BARBARA IMPERIALI: OK, I want to walk us
through a bit of an exercise to understand
what happens when people become resistant to an antibiotic.
What's the molecular basis for resistance?
It's nothing magical.
It's really things that you can understand
based on what you've learned during various parts
of the course.
But I just want to remind you about this dreadful schematic
here, which shows how rapidly resistance
emerges to different antibiotics by showing you the year
that the drugs are introduced and the year that resistances
develop.
One of the newest antibiotics to be introduced--
people thought, oh, it's a different mechanism of action.
It should be pretty resilient.
It should last for a while.
It should be useful with daptomycin.
It's a cyclic peptide antibiotic,
which has a particular structure that doesn't
look like a lot of the others.
And honestly, it was two to three years
before resistance emerged.
So what I want to do is think together
about what are the ways in which a bacterium could evolve
to develop resistance against an antibiotic?
So here we've got the target.
We know that the antibiotic is very
effective against the target.
What types of things could happen in the bacterium
to make it manage to just ignore the antibiotic
and resist the antibiotic?
Any suggestions?
So it's very simple.
There's a molecular target.
It could be topoisomerase.
It could be in fact the ribosome and the machinery
for synthesizing proteins.
It could be the machinery that cross-links peptidoglycan.
What sorts of approaches and what sorts of strategies
might evolve to make that antibiotic stop working?
OK, fire.
Yes.
AUDIENCE: When two hydrogen-holding enzymes
at-- create things that are not [INAUDIBLE] absorbing.
BARBARA IMPERIALI: OK, right.
So antibiotic gets in.
The enzyme breaks up the antibiotic, so evolution
to destroy the antibiotic.
And that's very much what happens with penicillin.
The key aspect of the structure that's so useful
suddenly becomes invalidated through a degradation
of the beta-lactam bond.
So that's one of them.
What's next?
Yeah.
AUDIENCE: [INAUDIBLE]
BARBARA IMPERIALI: Ah, so maybe there
could be uptake decreased, so that's quite hard,
but there could be some evolution of the cell wall
to make it less permeable to the antibiotic
because we're usually relying on antibiotics to diffuse
in passively.
So if the membrane--
this could be in a membrane of a Gram-negative bacterium,
or the outer membrane of a Gram-negative bacterium that
has a slightly different composition,
could physically change its structure.
These are tough things to evolve all at once,
but it's certainly a possibility.
We've talked about uptake.
What about-- what else could happen?
Yes.
AUDIENCE: When you get a [INAUDIBLE] out,
such that they have oxygen [INAUDIBLE]..
BARBARA IMPERIALI: OK.
So this guy could just--
we've got a circular antibiotic usually,
but this just changes--
the target just changes.
It can't bind anymore, through mutation,
so that the antibiotic simply doesn't bind.
It gets in, but it's changed, and that happens a lot.
It also happens a lot--
one can think of antibiotic resistance
very much along the same veins as one thinks of resistance
to chemotherapeutic agents.
You're targeting a kinase.
Your drug works great.
A year later, the cancer comes back
because there's a single mutation in your target.
This happens a lot with the EGF, kinase, RAS's and so on.
There's a dramatic change.
So this change would be a change in the target.
You mentioned two things, right?
I thought.
Maybe not.
AUDIENCE: Well, like I said, there
were some for that [INAUDIBLE].
BARBARA IMPERIALI: Ah.
On the surface.
AUDIENCE: A couple of days you're going back, so.
BARBARA IMPERIALI: OK, so there could be
some kind of import strategy.
So some antibiotics just diffuse.
Some go in through targeted import,
and that might change so that the antibiotic can't
get in anymore.
Other thoughts?
There's a couple of other sneaky ways.
I mean, you've got to sort of give these bacteria credit
for maximum sneakiness.
So if influx is an issue, what about efflux?
The biggest problem with antibiotics
against Gram-negatives is that they way upregulate
efflux pumps.
They just, like, cover their cells with pumps that just go,
you're going to give me an antibiotic?
I'm just going to lob it straight back out to you.
So the efflux pumps increase.
So their molecules, we have a lot of efflux pumps
to just kick out things that are not--
that we don't want in our cells.
The bacteria have similar things.
They will-- they're fairly promiscuous,
exporting pumps that will bind to things
that don't look like things that should be in a cell,
and literally bind to them on the inside of the membrane,
[MAKES SQUIRT SOUND] send them back
to the outside of the membrane.
So Gram-negative bacteria can massively
upregulate the production of a pump
that they already have, but they just make much more of them.
So in many cases, you can hardly test a new compound
because it's getting pumped out as fast as it gets pumped in.
What could be a strategy when this happens?
Because people are doing this.
You inhibit the pump.
So you make your antibiotic--
it works great, but you stop the pump working.
So you have to give two drugs, the drug that's
the antibiotic to the target and the drug that inhibits
the pump, and that happens.
Similarly, with this mechanism, where the antibiotic gets
destroyed, you can recover from this
by inhibiting the destroying enzyme,
and then your antibiotic doesn't get destroyed
when it gets into the cells.
So there's one extremely important formulation
of antibiotic that is used.
It's called Augmentin.
And what it is is a penicillin plus
a beta-lactamase inhibitor.
It's the drug that works plus a drug that
inhibits the enzyme that destroys the drug.
People get this all the time.
Every day of the week, this stuff is prescribed.
It's a two-compound cocktail that
has something to overcome the resistance so that your drug
still works in a cell.
All right?
And there's one more key mechanism,
and what bacteria will just do is they say, well, you know,
I'm getting dosed with this much antibiotic.
What's a good way around it is to massively upregulate
the biosynthesis of the target to a state where you just
can't saturate it all.
So upregulation of the target is a very, very common thing.
So you-- this should have just increased the number
of transcripts being made.
You increase the amount of target being made so
that, even if antibiotics are flooding into cells,
there's just not enough to inhibit all of the target
because it's been upregulated by 10 or 100-fold.
So what I think is cool about all these mechanisms
is they all make sense.
You just kind of have to think of them--
do I stop the drug getting in?
Do I stop it getting pumped out?
Do I stop it getting degraded?
Do I make more target?
All of those things are very viable,
and they are strategies that are used quite commonly.
So very commonly, both in bacteria and in viruses,
we seldom give one compound.
We commonly give multiple compounds
to sort of hit multiple targets, because if you
gave a two-drug cocktail to a bacterium,
but you knew there was going to be upregulation of a target,
you could hope that the other enzyme is still a target.
So you give cocktails of drugs, as opposed to single drugs.
And you're going to see that very relevantly when
we talk about the HIV virus because it's only
been that HIV has become--
HIV-AIDS has become a treatable condition
because of drug cocktails, not because of singular drugs that
inhibit one step.
And you'll see it very, very commonly there.
Any questions about this stuff?
OK.
So we're going to move on to viruses.
And so I will actually update the slides that are on the web
to give you this set of information
so you can see it in one place.
OK, viruses.
Viruses are fascinating organisms.
They don't have the right to be alive
because they don't have the machinery to be alive,
but they exploit the host's mechanisms
for completing their viability.
So viruses, more or less, I think
we like to think of them as living a borrowed life.
And they only survive if they have spent
some time inside a host cell.
So we will see with viruses, some viruses specifically
target humans.
Other viruses may spend some time in different organisms,
and then target humans, and be carried around
amongst different organisms.
But the key thing is that viruses can only
actually replicate once they're inside a host cell
because they basically exploit all of the host cell's
machinery to do that.
So viruses don't make many of their own enzymes.
They don't have their own amino acid supplies
or all the metabolic enzymes that
are required for life, all the replication, transcription,
translation machinery.
They just borrow the host's machinery,
but there are occasionally individual components
that the virus will bring along with it
to cover certain things that are not provided by the hosts.
But viral genomes are tiny.
They may comprise maybe eight genes.
Some of them are a lot-- are bigger,
but they are very, very small genomes.
They're very, what we call, parsimonious genomes,
so there's overlapping genes, so you can keep
the genome tiny by having--
compacting the size of the genome.
And then there are bigger viruses.
Some of the biggest viruses approach the sizes of bacteria,
like the mimiviruses, and they may
have been an intermediate step from virus
to more elaborated organisms.
And those viruses have a bit more machinery
within their contexts.
People-- obviously, there's no fossil record for viruses.
It's not like we can go, you know, go exploring
and find a fossil record.
But where these viruses are being found
is in the permafrost, so they're frozen.
They've been frozen there for centuries.
So people are finding really sort of scary things
in the Siberian permafrost because the viruses are
preserved there.
And some of these giant viruses are being
discovered in those locations.
And if that's not the subject for wonderful sci-fi books,
I don't know what is, because there are-- and I
tend to read those things because my favorite thing is
finding mistakes in them.
So there's a lot out there about those kinds of things.
So let me just show you a tiny bit about--
you know, this is that boring old "learn genetics" thing
right from the beginning, but what I want to take you back to
is sizes.
So we know all this stuff.
We've learned it to death, hemoglobin, antibodies,
and ribosome.
But what I really want to point out on this slide is that
the smallest viruses, like the rhinovirus--
that's the common cold--
or the hepatitis virus are not barely any bigger
than the ribosome.
So obviously, there's not much in the virus,
but all the components of the virus
have evolved to enable them to sneakily get into host cells,
exploit the host cell machinery, and then replicate
inside host cell, and then get out of the host cell
and ready to infect another host cell.
So I want you to really notice these sizes.
So the rhinovirus is similar to a ribosome,
but some viruses, which we will talk about,
the influenza virus and the HIV virus are a little bigger,
but none of them compete up to the size of a bacterium.
And just to get you into that mode, there are the bacteria,
and there's the mitochondria, and remember
endosymbiotic theory, bacteria, similar size to mitochondria,
and much, much bigger than any typical virus.
But giant viruses approach some of these bigger sizes.
They're a different ballgame altogether.
And we won't talk about them, apart from the fact
that they're really cool, and they're in the permafrost.
All right, so another impressive thing
about viruses, as they look-- some of them like this.
Phage, a bacterial virus, they look like things,
lunar landers, for example, or sort of other kinds of things.
Some of them are linear.
Some of them are different kinds of shapes.
A lot of viruses are icosahedra.
We'll talk about that in a moment.
But the fact sheet about viruses is first of all sizes.
And the typical viral size, if there is something typical,
expand from 20 to 400 nanometers in diameter.
So remember, the ribosome sits right
at this end with respect to size, but bacteria--
oh, yellow, I can't do a yellow lecture here--
remember, are 1 to 10 micrometers in length,
depending on what dimension you're measuring,
so considerably smaller, nanometer scale,
micrometer scale for bacteria.
So that's the first thing that it's important to know.
They're very small.
The next critical thing is what's in a virus?
What is its-- what's the blood and guts of a virus?
And it's either DNA or RNA, and it
can be single-stranded or double-stranded.
So it has its genetic material.
Its genetic material is usually dedicated
to making more copies of itself.
So if the virus has a coat, a coat of proteins,
the virus has to have a gene for that
because the host isn't going to have a coat for a virus.
So the virus has to have certain specialized things that
complete itself that can't be borrowed from the host cell.
And they can be--
let's see-- they can be what are called capsid viruses
or enveloped.
Capsid viruses just have a protein coat.
The enveloped viruses have a membrane surrounding them
with proteins stuck into them.
So the enveloped viruses have an outer membrane
which is studded with proteins.
But what is cool about the virus is
it never makes its own membranes.
It doesn't make its phospholipids.
It just, as it emerges from a host cell,
pinches a piece of the cell surface.
It steals the cellular membrane with it,
as it's emerging from a cell.
And you'll see this in a video, how cool that
is, all the proteins that-- all the components of the virus
cluster near the surface of a membrane,
and then you have this wonderful endocytosis
using the host membrane.
So the virus never has to make it own membrane.
And not all viruses are enveloped, just some of them,
and you'll see examples of each.
So the definition really is that they're
small, infectious agents, that they only
replicate inside living cells because they
have to exploit a lot of the machinery of living cells.
And they can infect humans, other animals.
There are plant viruses.
Bacteria have viruses.
So all living organisms have viruses that infect them.
But viruses are usually targeted very specifically to the cells
that they infect.
And, in fact, you will see with HIV,
it's not just a virus that infects a human host.
It infects specifically, and that
was why it was so terrifying, this-- actually T cells.
That's the one cell type in the host that it goes after.
So viruses very often target to particular organs
within their hosts, and that's why
we know some of the viruses.
And you'll see that the names of the viruses
are related to the organs that they may infect.
So I want to just briefly describe the terms.
We talk about these with all infectious diseases,
that they may be endemic, epidemic, and pandemic.
Endemic is the term that we use for, there's
a very low level of an infectious agent
in the population.
It's completely out of--
within control.
There's a few cases, but there's not
a transfer from person to person or animal to animal.
We would call that endemic, a very, very low level of virus
that doesn't cause any threat.
As soon as the virus or bacterial infectious agents
starts spreading amongst a local population,
we would call that a local epidemic, so
all of a community, all of a country,
so very much defined geographically
into a particular space where there's transmission of viruses
from person to person or animal to person within a community.
There has to be direct contact.
But now, with travel, many viruses
reach pandemic stages, which means worldwide.
So plane travel really caused enormous trouble
because you can have a virus in Africa or Asia.
Somebody gets on a plane and ends up somewhere else,
and the virus has been moved to a new country.
I made the terrible mistake of reading Hot Zone on a plane one
time, which is about Marburg virus, which
is where people basically just start bleeding out in the spot.
And I'm reading this book, and it's
describing the steps of someone who
had Marburg and was just sort of bleeding out next to them
on the plane.
And I'm like, are you crazy, reading this book on a plane?
Because they were describing how Marburg was just
moved from its country of origin to New York City,
or something like that.
So you remember when we had the Ebola concerns.
There was a real, genuine worry that Ebola
would jump through flight travel,
through people coming in at airports,
and end up with a pandemic of Ebola.
When there was a real problem with the avian flu in Asia,
Singapore, that's very, very protective of its territory,
had sensors that would-- you would go into Singapore,
and you'd go down these two huge escalators.
And they had sensors measuring people's temperature
at a distance as they came down the escalator, and hauling
people over, and sort of interrogating them,
where have you been?--
to see whether they would be allowed to enter Singapore,
because the flight travel, people getting on planes,
spreading a very contagious virus to a new country
is very, very realistic.
The issue with spreading to pandemic situations
is very, very important when one thinks of history,
because when the Europeans were conquering the Americas,
in particular South America and Central America,
they brought with them a lot of viruses.
But there was an innate sort of resistance
to-- because of years and years of exposure.
But these communities have never seen these viruses,
so millions of people died because they were suddenly
exposed to a human virus that they had never seen before,
through transmission from a country where there wasn't
such a problem with the virus.
So the indigenous peoples of the Americas, Australia,
and New Zealand had terrible consequences there.
Some of you have probably heard of the Spanish flu,
and that was towards the tail end of World War I
and is thought to have killed as many as 100 million people.
And that, in fact, is quite interesting.
It's called the Spanish flu, but there's some evidence
that it might have originated in the Americas,
in the boats that took troops over to Europe
to help at the tail end of the First World War.
And there's a really interesting book about that whole story,
that the Spanish flu may not have originated in Spain.
And that's a-- it's definitely a worthwhile read.
So that tells you a lot about the statistics of viruses.
I just want to highlight here, we talk about HIV
as a very serious virus.
It emerged in the early '80s to this current--
well, in 2011, there were 35 million people infected.
There's about 2 and 1/2 million new cases a year.
But what's fascinating about HIV--
there was a stage before the really good antivirals
were available that, if the mother had HIV,
the baby would get HIV.
But now, if there's treatment of the mother,
and the baby is delivered, often by a Caesarean section,
the baby can escape being infected
with the virus due to the new antivirals.
So that's really important, that the--
originally, there were a lot of cases of newborns who
simply got HIV during birth.
But now that can be-- there's escape from that,
which is really, really cool.
The viral load can be brought really low
with the common antivirals against HIV,
and that next generation doesn't have that sentence.
So I mentioned to you that a lot of viruses
are basically named after the organs that they hit.
So I've just got a human being here
with a lot of different viruses that hit different places,
and I just want to point out a few points.
Viruses may be targets nowadays of childhood vaccinations,
and many of you--
I hope all of you--
have had vaccinations to many of these common viruses.
There is a concern now with communities that are deciding
not to vaccinate children.
That's a huge social problem that may, initially, sort of,
people can get away with it because there's
community vaccination.
You're in a community where a lot of people
have a resistance or some sort of immunity to a virus.
But as communities become less and less vaccinated,
than later generations will start
to get the disease seriously.
And that's actually happening in parts of the world where
there's--
there used to be no polio, and now there's
polio emerging because the community immunity has
been-- is fading away.
So we hope that people get vaccinated.
That's for sure.
The vaccinations work.
Several vaccinations-- several viruses
were pretty much eradicated.
Smallpox and polio were two of the real poster examples
of childhood vaccinations that worked
and worked amazingly well.
But now, there's a problem with failure
to vaccinate in certain parts of the world.
So that's a concern.
And then, another interesting thing is that some viruses--
whoops, oops, go back.
Sorry.
Go back, back, back, back.
Don't now-- that's all a secret.
You can't see that just yet.
Some viruses lead to cancer, so human papilloma virus,
where there is a vaccine, the people who have HIV--
some of the types of hepatitis and Epstein-Barr
are all associated with later cases of cancer.
That's important to know.
So often cancers are named by the organ that they attach,
so even though the three--
the five hepatitises all attack the liver, they're not related.
They're just five viruses that go off to the liver.
So if you've had a vaccination against Hep A,
It doesn't protect you from Hep B or C by a relationship.
They're very, very different, so you have
to have different vaccinations.
So this just gives you a nice view of human viruses,
what their names are, what organs they may attack,
what sorts of things they might be associated with.
But the trouble is, this nomenclature doesn't get you
anywhere towards understanding the mechanism of a virus.
So what we will focus on is a much better system
for describing viruses that's based
on whether they have DNA or RNA within the genomes
that they import into host cells,
and whether that DNA or RNA is single-stranded or
double-stranded, because that truly tells us
a lot more about the virus and maybe the steps that
could be inhibited to prevent the viral infections.
But first of all, just a few pictures--
here's some-- so viruses can be rod-shaped.
They can look like--
they can be icosahedra.
They can just have a capsid.
So I mentioned they may just have a protein
coat, the sets of repeating proteins that
pack into a beautiful structure, very commonly an icosahedron,
and I'll show you why that is.
Or they may be enveloped viruses,
like, influenza has a membranous surface around where
the DNA is packaged.
All of these have nucleic acids packaged within them,
DNA or RNA, single or double-stranded.
And in the case of the enveloped viruses,
that membrane-- it's a normal membrane.
It's just like your membrane.
In fact, it is your membrane--
will have proteins dotted within it
that's actually-- serve as recognition to the host cells.
They'll grab onto host cells and be the source of the infection
into the host cells.
And this is a bacterial virus, and as I said,
I just love the way they--
I mean, they really look like this.
You know, the cartoon is really the cartoon
of what the thing looks like, and they're sort of
pretty amazing.
And they kind of--
they keep their nucleic acid in the head here.
They land on their sort of feet, and they shoot the nucleic acid
material into the host cells.
So that's very interesting.
Of course, this thing is--
OK.
So why are many viruses that are capsid viruses icosahedra?
So it ends up being a problem of geometry.
So how can you make a perfect coat around something
with very, very few building blocks of different types?
Like, if every building block in that coat was different,
the virus would have to have genes for all of them.
What viruses can do is they can have
genes for, like, three pieces of a module of the virus.
So I'm going to show you how these capsid viruses get
assembled.
So here, color-coded, is an icosahedral virus,
where I've coded in the red, green, and blue,
a triangular component-- this is really cool--
that is a single sort of panel on that icosahedral virus that
comes together as a triangle through
noncovalent interactions between three proteins.
You see that panel there.
What you can then do is see how that panel would
fit into a pentagon with an extra triangle stuck onto it,
and you can fit that triangle into the pentagon
and also into the additional piece.
And then you can start to visualize
how you could build an icosahedron from those pieces
because they represent each of those faces within the virus.
So you can go from this, which is a set of building blocks
that I just showed you--
then you can assemble them like this.
And one of these would be this part of the icosahedron,
and then you just have a bunch of copies of it.
And you can see how you would assemble that.
And years ago, I decided to decorate my Christmas tree
with icosahedra.
So I went through this geometrical thing,
and believe me, it works really nicely.
You can put together an icosahedron
and build an icosahedron.
You could spray it gold and put it on your Christmas tree.
It's kind of fanatical, but it really-- it's
highly recommended.
All right, so let's now get down to something a little bit more
serious than Christmas trees and things.
All right, so I told you that the classification of viruses
by what organ they attack or who discovered them or anything
is just--
is a vagary that's not so useful to the non-physicians
because you can't immediately know,
oh, this is how the virus gets into the host cell.
This is how the virus uses its genetic material
to make new viruses.
So what was developed by Baltimore--
David Baltimore used to be at--
it was kind of interesting.
David Baltimore, a very famous person and Nobel laureate,
used to be at MIT when I was at Caltech,
and we moved in opposite directions.
I'm not sure it was a great trade for MIT,
but it was a great trade for Caltech.
So I ended up with David Baltimore's labs in Building 68
because we did that swap in 1999 or something like that.
So I thought that was pretty interesting.
Anyway, so what Baltimore decided
is-- was much better to classify viruses
by the type of genetic material, like, are they DNA or RNA?
Is that DNA or RNA single-stranded or
double-stranded?
Because, depending on what the genetic material in the virus
is, once that gets unloaded into a host cell,
certain steps have to happen in order for the virus
to be able to replicate that genetic material,
to convert it ultimately into the proteins
it needs, and then to package up new viral genetic material
into viral capsids so that they can then
be sprung out of the cell and go infect another cell.
So the classification basically went this way.
So if you think of it, what the major goal in the infected cell
is to get the virus to a stage where the virus has
plus-messenger RNA.
It has RNA that can be read by the host's ribosomes
and convert it into proteins.
So the overall goal of the virus,
if we give it sort of some conscience, shall we say,
is to make its viral material into messenger RNA.
Now, the virus doesn't include messenger RNA.
That's just what is made transiently,
but the virus may have single-stranded DNA.
It may have plus-sense RNA.
It may have negative-sense RNA.
It could have double-stranded DNA,
or it could even have double-stranded RNA.
And depending on what that genetic material,
is what the Baltimore classification of a virus
would be.
So depending on what's inside the virus,
then they can be classified.
And what we're going to go through today and on Friday
is examples of class I, class V, and class VI viruses,
so we can see how that genetic material ultimately
becomes a new viral--
a new virus within a host cell, or at least the components
thereof ready to be sprung out of a virus.
And there's one important point that I want to also address--
oops-- budding or lytic.
All right, there are two ways in which
viruses escape their host cell.
They may be budding.
So here you have a host cell.
The viral components all congregate
near the surface of the membrane from the inside,
and then the host cell buds off.
The viral components go with it, and the bud splits off.
So the host cell has its nucleus.
It's still intact.
HIV is such a virus.
HIV doesn't kill its hosts.
That's the best sign of a parasite.
It wants the host to stick around, so it just buds off.
The other types of viruses are lytic,
and, basically, the cell just bursts open and throws out
the virus.
So they're in two categories.
Some of them are budding, though the enveloped viruses
have to be budding because they're
going to take with them the membrane of the host cell.
All right?
So that's another important difference.
So what have we got here?
So ultimately, the goal is to be able to make a plus-strand mRNA
for protein synthesis.
So we really need to have the appropriate sense of the RNA
that will dictate the protein synthesis.
So let's first of all look at one of the simple versions,
a double-stranded DNA virus.
And this is represented by the smallpox virus.
So everybody's heard of that, and herpes simplex.
And these are both enveloped viruses,
so that means they have a membrane shell.
And so I'm just going to walk you
through the steps of going from the double-stranded DNA
to make a new virus.
So here's the virus.
It has a capsid, as well as a membrane envelope.
And there's recognition between the virus and the host cell.
And we'll talk very specifically about what that recognition is
when we talk about HIV, because that's very well categorized.
Once the virus gets into the host cell,
it sort of spills off all the coat and dumps
out its double-stranded DNA, the viral DNA, into the host cell.
And then that DNA can--
in the nucleus, can replicate into more copies
of the viral DNA, or it can be transcribed
into messenger RNA, which is then
the coat for all those capsid proteins that the virus needs.
And then these start to self-assemble within the host
cell where the capsid proteins wrap around
the viral genetic material.
They accumulate near the surface of the cell,
and then they bud off from the cell.
So that's how you go from simple DNA.
So these processes are completely
based on the human enzymes that do those processes.
Replication, we've got to replicate DNA.
We're going to have to do that in the nucleus.
Transcription, we're going to have
to ship out part of the DNA from the nucleus to the cytoplasm
and make--
we're going to have to make a copy of the messenger RNA
and ship it out to the nucleus.
And then we're going to use the host ribosomes, the host's
amino acids, the building blocks in everything,
to make a new protein that is not a host's cell protein.
It's the capsid protein.
Obviously, the human cell isn't going
to be making a capsid protein.
So that's the main thing that the virus had to encode.
It had to have the DNA to make that.
So that all looks sort of fairly simple,
and the steps make sense.
This is why we cover this virus first because it really--
it's kind of the most transparent to understand,
so this transient stage of sort of borrowing machinery.
And as I mentioned here, the virus
can spring out of the host cell.
Yes.
AUDIENCE: So all it means is-- one's that don't kill the host
cells, how do they, like, on the body, or the cells that they--
BARBARA IMPERIALI: They start to just be too much of a burden
onto the body, so they're just--
you know, if they're inside cells and exploiting
the resources of the cell, they're basically--
they're harming it, but they're not destroying it instantly
every life cycle.
They're just using resources to replicate, and then go--
get spread to another cell, and another cell,
where they'll keep using resources.
So it's really just an overload of the system.
It's a very good point.
But they can stick around a long time,
and with HIV, you're going to see
what really sneaky thing they do is
because they put their genome into the host genome.
And that's sort of really pretty terrifying.
I always ask this question, but it's kind of a silly one.
You know, what is life?
A virus is alive.
Well, they're kind of alive, but they're not really alive
unless they have some place to live.
But aren't we all like that?
So that's very philosophical.
So we'll move right on here.
So when you think of a virus, this
is the original central dogma, all
the moving parts of the central dogma.
And note-- so that when you think of a virus,
what double-- what does double-stranded DNA need
from the host?
It's got all of these things.
It's got the-- the host has the polymerase.
It has the DNA-dependent RNA polymerase.
It's got all the ribosomal machinery.
So the only thing that the virus needs
is the gene for its capsid proteins.
So you can peel out from that entire life cycle
the one unique thing about the virus.
So that's a double-stranded DNA.
Let's now move to a different type of V,
which is a negative-stranded RNA virus.
And these are quite important because these
form the basis for--
let me just go to the diseases.
This is the influenza virus, and I'm
going to mention some very important points
relative to influenza virus.
So influenza virus is what's known as a segmented virus.
And what that means is that its genome--
in this case, it's negative-stranded RNA--
is in pieces.
A lot of other viruses just have a single strand of genome,
a single nucleic acid strand.
So it's just one piece, where portions of that nucleic acid
code for different proteins, and they'll often
code for initially polyproteins that get broken up.
And we'll see a virus with a single strand
when we look at HIV.
But the influenza virus has a segmented genome.
And that's very relevant for its lifestyle
because we'll see in a moment how influenza virus can cause
more damage than we anticipate because of recombination
of different copies of the segmented virus
through differences.
But let's first of all take a look
at the life cycle of this virus, and then we'll
move on to dealing with the issue of the segmentation.
So here's a typical enveloped virus with a capsid.
Inside, there's the negative-stranded RNA that gets
into the host cell, and you make--
and you dump into the host cell the viral genomic RNA.
That can get copied.
The minus-strand RNA gets copied to the plus-strand RNA,
which becomes the messenger for protein synthesis in the cell.
So you've gone in with minus strand.
You've made the plus strand, which is the messenger,
and that encodes all the proteins that
are needed for a new virus.
And some of those proteins may have signal sequences.
They may be shipped to the surface of the cell,
and they may be planted in the outside cellular membrane
of the host cells.
And what you see here is copies of those proteins
actually in the surface of a cell.
So what happens with this virus is, once all the moving
parts are made, they congregate at the surface of a cell,
get packaged, and then bud off from the cell.
So remember all the rules you learned about where proteins
end up in the cell are all good still here
because the capsid proteins have to get to a cell membrane,
so they're translated with a signal sequence.
They congregate-- I don't know how this self-assembly occurs,
but it's a fascinating process, so that ultimately you
bud off an intact virion from the host cell.
But the key thing that the virus has to have
is something that will copy negative-stranded RNA
to plus-stranded RNA, which is going to be the messenger.
So the virus also has to code for a particular protein that's
unique to its lifestyle.
So it has an RA-dependent RNA polymerase.
We don't use an RNA-dependent RNA polymerase,
but the virus needs it to take its negative-strand RNA
to a plus-strand RNA, which will be the messenger.
So does that make sense?
So obviously, that's a moving part
that it needs to provide to the host.
Now, what's this about segmented viruses that's quite important?
Oh, and I just want to underscore here,
what defines the destination of these proteins,
whether they're capsid proteins or proteins that
are going to be packaged within the virus,
is basically just the same rules that
apply that we talked about when we talked
about protein trafficking.
So every year, there's a whole panic.
Did you get your flu shot?
Is it going to work this year?
Oh my god, millions of people are going to get sick.
Go get your flu shot.
It's tetravalent, it's trivalent, and so on.
So what we're trying to do every year
is predict what the virus is going to look like.
So we have to--
there are teams of people, who sometimes get it wrong,
who predict the variation in these genes.
And they look at winter in the Southern Hemisphere,
because that precedes us, and try
to guess what's going to happen in winter in the Northern
Hemisphere.
And we get to try and put together a vaccination package.
But the problem with the viral influenza virus
is that there can be not just a drift, like mutations,
small mutations happening a little bit at a time,
but there can be recombination of the genes,
because they are segmented, into totally new virus particles
that have different properties.
So viruses don't just drift in their genomic sequence.
They can have dramatic shifts in their sequences that occur--
whoops-- through combinations of viruses that come-- that
have infected different animals.
So some of the common strains, when
we talk about certain strains that have been very, very
troublesome to humans, may result from such a combination.
So this would be the Eurasian pig flu, the classic pig flu,
the human flu, the bird flu.
If, in certain communities where people often
live with their livestock, a cell
gets infected with viruses, a human virus
and the swine virus, they can mix and match together.
And you can make a totally different viral composition,
where you've got one piece of genetic information
from the swine flu and seven more from the human flu.
And what that can suddenly mean is
that the-- first of all, the vaccines don't work at all,
but that they may have very, very different properties
for infectivity.
The protein that is expressed that may cause
that very first attack of the virus on your cells
in the upper lungs may be very different to the type--
to the protein that comes from the swine flu
and may give you much more serious lung infections
because they can go deeper into the lungs.
So it can be very small changes by pulling
an enzyme, a piece of gene, from a completely different organism
and matching it up with the rest of the genes
from the human virus that makes for dramatic shifts
in viral infections that cause these sorts
of sudden tectonic shifts where we've really
got to deal with a virus.
There are two terms up here.
There's H and N. These are hemagglutinin and
neuraminidase.
They are two proteins that are in the viral coat,
so you'll often hear viruses referred to as H1N1, H3N3,
and it's just the variant of those proteins that
are in the viruses.
See these little terms here--
that's what that means, what type of hemagglutinin,
what type of neuraminidase, is on the surface of the virus.
So I am done for today, and next class
will be exclusively about the AIDS-HIV virus, where we'll
go into that life cycle and also talk
about resistance to therapeutic agents and combination
therapies.