this is chapter 8 part two so in part one of this lecture we left off talking about types of mutations um and how they mutate DNA sequences we're going to pick up uh kind of where we left off with talking about mutations a little bit more how the cells try to fix and correct any type of mismatches in base pairing or any other mutations the best that it can and then we're going to move on to horizontal Gene transfer and types of horizontal Gene transfer so let's talk a little bit about radiation there are two types of radiation that we are going to discuss ionizing radiation and UV radiation examples of ionizing radiation are xrays and gamma rays and these we call them ionizing because they cause the production of ions and this leads to Breaking the backbone of DNA so if you recall DNA the backbone of DNA are basically those main strands of DNA that are made up of deoxy ribos and phosphate ionizing radiation like x-rays like gamma rays these break the deoxy phosphate backbone of DNA and that's a really big deal UV radiation are like UV rays these end up causing thyine diers so a is supposed to bind with t right so adenine has to bind with thyine and thines don't bind with each other so I'm going to draw an image here so here I have my two strands of DNA right so these would be like the backbones and then I have my bases kind of sticking inward right so if I were to make the analogy of a ladder it's kind of the steps of the ladder and so I can have a here um I'll have another a and then maybe I'll have like a c whatever and then here the correct match would be t t and then here would be G right so these base pair with each other however UV rays actually cause thy Mees to bind to one another so I have a thyine here and a thyine here these will actually bind together they're not supposed to there's no binding that has to happen this way and there's no binding that has to happen between two thines so this would be a thyine dier and again that's caused by UV radiation so how is this repaired two ways um there's a lot of ways actually that this is repaired one enzyme that plays a big role are photol liases photol liasis are enzymes that will separate the thyine DI ERS that happen so that's one way to repair um what radiation has caused now the process of repair that we're going to learn about is nucleotide excision repair that's when you have a mismatch between the base pairs and we have enzymes that will actually cut out and remove the wrong base and replace it with the correct base so this process is called nucleotide excision repair so here let's say this is was the DNA was exposed to UV light and now we have a thyine dier so we have the thines next to each other there's an enzyme called an endonuclease and the endonuclease enzyme will remove this incorrect section DNA poase will come in and fill in the Gap um with the correct bases and then DNA ligase comes in and kind of seals everything together and in this way you repaired those thyine dimers okay so there are um ways to identify mutants mutants are basically mutated cells cells that have a mutation in there and they are basically different there is positive or direct selection and negative or indirect selection um positive selection is going to detect mutant cells because they grow or they look different than cells that are not mutated negative selection detects mutant cells that can't grow or they're defective and and they can't perform a function okay so how do we identify chemical carcinogens so these are chemical agents that cause cancer and mutations can lead to cancer um or do lead to cancer um there's one test called the Asim test and that exposes mutant bacteria or mutated bacteria to mutagens and measures the rate of reversal of the mutation and so this is how we test to see how mutagenic a substance is how how much of a mutation would that substance cause I'm not going to ask you about the as test um I'm also not going to ask you about positive or negative selection but it's something that is good to know okay so a couple of terms we have to Define here that maybe you're familiar with with previous bio classes genetic recombination genetic recom combination just think of genetic has to do with genes and recombination means it's recombining okay into something else so genetic recombination is the exchange of genes between two DNA molecules so for example let's say I have my DNA molecule and you have your DNA molecule we can exchange genes with one another that would be like a very simple um genetic re combination definition this creates genetic diversity because now for example I just had my own genes but now I have someone else's genes too which I never had before so things are becoming more genetically diverse okay um crossing over when two chromosomes break up and then they rejoin they result in foreign DNA entering into the chromosome this is kind of another example of creating genetic diversity breaking up two chromosomes and joining them with maybe another organism's chromosomes and now in that way foreign DNA or DNA that doesn't belong to the cell has entered into the chromosome okay so now we're going to move on to horizontal Gene transfer we have so far when whenever we talked about DNA replication we were talking about vertical Gene transfer right the transferring of genes from an organism to its Offspring cells and then to the Next Generation and to the next it's moving vertically horizontal Gene transfer is still a transfer of genes but it's between the same generation of cells so between cells that are the same generation so that's like me transferring my genes to a coworker okay you transferring your genes to one of your classmates that's horizontal Gene transfer we cannot do horizontal Gene transfer but bacteria can and it's a really really big deal because not only does it cause um pathogens to be more diverse and evolve um it also gives them resistance and so that's a survival Advantage for them but it's bad news for us if we get infected by one so the first uh subject that we're going to talk about are plasmids plasmids and transposons these two are examples of mobile genetic elements that means they are genetic elements or genes that can actually move they can move from one part of the DNA to another part of the DNA they can move from one cell's chromosome to another organism or another cell's chromosome and it doesn't have to be between cells of the same species a lot of times most of the time we're talking about bacteria of different species exchanging genes and that leads to a lot of diversity so plasmids and transposons can be moving around in procaryotic or eukaryotic microorganisms so let's talk about plasmids first plasmids are pieces of DNA that are circular but they're self-replicating they're not part of the typical chromosome or the typical DNA of a bacterial cell but they're kind of on the side they can replicate by themselves they're much smaller so they're about like 1 to 5% of the size of a regular bacterial DNA and a lot of times they C code for proteins that makes a bacteria more pathogenic makes the bacteria um more able to survive and more able to cause disease because a lot of times plasmids they um have resistance factors on them resistance genes that helps the bacteria survive in for example in the presence of an antibiotic so here is an example of a plasmid so in a regular cell you would have so let's say this is my cell and inside of my cell I have my bacterial chromosome my typical bacterial chromosome and so these plasmids are just smaller pieces of DNA sorry that are kind of hanging around okay all right so again plasmas can carry a lot of genes on them so this plasmid for example it can carry resistance genes that's resistance to tr sorry streptomycin resistant to sulfonamides resistant to Tetra cyclin resistant to Mercury so it helps them survive a lot and so these plasmids can actually travel around plasmids can travel from one bacterial cell to another bacterial cell and so they can keep passing around these resistance genes okay transposons are also mobile genetic elements these are again pieces of DNA but they can move from one region of the DNA to another region so these ones kind of stay on the typical on the regular DNA chromosome but they're we I call them jumping genes they're genes that can basically cut themselves out of one part of the DNA molecule and put them in put themselves into another part of the DNA molecule so jumping genes um so these transposons they contain these DNA sequences called insertion sequences and insertion sequences code for an enzyme called transposase transposase basically can cut out and resal DNA so it can literally jump to another section so it can cut it cut out the SE the sequence of DNA jump to another SE segment of DNA and resal we have complex transposons that can carry a lot of genes just like how plasmids can carry a bunch of genes transposons can carry like antibiotic resistance genes other factors that would make a bacteria more pathogenic so this for example um is a transposon so you see there is the transposase gene here so this whole segment is called an insertion sequence and the transposase gene is always between two inverted repeats inverted repeats are basically like um the same pattern but in the opposite direction so for example um the this would be ATC up here and then this is ATC up here so in the middle here you have transposase and that again is going to help cut out a gene and insert it somewhere else so these are jumping genes transposons okay we're going to move on to another method of horizontal Gene transfer and this is transformation transformation is a really really big deal not all bacterial species are able to undergo transformation but some are transformation is when genes are transferred from one bacterium to another bacterium as naked DNA in other words transformation is when a bacterial cell can take up naked DNA from its environment and bring it in and that naked DNA often can have genes that can help out this bacterial cell like resistance genes so taking up naked a piece of naked DNA from the environment that is transformation so if a bacterial cell was able to pick up genes from outside from naked DNA outside we would say that that cell has transformed okay so how did we discover transformation so there was um a scientist Griffith and so Griffith basically did an experiment and he noticed noticed that something different was going on and that's the first time he discovered transformation so he was working with mice okay and before I go over the steps I just want to tell you what encapsulated bacteria is encapsulated bacteria means a bacteria that has a capsule around it having a capsule around a bacterial cell makes the bacterial cell more pathogenic it helps it survive better it helps your immune system not be able to basically kill that cell so if I say there is an encapsulated bacteria in other words to put it simply it's a more pathogenic bacteria more dangerous for us okay so first Griffith injected this mouse with living encapsulated bacteria so it injected the mouse with the pathogenic more pathogenic bacteria what happened it caused disease and the mouth died okay then he injected another mouse with living nonencapsulated bacteria this is bacteria that does not have a capsule so it's not really that pathogenic since it's not that pathogenic the mouse remained healthy and lived and then he heat killed the pathogenic bacteria he basically injected the mouse with killed encapsulated bacteria killed pathogenic bacteria so it's still the pathogenic bacteria but the cells are all dead since the cells are dead they can't do anything so the mouse remained healthy and then he injected a mouse with both the dead pathogenic bacteria and the living nonpathogenic bacteria and he noticed that the mouse died and he thought okay that's weird because the one that's supposed to kill the mouse is the pathogenic bacteria but the pathogenic bacteria is dead the living bacteria is the non-pathogenic one without a capsule but yet the mouse still died so what's going on here and so he realized that the living non-pathogenic cells were able to take up the DNA or the genes from the dead pathogenic cells and it turned these non-pathogenic cells into pathogens and so they ended up causing disease and the mouse still died so the non capsulated or non-pathogenic bacteria was able to be transformed and so I picked up the genes to have a capsule and now it became more pathogenic okay so here is the mechanism of transformation so you have a bacterial cell it has its regular chromosome DNA inside and here is a naked DNA in the environment this bacteria if it's able to take up this naked DNA it can cause recombination remember recombination was the exchange of genes so it can undergo genetic Rec combination and basically exchange genes with that naked piece of DNA and now genes that don't belong to this cell are put into its regular chromosome and now those genes can code for a number of things that can make this bacteria now more resistant and it increases its survival and its Advan percentages so that's transformation so so far we looked at plasmids we looked at transposons and we looked at transformation now these were all methods of horizontal Gene transfer we're going to move on to our next method of horizontal Gene transfer which is conjugation so conjugation is when plasmids are basically transferred from one bacterial cell to another bacterial cells and this requires cellto cell contact and the cellto cell contact is through sex py so remember we talked about py or aillis is a singular version and it's it was kind of like an extension and it helped with attachment so these cells attach to each other through a pillis and then the plasmid is transferred from one cell to another cell so this is what it would look like and I'm going to go over what these cells are but one of the cells is called the f f plus cell or F positive the other one is f minus and here is the sex pillis um allowing these cells to have direct contact so genes can literally pass from one to the other and we call that a mating Bridge that's where genes are transferred okay so a couple of terms we have to Define first the plasma that we're talking about in conjugation we call that the F factor or the F plasmid so if a bacteria cell does have the plasmid it carries the F Factor we say that that cell is an f+ cell if a bacterial cell does not carry the F Factor plasmid we say that that cell is an F minus cell it doesn't have it or F negative okay we're going to come back to this HFR cell in a second so here I have a bacterial cell and this is an F positive cell right because you have it has its regular chromosome and it does carry the F Factor plasmid here I have an F negative cell because it does not have the plasmid so the bacterial cell the f+ bacterial cell that has the plasmid basically creates a mating Bridge with the F negative cell and through that mating Bridge it first copies its plasmid and then it transfers that copy of its plasma to the F positive cell so now they both carry the f F Factor so now the one that was F minus is now considered f+ this is conjugation now one more thing can happen that f+ cell that has a plasmid that's separate from its chromosomal DNA can undergo recombination if it chooses to where it literally inserts or integrates its F factor into its main chromosome in that case we would call it an HFR cell so if integration of the fact Factor happens and this recombination happens we would call that an HFR cell so one more time I have an F positive cell and an F minus cell right F positive cell carries the fact Factor plasmid but it can transfer that plasma to the F negative cell making the f- negative cell now an F positive cell if this F positive cells or even this one doesn't matter if the if an F positive cell chooses to undergo recombination and integrate the fact factor into its main chromosome then we would Now call that an HFR cell now an HFR cell doesn't have to permanently have the F Factor integrated at any time if it ever wants to or needs to depending on its circumstance it can cut out this F Factor cut it back out and leave it as a plasmid once again okay let's talk about about our next method of horizontal Gene transfer which is transduction so this is our last method transduction uses something called bacterial phages bacterial fages are are viruses that infect bacteria so just like how we have viruses like HIV or chickenpox that infect us bacterial phages are viruses that only infect bacteria now bacterial phases there's a bunch of different types of bacterial phages but what they can do is they can pick up DNA from one cell that they infected and take it to their next cell that they're going to infect so let's just look at that for a second now viruses and we're going to learn about this soon in a whole other chapter um viruses they need require a host cell right so whenever they enter the host cell they used the host cells um all of the host cell reactions and mechanisms to make a bunch of copies of themselves and then they leave the cell and then they each go on and they infect more and more cells so here is my bacterial cell and here's a bacterio phage the bacterio phage has its own DNA that belongs to it and the bacteria has its own DNA as well so this purple DNA is the bacterial DNA this pink DNA is the Fage DNA so the Fage enters into the bacterial cell it uses the bacterial cell Machinery to make a bunch of copies of itself it packages up all of its Offspring and The Offspring are ready to leave but notice how it accidentally packaged up some of the bacterial DNA inside of it so whenever it goes to the next cell guess what's it's guess what it's inserting into the next cell the bacterial DNA from a completely different cell so in that way bacterial DNA was transferred from one bacterium to another bacterium and it can be the same species it could be a different species but that way genes were horizontally transferred but in this case it was with the help of a bacteriophage and it's just by chance so there are two types of transduction that can occur generalize or specialized generalized transduction is what we looked at right now in that diagram where random bacterial DNA is accidentally packaged inside of a bacterial Fage and then it's transferred to the next bacterium that that bacteria agage is going to infect specialized transduction is when specific bacterial genes are packaged and still transferred okay so genes and evolution just to kind of tie it all together remember horizontal Gene transfer um and even mutations genetic recombination exchanging genes between different species of bacteria all lead to cell diversity they all lead to microbial diversity or pathogen diversity and diversity we've already learned um in previous classes it leads to Evolution natural selection is going to select for traits that help bacteria survive so if that mutation helped it survive better if recombination or transformation or conjugation helped it survive better it's going to keep those genes and so it's going to basically evolve so just to review what we did today um we talked about types of radiation remember there's ionizing radiation and UV radiation ionizing radiation which are X-rays and gamma rays they break the backbone of DNA UV radiation causes thyine diers enzymes called photol liasis will separate thyine diers and repair the mutations of UV radiation nucleotide excision repair is the whole process of repair where you have endonucleases coming in to cut out the incorrect bases DNA polymerase coming in to insert the correct new DNA and DNA liay sealing it all together and we also talked about mutants mutants are mutated bacterial cells or mutated cells and then we talked about horizontal Gene transfer that includes genetic recombination which is the exchange of genes between two DNA molecules and we talked about um how horizontal Gene transfer is within cells of the same Generation Um instead of going from parent to offspring two types of mobile genetic elements that are types of horizontal Gene transfer are plasmids and transposons remember that plasmids are self-replicating um they are smaller circular pieces of DNA outside of the typical chromosome and they can code for a lot of proteins a lot of genes resistance factors antibiotic resistance genes that lead to um making a bacteria more pathogenic and then we also talked about transposons they jump from one part of the DNA to the other part of so another part of that same DNA so one region to another region um and they contain insertion sequences and insertion sequences code for an enzyme called transposase that can cut and reseal DNA helping these jump genes jump from one region to another and these transposons can also carry antibiotic resistance genes and then we talked about transformation and transformation um are when genes are taken up naked DNA is taken up by um a bacterial cell and so we would say that bacteria has transformed conjugation uses a sex pillis between an F positive cell and an F negative cell right and the F Factor plasma is transferred to make that F negative into an F positive if that uh if an F positive cell wants to integrate its fact factor into it into its main chromosome we call that an HFR cell and lastly transduction is through bacterial phages they accidentally pick up some donor or cell uh bacterial cell DNA and then they transfer it to another bacteria and all of this leads to cell diver iversity it can make bacteria more resistant more pathogenic and um increase their survival