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Medical Microbiology > Viral Pathogens: Classification, Biology, Diseases I > Flashcards

Viral Pathogens: Classification, Biology, Diseases I Flashcards

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1
Q

How varying are viral structures?

A

Various different viral structures with varying genomes (RNA/DNA)

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2
Q

How does structure effect viral function?

A

Adenoviruses and influenza viruses cause significant respiratory disease in humans although they differ greatly in structure, pathogenesis and their molecular biology

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3
Q

Outline the various configurations of viral genomes

A
  • Single-stranded RNA (ssRNA)
  • Double-stranded RNA (dsRNA)
  • Single-stranded DNA (ssDNA)
  • Double-stranded RNA (dsDNA)
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4
Q

What maintains the double stranded genomes?

A

Double-stranded genomes have complementary base pairing

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5
Q

Describe the structure of RNA genomes

A

RNA genomes can be linear and segmented i.e. more than one RNA per capsid

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6
Q

What is the structures of DNA viral genomes?

A

DNA genomes can be linear or circular.

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7
Q

What is Baltimore classification?

A

Viruses are grouped together by the way their genomes are grouped together (RNA/DNA)

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8
Q

Which nucleic acid do all viruses produce?

A

All viruses produce RNA which can be transcribed into protein to make new viruses

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9
Q

Describe HIV structure

A

Contains 2 RNA strands encapsulated by a protein capsid all covered by a lipid bilayer gathered by the virus as it emerges from the cell

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10
Q

What is the role of surface glycoproteins?

A

Protein sites / protein envelope glycoproteins on the cell surface mediate entry into the cell

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11
Q

Name the enzymes in HIV

A

HIV also houses integrase, reverse transcriptase and protease enzymes

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12
Q

Describe the outer structure of mature HIV

A

The outer envelope of HIV consists of a lipid bilayer with protruding Env spikes (heterotrimers of SU3TM3).

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13
Q

What structures lie within the envelope of mature HIV?

A

Inside the envelope lie shells of Gag proteins

In the immature particle, Gag itself forms a single shell

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14
Q

How is the mature HIV conical capsid formed?

A

MA (matrix protein) associates around the membrane CA (capsid protein) to form the conical capsid

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15
Q

What is the role of the nucleocapsid?

A

Nucleocapsid coats the viral RNA genome and bridges the interaction between the genome and the capsid as the variant forms

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16
Q

What are the 3 polyproteins synthesised by retroviruses?

A
  • Gag
  • Pol
  • Env
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17
Q

What is contained within the HIV core?

A

The core contains two genomic RNA strands (plus strand) that the nucleosome binds, as well as tRNALys3, and ~50 copies of each viral enzyme (PR, RT, and IN).

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18
Q

What is the gag protein?

A

Gag; group specific antigen; viral core proteins; MA (matrix), CA (capsid), NC (nucleocapsid)

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19
Q

What is the Pol protein?

A

Pol; viral enzymes; protease (PR), reverse transcriptase (RT) and integrase (IN)

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20
Q

What is the Env protein?

A

Env; envelope glycoprotein; gp120 SU (surface); gp41 TM (transmembrane)

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21
Q

Name the accessory / regulatory HIV proteins present

A
  • Tat
  • Rev
  • Vif
  • Nef
  • Vpu
  • Vpr

Involved in immunoregulation to interact and try overcome complex human immune system

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22
Q

What is the role of the Tat accessory protein?

A

Potent activator of viral transcription

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23
Q

What is the role of the vpr protein?

A

Cell cycle, virus nuclear import (?)

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24
Q

What is the role of the regulatory Vpu protein?

A

immune modulator, virus release

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25
Q

What is the role of the Nef protein?

A

Immune modulator, T-cell activation, virus spread (?)

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26
Q

Describe the role of the regulatory Vif protein

A

Critical regulator of virus infectivity

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27
Q

Outline the role of the regulatory Rev protein in HIV

A

Mediates unspliced RNA nuclear export

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28
Q

What mechanism do retroviruses use to organise their genome?

A

Mechanism of Retroviruses: RNA is brought into cells via viruses and reverse transcribed into DNA

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29
Q

How is HIV RNA differentiated?

A

HIV RNA is split into different RNA structures that are recognised for different functions

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30
Q

What is the effect of reverse transcription in HIV?

A

Reverse transcription produces DNA version of the genes to be transcribed to produce all the protein products required as well as back into RNA

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31
Q

Describe the HIV outer envelope structure

A

HIV-1 Env consists of a trimer of gp41 and gp120 peptide subunits and is covered with glycans

These glycoproteins are large globular structures

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32
Q

How does HIV entry into cells differ from other retroviruses?

A

HIV entry at cell surface triggered by conformation changes driven by Env/receptor interactions

Contrasts with pH-dependent entry of adenovirus, influenza virus, etc

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33
Q

How does HIV gain entry into cells?

A

HIV-1 entry requires two membrane proteins:

CD4 (T-cells) and a chemokine receptor (CCR5/CXCR4)

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34
Q

How does HIV infection lead to immunodeficiency?

A

HIV-1 is tropic for CD4 expressing cells such as helper T cells and macrophages; the loss
of which results in immunodeficiency (& AIDS)

35
Q

Outline how HIV interacts with CD4 T cells

A
  1. HIV specifically binds to CD4 receptor on T cells
  2. Allows interaction with specific coreceptors CCR5 and
    CXCR4
  3. Produces 6-Helix bundle formation
  4. Envelope meshes viral and cellular plasma membranes
    together allowing entry into cell
36
Q

How does HIV travel through the cell?

A

HIV doesn’t travel passively through the cell, but alters it genome along the way

37
Q

Outline the first alterations HIV undergoes once inside the host cell

A
  1. Uncoating step: Lose capsid, exposing RNA genome covered by enzymes and nucleocapsid protein
  2. HIV moves down microtubules towards microtubule organising complex to allow directionality
  3. Undergoes intracellular trafficking to get into nuclear membrane
38
Q

What is the role of HIV degenerate nuclear entry pathways?

A

Intracellular trafficking pathways (e.g. microtubules) allows efficient movement of viruses through host cells

39
Q

What is the role of HIV degenerate nuclear entry pathways?

A

Each microtubule pathway has a different result that the virus selects

40
Q

How does HIV decide which pathway to take?

A

Molecules of capsid that enter cells with the virus help select which microtubule and destination on the cell nuclear membrane is used

41
Q

Outline the most efficient microtubular pathway to the nucleus

A

Most efficient pathway involves the capsid molecule directing the virus through cytoplasm to NPC (nuclear pore complex) used by virus to gain entry into nuclear space

42
Q

Outline the structure of reverse transcriptase (RT)

A

RT is a heterodimer of p66 and p51 subunits

43
Q

What are the roles of the 2 RT dimers?

A

Catalytic properties are in p66 subunit, p51 serves structural role and lacks RNAse H domain

44
Q

What are the 3 enzymatic activities of RT?

A

RT displays three distinct enzymatic activities:

  1. RNA-dependent DNA polymerase
  2. RNAse H (cleaves RNA from RNA/DNA hybrid)
  3. DNA-dependent DNA polymerase
45
Q

How does reverse transcriptase bind to Viral RNA?

A

RNA with smaller intrinsic RNA structures is recognised by RT
RT finds specificity within those structures and binds to it

46
Q

How does reverse transcriptase initially form more RNA?

A

RNA structure produced by RNA polymerase part of RT as well as an RNA primer which is moved to the other end of the genome (unknown reason) to enable even more RNA production

47
Q

How is DNA formed from RT?

A

DNA is primed as DNA Pol. component of RT takes over

The DNA primer is then used to produce more copies of DNA

48
Q

What is the significance of HIV RT?

A

HIV Reverse transcriptase contains both RNA and DNA polymerase functions together

⇒ produce DNA version of RNA genome

49
Q

Why must HIV integrate into the host cell DNA?

A

Cell nucleus is a highly regulated structure; In order to access nuclear components HIV requires to replicate, HIV DNA genome (provirus) is integrated into host chromosomes

50
Q

How is viral DNA integrated into the host cell?

A

DNA break repair enzymes are present in the genome. These find specific sequences and break them apart to insert new DNA in them to be copied - mechanism of Viral integrase enzyme

51
Q

Outline how integrase anneals viral DNA to cellular DNA

A
  1. Integrase loops target DNA
  2. Brings termini sequences into physical contact with the viral genome
  3. Integrase now has ability through chelation (use of divalent cations) to break open DNA
  4. One strand at a time anneals viral DNA to cellular DNA
52
Q

What is LEDGF/P75

A

LEDGF/P75 is a protein that binds HIV-1 integrase and facilitates targeting to chromatin

LEDGF/P75 isn’t a HIV viral protein but is picked up along the way

53
Q

How does LEDGF/P75 aid chromatin targeting?

A

As virus addresses nuclear membrane, LEDGF is bound by virus

Enables it through nuclear pore

LEDGF also allows integrase to recognise specific target sequences within host cell DNA

54
Q

How is viral transcription mediated?

A

Viral transcription is regulated by the binding of various Transcription Factors (TF) to the viral DNA in order to recruit polymerases

55
Q

Why are there so many transcription factors (TF) in HIV?

A

HIV contains many TF binding sites to ensure transcription will occur in any circumstance

56
Q

How is CD4 specificity aided by TF?

A

The HIV-1 promoter contains binding sites for transcription factors that are present in T-lymphocytes

57
Q

What is the purpose of the Tar-Tat complex?

A

The TAR RNA binds the Tat protein; TAR-Tat interaction is thought to preferentially bring RNA pol. to the viral genome and enhances elongation of RNA pol II

58
Q

How are viral proteins formed when HIV transcription occurs

A

The HIV-1provirus generates different mRNAs for the viral proteins via splicing

59
Q

How are different viral proteins made from the same HIV?

A

Splicing alters coding regions of the RNA to produce different proteins with varying functions

60
Q

What is the fate of the genomic viral RNA transcribed?

A

Nuclear export of unspliced retrovirus RNA (genomic RNA)

61
Q

What are the products of viral transcription?

A

Full length virus and primary transcripts of polyproteins (Gag / pol) produced

62
Q

What enables the formation of accessory viral proteins?

A

Splicing occurs to form Env protein which goes on to make further viral proteins

63
Q

How do the viral proteins produced help export the viral genome?

A

Virus produces advantageous Rev protein that interacts with RRE structure to bring other cellular proteins along to preferentially export genomic and spliced RNA out the cell

64
Q

What is the role of the HIV-1 Rev protein?

A

The HIV-1 Rev protein mediates nuclear export of unspliced and singly spliced viral RNA

65
Q

What is the significance of the HIV-1 Rev protein?

A

HIV Rev is essential for the nuclear export of intron-containing viral mRNAs

66
Q

When is Genomic RNA exported from the host cell?

A

The long genomic RNA contains introns and is only removed from the the cell when HIV-1 Rev protein interacts with Crm1 and the RRE RNA

67
Q

How is genomic RNA export mediated?

A

Regulated by the fact the cell doesn’t contain any machinery enabling intron containing RNA to leave the nucleus

68
Q

Why does the viral proteins and RNA assemble at the host cell membrane?

A

The virus assembles at the plasma membrane so it has less distance to travel

69
Q

Describe the different RNA products present at assembly

A

The unspliced HIV-1 RNA is the mRNA for Gag and Gag-Pol proteins. Spliced full length RNA genome has 2 copies in the virus

70
Q

What mechanism enables the virus to leave the cell?

A

Interaction of the 2 RNA genomes occurs surrounded by protein causing the virus to be pushed out of the host cell

71
Q

Outline how RNA interaction leads to exportation of the virus

A

Kissing loop complexes in SL1 and SL4 domains of side structures allows interaction of the 2 RNA genomes at the membrane

Dimerisation of unspliced viral RNA allows packing of two genomes

72
Q

What proteins are formed from the viral polyproteins gag and pol?

A

Gag and Gag-Pol proteins assemble viral particles

  • Gag produces structural proteins
  • Pol produces viral enzymes
  • Env produces envelope glycoproteins
73
Q

How are various polyproteins formed?

A

Long genomic RNA undergoes slippery sequence translation to form different polyproteins

74
Q

What is slippery sequence?

A

Slippery sequence is when ribosome misreads RNA causing a frameshift to produce different polyproteins

75
Q

Describe the translation slippery sequence that occurs to form gag and pol

A

Gag-pol protein is generated by -1 ribosomal frameshifting induced by a ‘slippery’ sequence and an RNA hairpin structure

76
Q

What is myristolation?

A

Myristoylation is a post-translational modification that proteins undergo enabling them to interact with the plasma membrane

77
Q

What modification process allows Gag to interact with plasma mebrane?

A

Myristoylation (Myr) of Glycines in MA domain of Gag mediates association with plasma membrane

78
Q

Which structures are involved in HIV budding?

A

The HIV-1 PT(S)AP motif is required for virus budding and mediates binding of the host Tsg101 protein

Myr binding shows interaction with the membrane

79
Q

What is the role of the P6 protein in viral budding?

A

P6 protein responsible for pushing out virus from cells; used in cytokinesis of daughter cells
part of ESCRT machinery

80
Q

How is ESCRT machinary altered in HIV?

A

The ESCRT machinery is hijacked by HIV to perform membrane abscission during viral release; P6 binds Tsg101 protein to push out virus

81
Q

Why are polyproteins cleaved at the membrane?

A

Polyproteins at the membrane get cleaved by protease to produce individual proteins that form the capsid

82
Q

How does protease form viral capsids?

A

Protease releases the individual proteins from Gag and Gag-Pol polyproteins

83
Q

Describe the immature structure of virion?

A

The immature virion contains ordered arrays of polyproteins (green) surrounded by membrane

84
Q

Outline the structure of a mature virion

A

Mature virion has viral protease (Pr) encoded in Gag-Pol polyprotein to digest immature polyproteins to produce individual proteins that come together to form the mature virion

Envelope glycoprotein produces 2 glycoprotein spikes (yellow) that are already at membrane and taken up as virion is pushed out

Medical Microbiology (15 decks)

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