Viruses - Online Tutor, Practice Problems & Exam Prep

Virus Structure

Hi. In this video, we're going to talk about viruses, which are much smaller than your average cell. In fact, viruses are significantly smaller than even the smallest bacteria, and this is because viruses lack many 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 vessels for genetic material. And the protective coating over that genetic material is called the capsid. This is really just a protein coat that covers the viral genome and is made up of little subunits we call capsomeres. So, you can see in this image right here we have this virus, and it has a capsid. This blue structure is made of all these little balls you see here. Each one of these little blue balls is a capsomere.

Now, viruses, as I've said, are 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've 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. There is such a wide range of viruses and what they're all capable of that we're really just going to talk about generalities here. However, we are going to focus in on a particular class of virus called bacteriophages because these have been very heavily studied, and we have a lot of good information. Sometimes just called phages for short is that they're viruses that infect bacteria, and they actually have some pretty complex capsids. So, this right here is a bacteriophage, and you can see that compared to its neighbor, this bacteria or this virus's capsid structure is much more intricate-looking. In fact, that's because this capsid has to carry out a pretty specialized function that we'll get to a little later in the 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 are 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 membranous 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's membrane to form a viral envelope around itself. Now, in addition to these viral envelopes, viruses have important structures on their surfaces that you can see labeled here. We have these glycoproteins, and these in addition to some other structures that I'm not going to mention define the virus's 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 glycoproteins or other various protein structures on the surface of the virus will actually determine its host range. Alright.

Now let's flip the page.

Virus Replication

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 bacteriophage 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 bacteriophage have a more complex capsid than other viruses because that capsid actually has to function almost like a syringe injecting the genome which we see in green right here. Let me actually change my pen color so it's easier to see. Right there. So that viral genome gets injected into the host bacteria.

And this happens because of the surface of the bacteria cell inserts 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 endocytosis. Others actually fuse their membranes. Remember those structures we were just talking about? They fuse their membranes with the host's 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 are 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 their knowledge, provide nucleotides, enzymes, ribosomes, tRNA, amino acids, and even ATP to the virus so that the virus can replicate its genome and create new viruses and other viral products. Now, through this replicative process, the most important products to be produced are nucleic acids, right? The virus needs to replicate its viral genome and also capsomeres. The virus needs to build the components necessary to build a capsid to house the replicated viral genome so that it can create more viruses. Right? Its main goal, more or less, is to produce more of itself.

In this process, the virus actually doesn't have to go through the trouble of assembly. What's pretty amazing is in producing the viral genome and these capsomeres, 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 phospholipids arrange themselves into the proper orientation so that we produce the lipid bilayer. Now much like that, viruses also spontaneously assemble when the proper components are produced.

Lytic and Lysogenic Cycles

Bacteriophage can actually use two different types of cycles to replicate themselves and here, we're going to talk about both. Now, the first one we're going to talk about is the lytic cycle and this is phage replication that ultimately results in the death of the host. Lytic, 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 will basically fill up the cell to the point of bursting and it's going to lyse, burst open with all those viruses, releasing them to the environment so that they can infect other cells. So, the lytic cycle, scroll down a little bit, actually begins with the injection of the viral genome as you see right here. So I'll just label this number 1. Now, the bacteriophage 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 bacterial. I'm just going to abbreviate that back. So that's the bacterial portion that was originally in the cell. That's the bacteria's genes. And the virus is actually going to cause its own genes to be replicated and it's actually going to degrade the host genome so that only its genes are being produced. And you can see that happening over here in this third image in the sequence. Now, from its genome, it's going to lead to the production of capsomeres, right? Those components necessary to build new viruses. So here we can see some capsomeres being produced. And eventually, all the components will be produced like we see here in image number 5. And from there, they will spontaneously assemble into phages and those phages will lyse from the cell like we see here in image number 6. That is the basic. Those are the basics of the lytic cycle. A couple of things to note: a virulent phage is a phage that replicates by the lytic cycle only. Now, there are many phages which can enter either cycle and can actually switch between them, but there are some that only use the lytic cycle and we call those virulent phages. Now it's also worth noting that over years, bacteria actually have defensive mechanisms against these bacteriophages. 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 lysogenic cycle, and this involves replication of the viral genome without actually killing the host cell. As a result, we refer to phages that are capable of replicating through both lytic and lysogenic cycles as temperate phages, right? They're more tempered. They have a 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 phages are more even tempered. Now, how does the lysogenic cycle actually go down? Well, again, first, the phage inserts its DNA into the host just like we saw before. So this is still our first image of the lysogenic cycle and again, 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 it's getting a free ride. And of course, the bacteria will replicate its genome and eventually divide in a process that we know as binary fission which we can see right here. We have 2 daughter bacterial cells. Now, each has that viral genome incorporated into its own genome. Eventually, what will happen is, at some point, the virus will say, well, not going to lay dormant forever and it will divide into 2 like we see here. And from there, it will follow the lytic cycle that we traced before. A couple of points of terminology, prophage: a prophage is when the viral DNA has been integrated into the bacterial chromosome. And you can kind of think of this as the term prophage kind of being like prephage, right? That prefix pro means before kind of. So this is like a protophage in a sense. It's the precursor to the actual phage. So these two cycles can feed into each other. As we saw, the lysogenic cycle will feed into the lytic cycle at some point. However, the lysogenic cycle can repeat itself many times so that, from one single infected bacterium, there could be hundreds of bacteria with prophage inside laying dormant, waiting to enter the lytic cycle, replicate all the necessary capsomeres, self-assemble a bunch of new bacteriophages and lyse the cell to infect more host cells. Alright, let's turn the page.

Animal Viruses and Retroviruses

Animal viruses behave differently than those bacteriophages 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 membranous, accessory structures that are often derived from the host cell's own membrane. They also tend to have RNA genomes unlike those bacteriophages that had DNA genomes. Now, animal virus replication involves entry into the cell just like we saw with bacteriophages 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 a variety of specific ways that this can happen but think of endocytosis. Think about those endocytotic processes we took a look at, way back in cell signaling. And what happens there is you have little molecules, ligands, bind 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 are going to bind to receptors on the host cell and it's going to cause the host cell to take the virus inside. Right? These viruses are very tricky. They trick the host cells. 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 mRNAs will be synthesized by a special viral RNA polymerase. Retroviruses are a special type of animal viruses. And these are viruses with RNA genomes that actually instead of just putting that RNA out there to make copies of mRNA 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 what 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 transcribe 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, because of the discovery of reverse transcriptases, we've actually been able to advance a lot of fields of biotechnology. These are very helpful enzymes. And much like we were talking about the prophages, which are those viral genomes inserted into the bacterial genome. Right? Those precursor phages more or less. Well, when a retrovirus has inserted its viral genome into the host cell's genome through that reverse transcription process, we call that a provirus. So provirus, very similar to prophage except to become a provirus, you have to have this special reverse transcriptase enzyme. So in a way, proviruses are kind of a little fancier than prophages. 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 bilayer 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 a viral envelope and it will go infect a new cell.

Alright. Let's turn the page.

Viral Genetics

Hello everyone. In this lesson, we are 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 an RNA virus. Meaning that they can have a DNA genome or an RNA 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 the S phase. Double stranded DNA viruses often integrate themselves into our genome, so that anytime 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 RNA viruses. 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 cytosol, and because they are double stranded RNA viruses, they can serve 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 RNA 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 a 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 RNA viruses. Now, we're going to talk about single stranded RNA viruses, which are going to be the most common type of virus that you will ever hear of. Now, if you guys wanted some examples of Double or if you wanted some examples of DNA viruses, Smallpox is a DNA virus, herpes is a DNA virus, and chickenpox, I also believe, is a DNA virus. Most viruses we're familiar with are going to be RNA viruses and most of those are 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 2 forms, but I wanna 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 already learned about whenever we learned about DNA expression. So, this is the process of transcription and this mRNA in blue is being made by the RNA Polymerase actually reading the genetic code, the DNA, and building an mRNA strand off of this genetic code. So this is the DNA, and then we have our RNA polymerase. Now, whenever we talked about creating mRNA, 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 3 different names. Remember, the coding strand is going to have the same exact code as the mRNA. So the coding strand equals the code of the mRNA. 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 antisense 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 antisense strand and the minus strand. And the template strand is going to be complementary to the mRNA. So, the template strand is complementary to the mRNA. And that is because the template strand is utilized to build the mRNA. So they're going to be complementary to each other while the coding strand and the mRNA are going to be exactly the same code. Now remem

Viroids and Prions

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 viroids. 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 viroid, and you can see it starts with this c base pair right here labeled 1. 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 are 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 tiny stretch of RNA. And yet, this is a pathogen. It infects viroids infect mostly plants, and they tend to disrupt plant growth. So, plants infected with viroids tend to be short or stubby or malformed because their growth is somehow disrupted. Now, viroids do not actually encode proteins like viruses. They simply replicate themselves using the host's enzymes, and this self-replication ultimately leads to problems for the host and propagation of the viroids. So kind of a similar idea to viruses there.

Now, there are actually other tiny infectious agents called prions. Now these are bigger than viroids. They're actually proteins, and these instead of affecting plants, tend to affect animals, specifically, 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. You 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 the green folded protein to end up being misfolded as we see there. And this leads to an accumulation of these misfolded proteins and protein gunk buildup in nerve cells, which is actually very toxic and harmful to the nerve cells. It causes nerve cell death. In fact, protein-like garbage protein buildup 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, but it is actually very harmful to cells. So that's how these prions 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.