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MolMic > Viruses > Flashcards

Viruses Flashcards

1
Q

What types of genomes do viruses have?

A 
dsDNA
ssDNA
dsRNA
ssRNA
Circular
Linear
Non-segmented
Segmented
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2
Q

How are viruses classified?

A

Baltimore classification - how they replicate genome and produce mRNA

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3
Q

Do viruses generally insert their genome into the host cell genome?

A

No - only retroviruses do

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4
Q

What does reverse transcriptase do?

A

Makes DNA from RNA

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5
Q

How do DNA viruses express their genome?

A

Same flow of info as cell: DNA -> RNA -> Protein

Make use of cell transcription and translation machinery

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6
Q

How do RNA viruses express their genome?

A

Eukaryotic cells don’t have RNA dependent RNA polymerase
Eukaryotic cells don’t often encode for more than one protein on each mRNA
All encode RNA dependent RNA polymerase

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7
Q

How do +ve strand RNA viruses replicate?

A

Genomic RNA acts as mRNA on cell entry

Translated to produce polymerase

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8
Q

How do -ve strand RNA viruses replicate?

A

Need to carry polymerase in virion

Required to convert -ve RNA to +ve RNA after entry

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9
Q

How does dsRNA replicate?

A

Have segmented genomes
+ mRNA produced
Produces proteins and +/- RNA

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10
Q

How does ssRNA replicate?

A

+ve sense produces protein, a -ve RNA to produce a +ve mRNA or genomic RNA packaged into virion

-ve sense produces +ve mRNA to produce protein or +ve RNA to produce -ve RNA

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11
Q

What are some +ve stranded RNA viruses?

A 
Picornaviridae
Coronaviridae
Flaviviridae
Alphaviridae
Calciviridae
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12
Q

What are Picornaviruses?

A

Non-enveloped
Icosahedral
Diverse - over 200 serotypes

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13
Q

What are the groups of picornaviruses?

A

Enteroviruses
Eg. Poliovirus
Faecal-oral transmission
Poliovirus can cause paralysis in most virulent strains

Rhinovirus
Many serotypes
One cause of the ‘common cold’

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14
Q

What does the picornavirus genome look like?

A

Small section of ssRNA, +ve sense - 7.2-8.5 kb
Has virus protein at 5’ end - caps it
Long UTR at 5’ end
3’ end polyadenylated
Encodes single polyprotein in one reading frame

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15
Q

How does viral receptor binding occur?

A

Binds to specific receptor - CD155 in polivirus
Endocytosis to uptake virus
Loss of VP4 allows RNA to exit plasmid and enter cytoplasm

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16
Q

How long does gene expression take for +ve sense RNA viruses?

A

Picornavirus very rapid - 5-10 hours
Genomic RNA directly translated by ribosomes
~30 min after infection, cellular protein synthesis declines sharply - ‘Shutoff’

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17
Q

What is ‘Shutoff’?

A

Cleavage of ‘cap-binding’ complex’ (CBC)
Involved in binding the m7G cap structure at the 5’ end of all eukaryotic mRNAs during initiation of translation
CBC cleaved by poliovirus protein 2A

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18
Q

How is viral RNA recognised and translated after Shutoff?

A

5’ UTR contains IRES: Internal Ribosome Entry Site
Overcomes need for 5’ cap
Allows translation of viral mRNA

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19
Q

What happens to the polyprotein?

A

Proteases encoded within the polyprotein which cleaves itself to produce smaller proteins

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20
Q

Why is the Vpg protein important?

A

Acts as a primer for complimentary strand synthesis
2 uracils attached to Vpg by viral RNA polymerase 3D
Base pair with Adenosines in polyA tail

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21
Q

How are virus particles assembled for Picornavirus?

A

Capsids preform and RNA packaged in

Formation of capsid - polyprotein cleaved to form VP0, VP3, VP1 complex
As matures virus cleaves VP0 to VP2 and VP4 which seal the capsid

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22
Q

What are some examples of -ve RNA viruses?

A

Orthomyxoviruses - influenza
Rhabdoviruses - rabies
Paramyxoviruses - mumps, measles, RSV
Filoviruses - ebola

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23
Q

What are the different types of influenza?

A

Influenza A - infect wide variety of hosts, epidemics and pandemics
Influenza B - not as severe as type A, seasonal epidemics
Influenza C
Influenza D

A and B have annual vaccines

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24
Q

What is the structure of -ve RNA viruses?

A

Pleiomorphic - mostly spherical
Lipid envelope and glycoprotein spikes - haemaglutinin trimer (HA) for receptor binding and entry, neuraminidase tetramer for exit cell efficiently
Inner side of envelope lined by matrix protein M1
8 genome segments packaged into core
‘RNP’ (RNA and nucleoprotein) in helical form

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25
Q

How does attachment occur for -ve RNA viruses?

A

HA spikes bond to mucoproteins with terminal sialic acid
HA monomers have 2 disulphide linked domains, HA1 and HA2
Interaction can be reversed by polysaccharide cleavage by NA spikes

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26
Q

How does entry occur for -ve RNA viruses?

A

Particle engulfed by endocytosis
Endocytic vesicles acidified by cell - M2 protein
Low pH results in conformational change in HA
Activates membrane-fusion function in HA2
Fusion of viral envelope with endosomal membrane - releases RNA genomic segments into cytoplasm

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27
Q

How does gene expression and genome replication occur?

A

Nuclear targeting sequences in NP protein - translocates into nucleus through a nuclear pore
-ve sense genomic segment can be used as a template for mRNA or a cRNA intermediate to make more copies of genomic RNA

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28
Q

How does host protein ‘Shutoff’ occur for -ve sense RNA viruses?

A

Steal cellular mRNA caps for their own protein synthesis
PA, PB1, and PB2 bind to cap and cleave it, added to viral -ve RNA segments
Uses cap as a primer and encoded a polyA tail
Destroys cellular mRNA

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29
Q

How does viral assembly occur for -ve RNA viruses?

A

Nucleoprotein (NP) migrates back into nucleus
Associated with newly-synthesised vRNA to form nucleocapsids
Migrate back out into the cytoplasm and towards cell membrane - higher level of free NP = more cRNA synthesis

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30
Q

What are some viruses with dsDNA genome?

A

Papillomaviridae, Adenoviridae, Herpesviridae, Polyomaviridae, Poxviridae

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31
Q

How do dsDNA viruses replicate?

A

+/- DNA can be transcribed to mRNA for translation of proteins to make capsid
OR
Can be replicated to produce more dsDNA

32
Q

What are some examples of ssDNA viruses?

A

Circoviridae, Parvoviridae

33
Q

How so ssDNA viruses replicate?

A

DNA used as template to produce dsDNA
dsDNA used to produce mRNA to make proteins
OR
Split in to + and - DNA, + strand packaged in to virion

34
Q

What do all DNA viruses have?

A

Origin of replication:
Hairpin structures eg. parvovirus
Multiple origins in some eg. herpesvirus
Can be at the end and use a terminal protein to initiate replication eg. adenovirus
Can have a looped DNA structure that initiates replication eg. poxvirus

35
Q

What are the 2 mechanisms of DNA synthesis?

A

Replication fork - RNA primers

Strand displacement - never RNA primed

36
Q

Which viruses use a replication fork for DNA synthesis?

A

Papillomaviruses, Polyomaviruses, Herpesviruses, Retroviral proviruses

37
Q

Which viruses use a strand displacement for DNA synthesis?

A

Adenoviruses, Parvoviruses, Poxviruses

38
Q

How does the replication fork mechanism work?

A

Leading and lagging strands as can only synthesise in 5’-3’ direction
Produced replication bubble as in bacteria

39
Q

How does strand displacement work?

A

Template strand copied by polymerase
Non-template strand displaced and coated in ssDBP
When DNA sythesis of template stand complete displaced strand circularises as it base pairs with itself
This is then bound by a polymerase and DNA synthesis occurs, removing ssDBP

40
Q

How does parvovirus prime itself for replication?

A

Self base-pairing loop acts as a primer for DNA replication

41
Q

What are papovaviruses?

A

2 genera of oncogenic viruses:
Papillomaviruses - eg. HPV
Polyomaviruses - eg. SV40

42
Q

What is HPV?

A

Human Papillomavirus
>160 types
Ubiquitous - infection can be completely asymptomatic
BUT
Some can cause benign skin warts - papillomas
Others cause cervical cancer - HPV16 and HPV18

43
Q

What is the structure of HPV?

A

Non-enveloped DNA genome in icosahedral capsid
L1 makes up capsid as well as varying amounts of L2
Current vaccine targets L1

44
Q

What is the genome structure of HPV?

A

8 kb
Circular dsDNA, persists as an episome ie. doesn’t normally integrate into host DNA
Genome divided to late and early regions
Late - capsid genes: virion formation, genome encapsidation, membrane penetration, post-entry trafficking

45
Q

Which are the oncogenes?

A

E6 and E7
Immortalise the cell and prime it for viral DNA replication by disrupting the cell cycle
Mediate inhibition of p53 and pRB tumor-supressor genes that block cell cycle from G phase to S phase

46
Q

What are the other functions of E6 and E7?

A

E6: activates telomerase
E7: triggers chromosomal instability - could be why HPV can integrate into genome
Both essential for maintenance of HPV-transformed cells

47
Q

What’s the function of E1?

A

Helicase starts replication fork/bubble, recruits cellular DNA polymerase to Ori

48
Q

What’s the function of E2?

A

Transcriptional regulation
Recruit E1 to Ori
Tethers viral DNA to chromosomes during cell division

49
Q

What is the HPV lifecycle?

A

Needs access to basal layer

Expression changes as the host cells replicate and move further to the upper layers of cells

50
Q

Is HPV enough to cause cancer?

A

No, probably requires co-factors
High infection rate but only a small % progress to invasive cancer
Long latency period

51
Q

What is required for cervical carcinoma?

A

HPV DNA integration is required in most
When genome integrates often a part of the HPV E2 protein deleted - regulates expression of E6 and E7
Leads to overexpression resulting in unregulated cell cycling

52
Q

What are the 3 sub-families of herpesvirus?

A

Alphaherpesvirinae - HSV-1, HSV-1, VZV
Betaherpesvirinae - CMV, HHP-6, HHP-7
Gammaherpesvirinae - EBV, KSHV
All associated with long latency period

53
Q

What’s the structure of herpesviruses?

A

Large DNA genome
Icosahedral capsid
Protein tegument surround the capsid
Envelope contains many glycoproteins

54
Q

What’s the genome structure of herpesviruses?

A

Unique long (UL) and unique short (US) regions bounded by inverted repeats

55
Q

How does cellular entry occur for herpesviruses?

A

HSV envelope contains at least 9 glycoproteins
Some initiate attachment and others the process of fusion
Capsid migrates to the nucleus - enters via nuclear pore, genome is circularised

56
Q

How does herpesvirus latency occur?

A

Viral genome exists as episome in circular form and produces very few if any proteins
No antigens for cell to recognise
Only starts producing proteins when activated

57
Q

How does gene expression occur in herpesviruses?

A

3 classes of mRNA made:
Alpha - immediate early (IE) mRNAs
Regulators of virus transcription

Beta - (delayed) early mRNAs
Non-structural regulatory proteins and minor structural proteins
DNA replication enzymes

Gamma - late mRNAs
Major structural proteins

58
Q

How does genome replication occur for herpesvirus?

A

In nucleus
Virus-encoded DNA-dependent DNA polymerase and DNA-binding protein involved
Rolling circle replication - nick introduced, replication starts and strand displacement which is replicated, produces genome lengths which are cleaved and circularised

59
Q

What are retroviruses?

A 
Enveloped viruses
ssRNA genome
2 copes of genome - diploid viruses
Replication involves:
reverse transcription of RNA genome into DNA
integration of DNA into host chromosome
60
Q

How do retroviruses replicate?

A

RNA to -DNA to dsDNA - integrates into host genome
+mRNA produced to make proteins
OR
Genomic +RNA produced packaged into virion

61
Q

What is the structure of retroviruses?

A

Host-derived lipid bilayer envelope
Surface glycoproteins
Matrix
Capsid containing RNA in nucleocapsid, protease, integrase, and reverse transcriptase

62
Q

What is retroviral genome structure?

A

RNA
5’ Cap structure
3’ polyA tail
Protein coding region with: gag, pro, pol, env
Always in that order
Encapsidation signal shows which RNA should be packaged into capsid

DNA
Long terminal repeats at either end containing promoter and enhancer elements

63
Q

What are the retroviral proteins?

A

Gag - structural components eg. capsid proteins
Pro - protease important for maturation of virus
Pol - reverse transcriptase, Rnase H, and integrase
Env - envelope proteins

64
Q

How does reverse transcriptase occur?

A

tRNA binds at a PBS near 5’ end
This primes the start of reverse-transcription, which proceeds through a unique sequence and then repeat to 5’ end on RNA template
Repeat sequence of new DNA can now bind 3’ end of RNA
Primes continued reverse transcription through whole TE transcript
RNA template degraded by RNAse H leaving a fragment that primes 2nd strand DNA synthesis
Synthesis moves through 3’ unique sequence, the repeat and 5’ unique sequence
This fragment primes from 5’ end
Synthesis completes in both directions
Resulting dsDNA enters nucleus with viral integrase allows 3’ OH of each strand to attack target at sites a few bps apart - short target site duplication

65
Q

How does HIV attachment and entry occur?

A

SU protein attaches to CD4 on target cell - expressed on CD4 T-lymphocytes and macrophages
CD4 not sufficient, co-receptor required, chemokine receptors
Conformational change causes membrane fusion

66
Q

How does HIV get a range of proteins from one transcript?

A

Alternative splicing using host cell machinery

67
Q

How does HIV maturation occur?

A 
Driven by viral protease
Cleaves nucleocapsid matrix proteins to rearrange and form final structure
Immature -> mature virus particles
Essential for HIV to be infectious
Target for anti retroviral drugs
68
Q

What are the three types of retroviral transformation?

A

Acutely transforming
Viral oncogenes
Growth factors, transcription factors, kinases
Eg. Rous Sarcoma Virus

Insertional mutagenesis
Viral integration near cellular proto oncogene - myc
Eg. avian leukosis viruses

Transacting functions
Transactivation of cellular genes - HTLV-1 Tax gene

69
Q

What are oncogenes?

A

Several protein families involved in regulation of cell growth and replication
Growth factors and receptors
Signal transduction pathways
Transcription factors

70
Q

What are cancer associated features of retrovirus replication?

A

Reverse transcription of diploid RNA genome to dsDNA genome - recombination
Integration into target cell DNA
Transcription of viral genes controlled by promoter and enhancer elements in LTR

71
Q

How do acutely transforming retroviruses cause oncogenesis?

A

Cause tumours rapidly
Carry cellular oncogene in genome - captured
Almost all defective and require helper virus
Tumours polyclonal

72
Q

How does oncogenic capture occur?

A

Integration adjacent to proto-oncogene
Read-through transcription
Co-packaging
Recombination during reverse transcription
Integration of resulting DNA genome containing onc
Transcription of viral RNA containing onc controlled by viral LTR

73
Q

How do insertional mutagenesis retroviruses cause oncogenesis?

A

Activate cellular oncogene by provirus insertion
Non-acute-transforming retroviruses
Tumours develop slowly
No cellular oncogene
Replication-competent
Tumours monoclonal
Transform cells by insertional mutagenesis

74
Q

How do transacting functions retroviruses cause oncogenesis?

A

Encode viral oncogene with no cellular homologue
Can activate cellular gene transcription
OR
Directly oncogenic

75
Q

What are the human retroviruses that cause cancer?

A

HLV1
HLV2
HIV1
HIV2

76
Q

What is HLV1?

A

Deltaretrovirus
Complex genome
Lacks classical oncogene
Tax protein involved in oncogenesis - causes ATLL
Also trans-activates expression of cellular genes
Lead to T-cell activation and proliferation

77
Q

How can HIV 1 lead to oncogenesis?

A

NO direct cause but immunodeficiency can leave person susceptible to other oncogenic viruses

MolMic (5 decks)

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