five Prime to three prime Direction now I do want to point out that in Connect all the answers get presented five to three and I can't control that so just pay attention to the fact that even though it is anti-parallel they are giving you all the answers in the same format and students are looking for that flipped orientation and the multiple choice responses and they're not giving it to you they're presenting them all in that five to three format because it's made five to three but they're presenting it like they would read it so this answer here if it were connect the answer would have been c g g a t and then three prime yeah they they started they present it from here first and then they give you the enzymes in that backwards orientation it's still right but that's how DNA is working and so the logic and I've asked the rep about this the logic is DNA is made five to three so that's the direction you would read it in so they give you all your answers that way I'm not going to do that because on the test you're trying to go you're timed right I'm going to present it so that you're just type it so that it lines up it's hard enough to take a test with that stress without having to look for it so I can't change that and connect it's a connect system uh question but on the test you know no it's anti-parallel and just know that connect is something that I cannot cannot control um so this is from chapter 14 last week and in lab I started central dogma and I gave you guys a handout and the handouts posted in this week's module so if you didn't get it you can see it in the module so you're not missing anything but central dogma just involves transcription and translation so replication happens in the S phase of the cell cycle we learned that back in chapter 10 when we talked about the cell cycle so replication a to T C to G is happening in the S phase transcription translation these are happening in the G phases the the cell is doing its job it's making the products it needs to be whatever cell type it is and so transcription is taking DNA and turning it into and I introduced messenger RNA in lab last week we're going to see it in chapter 15 this week and because we're making RNA this added a new enzyme to your list of of enzymes and that's RNA polymerase so it follows sargov's rule but RNA doesn't have thiamine so shardoff's rule tweaks for transcription and you're going to have a to U and C to G now notice that when there's a t right here see that t it puts an a that's the only place I see students mess up so I'm going to be looking for it and it's worth one point because CNG don't change so whether you're replicating or transcribing it's all the same but what you have to be careful about is if DNA says T you have to think about what does RNA have it has an A so I can put an a here but if the DNA says a we can't put T that's the only place that we see a change in transcription is we just replace what would have been a t with a u so Charlotte's rules a to U and C to G is really just changing what base pairs to that a when I'm writing down the RNA strand so this is a short answer question on the test this figure came from your book you have an activity for transcription we looked at it in lab but I'm going to give you a strand of DNA and it's going to be kind of the same approach and I can't remember what I wrote down before I think it was like this right so I'm trying to be consistent so when I say transcribe and I give you this strand you still have to keep in mind it's anti-parallel it's still only going to go five to three because DNA and RNA both have a five Prime phosphate so you can never have two five Prime ends together just never gonna happen so you're always going to flip the ends and it's going to work in the five to three Direction because of that the difference is what you write so when I transcribe if DNA says a I write a u I can't put down T because RNA does not have one everything else is the same so a g g c no change okay so the only difference for transcription and I'm going to go over this this is in this next lecture I'm just showing you the application from last week's lab and then I'll uh cover it more than you care for has to do with watching what RNA has versus what DNA has the second step for central dogma after transcription is translation where we then start reading these bases of mRNA we read in three three bases at a time this is called translation and we're going to start building our protein so this blue structure here represents the ribosome remember the job of the ribosome from chapter four is protein synthesis so now this is the chapter where we see how do ribosomes which are just made up of RNA actually turn it into protein and what it comes down to is for every three bases of mRNA it correlates to a single amino acid so this is the genetic code table that we were introduced to last week so for uh and I'm just going to give you a strand of mRNA here and I'm going to make it stupid short just for this purpose um on the test you're going to have one translation problem I'm going to give you the code table no need to memorize it it's not applicable you get that in biochem they'll talk to you about it then what I want you to know is just how to use it so I'm going to have you apply the genetic code table on a couple of problems but the short answer question I'm going to assign you is I'm going to give you a strand and I'm going to say translate this so all you have to do is know where to start where to stop and then how to actually apply the table so every protein in our body starts with a very specific amino acid called methionine met for short you see it in green on this table so what that means is on the test if the first triplet codon that I give you and that's what we're looking at when I say codon it's three bases of mRNA so a codon is three bases of mRNA that's the only thing you can use on this table you can't use DNA can't use anything else it's got to be three bases of mRNA if the first three bases are not a U or Aug you're not going to do anything with it because we can't start making a proton a protein until we find Aug so you would just ignore anything that's not Aug when you get Aug that's when you start translation and while it says start I want you to ignore the word start it'll start the process and code for methionine there's no start it's always methionine so you can have it multiple times it doesn't affect it so if I had done Aug in in triplicate right three augs in a row it would just be met met met three times it doesn't do anything it's just the first amino acid in the sequence so all you would do for translation is you would write down that code m-e-t so what would we use for the second codon Pro right right so this codon sheet tells you okay if my first base is C it's going to be somewhere in this row second base is C it's going to be in this column so that narrows it down to a box third base is C and it's right there you could of course read every single one if you wanted to but the outer directions are telling you it's going to be in this row this column and then it directs you directly to that base so there are 64 codons here and in this chapter we're going to talk about how they figured those out um and why we see thumb repeat so if you look at glycine right here there's one two three four different ways for glycine so there's a phrase where we say redundancy but no ambiguity the redundancy is there are four different ways to code for glycine no ambiguity is if I have ggu it's always glycine and so with our code we can have a problem think about what happens if I change this C to something else let's say I mutate just the C to a g what does GCU give you right okay so that is a single base change but I've just changed my amino acid and again we talked about sickle cell anemia sickle cell anemia is one base change in DNA you change the structure of the DNA you change the amino acid that's coming into play that changes how your protein is going to shape structure equals function all the way down and that leads to the disease state of having Sickle Cell now you have a blood cell that cannot transport oxygen properly and guess what we kind of need oxygen so when we're talking about the order of this the the order is incredibly important so you have to think about what happens to us if we delete a base if we add a base we read in threes so if you delete or add you've shifted everything over this is called a reading frame shift and you've altered every Gene from that point on so we talked about those thymine dimers and replication remember we're two adjacent thymines Bubble Up in response to UV radiation that essentially acts as a deletion we just took out two bases everything is going to shift over because of that which means you have multiple errors on a strand which increases your rate of what when you're exposed to sunlight all the time tanning whatever UV radiation cancer right so this is why it's important to understand structure equals function down to the DNA level because it affects everything afterwards so that's what we're going to be looking at this chapter and we're going to look at mutations specifically whether it's within a gene or the entire chromosome specifically because again if you remove just a single one it changes everything from that point down which changes the the goal of that Gene to begin with and then of course we're also going to be looking at variations and eukaryotes get more complicated because we have 46 linear chromosomes as humans prokaryotes just have this one Loop so in eukaryotes we have something called RNA processing where your DNA by itself is not the end of what you're going to make because we can alternate it and change it so we have human genes that make three different products through this process of alternative splicing where we will cut out different parts and join them together so when we talk about the human genome and we say we only have this many genes but we have this many proteins it's because we mix and match what we have and we make multiple products and again our body wants to be you know mindful of our resources so if we start to make something and then the body's like never mind I don't need it it's like I started to make this can I turn it into something else that's the goal of RNA processing is I already transcribed this I don't want to waste the effort I just put into it and so that's what we're going to be looking at this week as we're in module 10. is how do these genes work and again we're looking at prokaryotes and eukaryotes and the scientists who studied them so looking at genes there's a lot of interest here and we've talked about this in the context of genetics as as we start to figure out there are actually factors being passed on from one generation to the next and some of these factors can lead to diseases scientists became incredibly interested in well what is it that's being passed on so 1900s again this is before Hershey and Chase this is before we prove that it's DNA but there's a scientist by the name of Archibald garrid who is a family doctor and in the 1900s doctors ran in families if your dad was a doctor he was going to train you to be a doctor and so on and so on so you kept charts and so Dr Garrett had his father's charts and his grandfather's charts on all the families in the area that he treated and with this he noticed that there was a condition called alcaptainuria it's actually one of the case studies I posted for you back when we had to do pedigrees remember I talked about squares or males circles or females there was a condition called alcoctinuria that I put as a case study for you to work and what Dr Garrett noticed was this ran in families and so he proposed that this particular condition Al Captain Maria was being passed on because this family missed a crucial enzyme in breaking down proteins now Al capitanuri is commonly referred to as blue diaper syndrome and it's because the body cannot break down our captain so it's released in the urine and when it's interacting with oxygen it changes color it oxidizes and turns blue and so that's why it was called Blue diaper syndrome was you couldn't tell by looking at the baby they had it but when you went to change their diaper it would be blue and so this was supported by the idea that he had a family record showing hey it's just in this family that this is popping up so they're passing something on that's not allowing them to metabolize this and this proposed the setup for there's something genes we didn't know that they were genes at the time that corresponded to enzymes that break things down so 40 years later we have Beetle and Tatum who decide to actually test this and they worked with a mold called neurospasa neuro spora crossa and again radiation is being used here they're messing with the DNA to intentionally cause mutations to see what effect that would have on the bread molds by the way if you're paying any attention to the news right now fungal infections are out of control like yeah um so so there's The Last of Us right the the show the game all of that stuff we're talking about a specific type of fungus that essentially eradicates humans right now there are about four different species of fungi they're a wrecking havoc on humans and one of them has a high fatality rate we're about 30 to 60 percent of patients who get it are dying um so so the world is like in chaos right now and so we're studying things and it's it's helpful to know how they work because when something like this happens it gives us an approach okay this is how it works how can we treat it um with the mutations we're seeing right now there's not a lot of treatment options but um I digress so with bead on Tatum they're looking at this bread mold and so I want to briefly mention uh let me jump back to this nutritional media so with this uh nutritional media they use something called a slant tube and so a slant tube is you have media at a slant and when we're talking about this minimal media minimal media has just the essentials that this organism needs to grow it has all the enzymes to process that and then it will grow what they're doing with the radiation is damaging the mold so it cannot produce an enzyme it needs to grow on that minimal media it's going to be deficient in something so that's what they're doing is causing these mutations so that the minimal media is not enough anymore and now they're looking for okay we've caused some mutations what did we mess up it's going to be a gene that corresponds to an enzyme that allowed them to digest that minimal media now they can't do it anymore again think about lactose intolerance people who are lactose intolerance don't have the enzyme lactase they can't break down lactose so they used radiation to mess with the fungus so that the fungus could not digest the minimal media it's deficient in something and they're trying to track what it is that they cannot make anymore and it had to be essential to their life so these mutations ended up blocking their ability to produce crucial amino acids again there are 20 natural amino acids so Beetle and Tatum went through thousands of these tubes and you've worked with tubes before right we've had the little you've seen the little tubes um in some of your virtual Labs since you guys have pure Labs online but they were starting to identify some of the mutations that they caused and they came up with an idea that these enzymes were coded for by a specific Gene do they propose one gene codes to one enzyme that has since been changed because enzymes are proteins and remember when we covered proteins we talked about the four levels of protein structure right primary secondary tertiaries were most stopped they get 3D structure but there was that quaternary level that fourth level where you had two or more polypeptides that interacted and so I gave you the example of hemoglobin because I knew I was going to cover sickle cell anemia hemoglobin is four polypeptides so it was one gene one enzyme but we now know that some enzymes are made of multiple polypeptides and so we've modified it to one gene codes for one polypeptide and that's what happens in Sickle Cell you just mess with one of the polypeptides so lots of experiments are done by Beetle and Tatum where they're tracking where did the mutation occur so they have tubes for every specific area but essentially they get a metabolic pathway and they can tell I made a mistake at this point with the UV radiation not eye the UV radiation uh affected an enzyme that allowed for the conversion of this product to this product it blocked it at one step and you could not progress how did they know that they gave it each of this that's what this is showing you okay I'm just going to give it this level does it grow or not and so at the point that they see no growth they know okay this mutant could not grow without this enzyme so if we're we're tracking where that mutation occurred now what this correlates to is what Francis and Crick did with DNA to RNA that transcription step and then RNA to the protein or polypeptide that translation step so you're not going to have to explain Beetle and Tatum's experiment to me you're going to have to transcribe a sequence you're going to have to translate a sequence and so that's what this led to is understanding what happens in a cell when we're looking at central dogma the transcription and translation step and this is going to be similar in approach for prokaryotes and eukaryotes because the language of DNA is universal four bases of DNA four bases of RNA so transcription and translation in approach is the same but there are some modifications because of the presence of the nucleus itself so this is a very wordy slide but what it's saying is with transcription you're just changing out that U for the T that's it right so it's RNA polymerase that's reading your DNA and we're going a to U instead of a to T because that does not exist in RNA that's going to give us our mRNA and that m stands for Messenger we use that for translation to actually make the polypeptides and that's where the ribosome comes in and another type of RNA called Transfer RNA so I use this slide to introduce all the rnas we've already seen messenger RNA we produce this directly from DNA ribosomes were not organelles and so some of you got that on the exam where I said name two eukaryotic organelles and some of you put ribosomes and I didn't give you credit for it because ribosomes are not organelles an organelle is a membrane enclosed structure ribosomes are naked RNA so our RNA stands for ribosomal RNA and that makes up the two components that we see in a ribosome in this chapter we add the third one the TRNA T stands for transfer this carries your amino acid so how many amino acids are there again 20. so we have 20 trnas each one carrying a specific amino acid and we're going to look at the wobble rule that explains where that redundancy comes in it's that third base it wobbles and so it allows this Transfer RNA to match a couple of different codons in certain places and then I gave you a couple of others and the only reason I did this is because in the last 10 years there's now a new field of RNA biology and it's really a decade you can get your PhD just studying RNA a specific type of RNA and still not know everything about it at last count there were over 30 types of RNA now and remember we talked in replication about the fact that you cannot replicate DNA without RNA which means RNA came first but we are just now coming around to understand the importance of RNA when we talk about epigenetics or you hear about epigenetics in the media it's really a lot of that is mitigated by RNA controlling the expression of our genes and I'll give you kind of a taste of that but um here's a couple the small nuclear RNA the signal recognition particle RNA we're going to see some of these in this this chapter and then we have small even smaller rnas called micro rnas and silencer rnas they're using this in gene therapy right now because in order to translate something you have to be able to bind to the MRNA and then read it so for certain cancers for example that have abnormal gene expression you can actually use micro RNA or silence or RNA to bind to the cancer mRNA and not allow it to be translated which allows your immune system time to attack that cancer and there are no side effects from this treatment because the cancer genes making something you don't need or don't have to just support itself so imagine a world where we can Target your cancer sequence it and then block its growth and development and you're not going to feel any sicker or even know that it's happening while it's being expressed in your body because you're just blocking it and then your immune system does its job so knowing how these work have applications and so that's why I just wanted to kind of highlight a couple of those so with this genetic code table I told you I'd talk briefly about how we got to these codons and when we look at a codon oh that should say mRNA that's not DNA I'll need to change my slides um we're looking at three sequences of mRNA that are going to code to an amino acid now on um your test I usually do it as a bonus question specifically I like to give you a sentence and I don't like you to have to track aucg like in a long strand so I do something like this where I give you a sentence where all the words are three letter words like why did the bat red bat eat the fat rat so you can see the effect of a mutation because if you substitute a single letter or delete a single letter it changes so this is a deletion you deleted the T now what normally happens is it faces it all over so when we delete a letter everything shifts over because we have to read in threes so this is emphasizing that it's in threes if you delete or add everything shifts over so this is called a reading frame shift and the type of mutation is a frame shift mutation so if you add or delete you shift the entire message over so I do this as a bonus question and I'm going to pick something like um just like that the fat cat ate the rat where every word is three letters and I'm gonna say delete yes or change the F because that could be a substitution and the fat cat ate the rat there's only one F right so there's no confusion about well if I said atcg or aucg and I said change the C and you've got lots of C's that gets complicated so that's why I use the sentences you see the effect in the mutation directly in the the expression of that sentence so I'll have this as a bonus question where I'm going to give you a sentence and I'm going to either ask you to show me the effects of an insertion or deletion with a specific letter or a substitution where you change it but we're talking about specific codes here and again if you make a change so here shows you a deletion of one base it's going to change um everything from that point because we shifted all over so that's all this is showing and again it it it's a bunch of letters it's harder to express in this way that's why I do the bonus with sentences at the end of the day what this translation process has shown us is that each three bases notice they all start Aug first one's always methionine right so here's our mRNA start codon translation is I wrote m-e-t there were multiple ways to get to Proline for my example before I did CCC that corresponded to Proline so this shows us redundancy CCU also corresponds to Proline so while there's some redundancy your start codons always aug this other end of this that we don't see is that we have some stop codons so of the genetic code table that was created by Nuremberg Corona and a couple of other science scientists so this is just showing you the first name it's nurnberg at Al they started with that uu and why did they do this well because you you you only exist in RNA so they knew it wasn't anything to do with DNA and they looked at what amino acid was coded and when they did this I'm going to come back to the slide I just want to show you the genetic code table as I talk about this they saw a chain of phenylalanine because uu codes for federality so then they started deleting it because they were trying to figure out how many mRNA molecules does it take to get an amino acid it's clearly not one to one because we have four RNA bases but 20 amino acids and they were confused because if you think about this mathematically right it's it couldn't be this because that just codes for four bases if you do four squared that's 16. if you do 4 cubed that's 64 and so the confusion was there are 20 amino acids so what number of RNA molecules code for an amino acid if you notice on this table there's 64 coats and so that's why we're redundancy came from is there are 64 different coats but only 61 of them code and that's because three of them are stop codons so jumping back these are your three stop codons UAA UGA and UAG when you get one of these they call in not a transcription Factor but they call in a release factor and that release Factor happens to be water what happens when you add water to something we see a process called hydrolysis are we building or breaking we're breaking right hydrolysis means we've added water and it's breaking something apart so with these stop codons do is they call in a release factor which brings in essentially a molecule of water and so that growing chain of amino acids that we have gets released and now it can fold and become the final product or be modified or whatever so while making a protein requires a start codon it requires a stop codon as well or you never release your product so that it can form so when we're talking about mutations it's you have to have a start codon you have to have a stop codon and everything in between has to go flawlessly because any mistake in any of those spots leads to a problem so I will ask you about the stop codons probably as a multiple choice question on the test you don't have to memorize it because the genetic code table will be on the test so these are the three stop codons UAA UAG and UGA and they just call in that release Factor so the great thing about this is the code is universal prokaryote Eukarya animal plant fungus protist doesn't matter and so that lets us know that we probably all shared a common ancestor and we've just accumulated mutations along the way and this has led to speciation we'll talk about this later in the course but it also means that we can manipulate genes and this has led to advances in genetic engineering and remember the nucleus is not the only organelle that has DNA the mitochondria has its own DNA the chloroplasts have their own DNA which means we can manipulate those as well so here's two pigs they added the green fluorescent protein which fluoresces under light to this pig to its in in place of keratin and so we can genetically manipulate things you see this when you go to the grocery store and you buy something like a grapple an apple that's supposed to taste like a grape remember genetic engineering does nothing to us because we don't really get anything from DNA we chop it up it's not going to harm us when we talk about eating a genetically modified organism what harms us is what was it genetically modified to do and so when it comes to plant-based products and again you have to pick and choose what your what you're processing from the media they talk about oh you know it's not this is a non-GMO that the issue has been that if you genetically modified a plant product to be resistant to an herbicide and a pesticide and then we go by in that product and eat it it's not the genetic modification that makes us sick it's herbicides and pesticides which are mostly going to be fat soluble so they don't wash away in water and then you eat those and those pesticides and herbicides accumulate in your body so what's making you sick is not that you ate a genetically modified organism but that you started consuming herbicides and pesticides from those products so again you see babies in the grocery store eating grapes out of the bag right and yeah right yes clean it because you don't know what the reading that's also technically stealing right you're decreasing the weight but um genetic modification does not make you sick it does not affect you unless the gene modification would alter your DNA which it won't unless it causes a mutation and herbicides and pesticides can do that so genetic modification not harmful to humans unless the intended goal was to change our our DNA specifically now prokaryotes are a little bit different in all of this they still use RNA polymerase but remember their chromosome is in a loop so we have linear chromosomes so we see transcription happen wherever we need it to in a prokaryote we're going to look at this in the next couple of chapters they have a loop of DNA and so when they're reading a gene we have an area that we want to open up and the area we will Target is called the promoter that promoter is where RNA polymerase is going to bind to an RNA polymerase again does transcription so when we're reading their sequence that starting site that it looks for tends to be what we call a Tata box t-a-t-a so when scientists are studying bacterium specifically they look in the sequence for where do we see Tata because it's it's a clue that this is starting a gene and then we can look at the sequence Factor we can figure out what it's going to be because we know about transcription and translation we can read DNA and transcribe it then we can take that to the genetic code table and figure out what the amino acids would be and then we can kind of figure out uh what that potential product is going to be so it's still RNA polymerase we're still dealing with antiparallel structures everything we talked about that I can't put on the test I'm just going to say transcribe and give you a strand that's as simple as it's going to be on the test but this is showing you the science of how they figured out the sequences in most prokaryotes that we know about and how we're reading off of the DNA working in a five Prime to three prime Direction Where RNA polymerase reads the template and makes the transcript so what that's going to correlate to for you being is I'm going to give you a strand of DNA and I'm going to give you the the ends 5 and 3 and I'm going to say transcribe it you use shardoff's rule flip the ends three to five and then a to you and C to G you're not going to have to worry about start or stop because the test is timed right but again when we take this transcript and we want to end the process just like there's a stop codon for translation there's a release Factor that's going to end transcription as well and this ends up changing the structure so we see this hairpin Loop that forms and that causes RNA polymerase to stop when it reaches it it's based on the codes that are that are processed there so in chapter 16 I'm going to be looking at an operon and I mentioned in the review um so I did not Pitch 16 on the board because I'm not covering it today I mentioned in the review that I'm going to cover the Lac operon and the trip operon these specifically apply to prokaryotes it's how prokaryotes control their genes so two short answer questions I said you'd have to prepare for for the test would be one looking at the operon model either a lacquer trip I'm covering that in the next class not this lecture because this is a lot and your brain gets fried but then I'm going to also show you how eukaryotes have all of this diversity in gene expression and so I'm going to save those two for the next lecture keep in mind that prokaryotes do not have a nucleus so when I'm talking about transcription and translation there is no pause because there's no nuclear membrane to protect the transcript that's been made so this is transcription you're making mRNA as soon as it comes off these little golden circles represent ribosomes they jump on it and translation starts and so you make multiple proteins from one strand of mRNA because it just continues it's not even finished it hasn't even released yet and you're already making protein products because every three bases as it leaves another ribosome jumps on it so the the idea behind this figure is we call these polyzomes or poly ribosomes where you have many ribosomes on one mRNA transcript we don't just do transcription and translation to get to one protein even in eukaryotes we make lots of products when we undergo transcription it translates into lots of different protein products and we'll talk about that more uh in chapter 16. lots of RNA polymerases you don't have to know any of these because I'm not going to have you know those specifically just know that RNA polymerase is what puts together the transcript that we're going to look at so just like prokaryotes have that Tata box so do eukaryotes so this is eukaryotic transcription so here's the Tata box the difference in a eukaryotic gene expression is we have these linear chromosomes and we have to open our DNA at multiple spots so what our Tata box does is it binds to transcription factors and you'll learn this in genetics each of these comes in in a specific order so we call these transcription factors TF for short and so they'll come in tf2d tf2e they come in and that's how their name transcription factor and then Roman numerals and then letters I don't have you know that but these transcription factors act like a jack lifting the DNA apart so that RNA polymerase can squeeze in so here's RNA polymerase it can squeeze in there and start transcribing the RNA itself and because there's the nuclear membrane that transcript is going to get altered so this is where I said but wait there's more that mRNA does not directly go into translation we have time to change it and these are the three major changes we do for our mRNA we have a five Prime cap that's going to be GTP so it's got three phosphates it's negative it leads it leads the process for translation and it's protective on the three prime end we ought to poly a tail poly means what many right so we just had a bunch of A's they end up being decoys because once we leave the nucleus they're enzymes that are going to start chopping it up so they can approach the five Prime end because it's highly negative so it's protected the three prime end has this long chain of decoy bases and so they're just chewing off decoy bases it buys your transcript time to be translated but this is where we see the most variation where we have the removal of the introns and the coding joining of different axons so this midpoint here is where we see splicing take place so this is what GTP looks like this is your poly a tail and introns and exons will be on the test so I wanted you have definitions introns used to be called Junk DNA in the 80s and 90s it was junk DNA we now know these introns are just not coding for the product we're making at that time but they anticipate oh you're making this you're about to need this or I should turn that off we're talking about mRNA so this is where RNA science has exploded these introns act as transcription factors to turn on genes elsewhere or to block expression of genes somewhere else so they're not junk at all they're helping control our entire metabolic process if you're making this I need to turn this off and turn this on so we used to call them junk DNA in the 80s and 90s now we know these are control mechanisms they're not actually being wasted the exons are the sequences that are actually going to be coated and these are individually targeted by another group of RNA called snurfs small nuclear riboproteins so we call them snurps for short they read the transcript and cut out the pieces that we don't want so the snerps these small nuclear riber proteins make up what we call a splice Zone and they cut out different sequences those introns then go and control genes somewhere else so this entire process is called alternative splicing one gene will have different products made from it based on what's needed at that moment and there are all kinds of studies that suggest most mammals use alternative splicing to spread our genome for multiple products though just giving you one study here that says 95 of mammalian genes okay undergo alternative splicing to make different products so we have about 20 000 genes that we've mapped out at the time of printing this book those 20 000 different genes make over a hundred thousand different proteins because of alternative splicing so this gives us an edge in making our our products so I'm going to stop right here with alternative splicing and I'll pick up and we'll finish um

we're in module 10. so if you've looked at the uh syllabus we we're almost there right um exam Three is coming up and it's going to cover chapters 10 through 17. so I did a review last week it's it's going to be there if you didn't watch it please watch it because the exam is coming up so you need to have time to practice those genetics problems as we went over them a monohybrid in complete dominance sex-linked blood type and there will be a dihybrid question about phenotype uh ratio so that's chapters 12 and 13 looking at those types of problems for chapter 14 this was replication so we worked on that last week as far as sharkov's rule a to T C to G so it should be a fairly easy short answer question for that one you flip the ends and you use those base pairing rules and that should be pretty straightforward and then transcription and translation I introduced as a lab concept so if you watch the lab video from last week in module nine I covered it that comes from this week's lecture in chapter 15. so we're going to go over that in more detail but there will be one transcription question one translation question on the short answer portion so the bulk of your short answer problems are genetics one replication one transcription one translation and those are things that you have to practice it's not just I'm going to memorize a fact and regurgitate it you're going to have to actually work something and so that's why I'm saying practice that the test is coming up these things require you to look at them a couple of times so just to give you an example let's just do two genetics problems real quick let's do a blood type um let's say uh mom has blood type O and dad has blood type B on the test I'm going to ask you what are the genotypic and phenotypic ratios possible for The Offspring and then probably a probability question okay so I'm going to tell you mom has blood type O dad has blood type B give me the genotypic and phenotypic ratios that are possible from this cross and so you just get the blood type you have to know what the genotype is for that so remember with blood type O it can only be one way it looks like this you do those two little recessive alleles for blood type B while there are two ways to be blood type B I told you just to remember the heterozygote version for both B and for a so you would just write that down that way you never miss a possibility in doing that cross and so then I really need a finer tip stylus that door will never be open just so you know um so then this is what the the cross ends up looking like and genotypically you write what you see so you can just make a list two that look like this and two that look like that that's genotypic you're showing me the genetic makeup so that's what I want to see for the genotypic ratios phenotypically you would have two blood type B possibilities two blood type O possibilities and then I'll ask that probability question so if I had asked what's the probability they'll have a child with blood type B it's two out of four one half or 50 percent and again I give you all those options not because you have to put that on the short answer portion of the test but because the multiple choice you will see sometimes it's a fraction response sometimes it's a percentage and I want you to know it's all coming from the same cross it's just giving it to you in a different version so on the short answer portion you just have to give me one answer but just know that when we work across it could be any of those so guaranteed one blood type question on your exam it's a short answer question you'll have to give me genotypic and phenotypic ratios and then I'll ask a probability as always with my exams you get partial credit so even if you only can give me one part you're going to earn something as opposed to just leaving it blank okay and again you'll get to use a scratch sheet of paper I know you need to work this out so you'll just show that blank sheet of paper both sides to the camera that way you have something to work this on um and I I turned off the flag setting so it won't flag you for lifting your head and not looking directly at the screen the whole time a Sex Link problem um let's do one of those just real quick before we add on um sex linked I could say mom's a carrier for red green color blindness if I say she's a carrier she looks like this males are Hemi zygous they cannot be heterozygous which means they can never be a carrier so let's say Dad has red green color blindness he's gonna look like this all of our sex link crosses for this class are going to be x-linked recessive conditions when you get to genetics you'll see that's not the only the genetics course uh not not the topic uh you'll see that's not the only type of x-linked or sex-linked problem that can occur there are y-linked problems there are dominant genes that uh get carried by the X chromosome but I like consistency for the first time I introduce something so I'm only going to give you x-linked recessive because that's what the book highlights and that's all the problems that we've done so just know that on your test it's going to be a problem that we've seen for a disease that we have seen or at least talked about so for sex linked it looks kind of like wood types because you are tracking the allele that's raised to the chromosome that's representing where it's being carried so you have to use the sex chromosomes for this you always keep that dominant allele first and then when you analyze the results it's gender specific so if I say what are the odds that you're going to have a son that's affected it's not one out of four it's one out of two so it's a 50 chance that you're going to have a male that's affected so gender uh specific questions or sex-linked questions you just look at the two males and you assess those if I ask a male question if I ask a female question you look at it that way as well so these questions are both on your lab exam and this lecture exam so the lecture exam I have the dates on the board your lab practical exam is at the end of the the same month end of April okay and you'll see this problem so I'm asking you an x-linked cross problem on the lab practical and questions a b c d will be that you just list the genotypes for that cross so as you're studying for this test just know that you're helping yourself out by preparing for that lab exam as well because blood type will be on the lab practical as will sex linked so you want to get it now because it'll help boost your grade if you get right on both both problems so genotypically you just list everything that you see in the cross so that's genotypic phenotypic you'd have one daughter who's a carrier one daughter who is affected one unaffected male and one effective male and since this is red green color blindness that's we're looking at affected by red green color blindness and then I could ask that probability question and again you just look at it based on which gender I'm asking for so questions on blood type or sex linked and then again you'll have a dihybrid question and so um remember with dihybrid we're looking at the law of segregation and the Law of Independent Assortment just in gamete formation so what you learned about in meiosis which was chapter 11 we are seeing applied in genetics so the the order of the book may seem random and you think we're jumping around but it's setting the Precedence for why these things happen and why we see things skip Generations or recombine Etc so for gamete formation here you can only have one R and one y in each of The Offspring That's the Law of segregation you're separating them out and the Law of Independent Assortment says you've got to look at all the possible combinations between these two genes so this is dihybrid looking at two different traits so I told you you could use foil or I said you could take the first set of genes write them out once like that and then take the second set of genes and write them once for each letter that you just separated before so the Y goes here and then you do the same thing for this that gives you all four possible gametes right so you won't miss a combination because you'll catch them all so on the exam that you have coming up I'm going to ask you a dihybrid question but just about the phenotypic ratios so I'm just going to make this easy so I can actually get started with new materials so let's say we cross the same setup and this is Mendel's ratios um where we can put them together and again this makes it more apparent why you keep dominant alleles first and you keep same genes together because that will make it easier to read rather than if you just start scrambling R's and y's and then it doesn't matter where you start because that rule of keeping the dominant Gene first and similar letters together will make it easy to interpret no matter where you start it at I shouldn't have picked the why that makes it hard here and I gave myself very little room ah I don't know what I hit  writing on this screen is uh new experience for me okay so then we track them and so remember with Mendel's ratios the first thing he looked for was dominant for both traits so a dominant r a dominant y once you use it towards that end you cannot use it again so you just need one of each and then that means you've counted it for dominant for both particular um areas so if you count all of those one two three four five six seven eight nine Mendel's ratios told us that first number for two heterozygous being dominant for both having a Big R and A Big Y he gave us this 9331 ratio so I'm just showing you where it came from once you've counted it towards something you can't use it again so your number should always add up to 16 every time you do a cross second trait that you track should be dominant just for that first Gene so you're just looking for the dominant R so we have one here two three and so that's what we're looking at here second one would just be dominant for the Y the one two three and then that last one is going to be recessive for both and there's just one so nine plus three plus three plus one adds up to your sixteen we've accounted for all of them this is a phenotypic ratio so the short answer question is not going to be two heterozygous cross but the approach is the same you're just going to set up the gametes for both parents put them at the top and the side and then fill those in and then just count how many are dominant for the verse for both dominant for the first dominant for second and recessive for both and you're just giving me those numbers you don't have to write all the genotypes you don't have to do anything crazy if you present it in this order that's all I'm asking you for for that question okay so again I'm always recording these so you can go back and and watch them and I gave you lots of practice problems in the genetics uh module um which I think was like module eight seven or eight somewhere around there um we had a lab so you had lots of PDFs that I did not take for grades just so you'd have something to try it on and then you could come back to me with hey I don't know this problem or hey can you verify I did this right however you want to approach it you can even send me a picture and say can you look at this and tell me if I did it correctly and that way you know you're on the right track so you've got some time but these are the kinds of things that I'm saying you need to practice you can't just put this in your head and then regurgitate it on a test this is this is very much going to require some practice oh last last week we were talking about DNA we've talked about the structure we know it's a double helix we know it's anti-parallel we know the monomer form is a nucleotide so we have a five carbon sugar we have a phosphate group and we have a nitrogenous base and we talked about schargov's rules the Ada T C to G I also introduced you to all the enzymes and I made a list last week in the recording so you can go back and track those those enzymes and so the short answer question I'm going to ask you about on replication on your exam is not about these enzymes those are going to be on the multiple choice where you're what what enzyme does this or what what uh protein does this um problem instead what I'm going to do is I'm going to ask you to replicate a given strand so if I tell you that this is the parent strand I'm just going to make it short that's what you're going to see typed on the test I'm going to say replicate this strip what direction does replication go does anyone remember right so the ends are going to flip and it always goes five to three but on a tight test I can't tell if you start on this end so replication goes 5 Prime to 3 Prime because of the orientation of the phosphate group on that five Prime end but you do have to flip the ends you're typing this so you're gonna you know on this end you would type a three on the other end you're going to type a five in a Cell it's going to start at that five Prime in and work to the three prime Direction but on the test I'm looking for did you flip the ends that shows me you know it's anti-parallel we can't have two five Prime ends on the same side they would repel each other because they're both negative charges and then I'm looking for chargoff's rule for replication that is going to be a to T and C to G so for this strand what would the daughter strand be it's it's that easy the short answer question is going to be that easy what enzyme makes DNA I'm going to ask you that on the test and remember there's multiple different DNA polymerases I'm only having you know two DNA polymerase 3 and DNA polymerase one Paul one is the proofreader it removes the okazaki fragments the the little primers that are RNA it removes those and then puts in DNA but actually synthesizing DNA is DNA polymerase 3 and again it works in the five Prime to three prime Direction now I do want to point out that in Connect all the answers get presented five to three and I can't control that so just pay attention to the fact that even though it is anti-parallel they are giving you all the answers in the same format and students are looking for that flipped orientation and the multiple choice responses and they're not giving it to you they're presenting them all in that five to three format because it's made five to three but they're presenting it like they would read it so this answer here if it were connect the answer would have been c g g a t and then three prime yeah they they started they present it from here first and then they give you the enzymes in that backwards orientation it's still right but that's how DNA is working and so the logic and I've asked the rep about this the logic is DNA is made five to three so that's the direction you would read it in so they give you all your answers that way I'm not going to do that because on the test you're trying to go you're timed right I'm going to present it so that you're just type it so that it lines up it's hard enough to take a test with that stress without having to look for it so I can't change that and connect it's a connect system uh question but on the test you know no it's anti-parallel and just know that connect is something that I cannot cannot control um so this is from chapter 14 last week and in lab I started central dogma and I gave you guys a handout and the handouts posted in this week's module so if you didn't get it you can see it in the module so you're not missing anything but central dogma just involves transcription and translation so replication happens in the S phase of the cell cycle we learned that back in chapter 10 when we talked about the cell cycle so replication a to T C to G is happening in the S phase transcription translation these are happening in the G phases the the cell is doing its job it's making the products it needs to be whatever cell type it is and so transcription is taking DNA and turning it into and I introduced messenger RNA in lab last week we're going to see it in chapter 15 this week and because we're making RNA this added a new enzyme to your list of of enzymes and that's RNA polymerase so it follows sargov's rule but RNA doesn't have thiamine so shardoff's rule tweaks for transcription and you're going to have a to U and C to G now notice that when there's a t right here see that t it puts an a that's the only place I see students mess up so I'm going to be looking for it and it's worth one point because CNG don't change so whether you're replicating or transcribing it's all the same but what you have to be careful about is if DNA says T you have to think about what does RNA have it has an A so I can put an a here but if the DNA says a we can't put T that's the only place that we see a change in transcription is we just replace what would have been a t with a u so Charlotte's rules a to U and C to G is really just changing what base pairs to that a when I'm writing down the RNA strand so this is a short answer question on the test this figure came from your book you have an activity for transcription we looked at it in lab but I'm going to give you a strand of DNA and it's going to be kind of the same approach and I can't remember what I wrote down before I think it was like this right so I'm trying to be consistent so when I say transcribe and I give you this strand you still have to keep in mind it's anti-parallel it's still only going to go five to three because DNA and RNA both have a five Prime phosphate so you can never have two five Prime ends together just never gonna happen so you're always going to flip the ends and it's going to work in the five to three Direction because of that the difference is what you write so when I transcribe if DNA says a I write a u I can't put down T because RNA does not have one everything else is the same so a g g c no change okay so the only difference for transcription and I'm going to go over this this is in this next lecture I'm just showing you the application from last week's lab and then I'll uh cover it more than you care for has to do with watching what RNA has versus what DNA has the second step for central dogma after transcription is translation where we then start reading these bases of mRNA we read in three three bases at a time this is called translation and we're going to start building our protein so this blue structure here represents the ribosome remember the job of the ribosome from chapter four is protein synthesis so now this is the chapter where we see how do ribosomes which are just made up of RNA actually turn it into protein and what it comes down to is for every three bases of mRNA it correlates to a single amino acid so this is the genetic code table that we were introduced to last week so for uh and I'm just going to give you a strand of mRNA here and I'm going to make it stupid short just for this purpose um on the test you're going to have one translation problem I'm going to give you the code table no need to memorize it it's not applicable you get that in biochem they'll talk to you about it then what I want you to know is just how to use it so I'm going to have you apply the genetic code table on a couple of problems but the short answer question I'm going to assign you is I'm going to give you a strand and I'm going to say translate this so all you have to do is know where to start where to stop and then how to actually apply the table so every protein in our body starts with a very specific amino acid called methionine met for short you see it in green on this table so what that means is on the test if the first triplet codon that I give you and that's what we're looking at when I say codon it's three bases of mRNA so a codon is three bases of mRNA that's the only thing you can use on this table you can't use DNA can't use anything else it's got to be three bases of mRNA if the first three bases are not a U or Aug you're not going to do anything with it because we can't start making a proton a protein until we find Aug so you would just ignore anything that's not Aug when you get Aug that's when you start translation and while it says start I want you to ignore the word start it'll start the process and code for methionine there's no start it's always methionine so you can have it multiple times it doesn't affect it so if I had done Aug in in triplicate right three augs in a row it would just be met met met three times it doesn't do anything it's just the first amino acid in the sequence so all you would do for translation is you would write down that code m-e-t so what would we use for the second codon Pro right right so this codon sheet tells you okay if my first base is C it's going to be somewhere in this row second base is C it's going to be in this column so that narrows it down to a box third base is C and it's right there you could of course read every single one if you wanted to but the outer directions are telling you it's going to be in this row this column and then it directs you directly to that base so there are 64 codons here and in this chapter we're going to talk about how they figured those out um and why we see thumb repeat so if you look at glycine right here there's one two three four different ways for glycine so there's a phrase where we say redundancy but no ambiguity the redundancy is there are four different ways to code for glycine no ambiguity is if I have ggu it's always glycine and so with our code we can have a problem think about what happens if I change this C to something else let's say I mutate just the C to a g what does GCU give you right okay so that is a single base change but I've just changed my amino acid and again we talked about sickle cell anemia sickle cell anemia is one base change in DNA you change the structure of the DNA you change the amino acid that's coming into play that changes how your protein is going to shape structure equals function all the way down and that leads to the disease state of having Sickle Cell now you have a blood cell that cannot transport oxygen properly and guess what we kind of need oxygen so when we're talking about the order of this the the order is incredibly important so you have to think about what happens to us if we delete a base if we add a base we read in threes so if you delete or add you've shifted everything over this is called a reading frame shift and you've altered every Gene from that point on so we talked about those thymine dimers and replication remember we're two adjacent thymines Bubble Up in response to UV radiation that essentially acts as a deletion we just took out two bases everything is going to shift over because of that which means you have multiple errors on a strand which increases your rate of what when you're exposed to sunlight all the time tanning whatever UV radiation cancer right so this is why it's important to understand structure equals function down to the DNA level because it affects everything afterwards so that's what we're going to be looking at this chapter and we're going to look at mutations specifically whether it's within a gene or the entire chromosome specifically because again if you remove just a single one it changes everything from that point down which changes the the goal of that Gene to begin with and then of course we're also going to be looking at variations and eukaryotes get more complicated because we have 46 linear chromosomes as humans prokaryotes just have this one Loop so in eukaryotes we have something called RNA processing where your DNA by itself is not the end of what you're going to make because we can alternate it and change it so we have human genes that make three different products through this process of alternative splicing where we will cut out different parts and join them together so when we talk about the human genome and we say we only have this many genes but we have this many proteins it's because we mix and match what we have and we make multiple products and again our body wants to be you know mindful of our resources so if we start to make something and then the body's like never mind I don't need it it's like I started to make this can I turn it into something else that's the goal of RNA processing is I already transcribed this I don't want to waste the effort I just put into it and so that's what we're going to be looking at this week as we're in module 10. is how do these genes work and again we're looking at prokaryotes and eukaryotes and the scientists who studied them so looking at genes there's a lot of interest here and we've talked about this in the context of genetics as as we start to figure out there are actually factors being passed on from one generation to the next and some of these factors can lead to diseases scientists became incredibly interested in well what is it that's being passed on so 1900s again this is before Hershey and Chase this is before we prove that it's DNA but there's a scientist by the name of Archibald garrid who is a family doctor and in the 1900s doctors ran in families if your dad was a doctor he was going to train you to be a doctor and so on and so on so you kept charts and so Dr Garrett had his father's charts and his grandfather's charts on all the families in the area that he treated and with this he noticed that there was a condition called alcaptainuria it's actually one of the case studies I posted for you back when we had to do pedigrees remember I talked about squares or males circles or females there was a condition called alcoctinuria that I put as a case study for you to work and what Dr Garrett noticed was this ran in families and so he proposed that this particular condition Al Captain Maria was being passed on because this family missed a crucial enzyme in breaking down proteins now Al capitanuri is commonly referred to as blue diaper syndrome and it's because the body cannot break down our captain so it's released in the urine and when it's interacting with oxygen it changes color it oxidizes and turns blue and so that's why it was called Blue diaper syndrome was you couldn't tell by looking at the baby they had it but when you went to change their diaper it would be blue and so this was supported by the idea that he had a family record showing hey it's just in this family that this is popping up so they're passing something on that's not allowing them to metabolize this and this proposed the setup for there's something genes we didn't know that they were genes at the time that corresponded to enzymes that break things down so 40 years later we have Beetle and Tatum who decide to actually test this and they worked with a mold called neurospasa neuro spora crossa and again radiation is being used here they're messing with the DNA to intentionally cause mutations to see what effect that would have on the bread molds by the way if you're paying any attention to the news right now fungal infections are out of control like yeah um so so there's The Last of Us right the the show the game all of that stuff we're talking about a specific type of fungus that essentially eradicates humans right now there are about four different species of fungi they're a wrecking havoc on humans and one of them has a high fatality rate we're about 30 to 60 percent of patients who get it are dying um so so the world is like in chaos right now and so we're studying things and it's it's helpful to know how they work because when something like this happens it gives us an approach okay this is how it works how can we treat it um with the mutations we're seeing right now there's not a lot of treatment options but um I digress so with bead on Tatum they're looking at this bread mold and so I want to briefly mention uh let me jump back to this nutritional media so with this uh nutritional media they use something called a slant tube and so a slant tube is you have media at a slant and when we're talking about this minimal media minimal media has just the essentials that this organism needs to grow it has all the enzymes to process that and then it will grow what they're doing with the radiation is damaging the mold so it cannot produce an enzyme it needs to grow on that minimal media it's going to be deficient in something so that's what they're doing is causing these mutations so that the minimal media is not enough anymore and now they're looking for okay we've caused some mutations what did we mess up it's going to be a gene that corresponds to an enzyme that allowed them to digest that minimal media now they can't do it anymore again think about lactose intolerance people who are lactose intolerance don't have the enzyme lactase they can't break down lactose so they used radiation to mess with the fungus so that the fungus could not digest the minimal media it's deficient in something and they're trying to track what it is that they cannot make anymore and it had to be essential to their life so these mutations ended up blocking their ability to produce crucial amino acids again there are 20 natural amino acids so Beetle and Tatum went through thousands of these tubes and you've worked with tubes before right we've had the little you've seen the little tubes um in some of your virtual Labs since you guys have pure Labs online but they were starting to identify some of the mutations that they caused and they came up with an idea that these enzymes were coded for by a specific Gene do they propose one gene codes to one enzyme that has since been changed because enzymes are proteins and remember when we covered proteins we talked about the four levels of protein structure right primary secondary tertiaries were most stopped they get 3D structure but there was that quaternary level that fourth level where you had two or more polypeptides that interacted and so I gave you the example of hemoglobin because I knew I was going to cover sickle cell anemia hemoglobin is four polypeptides so it was one gene one enzyme but we now know that some enzymes are made of multiple polypeptides and so we've modified it to one gene codes for one polypeptide and that's what happens in Sickle Cell you just mess with one of the polypeptides so lots of experiments are done by Beetle and Tatum where they're tracking where did the mutation occur so they have tubes for every specific area but essentially they get a metabolic pathway and they can tell I made a mistake at this point with the UV radiation not eye the UV radiation uh affected an enzyme that allowed for the conversion of this product to this product it blocked it at one step and you could not progress how did they know that they gave it each of this that's what this is showing you okay I'm just going to give it this level does it grow or not and so at the point that they see no growth they know okay this mutant could not grow without this enzyme so if we're we're tracking where that mutation occurred now what this correlates to is what Francis and Crick did with DNA to RNA that transcription step and then RNA to the protein or polypeptide that translation step so you're not going to have to explain Beetle and Tatum's experiment to me you're going to have to transcribe a sequence you're going to have to translate a sequence and so that's what this led to is understanding what happens in a cell when we're looking at central dogma the transcription and translation step and this is going to be similar in approach for prokaryotes and eukaryotes because the language of DNA is universal four bases of DNA four bases of RNA so transcription and translation in approach is the same but there are some modifications because of the presence of the nucleus itself so this is a very wordy slide but what it's saying is with transcription you're just changing out that U for the T that's it right so it's RNA polymerase that's reading your DNA and we're going a to U instead of a to T because that does not exist in RNA that's going to give us our mRNA and that m stands for Messenger we use that for translation to actually make the polypeptides and that's where the ribosome comes in and another type of RNA called Transfer RNA so I use this slide to introduce all the rnas we've already seen messenger RNA we produce this directly from DNA ribosomes were not organelles and so some of you got that on the exam where I said name two eukaryotic organelles and some of you put ribosomes and I didn't give you credit for it because ribosomes are not organelles an organelle is a membrane enclosed structure ribosomes are naked RNA so our RNA stands for ribosomal RNA and that makes up the two components that we see in a ribosome in this chapter we add the third one the TRNA T stands for transfer this carries your amino acid so how many amino acids are there again 20. so we have 20 trnas each one carrying a specific amino acid and we're going to look at the wobble rule that explains where that redundancy comes in it's that third base it wobbles and so it allows this Transfer RNA to match a couple of different codons in certain places and then I gave you a couple of others and the only reason I did this is because in the last 10 years there's now a new field of RNA biology and it's really a decade you can get your PhD just studying RNA a specific type of RNA and still not know everything about it at last count there were over 30 types of RNA now and remember we talked in replication about the fact that you cannot replicate DNA without RNA which means RNA came first but we are just now coming around to understand the importance of RNA when we talk about epigenetics or you hear about epigenetics in the media it's really a lot of that is mitigated by RNA controlling the expression of our genes and I'll give you kind of a taste of that but um here's a couple the small nuclear RNA the signal recognition particle RNA we're going to see some of these in this this chapter and then we have small even smaller rnas called micro rnas and silencer rnas they're using this in gene therapy right now because in order to translate something you have to be able to bind to the MRNA and then read it so for certain cancers for example that have abnormal gene expression you can actually use micro RNA or silence or RNA to bind to the cancer mRNA and not allow it to be translated which allows your immune system time to attack that cancer and there are no side effects from this treatment because the cancer genes making something you don't need or don't have to just support itself so imagine a world where we can Target your cancer sequence it and then block its growth and development and you're not going to feel any sicker or even know that it's happening while it's being expressed in your body because you're just blocking it and then your immune system does its job so knowing how these work have applications and so that's why I just wanted to kind of highlight a couple of those so with this genetic code table I told you I'd talk briefly about how we got to these codons and when we look at a codon oh that should say mRNA that's not DNA I'll need to change my slides um we're looking at three sequences of mRNA that are going to code to an amino acid now on um your test I usually do it as a bonus question specifically I like to give you a sentence and I don't like you to have to track aucg like in a long strand so I do something like this where I give you a sentence where all the words are three letter words like why did the bat red bat eat the fat rat so you can see the effect of a mutation because if you substitute a single letter or delete a single letter it changes so this is a deletion you deleted the T now what normally happens is it faces it all over so when we delete a letter everything shifts over because we have to read in threes so this is emphasizing that it's in threes if you delete or add everything shifts over so this is called a reading frame shift and the type of mutation is a frame shift mutation so if you add or delete you shift the entire message over so I do this as a bonus question and I'm going to pick something like um just like that the fat cat ate the rat where every word is three letters and I'm gonna say delete yes or change the F because that could be a substitution and the fat cat ate the rat there's only one F right so there's no confusion about well if I said atcg or aucg and I said change the C and you've got lots of C's that gets complicated so that's why I use the sentences you see the effect in the mutation directly in the the expression of that sentence so I'll have this as a bonus question where I'm going to give you a sentence and I'm going to either ask you to show me the effects of an insertion or deletion with a specific letter or a substitution where you change it but we're talking about specific codes here and again if you make a change so here shows you a deletion of one base it's going to change um everything from that point because we shifted all over so that's all this is showing and again it it it's a bunch of letters it's harder to express in this way that's why I do the bonus with sentences at the end of the day what this translation process has shown us is that each three bases notice they all start Aug first one's always methionine right so here's our mRNA start codon translation is I wrote m-e-t there were multiple ways to get to Proline for my example before I did CCC that corresponded to Proline so this shows us redundancy CCU also corresponds to Proline so while there's some redundancy your start codons always aug this other end of this that we don't see is that we have some stop codons so of the genetic code table that was created by Nuremberg Corona and a couple of other science scientists so this is just showing you the first name it's nurnberg at Al they started with that uu and why did they do this well because you you you only exist in RNA so they knew it wasn't anything to do with DNA and they looked at what amino acid was coded and when they did this I'm going to come back to the slide I just want to show you the genetic code table as I talk about this they saw a chain of phenylalanine because uu codes for federality so then they started deleting it because they were trying to figure out how many mRNA molecules does it take to get an amino acid it's clearly not one to one because we have four RNA bases but 20 amino acids and they were confused because if you think about this mathematically right it's it couldn't be this because that just codes for four bases if you do four squared that's 16. if you do 4 cubed that's 64 and so the confusion was there are 20 amino acids so what number of RNA molecules code for an amino acid if you notice on this table there's 64 coats and so that's why we're redundancy came from is there are 64 different coats but only 61 of them code and that's because three of them are stop codons so jumping back these are your three stop codons UAA UGA and UAG when you get one of these they call in not a transcription Factor but they call in a release factor and that release Factor happens to be water what happens when you add water to something we see a process called hydrolysis are we building or breaking we're breaking right hydrolysis means we've added water and it's breaking something apart so with these stop codons do is they call in a release factor which brings in essentially a molecule of water and so that growing chain of amino acids that we have gets released and now it can fold and become the final product or be modified or whatever so while making a protein requires a start codon it requires a stop codon as well or you never release your product so that it can form so when we're talking about mutations it's you have to have a start codon you have to have a stop codon and everything in between has to go flawlessly because any mistake in any of those spots leads to a problem so I will ask you about the stop codons probably as a multiple choice question on the test you don't have to memorize it because the genetic code table will be on the test so these are the three stop codons UAA UAG and UGA and they just call in that release Factor so the great thing about this is the code is universal prokaryote Eukarya animal plant fungus protist doesn't matter and so that lets us know that we probably all shared a common ancestor and we've just accumulated mutations along the way and this has led to speciation we'll talk about this later in the course but it also means that we can manipulate genes and this has led to advances in genetic engineering and remember the nucleus is not the only organelle that has DNA the mitochondria has its own DNA the chloroplasts have their own DNA which means we can manipulate those as well so here's two pigs they added the green fluorescent protein which fluoresces under light to this pig to its in in place of keratin and so we can genetically manipulate things you see this when you go to the grocery store and you buy something like a grapple an apple that's supposed to taste like a grape remember genetic engineering does nothing to us because we don't really get anything from DNA we chop it up it's not going to harm us when we talk about eating a genetically modified organism what harms us is what was it genetically modified to do and so when it comes to plant-based products and again you have to pick and choose what your what you're processing from the media they talk about oh you know it's not this is a non-GMO that the issue has been that if you genetically modified a plant product to be resistant to an herbicide and a pesticide and then we go by in that product and eat it it's not the genetic modification that makes us sick it's herbicides and pesticides which are mostly going to be fat soluble so they don't wash away in water and then you eat those and those pesticides and herbicides accumulate in your body so what's making you sick is not that you ate a genetically modified organism but that you started consuming herbicides and pesticides from those products so again you see babies in the grocery store eating grapes out of the bag right and yeah right yes clean it because you don't know what the reading that's also technically stealing right you're decreasing the weight but um genetic modification does not make you sick it does not affect you unless the gene modification would alter your DNA which it won't unless it causes a mutation and herbicides and pesticides can do that so genetic modification not harmful to humans unless the intended goal was to change our our DNA specifically now prokaryotes are a little bit different in all of this they still use RNA polymerase but remember their chromosome is in a loop so we have linear chromosomes so we see transcription happen wherever we need it to in a prokaryote we're going to look at this in the next couple of chapters they have a loop of DNA and so when they're reading a gene we have an area that we want to open up and the area we will Target is called the promoter that promoter is where RNA polymerase is going to bind to an RNA polymerase again does transcription so when we're reading their sequence that starting site that it looks for tends to be what we call a Tata box t-a-t-a so when scientists are studying bacterium specifically they look in the sequence for where do we see Tata because it's it's a clue that this is starting a gene and then we can look at the sequence Factor we can figure out what it's going to be because we know about transcription and translation we can read DNA and transcribe it then we can take that to the genetic code table and figure out what the amino acids would be and then we can kind of figure out uh what that potential product is going to be so it's still RNA polymerase we're still dealing with antiparallel structures everything we talked about that I can't put on the test I'm just going to say transcribe and give you a strand that's as simple as it's going to be on the test but this is showing you the science of how they figured out the sequences in most prokaryotes that we know about and how we're reading off of the DNA working in a five Prime to three prime Direction Where RNA polymerase reads the template and makes the transcript so what that's going to correlate to for you being is I'm going to give you a strand of DNA and I'm going to give you the the ends 5 and 3 and I'm going to say transcribe it you use shardoff's rule flip the ends three to five and then a to you and C to G you're not going to have to worry about start or stop because the test is timed right but again when we take this transcript and we want to end the process just like there's a stop codon for translation there's a release Factor that's going to end transcription as well and this ends up changing the structure so we see this hairpin Loop that forms and that causes RNA polymerase to stop when it reaches it it's based on the codes that are that are processed there so in chapter 16 I'm going to be looking at an operon and I mentioned in the review um so I did not Pitch 16 on the board because I'm not covering it today I mentioned in the review that I'm going to cover the Lac operon and the trip operon these specifically apply to prokaryotes it's how prokaryotes control their genes so two short answer questions I said you'd have to prepare for for the test would be one looking at the operon model either a lacquer trip I'm covering that in the next class not this lecture because this is a lot and your brain gets fried but then I'm going to also show you how eukaryotes have all of this diversity in gene expression and so I'm going to save those two for the next lecture keep in mind that prokaryotes do not have a nucleus so when I'm talking about transcription and translation there is no pause because there's no nuclear membrane to protect the transcript that's been made so this is transcription you're making mRNA as soon as it comes off these little golden circles represent ribosomes they jump on it and translation starts and so you make multiple proteins from one strand of mRNA because it just continues it's not even finished it hasn't even released yet and you're already making protein products because every three bases as it leaves another ribosome jumps on it so the the idea behind this figure is we call these polyzomes or poly ribosomes where you have many ribosomes on one mRNA transcript we don't just do transcription and translation to get to one protein even in eukaryotes we make lots of products when we undergo transcription it translates into lots of different protein products and we'll talk about that more uh in chapter 16. lots of RNA polymerases you don't have to know any of these because I'm not going to have you know those specifically just know that RNA polymerase is what puts together the transcript that we're going to look at so just like prokaryotes have that Tata box so do eukaryotes so this is eukaryotic transcription so here's the Tata box the difference in a eukaryotic gene expression is we have these linear chromosomes and we have to open our DNA at multiple spots so what our Tata box does is it binds to transcription factors and you'll learn this in genetics each of these comes in in a specific order so we call these transcription factors TF for short and so they'll come in tf2d tf2e they come in and that's how their name transcription factor and then Roman numerals and then letters I don't have you know that but these transcription factors act like a jack lifting the DNA apart so that RNA polymerase can squeeze in so here's RNA polymerase it can squeeze in there and start transcribing the RNA itself and because there's the nuclear membrane that transcript is going to get altered so this is where I said but wait there's more that mRNA does not directly go into translation we have time to change it and these are the three major changes we do for our mRNA we have a five Prime cap that's going to be GTP so it's got three phosphates it's negative it leads it leads the process for translation and it's protective on the three prime end we ought to poly a tail poly means what many right so we just had a bunch of A's they end up being decoys because once we leave the nucleus they're enzymes that are going to start chopping it up so they can approach the five Prime end because it's highly negative so it's protected the three prime end has this long chain of decoy bases and so they're just chewing off decoy bases it buys your transcript time to be translated but this is where we see the most variation where we have the removal of the introns and the coding joining of different axons so this midpoint here is where we see splicing take place so this is what GTP looks like this is your poly a tail and introns and exons will be on the test so I wanted you have definitions introns used to be called Junk DNA in the 80s and 90s it was junk DNA we now know these introns are just not coding for the product we're making at that time but they anticipate oh you're making this you're about to need this or I should turn that off we're talking about mRNA so this is where RNA science has exploded these introns act as transcription factors to turn on genes elsewhere or to block expression of genes somewhere else so they're not junk at all they're helping control our entire metabolic process if you're making this I need to turn this off and turn this on so we used to call them junk DNA in the 80s and 90s now we know these are control mechanisms they're not actually being wasted the exons are the sequences that are actually going to be coated and these are individually targeted by another group of RNA called snurfs small nuclear riboproteins so we call them snurps for short they read the transcript and cut out the pieces that we don't want so the snerps these small nuclear riber proteins make up what we call a splice Zone and they cut out different sequences those introns then go and control genes somewhere else so this entire process is called alternative splicing one gene will have different products made from it based on what's needed at that moment and there are all kinds of studies that suggest most mammals use alternative splicing to spread our genome for multiple products though just giving you one study here that says 95 of mammalian genes okay undergo alternative splicing to make different products so we have about 20 000 genes that we've mapped out at the time of printing this book those 20 000 different genes make over a hundred thousand different proteins because of alternative splicing so this gives us an edge in making our our products so I'm going to stop right here with alternative splicing and I'll pick up and we'll finish um

Transcript for:Genetics and Molecular Biology Exam Prep

Transcript for:
Genetics and Molecular Biology Exam Prep