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Virology > Lecture 6 - DNA Virus Replication > Flashcards

Lecture 6 - DNA Virus Replication Flashcards

1
Q

Cellular polymerase that makes mRNA from DNA

A

RNA polymerase II

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2
Q

Where does RNA polymerase II terminate elongation?

A

At AATAAA (poly-A signal)

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3
Q

Parts of the core promoter

A

1) TATA sequence

2) Initiator sequence

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4
Q

Role of the initiator sequence

A

Lies just before what is to be transcribed into mRNA.

Occupies +1 position of gene

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5
Q

Role of TATA sequence

A

Recruits RNA polymerase II

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6
Q

Components of the promoter

A

1) Local regulatory sequences

2) Core promoter

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7
Q

Local regulatory sequences in the promotor

A

Factors that define whether a gene is transcribed or not.

Often binding sites for transcription factor proteins.

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8
Q

Components of the transcriptional control region upstream of a gene

A

1) Distant regulatory sequences

2) Promoter

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9
Q

Distant regulatory sequences

A

Enhancers, silencers

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10
Q

Ways in which enhancer-binding proteins can act

A

1) Additively, where their action adds together

2) Synergistically, where they complement each others enhancement

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11
Q 
ds DNA replication
1)
2)
3)
4)
5)
A

1) Parental DNA is unwound by a helicase
2) Short RNA primers complementary to the template are synthesised by a primase
3) Other DNA-binding proteins keep the replication bubble open
4) DNA polymerase grows primed template in5’ to 3’ direction for both strands (lagging and leading strand)
5) Free ends are ligated

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12
Q

Name for short, newly synthesised, discontinuous portions of DNA on lagging strand

A

Okazaki fragments

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13
Q

Baltimore I

A

dsDNA –> (+) mRNA

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14
Q

Examples of Baltimore I viruses

A

Papovaviridae
Adenoviridae
Herpesviridae
Poxviridae

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15
Q

Baltimore II

A

ssDNA –> dsDNA –> (+) mRNA

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16
Q

Which Baltimore class does papovaviridae belong to?

A

Baltimore I

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17
Q

Example of a Baltimore II virus

A

Parvoviridae

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18
Q

Where do DNA viruses replicate?

A

In the nucleus

EXCEPT POXVIRUSES

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19
Q

Example of a papovavirus

A

Simian virus 40 (SV40)

20
Q

SV40

A

Naked, dsDNA papovavirus

21
Q

SV40 genome

A

dsDNA, circular, complexed with histones to form a mini-chromosome

22
Q

SV40 genome gene architecture

A

Circular.
Counterclockwise are early genes (LT, ST)
Clockwise are structural proteins (VP2, VP3, VP1).
There are overlapping reading frames of genes (VP2 and VP3).

23
Q

LT role

A

Large T antigen.

Non-structural SV40 protein. Promotes genome replication.

24
Q 
SV40 replication
1)
2)
3)
4)
5)
A

1) Genome released into nucleus, early RNA transcripts made with cell RNA pol II. Transcription factors (EG: NF-kB) bind promotor of early genes (‘early promoter’).
2) Alternative RNA splicing, RNA moves to cytoplasm, translation of early proteins.
3) Large T protein enters nucleus, binds origin on viral genome, promotes genome replication
4) Late promoter is antirepressed as viral genome reaches a certain concentration.
5) Structural genes transcribed, translated

25
Q

How does LT promote genome replication?

A

LT binds sequences flanking the core promoter, and assists in unwinding DNA genome, accelerating initiation of replication.

Binds as a hexamer.

Allows binding of single-stranded DNA binding protein, replication protein A, DNA polymerase alpha-primase.

26
Q

Motif in SV40 that promotes RNA pol II transcription of early genes

A

72bp enhancer repeat. Increases RNA synthesis by 100x

27
Q

How does LT switch the activity of the promoter?
1)
2)
3)

A

1) LT initiates viral DNA synthesis.
2) Cellular inhibitory binding proteins (IBP) inhibit late promoter.
3) LT causes genome to increase relative to IBP, diluting IBP, until the late promoter is no longer inhibited.

28
Q

How does SV40 keep the leading strand and lagging strands together in DNA synthesis?

A

A loop of template strand is formed at the replication complex

29
Q

Two types of viral DNA synthesis

A

1) Fork

2) Displacement

30
Q

Fork DNA synthesis
1)
2)
3)

A

1) Can initiate at an origin sequence
2) Always uses an RNA primer
3) Always has a leading and lagging strand

31
Q

Displacement DNA synthesis
1)
2)
3)

A

1) Doesn’t use an RNA primer
2) No lagging strand
3) Commonly initiates at free DNA ends, uses a viral polymerase

32
Q

Viruses that use fork DNA synthesis

A

1) Papovaviruses

2) Herpesviruses

33
Q

Viruses that use displacement DNA synthesis

A

1) Adenoviruses (protein)

2) Parvoviruses (DNA hairpin)

34
Q

Herpesvirus genome

A

dsDNA, linear.
126kb.
Complex. Many open reading frames, internal inverted repeats.

35
Q

Herpesvirus replication
1)
2)
3)

A

1) VP-16 (tegument layer) initiates transcription of immediate early promoter
2) ICP0 and ICP4 change RNA transcription to early genes
3) Early genes activate transcription of late genes

36
Q

Type of viral replication used by herpesviruses

A

Fork replication

37
Q

Direction that DNA is assembled in

A

5’–>3’

38
Q

Adenovirus genome structure

A

dsDNA, linear.

Origins at extremes of genome, use terminal proteins rather than RNA primer to initiate transcription

39
Q 
Adenovirus replication 
1)
2)
3)
4)
5)
6)
A

1) Genome to nucleus.
2) Cellular RNA pol II transcribes immediate early genes, these are alternatively spliced
3) E1A is transcribed and translated, protein brought into nucleus
4) Increased E1A concentrations lead to transcription of early genes, including genes for viral DNA replication
5) Early proteins increase viral DNA replication, lead to transcription of late genes, which encode viral structural proteins
6) Virion assembly occurs in the nucleus

40
Q

Where does adenovirus virion assembly occur?

A

Nucleus

41
Q

How is DNA replicated in adenoviruses?

A

No lagging strand.
Continuous DNA synthesis from each end of the genome.
Displacement.

42
Q

Parvovirus DNA replication
1)
2)

A

Displacement

1) Terminus of parvovirus ssDNA genome has an inverted terminal repeat
2) ITR folds into a hairpin structure, which serves as both a primer and template for dsDNA synthesis

43
Q

Inverted terminal repeat

A

Composed of a central and flanking palindromic repeat sequence.

In parvoviruses, folds to form a hairpin structure, which acts as a primer and template for ssDNA genome replication

44
Q

Example of a parvovirus

A

Adeno-associated virus

45
Q

Poxvirus replication oddity

A

DNA virus, but replicates in the cytoplasm.

Therefore RNAs don’t splice alternatively

46
Q

How can poxviruses replicate in the cytoplasm?

A

Encode their own polymerases

Virology (29 decks)

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