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MICI 2100 > Lec 14-Genomes And Antiviral II > Flashcards

Lec 14-Genomes And Antiviral II Flashcards

1
Q

What does (+)-ssRNA virus genome do?

A

Mimics host mRNA and is directly translated into cytoplasm to make polyproteins. Viruses are always finding ways to mimic mRNA, just not always with a cap and poly-A tail

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2
Q

What do enveloped (+)-ssRNA viruses usually make? Where?

A

Make polyproteins at ER with many transmembrane domains

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3
Q

What do host and viral proteases do?

A
  • Cut up long polyproteins into indiv proteins. Viral proteases typically cut themselves out
  • Make RdRp’s
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4
Q

What do RdRp’s do?

A

Transcribe the gene to replicate it and make more RNA products such as (-)ssRNA intermediates and(+)ssRNA genomes. Viruses cannot have host enzymes do this, they have to make new genomes themselves

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5
Q

What does gene expression of (+)ssRNA on a zika virus translate?

A

The polyprotein translated is polymerase

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6
Q

What does (+)ssRNA make?

A

(-)ssRNA intermediate

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7
Q

What does (-)ssRNA intermediate make?

A

(+)ssRNA progeny genome

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8
Q

(+)ssRNA viruses will make ____ strands, used as template to make ___ strands

A

-, +

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9
Q

Polymerase reads ___ to make ___ or ___ to make ___

A

-, +, +, -
**will compliment any strand with its antiparallel strand

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10
Q

What is Ribavirin?

A

An antiviral drug

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11
Q

What are nucleoside analogs?

A

Many antiviral drugs are nucleoside analogs, meaning they resemble resemble a nucleoside

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12
Q

What virus does Ribavirin target?

A

Lots of them

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13
Q

Ribavirin is an inactive pro-drug. What does this mean?

A

Not activated until it is metabolized—is activated by phosphorylation

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14
Q

Incorporation of Ribavirin into RNA

A

Incorporated into RNA during genome replication:
- Ribavirin is chemically different enough that it loosens strict pairings of A-T and C-G
- Ribavirin is analogous enough to A and G both that it can bind to U or C
- Induces hypermutation in viruses that depend on RdRp
- This can be lethal to RNA viruses

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15
Q

Lethal hypermutation…what exactly happens?

A

Eg. (+)ssRNA original sequence
(-)ssRNA has R (ribavirin) replacing both A’s and G’s
(+)ssRNA doesnt know whether to bind C or U to R,
resulting in 2^n possible outcomes

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16
Q

How is hepatitis C transmitted?

A

Via blood

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17
Q

What does hepatitis C cause?

A

Hepatitis (liver disease) and liver cancer. People with chronic hepatitis C may need a liver transplant

18
Q

Can hepatitis C be CURED?

A

Yes, with new anti-HCV drugs

19
Q

How is HCV transmitted?

A

It is hard to transmit. Done through unprotected sex, blood/bodily fluid exposure, IV drug use

20
Q

Can HCV be passed to animals?

A

No

21
Q

What does Dr Lisa Barrett do?

A

Leads HCV elim in PEI and NS

22
Q

What does Sofosbuvir do in HCV?

A

Sofosbuvir inhibits RdRp, resulting in no viral RNA synthesis. It is a prodrug for hep C, is metabolized into a nucleotide monophosphate to get phosphorylated and become an active triphosphate. This will be incorporated into the growing hep C molec, causing chain termination (stops the growing chain bc structure of ribose sugar in triphosphate inhibits elongation of new viral RNA)

23
Q

Steps of coronavirus gene expression:

A
  1. Virus binds to host
  2. Attachment and endocytosis
  3. Release of viral genome into host cytoplasm. Has a (+)sense genome
  4. Engages with ribosome, starts making viral proteins through polyprotein synth
  5. Intermediate (-)sense genome is made
  6. Final (+)sense strand is made
24
Q

What do polyproteins do in coronavirus gene expression?

A

Have 5’ cap. They dont go all the way to the end of the genome but they span most of it

25
Q

Covid gene products:

A

Translation of 2 products:
1. ORF1A translates the shorter
2. ORF1A and ORF1B together translates the longer

  • Covid makes their own proteases which are represented on both polyprotein products
  • If it didnt make ORF1B, it couldn’t make polymerase as it is only encoded on 1B not 1A
26
Q

Paxlovid on covid polyprotein:

A

Paxlovid targets a protease and prevents RdRp release. The protease should be cutting a lot of downstream things, but Paxlovid is encoded in the small, ORF1A produced polyprotein. This means that Paxlovid inhibits the entire second half of the protein

27
Q

Why does processing with ORF1B result in longer polypeptide?

A

At stop codon on 1A, ribosome doesnt stop, instead slips into new reading frame to make another polypeptide

28
Q

What causes an RNA pseudoknot?

A

Pseudoknot is a secondary structure just below reading site, makes ribosome pause to work through its complex structure

29
Q

What does pausing at pseudoknot cause?

A

Ribosomal frameshifting: Ribosome slips while stalled, causing -1 slip that shifts reading frame

30
Q

What viruses have ribosomal frameshifting?

A

Coronavirus, influenza, HIV

31
Q

Why is ribosomal frameshifting beneficial to viruses?

A

Use this strategy to maximize potential of genome and make many types of proteins

32
Q

Are ER-localized transmembrane coronavirus proteins in progeny?

A

No. They are nonstructural, meaning they aren’t in progeny

33
Q

How many types of ER-localized transmembrane coronavirus proteins?

A

3

34
Q

What enzyme do we need frameshifting to make?

A

RdRp, because it is only in the long polyprotein. So, we need to get past the stop codon using frameshifting in order to get to the 2nd half

35
Q

What is Remdesivir?

A

Paxlovin is the first line of defence against coronavirus, remdesivir is the second. It inhibits RdRp causing chain termination and prevents viral RNA synthesis

36
Q

What do ER-localized transmembrane coronavirus proteins do?

A

Sit in ER membrane, crossing it many times. Drive creation of viral factories in cytoplasm that are known as replication organelles. To do this, they steal ER membrane to make a compartment where viral RNA can be secretly replicated. We want this to be secret so immune system patter-recognition receptors dont recognize the foreign viral RNA products

37
Q

What did the Dr Montserrat Barcena lab look at?

A

How do replication products made in secret get out? They discovered it is from a molecular pore around a replication organelle

38
Q

Cryo-electron tomography

A

Cross-section of cell —> computer reconstruction to go to 3d. Many images combined can represent accurate structures. Was used to see the pore in which viral RNA escapes in Montesserat lab

39
Q

What 2 things does RdRp do?

A
  • Copies genome (+ genome to – intermediates to + product)
  • Makes shorter sub-genomic +ssRNAs that encode structural proteins like spike
40
Q

2 features of replication organelles:

A
  • Hides viral RNA from PRRs
  • Crown shaped pore allows ribonucleotides in, lets viral RNAs exit to be translated in cytoplasm or full-length genomes to be packaged into new viral particles

MICI 2100 (11 decks)

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