hello bisque 132 this is the beginning of recorded lecture one two uh last time we started our chapter on viruses and had some a brief introduction about you know just some of the terminology of uh what they look like uh now that we know their structure let's talk about what they actually do how how does a virus infection actually run uh well viruses are here's another mouthful of a phrase obligate intracellular parasites that's a lot but i mean parasite means that you know they have a host and they they steal nutrients or they steal energy and they harm the host intracellular means they get inside of a cell so they have their host as a parasite they have to get inside of the cell of their host and obligate means they have an obligation to do this they have no other way of i mean i can't say living because they're not alive they have no other way of doing their thing other than being intracellular parasites obligate intracellular parasites to say another way they require a host cell for replication they cannot make more of themselves on their own they need a host cell to do this now there are two types of viral infection cycle uh i'll start with the simpler of the two something called the lytic cycle defined in the key terms type of virus replication in which virions that's just virus particles are released through lysis or bursting of the cell anyway so this is a smash and grab job this is going to get in make more of yourselves get out this starts with attachment so here's a diagram that's going to work our way through the whole process attachment is exactly what it sounds like it's the virus attaching to the cell i do want to point out that when a virus particle a capsid attaches itself to the the membrane or the cell wall of a host this involves very specific protein protein interactions very specific interactions between proteins of the the capsid or the envelope uh and the the cell membrane this is and i'll bring this up again this is why viruses are going to be very specific for the types of cells that they can infect a virus that infects bacteria for example and that's what this example is this virus is not going to be able to infect a human cell we don't have the same proteins on the surface of our cells so this very first step is just not gonna happen so this attachment involves specific protein protein interactions next the virus is gonna get into the cell one way or another this particular diagram is only illustrating one way of doing this uh this is this is called penetration where the genetic material is injected into the cell but there are a couple of different ways to do this so i'm just calling this uh entry this can be injection of genetic material into the cytoplasm of the host or sometimes the host can take up the entire caps head so here's an example of this there's a viral capsid again it's making use of specific protein protein interactions here in the host cell membrane the host takes up this capsid in a vesicle and then through some mechanism the the virus particle escapes that and is now inside the host cell or there's another way uh the viral envelope can fuse with the host cell membrane so obviously this only works if we're talking about an enveloped virus but again specific protein protein interactions is meant to show a bunch of those different specific proteins present on the surface of the envelope the lipid bilayer of the envelope fuses with the lipid bilayer of the host membrane and now the capsid and all the genetic material is inside of the cell so any of these three can occur depending on the virus in its host but we can collectively call these just entry now that the virus is inside either the whole capsid or sometimes it's just its genetic material it's going to make more of itself this is called here it's called synthesis but i'm going to call it replication host energy and enzymes are used to make viral proteins and genomes so again viruses are parasites they're obligate parasites there there is no virus that is not a parasite it cannot do its thing without in some way harming the host they do not make their own energy they don't do cellular respiration the only way they can they can get energy to make more of themselves is by stealing host energy uh and they don't have a lot of their own enzymes either so they have to hijack the host cell machinery for doing transcription or translation making more of themselves making more viral proteins like capsid proteins and making genomes whether they're dna or rna next is assembly so all this stuff comes together really rather remarkable how these capsid proteins will assemble into the sometimes very complex capsid uh morphologies but that's what's going on assembly capsida symbols and with the genome inside and finally you gotta get out the virus is going to exit the cell one way or another this diagram is showing something called lysis uh lysis of the cell where the the cell wall actually bursts open so i'm collectively calling this egress you know getting out lysis defined in the key terms uh as uh bursting of a cell or another way to do this is budding so it's not shown here but here is a different viral infection cycle influenza virus don't sweat the details here but again this is just showing you a taste of how specific all these proteins are but budding is how an enveloped virus gets its envelope so here's the viral capsid uh you know stealing and sort of pinching off part of that cell membrane to use as its envelope budding is defined in the key terms as a method of exit from the cell in certain animal viruses where virions leave the cell individually by capturing a piece of the host plasma membrane a bit of a mouthful but you know pictures worth a thousand words it steals some membranes as it leaves and i do want to point out that you know i number these steps just to you know sort of walk you through the the basic cycle here i'm never going to ask a test question like what's step three you know the numbering is it's not a big part of things it's just to to walk us through the steps so uh but yeah whether it's lysis or budding now the virus particle is free ready to start the whole thing over again so this was the lytic cycle uh the lysogenic cycle because remember i told you there were two types uh is very similar so in fact this should look familiar to you uh the lysogenic cycle is basically an offshoot of this lytic cycle has a few extra steps but it has all these same steps in common so if we want to talk lysogenic cycle step one is attachment all the same things i said before about protein protein interactions i'm not copying that over uh entry you know one way or another it's got to get into the cell but here's where we come to something different instead of immediately making more of itself in a lysogenic infection cycle we have something called integration this is where the viral genome uh inserts itself into the host chromosome so at this point it is basically hiding out it's not actively you know building more of itself it's not actively destroying the cell but it is silently part of this host chromosome so integration viral genome integrated intel's chromosome viral gene expression shut off it wants to you know lay low for a while it is now referred to as a pro virus when it's in this state of being integrated into the chromosome and even though it's not you know actively making more of itself like it would in the lytic cycle it is making more of itself because as a copy you know as a part of the host chromosome every time this host cell divides itself it's going to be dividing that pro virus along with it because you know you know how dna replication works and how mitosis or binary fission works it's it's going to replicate the entire genome so every single daughter cell created from this you know original integration is going to have pro virus as part of its genome as well so it is silently making more of itself uh called propagation where viral dna replicates with the host cell it's just part of the chromosome now this can go on for for many generations for generations generations generations the only reason this will ever stop is if the cell gets stressed out uh and you know stress can mean you know low on nutrients or you know hypoxia or you know messing with the ph you know some sort of cellular stress is going to cause this virus to want to get out like rats leaving a sinking ship once this cell looks like it's in trouble you're gonna have something called induction and this pro virus is gonna just switch right back to the lytic cycle synthesis assembly and release and just do all the stuff we talked about before so induction this is where stress triggers the linux cycle viral gene expression is then turned on we have replication assembly egress all that stuff we talked about before um this uh example both of these examples of the lytic cycle and the lysogenic cycle uh this was um showing a a virus that infects bacteria but just to give you a couple examples um flu is a lytic cycle virus influenza virus a good example to sort of just get in your mind about stress triggering induction uh cold sores herpes simplex virus ii uh they are an example of a human virus that does this lysogenic cycle and during stress usually cold parts of the year hence the term cold sores that is the kind of stress that temperature change maybe finals week or you know something like that that can trigger the lytic cycle on that that dormant herpes simplex virus can you know come out again uh as an active cold sore so just an example of something uh that's uh that's human focused instead of this bacterium example so uh going off of that uh it's important to note that all living things whether we're talking animals plants bacteria if if it's alive there's a virus for it all living things have viruses that parasitize them and as i noted before when we were talking about protein protein interactions and attachment each virus is specific for a certain host and i mean there could be a little bit of crossover like sometimes you know uh influenza for pig can infect a human but you know bacteria viruses are definitely not infecting animals and plant viruses are not infecting bacteria each virus is pretty specific for a certain host or or a narrow range of hosts and an example of this specificity another thing from the key terms uh is the term bacteriophage a bacteriophage also just called a phage is the name for a virus that infects bacteria and it's just a term that's used a lot so actually this that we've been looking at in this figure this is this is a phage this is phage replication this is a phage cycle um you should just be familiar with this bacteriophage or phage these are the viruses of bacteria we know a lot more about them than other viruses because it's easier to grow bacteria and examine how how they are infected now one of the many learning outcomes here in this section is to explain the transmission of plant and animal viruses and this is very cool and interesting but uh man this gets overwhelming really quickly if you're reading through through the textbook um don't memorize all of this but i mean in a broad sense it is important to um remember that there are a lot of viruses that infect plants and a lot of these are you know affecting plants uh that we care a lot about you know things that we use for food lettuce sugarcane cauliflower corn is a big one peanut uh yeah there are a lot of viruses that affect plants so all i'm going to say for this giving this this big section from the textbook not making you memorize plant viruses many viruses are responsible for plant diseases and they end up having a significant economic impact that's plants but the same thing can be said of humans don't memorize all of this you can read more in this section uh in the textbook if you want some uh more specific information but i don't want to make you memorize all of this stuff but yeah there are a ton of viruses that infect humans in a lot of different places you know whether it's the skin or the lungs or the gastrointes intestinal tract uh just all over the body so i'm not making you memorize this uh all i'm going to say many viruses infect humans and these have a significant impact uh on public health um a couple other things though about these human infections um we're familiar with with most of these i mean uh you know some of these smallpox we're probably not actually familiar with but you've heard of smallpox before but um a lot of these if you are infected with let's say uh a cocksackie virus it's a hand-foot mouth disease um there's no cure for that uh if you're infected with uh you know some adenovirus or rotavirus uh some something in the gut that's giving you horrible gut problems uh there's there's no cure for that you you treat the symptoms you know you drink plenty of fluids and electrolytes to alleviate the symptoms of these uh gastroenteritis viruses uh but there's there's no specific cure that's true for a lot of these so anti the reason for this antiviral compounds are not widely available for most viruses uh it's you know we'll talk about antibiotics when we get to the bacteria chapter and there are a lot of ways that we could you know sort of hit bacteria you know take them out but viruses are really hard to target because they're using our stuff they're using our energy and our enzymes so it's hard to shut them down without shutting our own cells down so for a lot of these uh viral infections they end up being self-limiting that means you know you get sick with the adenovirus and you treat the symptoms but your body fights it off and and you get over it um you know even the extremely deadly viruses uh like like smallpox or ebola they'll either kill you or you will survive it and uh the the infection itself is self-limiting so a lot of the the cure that you have is just you know treating the symptoms waiting for that infection to resolve itself uh and so rather than antiviral compounds a good strategy to try to uh you know fight against viruses is to prevent them in the first place so vaccines are much more effective uh control mechanism for viral infections than trying to use antiviral compounds and in order to understand vaccines you have to understand the immune system so we will bring up vaccines uh again when we get to our immune system chapter much later in the quarter but you know definitely worth noting here uh that you know among all of these uh some of these uh stick with you like there's a herpes simplex virus or hiv but a lot of these are are self-limiting and uh the best strategy is to try to prevent them with vaccines now and yeah i'm skipping this sort of list of illnesses if you're interested in public health stuff yeah just read these sections they're kind of cool and interesting but not going to make you memorize all this stuff now there is one last section in this chapter and i'm going to present this as a bit of a mystery so let's talk about a few neurological diseases one of these is called bovine spongiform encephalopathy ooh uh abbreviated bse because that's a mouthful uh or even more colloquially known mad cow disease uh this is you know a disease that infects cattle uh causes a lot of horrible neurological symptoms increa including an increase in aggressive tendencies hence the mad cow part of it um and it ultimately leads to death so a very scary thing there's another neurological disease called scrapey uh it's very similar in many ways and that it you know attacks the brain and just shuts the the brain down in many different ways across the board damage this is not in cows this isn't sheep it's called scrapey because one of the symptoms is causing them to sort of compulsively scrape themselves against fence posts or walls of a barn or trees or whatever they can find looks pretty rough here there are even more gruesome images because they'll continue to scrape themselves until they break the skin and just keep doing that so this is just horrible across the board brain damage and there's a version for humans as well uh kuru also known as kreutzfeld jacob disease is the version of this uh that infects humans and again this is probably telling control brain kuru brain uh just you can see how much deterioration has occurred just across the entire brain so the the symptoms here it's just a huge list of symptoms because everything is just deteriorating and this is uh there's no cure for this this is lethal so it's very very scary so the question is what is causing all of these things and you know let's go through this like this were you know an episode of house md or something like that one thing we can rule out is this is not caused by a toxin or a poison you know it's not like heavy metal poisoning or uh you know a toxin produced by some uh insect or something like that uh the reason why it's not a toxin or a poison is because it can be transmitted from infected individuals from nerve tissue so you can't you know poison it poisoning is not contagious from person to person but all of these disorders can be spread specifically from nerve tissue and you don't have to be eating brains to acquire this disease there is nerve tissue underneath your skin so eating you know muscle meat from an infected cow can spread this to humans for example so it's not a toxin or a poison okay well the next suspect i mean we're in the chapter on viruses so viruses are probably a pretty good suspect if you're thinking about things that way well we can rule that out uh these diseases are not caused by a virus and they're not caused by a living organism and that's a huge swath of things to rule out so it's not a bacterium uh not you know a worm or some sort of eukaryotic parasite and it's not a virus either we rule all this stuff out because if you take that nerve tissue and you irradiate it which would destroy dna and rna any genetic material so that would shut down a living thing that would shut down a virus if nerve tissue is irradiated it still transmits that disease so this was a real puzzler for quite a long time uh it was eventually discovered that these neurological diseases are caused by a misfolded protein called a prion so this is the viruses chapter and this is not a virus but there's no better chapter to to put this in so this is a in a section called other acellular entities because just like a virus this is not a living thing uh it is a misfolded protein so here's a sort of diagram working you through this and the terminology here gets a little hairy because we all have this protein in our nerve cells what causes the disease is a misfolded version of it so we can refer to the normal protein as p r p c that's capital p lowercase r capital p uh superscript c the messed up version is p r p superscript s c named after scrapey if you're curious so this misfolded version is thought to come into contact with the normal version and cause it to convert into this misfolded version and that'll go off and do the same thing again all of these weird messed up uh misfolded versions converting all of these normal versions into messed up misfolded versions and the accumulating accumulation of this prpsc all across the brain leads to you know huge laundry list of symptoms associated with this neurodegenerative disease um this is not unlike a zombie apocalypse scenario where you have humans and altered humans if you want to think of zombies as that way the zombies uh convert the humans into more zombies and then the whole thing just uh cascades out of control so again the terminology here is weird but this is uh this is how the disease is propagated it's a protein a misfolded protein so here's my summary of all that caused by misfolded protein called a prion we all have prpc the disease causing protein is prpsc when prpsc comes into contact with prpc it converts it to prpsc again that's quite a mouthful but hopefully it makes sense if you understand the terminology here and yeah it's prp sc that causes these lesions in the brain so uh very scary uh and no known cure at all uh you can rest assured though that this is incredibly incredibly rare and uh you know when it does break out very very well uh contained and controlled um very fun episode of classic x-files where a town of cannibals is all getting this disease because they're eating brains from someone who is infected that's besides the point uh but yeah it's in this chapter because it's another uh acellular entity uh speaking of which there's actually one more acellular entity uh something called a viroid um vibroids are like viruses uh but they don't even have a capsid or an envelope and if you remember a virus was a capsid with genetic material if you don't have a capsid you're just genetic material so a viroid is uh just rna there are no dna thyroids now just that's why i don't have a picture to show you this is just a sequence of rna and somehow being just a sequence of rna it's able to do all the same stuff that viruses do it's able to get into a host cell replicate within a host cell and spread itself uh to other host cells without a capsid just as a sequence of rna these are very rare uh the only viroids known to exist uh infect plants so here's potato spindle tuber viroid that's all i have to say about viroids but yeah they belong in this chapter because they are other acellular entities and that does it for the viruses chapter but we still have enough time in this uh lecture period to start on the next chapter chapter 22 uh prokaryotes so this might be kind of a weird word for you you know we're done with uh you know the non-living or acellular entities we we should be making our way onto you know one of these domains in the phylogenetic tree of life but prokaryote isn't any of these three well prokaryote is a group that includes bacteria and archaea and if you remember that first chapter we did if you were to draw a line around bacteria and archaea but not eukarya this would not be an ancestor and all of its descendants that there's there's no way to draw a line i mean bacteria is a clade rk is a clade you carry is a clade but you you can't make a clade that includes bacteria and archaea without excluding or cutting through eukarya if you remember back to this uh that is an example of a paraphyletic group so prokaryote this this term this this grouping uh refers to bacteria and archaea but it's a paraphyletic group it's not a clade prokaryote is one of those uh traditional groups like reptiles that's you know been part of science for a really really long time that despite you know not having evolutionary significance as a clade is still just embedded in the collective minds of of biologists it's a group that exists uh even if it is paraphyletic so why would people do this why would this group exist why would you lump bacteria and archaea together like this well it's actually a very easy thing to do if you're just looking at these things under a microscope and you don't have gene sequences available uh both bacteria and archaea are small single-celled organisms that don't have a nucleus so it's it's easy to conclude that they're related to one another even though that's an incorrect occlusion conclusion prokaryotes is again not acclaimed it is a cell type it refers to cells that do not have a nucleus so that's what holds um bacteria and archaea together not an evolutionary relationship they are ubiquitous uh which means they are basically everywhere uh they're on your skin right now uh they're in your mouth right now they're on your your desk or your phone or you know whatever your computer whatever you're using to to view this they are everywhere in us on us around us uh and yeah single-celled organisms just important to to note just how these things exist in every ecosystem on the planet all around us so a bit of a history of the world we'll do this again when we get to vertebrates but uh it is important to note that the oldest living things on earth uh were prokaryotes had this simple cell structure with without a nucleus and they got their energy from hydrothermal vents so here's a hydrothermal event these things still exist today they're defined in the key terms as a fizzier in earth's surface that releases geothermally heated water and yeah the ancient ancient prokaryotes the oldest life we've been able to find but they're they're still alive today still doing their thing because these vents still uh exist today um so this is the first way of getting your energy from you know this uh this this goop coming out of these vents um photosynthesis changed everything for the planet so the evolution of photosynthesis among prokaryotes this is one way to say it dramatically altered the atmosphere of earth uh the pbs eons has a channel uh cheek has a video cheekily named that time oxygen almost killed everything so this is very on point because again if we're talking about history of the world this is the first way to live doing photosynthesis uh released oxygen into the atmosphere for the first time in high quantities and yeah it was the greatest extinction event that this planet had has ever known and almost destroyed everything um and yeah that does as far as i'm going to go as far as history of the world goes well we'll do this again when we get to vertebrates but yeah starting from hydrothermal vents moving on to photosynthesis and now prokaryotes live a lot of different ways in modern times a couple of other things to note some prokaryotes are what we call extremophiles and you can maybe guess the definition just based on extreme but it's defined on the key terms an extremophile is an organism that grows under extreme or harsh conditions so this can be extreme temperature extreme ph extreme salt content here's a very beautiful example of a hot spring environment against its blue color from prokaryotes that live inside here this is in yellowstone i believe very very very hot uh and of course there are others don't memorize this table but yeah there are all sorts of extremophiles living in acidic environments basic environments hot environments very hot environments you know all of these other things you you just need to know what extremophiles are and you know basically what this means uh this goes back to my point uh that these are ubiquitous these are basically everywhere not just on us in us around us but even in places where you might think nothing could possibly exist prokaryotes have have found a way now bacteria and i'm going to be very careful when i you know say prokaryotes and when i say bacteria and when i say archaea bacteria are often cultured which means grown in a medical lab as a diagnostic tool this is a very common thing in a hospital lab to you know get a sample from a patient whether it's sputum from a lung or a pus from an infection or whatever it is and try to grow this on plates to see what is causing that infection and it's you know it's very useful you'll detect the things that are growing and you'll know what's causing that infection and that can that can help you treat it appropriately um however bacteria are very very picky they're very specific about the conditions under which they can grow you you would think that you know being able to live in these extreme environments would make bacteria like these these super organisms that can survive anything but that's only true up into a point these acidophiles do great in this environment where no one else could survive but you put them in a normal ph environment they'd be dead and that's true for any of these even bacteria that you know that grow under you know less extreme conditions you put them in a in a plate that doesn't have the right nutrients or you know isn't the right temperature or doesn't have the right amount of carbon dioxide and they're just not going to grow so bacteria have very specific requirements for their growth they can be very picky many will not grow under common conditions so the the bacteria that we can grow tend to be the ones that are relevant in a medical lab because we have an incentive to figure out how to grow these pathogens so we can identify them but there are a lot of bacteria out there that are what's called unculturable and that makes it very difficult to learn more about them because if you if they don't grow under normal conditions and it's hard to figure out how they grow they're going to be invisible to us and so it's a very interesting anecdote about genome sequencing and sequencing a milliliter of ocean water and discovering all these bacteria that had never been found before uh because they just you couldn't grow them and so you couldn't understand them so it's very important to note all of these points um the reason i've been saying bacteria on this slide is in contrast archaea are almost all unculturable maybe you know i'm sure everyone's heard of bacteria before this lecture but it's very possible that you may have not heard of archaea before before listening to this and a large part because almost all archaea are unculturable and so we know very little about them because you know we can't grow them and study them as as readily as we're able to grow and study bacteria okay let's talk about structure now so there we did this with viruses we'll do this with bacteria there are three common bacterial cell morphologies that just means the shape they can have uh bacteria can be cocci that's basically a circle or a sphere uh they can be bacilli that's a rod or less common a uh spirulum which is like a corkscrew or a spiral so caucus or cocksie or spheres bacillus or bacilli or rods spirulium or spiruli are these spiral corkscrew things there are other morphologies that get wackier than this but these are the three basic ones these are the three ones you should definitely be uh familiar with and a lot of uncreative taxonomists will name things just based on their shape like streptococcus or bacillus anthracis just naming them off of the morphology in addition to this shape some cells have pili and or flagella so to look at a typical prokaryotic cell a figure that might look uh familiar to you from disc 130 here's the the optional structure the this is a single pillars multiple together it's called pili pili are defined in the key terms as a surface appendage of some prokaryotes remember this is an optional structure used for attachment to surfaces including other prokaryotes so a lot of pathogens will have these trying to attach themselves to a host the flagella here's a flood gel um is singular flagella is plural this is also in the key terms a long hair-like structure that extends from the plasma membrane and moves the cell so it helps it swim around and get from one place to another but again i said some have pili and or flagella plenty of these have neither just have other mechanisms for living so everything has a shape some have pili and or flagella all right there's more to be said definitely about prokaryotes but this is typically where i run out of time so this is the cut off this is the end of recorded lecture one two