hello and welcome to chapter 16.3 viruses um this is the only part right now of chapter 16 that we're going to cover we'll talk a little bit about some more of it later but let's go ahead and get started all right we have just finished talking about cells we said that cells are the basic unit of life we talked about cells theory but when we look at cells we also need to consider viruses viruses are not considered to be truly living forms actually the term virus refers to something that would be borrowed so it's something in between real living organisms and just a container of chemicals if you look at the diagram here that's on the screen this is going to be a bacterium these little guys right here that are covering that bacterium are actually bacteriophages or in this case they're viruses that reproduce by invading these bacterium so if you look at viruses they are very small we've already talked about eukaryotic cells over here that are going to be much larger compared to your typical prokaryotic cells now the prokaryotic cells that we're showing right here are going to be e coli but this one is your cyanobacteria that we also mentioned so some of them are going to be larger some are smaller staphylococcus is of course is a lot smaller than either of the other two bacteria but if you look here in the very bottom right at the viruses they're the smallest of all now there's a lot of different kinds of viruses but again they're not cells they're just infectious particles these particles are going to contain a couple of things one of them is they're going to have a protein coat now this protein coat in some cases may also include an envelope on top of that and we'll look at this but inside of this they are going to contain some genetic material now that genetic material or in this case their genome will contain either dna or rna and dependent on which kind then we call it a dna virus or an rna virus but that genetic material is going to be housed inside of a protein shell this protein shell then is referred to as a capsid when we look at capsid there's different types in this case over here on the left this would be a helical capsid whereas over here on the right this is much more complex it's going to contain multiple types a helical the head up here at the top uh the tail fibers you know it's a combination of many of these but all of these are going to be made up of little protein subunits so each of these little subunits then is referred to as a capsamerin altogether then you have what we call the capsid now some of these guys will also have an envelope on the outside and if you think about it the envelope if it's going to contain one is going to be important for that virus to be able to reproduce so they actually have this viral envelope surrounding or in addition to that capsid now this is normally found in animals well think about why in the world would you have them in animals why don't you need them in plants what do you know that's different from animals and plants animals only have a plasma what membrane whereas if you're looking at plants we said the animals only have a plasma membrane but the plants on the other hand in addition to the plasma membrane or the cell membrane will have a cell wall each of these envelopes if they have them surrounding them are going to contain a combination of not only virus materials but host cell molecules specifically if you look here on the outside it's going to have different markers so it will have different proteins or different glycoproteins here these glycoproteins are actually going to be receptors and if you have these receptors it's going to allow you to bind to the host cell and the host cell will recognize it is something that needs to come in that way this virus can actually infect that particular organism so if you're looking at viruses that would be able to be generally infecting animals they're going to have either a membranous envelope like this guy here or at least some type of glycoproteins on the outside whether it has the membrane or not so look at it you've got the flu viruses here and adenoviruses both of these are going to be ones that affect animals uh you know what the flu is an adenovirus is going to be like we get colds whereas over here on the left this tobacco mosaic virus is actually going to allow these viruses to go ahead and infect or plunge their genetic material into a plant whereas over here the bacteriophages it's going to be able to penetrate into in this case bacterium both of these are going to have cell walls your plants over here with the tobacco mosaic virus and then the bacteriophages that are going to infect bacteria that also have cell walls so the structure like we say multiple times is very important to the function now if you look at the structure we've already mentioned in this picture before if you have a particular protein over here that protein shape is going to be very very important because if you mess up this shape right here this portion of an antibody protein is going to be very specific to attack this or to attach to this part of a protein from a flu virus so if you've changed either one of these they're not going to bind properly now if you look at viruses then and we said again that these guys are what is referred to as an obligate intracellular parasite they're obligated or obligate because this is their only option they're a parasite because they cannot replicate on their own they cannot do everything they need to to produce their own food to metabolically be successful and the fact that they are going to invade and go into the inside of another organism that's why we use the term intracellular so that's why we get an obligate intracellular parasite is a definition used for viruses now each virus has a very specific range it can't just infect any and everything again that's why you know if you're looking at this picture here this is why you have very specific shapes but you may also have very specific glycoproteins on the outside that allow them in so there's a host range for each of these organisms and every year we have to get new virus well every year because we get new viruses that are modifying themselves we have to have flu shots that are different every year now we'll find out later that viruses unlike normal eukaryotic cells have a lot of mistakes that happen and these mistakes then will cause them to change their genetic makeup well if they're changing their genetic makeup then that would mean that let me move this pointer out of the way if they're changing their genetic makeup that means they're going to make slightly different proteins which means that we can't recognize them the same and our body can't defend us from that particular virus because it has modified now in eukaryotes we're going to have a system of checks and balances that stop this change from occurring so rapidly but for the viruses is actually a beneficial thing so that's why they go all over the world scientists do and they bring things back to the different world health organizations cdc capitals are not capitals but centers in different capitals of the world or regions of the world but one of the big places that they like to look at it's not the only place but it happens to be china and one of the main reasons here is because of the individuals that live in close proximity to each other now in china you've got an awful lot of people okay so you've got this person over here and a bunch of other people but they can give a virus from one individual to the other but it's still going to be a human so it's going to have the same markers on the outside it's not a big deal yes we pass it on to each other but that's not going to cause it to evolve or change or make it something that we can't recognize and make it terribly dangerous however we happen to know that there is another organism in this case pigs that and excuse my drawings here because they're not going to be that great but we're going to try see if i can kind of sort of make a half happen hap hazard rather go at a pig here okay so here's the squiggly little tail and here's the other legs coming down here all right so there's my pig i happen to know that it's very easy to interchange between humans and pigs because my father before he died ended up having heart surgery in which actually he had multiples but one of them they put in a valve from a pig into his heart and i was very excited that they were able to do that because i ended up having my father for another five years and that was really important to us because of me being the only parent and having no husband he was there for my boys but this is because we don't interact as a general rule in fact that's where we used to get insulin from was from pig insulin to give to individuals unless they had a religious reason that they didn't want to so we can exchange information very readily pigs can also pick up genetic information from and this is my bad drawing here but domesticated fouls so things like chickens okay so if you're looking at your chicken here let's make this a rooster okay so there's a rooster they can readily pick up diseases or share things from these fouls here that are domesticated and people will live in close proximity where they have their pigs and they'll have their you know chickens or they'll have their geese things like that but you also have waterfowl that are not domesticated so if you're looking at this guy here like a goose or a duck these guys over here oops and that wasn't a very good drawing i think i need to give up i'm not an art student but anyway that's close enough they can share but not as well with pigs but they're really good at sharing with the chicken and you can we can get a little bit from them but what's important is when you look at this if we have certain markers over here in our bodies but yet we don't really recognize anything over here from the waterfowl this guy over here we don't readily recognize information from him so if we were to get some of those markers our body is not going to recognize them same thing we can't get any at all from this chicken it just doesn't work there's no exchange of information here but if you have a virus that this chicken has and they give it to the pig then we can get it from the pig even though it's going to be foreign to our body and that's what you know if we talk about swine flu well it's something that you know we got up here from the pig but if we talk about bird flu it's going to have come via the pig to us so these things are really important the viruses replicate only in specific host cells but if they have a membrane on the outside what will happen is that the information from this chicken or other domesticated animal will be transferred to the pig and then the pig will give it to us the thing is our body has never seen that before and that's why we can't like back here in this picture we cannot recognize this protein if we don't recognize this protein then there's no way we can fight against it and that's why we get so ill and these spread so violently and we have problems okay so let's look at the cycles of these guys the two main cycles when you are looking at viruses one is the lytic cycle with the lytic cycle and they studied it first in bacteriophages so there would be your bacteriophage that attaches to a particular bacterium and what it does is it has genetic material up here on the inside of the capsule and it's going to inject them when it injects this then into your bacterium you can see here's your genetic material that went in it also chops up all the other dna that the bacteria has and gets rid of it so that it's the only dna left and it causes because it's hijacking the cell it's a terrorist it's hijacking the cell it causes the cell forces it to make all the components for the virus itself it can't do its on its own but it can hijack another cell and now when all these guys are in here they get assembled now they do it on their own they self-assemble and when they assemble all of a sudden you have this very large particle which is much larger than your cell so what happens is when the phase starts assembling it causes the cell to burst and it dies so that's the lytic cycle so it's actually one that's going to cause the death of your host cell so make sure you know what a lytic cycle is it produces your new phages but it causes it to lysis that's why it's referred to as a lytic cycle because it breaks open this host cell wall and releases the viruses outside now the term that's used for these phases or viruses that reproduce only by the lytic cycle is virulent so when we say something is extremely virulent we mean that you know and when it reproduces it's very deadly to that cell okay now the fact that we have studied bacteriophages so long what the viruses that infect bacteria has led us to a number of things one of which is restriction enzymes that we're going to talk about in a minute because remember we mentioned here that it actually chops up the dna into all these little pieces so that means it has the ability to destroy the dna but the bacteria can actually fight if they recognize this soon enough they can turn the tables and they can chop up the viral dna and defend themselves so one other cycle is the lysogenic cycle if you're looking at lysogenic this isn't lysing it's not bursting or breaking over open but what happens instead is when the bacteriophage inserts its dna what happens is that instead of it automatically taking over the cell and forcing it to form new viruses it instead goes ahead and integrates this dna into the genome and that means that every time your bacteria pinches off in half and forms two new cells you've got one cell over here that's full of virus and another cell over here that has your virus in it i'm not doing a very good job with that arrow am i okay another cell over here that has again that viral genome or that viral dna now we refer to this as a daughter cell with a prophase the prophage is telling you that the genetic material is actually integrated into the bacterial chromosome and that's why we refer to it as a prophase so here's the definition at the bottom of a prophase but sometimes there will be things that cause this piece of genetic material to be excised in other words it will come out so if it comes out and it's excise now it very frequently will then go into that lytic cycle okay so make sure you know the difference the lytic cycle is the one that bursts the lysogenic cycle is guess gonna replicate your phase genome but it doesn't do it by bursting open the cells it actually does it by integrating this viral dna into the bacterial dna and that's where you get the term prophase from so every time it divides if it's in the lysogenic cycle you're just copying the entire cell but with that you are copying the phages dna now sometimes these guys will just do one or the other but other times they will end up going through both cycles and a good example for humans although this diagram here is showing you phages and again phages are the ones that infect bacteria but you can go through the lytic cycle and the lysogenic cycle most humans actually have a particular herpes virus which causes us to have cold sores this is not sexually transmitted it's just a different type of herpes virus so most of us get it when we're born from our mothers but if you've ever had a fever blister or an ulcer in your mouth you know that you don't have them all the time but if you get stressed or maybe you bite the inside of your mouth or something like that you may end up getting one well the thing is that genetic information from the virus because this is viral dna is actually going to be a part of your genome it was integrated early on when you were a little kid or you know after you were born and it has become part of your genetic material again you're not a bacteria but you get the idea and then every time your cells reproduce you've made a copy of that virus so that inside of your mouth then if you get stressed to your bite some of it not all of it but those particular areas will excise and take out that genetic information and then that's why you get a hole in your mouth because it goes through now the lytic cycle and it burst your cell open and when you kill the cells you end up with a hole and that's what for humans would be one example of a temperate type of life cycle for your virus again it's not going to be a phage because we're not bacteria but it's still going to be a temperate cycle all right so let's look at the two types of genetic material again we said you could have dna or rna as your viral genetic material and we'll just quickly go through some examples so one of them warts you know different types of herpes viruses like we've already mentioned one but most of these are going to have dna as their viral genome again that's why it can incorporate into your genome and glue itself in but they don't all do that but regardless the dna when it gets in through the membrane you have this dna then that will from there make copies of messenger rna which then make your proteins and they assemble and they're going to leave okay so that's one way is dna the other is rna now this is typical of most of your influenzas they have this lovely capsule out here with all these glycoproteins so your body says oh this is supposed to be here and it lets it right in once once it gets inside then it will release that viral genome in this case made up of rna and then the rna will make other copies and from there now that you have copies of this rna you have also taken these copies and used them to make proteins now again it hijacks your cell and tells it to go ahead and make the proteins which happen in your er you know you go from your instructions here to the proteins well that assembles and makes your little capsule here which it puts in its rna and it comes out a third type is going to be retroviruses now retroviruses are still going to have rna as your genetic information but what's unique about retroviruses is they start out with rna but they also have a little enzyme in here called reverse transcriptase and this reverse transcriptase when you look at this guy right here this reverse transcriptase is an enzyme that allows your piece of rna to go backwards it goes from rna to dna and it has a hybrid and then eventually it forms a double-stranded dna which does get incorporated into your genome and becomes a pro virus not a prophase but in this case a pro virus and then from that that means it's permanently in you and it will go ahead make copies of rna and then cause that to through your er make copies of your protein and then send these guys out to infect somebody else one of the examples the one you probably most common with would be hiv okay now again bacteriophages are the ones that infect bacteria a lot of times we just refer to them as phages and typically they're going to have more of a structure here where you see a very complex structure that has this capsule up here this capsid head very frequent it very frequently it will have not only your rod shape but then it will have the tail portions here these tail fibers and that kind of helps it attach and insert the genetic material but by studying these guys this is where we got the field of molecular biology because we discovered that again the bacteria would try to protect themselves and they did this by cutting up and invading any foreign dna in this case from the viruses so if they could kill the virus by chopping up the dna then they wouldn't end up dying themselves and so we looked at the enzymes they had to chop up the viral dna and we now use it for these things here to clone genes to produce the gene copies that we want in that way it lets us make more proteins targeting for you know a very specific thing like maybe insulin human insulin so we don't have to get it from pigs again so let me go ahead and show you this little video here restriction enzymes are enzymes isolated from bacteria that recognize specific sequences in dna and then cut the dna to produce fragments called restriction fragments different restriction enzymes recognize and cut different sequences of dna this restriction enzyme recognizes the dna sequence i don't know what happened let me try this again g-a-a-t-t-c it cuts the dna strands between the bases a and g the resulting single-stranded sticky ends have the base sequence aat this restriction enzyme recognizes the dna sequence ctgc ag it cuts the dna strands between the bases a and g the resulting single-stranded sticky ends have the base sequence ac gt this restriction enzyme recognizes the dna sequence cc cgg it cuts the dna strands between the bases c and g the resulting dna fragments have no single stranded sticky ends okay so you can see there are a couple of different kinds of restriction enzymes when we look at these some of them when they cut if this is your piece of dna and it's double stranded when it cuts it cuts right in the middle which means you end up with blunt pieces like you see up here but some of them on the other hand when they cut this double strand here it would cut so that you end up with an overhang on one side and then of course the corresponding overhang on the other so you're going to have these extra base pairs here that can bind to something else that's going to be important that we'll talk about because they let us cut out one piece from one in this case human dna and insert it into a plasmid now plasmid is an extra circular piece of dna that's found in a lot of bacterium so we can cut this open and we can glue in our particular gene so you have this gene of interest that you want to glue in well you put it in now that you get this plasmid back into your bacterium here that allows you to grow it up and they do it in big vats and then you can insert it back into an organism if you want to over here like for plants or you may just take this guy right here if it's something that you wanted to insert with bacteria for the ability to chop up or to digest or eat petroleum-based products sometimes we don't want to put it in anything what we actually want to do is have this gene right here be a gene that actually makes some particular protein and we'll grow this up where it makes lots and lots of proteins in bats and then we're going to harvest this protein that would be what happens here with human growth hormone and now insulin this is why we do this not only do people not have any reactions to a human gene but even with the pig i mean there were a few people that had a few reactions but a lot of people had religious reasons that they didn't want to use pig insulin but if you're using human insulin there's no problem or we may use it for blood clot dissolving agents all sorts of things that we can use human genes for and if you're interested in this kind of stuff we do have biotechnology here at blend that you can look at but we also use this stuff to make vaccines um the technology anyway we use to make these vaccines now vaccines are going to be something that's harmless it's a derivative from the viruses itself either it's going to be one that's been heat inactivated so that it's got all the markers on the outside from the envelope the glycoproteins etc but it doesn't have any of the genetic material inside that can infect you or it may be attenuated so there's different things but that's why we go ahead and give ourselves shots because it allows us to recognize the outside and say hey this is something that doesn't belong give us time to mount a defense so that if we do encounter the actual virus later our body will recognize it and we can go ahead and kill it before we end up getting sick so a couple of things right here at the end if you are looking at plants there are also something we refer to as viroids these are small circular rna molecules that actually infect plants there are also something called prions when you look at prions they are actually going to be proteins that are misshapen and they kind of mess things up so they mess them up to the point that not only are they going to cause problems but right here they actually cause normal proteins that are minding their own business to convert into the messed up version the prion version and examples here would be mad cow disease you've all heard of that which in humans we refer to that as crutchfeld jacob disease but these are all going to be prions and what happens is that you have one messed up protein when you've got all the normal ones you think that's not a big deal but it is because these prions will bind to a normal protein here and cause it to mess up its shape and then they will bond others and eventually all you have are misshapen proteins and we know that that means nothing's going to work properly right that takes care of chapter 16.