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Module 2 > Retroviruses: Structure and Function > Flashcards

Retroviruses: Structure and Function Flashcards

1
Q

What are endogenous retroviruses?

A

remnants of historical infection, usually incomplete genomes which are transmitted in the germline

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2
Q

How much of the human genome do endogenous retroviruses make up?

A

8-12%

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3
Q

What is the common mechanism of replication of all retroviruses?

A

integrate into the host genome via reverse transcriptase

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4
Q

Give an example of insertional mutagenesis involving retroviruses?

A

in SCID gene therapy patients using retroviruses some patients got leukaemia as a result

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5
Q

How was retroviral taxonomy originally carried out?

A

based on morphology- size; shape of core; length of spikes, under electron microscopy

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6
Q

What are the gag proteins?

A

matrix; capsid; nucleocapsid

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7
Q

What are the structural components of a virion?

A

gag proteins; env proteins; lipid envelope

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8
Q

Where does the membrane envelope of a virion derive from?

A

host cell plasma membrane during virion production

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9
Q

What lines the membrane envelope?

A

gag-encoded matrix protein

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10
Q

What are the 2 env encoded glycoproteins?

A

transmembrane compoenet and surface component

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11
Q

What si the function of the TM env encoded glycoprotein?

A

contains peptide that promotes fusion of virion memrbane with target cell membrane

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12
Q

How is the SU glycoprotein attached to TM?

A

non-covalently

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13
Q

What is the virion core?

A

round or triangular structure somposed of gag-encoded capsid protein

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14
Q

What is found within the virion core?

A

2 copies of viral genomic RNA coated by gag-encoded nucleocapsid protein and pol-encoded enzymes

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15
Q

What are the 2 types of retroviral genome?

A

simple and complex

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16
Q

Rather than morphology, how are retroviruses now classified?

A

according to their genome organisation (simple/complex) and sequence analysis

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17
Q

Give an exmample of a virus with a simple genome?

A

murine leukaemia virus

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18
Q

What makes up a simple retrovirus genome?

A

LTRs at either end with gag, pol and env genes in between

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19
Q

What is a major determinant of virus phenotype?

A

virus envelope protein

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20
Q

What are the 6 additional genes that HIV possesses in addition to the simple genome?

A

Vpr; Rev; Vif; Tat; Vpu and Nef

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21
Q

Which of the 6 extra genes that HIV-1 has are absolutely essential for replication?

A

Tat and Rev

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22
Q

How are the simple genes encoded?

A

as polyproteins which have to then be cut down to size

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23
Q

What 4 proteins are encoded by HIV pol?

A

reverse transcriptase; protease; integrase and RNAase

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24
Q

What is the function of RNAase encoded by HIV?

A

eliminates RNA

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25
Q

What is the TM glycoprotein of HIV?

A

gp41

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26
Q

What si the SU glycoprotein of HIV?

A

gp120

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27
Q

What is the function of Tat?

A

transactivates transcription- produces protein which binds to LTR and activates viral transcription

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28
Q

What si the function of Rev?

A

regulates splicing- has a nuclear location signal and controls which RNA moves in and out of nucleus: without, all mRNA stays in nucleus

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29
Q

What is the function of Nef?

A

immune evasion- decreases MHC-I and Cd4 on surface of cell- without HIV grows very slowly

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30
Q

What is the function of Vif?

A

involvedi n viral assembly and increases viral infectivity- without decreased level of replication

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31
Q

What is the function of Vpu?

A

modulates CD4 and apoptosis

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32
Q

What is the function of Vpr?

A

allows nuclear import via importin interaction: most viruses need a cell to be rpelicating to access nucleus as in mitosis nuclear breaks down, this allows HIV to get in without replication

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33
Q

What is the most diverse part of the virus?

A

the envelope- in order to evade the immune system

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34
Q

What are the 2 types of retroviral phylogeny?

A

orthoretrovirinae and spumaretrovirinae

35
Q

Where does reverse transcription happen in the host cell?

A

cytoplasm within a copmlex of viral proteins

36
Q

What are the functions of the envelope protein?

A

determines viral tropism and viral diversity; repsonsible for cytopathic effect and is the target of humoral repsonse

37
Q

Give an example of a cytopathic effect of retroviruses?

A

HIV infected T cells in vitro causes multinucleated syncytia

38
Q

What are the 3 components of reverse transcription?

A

template; primer and revers transcription

39
Q

What is the template for reverse transcription?

A

viral genomic RNA

40
Q

What si the primer for reverse transcription?

A

a specific tRNA taken from the producer cell during viral assembly that anneals to homologous sequences- primer binding site of viral RNA

41
Q

What are the functions of reverse transcriptase?

A

a viral DNA polymerase that utilises RNA or DNA as template, also posseses RNAase activity that degrades RNA when complexed with DNA

42
Q

What are the steps of reverse transcription?

A

tRNA extended to form a negative strand; RNAase removes RNA hybridised to DNA; first jump: neg strand DNA hybridises with remaining R sequence; then neg strand DNA extended; majority of RNA removed; 3’ end of plus Dna strand extended as PBS attaches to tRNA; RNA and tRNA removed; second jump so that both PBS are joined together; both DNA strands completed

43
Q

What makes up the LRRs?

A

U3(located at 3’ end); R and U5(located at 5’ end)

44
Q

What was syncytial induction of CD4 T cells by HIV used for?

A

a quick assay to determine during efficacy against HIV

45
Q

What is integration?

A

covalent linkage of the dsDNA copy of hte viral genome to host chromosomal DNA

46
Q

What type of enzyme is integrase?

A

a nuclease

47
Q

How does integration work?

A

integrase clips 2 nucleotides from the 3’ end of the 2 LTRs then makes a staggered cut in host chromosomal DNA in a random location and ligates the clipped 3’ ends of the viral DNA to host DNA; host enzymes then repair the 5’ ends of the viral DNA

48
Q

What does retroviral genomic RNA incorporation in to virions require?

A

a cis-acting structure at the 5’ end of hte RNA called psi; a trans-acting factor, the zinc-fingers in the gag polyprotein

49
Q

What is the function of the gag polyprotein in HIV-1 virion assembly?

A

directs virion budding and release- myristylated atthe amino-terminus and accumulates the cytoplasmic membrane where is multimerizes to form the virion macromolecular complex

50
Q

Where are the zing-fingers which help incorporate viral genomic RNA into virions?

A

in the nucleocaspid domain of hte gag polyprotein

51
Q

How is the envelope glycoprotein cleaved?

A

by a cellular protease in the golgi to produce TM and SU

52
Q

What does the gag-pol polyprotein consist of?

A

gag polyprotein fused to the pol-encoded enzymes which in HIV-1 is produced by a ribosomal frameshift between the gag and pol reading frames

53
Q

How is the gag-pol polyprotein integrated into nascent virions?

A

via interactions with the gag polyprotein

54
Q

What needs to happen to create a mature virion?

A

when virions exit the cell, the gag and gag-pol polyproteins are intact, but once virion is released, protease is activated and the polyproteins cleaved–mature

55
Q

What are the primate retroviruses in order of pathogenicity?

A

SIV–STLV–SRV–PFV

56
Q

What subfamily do HIV and SIV belong to?

A

lentiviruses

57
Q

What are the 2 families of complex retroviruses?

A

spumaretroviruses and deltaretroviruses

58
Q

What family does SRV belong to?

A

betaretrovirus

59
Q

What family does PFV belong to?

A

spumaretrovirus

60
Q

What is the difference in morphology between SIV and HIV?

A

no difference

61
Q

What is sooty mangaby SIV the originator of?

A

HIV2

62
Q

What is chimpanzee SIV the origin of?

A

HIV-1

63
Q

What are the serological similarities of HIV-1 patients to monkets with SIV?

A

share same antibodies to core proteins but not to envelope proteins

64
Q

What happens when Asian macaques are given sooty mangaby SIV?

A

get SAIDs

65
Q

What has SAIDs shown for humans?

A

given a parallel model to study; vaccine has been created for SAIDs using a fixed form of virion- shows that virus can be vaccinated against if the right immunogen is found

66
Q

Which primates are infected with SRVs?

A

mainly macaques

67
Q

Where can SRV be foudn in infected monkeys?

A

in all bodily fluids

68
Q

What does SRV infection result in?

A

an immunodeficiency profile similar to AIDs and SAIDs- no genetic or morphological similarities however

69
Q

What is the difference between different SRV serotypes?

A

different evelopes which causes variation in severity of disease; the macaques infected and the disease manifestations

70
Q

What is a serotype?

A

a serologically distinguishable strain of a microbe

71
Q

Why did SRV cause problems in HIV vaccine research?

A

it was possible to create a vaccine inducing neutralising antibodies which totally protected the monkeys whereas in HIV, even having lots of neutralising antibodies does not protect

72
Q

Why are foamy viruses called such?

A

see lots of bubbles in cells infected

73
Q

Why may foamy virus research be useful?

A

doesn’t cause disease; can be grown in pretty much every cell- good vector for gene therapy- no human disease and one of biggest retroviruses so could incorporate large genes into it

74
Q

What is zoonosis?

A

emergence of novel viruses in humans as a result of interspecies transmission

75
Q

What type of genome does SRV have?

A

simple

76
Q

What family does HFV belong to?

A

spumaretrovirinae (only has one genus- SFV and HFV)

77
Q

What are the first steps that should be taken in a new epidemic

A

case definition; facilitate suveillance and quarantine; safe body disposal; protect health services; facilitate collection of samples

78
Q

What is the diference between plasma and serum?

A

plasma has been treated with anti-coagulatants; whereas serum is liquid part of blood after coagulation- devoid of clotting factors eg fibrinogen

79
Q

What does identifying the tropism of hte virus allow you to do?

A

identify the cellular receptor it uses- inhibitor mechanism; virus neutralising target and possible inhibition of virus

80
Q

What is a precipitin?

A

an antibody that can precipitate out of solution upon antigen binding

81
Q

What is a precipitin line?

A

line formed by the binding of blood serum to antigen on a plate

82
Q

What is the difference between direct/indirect ELISA and sandwich ELISA?

A

sandwich ELISA is measuring antigen detected by antibody bound to the plate wherease direct/indirect ELISA is looking at antibody which binds to the antigen coated well

83
Q

What metals does reverse transcriptase need to work?

A

magnesium or zinc

Module 2 (38 decks)

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