so chapter 11 covers viruses throughout human history viral epidemics have caused us to become more aware of the impact microbes have on our lives and on the course of history some forms of cancer are definitely caused by viruses viruses that we know are transmitted from person to person so what are your chances of catching cancer this is just one of the questions surrounding our knowledge of viral infections today this chapter examines the structure and behavior of viruses and virus-like agents by the end of this chapter you will have a better understanding of and an appreciation for one of Nature's tiniest eyes but most dangerous group of microbes the name virus itself comes from the Latin word meaning poison so what are viruses viruses are infectious agents that are too small to be seen with a light microscope so even if we had viruses on our slide looking under the microscope we would not be able to see them they have no cell nucleus no organelles or cytoplasm when they invade susceptible host cells viruses display some properties of living organisms and appear to be on the borderline between living and non-living so we say that they are non-living because they can't replicate on their own but once they get inside of a host cell they are able to replicate so that's why they are on the borderline between living and non-living they can replicate or multiply only in a living host cell so they are considered obligate intracellular parasites so components of viruses a typical viral component as you can see here also on figure 11.1 consists of a nucleic acid core and a surrounding protein coat called a capsid which we can see here and purple here some viruses have a surrounding lipid bilayer membrane called an envelope we could see those hydrophilic heads and hydrophobic tails and that lipid bilayer so a complete virus particle including its envelope if it has one is known as a viron viruses are a piece of bad news wrapped up in protein the bad news is the DNA or the nucleic acid because they use their genome to replicate themselves in host cells the result is often A disruption of host cellular activities or death of the host that it's in viral nucleic acids can be single stranded or double stranded they can be linear circular or even segmented like the ortho mixoviruses are segmented into eight segments so looking at the first component of the virus the capsid the nucleic acid of an individual viron is in most cases enclosed within a capsid that protects it and determines the shape of the cell the capsa does play a key role in the attachment of some viruses to host cells the envelope as we mentioned earlier usually has that typical bilayer membrane outside of the capsids such viruses acquire their envelope after they are assembled in a host cell and as they go through a process known as budding or moving through the host cell membranes of Iron's nucleocapsid comprised comprises the viral genome together with the capsid viruses with only a nucleocapsid and no envelope are known as naked or non-enveloped viruses combinations of lipids proteins and carbohydrates make up most envelopes that we see there on viruses and then depending on the virus projections known as spikes as we can see here sometimes the viruses will have spikes that extend from the viral envelope these surface projections are glycoproteins that serve to attach the virus to a specific receptor sites on the host cell so sizes and shapes of the virus various viruses we can see that on figure 11.2 almost viruses are too small to be seen with a light microscope they do have a variety of ranges as we can see all of these viruses sit inside of a bacillus the largest viruses are between 1200 and 1500 nanometers remember nanometers is 10 to the negative ninth among the smallest viruses known are the enteroviruses which are less than 30 nanometers in diameter so as figure 11.2 shows most viruses are quite small when compared with the bacteria or even eukaryotic cell many bacteriophages or viruses that infect bacteria have a complex shape that incorporates specialized structures such as heads tails and tail fibers like the spikes mentioned earlier the tail fibers are also used to attach the virus to a bacterial cell so origins of viruses viruses are quite clearly different from cellular microbes free viruses are incapable of reproduction they must infect a host cell uncoat their genetic material and then use the host Machinery to copy or transcribe the viral genetic material so there is some debate as to whether viruses are living or non-living because viruses cannot reproduce or metabolize or perform metabolic functions on their own some scientists say they are not living other scientists claim that because viruses have a genetic information for replication and this information is active after infection they are living so like I mentioned earlier we're still on the fence about whether viruses are living or non-living we cannot yet categorize them as one or the other before they knew much about the structure or chemical properties of viruses virologists classified viruses by the type of host infected or by the type of host structures infected so viruses have been classified as bacterial viruses plant viruses or animal viruses as Moore was learned about the structure of viruses at the biochemical and molecular levels classification of viruses came to be based on the type and structure of their nucleic acids including method of replication also Host range and other chemical and physical characteristics and as more viruses were discovered today over 40 000 strains of viruses exist in the international committee on taxonomy of viruses or the ictv which establishes the rules for classifying viruses because they are so different from cellular organisms it is difficult to classify them according to their typical taxonomic categories as we categorize everything else using uh domain kingdom phylum class order family genus and species so the family is the highest taxonomic category used when uh differentiating between viruses themselves major groups of viruses are distinguished by their nucleic acid content as either DNA or RNA subsequent subdivisions are base based largely on other properties of nucleic acids the RNA viruses can be single stranded or ssrna or double-stranded dsrna although most are single stranded because most eukaryotic cells do not have the enzymes to copy viral RNA molecules the RNA viruses must either carry the enzymes or have the genes for those enzymes as part of their genome so they need to bring with them whatever is required to replicate inside of the cell if the cell does not have that available for them many single-stranded RNA viruses contain positive sense RNA meaning that during infection the RNA acts like mRNA and can be translated by the host ribosomes so remember when we talked in chapter 8 about DNA and we said that whenever you build a DNA strand it has to be built in the five Prime to three prime Direction so whenever we're using this strand of DNA to make mRNA we want to use the three prime to five Prime strand which is going to be the leading strand or the template strand so that when we build the complementary strand or the MRNA it runs in the five Prime to three prime Direction so once we build our strand our five Prime to three prime a strand of Mr and a when we were looking at transcription and translation we can take that five Prime to three prime strand of mRNA from transcription directly into translation put it on a ribosome and translate it into proteins so we're here we're saying that if it is a positive since RNA when it infects a host the RNA is in the five Prime to three prime Direction already it acts like mRNA goes directly to translation and can be translated into viral proteins other single-stranded viruses have negative sense RNA negative since RNA means that it comes in in the three prime to five Prime Direction so it cannot act like mRNA because it's going in the wrong direction so in such viruses the RNA acts like a template during transcription to make a complementary positive sense mRNA after a host cell has been entered so if we get a negative sense RNA it's coming in at 3 Prime to five Prime and we have to read that to make a five Prime to three prime strand once we build that five Prime to three prime strand that's going to act like our positive sense RNA act like mRNA go to translation and be translated by host ribosomes into viral proteins in order to pour to perform the transcription step if we're looking at the negative sense RNA those negative sense viruses also need an RNA polymerase with them so because remember uh the polymerase is what's going to read The Strand to build the complementary strain so if we're going to have to build anything the virus needs to bring the polymerases necessary to build whatever it needs we can use the following charts to classify major groups of RNA viruses that cause human disease both positive sense RNA viruses and negative since RNA viruses as well as double-stranded RNA viruses along with double-stranded and single stranded DNA viruses so for each virus shown on the tables that we're going to look at you will need to know the following so you'll need to know the family name whether it has an envelope and its capsid shape and the infection or disease it causes so I've put a few charts here and the first one is going to give us those positive sense RNA viruses we know that these guys here are going to come in and act like mRNA and go directly to translation so I want you to know the family name picorno virus toga virus Flava virus and retroviruses whether or not they have a capsid and an envelope so naked no envelope the capsid shape is polyhedral this one is enveloped capsid shape is polyhedral enveloped with a polyhedral enveloped in a spherical shape and then I also want you to know the infection or disease it causes so picornoviruses cause polio common cold hepatitis a toga viruses rubella German Measles and equinine encephalitis flavor viruses cause yellow fever and retroviruses cause adult leukemia tumors and AIDS all right so these are our negative sense RNA viruses remember they're coming in at the three prime to five Prime Direction they are not in the correct form to act like mRNA so they will need their replication enzymes with them to transcribe that three prime to five Prime strand into a five Prime to three prime strand okay so the paramixovirus enveloped helical causes measles rhabdoviruses enveloped helical causes rabies Ortho mixaviruses the one I mentioned that has eight segments enveloped helical causes flu both A and B ilobir viruses are the ones that cause Ebola and marabug and then the uh Honda virus here enveloped spherical respiratory distress and hemorrhagic fevers remember these are our negative sense RNA viruses and then we have a double-stranded RNA virus Rio viruses naked polyhedral cause respiratory and gastrointestinal infections and then we have our double stranded DNA viruses so our adenoviruses are naked polyhedral cause respiratory infections herpes virus enveloped polyhedral gives us things like herpes chickenpox and shingles pox viruses give a smallpox cow pox those are usually enveloped with a complex shape papoviruses like human uh papillary viruses warts cervical and penile cancers these are naked with the polyhedral shape Adine usually gives us those hepatitis viruses hepatitis B then we have single stranded DNA viruses paroviruses naked polyhedral usually gives us a fifth disease all right so moving on to viral replication we're going to summarize the general functions here of viral replication and then we're going to talk about the lytic cycle and misogynic cycle in more detail so if you'll turn to figure 11.12 in the viral replication the general characteristics or the five steps the first one is adsorption here we can see that the virus attaches to the bacterial cell wall that happens in a very specific manner penetration is next we see that the DNA of the little red squiggly line the DNA from the virus gets injected into the bacterial cell now we see that only the DNA gets injected not the virus itself synthesis is a little bit more complex here the viral DNA takes over the host cell breaks up the host cell's DNA and uses their nucleotides to form viral proteins maturation those viral proteins come together in a very specific manner and then release those viral proteins are released from the bacterial cell they were inside and in doing so kill the bacterial cell okay so looking at replication of bacteriophages which usually go through the lytic cycle and lysogenic cycle bacteriophages are simply phages or viruses that infect bacterial cells specifically bacteriophages are highly specific attacking only the targeted bacteria and leaving potentially beneficial bacteria that normally inhabit the human digestive tract in other locations alive they are also cheap effective in small doses and rarely cause side effects so using bacteriophages on humans inside and on um like biofilm infections are very effective because the bacterial phage only targets and kills the specific bacteria we are trying to get rid of or trying to kill and leaves our other good bacteria alone so a typical treatment was 10 tablets or an aerosol spray and Recovery could be as rapid as one or two days the Polish microbiologist Stefan slopeck and his colleagues successfully used phages to treat 138 patients with long-term antibiotic resistant bacterial infections all patients benefit from benefited from the treatment and 88 percent were completely cured so this is long term this is patients that were on antibiotic regimens for years usually these patients would end up with amputations of the foot because these diabetic foot ulcers are unable to be cleared so these were cleared very quickly 88 percent completely cured phage therapy is especially effective in treating biofilm infections such as diabetic foot ulcers or like the Rim ring around your tub or in your toilet also biofilms many amputations could be prevented this way currently Clinic trials are underway in the U.S for phage therapy for chronic treating chronic wounds all right so properties of bacteriophages we can see what that little guy looks like there figure 11.11 like other viruses bacteriophages can have their genetic information in the form of either double-stranded or single stranded RNA or DNA they can be relatively simple or complex and structure so to understand understand phage replication we will examine the T even phages these phages designated T2 T4 and T6 are complex but well-studied naked phages that have double-stranded DNA as their genetic material so the most widely studied is the T4 obligate parasite of common E coli so this one infects and kills E coli specifically T4 has a distinctly shaped capsid made of a head collar and tail the DNA is packed in the polyhedral head which is attached to the helical tail okay so again we're going to go through one two three four five steps of the lytic cycle but this time we're going to look at those steps in more detail so here adsorption the T4 phage collides in the correct orientation with the host cell the phage will attach to and absorb onto the bacterial cell wall this is a chemical attraction and requires specific protein recognition factors found in the phage tail fibers that bind to specific receptor sites on host cells the fibers Bend and allow the pins to touch the cell surfaces so let's go ahead and look at that in just a little bit more detail here all right so looking at adsorption we have our bacterial cell here so this is going to be our E coli and then we have our virus our T4 bacteriophage and basically on the surface of the bacterial cell there are receptors so I'm just going to draw The receptors to look like this and there are receptors both inside and outside of the cell so there's also receptors on inside of the cell like that and what happens is the tail fibers which I'm drawing here in red of the virus attached to the receptors of the bacterial cell wall by way of a chemical attraction not reaction so the tail fibers of the virus attach to the receptors on the bacterial cell wall by way of a chemical attraction okay next is penetration lysozyme which is present within phage tails weakens the bacterial cell wall when the tail sheath contracts the hollow tube or core in the tail is forced to penetrate the weakened cell wall and come in contact with the bacterial cell membrane the viral DNA moves from the head of the virus through the tube and into the bacterial cell wall so we'll go ahead and take a look at that okay so we have our bacterial cell we have the virus we know that the virus was already had its tail fibers stuck into the receptors of the host cell wall there are these little pins here that I'm drawing and when the tail fibers release the enzyme lysozyme so the lysozyme is in blue the lysozyme is actually going to weaken or thin out the cell wall so it's going to make let's see it's going to make the cell wall Very Thin so I'm just gonna cell wall here has been thinned out compared to the rest of the cell wall here like that and once the cell wall has been thinned out what's the DNA there the virus is going to come down or retract and once it does that the pins here are going to Nick or make a hole in the bacterial cell wall so when they make a hole in the bacterial cell wall the DNA goes through the tail sheath and moves from the virus into the bacterial cell itself okay synthesis viral genomes consisting of an only a few thousand to two hundred and fifty thousand nucleotides are too small to contain all of the genetic information to replicate themselves therefore they must use biosynthetic Machinery present in the host cell so that's saying that the viral DNA is not big enough to make the MRNA it needs so it's going to use the host cell's DNA instead once the phage DNA enters the host cell the phage Gene take control over the host cell's metabolic Machinery bacterial DNA is disrupted so the nucleotides of the hydrolyzed nucleic acids can be used as building blocks for the new phage phage DNA is transcribed into mRNA using the host cell's Machinery the MRNA is translated on host ribosomes direct synthesis of the viral capsid proteins and viral enzymes some of these enzymes are DNA polymerases that replicate the phage DNA thus phage infection directs the host cell to make only viral products that is viral DNA and viral proteins so what's happening here is that the virus hydrolyzes the bacterial DNA so it breaks the bacterial cells DNA down virus uses those nucleotide bases to form its own mRNA by blocking RNA polymerase from reading the leading strand all right so now we are inside the bacterial cell this is the bacterial cells DNA remember a t c g and then it's um pair here and this goes all the way around right so what it's going to do is it's going to break these bases down and just allow these nucleotides to be free here and the viral DNA that got inside of the cell it is going to then take these free nucleotides and build its own code this is going to be viral mRNA it's going to go into 5 Prime to three prime Direction now remember before whenever the bacterial cell went through DNA and replication and then it went through transcription and translation and when it went through transcription it made m actually this is viral mRNA so this should be our use here instead it made a specific uh code here and I think it was something like this and that specific mRNA went to the cytoplasm step to our ribosome and when the trnas came in and read it we were able to literally build the enzyme or whatever protein we were wanting to build based off of this very specific code so the bacterial cell thinks that this is what it's making it's making this mRNA code to build a enzyme and when the viral DNA comes in and takes over the virus actually builds this code viral mRNA code instead of the bacterials MRNA code it was wanting so when the virus takes this and sticks it to the ribosome and builds the protein it's going to build this protein which is a viral head instead of this bacterial cell protein and then it's going to build tail fibers and pins and collars and sheaths and continue to build all these viral Parts all these viral proteins rather than the bacterial cells proteins that it needs so then we see here at the end of synthesis that we've just built a whole bunch of viral parts right here rather than the enzyme or the ribosome or whatever the bacterial cell was wanting to build now in maturation the head of the T4 phage is assembled in the host cell cytoplasm from newly synthesized capsid proteins a viral double-stranded DNA molecule is packed into each head so while the DNA molecule is being packed inside of the head of the virus phage tails are assembled from newly formed base plates sheaths and collars when the head has the DNA and the tails are formed they come together and then once they come together the tail fibers are attached last and those are the infective portions here so looking at maturation here inside of the bacterial cell inside of E coli now we have a lot of proteins that were made and those proteins were all of these parts right here so the first thing that happens is that the double-stranded DNA is packed inside of the head and once the double-stranded DNA is packed inside of the head that part is ready to go but as that's happening the tail sheath and the tails are coming together so those two things are happening at the same time once the tails are ready and the DNA is packed inside of the head the virus comes together completely and then the last thing to be added is going to be those tail fibers so Those infective portions or those tail fibers are added at the very end okay release the enzyme lysozyme breaks down the whole cell while allowing viruses to escape in this process the bacterial host cell is lysed thus T4 phages are called virulent lytic phages because they kill the host cell the released phages can now infect more susceptible bacteria starting the infection process all over again such infections by virulent phages represent a lytic cycle so now that we have all of these viruses that have been made inside of the bacterial cell so I'm just going to draw now we have our viruses with their DNA the virus tail fibers are going to stick to those receptors inside of the bacterial cell wall so virus tail fibers and red stick to the black receptors inside of the cell wall and this is happening all over the cell right 50 to 200 viruses were made here once that happens the tail fibers Again release lysozyme we know that lysozyme weakens the cell wall but we have 50 to 200 viruses doing that so in that case it's not just going to weaken the cell wall but it's going to lyse or break open the cell wall here once the cell wall has been broken open all of those viruses are released and are able to infect a new cell the time from adsorption to release is called the burst time it varies from 20 to 40 minutes for different phages the number of new virons released from each bacterial host represents the viral yield or burst size in phages such as T4 anywhere from 50 to 200 new phages may be released from one infected bacterium all right so then looking at the opposite of that lysogyny different type of virus also infects E coli but is not a virulent phage it does not kill its host so temperate phages do not always undergo a lytic cycle the majority of the time they will exhibit lysogyny which is a stable long-term relationship between the phage and its host in which the phage nucleic acid becomes incorporated into the host cells DNA such participating bacteria are called lysogenic cells one of the most widely studied lysogenic phages is the Lambda phage again infecting E coli Lambda phages attached to bacterial cells and insert their linear DNA into the bacterial cytoplasm once in the cytoplasm the phage DNA circularizes and integrates into the circular bacterial chromosome at a specific location the viral DNA within the bacterial chromosome is called a prophage and the combination of the bacterium and a temperate phage is called a lysogen insertion of Lambda phage into a bacterium Alters the genetic characteristics of the bacterium two genes present in the prophage produce proteins that repress viral replication the prophage also contains a gene to confer immunity so if another virus of that specific type tries to attach to the bacteria it cannot this whole process is called lysogenic conversion and it prevents the absorption of biosynthesis of phages of the type whose DNA is already carried by the lysogen so only one particular virus of that type can infect one cell the gene responsible for such immunity does not protect the lysogen against infection of a different type of temperate phage so you can be infected with multiple different types of viruses in one cell just not the same one so let's go ahead and draw um or let's look at this next slide here so we can see lysogeny we see that very similar things happen here the DNA gets inside of the host cell very similarly the same way that linear DNA the viral DNA is red it's going to actually just incorporate itself into the host cell's DNA so it just kind of injects itself inside of the host cell's DNA now when the host cell goes through DNA replication it's going to make a copy of its own DNA as well as the viral DNA so every single time the bacterial cell replicates it not only replicates its host cells DNA but the viral DNA as well so basically the virus gets a free ride once it injects itself in the host cell's DNA the whole cell stays in control it doesn't allow the virus to take over and the host cell blocks the virus from being able to replicate on its own and it also blocks its receptors so another one of those same viruses can't bind to and get inside of the cell but then the bacterial cell is just going to go through binary fission over and over and over again and this time when it does it's going to replicate both its bacterial cell DNA and purple as well as the viral DNA in red and so each new cell that forms has the infective portion of the viral DNA in it so whenever we're looking at just the DNA itself just the DNA with the viral DNA in it that's called a prophage and the entire cell with the viral DNA and the bacterial cell CNA the entire cell is called a lysogen so once established as a prophage the virus can remain dormant for a long time each time a bacterium divides the prophase is copied and part of the bacterial chromosome in the progeny is in the progeny bacteria that's this period of bacterial growth with the prophage represents a lysogenic cycle so the virus is just going to take a free ride and live in that bacterial cell and allow that bacterial cell to go through binary fission hundreds of thousands of millions of times now let's say this happened in a Petri dish and the virus infected the bacterial cell of a petri dish and the bacterial cell went ahead and went through binary fission and made lots and lots and lots of colonies eventually we're going to run out of food and water in the petri dish and the bacterial cells are going to die so in this case the virus can sense that the living conditions aren't great and since the living conditions aren't great there's lots of toxic waste or chemicals being built up the virus can actually go through a process of induction and remove itself from the host cell's DNA once it removes itself from the whole cell's DNA it can go through a lytic cycle and the purpose for going through a lytic cycle is to lyse the host and once it lyses the host it's able to get out in hopes of finding a new home of course in the petri dish it wouldn't be able to do so but if we were transferring bacterial cells to a new petri dish then those viruses could find better bacterial cells with a better environment to live in once they got inside those new bacterial cells though the viruses would exhibit lysogyny again so they really only go through induction and go through the lytic cycle when they are sensing a bad environment and want to find a new home most of the time they will exhibit lysogyny going through a lysogenic cycle allows temperate phages to infect more bacteria without forming new bacteriophages as a result of binary fission a copy of the phage DNA is distributed to each new bacterial cell so this is kind of the lazy way but in the end all these viral dnas are getting incorporated into all the bacterial cells that are going through binary fission if they all go through the lyric cycle and get released then there are a lot more viruses that were made by way of lysogyny than going through the lytic cycle doing all the work and then just making 50 to 200 viruses after each replication okay so now we're going to move to replication of animal viruses and talk a little bit about this replication of animal viruses there's a lot of similarities in animal viruses when compared to the bacterial viruses or viruses that were infecting bacteria it was just a few differences and we're going to look at those differences in a bit more detail so like other viruses animal viruses invade and replicate in animal cells by processes of adsorption penetration synthesis maturation again and release so all of that then is very similar the same stuff there just how they go through those steps are a little bit different all right so looking at adsorption as we have seen bacteriophages have specialized structures for attaching to bacterial cell walls although animal cells lack cell walls animal viruses have ways of attaching to host proteins specificity involves a combination of virus and host cell recognition naked viruses have attachment sites or proteins on the surface of their capsids that bind to corresponding sites on appropriate host cells for example virologists have shown that rhinoviruses have Canyons or depressions in their capsids to bind to a specific membrane protein normally involved with cell adhesion conversely envelope viruses such as HIV have spikes that recognize in part a membrane protein receptor on the surface of certain specific immune defenses so lots of ways here in animal viruses lots of ways that these viruses can be absorbed or taken in to the cell um remember here though most of the time we are taking in the whole virus here so not just the DNA as we saw in the lytic cycle in lysogenic cycle but the entire virus gets taken in to the cell so since that's the case we have to get that DNA out and we do that in the next step here so penetration follows quickly after absorption of the viron to host Plasma's membrane unlike bacteriophages animal viruses do not have a mechanism for injecting their nucleic acid into the host cells thus both the nucleic acid and the capsid usually penetrate animal host cells most naked viruses enter the cell by endocytosis than if they're naked viruses with no envelope and then enveloped viruses May fuse their envelope with the host plasma membrane or also enter by endocytosis once the animal virus enters the host cell's cytoplasm the viral genome must be separated from its protein coat or capsid and is released through a process known as uncoding so once the virus gets absorbed into the animal cell here we have to get that DNA out of the virus here and that process is known as uncoding now synthesis the synthesis of new genetic material and proteins depends on the nature of the infecting virus be it at DNA animal viruses or RNA animal viruses or retroviruses we will focus our attention on synthesis in retro viruses such as HIV sure that we're skipping over those other two this time okay so we're gonna skip right to retroviruses such as HIV here so synthesis and retroviruses such as HIV the two copies of two copies of positive sense RNA do not act as mRNA rather they are transcribed into single-stranded DNA with the help of reverse transcriptase let's go ahead and take a look here I think I have a video that I'm going to show you just a bit okay so what's happening here is that reverse transcriptase is going to take the copy of positive sense RNA and turn it into DNA and then the single stranded DNA is replicated through complementary base pairing to make double-stranded DNA so what we normally do is we start with DNA as the template and from DNA we copy it to make either more DNA and DNA replication or we use DNA to make mRNA in transcription in this case the virus is coming in as a positive sense RNA and so that positive sense RNA needs to be converted into double-stranded DNA instead of single stranded RNA because our genome has double-stranded DNA so what we have to do is we have to take the single stranded RNA coming from the HIV virus and turn it into double-stranded DNA and we do that by using an enzyme called reverse transcriptase to make a single stranded DNA molecule and then we copy that single stranded DNA molecule into a double stranded DNA molecule once in the cell nucleus this molecule inserts itself as a pro virus inside the host cells chromosome that's the viral genetic information is passed to progeny host cells so then it gets inserted kind of similar to lysogyny it's in the DNA so it can be accessed at any time unlike prophages however the pro virus cannot be excised if an invent occurs that activates the pro virus its genes are expressed that is the genes are used to make viral mRNA which directs the synthesis of viral proteins so not only is it Incorporated in the DNA it can also be used to make more HIV viruses so in order to do that we make full length positive sense RNA molecules transcribed two copies of the positive sense RNA are packaged into each viron and then we use that along with this enzymes and those will have a capsid formed around them and they will Bud out of the cell so as I mentioned I have this video here that I want to show you the video is going to just explain the replication of animal viruses the retroviruses here and then this is the information from the video that I want you to know so I wrote that out there so you don't have to take notes from the video and then I'm going to redraw this and explain this synthesis part again so let's go ahead and take a look at the video here targeting HIV replication the replication of hiv-1 is a multi-stage process each step is crucial to successful replication and is therefore a potential Target of antiretroviral drugs Step One is the infection of a suitable host cell such as a CD4 positive T lymphocyte entry of HIV into the cell requires the presence of certain receptors on the cell surface CD4 receptors and co-receptors such as ccr5 or cxcr4 these receptors interact with protein complexes which are embedded in the viral envelope complexes are composed of two glycoproteins and extracellular gp120 and a transmembrane gp41 when HIV approaches a Target cell gp120 binds to the CD4 receptors this process is termed attachment it promotes further binding to a co-receptor co-receptor binding results in a conformational change in gp120 this allows gp41 to unfold and insert its hydrophobic Terminus into the cell membrane [Music] gp41 then folds back on itself this draws the virus towards the cell and facilitates the fusion of their membranes the viral nucleocapsid enters the host cell and breaks open releasing two viral RNA strands and three essential replication enzymes integrase protease and reverse transcriptase reverse transcriptase Begins the reverse transcription of viral RNA it has two catalytic domains the ribonuclease H active site and the polymerase active site here single-stranded viral RNA is transcribed into an RNA DNA double helix ribonuclease H breaks down the RNA the polymerase then completes the remaining DNA strand to form a DNA double helix now integration's into action it Cleaves a dinubleotide from each three prime end of the DNA creating two sticky ends integrase then transfers the DNA into the cell nucleus and facilitates its integration into the host cell genome the host cell genome now contains the genetic information of HIV activation of the cell induces transcription of pro-viral DNA into messenger RNA the viral messenger RNA migrates into the cytoplasm where building blocks for a new virus are synthesized some of them have to be processed by the viral protease protease Cleaves longer proteins into smaller core proteins this step is crucial to create an infectious virus two viral RNA strands and the replication enzymes then come together and core proteins assemble around them forming the capsid immature viral particle leaves the cell acquiring a new envelope of host and viral proteins the virus matures and becomes ready to infect other cells HIV replicates billions of times per day destroying the host's immune cells and eventually causing disease progression drugs which interfere with the key steps of viral replication can stop this fatal process entry into the host cell can be blocked by Fusion inhibitors for example [Music] inhibition of reverse transcriptase by nucleoside Inhibitors or by non-nucleoside reverse transcriptase Inhibitors is part of standard antiretroviral regimens the action of Integris can be blocked [Music] protease Inhibitors are also part of standard antiretroviral therapy each blocked step in viral replication is a step towards better control of HIV disease [Music] okay so as I mentioned we are using a single stranded positive sense RNA virus with a DNA intermediate here so we're just going to go back over the steps in the video so the first one the viral nucleocapser capsid enters the host cell and it releases these things right here it releases two viral RNA strands here and the five Prime to three prime Direction but these are not going to act as RNA and just translate proteins because we want them to be converted into double-stranded DNA to go inside of the host cell's DNA we also see three enzymes protease integrates and reverse transcriptase these enzymes are needed to convert our single stranded m or our single-stranded RNA into double-stranded DNA okay so the next reverse transcriptase begins reverse transcription of viral RNA going from RNA to DNA so we're taking our single stranded RNA and we are just going to copy it here and once we copy it we get our single stranded DNA or complementary DNA so we're going to read this strand here make our copy and then this is our copy going in the three prime to five Prime Direction now so this is our single stranded DNA that we just built after we separated it from our RNA DNA Helix here so basically what we did was we took the RNA that we started with the viral RNA we copied it and we have a single stranded RNA we have a single stranded DNA those two come together and make an RNA DNA double helix once we make that RNA DNA double helix we're going to separate the DNA out and have a single stranded DNA so in order to do that ribonuclease H breaks down the Helix and the RNA is hydrolyzed and now we're just left with our single stranded DNA now that we have our single stranded DNA DNA polymerase is going to read that strand to build a complementary strand we see here in red so now we're left with a double-stranded DNA Helix and that's the form it needs to be in to go into our DNA so we went from a single stranded RNA molecule to a RNA DNA double helix to a single stranded DNA molecule and then a double-stranded DNA molecule and now we can put that double-stranded DNA molecule into our DNA so our DNA is the black double-stranded DNA molecule this is the one that we just made our double-stranded DNA from the virus itself that gets incorporated into our own DNA there integrace puts the double-stranded DNA into the host cell's DNA the viral DNA goes through transcription to make viral mRNA so then now the um viral DNA is going to go through transcription as we read that we're going to just read that one strand here the leading strand of that double helix that we made we'll just read this three prime to five Prime end to make our m r n a here now we have our mRNA coming from the whole double helix there the viral mRNA that we just made goes to the cytoplasm to go through translation to make viral proteins AKA viruses we then take our two viral RNA strands and replication enzymes put them together with proteins and form a capsid around them and then the viral particle leaves acquiring an envelope by way of budding so it buds out of the cell here and we can see that budding occurring in this picture where the viruses are budding out of the cell okay so in maturation once an abundance of viral nucleic acid enzymes and other proteins have been synthesized assembly of components into complete viron's start and that constitutes the maturation or assembly of progeny viruses maturation of envelope viruses is a longer and more complex process than that of most bacteriophages so you can see the book for details if interested just know that during maturation all of these viral proteins the RNA and the enzymes here are going to come together in the capsid there and once they come together in the capsid that kind of constitutes maturation there and then it leaves the cell by way of budding that process is known as release the budding of new virons through a membrane may or may not kill the host cell just kind of depends on how many viruses are leaving if a lot of viruses are leaving so we can make billions every day then that may kill the whole cell because remember it acquires its Envelope as it leaves and that envelope is coming from that host white blood cell human adenoviruses for example Bud from the host in a controlled manner the shedding of new virons does not lyse the host cell when an infected animal cell is filled with progeny virons the plasma membrane lyses the progeny and the progeny are released lysis of the cell often produces the clinical symptoms of the infection or disease so as long as it's in a controlled manner it doesn't usually kill the cell but if it is not in a controlled manner then lots of viruses are butting out and that is going to kill the cell the herpes virus that causes cold sores destroy skin cells as a result of viron release table 11.5 gives a good summary of the comparison of bacteriophages and animal virus replication so make sure you take a minute to look at that table there individuals experience their recurrence of skin eruptions commonly called cold sores or fever blisters these are caused by the herpes simplex virus a member of the herpes virus as we saw earlier these are double-stranded DNA viruses that can exhibit a lytic cycle so these make up our latent viral infections they can also remain latent within the cells of the host genome or the host organism throughout the individual's life not in the skin cells we associate them in but in nerve cells and when activated whether by a cold or a fever or by stress or immunosuppression they once again replicate resulting in lysis so basically in these latent viral infections these viruses live in the nerve cells in the ganglion of our spine spinal cord and in our brain and once we become sick or our immune system weakens and we don't have those cells those white blood cells as protection anymore then the virus tries to escape because it knows that its host is weak and the virus senses that the living conditions aren't great so the virus will try to escape and once it escapes it goes through the lytic cycle and our skin cells especially with the herpes virus the one that causes herpes and that's why you see those cold sores or blisters in the HSV-1 around your mouth because the herpes viruses are going through the lytic cycle and breaking the skin cells to get out of the body so that ability to become latent is held by all herpes viruses another herpes virus the one that's responsible for Chickenpox also remains dormant within the central nervous system so we see those red um blisters with chickenpox as well as those viruses are trying to exit or leave the body they have those fluid filled turbid fluid blisters there as chickenpox so that's when you are very contagious or infective because the virus is trying to leave the body and that's why the fluid is turbid because it does contain those viruses in it with chickenpox however you usually get two viruses together so that's the vzv varicella zoster virus and the varicella portion is the chickenpox portion and the zoster portion of the virus is the shingles so the reactivation is known as shingles usually when you get Chickenpox the shingles virus is already inside of you stays dormant in your body until your immune system is compromised usually as you get older and then it will reoccur as shingles later on many individuals carry these viruses throughout their lives never exhibiting any symptoms at all okay so moving to human cancer viruses after many years of research and testing we know now of at least six viruses that are associated with human cancers there are probably many more yet to be identified several of the human papillomaviruses or HPV have shown a strong correlation with some human cancers although some of these DNA viruses cause only benign warts other types hpv8 and hpv16 lead to a carcinoma of the uterine cervix that usually is cancer literally 99.7 of all cases of cervical cancer are caused by HPV in our sexually transmitted another potential cancer-causing DNA virus is Hepatitis B virus or hbv it causes inflammation of the liver and leads to about 80 percent of all liver cancer so how cancer viruses cause cancer like bacteriophages some animal viruses that infect animal cells often cause cell death through lysis other animal viruses can infect cells and form Pro viruses in some cases these infections result in physical and genetic changes to host cells the papillomavirus that causes human cancers infect cells but their viral DNA remains free in the cytoplasm of the host so we can see that papillomaviral DNA here free in the cytoplasm of the host and that's fine a few genes of the papillomavirus are active so that the virus can replicate with each cell division but it has to stay free in the cytoplasm of the host here should the viral DNA accidentally integrate into the host cell's DNA so we see here that integration of the host cell's DNA then we have unregulated replication of viral proteins occurring so then the cell starts replicating uncontrollably and we have lots and lots of cells being made and that's the malignant part that is the cancer the malignant tumor unregulated replication of these cells so the cells are dividing uncontrollably and that gives us the malignant tumor some of these viral proteins block the effects of tumor suppressor genes which prevent those uncontrolled cell divisions without the products of the genes the host experiences uncontrolled cell divisions and that tumor there or cancer develops so as long as the papilloma virus stays free in the cytoplasm and doesn't get integrated into the host cell's DNA you will not get cancer forming from that HPV okay so that sums up chapter 11 and sums up viruses