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MCAT
Course: MCAT > Unit 6
Lesson 7: Viruses- Virus structure and reproductive cycle questions
- Mini MCAT passage: Molecular targets of antiretroviral therapies
- Mini MCAT passage: Gene therapy using retroviruses
- Are viruses dead or alive?
- Virus structure and classification
- Viral replication: lytic vs lysogenic
- Retroviruses
- Subviral particles: viroids and prions
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Retroviruses
Retroviruses, like HIV, have a unique replication process combining lytic and lysogenic elements. They enter cells through direct fusion and use reverse transcriptase to create complementary DNA (cDNA) from their RNA. Integrase integrates viral DNA into the host genome, forming a provirus. Viral mRNA is produced, translated into proteins, and assembled into new viruses that bud off with an envelope. Protease matures the viruses before they infect other cells.
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- the two cDNAs made by reverse transcriptase are not complimentary to each other, they are both complimentary to the viral RNA so how do they combine with each other?
Shouldn't reverse transcriptase use the newly made cDNA as a template to make the second strand of DNA that is complimentary to the first?(30 votes)- I think the description in the video may be incorrect.
Using the viral RNA as a template, reverse transcriptase creates a DNA-RNA complex. Another enzyme unzips this complex to create a single strand of cDNA. That piece of cDNA is then acted on by reverse transcriptase again to create the cDNA's complementary strand. This yields double stranded DNA. I think the video is wrong in saying that reverse transcriptase uses the same viral RNA to create two separate cDNA strands. Otherwise--like you said--the cDNA strands created would be identical and not complementary.(51 votes)
- I know it might seem like I'm splitting hairs but at, when the video refers to viral integration into the host (human) genome, isn't the representation of circular DNA now inaccurate? 4:15(12 votes)
- Doesn't seem like splitting hairs to me; this is a pretty blatant mistake(17 votes)
- Atshe draws reverse transcriptase binding to the 5' end of the viral RNA, but shouldn't it bind to the 3' end of the RNA if it is to synthesize the complementary DNA in the 5' to 3' direction? 1:52(14 votes)
- This seemed wrong to me as well, and when I checked other sources they all agree that reverse transcriptase binds to the 3' end of RNA instead of the 5' end as shown in the video. cDNA is synthesized 5' to 3' just as in normal transcription. This is a good image: https://www.thermofisher.com/content/dam/LifeTech/global/life-sciences/Cloning/Images/0816/reverse_transcription_process.png(7 votes)
- What does protease do? Why is the virus considered immature until the protease cleaves them? What does it cleave? Why does it need to cleave it before the protein is functional?(13 votes)
- Remember, DNA -> RNA -> Proteins. When mRNA is translated, polypeptide proteins are formed. And the role of proteases are to split the polypeptides chain at specific points (cleave) to make sure that the proteins it wants are made.
By cutting other proteins off of the polypeptide chain, the proteases basically shape the new proteins (think primary structure) and this is called maturation of the proteins.(1 vote)
- At, she mentions that the protease "cleaves the other proteins to make sure that they're fully functional." How does cleaving proteins make them functional? And is this the step that makes the virus "mature"? 7:03(6 votes)
- Viral RNA is translated into a single long chain that includes reverse transcriptase, integrase, and protease which can't function because they're in a long chain. Protease cuts them from the chain into their individual enzyme components so they can be used to produce new viruses.(7 votes)
- How come the host cell is unable to detect the presence of viral RNA?(7 votes)
- Would the retrovirus be a + sense or a - sense strand or that would not apply here?(4 votes)
- HIV is classified as a single-stranded positive-sense enveloped RNA virus
https://en.wikipedia.org/wiki/HIV
but I don't know if this applies to all retroviruses(1 vote)
- This video should be redone as there are numerous errors. HIV does not enter host cells through direct fusion; it's through attachment of 2 receptors; CCR5 & CD4. The capsid does NOT open; if it did, ribosomes would transcribe the +RNA right there. Rather, the capsid shields the +RNA strands from those ribosomes. While inside the capsid, in the cytosol, reverse transcriptase creates the DNA strands (RNAse H chews up the original RNA template strand as first DNA strand is made); the DNA goes into the nucleus, integrates and becomes a provirus. The DNA gets transcribed to form mRNAs which give rise to all the proteins needed to make viral particles. There are numerous mistakes in this video and even address a few. Dismissal of subbing a prokaryotic cell for eukaryotic as simply not being "super accurate" is bad form (). Numerous mistakes, using a prokaryotic cell with circular genome, etc, etc.; dismissal of the details, important details, is a disservice to your students. Can you please remake this video? 3:48
Also, all viruses can be categorized by the Baltimore Classification (ref: David Baltimore, Nobel laureate for his discovery of retroviruses)(4 votes) - i didnt understand the function of integrase (regarding 3' ends n sticky ends) and protease.... please explain.(2 votes)
- Please have another teacher remake the video. She is in sharp contrast to many of the other teachers in KA. She seems rough, unfriendly more like a machine instead of a person who wants to teach(2 votes)
Video transcript
- 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 enveloped, single-stranded RNA virus. And inside of this envelope it also carries three special proteins. And right now just be aware that they are three special proteins. I'll talk about them more when we get to each step
where they're important. So as you know, enveloped 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 nucleocapsid
is inside the cell, it actually has to undergo
a step called uncoating where this purple capsid is dissolved. Oh, and we forgot about the protein, so let me redraw those in right now. So these are the proteins that were originally inside of the 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, and it reverse 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. But 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 this 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 strand's three
prime end is over here. And while the first one is
actually clearly labeled as this is the three 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 host's DNA. And one thing I would 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 the viral DNA integrate with the host, like its name, integrase, 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'd 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 host's DNA is transcribed. So since the host's 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 exists 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 of the parts that can self-assemble into new viruses. So again, all of these
viruses that are formed will have the RNA, 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 want in here and
this will want to enter here. Oops, and that's missing a border, I just realized, so there you go. And they will bud 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.