welcome to section 8 of microbiology fundamentals in this section we'll be discussing viral genomes and replication let's get started viral genomes come in two broad categories rna and dna rna viruses are single stranded and dna viruses are double-stranded now these facts are fairly intuitive we typically see dna as double-stranded and we think of rna as single-stranded for example mrna but there are some exceptions rio viruses are actually double-stranded rna and we will help you remember this unique fact when you watch the video on rio viruses an exception to dna viruses being double-stranded is parvovirus parvovirus is a dna virus that is single-stranded and again when you watch the video on parvoviruses we'll help you memorize that fact now let's discuss positive and negative sense rna positive sense rna resembles eukaryotic mrna the host ribosomes recognize it and can translate it in a five to three prime direction this means that when the host cell is infected with a positive sense virus translation of the virus can begin immediately however with regards to negative sense rna these must first be transcribed from a negative to a positive sense strand for this reason these viruses must carry with them their own rna-dependent rna polymerase to create that positive strand and they need to carry it themselves because host eukaryotic cells lack that polymerase and just so you're not freaked out know that every rna video in our collection has a way to help you memorize which ones are positive sense and which ones are negative sense on the left you can see how negative sense viruses are translated and on the right you can see how positive sense viruses are translated let's focus on the right first notice that a positive sense sequence of rna just means that it's oriented in a five to three prime direction this is important because host cell machinery such as the host ribosome and host trna only function in the five to three prime direction so we can see that the viral strand of rna enters the host cell and is directly translated into protein using host cell machinery if we look at the left we can see that a sequence of negative sense rna is oriented in the three prime to five prime direction therefore negative sense viruses cannot be directly translated into protein because the host cell machinery is incompatible with the orientation of the sequence of rna this is why negative sense viruses have to bring along their own rna-dependent rna polymerases which you can see represented right here these enzymes allow the virus to be converted into a positive sense strand meaning that the sequence of rna is reoriented in the 5 prime to 3 prime direction once this occurs the rna can be utilized just like a positive sense strand of rna as you can see with this image rna viruses are listed on the right they are further divided into enveloped and naked viruses from there they are subdivided into positive sense and negative sense viruses i only point this out to you so that you recognize that positive and negative sense is only a term relevant for rna viruses not for dna viruses now let's discuss the infectivity of purified viral genomes when we discuss purified nucleic acids this simply means that everything but the nucleic acids or viral genome has been removed this concept helps reinforce how vital rna-dependent rna polymerase is to negative sense rna viruses let me explain why following purification the following viruses will be infectious these include positive stranded rna viruses and dna viruses with the exception of poxviruses and hepatitis b virus i'll explain why poxvirus and hbv are exceptions in a moment before i dive into those details though i want you to know that when we're referring to infectious in this instance it's really only in a research setting in other words the virus needs to be injected directly into the host cell after all we already know how important those viral particles are for adsorption of viruses whether the particles are on the capsid or the envelope they are vital and purification means that everything except for the nucleic acids are gone including those viral particles so those viruses would not be infectious unless you force them into the cell by injecting them so again this is really only in a research setting that these would be infectious and the reason that positive stranded rna viruses and dna viruses can be infectious after purification is because they don't need any polymerases with them they just enter the cytoplasm and the host cell takes care of everything else it can start translating the rna the host cell has all the machinery necessary for the rna viruses that are positive stranded and dna viruses to replicate now let's talk about the viruses that would not be infectious following purification even if they were injected directly into the host cell cytoplasm these include negative stranded rna viruses these would not be infectious because they lack that rna-dependent rna polymerase the host cell doesn't have this and the host cell can't start translating this negative stranded rna until it gets converted to a positive strand and that can't happen unless there's rna dependent rna polymerase with the virus as we described with this image negative sense rna viruses require their own viral rna-dependent rna polymerase and the host cell can't start working on it until it gets converted to this five prime to three prime positive strand that means if you purify this nucleic acid then it won't have this rna polymerase and it is not infectious i mentioned before that dna viruses are all infectious following purification with the exception of pox viruses and hepatitis b i've listed them down here as well so now let's explain why they would not be infectious for pox viruses they require their own dna-dependent rna polymerase they need this for transcription in order to make mrna from its genome let me show you why they need this this diagram shows poxvirus replication which takes place in the cytoplasm normally dna viruses replicate here in the nucleus in there they can use the host rna polymerase and this would make mrna but pox viruses do not replicate the nucleus which is what makes them unusual and since they don't replicate in the nucleus and rather they replicate in the cytoplasm they need their own dna-dependent rna polymerase but why would they need their own if the host has it as we just explained well the host dna dependent rna polymerase doesn't leave the nucleus why would it it just stays in the nucleus to do its work on dna so if the pox virus is to be infectious it needs to bring with it its own dna dependent rna polymerase now hepatitis b requires its own dna polymerase as well this diagram shows the basic structure of hepatitis b and it's described as well as all the detail you need to know about hepatitis b in the hepatitis b virus lecture right now i only want you to look at this dna polymerase you can see that the virus carries this with it because it needs it at some point during its life cycle it's not even important for you to know when or how it uses this you just need to appreciate the fact that it needs its own dna polymerase or else it wouldn't be bringing the enzyme with it it would just rely on the host machinery like all other viruses do so again negative stranded rna viruses and two dna viruses pox viruses and hpv will not be infectious even if they're purified and injected directly into host cells because they all need to bring with them their own polymerase it's important now to focus on translation itself and replication so whether we're referring to rna or dna viruses translation will result in new proteins and these protein products include everything needed to make the new virions for example capsids or the viral particles needed for adsorption or polymerases for replication or any of that stuff and with the production of all these proteins replication can occur and replication simply refers to copying the viral genome for rna viruses this replication will happen in the cytoplasm for dna viruses this replication will happen in the nucleus except of course for pox viruses which we discussed earlier this diagram shows a host cell and this shows the translation and replication for an rna virus there's adsorption penetration and encoding which we covered before and then translation and replication can begin so with uncoding the rna virus remains in the cytoplasm and you can see that host cell ribosomes will translate this rna and make viral proteins these proteins can help form the capsid or anything else for new and complete viral progeny some of those proteins will be polymerases which can help replicate the viral genome now i made a special note here with this star and is to point out that negative sense rna viruses must first be converted to positive strands and this item is not shown in other words if we're dealing with a negative sense virus there's an additional step right here now let's discuss dna virus replication first as adsorption penetration uncoding and then we see the dna virus enter the nucleus it then gets transcribed through a host cell rna polymerase and makes rna this rna then enters the cytoplasm and hosts cell ribosomes can translate it into proteins which you can see here now going back to the nucleus we can see there's a dna polymerase and this will allow viral replication and you can see this little copied dna right here now let's make a few notes about polymerases in general we already discussed rna-dependent rna polymerase these are found only in negative sense rna viruses and they function to make a positive strand which is basically mrna now let's discuss rna dependent dna polymerase this is just another way of saying reverse transcriptase and reverse transcriptases are found in retroviruses for example htlv and hiv as well as hepatitis b which is not a retrovirus in other words there are three viruses that have reverse transcriptase and they're all listed here and i just want to prove to you that rna-dependent dna polymerase is the same thing as reverse transcriptase so here's an rna virus and here's a polymerase which is rna-dependent dna polymerase the polymerase is rna-dependent because it uses rna to make its product and the fact that it's a dna polymerase indicates that it makes dna so here's that dna product made from that rna-dependent dna polymerase so which viruses start with rna and then make dna those would be hiv and htlv and they need to convert things into dna in order for their dna to be integrated into the host genome after all our genome is dna not rna and then of course remember that hepatitis b also requires reverse transcriptase we discussed the basic structure of envelopes now let's discuss how envelopes form envelopes that viruses have are basically stolen from the host cell most of the time the varions exit and they just take a piece of the lipid bilayer from the plasma membrane from the host cell as they leave the only exception to this are the herpes viruses which actually steal some of the lipid bilayer from the nuclear membrane otherwise just expect that viruses get their envelope from the cell membrane now let's do a question to apply what you've learned newly synthesized virions of a dna virus obtain a lipid bilayer from the cell membrane of a eukaryotic cell this virus is not known to infect hepatic cells which of the following occurred at some point during the life cycle of this virus a dna formation from an rna-dependent polymerase b rna formation from an rna-dependent polymerase c lipid membrane fusion with host cells or d invagination of host cell membrane hopefully from the question stem you notice that this virus is an enveloped virus after all it obtained a lipid bilayer from the cell membrane this is how all enveloped viruses obtain their envelopes with the exception of herpes viruses which get their envelope from the nuclear membrane also we know this is a dna virus and lastly it's a virus that does not infect hepatic cells this fact basically tells us that this is not a hepatitis virus with these facts in mind which of the following occurred during the life cycle of this virus that would be choice c lipid membrane fusion with host cells this simply describes the penetration step of enveloped variants this image depicts how the viral particle on the envelope attaches to the host cell which we can see here this is adsorption then penetration occurs which is just fusion of the lipid membranes which is choice c now choice a is wrong because this describes forming dna from rna in other words this is an rna dependent rd dna polymerase also known as reverse transcriptase and which viruses use reverse transcriptase hiv and htov both of which are rna viruses and that doesn't fit with the dna virus in the question stem you may have been attracted to choice a thinking about hepatitis b and how it has a reverse transcriptase and also it's a dna virus however the question stem specifically states that the virus is not known to infect hepatic cells and hepatitis b definitely infects hepatic cells so we can rule this out so again we have no reason to believe that the virus in the question stem would use reverse transcriptase now choice b is wrong because this describes rna-dependent rna polymerase rna-dependent rna polymerases are only used by rna viruses recall from earlier in our discussion that there are instances in which rna will be made from an rna template during rna virus replication rna polymerase will replicate the rna virus it does this using an rna strand thus it's an rna-dependent rna polymerase we also discussed how negative sense rna viruses need to bring with them an rna-dependent rna polymerase and they do this in order to convert the virus into a usable positive strand regardless of which circumstance you're thinking of rna-dependent rna polymerase is only used by rna viruses and the virus in the question stem is a dna virus lastly choice d is wrong because this describes endocytosis and invagination of the host cell membrane endocytosis is needed for naked viruses to penetrate the host cell recall from section 6 that naked viruses depicted here attach to the cell surface and then they are brought into the cell through endocytosis and as you can see the cell membrane invaginates during this process the point here is that endocytosis is how naked viruses enter the cell and the virus in the question is an enveloped virus not a naked one and that covers viral genomes and replication