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Virology > Exam II - review > Flashcards

Exam II - review Flashcards

1
Q

Topic 6, slide 6

Why would a DNA virus and a Retrovirus be affected by Actinomycin D?

A

They use cellular RNA Pol II that is inhibited by Act. D

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2
Q

Topic 6, slide 15

Which polynucleotide polymerases require divalent metal ions?

Bank: RdRp, DdRp, DdDp and RT

A

All of them

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3
Q

Topic 6, slide 16

What attributes the NTP specificity over dNTPs in RNA polymerases?

A

The 2′hydroxyl of the ribose sugar

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4
Q

Topic 6, slide 17

What domain of the hand ( fingers, thumb, palm ) is the RNA dependent RNA polymerase active site located in?

A

Palm

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5
Q

Topic 6, slide 22

In dsRNA viruses ( Reovirus) , RNA dependent RNA polymerases are located in the viral core.
What special structure is here and what does it do?

A

Turrets ( 12 )

Each turret is associated with one of the RNA dependent RNA polymerases

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6
Q

Topic 6, slide 24

In dsDNA viruses ( Reoviruses ), which of the following is correct?

A) The mRNAs are produced inside the viral core particle and never synthesized in the cytoplasm

B) The RNA dependent RNA polymerase is located inside the viral core below the turret proteins which synthesize the mRNAs

C) One of each of the 10 segments of double-stranded genomic RNA is associated with a viral RNA dependent RNA polymerase and is located under each “ turret proteins ” in each fivefold axis which synthesizes the mRNA

A

All of them

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7
Q

Topic 6, slide 32

In which of the following ways are Poliovirus and Coronavirus replication strategy similar ( both + stranded RNA )?

A) Circularization of template for initiation of RNA synthesis

B) Extensive RNA secondary structures such as stem-loops

C) Long distance RNA -RNA interactions

A

All of them

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8
Q

Topic 6, slide 38

What is the major difference between the Vesicular Stomatitis Virus (VSV) and Influenza Virus mRNA synthesis?

A) Genome is unimolecular (1 segment)

B) mRNAs and genomic RNAs are synthesized in the cytoplasm by viral RdRp

A

B; in the Flu, this occurs in the nucleus

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9
Q

Topic 6, slide 41

In - strand RNA viruses ( VSV ), what causes polyadenylation of mRNA?

A

Slippage of the RNA polymerase and recopying over a seven-residue uridine (U7) at each intergenic region

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10
Q

Topic 6, slide 42

In - strand RNA viruses ( VSV ), what causes genome RNA synthesis?

A

Encapsidation of the “leader RNA” by N protein acts as the “switch” from mRNA synthesis to genome RNA synthesis

RdRp reads through the intergenic region all the way to the end of template to synthesize the genome RNA

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11
Q

Topic 6, slide 46

In - strand RNA viruses, ( Influenza virus ), what is the mRNA synthesis primer?

A

a snatched Portion of 5′ Capped of Host Nuclear Pre-mRNA

The 5’ cap is cleaved and snatched from host nuclear pre-mRNAs

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12
Q

Topic 7, slide 56

Transcription of most but not all DNA viruses are carried out by RNA pol II – what is the exception?

A

Pox and giant viruses

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13
Q

Topic 7, slide 58

What does TfIID bind to?

A

the TATA sequence

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14
Q

Topic 7, slide 60

DNA binding protein can be enhancers or silencers. What are two examples of enhancer binding proteins?

A

Transcription factors in cis - within few 100 basepairs of the transcription initiation site

Transcription factors in trans - can be 1000s of base pair away from the transcription initiation site

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15
Q

Topic 7, slide 62

Signature structure of a DNA binding domain of a transcriptional activator protein is ________

A

the Zinc Finger

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16
Q

Topic 7, slide 66

When is the LT ( large T antigen ) created in SV40? What does it do?

A

the EARLY phase of transcription

Regulate DNA replication and expression of late genes

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17
Q

Topic 7, slide 67

What binds to the initiator sequence in SV40 in order to repress regulation?

A

Ibp = initiator binding protein, a cellular protein

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18
Q

Topic 7, slide 69

In Adenovirus transcription, what is produced…

  • in the early phase and controls early gene expression?
  • by the early phase that causes DNA replication and anti repression?
  • in the late phase (2) and enhances the late phase gene expression?
A
  • E1A
  • E2
  • IVa2 and L4
  • Might be an exam question about which one is correct – all of them are correct
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19
Q

Topic 7, slide 70

In Adenovirus transcription, E2F recruits the histone deacetylases ( Hdacs ). What is the result?

A

the DNA is wrapped more tightly and reduces transcription

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20
Q

Topic 7, slide 72

The “ immediate early ” transcription factor ____ is packaged into the Herpesvirus virion because otherwise it cannot be recognized.

A

VP16

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21
Q

Topic 7, slide 73

In Herpesvirus, transcription initiated by ____.
What is this the promoter of?

A

VP16

IE (immediate early ) transcription

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22
Q

Topic 7, slide 75

In the modification of mRNA, in the 5’ cap structure, what is the first capping nucleotide? What is the second connected by? What do the second and third base have?

A

guanine ( at the seventh position )

a 5’ – 5’ triphosphate linkage

an O methylation ( can be viral or cellular )

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23
Q

Topic 7, slide 77

In the modification of mRNA, where is Poly A added?

A

The cleaveage site of the pre mRNA

  • No polyU tracts, no slippage
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24
Q

Topic 7, slide 78

How is a poly A tail of mRNAs added to:

1) Adenovirus, HBV, HDV, Herpesvirus, Retrovirus

and

2) Influenza virus, VSV

and

3) Poliovirus, Coronavirus?

A

1) Cleavage of pre mRNA followed by polyadenylation
2) Copying at stretches of U in template RNA
3) Copying of long U stretch template RNA

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25
Q

Topic 7, slide 80

How many trans-esterification reactions take place in the splicing of pre mRNA?

A

2

26
Q

Topic 7, slide 82

What does alternative splicing do?

A

creates different mRNAs and proteins so in a limited size genome, more proteins can be created

27
Q

Topic 7, slide 84

Why is splicing mRNAs necessary?

A

for the binding and activation of the nuclear export proteins for most viral mRNA export into the cytoplasm from the nucleus

28
Q

Topic 7, slide 85

To transport unspliced viral pre-mRNAs, Retroviral mRNAs must have a nuclear export signal known as _____. What is this is HIV?

A

CTEs ( Constitutive transport element )

RRE ( Rev responce element )

29
Q

Topic 7, slide 86

Why do mRNAs in HIV need RRE in order to be transported?

A

because it is unspliced ( not spliced)

30
Q

Topic 8, slide 92

Why do viruses need hosts for DNA replication (3)?

A

1) Viral DNA replication always requires synthesis of at least one viral protein, sometimes many (hence always delayed after infection)
2) Simple viruses require more host proteins - smaller genomes
3) Complex viruses encode many, but not all proteins required for replication

31
Q

Topic 8, slide 94

Which of the following proteins / enzymes is not involved in viral DNA replication?

A) Helicases
B) Topoisomerases
C) Exonucleases
D) None of the above

A

D

32
Q

Topic 8, slide 98

In the SV40 large T antigen, what does the host range have?

A

the ATPase function, helicase function, and the phosphorylation of the threonine ; needed for binding the Rb

33
Q

Topic 8, slide 100

What is Rb loss associated with?

What binds to Rb and makes it lose its function?

A

Tumors; it is a tumor suppressor gene

LT; makes tumors

34
Q

Topic 8, slide 101

___, ____ or ___, ___ can all bind to Rb. Makes the Rb not able to bind ( causes tumors ).

A

SV40

HPV-16 or HPV-18

Ad5

35
Q

Topic 8, slide 106

In SV 40…

LT is a ____ that binds on the opposite side of the origin

____ ( single strand binding protein ) binds LT

LT shows helicase activity when bound to ___

LT has intrinsic ____ helicase activity

A

hexamer

RpA

RpA

3′→ 5′

36
Q

Topic 8, slide 107

In SV40 synthesis of leading and lagging strands, what is the clamp and what is the clamp promoter?

A

PCNA

RFC

37
Q

Topic 8, slide 108

In SV40 synthesis of leading and lagging strands, what does gap repair?

A

DNA pol delta ( δ )

38
Q

Topic 8, slide 110

During DNA replication, _____ or ____ reduced the strain on the supercoiling ( relaxes )

At the end, the _______ does the resolution

A

topoisomerase I or II

topoisomerase II

39
Q

Topic 8, slide 112

In Parvoviruses, DNA replication, what does Rep78/68 do?

A

required for initiation and resolution: endonuclease, helicase, binds 5′-terminus

40
Q

Topic 8, slide 117

In Herpesvirus ignition of DNA replication, what is responsible for circularization of the incoming viral DNA immediately after its delivery into the nucleus?

A

DNA ligase IV/XRCC4

41
Q

Topic 9, slide 129

( +) strand RNA viruses usually have naked genomic RNA ( no nucleocapsid ), exceptions are what (2)?

A

Retroviruses and Coronaviruses

42
Q

Topic 9, slide 133

Every virus that codes reverse transcriptase (does or does not) have integrase to integrate the converted DNA

A

does not

43
Q

Topic 9, slide 137

In HIV-1 reverse transcriptase, how many divalent metal ions are needed?

A

4

44
Q

Topic 9, slide 139

Why are retroviruses relatively resistant to UV and ionizing radiation?

A

Copy – choice rebuilds the genome ( two copies of all genes into one )

45
Q

Topic 9, slide 140

What is the signature structure of the tRNA used in the reverse transcription of the primer and the binding of the primer binding site in a retrovirus?

A

ΤψC ( T psi C ) loop and arm is the pbs ( primer binding site )

46
Q

Topic 9, slide 141 / 142

In Retroviral Reverse Transcription, first template exchange (of 2)…

Priming of (‒) DNA strand synthesis is from ___

Priming of (+) DNA strand synthesis is from ___

A

tRNA

PPT (polypurine tract; A and Gs)

47
Q

Topic 9, slide 143

In Retroviral Reverse Transcription, what happens (2)?

A

In two different template exchanges…

1) Degradation of the viral RNA by RNase H
2) Generation of two LTRs ( at each end of the DNA )

48
Q

Topic 9, slide 148

What is the BAF? What does it do?

A

BAF = barrier of autointegration factor = prevents autointegration of the retroviral DNA

Tick question: Which interaction is incorrect? All interactions are correct

49
Q

Topic 9, slide 153

More than ___% of the human genome comprises mobile genetic elements, including endogenous proviruses and other retroelements

A

40

50
Q

Topic 9, slide 154

________ and _______ both have LTRs

________ and ________ do not have LTRs

A

Endogenous retrovirus

retrotransposons

LINEs

SINEs

51
Q

Topic 9, slide 156

______ are produced during normal human embryogenesis

A

HERV-K mRNAs

52
Q

Topic 9, slide 158

How does a capsid allow entry into a cell?

A

Has a pore

53
Q

Topic 9, slide 159

_____ happens only in the core particle with partially assembled capsid

A

Reverse transcription

54
Q

Topic 9, slide 161

A Second template exchange is what kind of formation?

A

Hairpin

55
Q

Coronavirus RNA Synthesis, slide 165

What is the structure of the Coronavirus and what is it similar to?

A

Plus ( + ) strand RNA viruses with encapsidated genomic RNA in the form of the nucleocapsid also seen in retroviruses

56
Q

Coronavirus RNA Synthesis, slide 167

In the full length genome, what is manufactured first?

A

Two long polyproteins are translated by the ribosome by ribosomal frameshifting

57
Q

Coronavirus RNA Synthesis, slide 170

In differential synthesis, what would happen with…

No slippery sequence & yes pseudoknot

or

No slippery sequence & no pseudoknot

A

No slippery sequence & yes pseudoknot – add viral genome and translation – small amount of transcription product

No slippery sequence & no pseudoknot – add viral genome translation – virus dead

58
Q

Coronavirus RNA Synthesis, slide 173

What do NSP7 and NSP8 do?

What is responsible for genome maintenance?

A

processivity factors and confer the stability of the RNA duplex

Exonucleases and endonucleases

59
Q

Coronavirus RNA Synthesis, slide 178

Coronavirus produces two polyproteins – ______

Subgenomic mRNAs are of ____ lengths

Only the _____ is translated

A

1a and 1ab

variable

first open reading frame

60
Q

Coronavirus RNA Synthesis, slide 180

_____ of template for initiation of RNA synthesis with the help of extensive RNA secondary structures such as stem-loops and long-distance RNA -RNA interactions

A

Circularization

Like poliovirus!

61
Q

Coronavirus RNA Synthesis, slide 181

What does the cap do? What does it not do?

A

Cap confers stability to the genome/mRNA but NOT maintenance of large genomes

Virology (3 decks)

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