MIMM 324 > 28. Coronavirus 2 > Flashcards

28. Coronavirus 2 Flashcards

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1
Q

why are spikes under immune selection?

A

immune pressure from Ab causes spikes to mutate

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2
Q

initial monoclonal antibody therapy

A

used COVID-19 convalescent plasma that has Ab from patient who had recovered from infection

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3
Q

2 examples of therapeutics MAb

A
  1. Bamlanivimab
  2. Bebtelovimab
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4
Q

describe Bamlanivimab

A

used as early therapy but the virus evolved so became ineffective

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5
Q

describe bebtelovimab

A

used as early therapy for patients with high risk of disease progression

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6
Q

3 benefits of MAb therapies

A
  1. good safety
  2. moderate efficacy
  3. good for emergency use when no drugs or vaccines are available
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7
Q

3 downsides of MAb therapies

A
  1. resistance mutations in spike
  2. variants have many mutations that make Ab not effective
  3. vaccines are better
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8
Q

what was another consideration that had to be made in addition to developing a vaccine that allows the body to make spike proteins?

A

had to make sure the immune system didn’t react to mRNA

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9
Q

what are the 2 fates of genomic +RNA

A
  1. +RNA copied into -RNA for replication
  2. +RNA copied into subgenomic -RNA
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10
Q

role of subgenomic RNA

A

to make structural and accessory proteins

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11
Q

mechanism of producing subgenomic -RNA

A

when viral RNA pol makes -RNA, it can stop at TRS-B btwn each protein and switch back to the leader TRS-L, giving short pieces of -RNA

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12
Q

what does TRS stand for?

A

transcription regulatory system

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13
Q

4 proteins in RNA replication/transcription complex

A
  1. NSP7
  2. NSP8
  3. NSP12
  4. NSP13
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14
Q

what is the most important protein in RNA replication/transcription complex?

A

NSP12 –> RdRP

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15
Q

role of NSP13?

A

sits at the top of the complex –> RNA helicase to open up dsRNA for RNA synthesis

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16
Q

what is the role of NSP14? why do we need it?

A

NSP14 = proofreader

needed bc long genome allows for mutations

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17
Q

what is the co-factor for NSP14?

A

NSP10

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18
Q

2 activities of NSP14

A
  1. 3’ to 5’ EXOribonuclease
  2. adds methyl group to cap on mRNA
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19
Q

why does the viral RNA have a cap? (2)

A
  1. improve viral protein translation
  2. avoid host immune detection
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20
Q

what are the 2 viral RNA capping enzymes?

A

both add a methyl:

nsp14 –> guanine-N7 methyltransferase
nsp16 –> 2’ methyltransferase

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21
Q

what happens if NSP16/NSP14 is mutated and there is a bad RNA cap?

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A

body can shut down the virus

22
Q

what is REMDESIVIR?

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A

Chain terminator –> nt analog that is added to the chain but has no OH so no new nt can be added

targets RdRP

23
Q

what is MOLNUPIRAVIR?

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A

Increases frequency of viral RNA mutations and impairs replication

24
Q

how does molnupiravir work?

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A

RdRP uses the drug as a substrate instead of CTP or UTP –> incorrectly incorporates G or A leading to mutation

25
3 proteins involved in replication factory
1. NSP3 2. NSP4 3. NSP6
26
where does replication occur and why?
replication occurs in double membrane vesicles to concentrate all components required and shield mRNA from the cell
27
how do components for replication enter the DMVs?
there are pores/gates for substrates to enter and mRNA to leave
28
how does the RNA get coated with nucleocapsid protein?
when the viral RNA leaves the DMV via the pores, the nucleocapsid coats the RNA
29
what is the major component of the replication factory? what is its role?
NSP3 --> protease that cleaves so proteins can mature
30
3 mechanisms of coronavirus gene expression
1. protease cleavage of polyprotein 2. ribosomal frameshift 3. discontinuous transcription
31
how does ribosomal frameshift help coronavirus gene expression?
shift by -1 bases to regulate abundance of non-structural proteins
32
2 components of PAXLOVID
1. Nirmatrelvir 2. Ritonavir
33
function of nirmatrelvir
binds nsp5/Mpro --> forming covalent bond so nsp5 cannot recognize protein --> blocks protein processing
34
function of ritonavir
targets CYP3A4 to increase plasma concentration of nirmatrelvir
35
where does coronavirus assemble?
in SINGLE membrane vesicle
36
6 steps of virus assembly + exit starting from replication
1. RNA replicates in DMV 2. RNA leaves DMV via pores 3. structural mRNAs are translated to make proteins 4. proteins go to ER and golgi to be glycosylated 5. structural proteins meet with mRNA/nucleocapsid at SMV 6. particles leave the cell
37
what protein drives SARS-CoV-2 assembly?
M protein
38
3 domains of M protein
- N-terminus has extravirion - 3 transmembrane (TM) domains to anchor in viral envelope - C-terminus has beta sheet domain (intravirion)
39
how does M protein form virus vesicle?
M oligomerizes so membrane can curve - weak interaction with N or RNA individually - strong interaction with RNA coated by N this strong interaction can recruit S and E proteins to form virus particle
40
what is the role of E protein?
Envelope protein: VIROPORIN --> forms ion channel in membrane - ions move between lumen and cytoplasm
41
when is E pore open / closed?
low pH = open (golgi) neutral pH = closed (ER)
42
what is the general role of N protein?
for RNA binding and packaging
43
what parts of N protein interact with RNA?
basic parts of N protein interact with RNA
44
2 parts of N protein, which binds RNA?
N-terminus and C-terminus C-terminus binds RNA
45
which 2 non-structural proteins have unknown functions?
nsp2 and nsp11
46
what is the first protein on the N terminus of the genome? why is it first?
NSP1 --> suppresses host cell translation
47
how does NSP1 block host cell translation?
NSP1 C-terminus binds mRNA channel in 40S ribosomal subunit so it cannot bind host mRNA
48
what protease processes NSP1?
NSP1 processed by PL protease
49
if NSP1 blocks 40S subunit of ribosome, how does viral translation occur?
viral RNA has leader sequence on 5' end that competes with NSP1 and takes over the 40S subunit to start synthesis of viral proteins
50
general role of accessory proteins
delay or block immune response in early stages of replication
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