Retroviruses

so you might have an understanding of viral replication but there's one special case that doesn't quite fit neatly into the box of lytic or lysogenic and that's what we're going to talk about so that special case is called a retrovirus so first let's zoom in and take a look at some unique things about the retrovirus that make it different from other viruses so first of all it is an envelope to single-stranded RNA virus and inside of this envelope it also carries three special proteins and right now just be aware that there are three special proteins I'll talk about them more when we get to each step where they are important so as you know envelope viruses can enter in one of two ways either through tricking receptors receptor mediated endocytosis or through direct fusion and it just so happens that in our example and we're talking here about the retrovirus HIV this retrovirus will enter the cell with direct fusion so now that this nucleo capsid is inside the cell it actually has to undergo a step called encoding where this purple capsid is dissolved oh we forgot about the protein so let me redraw those in right now so these are the proteins that were originally inside of that capsid so everything inside of that coat is released and this is where the first special step occurs so we're going to say that this red protein is reverse transcriptase so reverse transcriptase will hop on to the RNA it reversed transcribes the RNA which means that so it reads from five prime to three prime end and you will form complementary DNA shown here in pink and the reason it's called reverse transcription is usually you take DNA to make RNA in this case you take RNA to make DNA and because this is the complementary DNA strand we call this cDNA complementary and then reverse transcriptase will work again on the same RNA to make another cDNA strand because it's the same exact code it can recombine with the other cDNA strand to make a double-stranded DNA and so now what happens is you have integrase coming along and let's make integrase blue so integrase comes along Clips off each of the three prime ends so now these are slightly shorter on each end and sorry this is a bit hard to see because this strands 3 prime end is over here and the while the first one is actually clearly labeled as this is the 3 prime end and by clipping off those three prime sections they form these sticky ends because unpaired DNA wants to be paired and integrase has suddenly removed that part and you might be wondering what happens to this RNA and what happens is that it actually gets degraded by normal ribonuclease so that's no longer there and integrase does exactly what it says it will follow this path and integrate this HIV DNA into the hosts DNA and one thing I just want to very quickly mention is that if I had drawn this to be super accurate this would need to have a nucleus around it because the HIV retrovirus infects human eukaryotic cells which have a nucleus so it actually will travel through the nuclear membrane to get to the genome and here integrase helps viral DNA integrate with the host like it's named interets integrate so just imagine this is all double-stranded but just for simple drawing sake this will just be one line so this is viral DNA and this is called the provirus stage so you can see that this is similar to the lysogenic cycle that we talked about before but unlike the regular lysogenic cycle it's not dormant or latent it actually does not have that repressor gene that typical lysogenic viruses have so it is actively transcribed whenever the hosts DNA is transcribed so since the host cell thinks this is normal DNA it will make RNA and I just wanted to call this viral mRNA so you have an idea that the cell cannot tell that this mRNA shouldn't have happened so this mRNA exits the nucleus and these viral RNAs are now in the cytosol again once this viral mRNA exits the nucleus and it goes into the cytoplasm it's just like any other RNA and some of these will be translated into proteins like the capsid proteins and of course the three proteins that we begin with which are the reverse transcriptase the integrase and actually the last one we haven't yet mentioned is the protease the green here is protease and we're going to hold off a little bit on what protease does but here it's formed and you can see that you now have all the parts that can self-assemble into new viruses so again all of these viruses that are form will have the RNA they're the reverse transcriptase the integrase and the protease so you'll notice that these are actually missing one thing they're missing their envelope and so they're called immature viruses and unlike the typical lytic cycle it doesn't just break open the membrane in fact it takes advantage of the membrane and so these viruses will come along and they will bud off so this will wander here and this one will enter here oops and that's missing a border I just realized so there you and they will butt off and that will be their envelope and sorry they're missing the proteins and I'll just draw them in again so again these are still immature right and before they go on to infect other cells they have to mature somehow so what happens is that protease inside of here will cleave those other proteins to make sure that they're fully functional before the virus enters another cell and starts this cycle all over again and so retroviruses replicating are a bit more complicated than traditional replication so it's not just lysogenic or lytic it actually has elements of both