Viruses

hi. In this video, we're going to talk about viruses, which are much, much, much, much, much smaller than your average cell. In fact, viruses are significantly smaller than even the smallest bacteria, and this is because viruses lack a lot of the necessary structures to sustain life that you'd find in cells. They don't have the machinery necessary to carry out metabolic processes or to process their genetic information through transcription and translation. Now, because of this, you could almost think of viruses as these vessels for genetic material, and the protective coating over that genetic material is called the Caps it. And this is really just a protein coat that covers the viral genome, and it is made up of little sub units we call caps Amir's so you can see in this image right here we have this virus, and it has a caps it. This blue structure made of all these little balls you see here. Each one of these little blue balls is a cap Samir now viruses. As I said, they're basically vessels for genetic information. But what kind of genetic information well, that actually can vary depending on the type of virus, so a virus could contain double stranded DNA, single stranded DNA, double stranded RNA. Believe it or not, that's not something we really encountered yet, and we probably won't really bring it up again. But it can happen, and they can also have single stranded RNA. And there's such a wide range of viruses and what they're all capable of, that we're really just gonna talk about generalities. Here, however, we are going to focus in on a particular class of virus called bacteria fage. And that's because these have been very heavily studied, and we have a lot of good information about how these particular types of viruses operate. Now what's defining about bacteria pages, or sometimes just called fage is for short is that their viruses that infect bacteria and they actually have some pretty complex caps is so this right here is a bacteria fage, and you can see that compared to its neighbor, this bacteria or this virus is struck. Capsized structure is much more intricate looking. In fact, that's because this caps it has to carry out a pretty specialized function that will get to a little later in lesson. But for now, just note that this protein coat encapsulates the viral genome right here. So that's our viral genome. And, well, there's a lot of other bells and whistles down here, and we'll get to what those do later. Now. Some viruses. Not all viruses, but some viruses have what's called a viral envelope, and this is an accessory structure, so it's not necessary for viruses. But some viruses have them frequently animal viruses, and these are member Enis structures that are often derived from the membrane of the viral host cell. So what that means is the virus will actually take a portion of the host membrane to form a viral envelope around itself. Now, in addition to these viral envelopes, viruses have important structures on their surface that you can see labeled here. We have thes glycoprotein and these, in addition to some other structures that I'm not going to mention define the viruses host range, which is the collection of hosts that a virus can enter and infect, and viruses identify their hosts based on these surface proteins that detect specific receptors on the host cell. So that's why I said these gallego proteins or other various protein structures on the surface of the virus will actually determine its host range. All right, now, let's flip the page

viral infection begins when the virus binds to the host cell. Following that, the virus has its viral genome. Enter the host cell through some manner. Now some viruses, like the bacteria, fades. We were just talking about actually inject their genome into the host. And you can see that happening right here in this image. And now you might have a better understanding of why those bacteria fage have a Mork complex caps ID than other viruses because that caps it actually has to function almost like a syringe. Injecting the genome, which we see in green right here, I mean, actually change my pen colors. So it's easier to see right there so that viral genome gets injected into the host bacteria. And this happens because of the specialized caps it which lands on the surface of the bacteria cell and inserts um a portion into the actual exterior membrane of the bacteria and then allows for the entry of the viral genome. Now, this is a more complex process than many viruses employ. Many viruses get their genome inside the host cell by simpler means. In fact, some are merely absorbed into the host by a process like and associate Asus. Others actually fused their membranes. Remember those accessory structures we were just talking about? They fuse their membranes with the hosts membrane, allowing the entry of the viral genome into the cell. Now, once inside the cell, the virus hijacks the machinery that the host cell uses in order to replicate itself. So remember, viruses air really small, and they don't have all those necessary structures that are required to sustain life. So they have to use the structures that the host cell has in order to carry out those processes. So these host cells unwittingly, without without their knowledge, they provide nucleotides. They provide enzymes, ribosomes, tr, nay, amino acids and even a teepee to the virus so that the virus can replicate its genome and create new viruses and other viral products. Now, through this replica of process, the most important products to be produced our nucleic acids right. The virus needs to replicate its viral genome and also caps Amir's um, the virus needs to build the components necessary to build a caps ID to house the replicated viral genome so that it can create Mawr viruses right, its main goal more or less is to produce more of itself. Um, in this in this process, the virus actually doesn't have to go through the trouble of assembly. What's what's Pretty amazing is in producing the viral genome and these caps Amir's. These viruses actually spontaneously assemble now. Spontaneous assembly is an idea we touched upon a long time ago when we were talking about membranes, cell membranes. And we said that cell membranes spontaneously assemble in an aqueous environment, meaning that those fossil lipids arrange themselves into the proper orientation so that we produce the lipid beyeler. Now much like that, viruses have their caps. IDs. I'm sorry caps Amir's spontaneously assembled into the proper caps it. So just like cell membranes, viruses also spontaneously assemble when the proper, uh, components are produced. Let's turn the page.

bacteria, Fage actually can use two different types of cycles to replicate themselves, and here we're actually going to talk about both. Now, the first one we're going to talk about is the light IQ cycle, and this is fade replication that ultimately results in the death of the host light IQ. That term you see there, think of that as lice, right? When a cell bursts open, this cycle is going to result in tons of viral replication that actually will basically fill up the cell to the point of bursting. And it's going to lice burst open with all those viruses, release them to the environment so that they can infect other cells. So the light X cycle scroll down a little bit actually begins with the injection of the viral genome, as you see right here. So just label this number one. Now the bacteria Fage injects its viral genome into the cell, and then it will incorporate into the host cell's genome. Like you see, right here here we have the viral, and here is the bacterium's going abbreviate that backs. That's the bacterial portion that was originally in the cell. That's the bacteria's jeans and the viruses actually going Thio cause its own genes to be replicated, and it's actually going to degrade the host genome so that Onley its genes are being produced. And you can see that happening over here in this third image in the sequence now from its replicated genome, it's going thio, uh, lead to the production of caps and years, right, those components necessary to build new viruses. So here we can see some caps Amir's being produced, and eventually all the components will be produced like we see here in image number five. And from there they will spontaneously assemble into Fage is and those pages will lice from the cell like we see here in image number six. That is the basic those air, the basics of the light X cycle. A couple things to note. A. A virulent Fage is a fage that replicates by the light X cycle on Lee. Now there are there are many Fage is which can enter either cycle and can actually switch between them. But there are some that Onley used the light X cycle, and we call those virulent pages now. It's also worth noting that bacteria aren't total suckers to this. They've been around the block for a really long time, right? Billions of years, in fact. So bacteria actually have defensive mechanisms against these bacteria pages, and those come in the form of restriction enzymes that actually degrade the viral DNA that enters the host cell. Now the other cycle is the lice a genic cycle, and this involves replication of the viral genome without actually killing the host cell. As a result, we refer to Fage. Is that air capable of replicating through both lighting and Lissa genic cycles? Temperate pages, right? They're more tempered. They haven't more even temper, let's say, because they can kill off the host cell when they want to replicate a bunch of viruses. But they can also coexist with the cell without actually really harming it too much. So let's say those temperate pages arm or even tempered. Now, how does the Lissa genic cycle actually go down well again? First, Thief Age inserts its DNA into the host, just like we saw before. So this is still our first image of the lycee genic cycle, and again, the second is are The second phase is when the viral genome inserts itself into the bacterial genome. But now, instead of actually degrading the bacterial genome and replicating its own genome, the viral genome more or less lays dormant. And it allows the bacterial cell to replicate its own genome along with the viral genome, which is what we see happening here. You see how the bacterial genome is replicating normally, but because the viral genome has been incorporated into it, the viral genome is getting replicated, kind of like getting a free ride. And, of course, the bacteria will replicate its genome and eventually divide in a process that we know as binary vision, which we can see right here we have to jot er bacterial cells. Now each has that viral genome incorporated into its own genome. And eventually what will happen is at some point the virus will say, Well, not gonna lie dormant forever. And it will enter the light X cycle going from this image, five more or less back into to like we see here. And from there it will follow the light X cycle that we traced before couple points of terminology. Pro fage a pro fage is when the viral DNA has been integrated into the bacterial chromosome. And you can kind of think of this as the term pro fe, just kind of being like pre fage, right? Um, that that prefix pro means before kind of. So this is like a proto fage. In a sense, it's the precursor to the actual fage, um, so these two cycles can feed into each other. As we saw, the lycee genic cycle will feed into the light X cycle. At some point, however, the lice of genic cycle cycle can repeat itself many, many times, so that from one single infected bacteria there could be hundreds. Hundreds of bacteria with pro fage inside, laying dormant, waiting to enter the light X cycle and replicate all the necessary caps. Amir's self assemble a bunch of new bacteria pages and lice the cell to infect mawr host cells. All right, let's turn the page

animal viruses behave differently than those bacteria fades. We just took a look at, in fact, just down to their structure. Animal viruses look different, so animal viruses tend to have viral envelopes, right. Those member Enis accessory structures that are often derived from the host cells own membrane. They also tend to have RNA genomes, unlike those bacteria fades that had DNA genomes. Now animal virus replication involves entry into the cell, just like we saw with bacteria fage. But this time the whole virus is going to enter the cell, and it's going to do that through cell surface protein receptor recognition. Right? So there are, you know, a variety of specific ways that this can happen. But think Endo site Asus. Think about those Endo site tot psychotic processes. We took a look at way back and cell signaling, and what happens there is you have little molecules wagons find to these cell surface receptors and that causes the membrane to fold inward and pinch in well similar to that these viral cell surface proteins they're gonna bind to receptors on the host cell and is going to cause the host cell to take the virus inside right. These viruses are very tricky. They trick the host cells. Uh, the viral RNA. Once inside the cell serves as a template for replication by the viral RNA polymerase so that RNA will serve as a template from which marinas will be synthesized by a special viral RNA. Polymerase retroviruses are a special type of animal viruses and these air viruses with RNA genomes that actually instead of just putting that RNA out there, thio make copies of Marna from it. Instead of doing that, these retroviruses actually do something called reverse transcription, Right? So transcription is when you take DNA and you copy over the message into an RNA code. But with these retroviruses do is they take their RNA code. That's their genome, and they turn it back into DNA, which they insert into the host cell's genome. So let's just cover that one more time. These viruses have an RNA genome. They reverse transcribed that RNA into DNA and then insert that DNA into the host cell's DNA genome. Now they use a special enzyme called reverse transcriptase. To do this, it's a special enzyme that can catalyze that RNA to DNA transcription. In fact, uh, because of the discovery of reverse transcriptase is we've actually been able to advance a lot of fields of biotechnology, these air, very helpful enzymes and much like we were talking about the Pro Fe Ages, which are those viral genomes inserted into the bacterial genome, right? Those precursor fage is more or less well when a retrovirus has inserted it's viral genome into the host cell's genome. Through that reverse transcription process, we call that a pro virus so pro virus very similar to pro fage, except to become a pro virus. You have to have this special reverse transcriptase enzyme. So in a way, pro viruses air kind of a little fancier than pro fage is now. We can see examples of this right here with a very famous virus. Human immunodeficiency virus, better known as HIV. HIV is an animal virus. It's also a retrovirus. It has a lipid bi, bi layer viral envelope accessory structure, and it has that reverse transcriptase enzyme. You can see it right here represented by this little blob right here, and it has an RNA viral genome. It interacts with this particular type of cell surface receptor, allowing its viral genome to enter the cell. And here we can see the steps of reverse transcription playing out whereby the viral genome is converted to DNA, that DNA is inserted into the host cell's genome, and from there viral products can be produced. And ultimately, the ultimate goal is to produce the proper viral products. To then create a new virus, which will leave the host cell taking some of its membrane with it to act as in viral envelope, and it will go infect a new cell. All right, let's turn the page.

Hello, everyone. In this lesson, we're going to be talking about the different groups and classifications of viruses, depending on the amount and type of genetic material that they have. So viruses, even though they are not alive, are going to have genetic material that contains the blueprints for new viruses. And they can either have a DNA virus or RNA virus, meaning that they can have a DNA genome or a Arna genome. Now these different genomes can come in the form of double stranded DNA or RNA, or single stranded DNA or RNA. So first, let's talk about double stranded DNA viruses and double stranded RNA viruses. Double stranded RNA viruses are going to have a genome that's very similar to ours. They're going to have double stranded DNA to make up their genetic material. And because it's so similar to our genome, whenever the virus enters into the cell, it can easily be replicated because it often replicates with the genome. During s phase, Double stranded DNA viruses often integrate themselves into our genome so that any time we replicate our genome, the viral genome is replicated as well. Now they're going to infect a wide array of organisms, including US, including bacteria, including all sorts of organisms except land plants, which I always thought was interesting. Land plants don't have double stranded DNA viruses. Now there's also double stranded are in a virus is double stranded. RNA viruses are not as common as single stranded RNA viruses, but they're still very important. Double stranded RNA viruses are going to be a little bit different. They are going to enter. The site is all, and because they are double stranded, are in a viruses they conserve as a template for synthesis. They can actually serve as a template to create the viral proteins that are needed because it's already RNA, and it's already going to have our name molecules that can be translated. So this allows the viral enzymes to be made. And then these viral enzymes are made, and then the viral genome can be replicated as well. And this is going to include ah whole bunch of organisms that can be infected, including fungi, plants, vertebrates, bacteria and insects. So a ton of different organisms are infected by double stranded Arning viruses. Now we're going to talk about single stranded RNA viruses, which you're going to be the most common type of virus that you will ever hear off. Now if you guys wanted some examples off double or if you wanted some examples of DNA viruses, smallpox is a DNA virus. Herpes is a DNA virus, and chicken pox, I also believe, is a DNA virus. Most viruses where familiar with they're going to be RNA viruses, and most of those were going to be single stranded RNA viruses. Now I'm going to go over this topic first before we talk about single stranded RNA viruses because single stranded RNA viruses can come in two forms. But I want to go over a concept before we talk about those two forms. So what do we have here? Do you guys know? Well, this is the process of transcription whenever we which we already learned about whenever we learned about DNA expression. So this is the process of transcription, and this Marna in blue is being made by the RNA prelim race, actually reading the genetic code, the DNA and building an m. R n a strand off of this genetic code. So this is the DNA, and then we have our RNA pull. Emory's Now, Whenever we talked about creating Marna, we talked about the coding DNA Strand and the template DNA strand. Now there are many names for the coding strand, and there are many names for the template strand. You guys might also remember that the coding strand can also be called the Sense Strand, and it's also called the Positive Strand. For whatever reason, the coding strand has three different names. Remember the coding Strand is going to have the same exact code as the Marna. So the coding strand equals the code of the Marna. They have the same exact code. Now. We also have the template strand here, which is very important. The template Strand also has its own unique names. It's either called the Template strand. It's either called the anti sense strand or it's called the Minus Strand. Now I know that it sucks that we have to remember all these different names of these DNA strands, but they are going to become very useful. Let me rewrite that since you guys can't really see it. So the minus strand. Okay, so the template strand is called the anti Sundstrand anti minus strand and the template strand is going to be complimentary. Thio. The M r N A. So the template strand is complimentary to the Marna. And that is because the template strand is utilized to build the Marna. So they're going to be complementary to each other while the coding strand in the Marna are going to be exactly the same code. Now, remember that the coding strand is also called the plus strand, and the template strand is also called the minus strand. So now we know what plus and minus actually means. Plus strands have the same code as the Marna minus strands have the complementary code to the Marna. That's going to become very important because, as you guys will see, there are two different types off single stranded RNA viruses. You can have a positive sense strand RNA viruses, and you can have negative or minus since strand RNA viruses. And this is going to tell you whether the single stranded RNA genetic code off this particular virus is equal to the Marna or complementary to the M R N A. That is made for this virus. So we have these two different types. We're going to have the positive sense strand and the negative sense strand for the RNA virus. So the positive sense are in a virus is a single stranded RNA virus. So just you guys know these air all single stranded Arnie. It's gonna be a single stranded RNA virus genome that contains the same sequence needed to produce the viral proteins. So that means that this particular genome is the coding strand. So the genome equals the coding strand or the positive strand. Okay, So because it is the coding strand, that means that the genomes code is exactly the same as any more n A. That would be made from that genome. So what does that tell us? Well, that tells us that the genome could enter the cell the host cell and immediately transcribed into translate. Excuse me? That is a type of immediately translate into proteins because the coding strand is the exact same code as the Marna. Well, the virus could simply send its genetic material in and translate that genetic material into viral proteins, which will then begin to build and replicate that virus. So the positive sense are any viruses are very simple. They are the coding strand, which is equal to the Mariana Strand. And when that goes into the host cell because it is equal to the mRNA Strand, it could be directly translated into viral proteins, and that virus will be immediately replicated now. Negative sense are any virus is not so easy. Negative sense aren't a Viruses have a genome that contains the complementary sequence to those that code for the viral proteins. So what does that mean? That means that the genome is the template strand. So what does that mean? Well, that means it's the minus strand, meaning that we have to make an M R N A from this template genome strand to begin creating viral proteins. So we have to make the marina. Where, in the positive sense RNA virus. We didn't have to make the marina because the Marna was equal to the genetic code. So the negative sense strand RNA viruses have an extra step. They have to make an mRNA so viral RNA polymerase must always accompany these viruses into the cell so that the viral RNA preliminaries once this viral genome enters the cell, can transcribe it into the viral M RNA. So viral viral RNA Flynn race must accompany genome to transcribe the RNA into the viral marina so that those viral proteins can be generated. So those were the two different types of single stranded RNA viruses. Now there's another very important type of virus that I would like to talk about. Those air gonna be retroviruses, retroviruses. I'm sure you guys have heard of before. Retroviruses are incredibly interesting because they're able to change their genetic code and have intermediate genetic code. Retroviruses have a very important protein called viral reverse transcriptase, and what's going to happen is thes retroviruses are going to be positive. Single stranded are in a viruses, and they're going to use their viral reverse transcriptase to create complementary DNA from that single strand RNA genome. And then that single stranded DNA complementary DNA is created into double stranded DNA and then inserted into the host genome. Do you guys have any examples, or do you guys know of any examples of retroviruses Really, really good example of a retrovirus? Is HIV HIV does this and it is going to be an RNA virus that is going to use the reverse transcriptase to create a DNA version of its viral genome And then that DNA version will be inserted into the host genome. Okay, everyone All right. So now I wanted to go over one more thing before we end. And that is three different classifications off viruses. You can actually put viruses into groups groups one through seven. So group number one is going to be double stranded DNA viruses, group number to a single stranded DNA viruses, three double stranded RNA viruses, four single stranded plus RNA viruses or plus single stranded RNA viruses. And then you're going have the negative single stranded RNA viruses and group number five and then the last two groups are interesting. So the number six Group six is going to be the single stranded on RNA virus that is going to have reverse transcriptase. So this one here is a retro virus. So these air retroviruses in Group number six group never seven. I didn't particularly talk about because it's very uncommon group of viruses, but these were going to be called Pera Retro viruses. Pere retro viruses are going to be viruses that have double stranded DNA, but they're going to replicate via a single stranded RNA intermediate. They're not very common whatsoever they're not generally talked about. I doubt you guys will be tested upon thes because they are so uncommon. But that is group number seven. Now, if you guys were wondering what some examples of single stranded viruses were for positive, since Strand single stranded are in a viruses three West Nile virus. So this group right here, Group number four, you're going to have the West Nile virus. The common cold is also in group number four, and hepatitis C is also in group number four. But there are a lot of RNA viruses, like a ton of RNA viruses. Rabies, I believe, is also an RNA virus. Ebola, I believe, is also an RNA virus. Influenza and polio are also RNA viruses, so most of the ones we combat on a regular basis we're going to be RNA viruses. But I just wanted you guys to know the difference between our RNA and DNA viruses, single and double stranded viruses. And I wanted you all to know the different groups of viruses that you may need to understand, or you may encounter on a quiz or test. Okay, everyone, let's go on to our next topic

I know at the beginning of the lesson I was going on and on about how small viruses are. Well it turns out they're actually not the smallest infectious pathogens. There are actually smaller infectious agents known as Vai roids. And these are actually the smallest pathogen known and they consist of a short circular single stranded piece of RNA pictured right here. This is an actual image of a viral oid. And you can see it starts with this c base pair right here, labeled one. You can see the one right there, it goes all along this way, there is some base pair binding as it folds back in on itself. You can see there's these stretches of base pair binding. I'm kind of just running my pen through those bonds. It's almost like I'm cutting them and so it folds back in on itself and ends with base 359. So this is not even 500 bases long. This is a teeny stretch of RNA And yet this is a pathogen. It infects Vai Roids infect mostly plants and they tend to disrupt plant growth. So plants infected with virus roids tend to be short or stubby or malformed because they their growth is somehow disrupted. Now Vie Roids do not actually encode proteins like viruses. They simply replicate themselves using the hosts enzymes and this uh self replication ultimately leads to problems for the host and propagation of the virus roids. So kind of similar idea to viruses there. Now there are actually other teeny infectious agents called prion. Now, these are bigger than Vai roids. They're actually proteins and these instead of affecting plants tend to affect animals, specifically the brain tissue of animals. The way prions work, you can kind of think of a prion as a weirdly folded protein. And essentially these weirdly folded proteins can interact with normal proteins that have their proper folded form and cause them to get all misfolded and bent out of shape. So in that sense they self propagate misfolding in other proteins. And we can see a little simplified diagram of that happening right here. So here these green balls that's the proper fold for the protein. It interacts with this weird fold in this protein seen in red with little spiky balls around the outside and that causes see the green properly folded protein ends up being misfolded as we see there and this leads to an accumulation of these misfolded proteins. And protein gunk build up in nerve cells is actually very, very toxic and harmful to the nerve cells causes nerve cell death. In fact, protein like garbage protein build up is also implicated in diseases like Alzheimer's as the cause for cell death in those diseases. So building up garbage protein might not sound like it's that bad actually very harmful for cells. So that's how these pry UN's can actually cause a lot of cell death in the brain and lead to a variety of diseases. Now that's all I have for this lesson. I'll see you guys next time