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00:01 OK, folks. Um Welcome. As I expected several started spring break

00:10 . So don't blame me. Um remember, don't come to school next

00:17 . Uh There's no classes. So um do do uh don't make it

00:25 work next week, do take do, do something fun next

00:29 whatever that may be. Um So that point, uh that's kind of

00:35 the nine weeks. So basically get another six weeks once we come back

00:41 the end of the semester. um so we'll continue on with chapter

00:47 , which is the end of the two stuff, which will finish up

00:52 we come back and then uh the week on the 25th starting the third

01:00 . And so um the uh so exams at the end of the

01:05 So remember that, that scheduler opens Thursday, the 14th. OK.

01:12 And you remember the, the new for that? Uh So anyway,

01:18 uh the quiz, so this is one canvas quiz that uh you have

01:24 uh 10 days, 10 days to . It's not due until the Monday

01:29 the week we come back. And um smart work as well. Not

01:34 due until 18th. So lots of for those. So, uh what

01:40 ? So what we're gonna do today finish up viruses in terms of like

01:48 the structure and um make up, up a virus and then get into

01:53 cycles. Um We start with kind start with simple life cycles which involve

01:59 bacterial viruses. And then when we back, we'll, we'll get into

02:04 animal virus life cycles uh which are little bit more complicated only because they

02:12 in a more complicated host cell host , right? Ear cells a little

02:17 complicated than a bacterial cell. and as a result, the virus

02:22 is a little, a little more by comparison. But uh we'll go

02:27 all that. Uh So let's just look at um uh recap.

02:35 So he went through definition of a , how to describe them a little

02:40 about um a little bit about structure not completely. And so remember that

02:47 number one thing is they're not OK. So I remember they do

02:51 some cell properties, right? Like they can um evolve, they can

03:00 um they do uh replicate but they only inside of a cell,

03:05 Not, not outside of the They um they rely on the host

03:11 most things. OK? But not we'll talk about a little bit about

03:15 . Here in a second. So because we need a host, we

03:19 them uh parasites. OK. Uh obligate because they are required to do

03:28 . That's the only way they can . They're tied to that host

03:33 OK. And of course, they their activities inside the cell, hence

03:38 . OK. So the most, viruses had the most basic structure of

03:44 protein covering what they call a Uh And the genome inside RN A

03:52 , single or double stranded. That all viruses have that.

03:57 We'll see that you can build on and have variations and additional things and

04:02 forth. OK. Um Also know we're also gonna talk about thyroids and

04:11 in a little bit. Those are viruses. OK? So think of

04:16 is, that's why there's kind of categories here, the viruses, virus

04:20 prions because these, these differ, don't have that this kind of a

04:26 . OK. Uh They're simpler, fact. OK. Um And so

04:32 in terms of, you know, um uh other like uh like

04:37 cells can have different sizes and so . So can viruses, they can

04:40 different uh shapes and uh lengths, and so forth. But they're mostly

04:47 the nanometer scales, right? So than one micron, uh we'll see

04:53 variations on that. But for the part, that's where they reside.

04:58 um the uh all right, are , so, and then we looked

05:10 a little bit of a basic life . So remember the part that all

05:15 do, it's gonna be this, ? This part will vary,

05:26 Not all viruses can integrate into a chromosome, but they'll all, you

05:32 . And so it really begins or here with recognizing the host, then

05:37 is inside the cell gets copied, , translated to make viruses, viruses

05:42 . So that's, that's common to kind of virus. OK.

05:46 there's gonna be variations in how this and, and done in different

05:52 Um What they need from the hosts vary. Some come with their own

05:57 , some do not, but they will need uh ribosomes, Trnas and

06:03 to do protein symptoms. They don't that with them. OK. Uh

06:07 of course, these other things. uh so again, remember they don't

06:11 a metabolism, you can't say here's glucose, start respiring, they

06:15 do that. OK. So, uh using the host for these

06:20 OK. So remember though, always in mind that while doing this,

06:26 ? The the effects on the host , right? Because the host cell

06:32 getting its resources used to support this while it's replicating. So that means

06:39 host cell suffers in terms of how it can grow and these kinds of

06:44 . OK. We'll see that the especially with animal viruses and, and

06:49 bacterial viruses, the whole cell can a whole spectrum of virus infects,

06:55 cell. Boom. That's it. virus can just live inside the cell

06:59 a long time before it does anything it, to everything in between.

07:04 . That's especially true. Uh, animal viruses. They have so many

07:08 types of um life cycles and variations they can do. OK. Um

07:17 of course, those, those, know whether and those will have differing

07:22 on the whole self and being killed to almost immediately to, to be

07:26 to live a somewhat normal life to between. OK. Um All

07:35 let's see. Oh, when we on this right host range and,

07:38 tropism. So remember uh all that really about the interactions right between the

07:46 and host, right? Um recognizing specific proteins, glycoproteins molecules on the

07:56 many times what these are on the cell are already existing um receptors of

08:04 types that the cell would use for functions. So one example is our

08:10 have receptors for cholesterol, right? is part of our membrane in our

08:15 . And so our cells take these and there are viruses that use those

08:20 their way to get in. So very often is gonna be existing receptors

08:25 of different types of viruses that use well. OK. But it's it's

08:29 specific interaction though. OK. So Coronavirus recognizes, recognizes these specific receptors

08:37 are present on cells in your in lungs. Ok. Uh But another

08:43 type won't recognize that. So a virus which is also a respiratory infection

08:49 flu virus will recognize other types of . Ok. Um Now remember the

08:56 versus narrow, right? And in of host range and what I call

09:02 specificity. The fancy name is Ok. So uh rabies virus is

09:09 good way to remember this. So rabies can infect all different types of

09:13 , right? Dogs, cats, , rats, mice, whatever.

09:17 within that specific host, it can infect nerve cells, right? So

09:23 a squirrel, a cat and a and a bat, they're only gonna

09:27 nerve cells. So it's a very in terms of tissue specificity.

09:32 Um But broad in terms of the of different types of animals, they

09:37 infect. Ok. So viruses vary on that. So uh HIV has

09:42 narrow host range and also a narrow specificity. Um The uh Ebola narrow

09:54 , in fact, bats but uh humans but um broad tissue specificity in

10:01 many different types of of tissue Ok. And um that's generally,

10:08 was if I was gonna say a rule here is that most viruses do

10:14 a narrow tissue specificity, ok. either cells to the respiratory system.

10:21 a if it's a respiratory virus or system. So for the most

10:25 they're narrow, it's Ebola is kind one of those types, uh,

10:30 can infect different tissues and there's, some others, right? But those

10:34 do that tend to be pretty right? Because they, they can

10:39 different tissue types in your body. a lot to have to overcome.

10:44 . It's no wonder that Ebola has a very high mortality rate.

10:50 , if you contract Ebola it's upwards 90% mortality, only 10% chance of

10:56 . And that's, and it's really of different tissue types, it can

11:00 . OK. So uh so all this um is all about this

11:06 . OK. What does it recognize ? Um All right, any questions

11:12 that? OK. So let's look this question. So we'll get into

11:15 little more about structure of a So let's look at this question

11:20 So the naked virus is lacking or what? So remember as with any

11:29 these kinds, these kinds of if you don't see an answer,

11:34 , then that's your answer, Yeah. OK. Speed this up

11:53 little bit here. So, all . Thank you now. Mhm

12:13 Um So the thing that's missing is envelope? Yeah, it's envelope.

12:22 you don't see envelope listed here. it's uh that on the lope.

12:31 . Um All right structure. So granite, the classification here is kind

12:36 based on symmetry. So uh s viruses um you know, you can

12:42 it, cut it in half and have identical halves, right? That's

12:45 . So uh very often these types a um this icosahedra that's a 20

12:53 uh geometric structure. Uh So remember caps is made up of capsule

13:01 And so, but don't think every uh in this diagram, every

13:06 block right is a one of those , the capsule. OK. So

13:12 , this will have lots of capsule . But in terms of being different

13:19 , in terms of structure, this has three, right? 123,

13:23 one has four I'm sorry, uh . So they have um on the

13:29 the surface. So three different caps proteins on the surface, right?

13:34 so um but remember that the genome a virus is pretty small. So

13:39 can't have a lot of genes for things. So you kind of consolidate

13:44 you you, you limit your different types to maybe 3 to 4

13:49 5 in that range and then they of assemble the form of structure.

13:54 . Um The oops sorry, the envelope viruses. So this this right

14:01 as shown would be a naked right? It's just a capsule.

14:07 if it's doesn't has an envelope, you're gonna have a layer around

14:11 OK? As you see here, is the caps structure, there's a

14:17 there and surrounding it is an OK. So um so the envelope

14:22 from the host cell, right? this is basically a lipid bilayer coming

14:27 the, that that originates from the cell membrane. So as the virus

14:32 assembled and exits the cell, that wraps around it. OK. But

14:39 the course of the infection, as see, I'm talking about this uh

14:44 when we come back. But uh the virus is being um replicates,

14:49 genome makes vowel proteins, many of proteins then go to the surface of

14:55 host cell. And then as the exits, it gets the envelope plus

15:01 viral proteins on the surface that it's to have, right? So that's

15:06 of how that works. And so the envelope is a feature as far

15:14 I know of only animal viruses, ? Because uh typically with bacterial

15:22 uh they don't have an envelope, have uh just a capsid uh but

15:28 don't have some other different structures. , envelopes are typically only a feature

15:31 animal viruses. OK? Um uh let's see here. OK.

15:38 glycoprotein spikes, OK. So these a feature of many viruses. Um

15:44 may not be uh so prominent and like like these are OK. But

15:52 these are gonna be um you anything on the surface generally is about

15:56 the host attaching. Uh it it also be for help helping in in

16:02 from the cell as well, So that's kind of what the features

16:06 of these surface viral proteins. Um, filamentous types. So,

16:14 types are gonna be like strings like . Um, they can, uh

16:19 will have a, can have a on as well as you see

16:23 Ok. Um Tobacco mosaic virus uh have the capsule has, doesn't have

16:30 uh envelope, sorry, but it have the capsules here. You see

16:33 blue red is the genome. Uh it will be a long kind of

16:38 strand. OK. The um tailed , depending on the textbook, they

16:45 these different things. Uh some can call these uh complex viruses because they're

16:50 of a combination of forms. So see the the geometric caps in

16:56 but then it has in addition to um these other structures. So this

17:01 of tube here is a um will . So when this thing attaches to

17:08 cell and this is a typical for bacterial virus, OK. So it

17:14 a whole cell sitting here. It , it will recognize the whole hotel

17:22 tail fibers. OK. So that's of what rests on the cell.

17:28 this part comes down and it will compress and pressure shoots the genome into

17:37 cell, right. So the genomes here and it will enter the cell

17:43 all this will stay behind. Stays outside the cell. And that's

17:49 for bacterial virus. Genome comes Everything else stays out. OK.

17:56 um so asymmetrical viruses are not so viruses. You can, you can

18:02 identical halves of the virus, more kind of think of it as

18:09 , a roundish roundish blob ish OK. Not completely symmetrical but kind

18:18 some are more blobby than others. . Uh COVID is like this flu

18:23 has this shape. Um uh And they're more kind of amorphous in a

18:29 , not a uniform circle. Uh But aside from the shape,

18:34 know, they do have the typical , right? Uh This one has

18:37 envelope flu virus has an envelope, have the capsid, then you have

18:41 thing called the nucleo protein. We're gonna talk about that here.

18:48 . So um Coronavirus has that as . And so for Coronavirus, we

18:55 the envelope structure here, right? Despike proteins. OK? And then

19:02 this genome. OK? This is A genome. So you don't see

19:08 little house, that's the caption, ? Something like this. All

19:14 This is what we've been seeing. . This one uh has its genome

19:22 of covered with a capsule that looks this. So this is what we

19:28 nucleo N because it, it attaches the nucleic acid in this case,

19:33 A. OK. So these are and this is in essence the cap

19:39 if you will. OK. So not a structure like this, it's

19:44 attached to the chrome to the to genome. OK? And in that

19:49 serves the same purpose it, it , it, protects the genome.

19:54 . So, um, but that's a variation, you'll see.

19:57 even the, um, going back , even the, uh flu

20:03 it does have a capsule in but it has that as well on

20:06 genome. Those nucleocapsid proteins. So, actually has both, uh

20:13 has just the one type. Um, and you'll see this variation

20:19 , with different viral types. Um, what is it, what

20:25 it mean to have one over the ? I don't know if it

20:27 I don't think there's, it's known the significance is of that, but

20:31 you know, it is a way starting to protect the, protect the

20:36 . OK. Uh OK. So just talking only in general terms about

20:43 genomes, right? Just a couple things to point out. So one

20:47 , the size is based on the of the virus, right? Smaller

20:51 , smaller genome can accommodate fewer right? Larger spectrum. So something

20:56 a poliovirus is pretty big in terms genome sizes for viruses, it'll have

21:02 , more genes. OK. Um types of genes you find and you

21:07 need to know this uh memorize but the types of genes you find

21:13 of course, are are virus specific , right? So what is

21:16 what's the it the virus needs a to replicate? But even having said

21:23 the virus does have to contribute some things to it, right? Because

21:30 virus is made up of virus specific , right? So you have capsid

21:36 are gonna be things that are encoded the genome. Um you know the

21:40 spike proteins and things on the surface are part of recognition are viral.

21:45 that's gonna be coded for. And may be enzymes like you see here

21:50 are involved in the assembly and the the um exiting of the virus.

21:56 th those those will be virus So you'll have some of those in

22:00 . And so again, anything that help the virus replicate and exit the

22:05 or um um uh recognize, attach the cell or be be part of

22:13 catch. Those are all gonna be specific uh structures. OK? And

22:19 when we talk about uh dimensions are segmented, OK. So most viruses

22:28 will have a genome, something like . OK? It's one piece,

22:34 ? One piece. And um that's called non segmented. OK? You

22:41 the one thats what flu virus OK. So you see eight different

22:46 . Wow, eight different segments. . And uh that's a genome,

22:52 segments. OK. And so what enables and, and of course,

22:58 viruses, all viral types can, mutate, of course, and,

23:03 change. Um uh and also um for like say for a flu virus

23:11 , more than one flu virus can the same cell. OK? And

23:17 and so can other viral types. . And what that can do is

23:21 can have recombination of genomes in in the cell being infected.

23:28 So, especially with the flu virus has segments, these segments can

23:33 OK. And so when we look , for example, the there's different

23:38 of flu viruses, OK. And designated by the, OK. The

23:52 ones are involved in um attachment and getting into the host. The

23:58 ones are actually involved in exit. . But they, but they

24:03 they produce an immune response in the . Ok. Um And this is

24:09 changes, you know, because flu vary from year to year because the

24:14 is changing and, and the changes particularly in those in those outer ancient

24:19 proteins. OK. And so V flu virus originated in uh aquatic,

24:26 , birds of various like ducks, of wild, uh wild aquatic

24:33 And then, uh, then also the jump into uh domestic birds,

24:42 chickens, um uh domestic ducks, like that and then into swine,

24:49 ? Because there's swine flu as And so you can see the evidence

24:54 that in the genomes of viruses. this is kind of, you

24:57 simplifying it for you. But uh , they're, they're color coded here

25:02 the origins from the various bird species swine. OK. And so,

25:09 , and of course, one of forms of balance between humans OK.

25:15 so, you know, and all involves is getting changes in these proteins

25:20 the surface such that they, such they recognize um will recognize this receptors

25:27 a, on a human cell or virus re respiratory cells, right.

25:32 uh so they find the right change the right key to fit the lock

25:36 they get in right and cause So, uh so these of course

25:42 evolve uh year to year, of . And so we um we sequence

25:49 the, so we have a huge of, of information about the uh

25:56 sequence of the, of this And we look to see your year

26:01 changing, right? So specifically looking changes in these outer proteins,

26:07 then you try to predict OK, , what can we, what can

26:11 um put in our vaccine to uh ? You know, maybe, maybe

26:16 it'll morph into this form and that's of how we'll formulate our vaccine.

26:22 so a vaccine will be a combination different of these spike proteins in

26:28 And so the idea is that uh know, some years, it's

26:31 some years, it's not so And so it's all because you can

26:34 absolutely nail down how it's what form will evolve into. You can kind

26:39 just make a educated guess. um but that's, that's kind of

26:44 they do that. OK. Um general rule is, and this is

26:50 RN A virus. RN A viruses more prone to mutating because there's really

26:58 repair systems to fix mistakes. So we have repair systems without,

27:04 have DNA. Right. And, so D nav, uh D nav

27:11 A DNA viruses, uh can have ability to have mistakes fixed because of

27:17 because as humans have those capabilities. um ARN viruses can have more mutations

27:24 they can evolve uh a little bit in some cases. OK? Um

27:30 again, the, the changing is about acquiring changes in the genome to

27:36 change these outer proteins because that will how um the body sees it,

27:43 ? So it was, if it , if it was a new form

27:46 infectious, but the body hasn't seen before, then it, then,

27:49 you're, then you're more susceptible. anyway, so you, you

27:52 you try to come up with vaccines can hopefully deal with that variation.

27:58 ? Uh It's a, again, , it's, it's always a constant

28:02 battle. OK? Um Any questions genome structure thing? OK. So

28:11 uh switch gears a bit and look prions and thyroids. All right.

28:17 as you read these, uh you wanna pick the one, there's

28:23 true statement, the whole thing has be true. It could be

28:28 that some of these have half of right, half of it's wrong.

28:32 just make sure the whole thing is . OK. OK. Let's

29:18 So we'll flip ahead. We're gonna this question here again. OK.

29:27 let's um move ahead. So we'll with prions first. So pri uh

29:33 , excuse me, vids, so . Um So the, the neither

29:39 nor, nor prions uh well, with prions, it's the um mad

29:45 disease. Ok. Um That's the human disease caused by a prion and

29:54 chances of you catching that are next zero. There haven't been any cases

29:58 that in. I, I don't how many decades. Ok. So

30:03 I was gonna say was you, , you don't need to worry about

30:05 or prions as causing you an Ok. Um What's unique about these

30:12 things is that they are basically each infectious molecule. That's it. One

30:19 an RN A vy roids and one's protein and that's essentially the, the

30:25 in terms of structure. There's nothing to it than an RN A for

30:29 vid, a protein for prime. it. Ok. So they're not

30:33 because they don't have the typical virus . A protein coat a genome.

30:39 don't have that. Ok. So why they're kind of their own

30:43 Ok. Um Thyroids are a problem many, not many, but for

30:50 number of crops, particularly potatoes. That's probably the most well studied.

30:56 And so RNAs of course, aren't stranded like DNA, but they can

31:03 these secondary structures, right? It's all complementary base a AUGC,

31:09 And so, and that's secondary structure important for their functioning. OK.

31:14 what do they do? So they uh they um combined co again,

31:35 base pairing. So you may have message an MRN A by the

31:39 for example. And this RN it's give it the shape here,

31:49 ? And this would be the um , it could just buying complementary base

31:58 to AM RN A and that in can block a ribosome from translating

32:04 OK. So that's how it can uh gene expression. OK. Um

32:11 , it replicates itself by simply using host or a pli to make

32:17 OK. Um How it's transmitted to plants. Uh I don't know that

32:25 known, but it could be through seeds are formed. Perhaps. Um

32:32 if it's carried from plant to it would likely have to be some

32:37 of a, I would guess uh kind of insect carrying it from plant

32:41 plant. Uh because plants generally aren't to penetrate. And so usually it's

32:46 , a vector of some sort that a, like a, an insect

32:49 some sort that does that. Uh But anyway, so, you

32:54 , yeah, the uniqueness here, an infectious piece of RN A is

32:58 it is. OK. No human are known to be caused by these

33:03 . OK. Now, the prion uh again, infectious protein. All

33:10 . So that, and that's There's no other structures associated with

33:13 The um so mad cow disease, was kind of a bit of a

33:19 back in the eighties, but that really confined to England. Had,

33:25 some reported cases of this. Uh was one fatality in the US that

33:31 from a person who had come over England. So, uh I'm not

33:36 of any fatalities of this in the . But um it was discovered,

33:41 think in sheep, that's what scrapey to. This is what they called

33:45 in sheep. Um Apparently you can it if you're one of these tribes

33:50 the remote areas that practice cannibalism, can get it that way. Um

33:56 you know, if you do catch typically from um from contaminated meat,

34:02 ? Um Thing about this disease, a very slow progressive disease,

34:08 You don't even know you've ingested infected because you won't, you experience symptoms

34:14 it could be years, you before you experience any symptoms.

34:18 Uh And, and there is no for it. So if you do

34:21 symptoms, that's, you know, much it. But, you

34:25 it is a slow progressing illness. And so the uh there is some

34:33 to support that there may be a component. So apparently it can be

34:38 , I think they've traced some families generations have contracted this. Uh But

34:42 don't know how extensive that is, there is some evidence for that.

34:46 Now what? So, so the about this is there is a normal

34:53 of the protein, right? And part of your body, it um

34:59 a molecule in your cells, it's the membrane. OK? And you

35:04 uh a good portion of it in uh nerve cells in your central nervous

35:08 . OK. Now, what the form does? There's been a lot

35:13 debate. Uh Strangely enough, they it has something to do with copper

35:20 of all things. OK. So they know that if it becomes this

35:26 form, which is the normal, , it is all about the

35:29 OK. So you can see the here are these alpha heli helices.

35:35 the blue are kind of those beta if you remember your protein structure.

35:40 they have no forms uh acquire a of these um have this kind of

35:45 sheet structure, OK? And less . So, in any case,

35:50 so, ingestion of these normal forms through the 10 of meat can induce

35:57 formation of uh from normal to So it kind of looks something like

36:02 kind of simplistic, but you'd have prion form that can attach to a

36:09 form and that in itself produces the this abnormal form confirmation, right?

36:17 this uh keeps occurring as these ba the the mi uh shapen ones by

36:24 correctly shaped ones to change them into prion. And again, this process

36:29 over several years and the damage accumulates the cell cell dies and then those

36:37 can then be released and are taken by other cells and continues the

36:42 Ok. So what happens to a cell just quickly go, I'll come

36:47 to this. This could be a cell here. The green ones are

36:52 normal forms of the prions. Red are the misshapen ones. And so

36:56 they bind together, uh converting the into the red forms, uh these

37:02 in the cell and of course, damages function of the neuron. The

37:07 dies. Ok. And what's left because nerves don't s nerves to the

37:13 nervous system don't generally regenerate themselves. , um you're left behind holes in

37:19 brain tissues. This is a slice brain tissue of I I assume an

37:24 that's been infected with this uh prion protein and you see the results.

37:30 these these hole basically holes in the tissue. So that creates a very

37:35 texture to the brain. Ok. , um and so encephalopathy refers

37:42 you know, pathology of the brain . So it becomes very uh

37:47 obviously severe neurological impairment, motor function stuff like that uh worse as it

37:56 . Ok. Um Apparently these things also, I guess because of their

38:00 and how they fold, they're very to temperature chemicals and things.

38:05 um, you know, if you , although I don't know how,

38:08 know it, that you're eating contaminated , I, I cook the heck

38:13 of it. Right. If you're eat it. But, uh,

38:15 don't, I don't see that that's really a problem in the US.

38:20 . Or, I don't even know much elsewhere in the world is a

38:22 . But again, like with uh , the uniqueness is the, in

38:27 , it's an infectious molecule basically. . Um OK. Uh Let's try

38:36 one again. OK. If you like changing your answer or not,

38:41 uh while you're looking at this, there any questions, thyroids or

38:51 Anything? So, remember they're not of the other, other main things

38:55 they are not viruses. OK? their own unique thing. OK.

39:39 . Let's see here. Yeah, , it's, it's the, everybody

39:46 much answered it right the first So um so yeah, the only

39:50 fitting here is completely correct is So uh this one's uh um com

40:02 wrong. All right. There's no in a prion thyroids or RN

40:07 Um That's wrong. That's wrong. ST vs can, of course,

40:14 can both replicate, that's wrong. There, this is wrong. Uh

40:23 wrong. So uh well, they, they don't, of

40:25 But uh so yeah, d is only completely correct statement here. So

40:31 get into a little bit about, look at this question and we're gonna

40:34 about um classification of viruses but more about um because it can be a

40:43 bit confusing is the nature of, uh RN A viruses. OK.

40:50 is why I put this question up it can be as we go through

40:55 more when we come back from uh their life cycles could be a

41:00 bit uh may not make sense, there's a reason why they do what

41:06 do in the order, they do in China. So it's kind of

41:10 do a little bit of explanation on . Uh After we do this question

41:27 . OK. So we're asking about , what can they, so different

41:35 of RN A viruses and they use genome for different purposes depending on the

41:40 they are. OK. So, . So yeah, they can be

41:52 the above, right? So that's your, we call plus on

42:01 virus. There is a minus RN virus and this is a retrovirus.

42:12 . So um well, let's look , so, classification, right?

42:18 had a question last time about what the things you can look at to

42:25 viruses? You know, some of pretty obvious, right? You can

42:28 at, you know, what's the genome RN A DNA? What's the

42:33 does it have an envelope or Does it have uh uh with the

42:38 uh symmetry? Uh and so So, um generally, the classification

42:45 used this Baltimore system is uh based really the genome number one. All

42:53 . Is it DNA RN A? is it double or single stranded?

42:58 then uh it's the route to get the MRN A? So I would

43:05 this box. OK. Knowing that plus RN A is the MRN

43:14 OK? And being an MRN A you can be translated. So ribosome

43:20 pop on this and start translating. ? Um We call it the sense

43:26 A. So whether it's DNA or A, there's always a plus sense

43:32 and there is a minus anti sense . OK. So, so the

43:39 of getting to the MRN A. , it varies depending on how

43:42 how you get there varies depending on viral type. OK? Of

43:47 it's important because remember this is gonna needed to make the captured,

43:54 And the other viral components uh because gonna assemble all these things and then

43:58 gonna put a genome in, So let's take a detour for a

44:05 . OK? And look at OK. So um the language of

44:16 of nucleic acids, like when you about nucleic acids, there's certain things

44:20 are a constant, right? You that there's gonna be a five prime

44:26 three prime end, right? This all just relates to the, the

44:29 of nucleotide and putting them together, ? So there's a five prime and

44:33 prime end, it's complementary, Basically, they are complementary to each

44:39 . And so, so the they're identical, right? This, this

44:44 uh we're going to um uh one always designated the plus strand. The

44:50 is the minus strand. OK. so the um the uh and so

44:57 same rules apply whether it's DNA which is what our chromosomes are or

45:02 it's DNA RN A, right? happens during transcription, right? Our

45:07 , one of our DNA strands are strand is, is what we're going

45:12 do. We're actually gonna copy the strand. OK? Because it is

45:17 other thing, remember when you copy strand, you're gonna copy the

45:23 right? So if we copy we're gonna copy the plus, we're

45:26 make, we're gonna make a plus by copying this one. OK?

45:33 that plus strand will be orientation, ? Plus a GC, you,

45:43 it's going to be our name, ? Mr A? And we can

45:48 this is identical to that, And that's so because we're copying the

45:57 we call the template strand template or this is a coding strand. Ah

46:06 . This is the coding strand here the South, the way coding

46:13 So that contains the essential information that the information to make a protein.

46:19 we don't, we don't translate we translate RN A. So we

46:23 to make an RN A copy of and that's how it's done.

46:26 we copy the template because we know the minus strand gives us a

46:31 right? That's gonna be, that's to the DNA. Obviously, the

46:36 cells are in place of thymine. . So that's how we now have

46:41 , the coding information in the form RN A, right? Um

46:46 So our, our name that you see in eukaryote prokaryotes, you see

46:53 in viruses, OK? Um Because except viruses are DNA, right?

47:00 they're gonna be DNA, either DNA in their chromosome or when they're doing

47:06 , right? But you don't see . OK? And um so,

47:13 again, so for all three of groups, right? The same rules

47:16 . One's a plus one's a it's all complimentary five times three prime

47:20 just the lingo of, of nucleic , right? And so with RN

47:27 viruses, right, we can have plus single stranded RNA virus,

47:32 Which would be that OK. And can obviously have a minus RN A

47:38 . OK. Which would be something this, right? So when these

47:43 viruses then begin to replicate, Uh And then also translate OK into

47:52 , we're gonna copy OK. And OK. So you might be

47:57 having just learned that the plus strand for reference, right? Plus RN

48:07 uh come on plus R A equals . OK. So, um are

48:23 , so um So the MRN A be translated. So the cluster and

48:28 go, OK. Well, that's MRN A, that's all it

48:32 . It doesn't need to do anything , right? It can, it

48:35 express proteins from this and it's on way. OK. Well,

48:42 OK. Because, yeah, it , it could certainly express pro viral

48:47 with that. But what else is ? Right. The missing part

48:52 you only gotta think of the end here. This is the end

48:56 OK? In a basic simplified OK. Here's our virus.

49:05 Here is host cell. OK. gonna come out? Multiple viruses?

49:17 . Well, OK. Yeah, can make proteins with that but I

49:22 to put genomes and all these capsules making, right? So we're gonna

49:27 to make more copies of this right that genome because that's what the virus

49:33 , that's infecting, right? So are we gonna do that?

49:39 OK, we are going to, right, do this. Let me

49:48 if I can get this off of screen here. OK. I,

49:53 do it this way. OK. . There we go. What we're

50:01 do is copy that. We're gonna that into this. Now, it

50:09 be super simple, super easy as . If life would allow us to

50:14 copy that into a plus strand, happen, doesn't happen on planet

50:20 right? Maybe somewhere in some other where things work differently. Maybe it

50:26 but it doesn't. Right. Because copy it into a complementary strand.

50:32 . So we can't do that. right. So what we do is

50:43 oh goodness. Uh Here we I'm playing. OK. So what

50:47 gonna do is um OK. Go it. This thing will not let

50:56 erase this. Stupid. OK. right. So what we're gonna do

51:04 we're gonna make lots of copies of plus strand into minus. OK?

51:11 we're gonna take all those and copy into plus strands. OK? So

51:16 other thing here is it's a numbers . So if we have just one

51:19 two viruses infecting, you know, need that more than just that,

51:25 just one template, right? If wanna make lots of protein, you

51:28 , rather quickly. So the way get there is to make copies,

51:33 we can't go directly from plus to , we have to know what,

51:38 nucleic gasses let us do. Which is to make the complementary

51:41 which is negative, copy that into positive. OK. Um And now

51:47 get two things. We get expression the bowel proteins to make our capsules

51:53 we can stuff those caps with our . OK? And so each of

51:59 will have a captain around it. now we've completed the viral cycle and

52:06 can exit the cell and infect more . OK? Similarly, with the

52:10 RN A virus, we need lots stuff, right? So first we

52:15 to, we can't translate that at . We have to make that into

52:18 plus string. So we do it that. Now, we can translate

52:22 proteins, make our capsules. And then we gotta make negative minus strands

52:29 that's what our virus is, It's one of these, right?

52:33 then we do that, then we make a little cap house around

52:37 Right now. We've got a complete . It connects it and affect more

52:42 . So you just, it's, convoluted because we're just following the rules

52:47 nucleic acids. OK? Uh If is not because these are RN A

52:51 , it's just, that's the way stuff works. OK? So with

52:58 this other type, it's completely right? Retroviruses, right? So

53:04 uh have a plus single RN OK? But what they, their

53:09 is to take that and to copy the name. OK. So

53:15 you see it's the same rules, right, plus strand of R and

53:24 , we copy it into DNA. a minor strand, right? And

53:28 it actually uses um host DNA polymerase make the complimentary copy. OK.

53:38 it has to do that because it into the host chromosome, right?

53:42 if you're gonna do that, you to be DNA double stranded to do

53:46 . OK? And so that's a from these two other groups.

53:52 So again, it's, it's literally , you know, this is how

53:56 has to happen, right? it's what happens in us. You

53:59 , when we copy a copy the strand here we are. Uh I'm

54:06 copy that into um A plus RN and that's, you know what gets

54:12 . So uh it's nothing different than what happens in us. OK?

54:16 any living thing. OK. the other thing here is that this

54:22 of copying RN A into RN A everything that's happening here is all this

54:32 all, this is all RN A but, right? There's no DNA

54:40 in any of this when it's the A virus of these two types doing

54:45 thing. OK? No, OK. So eu periodic systems or

54:51 bacterial systems do not copy RN A RN A, right? We don't

54:58 that. The only copying we do RN A is from DNA, DNA

55:02 RN A, right? Um So of this type um have to have

55:10 own enzyme to do this, So what we have is what's called

55:17 DNA dependent rnap Premera, right? what does our transcription, what these

55:25 have is called an RN A dependent RN A lyra. OK. And

55:31 that's um that let's go back this . That is what's abbreviated here.

55:44 Right here, this enzyme, So it's a virus specific enzyme again

55:50 copy RN A to RN A. And so we just looked at so

55:56 double stranded group I didn't mention, , you know, it's gonna,

55:58 gonna follow the same rules, right? So they're, they're um

56:04 copy as well to produce transcripts and into protein. Um We have the

56:10 stranded plus group we just saw and our Mrnas plus strands and then this

56:18 here um into, into there. remember that what's not shown here is

56:25 then go from here, but the enzyme RP to a minus strand because

56:33 what we're gonna need those genomes to into our, our capsules.

56:38 So, um again, it's just uh nucleic acid rules here.

56:44 And the last one, the retrovirus copy DNA uses host prema to get

56:52 uh double strand. So when it's integrated into the host chromosome, it

56:57 actually in that state transcribe and it make viruses. So the retrovirus,

57:03 talk about that when we come but it's a unique one in that

57:07 can um sit in the chromosome but carry out replication of viruses as

57:13 OK. Um So yeah, we will revisit all this or get

57:19 animal virus life cycles again. So just kind of wanted to bring it

57:24 now. So you kind of get to it and you kind of have

57:27 absorb this to kind of, you , the whole plus the minus the

57:31 thing. OK? But it's, it's not kind of any kind of

57:35 . It's, it's, it's what when you're dealing with the cle

57:39 OK. Um, any questions about ? OK. All right.

57:47 uh, let's go forward here OK. Don't memorize this table.

57:53 only bring it up just to show some representative types that you're familiar

57:57 So, in these, uh DNA , so things like, uh,

58:02 HPV, uh very common STD, , can cause cervical cancer, uh

58:09 viruses in this group. Um It's type that can uh both of those

58:14 and HPV are types that can integrate the chromosome. Um The among the

58:21 A viruses, many, many human caused by RN A viruses of various

58:26 . Uh rabies COVID flu mumps, , West Nile, which is,

58:33 is endemic in this part of the uh around Houston and East Texas.

58:39 So lots of them in that group those groups. Uh So the one

58:43 retrovirus, of course, the uh oddball here is this group per

58:51 They're kind of a variation of retrovirus that. They, they have

58:57 But um they have to reverse transcribe RN A into, back into

59:07 OK. And uh that's how they their genome. OK. It's a

59:13 bit, a little bit different. . The one significant one there

59:18 in terms of human disease is the B virus, liver, liver,

59:22 disease. OK. Um OK. the OK, just recapping. So

59:30 the structure virus, remembering this. . Uh capture type genome type,

59:37 your envelope spikes, et cetera. And then uh we'll, we'll get

59:45 uh eco ecology and uh large viruses isn't that much. But I'm afraid

59:52 wait until the end, it'll be applicable there. So, uh so

59:57 went through the basics of a life previously. Uh So we're gonna,

60:04 this is just really just reiterating what talked about before. So remember it's

60:09 about host recognition that's, that begins cycle. Um Remember how this relates

60:15 host range and tissue specificity of recognizing host cell um entry. So the

60:23 structure may come into the cell and typical for animal viruses. Uh bacterial

60:28 know only the genome comes in uh , it's, you know, copy

60:34 genome, it could be integrating into genome, that's what they do.

60:38 If not, whatever the case, it's gonna replicate, it's gonna go

60:42 all these steps here. OK. we'll see different variations depending on the

60:47 type. OK. So let's uh with bacterial viruses the more simpler.

60:54 We'll start with this question here. . So we're looking at uh so

61:01 , remember, page is refers to viruses. OK. So we're looking

61:07 um uh which is not a part Atlantic Sage cycle. Hm. So

61:15 the operative term there. No. . OK. So the, the

62:10 that are um the F is So the, the two that are

62:13 here are which ones? Yeah. D and E if I heard

62:22 So um these are virulent page, temperate and uh that's false. Only

62:34 genome enters the cell. OK. we look at two types here.

62:39 so the same um with animal the same thing applies. So there's

62:44 animal viruses, lytic bacterial viruses. And so basically a light sage or

62:52 LAIC virus, their mode of operation recognize host infect host, make viruses

63:01 host. That's basically it. And um of course, like with

63:07 viral infection, we have recognition So very typical structure for bacterial virus

63:15 terminus that tailed virus, your book it. So a and that,

63:20 I mentioned that tube in the middle and so the genome enters everything else

63:26 outside. OK. Um Your lysogenic . So there's an equivalent in animal

63:33 , we call them um uh we call them lysogenic, we call them

63:38 viruses. OK? They form a state here. They call them

63:45 OK. And so uh actual integration the viral genome into the host

63:51 OK. So we call them temperate they can, you know, not

63:57 anything to the cell, leave the alone and they then they can kill

64:00 cell. OK. So a like page has a part portion of their

64:07 where they're just integrated into the host doing nothing, right? And the

64:11 cell is perfectly fine, just keeps no problems. But uh eventually it

64:17 gonna replicate, it will have to into the light cycle and to make

64:22 viruses. So it kind of goes both, both uh sides. And

64:27 it all depends on what is the of the host cell pretty much.

64:34 . And that determines which way it . OK. So with the lighting

64:39 , OK? Um It involves, me just go real, I'm gonna

64:44 you. So it involves all of . OK. That's a light

64:50 OK. So uh enter the And so again, only the genome

64:56 a page is entering OK. Then has uh produces viral enzymes to degrade

65:05 host chromosome, which is right degrades. It uses those nucleotides for

65:10 own use. Um transcribes, translates protein, assembles, um inserts the

65:18 into the caps and heads and then . And so at 200 to 500

65:24 , that's a lot of phage coming of a one host cell.

65:30 And typically, that's enough just to and kill the cell. They also

65:34 things like lysozyme that breaks apart the wall and uh basically just destroys the

65:41 . Um you can, and this acts very fast. So you can

65:46 if you have 200 to 500 of coming out, they'll quickly infect more

65:51 . And so it actually becomes like exponential, you know, exponential

65:57 Um And so, so that's a phase. Now, the lysogenic type

66:04 that, but it also has this . OK. But again, just

66:10 reiterate the lytic virus will not have as part of its thing, it

66:18 has just this lighting cycle. So misogyny um going this route means

66:26 integrates is the prophage uh in the . And so this is not detrimental

66:34 the host cell at all. Um it's no burden. So the host

66:39 can continue to replicate and this normal . OK. But even though the

66:46 isn't technically replicating forming new pages, is replicating its genome right as the

66:54 divides. So, of course, prophage is along for the ride,

67:00 . So each of these generations of , each containing that prophage,

67:07 So, you know how fast bacteria grow. So um you know,

67:12 several 100,000 cells can form and each them carrying a part of that carrying

67:17 prophage. OK. So then it an issue of OK. When do

67:22 go to the lighting cycle? Because that's ultimately how it's going to

67:28 more fate. OK. And so different cues for that. Uh very

67:34 it's um the, the health of cell. OK. So if you

67:41 to think in terms of, if it goes to the light

67:45 we're going to produce page particles and perpetuate, right? The species,

67:53 ? We want to be able to more cells, right? So you'd

67:58 there to be a enough host cells to be infected, right?

68:05 if you have, so the cells pretty healthy and they're growing like

68:11 Ok, then that's probably a good to say, ok, let's let's

68:19 cycle because we can be assured that gonna be lots of hotels around.

68:26 . And so, uh that's makes , right? So you have lots

68:30 susceptible hosts in the population that's growing quickly. You know, from the

68:35 of the age, that's probably a time to, to get into the

68:39 cycle and do that. Ok. not a good idea to do that

68:43 the cells are kind of starving, maybe limping along growing slowly because of

68:49 kind of a stress or something because there's probably not a lot of the

68:54 growth rate, there's probably not a of host cells in the population

68:58 right? So if they go through cycle, then these may not have

69:03 host to find and replicate. So that's kind of how the nutrient

69:10 or, or the state of the cell can kind of influence, influence

69:14 uh which way it goes. And you know, we didn't go

69:18 it. But, you know, prophet itself is, has some virus

69:25 proteins being made that kind of sense going on in the cell, there's

69:29 molecules in, in a host cell that, that, that can determine

69:34 kind of the energy state of the . OK. And, and the

69:38 has, has proteins that can kind sense, sense that. OK.

69:42 so it's kind of how it bases to stay or go into lighting

69:47 That's a fine line, right? even if the cells are stressed,

69:53 not growing well. And the page , OK, let's not exit

69:57 It could be that the whole cells so bad, but now they begin

70:01 die. And so of course, know, you'll want to want to

70:06 out of there because you're gonna go with the ship otherwise. So

70:10 it can be a fine line in of, uh, it's its own

70:15 preservation and when to kind of jump , so to speak. Ok.

70:22 , that makes sense. Yeah, think it makes sense. Um

70:29 please stop. That's probably a good . Um, any questions? All

70:35 . So, um, we'll see in a couple, uh,

70:39 after next week. So you got few days, uh, 10 days

70:42 so. So, um, have fun next week. We'll see you

70:52 .

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