BIO 205 Chapter 13 Viruses and Virus Like Agents

All right this narration is going to be about viruses and virus-like agents we see an example of a virus here in this picture so there's a bacterial cell colored green artificially colored green and the virus is on the outside so you see a few virus particles on the outside colored in Orange these are called bacteriophage and we will learn more about those in this chapter I want to start this chapter with a clinical application specifically I want to talk about the human immunodeficiency virus or HIV HIV infects immune cells called t cells so we're not

going to get into the function of T cells but for now I just want you to think of them as being very important part of our immune system in this picture we show or we see an example of HIV colored in yellow or orange those tiny round dots being Released from a T Cell host so that means that HIV has replicated inside of the T cell and is now budding or again being released from the T cell and this will likely kill the T cell HIV is associated with a disease called AIDS AIDS stands for

acquired immunodeficiency syndrome so this is a disease where an immunodeficiency is acquired meaning You're not born with it you got it from a virus it's not a genetic mutation um immunodeficiency that word refers to the fact that the immune system is deficient or in other words it's crippled it's weakened so this disease AIDS is basically a weakening of the immune system thanks to this viral infection and again really it all comes down to T cells T cells are the host cells of HIV and as T Cell numbers decrease the immune system is weakened so let's

look at these graphs down here and look at how Aids HIV infection and eventually AIDS progresses over time so on the x-axis we have time in years on the y-axis we have either viral count or T cell count and we actually have two traces in this graph we have a red line and a blue line And notice that they kind of have opposite trends so the red line is HIV load or HIV tighter in other words it's how much HIV how many HIV particles how concentrated is it in the body so early in an infection

the tighter skyrockets right so the amount of virus increases significantly in the blood notice in blue the blue line is going down at the same time and the Blue Line Stands for T cell count So that's how many T cells are in the blood so HIV is going up as it infects and replicates and is released from T Cell hosts T cell count is going down because they're dying in the process but it's not too long into the infection before viral load actually goes down pretty significantly which is kind of encouraging and T cell count

is able to bounce up and the reason is this process called Zero conversion means that the immune system is is ready now it's able to make the appropriate antibodies to attack HIV so initially there's some success but it doesn't take long before uh the viral load starts to increase again and it does that over many many years very slowly as T cell count very slowly decreases and there's there are a couple reasons for this First of all HIV mutates very frequently very quickly so as HIV mutates the immune system is continually guessing and has a

difficult time fighting all of the virus the other reason why this happens is because HIV is really good at hiding inside of of the T cell it's able to take its genome and stick it into the host cell genome and just hang out there All right so and it can do that for years so it's very very difficult to completely eradicate HIV from the blood and so over time HIV starts to win and as T cell count goes down that just means that our immune system is weaker and weaker and weaker and therefore more difficult

to fight HIV which is already difficult to fight and eventually there is this line that's reached and in this example it's eight years in But of course it varies this is just an example the clinical diagnosis of AIDS is when T cell counts so CD4 plus is just a type of T cell when T cell count is less than 200 T cells per milliliter so this microliter right here this is incorrect should be milliliter so less than 200 T cells per milliliter of blood that's the clinical diagnosis Of AIDS and what that means in real

terms is that this person's immune system is is very weak very crippled and so at this point the patient is extremely vulnerable to infections even just regular old infections that would normally not hurt someone you know let alone kill them can actually be lethal for an AIDS patient so we call these opportunistic infections you know pathogens that wait for a good Opportunity so what is an HIV patient to do how do we treat this disease well we treat it with different drugs and those drugs have different targets we'll look at some specific examples later but

here we're just going to take a hypothetical example with a single drug that has one target so in this graph we have time on the x-axis at the bottom and we have viral load on The y-axis you see that viral load is very high and as soon as the person starts taking the drug viral load goes down which looks great but remember we have a high mutation rate in HIV so there is a proportion of the viral load that actually becomes resistant to this drug again that's just due to mutation so HIV has mutated around

the Drug's ability to be effective And so as the sensitive population of HIV decreases almost to nothing the resistant population stays alive and eventually not technically alive sorry but stays around and uh eventually is able to increase significantly and so this is why this type of treatment called monotherapy does not work again because the high mutation rate of HIV So instead patients have to take a drug cocktail that targets at least three targets typically and that has been shown to be pretty effective overall where a patient with HIV can actually live a fairly normal life

and fairly normal lifespan so here on this slide are just some introductory things about viruses we can't call viruses cells because they're not cells so instead it's more Appropriate to call them particles and these particles are parasitic meaning they need a host so here's a fancy way of saying this they are obligate meaning they are requiring a host absolutely have to have a host obligate intracellular meaning they uh infect and replicate inside of a cell and they're parasitic which means they are requiring a host and they're doing damage to that host Um now viruses even

though they do replicate and contain some of the characteristics of life they can't produce energy on their own and they can't replicate on their own so they need a host cell for that therefore we cannot call viruses living right so they are not alive they're just sort of these inert infectious particles floating around waiting to randomly bump into a host cell when they can infect And their total goal in life is to make more copies of themselves and they're going to do that by hijacking a cell something to take over the cell use all the

cellular energy cellular enzymes for viral functions and basically turn that cell into a virus producing Factory all right now viruses on average are incredibly small so usually they're in the nanometer range so tens to maybe even hundreds of nanometers in size So let's look at some examples in this picture so we have a couple really small viruses you know 20 28 nanometers and let's compare those to a typical eukaryotic cell typical eukaryotic cell is maybe seven to ten microns or seven thousand to ten thousand nanometers as we see here so far smaller than a eukaryotic

cell and also far smaller than a bacterial cell so typical bacterial cell may be Um one two five microns which would be one thousand to five thousand nanometers far larger than a typical virus okay so as far as our microbes and a size scale viruses are are the smallest almost always they also come in a wide variety of shapes um there sometimes they have just a protein shell with nucleic acid inside other times they have a lipid membrane called an envelope as we're going to see Here in just a minute on a future slide so

their composition varies their shapes are a variable and their particular mechanisms of infection they're the infection cycle can vary as well so I'm not so worried that you remember the different types of shapes and sizes I just want you to know that there is a variety and we'll be using some representative examples as we go through this chapter we're going to use this kind of Stereotypical viral structure but like I mentioned there is a large variety of different shapes but let's take the psychosahedral shape there are sort of two major types of structures we have

those that do not have an envelope and those that do an envelope is this lipid membrane that surrounds a structure called the nucleocapsid so the nucleocapsid Is the the key component the indispensable component of a virus and the nucleocapsody consists of a genome inside of a protein shell The genome can be RNA DNA single stranded double strand there's a lot of variety there the protein shell is called the capsid and it's composed of subunits called capsimirs the cool thing about capsa Mirrors is first of all they can they can vary and function so maybe it's

not just a container maybe they also have an enzymatic function also they self-assemble so when new viruses are being made inside of a host cell these proteins can just kind of automatically come together to help assemble a new virus so capsa mirrors make up the capsid which is our protein shell containing And protecting the genome coming off of the nucleocapsid at least in the non-envelope virus we have proteins called spikes and spikes are often for attachment to a host cell but may also have other um other functions for example aiding in release from a host

cell over here on the enveloped form notice that the spikes are in the envelope Which makes sense we don't want the spikes underneath the envelope where they can't be exposed we want the spikes on the outside of the envelope where they're exposed and therefore useful for attachments or Detachment from a host cell okay once one of these things is all together fully assembled and capable of infection it's called a variant so Varian down Here it's basically just a an assembled virus particle capable of infecting another cell I mentioned in the previous slide that viruses can

have an envelope or not I also mentioned that their genome can vary you know DNA RNA and so on so if we kind of go into a little more detail here we can look at sort of how viruses are organized or in other words How they're classified which is their their taxonomy and they're classified by several different things several different ways so they're classified by the type of nucleic acid and whether or not it's single or double stranded and in the case of RNA if it's single stranded RNA it has either what's called a positive

strand a positive sense strand or negative strand so over here we can see DNA viruses at The top DNA viruses my writing is not working uh DNA viruses at the top RNA viruses at the bottom we see that they are either double stranded or single stranded genomes in both cases enveloped or not enveloped or not and in the case of single stranded RNA we also have the possibility that the single strands single stranded genome is Either the plus strand or the minus strand the positive strand or the negative strand okay so these are all the

different ways the viruses are classified um a couple things to note about DNA viruses is that this is kind of the easiest case because the DNA genome is already DNA um the DNA can be copied using host enzymes like DNA polymerase And transcription and translation can use host enzymes as well like RNA polymerase and ribosomes RNA viruses can be a little more tricky because they have to replicate their genome that means that they have to make more RNA copies from existing RNA copies so in other words if there is a virus that has an RNA

genome it needs to make more copies of its genome And so in order to do that it has to make more RNA from existing RNA and that's going to take an enzyme called rna-dependent RNA polymerase so it's a it's a new RNA polymerase we haven't heard of yet and this is a viral enzyme so this is not something that's in the host cell this is something that the virus has to come with has to come packaged with that there are some viruses that have these enzymes that we'll talk about later in More detail reverse transcriptase

and integrates these are also examples of viral enzymes that some viruses have and again we'll cross that bridge when we get to it in a little bit if you recall from the HIV example earlier in this lecture they mutate very very quickly which is why monotherapy is not effective so to clarify now that we have a little more information HIV is an RNA virus So you can see in this graph that RNA viruses have a very high mutation rate so on the y-axis we have mutation rates the higher higher we go on the y-axis the

more mutation and then the genome size is on the x-axis the further we go to the right the larger the genome so notice it notice where RNA viruses are they're at the top of the list for mutation rates and they have some of the Smallest genomes in fact viruses in general are kind of in another world as far as mutation rate goes and very small genomes so they're small particles with small efficient genomes that mutate quickly if you recall from our discussion of bacteria and mutation mutation is often beneficial it's not always bad sometimes it

has kind of this negative connotation but When we're talking about something like this that replicates very quickly huge populations these mutations can confer benefits and the survivors will pass those traits on to Future generations of either viruses or bacteria or whatever we're talking about so in other words the mistakes can be very beneficial for the population let's take a quick look at where we are so Humans specifically over here in the animal bubble some of the largest genomes and lowest mutation rates so for us that's good right but uh again viruses in a whole another

world one of the questions I brought up with HIV was why is it actually resulting in the death of T cells you know what is the goal of HIV why is it killing cells Well the answer is it's not out to just kill cells for the for fun the virus is driven to make more of itself it's driven to replicate so a virus is really going to have two goals when it infects a host cell it needs to make more virus particles so in other words it needs to make viral proteins to form the capsid

and it needs to make more viral genomes The capsid plus the genome equals a new virus and of course if we have to add an envelope to the outside we just take that from the host cell too so in order to make new viruses those are the goals now the very first part is just getting in the host so attachment to the host is Step number one and this is a very specific protein protein interaction between viral proteins and host cell receptors So note that this is usually quite specific which means that viruses are very

very specific for their host cells they are not just going to affect any old cell thanks to this specificity here step number two is to actually penetrate through the cell wall or the cell membrane depending on which host cell we're talking about and so we have to get the nucleic acid Into the cell somehow so we'll talk about a couple of ways that that happens then is the actual biosynthesis part remember I mentioned the two goals we need to make more genomes and we need to make more proteins then those can be assembled into new

particles virus particles and then release of the variance so this is going to occur through cell lysis or budding from the cell both are Often lethal to the host cell we're going to look at bacteriophage and its life cycle first I want you to keep in mind that some of the stuff we talk about here is going to also apply to animal viruses all right so when I talk about bacteriophage this is a a virus that is specific for bacteria so we don't have to worry about our cells getting hurt by bacteriophage Right they're specific

to bacteria and you can see that there is this spidery looking thing that grabs onto the outside of the cell and this is all protein except for the genome inside of the head so these tail fibers that look like spider legs are grabbing onto the host cell surface through very specific protein protein interactions so that's our attachment step and then there's some changes in shape Of these tail fibers that results in the bacteriophage kind of squatting down and injecting its DNA its genome into the host cell cytoplasm now once the genome is inside the cell

it can sort of take over and we're going to look at how that happens in in the next slide but here on this slide we can see attachment and penetration okay so now we can kind of finish the life cycle here on this slide Let's go to part a right up here sort of the top left we see bacteriophage on the outside of the cell we already know how it attaches and then it injects its DNA into the cell like that um now let's say that immediately this virus is going to make new variants So

in order to do that it's going to sort of follow this left cycle here and make more genomes through DNA synthesis so this is a DNA genome by the way Page DNA genome so DNA polymerase and all that stuff in the host cell is going to make new virus genomes and then transcription translation using host cell enzymes and ribosomes in order to make capsid proteins So that's the biosynthesis step and assembly as well as a kind of all shown here so in panel C we have the assembly has being shown so the biosynthesis piece have

been has been kind of omitted from this picture but in order to get to the assembly phase we have to first make those genome copies and those capsid proteins and then the final step then is release so this is done through lysis in this example And that's why this is called the lytic cycle this is a productive infection meaning virus particles are actively produced and released and now these bacteriophage can go infect new cells okay option number two for the phage that infects our host cell in panel a instead of staying through the lytic cycle

it can actually integrate its genome into the host cell chromosome and call and form what's called a pro virus Since we're talking about bacteriophage you see that it's called a prophage but to be a little more General we could just say Pro virus and so you see the viral genome integrated into the host chromosome and you know why would that be beneficial to the virus well for two reasons it's protected so it's it's not going to be detected the cell's not going to kill it it's just going to be kind of protected it's It's in

a genetic form and there's the second reason why it's helpful is shown right here in panel f where the host cell just reproduces it's happy it doesn't know that it's infected it reproduces and in the process it's reproducing the pro virus as well and at any time usually when the host cell is stressed in some way as you see in panel G the genome Cuts itself out And then we're going to enter the lytic cycle to make new virus particles which are then released so the lysogenic cycle like so-called lysogenic cycle is where the virus

just kind of hides out for a while and I can do that for quite a while but at any point it can take advantage of an opportunity re-enter the lytic cycle and form a productive infection again So the last thing I want to mention here is that this does not apply only to bacteriophage so the lytic and lysogenic cycle we're using bacteriophage as a way to explain it but it also applies to animal viruses too so some animal viruses only can do lytic some doolitic and lysogenic so again it's it's applying to bacteriophage and animal

viruses so we've seen the the five life cycle Steps for bacteriophage and now we're going to kind of do the same thing for some animal viruses first we're going to look at um attachment okay attachments penetration and then this uncoding step which we haven't talked about yet so the attachment depends on the presence or absence of an envelope so the top example is an enveloped virus you see the spike proteins protruding From the envelope and those Spike proteins are going to bind host cell receptors so that's a very specific interaction protein protein interaction which gets

strengthened as more receptors are kind of cruded to the area recruited to the area and eventually we have this membrane Fusion between you know the lipid envelope bilayer lipid bilayer envelope and the cell membrane which is also lipid Bilayer so they fuse and that kind of dumps in the nuclear capsid into the cytoplasm and then there are host cell enzymes called proteases that do quick work of that capsid so then we have the genome free in the cytoplasm and now The genome in the cytoplasm was the whole goal of this virus so now the genome

has the genes To take over the cell and turn it into a virus producing machine on the bottom panel B we see that it's a little different with a non-envelope virus we have the spike proteins coming off the capsid we have receptor Spike protein protein interaction you see that more receptors are kind of recruited to the area and we pinch off we pinch off the variant and bring it into the cell This is a form of endocytosis called receptor mediated endocytosis so after uncoding we have the genome free in the cytoplasm again to take over

the cell so for all animal viruses when I say an animal virus let me just clarify that means humans and other animals okay so these are viruses that that can affect us too the attachment penetration mechanisms are are going to be like we just saw in The previous slide now the rest of the steps are going to vary so the biosynthesis and assembly part this is going to vary depending on if the Genome of the virus is DNA or RNA and so we're going to look at both examples we're going to start with the easiest

case which is a a DNA virus so it has a double-stranded DNA genome so again easiest case scenario here in This particular example it's also enveloped so we're going to have attachment and penetration just like we did on the previous slide through membrane Fusion dump in the nucleocaps in uncoding and then we have the free genome and the cytoplasm now this genome is going to be transported to the cell nucleus again remember we're talking about animal viruses so we're always going to have a nucleus involved here and DNA synthesis occurs in the nucleus and transcription

always occurs in the nucleus of an animal cell and that's exactly the same thing here with uh even though it's viral DNA it's still the same thing so two objectives of the virus make more genomes and make viral proteins so here on the left Fork inside the nucleus you see that genomes are being replicated and that's using Host cell enzymes like DNA polymerase 3. we also have transcription occurring in the nucleus and translation occurring in the cytoplasm in order to make viral proteins so we have some capsid proteins that are synthesized and they are transported

back into the nucleus for assembly with the viral genomes so we form the nucleocapsids here also notice that we have some spike Proteins and the spike proteins we want on the outside of the envelope so the spike proteins embed themselves in this nuclear envelope and the nucleocapsid pinches off it kind of buds from the nuclear envelope picks up some of that membrane and that membrane is now the envelope and eventually this variant is released so this this release part and the budding part varies so the the envelope of the virus can be Picked up from

any from a variety of places uh inside the cell or the actual plasma membrane of the cell so it could be the nuclear envelope it could be other organelles like the Golgi there where it picks up its envelope uh or it picks up maybe its final version from the actual plasma membrane of the cell right so if it if it buds from the cell would look a little bit different from from this picture here but the concept Is the same before we leave the the DNA animal virus example I want to remind you that previously

we talked about how um in the genetics review chapter we talked about how transcription in the nucleus results in mRNA but the MRNA is not necessarily the final version that's going to be translated in the cytoplasm instead there's there's an RNA Processing step so for example here is our first mRNA from transcription and we have these introns that are cut out and removed the introns can have a variety of functions and the exons are spliced together now imagine this so-called mature mRNA now going out to the cytoplasm and being translated that's going to give us

one particular protein now remember that it doesn't always have To be exactly in this order where Exon 1 2 and 3 are just like that in this example maybe we have Exon 1 3 2 as another option so if if that's translated in it where these exons are sort of swapped reordered that would result in a totally different protein so some viruses are really really good at taking advantage of this where one gene And the DNA of the viral genome can code for up to 12 different proteins thanks to this RNA processing step called alternative

splicing so this is a great way for the the virus to maximize efficiency of its genome and to make its genome as small as possible so far we've talked about bacteriophage replication and recall that bacteriophage is basically a double-stranded DNA virus has a DNA Genome that infects bacteria only we then talked about animal viruses that have double-stranded DNA genomes and the life cycle steps there now we're going to talk about animal viruses that have RNA genomes and there are several varieties some of these RNA viruses have double stranded RNA genomes other RNA viruses have single

stranded RNA genomes either the plus strand so-called positive sense strand or the Negative sense strand or the minus strand so the difference between the plus and the minus strand is that well first of all they're complementary to each other that's important the second thing is the plus strand once is injected into the cytoplasm can it has the right coding it has a Right code to allow assembly of the ribosomes and translation Machinery to immediately start translating protein from it so in other words the positive sense strand acts like mRNA the negative sense strand is complementary

to the positive sense strand so it has a complementary sequence but by itself it does not have the right code to allow translation to occur all right so Let's take the case of [Music] a RNA virus that has the plus strand all right so we're going to kind of follow this flow at the bottom toward the bottom of the screen so attachment penetration those steps are pretty similar to what we've seen before endocytosis and uncoding and all those things occur and now once the genome is Inside the cell remember that a virus has two objectives

if it's to replicate itself it needs to do two things it needs to make more genomes and that's what we see on the top half of this here and it needs to make viral proteins once you have viral proteins and more genomes then these can be assembled to give us new virus particles so that's kind of the goal here all right let's take viral proteins First because this is the positive sense strand The genome is then as soon as it enters the cytoplasm ribosomes from the host cell grab onto it and start translating into viral

proteins so viral proteins are pretty straightforward um the next challenge is to make more genomes and so there's a couple things to note first of all We can't make plus strands from existing plus strands that's just not how the enzymes work we actually need to make a minus Strand and use that as a template to make more plus strands because remember the plus strands and the minor strands are complementary to each other so here is our plus strand we need to make a minus strand to serve as a template to make more plus trans So

you see that reflected here with the plus strand we make a complementary minus strand and with the minus trans we use those as templates to make more plus strands and that is our genome copying so we're we're making more genomes and now we have genomes and proteins can make a new virus so to make RNA strands that are complementary to other RNA Strands there's no host cell eukaryotic cell enzyme that does that there's no human enzyme animal enzyme that does that so DNA polymerase won't work the RNA polymerases that we have for transcription won't work

instead a viral enzyme called RNA dependent RNA polymerase that's the enzyme that can do it so again if we have a plus strand And we want to make minus strand that's complementary to it like that for reasons we talked about a minute ago then our enzymes won't do that the virus has to come with its own so RNA dependent RNA polymerase if we break it down makes a polymer that is RNA so it makes an RNA polymer and it does so from an RNA template okay now let's take the case of a single strand RNA

virus that has the negative Sense genome so we're just going to tweak the flow a little bit here so remember two objectives we need to make proteins and we need to make more genomes so the minus strand by itself can't do either of those so the first thing that has to happen is a positive sense strand is produced as you see here and the plus strands can be used to make more minus strands Those are the genomes that we want and the plus strands can also serve as mRNA for translation and now the combination of

genomes and proteins allow us to assemble new viruses as far as double-stranded RNA viruses go uh they're a piece of cake compared to the single strands because they have both the plus and the minus strands so the plus strand can immediately serve in for translation purposes make Proteins and each strand can serve as a template for the other strand to make more genomes so up to this point we've basically been talking about lytic Cycles where we're kind of assuming that we're immediately going to synthesize assemble new virus particles and then release them from the cell

through lysis or budding but for some viruses they may actually Form what's called a pro virus for a while maybe for a really long while and so this is what's called a latent infection where no viral particles are actively produced so this is in contrast to a productive infection so at a latent infection um the the viral genome integrates itself into the host cell chromosomes and we saw this with bacteriophage and its lysogenic cycle So hopefully it rings a bell all right so that's that's what our Pro virus is it's where the viral genome integrates

into the host chromosome and it can stay there for a long time and that's actually going to benefit the virus for example it's protected from our immune system if we're talking about a human example uh it's that you know the host cell doesn't know it's there and the host Cell might actually start replicating itself and in the process replicate the pro virus so again there are some viruses that can do this not all viruses can the double-stranded DNA viruses are probably the easiest case um we'll talk about those in a minute they just simply use

an enzyme called integrase to stick their double-stranded DNA genome into the double-stranded DNA Genome of the host cell so because the double-stranded DNA Genome of the virus is already in the right form it can just simply integrate itself but it needs a viral enzyme to do that called integrase um I also want to introduce to you retroviruses now these are RNA viruses in this group called retroviruses and they have RNA genomes so how is an RNA genome going to stick itself into a host cell DNA genome Well first the RNA genome has to be copied

into a DNA version of it and so there's a viral enzyme yet another viral enzyme called reverse transcriptase and reverse transcriptase makes a double-stranded DNA version of the viral RNA genome and this double-stranded DNA version can now be integrated into the host cell DNA chromosome using integrase so let's look at an example kind of this Flow down here so let's say we're starting with a retrovirus that has a positive sense single strand RNA genome with the help of reverse transcriptase which again the virus comes with right the virus has it in its capsid um with

the help of reverse transcriptase its RNA genome is copied into a double-stranded DNA version which is now the right form to be integrated As a pro virus into the host chromosome using another viral enzyme called integrase now it could stay there for a really long time maybe maybe years maybe a decade or more but at any point the the pro virus can enter the lytic cycle just like we talked about with bacteriophage where The genome which is in double-stranded DNA form again if we want to make new viruses we need to do two things we

need to make genomes we need to make proteins and so that's exactly what's what's going on here normal transcription with host cell RNA polymerase will give us mRNA well remember that mRNA is equivalent to the positive sense strand so basically just made some genomes there And the MRNA the positive sense genomes can be translated in the cytoplasm so we have genomes we have proteins those can be assembled to make a new virus and then of course lice or Bud from the cell so just to reinforce this concept let's take the flow charts on the previous

slide and see how this would look different if the genome was the minus strand So the minus strand reverse transcriptase doesn't care so it's still going to make a double-stranded DNA copy and that DNA copy can be integrated into the host's chromosome using viral enzyme into Grace and then at the bottom here double-stranded DNA so so at the bottom here this is when the pro virus wants to leave the lysogenic state it wants to enter The lytic cycle and so double stranded DNA can be transcribed into mRNA which is our plus strand but that's not

exactly what we want here we can use that for translation to make proteins and we use that as a template to make some minus strands so what do we have we have minus trans and proteins assemble them to make new virus before I leave reverse transcriptase I Want to provide a couple more details about it because it's a very important enzyme the reason why it's extra important is uh first of all HIV is a retrovirus so if we understand a thing or two about reverse transcriptase then that's going to help fight HIV which is notoriously

difficult to fight also reverse transcriptase is used a lot in the lab so in biotech labs and molecular biology Labs and so on and that's because RNA is not very stable it's kind of a short-term molecule and um so it's kind of convenient to make a double-stranded DNA copy of of RNA if you're working with it in the lab so let's look at how reverse transcriptase works now there's more detail on here than I care for you to know but there is a polymerase domain or area of the enzyme and there's a Nuclease domain or

area of the enzyme so in other words the polymerase domain is going to make uh make DNA and the nuclease domain is going to be cutting stuff up in this case cutting up RNA and so over on the left side we see that we're starting with a single stranded RNA template doesn't matter if it's plus or minus strand and we have polymerase activity We have a little bit of purple there that's DNA then we have some nuclease activity we just cut away some of the green and then we have more polymerase activity more purple being

made and then nucleus activity losing more green polymerase nuclease polymerase and look at what we end up with a double-stranded DNA version of the original single strand of RNA genome Now just because we converted it to DNA doesn't mean that we can't figure out what the original RNA strand sequence was okay because of complementary base pairing we can we can easily figure that out so we'll reverse transcriptase and its usefulness kind of goes beyond learning about viruses and fighting infections but we can actually use it as a tool in the lab as well So at

last we kind of have a visual summary here in this case it's HIV as well so HIV happens to be an enveloped virus it's an RNA virus that has a positive sense single strand RNA genome notice that there are two copies that's just something that HIV has it has two copies of its genome and it also comes packaged with reverse transcriptase because of course that's a um That is a viral enzyme all right so after attachment penetration we we have the genome inside and in this case the virus isn't going to make new viruses immediately

it's going to integrate itself and so first reverse transcriptase is going to synthesize a double-stranded DNA copy double strand DNA version of the viral genome and that with the Help of integrase can be integrated into the host chromosome it can stay there for for quite some time when the host is stressed in the case of a human maybe because the immune system is is weak the person is infected with something else or is taking immunosuppressant drugs then don't forget that this Pro virus can sort of leave this holding phase and enter the lytic cycle and

start making out new viruses as we talked a couple Slides back so it's really good information to know the the life cycle of molecular biology of viruses but when they infect a cell is there is there any other way that we can tell that they've been infected turns out that sometimes there is so not all the time but sometimes there are these so-called cytopathic effects and so we have a few examples here um basically it's a change In the cell's appearance under the microscope so um for example could just be the size of the cell

could be the shape it could have irregular nuclei or the nucleus of a cell could be could be odd looking oftentimes cells will kind of blob together and form these multi-nucleated multinucleated versions these Multinucleated cells called Synthesia and we have three examples here in these pictures sometimes it's also common to see inclusion bodies which are kind of storage sites but in this case for maybe viral Parts maybe kind of the viral assembly Factory going on so imagine you know a patient getting a pap smear and the physician is going to want or The pathologist anyway

is going to want to look at those cervical epithelial cells and and look for Oddities in their appearance like these here uh to maybe indicate a viral infection and in particular what they're usually looking for with that example is HPV which is a risk factor for cervical cancer so HPV is a virus the last major topic of this chapter is how viruses relate to cancer So let's start by talking about cancer cancer is where a cell basically loses control of itself it's unable to regulate itself or turn itself off its cell cycle stays on and

it just keeps replicating and replicating and replicating and as things get worse more mutations accumulate and so on and so oftentimes the morphology changes and the behavior changes and they're just kind of these Rogue out of control cells That can absolutely overwhelm organs and literally kind of eat them to death and of course they can spread from one place to another as well which is unusual so this uncontrolled behavior is basically the accumulation of mutations and these mutations can occur by genetic predisposition so some people just kind of born with a greater likelihood of having

this Mutation or they already do have these mutations of course environmental factors like UV radiation chemical carcinogens a wide variety of those and then infections can also contribute to cancer believe it or not and specifically viral infections we know of strongly linked to Cancers and these are called oncogenic viruses so these viruses that can cause cancer called oncogenic viruses And we can kind of summarize how they do this in in two major ways now it doesn't have to just be one or the other it could also be both so Uncle viruses can disrupt these genes

called proto-oncogenes so a proto-oncogene is a it's a normal Gene that we all have that produces um a regulatory component so um these protocol genes somehow regulate The cell cycle or produce a product that regulates the cell cycle so if these are mutated or disrupted then that could potentially contribute to the cell losing control so if they are mutated or disruptive disrupted these genes are now referred to as cellular oncogenes and that's bad so proto-alcogenes are good normal as long as they're not messed up If they are messed up then they're called cellular oncogenes which

are bad and could potentially lead to cancer it's not a guarantee but it's going to make the person more susceptible um possibility number two here is that oncoviruses also can inactivate what are called tumor suppressor genes or tumor suppressor proteins so tumor suppressor genes code for tumor suppressor proteins And tumor suppressor proteins are kind of guardians or Sentinels that act as checkpoints as well so if a cell is looking messed up if something is wrong these tumor suppressor proteins have the power to stop the cell cycle and either induce repair or induce apoptosis which is

where the cell commits suicide and so the body gets rid of this Abnormal cell so you can imagine if we mess up the tumor suppressor proteins or if we mess up the genes that code for those proteins that's going to make one more likely to develop cancer again not a guarantee but more susceptible so let's look at an example kind of visually now of how proto-oncogene can turn into a cellular oncogene and why that's bad So in this figure we have a normal cell and if we zoom into its DNA we see a gene here

it's proto-oncogene is able to turn on and off like normal so it's a normal Gene that's involved with the cell cycle and cell growth and because it's able to turn on and off we have normal cell division and cell growth all right if this Uncle if this protocol Gene is disrupted mutated its regulation is is screwed up or whatever it can Potentially sort of be permanently on so now that we call now we call this a cellular oncogene or sea ankh and this is where the cell loses control and oftentimes mutations accumulate over time and

it starts to look different so here's our tumor cell that has lost control of itself leading to tumor formation now let's look at kind of a visual representation of why tumor suppressor genes and tumor suppressor proteins are Important so at the top of this figure we have a normal cell that has normal tumor suppressor genes that make active tumor suppressor proteins so should the cell become abnormal it is told to either repair the damage or self-destruct apoptosis okay so again that's a good thing if this abnormal cell can't be repaired let's get rid of it

Down here in the bottom of the figure we have a a virus that has infected this cell messed up the tumor suppressor gene or the protein of course remember the gene codes for the protein so we can mess up the gene which messes up the protein or if we have a normal protein perhaps the virus screws screws with the protein product directly either way we have an inactive tumor suppressor protein so that if our cell becomes Abnormal it is not told to self-destruct we don't have that backup mechanism and it continues to lose control so

the additional piece of information here is that again viruses can can disrupt these tumor suppressor genes kind of mess this up as you see but we're going to see that some viruses contain cellular Olga genes that are actually called viral oncogenes Once they're packaged into the virus and we'll see how that works next so now let's look at how cellular oncogenes form and how viral oncogenes can form from that so here we have a virus looks like HIV again so this virus is integrating itself into the genome forming a pro virus through you know reverse

transcription integration and we get to the pro virus here in purple Now of course where this virus inserts itself is kind of critical if it should in its insert itself in an area that disrupts a proto-oncogene or its regulation then a sea Ankh may form right so you see that here where this Pro virus has interrupted kind of messed up this this Gene in green here and sort of turn it permanently on so We've formed a sea onk in this infected cell now this sea ANC may actually get packaged into a virus because remember the

pro virus can cut itself out and initiate the lytic cycle and in the process that cutting out is often not very precise and so it may actually capture this sea ankh and once that sea ank is captured into a virus particle it's now called a viral oncogene now imagine that this virus particle could Go off and deliver this defective oncogene to a potentially a healthy cell and screw up that cell too so now we've kind of had an overview of how viruses can contribute to cancer and how they can kind of spread Uncle genes between

cells as well let's look at some real examples so there are probably 10 12 Uncle viruses known we have some in the DNA category we have Some in the RNA category notice that most of them are in the DNA category have DNA genomes and the most noteworthy I would say HPV as I mentioned in a previous example human papillomavirus is associated with strongly associated with cervical cancer and it's thought that some high percentage like 70 80 percent of cervical cancers are caused by certain strains of HPV Also noteworthy here we have Hepatitis B virus and

hepatitis C viruses so these are both associated with liver cancer hepatitis and liver cancer now these again can disrupt Uncle genes and such but hepatitis C in particular can also contribute to cancer by just being there so it's kind of known for chronic Long-term infections that are fairly mild and um may be hard to detect and this chronic low level of inflammation can can contribute to the development of cancer even if it's not necessarily directly disrupting proto-oncogenes or tumor suppressor genes now that we understand a bit about viruses We can understand how to fight them

and if you think about the life cycle steps any one of those steps will be a great Target for an antiviral drug any one of the enzymes involved with those steps or proteins involved with those steps will be great antiviral targets and that's exactly what we see here so all these categories you know targeting penetration on coding biosynthesis uh You know these replication Inhibitors um assembly and release Inhibitors in the red box you see that repeated over and over blocking and coding blocking penetration blocking attachment and so on um one noteworthy example here is against

influenza A this is the the yearly flu that we get and it inhibits viral release by targeting in a spike enzyme called neurominidase This is the n Spike on influenza so when you hear H1N1 the N part is neurominidase and your metadase act this enzyme acts like molecular scissors that help make one final cut as influenza is budding from its host cell so naturally then that means it's pretty important so if the end Spike near minidase is targeted by a drug and influenza can no longer use near menidase then it can't release itself From a

host cell which is effectively going to help slow the spread it turns out that our bodies have kind of a built-in natural antiviral mechanism and that involves a protein called interferon so this is going to make more sense when you see the figure on the next slide but I'll try to summarize it here imagine an infected cell a cell has been Infected with a virus and that cell is going to die and the virus is going to successfully replicate and release from that cell so the cell as it's about to die does one last thing

it expresses its genes for interferon so through transcription and translation it produces interferon and then releases it to its surrounding cells and what it's trying to do is communicate to the surrounding cells that there's a bad guy In the neighborhood and get ready you know build up your defenses so when interferon binds your interferon receptors on those surrounding cells then those surrounding cells initiate expression of antiviral proteins and so there are a few examples here now should those surrounding cells become infected with the virus as well at least they're ready because they have these antiviral

proteins so often some Viral indicator like a double-stranded RNA intermediate or something like that will spark the the process of turning on these antiviral proteins and you see that in this case these antiviral proteins are going to Halt translation because all mRNA is going to be broken down and um protein synthesis the process is Inhibited as well so the key here though is that all translation is stopped meaning the host cell this um this cell here that was it was ready for the viral infection uh it was ready with its antiviral proteins it's going to

die but at least it's preventing the viral biosynthesis so by stopping all translation that includes host cell translation as well That means the cell is basically going to kill itself but it's going to prevent viral replication in the process so it's kind of doing it for the greater good so here's a visual way to depict what I was saying on the previous slide so we have an infected cell on the left so here's our virus it has infected the cell and as part of the viral life cycle for many viruses there's some sort of double-stranded

RNA intermediates This serves as a red flag for this cell and this cell is going to it is going to die right the virus is going to succeed and assemble new viruses and be released and so on but as kind of a Dying wish here this cell uses its last breath to synthesize interferon so transcription translation to make interferon which is released from the cell and it's going to bind surrounding cells and these surrounding Cells have interferon receptors on their cell surfaces and interferon initiates a Cascade of events that leads to transcription translation of antiviral

proteins so antiviral proteins there were a few examples on the previous Slide the specific names of those are not important just the concept is important so here we have antiviral proteins now this this uninfected cell here is going to sit and Wait so it's still alive it still goes you know along its normal duties interferon did not kill it but should it become infected it's now prepared it's ready so the virus infects the cell and again this double-stranded RNA intermediate serves as a red flag and these antiviral proteins are activated and translation is halted so

translation stops all translation Stops which means that the virus cannot replicate itself it needs to make viral proteins and it can't that also means that this cell is dead meat because it needs proteins to survive so if they can't make any proteins it's not going to survive so this cell is a goner but in the process it prevented the virus from replicating Now one last thing I want to note is that notice that interferon these antiviral proteins nothing directly attacked the virus nothing directly killed the virus all we did here is kind of indirectly stop

the spread of the virus by halting biosynthesis So speaking of antivirals here's a quick kind of comparison with antivirals and antibiotics another mode of action what they're used for or we get them and if Resistance is possible and you see that there are some similarities for example resistance is possible for both we can make both in the lab and we get some naturally one is for bacterial infections antivirals are for and for viral infections obviously but as far as mode of action goes one thing I want to to highlight here is that antibiotics directly kill

Bacteria or as antivirals do not kill the pathogen directly simply inhibits the development and interferon was a great example of that so we are now done talking about viruses but we have some loose ends here to take care of with the so-called virus-like agents and that includes an infectious protein referred to as a prion An infectious RNA particle referred to as a viroid so let's talk about prions first prions form Our Brands cause a disease a group of diseases referred to as spongy form encephalopathies and you can kind of see why they're named that because

the brain tissue starts to look like it has these these pockets in it like like holes in a sponge and this is because the nervous tissue is being destroyed And we have overall atrophy of brain tissue as you can see in these two brains compared side by side the one on the left has this disease kind of a wasting away of brain tissue on the upper right we have two molecular models of prions and notice that one of them has the word normal next to it so that is not a mistake we do have prions

that are normal so they are in all of us they are in our nervous tissue and they have normal Roles in nervous tissue the problem is with a very specific misfolding so on the right side we have this disease prion that obviously looks different in its shape the trick here though is that not only can this disease Prion make it into our body but it's able to replicate itself because anytime a normal prion which are normally in our body comes in contact With the disease Prion it misfolds so in other words the disease prion can

cause normal prions to misfold and you'll see that on the next slide as well so let's look at some of the names of these encephalopathies so they their names depend on which animal or animals we see this disease and so there's a cow version called mad cow disease Probably heard of that the sheep and goat version It's called scrapey chronic wasting disease is the elk and deer version and then the human version is Crutchfield Jacob disease all right um now let's talk about viroids a little bit and there's not much to say really except that

there are these infectious RNA particles that remain largely a mystery They're responsible for some plant diseases so we don't have to worry about them as humans so for example here's a picture on the bottom right of potato spindle tuber disease where the potatoes kind of have this unique shape they're relatively small RNA particles and even though we know that RNA can replicate itself we have no idea how how it causes this disease so kind of a mystery how it gets around And how it causes pathology of these these different plants just a visual to add

to the previous slide regarding prions I was mentioning how the disease prions can cause normal prions to misfold and so here's kind of a cartoon version of that so we have a grouping of three diseased prions forming this Filament and here is a normal Prion and when there's normal prion contacts the end of this filament like this that causes it to misfold so there's kind of a peer pressure thing going on here and that's how these develop they form these long filaments that become all tangled up and eventually are toxic and destructive to the neurons

which results in the characteristics observed by the disease