Transcript for:
Genetics (Chapter 8)

okay guys in our last chapter for unit 2 is going to be chapter 8 over genetics so overall genetics is just the science of inheritance or heredity basically how living things transmit properties from parents to their offspring how we express those traits once we have them we'll also look at how the genetic material dna rna is built how it works and then how that genetic material can change usually through things like mutations but we'll see a couple other instances as well so before we get too far into this let's do a couple definitions to get us started starting with genome so the genome when we're talking about any different organisms genome we're meaning all the genetic information of that organism so for eukaryotes this is going to include the nucleus as well as all the dna or rna in the mitochondria and chloroplasts because remember they do have their own set of genetic material and then for prokaryotes this will include the nucleoid which remember is just the kind of region inside the cell where they shove all the dna rna and then also those little plasmids when we say a chromosome you've probably heard that term before for example humans have 46 chromosomes this is just going to be a set of structures made of dna and for prokaryotes is where we'll focus most of our time this is just one large circular chromosome all bacteria just have one versus eukaryotes can have anywhere from five to two hundred a gene when we're looking at a gene is basically a piece of one chromosome a certain segment of dna that's going to code for one type of protein and then genotype and phenotype genotype is just an organism's genetic makeup their dna code or their rna code and then a phenotype is what that code gives them the expression of those traits so for example you can have the genetic code we'll see of a certain group of nucleotides that's for hair color and then the phenotype could be red hair or blonde hair or brown hair or black hair or whatever it is so this is just showing that difference in location for genomes so we said eukaryotes which is the big cell on the left there and then prokaryotes on the right and then viruses remember they're kind of their own little thing and the bottom right there eukaryotes they're going to have those chromosomes in the nucleus and then also some extra chromosomal dna in the mitochondria or chloroplasts if they have them and then the prokaryotes you can see that one circular chromosome as well as those little tidbits of dna that are in the plasmids now these are just two examples you don't have to memorize these numbers in fact please don't but just to kind of give you an idea of the different sizing of genomes there's a huge variance so we have two examples here with e coli or espressia coli a type of bacterium and then the human genome e coli those those are a prokaryotic cell right they're bacterium so they just have one chromosome on that one chromosome there's about 4 000 genes so each gene again codes for one thing in that cell and it's pretty small if it's totally unwound and stretched out it's only about one millimeter or one thousandth of a meter which is pretty long compared to the actual cell it's about a thousand times longer than the cell itself so it does take up quite a bit of space inside the cell so the nucleoid is fairly large for e coli for the human genome we have about 46 chromosomes and those are linear those kind of x-shaped ones that you saw in the image earlier and we have between all of those different chromosomes about 20 000 genes so a big difference here but we are a more you know generally complicated organism so that makes sense we'll see a little bit later that this doesn't necessarily mean that you have to be more complicated if you have more genes it's just in this case happens to be true um if we were to unravel all 46 of those chromosomes and lay them out end to end it would measure almost six feet long a little longer than six feet long and we shove all that into every single one of our teeny tiny little cells so let's do a little bit of review on the structure of dna and then add a little bit more to it so remember the monomer of nucleic acids or the building block of nucleic acids are nucleotides these are going to be the basic units of the genome for every organism whether they have dna or rna remember nucleotides are made up of three main parts a sugar which is either going to be deoxyribose and dna or ribose and rna a phosphate group and then some nitrogenous base now when we put a bunch of these nucleotides together that's when we get dna or rna when we have several nucleotides they're going to bond to each other what's known as a covalent bond which i don't care you know too much about but basically this is a really strong bond and it's going to attach and create this kind of backbone of dna or rna that's going to be made by the sugar and the phosphates of different nucleotides sugar of one nucleotide to the phosphate of another then another sugar then a phosphate sugar phosphate the sugar then is going to have this kind of repetitive pattern that comes out of it based on attaching to these different phosphates so you're going to see that this sugar is always a five carbon sugar whether it's deoxyribose or just ribose it's a sugar that has five carbon molecules in it and they go around and count them calling them one prime two prime three prime four prime or five prime carbons which you can either put the number with a little apostrophe or you can just write out whatever number prime but basically the one that's on the five prime carbon is going to be attached to one specific molecule and then the other is going to be attached to the three prime and this is going to end up creating a direction to the dna which sounds weird but we'll see it here in a second so when we're looking at this image you can see the little circles are kind of blown up on either side of this dna molecule you can see the counting of one two three four five primes around that yellow sugar molecule in this case deoxyribose because it's in dna and you can see coming off of the five prime carbon is a phosphate group on one end and then if you go to the opposite end of that dna if you're looking at like the top left and then go straight down to that other blown up phosphate group you can see the five prime of that sugar is still attached to a phosphate group but the three prime is attached to an o h group this is going to be known as the three prime end versus the five prime end on the other side is going to be the side that has that phosphate group on that little end that we first looked at then if you notice going across the way it's backwards you have the group with the oh group on top and then the group with the extra phosphate group on the bottom so this is going to give those two sides of dna if you notice those blue arrows one going down and on the other side one going up this is going to create a topic that we'll talk about on a second called antiparallel where the two sides of dna are running in different directions one is running five prime to three prime and the other side is running three prime it's a five prime so we said that the different nucleotides are going to bind between the phosphate and the sugar groups with that covalent bond a really strong bond then the nitrogen bases those kind of little third bits that we haven't talked about yet that make up a nucleotide those are going to join to complementary bases or basically they're matching side between the two sides of the dna molecule which you can see in the image here and those are going to be bonded with hydrogen bonds hydrogen bonds are the weakest of the three bonds so covalents are strongest hydrogens are weakest and so you can see that we have different pairings of these bases which you can see in the image and it's also written out there but for example at the start of the image here we have a t which is going to be known as a thymine is going to match to an a and name then if you go down you see g guanine is attached to a c cytosine and then vice versa going all the way down c to g cytosine the guanine adenine to thymine a to t this is always going to be the pairing for dna a is always compared to t g is always going to pair to c in dna in rna this is a little different because we don't have adenine we don't have that a so instead the a's will all be replaced with u's for uracil but we'll get to that here in a little bit so we end up with four bases for dna four bases for rna they're almost exactly the same except for that last one thymine and dna uracil and rna we can further break these down in both dna and rna into two groups purines versus pyrimidines now i don't care you know too much about this difference i just want you know which ones are purines which ones are pyrimidines but it's a structural difference the size difference it doesn't matter technically purines are a little bit smaller pyramidings are about a little bit bigger but for right now i just want you to know which ones are which so for purines in both dna and rna guanine and adding are going to be our purines and then pyrimidines are cytosine for both dna and rna and then those ones that switch thymine and dna uracil and rna so then when we match these guys up because remember a is always compared to t and dna a to u and rna and then c to g in both you're going to end up pairing a purine to a pyrimidine and you're going to end up having these different set of bonds it's going to be based on different structure changes that we don't care about i just want you to know that when we have adenine pairing to either thymine or uracil regardless of its dna or rna it's going to create a double bond versus cytosine and guanine are going to have a triple bond between them again structure we don't care about just want you know a pairs with a double bond to its partner c and g pair with a triple bond so then looking at this again so we see our double stranded dna here and then if we kind of unwrap that double helix structure kind of untwist that ladder now we can see the individual nucleotides with our phosphates and yellow our green sugars and then our different nucleotide bases in the center there and you can see our matching up of purines and pyrimidines our t's to our a's our g's to our c's so on and so forth and you can see again those hydrogen bonds the double hydrogen bond between a and t the triple hydrogen bonds between g and c and you can also see the difference between that five prime end and three prime end if you look in the purple boxes there in that backbone of the dna you can see the five prime end has that extra phosphate group and then the three prime n just ends with that sugar group or technically it's that oh group but in this image it just shows it's stopping so you see the left side in this case goes five prime to three prime if you're going down and then it switches on the other side and goes three prime to five prime so again this creates that idea known as anti-parallel dna where the two sides run in opposite directions another term that we need to know for dna is this idea of semi-conservative this we'll get into here in a second when we look at how dna replicates but essentially when we make a new dna molecule we are never starting from scratch which would be the conservative viewpoint semi-conservative means when we are replicating dna the new pieces of dna that we're making are each going to have a piece of the old dna in it which is shown by the blue see how it splits in the far right of that image and then the red is the new dna so we are going to have the semi-conservative model where both of these are basically going to be built off of a template from the old dna molecule and so this different ordering of those four nucleotide bases that's what creates all of the differences in every organism that we see think alone just of the different types of characteristics that people have right you have different color hair different heights different skin tones different you know builds of body all those different things that's just based on four nitrogen bases the a's the t's the c's and the g's then on top of that that's what makes up all living things just those differences in the order of those four nitrogen bases is what creates you know a bacterial cell versus a eukaryotic cell versus a human versus a plant versus e coli versus a virus right and that's because even though it's just four nucleotide bases we have all these different genes these different chromosomes so when you add a ton of them together it gives a ton of different sequence possibilities okay so now we're going to get into how we replicate that dna how we make new pieces of dna before the cell divides into create two new daughter cells so we want to take that double helix strand and make sure we get another double helix another double-stranded piece of dna there are going to be a lot of important players or important enzymes during this i mostly just want you to know these four helicase dna polymerase 3 dna polymerase 1 and ligase remember anything that ends in ace is generally an enzyme that's true for all of these so helicase job is going to be to unzip that dna double helix it's going to take the two sides of that ladder or that staircase and split them apart dna polymerase 3 is going to add on the new nucleotides and kind of proofread dna as it's building it for errors dna polymerase 1 we'll see we'll be removing a primer closing gaps and kind of fixing any mismatches that happen and then ligase will be the one that kind of puts the little last tidbits together and repairs anything at the very end so one thing to remember for dna replication is that dna is always going to be synthesized going from the five prime to the three prime direction which is why it was so important that we harped on it a little bit ago that there are different sides of that strand the problem with this remember is that dna is anti-parallel the two sides of dna run in opposite directions one is five prime to three prime the other is three prime to five prime so this is going to give us two different strands during replication a leading strand and a lagging strand the leading strand is going to be the one that's synthesized continuously because it's the one that's already going five prime to three prime as we're going to move down this dna replication fork the lagging strand on the other hand is the one that's going in the wrong direction so it's going to be synthesized discontinuously which basically just means that it's going to be made in pieces um roughly about a thousand nucleotides long i don't care you know that just know that it's synthesized in different pieces and then it's basically going to move in the opposite direction of the replication fork and then we're going to put those pieces together at the end so here's a nice overall image kind of showing this process so we have our enzyme there our helicase that's unzipping our dna it's not labeled helicase in this case it's just that number one that guy that's going to unzip the dna and you can see it's moving down that strand of dna then we're going to have some proteins kind of stabilize the two pieces that we've now unzipped that's going to give us our leading and lagging strand so as you can see dna polymerase will start on the top top one there it's going to be on the side that's already moving five prime to three prime because you can see the darker purple is the new side that it's making you can see the five prime n is where it starts and it's working its way towards a three prime end so that dna polymerase is just going to follow that helicase enzyme that enzyme that's unzipping it all the way down as it moves down this double helix so that is the leading strand the other strand the lagging strand is where we're going to run into issues because in this case dna polymerase again can only go from five prime to three prime but this side of the dna is flipped so it is going to be moving away from that replication fork from that kind of opening from the helicase molecule and so because of that every time that helicase moves down a little further on the dna it's going to leave a new gap which you can see there where it's not going to be replicated so dna polymerase is going to have to jump back okay remake that section as a helicase moves forward jump back remake that section helicase moves forward jump back remake that section technically this is done with several different dna polymerase molecules but what you end up having are these little segments known as okazaki fragments which i don't care you know that name for right now we'll get to it a little bit later but basically you can see these little pieces of that darker darker purple color that new section of dna that eventually dna ligase that last enzyme that we care about will come around and kind of join those little fragments together on that lagging strain which you can see it doing at number six there and so dna polymerase one that's going to move along removing those primers replacing them with sections of dna this can happen very very quickly just to give you some idea of how quickly this happens some bacteria can add nucleotides as quickly as 750 nitrogen bases per second at each fork and for different species of dna they're actually or sorry different species of bacteria they're actually multiple forks generally there are two that we'll see for bacteria so this is happening at both of those replication forks 750 bases every single second dna ligase then we said this is the one that's going to go along that lagging strand putting those little fragments together those okazaki fragments those little pieces of kind of incomplete dna and then dna polymerase 3 will come around again kind of fixing any mistakes that happened during replication which does happen fairly often but most of them are caught by dna polymerase 3 in this kind of second check so since this is a micro class of course we're going to focus more on the bacteria on the microbe side so in bacteria replication is always going to begin at this place called the origin of replication this is going to be where the membrane is also attached to the sorry the dna is also attached to the membrane and this is going to make sure that when the cell actually splits through binary fission each new cell is going to get a copy of the newly made chromosome another important thing for bacteria we just mentioned is that there are two replication forks and this is because we're going to have replication going bi-directionally around the chromosome remember bacteria have one circular piece of dna in order to speed up this process of replication for them because that's very important especially for like pathogens that get into a body and have to kind of fight with the like immune system of whatever organism they're in they need to replicate quickly so to kind of speed things up they have replication going either way around the circle and then meeting on the other end and you can see this happening here you have that origin of replication on the top left and kind of that greenish color and then you see the two replication works going either way around eventually you get a termination of the replication and you end up with two new sections of dna for that bacterium okay so that looked at replication of dna which is kind of the center of this image here replication of dna in order to make two new daughter cells but we also have different flow of genetic information with that horizontal gene transfer and then also we have the actual using of that genetic information to make the different parts of the cell to make the different proteins to make the cell do all the cell-like things so we're going to start with kind of looking at what is happening now within the cell once it's newly made with two processes transcription and translation and then we'll come back and look again at horizontal gene transfer where genetic info can be passed between cells in the same generation so remember we've said in earlier chapters that in order for cells to kind of function we have the central dogma of biology this idea of dna to rna to proteins so this process is actually broken down into two separate processes transcription and translation transcription is the process of going from dna to rna and then translation is going from rna to protein so you put the two together and you get that dna to rna to proteins how we get the genetic info and turn it into all the things you see and all the different things that an organism can actually do so we'll start with transcription converting dna into rna again there are tons and tons and tons of different players different enzymes different pieces to this i just want you to know a couple so the dna template is going to be important piece this is what's going to direct the synthesis of rna we're going to need another enzyme called rna polymerase in this case this is going to be building the rna piece by adding on different nucleotides don't let this confuse you with dna polymerase that we had in the previous section when we're looking at replication that's to make brand new piece of dna is dna polymerase rna polymerase is going to be making a piece of rna and then also we'll have a bunch of those rna nucleotides so we'll still have our adenines our guanines and our cytosines but remember instead of thymine now we have uracil and then some other important sites that we'll see on dna are going to be the promoter and the terminator sites the promoter site is where that dna polymerase or sorry that rna polymerase is first going to bind and start making the rna from the dna and then the terminator site is going to be where this rna polymerase is kind of released and the synthesis is over so here's just showing an overall image of that process so you can see the promoter is this kind of area of the gene that rna polymerase in blue there is going to latch on to and then it's going to start working its way down the dna building a new little section of rna and blue and you can see in this little blown up bubble it unwinds the dna in purple there it's going to read the one side and put the little matching pieces on its little blue rna section so you can see when it has a little a that it reads off the dna it's going to put a u because remember a matches to u for rna it sees a c it's going to put a g c is a t c a g c and so on and so forth building out this little blue rna molecule like you see in numbers three and numbers four eventually in number four there it hits that terminator site where the process is over rna polymerase is going to jump off and then you have your dna no worse for the where still in purple there and then a new rna molecule in blue so here i've kind of put a mock piece of dna in a mock piece of rna just to kind of simplify things for you so i have a piece of double-stranded dna at the top with a little section that's opened up as if the rna polymerase was about to read it and then the little piece of rna single stranded rna at the bottom so remember we are still going to create this just like in replication in the five prime to three prime direction so what happens when the rna polymerase opens up this dna molecule it's going to read the opposite side so it's going to read three prime to five prime in order to build the strand from five prime to three prime so it's going to read that top strand of dna in this image so the first nucleotide it will see is that t nucleotide and it knows okay t pairs to an a so it's going to put an a like in the rna on the middle of your slide there then it's going to keep reading all the way down that little section so the next one it comes into contact with is an a now remember instead of putting a t there because we're going from dna to rna instead we're going to add a u for uracil and then keep moving a c it's going to put a g sees another c it's going to put a g a g a c g a c so on and so forth until eventually it reaches the terminator sequence so we've mentioned all these things before but i thought i just have a slide with all of it written out for you that just there are a lot of similarities between rna and dna but there are some kind of key differences remember rna is always single stranded dna is double stranded i don't care you know so much that it has a helical form or that it has secondary tertiary levels of complexity it doesn't matter i do want to know that there are different forms of rna that we'll talk about here in a second mrna trna and rrna the mrna we just saw is going to be the piece that's made from dna we've so far just called it rna but it's technically mrna standing for messenger rna two other key differences is that it's going to replace thymine with uracil and that it's going to have a different sugar ribose instead of deoxyribose which is how it gets its name ribonucleic acid rna compared to deoxyribo nucleic acid dna and so here's a little closer look at those three types of rna so we said messenger rna or mrna that's the one that's going to go from dna to rna to proteins so it's made during that process of transcription then we have rrna and trna ribosomal rna and transfer rna ribosomal rna is going to just make part of the ribosomes which remember ribosomes job is to make proteins so this is a piece that's going to actually help build the protein from that messenger rna in the next step here in translation and then transfer rna is also going to help with that because it's going to carry the little building blocks of proteins amino acids to the growing protein chain so overall the process of transcription is going to result in a little kind of short-term copy of the gene that's basically an rna kind of replica from the dna and that's going to be used or red to build a protein so i kind of think of the mrna as like the blueprints for the actual protein so here's a closer look at our trna molecule that transfer rna molecule so this is the one we said is going to carry the amino acids to the building protein chain remember there are 20 different amino acids so he has to know which one or she i don't know it has to know which amino acid it has to bring in order to properly build that chain so basically we'll see here in a second that the dna and the rna are made up of what's called codons codons are just groups of three of these nitrogen bases so groups of threes of the a's the t's the cs and the g's or in the case of the rna the a the two the a the u the c and the g's can't talk so basically you'll get a code like a g g or a uc or something like that and it will code for a specific amino acid a specific building block of a protein the way that the trna molecule knows it's bringing the proper amino acid is because on the tna trna molecule there is an anti codon the anticodon is at the bottom there in yellow this is where those three little letters in this case an a an a and a g are going to match up to the side of the mrna molecule so when this comes up to the mrna molecule that's being read in the next part of translation that rna molecule is going to have uuc because that's going to be the complementary side so the codon would be uuc the anticodon on the trna molecule aag so that just knows that it's the correct amino acid that's going into place and then a couple other types of rna that we'll look at these are just little baby ones we won't look too closely at just basically know this slide and then we'll move on so we do have regulatory rnas primer rnas and ribozymes so regulatory rnas there are actually several different types including ribose switches small interfering rnas micro rnas antisense rnas basically these are all regulators for gene expression mostly in bacteria but a couple in eukaryotes as well another thing that these do is they act on coiling of the chromatin in eukaryotic cells so when a cell is going through replication when it's trying to make a new cell the dna condenses really really tight into those x-shaped chromosomes and eukaryotic cells but when the cell's not going through replication the dna isn't coiled real tightly like that it's kind of loose in the nucleus when it's loose like that it's called chromatin so this part of the regulatory rna job is basically just to kind of make sure that doesn't get tangled make sure that kind of coils up properly when it goes into the replication stages then we have primer rnas these are ones that occur during dna replication they kind of act like a template for dna kind of like the starter section for that rna or sorry that dna polymerase to come down and bind and start building the rna and these are found in both prokaryotic and eukaryotic cells and then finally the ribozymes basically these just remove unnecessary pieces from rnas in eukaryotic cells they basically take out what's known as introns these kind of unimportant little sections and get rid of them so we only focus on the important stuff okay so now let's actually move into the process of translation so we said central dogma is dna to rna to proteins transcription is that first half going dna to rna now translation is going to be going from the rna that we made that messenger rna to an actual protein so this is going to make that protein a couple important players again we're going to have the mrna that's going to act as the template or kind of the blueprints for the protein that's the one we just finished making in transcription then we'll have amino acids these will be the building blocks of proteins the trna is going to bring those amino acids over and then the ribosomes specifically made up of that rrna that ribosomal rna and then some proteins this is where we're actually going to have the building of proteins or protein synthesis so here's a closer look at those codons versus anticodons so the mrnas in the form of codons we said are groups of three nucleotides so for example say we have this stretch of mrna aug c u c a g a black whatever that's broken down into groups of threes so first one would be aug that's one codon gcc another codon the next codon cuc so on and so forth overall with those four nucleotides in rna adenine guanine cytosine and uracil there are 64 possible codons but remember there's only 20 amino acids that means that there are going to be several codons that lead to the same amino acid which is important because this redundancy or this kind of overlap is important so if there is a mistake made when we're making that mrna molecule say we replace a c with a g on accident or an a with a g on accident hopefully it will still lead to the same end result hopefully you will still get the proper amino acid in place so your protein will be built properly we'll see that that doesn't always work out but ideally that's what will happen i do want you to know the only codon i want you to to memorize is what's known as the start codon which is going to be aug this is going to encode for a specific amino acid known as methylene this is basically the kind of starting sequence for all proteins this is always the first codon then there are three stop codons i don't care that you memorize them doesn't matter but these are also sometimes called nonsense codons because this will kind of cancel protein synthesis it will stop the sequence the protein is now done and then as we're going forth just like we read the example up at the top of this slide codons are read sequentially just like we would read a book you'd read from right to left top to bottom type thing same thing here we always read right to left that five prime to three prime in case of the rna and that will give you your proper amino acid kind of order for the proteins and so here again don't memorize any of these except for that start codon that aug that leads to mephonine that's the only one i care about the rest of these do not memorize nobody cares but just to kind of show you how we have this overlap so you can see all the different possible codons in there for example if you look at the kind of top second row there there are four codons that lead to the same amino acid serine and actually there's two more in the last column third kind of third box down there's two more but again the overlap is if you notice they're relatively similar especially in that first box the only difference is that last letter in that group of codons so hopefully even if there is a mistake we get the same end result okay so now let's look at the actual process of translation so first you need all those different parts right the ribosomal rna you need the trna molecules bringing the amino acids and you need the mrna that was made in transcription once you have all those the ribosomal rna or the big ribosome is going to grab on to that mrna molecule and read that first codon which again will always be aug and it will bring methonine in then it will continue reading kind of working its way down that mrna molecule every time it reaches a codon the proper trna will bring the correct amino acid that's needed and it'll work its way down i don't care so much that you go no it goes from a p site to an a site nobody cares just know that they work their way down eventually you'll see a growing little peptide chain or a growing little protein chain like you see in step six there and at some point they'll reach one of those stop codons that will end the process of protein synthesis and you'll end up having a new kind of fully formed protein and then the ribosome will let go of the mrna and the process is all done so there are some differences here between prokaryotes and eukaryotes in terms of translation one of the biggest ones being that in bacteria in most prokaryotes but bacteria especially translation actually starts while transcription is still happening this is because both transcription and translation occur in the cytoplasm versus in eukaryotes the dna is housed in the nucleus so because transcription involves dna to rna and the dna is in the nucleus transcription has to happen there and then the mrna that's made has to leave the nucleus and go out to the cytoplasm where the ribosomes are so those two processes are separated in eukaryotes but in prokaryotes they can happen at the same time as soon as a little tidbit of mrna is made it can start going through translation another big difference is that there are actually what's called polyribosomal complexes which just means that there are several ribosomes that form on prokaryotic mrna because it's actually long enough that it can go through several ribosomes at once which means it can go through translation multiple times in one run versus the images we shot show already when we are looking at translation there is just one ribosome running along the mrna in a lot of prokaryotes there are actually several of those and they're just one after another going down the mrna chain which means you can make several proteins at once and this is a pretty lengthy process for both prokaryotes and eukaryotes and it's a pretty costly uh production on average for just like kind of a normal size protein and they're of course smaller and larger sized proteins on average it's about 1200 atps are required or 1200 of those little energetic batteries are needed in order to make one single protein and remember the best cell respiration that we looked at in the previous chapter only made at most 38 atp so this is a big big kind of energy input for cells some other differences here is that the start codon is that aug that methonine for both but in eukaryotes it actually has a slightly different form i'm fine if you just know them both as method but it's technically a different form overall another big difference is that the mrna in eukaryotes only codes for one protein versus bacteria oftentimes has several genes all on one rna and one gene codes for one protein so that means it codes for several proteins another one we already talked about is that transcription in eukaryotes happens in the nucleus versus in prokaryotes there is no nucleus so it all happens in the cytoplasm and then another big thing that we just briefly mentioned on a previous slide is that eukaryotic genes are not actually one long uninterrupted series of codes for a protein there are pieces that are used to make a protein and then there are pieces that are not and these are called introns and exons introns are pieces that are going to be cut out they're basically what's called kind of sometimes called junk dna although this is not a great term because we're finding out that there are things that it does it just doesn't code for a protein then the exons the pieces that are left are actually pieced together to form the actual gene and then a little look at gene expression and regulation of that expression we've looked at this a little bit in previous chapters um so some of this is a review some of it is new um so only about 60 to 80 of genes are actually needed all the time these are called constitutive which means they're always on they're never regulated because we need them all the time other genes we generally only turn on when a cell needs them because if a gene is turned on that means we're going to make a protein from it and we just talk about how that's a big energy expenditure so for this we either use repression or induction to either turn a cell on or sorry to turn a gene on or to turn a gene off as the cell needs it repression is going to inhibit that gene expression which means it won't go through transcription induction will turn on transcription so it'll start making that protein generally repression occurs when there's too much of a product or we have too many of those proteins or if there are repressors binding to that dna stopping that rna polymerase from binding and going through that transcription process induction on the other hand is where an inducer then binds to a repressor and basically stops the repressor from holding onto the dna so the repressor falls off and now rna polymerase can go and do its thing starting transcription so here's just that kind of breakdown with an image so on the left hand side you have without a repressor on the right hand side you have with a repressor so without a repressor you have rna polymerase it's going to bind to that promoter site and start transcription no problem but when you need a gene kind of shut off for a while you have essentially this roadblock that's the repressor so rna polymerase can't bind can't go through transcription because there is a literal thing stopping it from running down that dna so there are lots of different examples for repression in prokaryotes especially but the best understood one is one that's used for the repression induction of what's known as the lactose operon or the lac operon this was first seen in e coli bacteria in 1961 and it's basically how the cell regulates the breakdown or the metabolism of lactose which is a type of sugar found in milk if you've ever heard of someone that's lactose intolerant means they generally don't handle dairy very well it's because they don't have this enzyme to break down lactose so normally we'll see that most operons work the same way so when we're going through how this works it's going to mean for all of these repression systems it's just this one we understand the best so we're using as an example so there are three important features for any general operon system a regulator a control area and a structural area the regulator is going to be the gene that codes for the repressor protein that roadblock that we saw in the previous image the control center is going to be made of a promoter which remember is where the rna polymerase is going to bind and kind of signal the start of transcription and then an operator an operator is going to be a sequence that acts as the actual on and off switch for transcription and then finally the structural area this is generally made up of three genes each coding for a different enzyme in this case that catabolizes or breaks down lactose so you don't need to know like crazy lots of information about this just kind of giving you an overall image of this i do want you know for the most part what the lac operon system is and the different parts of it and roughly what they do but don't get crazy detailed here because again for the most part we're just trying to learn the operon system not this specific example but here you can see you have your regulator your promoter and your operator basically the regulator is going to be at the very start of this so when it's red when it's functioning it's going to produce this repressor protein that repressor protein is going to be the repressor that we saw in the previous image that's going to act as act as the roadblock it's going to attach itself to the dna and basically stop that rna polymerase from binding and going through transcription so when it's there it's not going to allow this to happen now in a normal e coli cell in this case this regulator is always turned on if they have another food source if they have something that they can break down other than lactose they're going to have this regulator on the repressor on so they're not going to go through transcription to make the enzyme needed to break down lactose because they don't need it they're eating something else usually glucose because it's a lot easier for the cell to break it down lactose on the other hand takes a lot of time and energy to break down i mean just here it takes three genes to make it right so they don't want to have to use that if they don't have to but if something goes wrong and if there's no glucose in the environment and they only have lactose that's going to trigger this event to turn this operator on so in this case the regulator is going to be shut off that repressor protein is going to be removed and the genes are going to be called what's known as induced or they're going to be kind of started so now that the repressor is gone like you see in the second half of that image the rna polymerase can bind and start the process of transcription it's going to start making those proteins to start breaking down lactose in this particular case in the lac operon it's going to end up producing those three separate proteins that you see in the bottom of the image there with three each one of those is going to work to start breaking down lactose for digestion as we start breaking down that lactose though at some point we'll run out of lactose ideally we'll get another food source like glucose back so we won't need to break down lactose anymore in this case that regulator is going to turn be turned back on the operator is going to be turned back off this means that that repressor protein is going to be made again and it's going to act as the roadblock again stopping transcription from continuing which means we won't make those proteins anymore which is good because we don't need to we have another food source okay so that was then the flow of genetic information within a cell we've already done the flow of genetic information between different generations with replication earlier now let's go to that far left side and look again at horizontal gene transfer most of which we've seen before so hopefully these next couple slides will be a review so remember our three types that we've seen before are conjugation transformation transduction remember conjugation is the one where you have that plasmid in one cell with the sex pilots or just the pilots that basically stabs a nearby cell yanks it close and then the plasmid is replicated and put into the new cell transformation that's where one cell comes across the kind of like tidbits or the fragments of dna from a cell that's been lysed some other time for whatever reason the cell picks up those pieces of dna for parts basically decides instead of breaking them down completely incorporates some of those genes into its own genetic information and then transduction involves that bacteriophage where you have the little virus of bacteria incorporates its dna into the cell but as it's building new viruses it incorporates a little bit of that bacterial dna into some of those phages so when they go around and infect cells later on some of that bacterial dna is put into the new bacterial cell a new thing for horizontal gene transfer that we haven't mentioned before are transposons transposons are what's known as transposable elements sometimes referred to as jumping genes but these are basically genes that are able to shift from one part of the genome to another specifically usually from the actual chromosome of a bacterial cell or some other prokaryotic cell to the plasmid or vice versa if they move to a plasmid that means that not only can they be replicated in the normal chromosome when they make new cells for a new generation but they can also get past new cells during conjugation so this is kind of like in addition to conjugation is they can pull these jumping genes into the plasmid as needed and then they can copy themselves back into the original cells chromosome so they don't lose that transposon and so this is just showing that image where a transposon exists in the actual bacterial cell and then it can move locations either just to different parts of that plasmid or it can duplicate itself like in 2b there where they now have multiple transposons or it can put itself into a plasmid in which case again it can go through that conjugation and pass that bit of information to an entirely new species of bacterial cells so when a transposon jumps around this essentially scrambles the genetic language it scrambles that dna or rna set up and this can be good or bad it kind of depends on where that transposon goes what kinds of genes are moved and also the type in cell involved but it can cause a lot of different changes it can cause things like colony morphology or color to change shape to change it can also replace damaged dna or it could transfer that drug resistance like we've seen in several species for example with mrsa and other antibiotic resistant species and the last section i want to look at for this chapter this unit really are mutations so mutation is just a change in genetic information that results in an altered protein now this is usually lethal if it involves a change to a necessary phenotype if it changes something that is needed by the cell every once in a while though it's beneficial maybe it gives like a bacteria antibiotic resistance which to us is not a benefit but to that bacterial cell is a benefit because it keeps it alive or it could have no effect at all but usually they are bad mutations overall are very important to evolution and these are actually how we've gotten all of the different species on our plant planet is through a mutation for example say there's a mutation that happens in a butterfly that is normally white that causes it to become brown this could be a benefit to that butterfly because maybe it's a butterfly that lives in a forest and now that it's brown it can hide better from predators versus the white butterflies stood out right this is a benefit to them because it's more likely to live long enough to produce more offspring which means it's now going to pass that mutation on to its offspring meaning the entire population of butterflies you will start to see more and more brown versus white because the white ones get picked off the brown ones survive and that's the basis of evolution eventually if this goes on long enough and there's enough changes you get entirely new species there are several different reasons for mutations called mutagens something that causes a mutation is a mutagen the two most common are chemical and radiation um so chemical you don't need to know the example but for example nitrous oxide alters adenine instead of it normally binding to thymine like it's supposed to nitrous oxide causes it to bind to a cytosine which when you break that dna apart and read it means you're going to build that opposite side of the dna wrong because it doesn't realize that there was that damage another example for radiation would be uv light uv light causes thymine dimers which just means that they basically stick together which again is bad because when they're building new dnas we don't know that that happens but uv light is in this thymine dimer is actually what ends up causing skin cancer so it's very common there are lots of different types of mutations these are just some of the most common ones but your textbook does have a few more for example so we're looking at three mutations here where you have the normal dna up top and then it's showing it's showing you the affected parts in different colors there for example the first mutation type is called a missense mutation this is where only one amino acid is changed in the polypeptide in this case an a is changed to a g or adding to thymine this causes that glutamine to be replacing that lysine or that glu replaces the lys and the image there but the overall chain is the same except for that one amino acid that's a missense mutation a frame shift mutation is far more damaging almost always results in a cell dying or not surviving almost always this is either caused by an insertion or a deletion where an amino acid is added in or removed or sorry a nucleotide is added in or removed and this changes the entire sequence of the polypeptide of the protein at the end you can see all of those amino acids after that frame shift have changed this is because it's going to change that codon grouping if you add or remove one in then that grouping of three is going to shift and so you're gonna end up with a completely different protein and then finally nonsense mutation these are again pretty rare but when they do happen it's just as bad because it changes that whatever codon it affects changes it to a stop codon which means the polypeptide's incomplete the protein is not finished which is usually bad because if we're making a protein it's because we need it so we said that we have mutagen that are likely to cause mutations things that make it more likely for mutations to happen but there are always there's always a risk for mutations even if you don't have those chemical or those radiation influences for example the average gene is roughly a thousand base pairs long and that's a huge um assumption that it can be anywhere from like 100 to 10 000 but just on average about a thousand the rate of mutation for spontaneous mutations is about one in every uh one billion genes so happens but kind of rare for example in a large bacterial population there are always a few mutant cells just because they reproduce so quickly and there are so many of them in their populations most of these mutations again are harmful or at least neutral but every once in a while you have a beneficial mutation where those cells are more likely to survive or more likely to reproduce for whatever reason and that's when you see the change in the actual species or a new species form because eventually that entire population will have that gene due to evolution and then if you have mutagens mixed in if you have those chemical or radiation influences that just increases the rate of spontaneous mutations sometimes depending on how much those mutagens are around up to a thousand times more likely so once we have these mutations once they get through that process of transcription translation they are permanent um and they will pass from organisms down through the offspring in either eukaryotic or prokaryotic cells or viruses most of these again are not beneficial but a small number of cases could be for example they could create different strains different ways of adaption survival reproduction really we don't see these benefits come about as long as the environment is stable for that population the mutants generally only com comprise or make up a sorry i lost that word for a second really only make up a small percentage of a population and it's not until that environment changes into some kind of negative effect that you generally see mutants kind of survive and thrive because usually for example say you have a mutation where that mutated cell can survive really high temperatures but normally the cell lives in a pretty steady environment say of you know 98.6 degrees and then it's not until all of a sudden the body gets a fever or something and it starts killing off those normal bacterial cells that are there now all of a sudden the mutants are like hey i'm still here i'm still good because they're the only ones that are left they end up reproducing now the entire population is temperature resistant same thing with drug resistance you really don't know you have drug resistance drug-resistant bacteria or cells until you introduce that drug and realize oh they're not dying great all right so there is one little section at the end of the chapter in the textbook called studying dna in the lab and genetic engineering we're not going to go over this section i won't ask anything about it on the lecture exam there may be a few homework questions on this just because connect covers the entire chapter but just try and bust through those because again we're not going to do it for the exam so just don't worry about that as far as studying goes okay and that is the end of unit 2 which means we are now ready for lecture exam two and this will cover everything from chapters six seven and eight