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Microbiology & Immunity > 4- Viral Pathogens I (HIV) > Flashcards

4- Viral Pathogens I (HIV) Flashcards

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Biology 101 flashcards
1
Q

what are the three types of infective agent?

A

viruses
bacteria
prions

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2
Q

what is a virus?

A

a small infectious agent, requires a host cell to replicate

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3
Q

what is a bacteria?

A

a single-celled organism with its own cellular structure of cytoplasm, cell membrane, DNA genetic material

  • capable of independent growth, metabolism and reproduction
  • often its unique cellular processes/ metabolism are targeted by antibiotics
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4
Q

what is a prion? how do they cause disease?

A

infectious agent composed of mainly protein, lack genetic material (DNA or RNA)

cause neurodegenerative diseases by inducing misfolding of normal cellular proteins, and propagate by inducing conformational changes in host cells

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5
Q

compare a virus to a bacteria & prions

A

genetic material
- virus has DNA/RNA genetic material surrounded by a capsid protein coat
- bacteria has DNA
- prions lack genetic material, have no nucleic acids

replication/ carrying other physiological processes
- viruses rely on host cell machinery for resources and replication
- bacteria are capable of independent replication, growth and metabolism
- prions don’t replicate as they have no nucleic acids, but propagate by inducing conformational changes in host proteins

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6
Q

describe how viruses are ‘obligate cellular parasites’

A

viruses can’t replicate or carry out metabolic processes outside of a host cell - rely entirely on host cell machinery for these processes

invade host cell, hijack cellular machinery and replicate their genetic material to make new viral particles

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7
Q

what is the central dogma?

A

the flow of genetic information within a biological system

genetic info transferred from DNA to RNA into a protein

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8
Q

list the five features of viral replication and propagation (three of which involve the central dogma)

A

genome replication
transcription
translation
assembly of viral components/particles
release of viral particles

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9
Q

describe how viruses use the central dogma

A

viruses use the central dogma to replicate and propagate within host cells - 5 stages/steps:

  1. genome replication = viruses hijack host cell machinery to replicate their genomes
    - DNA viral genomes use host DNA polymerase
    - RNA viruses use host RNA polymerase or viral RNA-dependent RNA polymerase
  2. transcription = viral genomes transcribed into mRNA by host or viral RNA polymerase
    - mRNA caries the genetic information needed for synthesising viral proteins
  3. translation = mRNA is translated by host cell ribosomes, synthesises viral proteins needed for assembly of new viral particles
  4. assembling viral components = viral proteins/genomes assembled into new viral particles within host cell, using viral proteins and other host cell components
  5. releasing viral particles = new viral particles released from host cell to infect and propagate the infection
    - released through cell lysis or budding from the host cell membrane
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10
Q

what is the Baltimore classification?

A

method for categorising viruses based on their genome type and replication strategy

seven groups (I-VII) = based on:
1. type of nucleic acid used for genome
2. how genome is expressed and replicated within host cells

dsDNA, ssDNA, dsRNA, ssRNA (+ve), ssRNA (-ve), reverse-transcribing viruses, dsDNA with RNA intermediates - viruses

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11
Q

list and describe the structural components of a mature HIV-1 retrovirus particle

A

viral core - two ssRNA molecules coated with nucleocapsids, contains approx. 50 genes encoding the three main viral enzymes - protease, integrase and reverse transcriptase

capsid protein shell - capsid proteins form a shell around the viral core, protects it from degradation

matrix protein shell - matrix proteins form a shell around the capsid shell, involved in assembly & budding of viral particles

outer envelope - lipid bilayer containing embedded glycoproteins (gp120, gp41) which form Env spikes which mediate viral entry into host cell

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12
Q

function of the viral core?

A

contains ssRNA genome - two identical ssRNA molecules coated with nucleocapsid proteins

contains approx. 50 genes encoding the three main viral enzymes - integrase, protease and reverse transcriptase - needed for viral replication and integration of the viral genome into the host cell genome

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13
Q

function of the capsid protein shell?

A

surrounds viral core, protects it from degradation

made up of capsid proteins

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14
Q

function of the matrix protein shell?

A

involved in assembly and maturation of viral particles

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15
Q

structure of Env spikes?

A

heterotrimer made up of three main subunits - short cytoplasmic tail, transmembrane gp and surface gp

consists of Env gp120 and gp41 coated with glycans= collectively called Env spikes that protrude from HIV-1 cell membrane

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16
Q

function of Env spikes?

A

mediate viral entry into the target host cell

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17
Q

function of gp120?

A

at the top of the Env spike - interacts with CD4+ T cell surface receptor and binds

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18
Q

function of gp41?

A

mediates fusion of HIV-1 & host cell membranes together - anchors them together through interlocking mechanisms, allows viral (core) entry into host cell cytoplasm

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19
Q

describe HIV-1 RNA viral genome organisation?

A

encodes genes for three main polyproteins - Env, Gag and Pol - which encode glycoproteins 120 & 41, structural proteins (nucleocapsid, capsid and matrix), and viral enzymes (integrase, protease and reverse transcriptase) respectively

encodes genes for accessory/ regulatory proteins - e.g. Tat, Ref, Nef - involved in viral entry, integration, replication and exit

encodes genes for regulatory RNA elements - e.g. RRE, TAR

LTR regions - long terminal repeat regions = contain regulatory sequences for viral transcription and genome integration

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20
Q

what are the three main polyproteins produced by the HIV-1 viral RNA genome?

A

Gag - group specific antigen
Pol - polymerase
Env - envelope (glycoproteins)

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21
Q

how does the HIV-1 viral RNA genome ensure different variants of the polyproteins?

A

differential splicing of viral RNA = allows for variable expression/ different polyprotein variants

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22
Q

function of Gag polyproteins?

A

encode the viral core proteins - nucleocapsid, capsid and matric proteins

important in assembly and maturation of the viral particle

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23
Q

function of Pol polyproteins?

A

encode the viral enzymes for viral replication & viral RNA genome integration into host cell genome

encode protease, integrase and reverse transcriptase

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24
Q

function of Env polyproteins?

A

encode glycoproteins - gp 120 and gp41 - which mediate binding and fusion/ viral entry into host cell

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25
Q

what do LTR regions of the HIV-1 viral RNA genome do?

A

contain regulatory sequences for viral transcription and genome integration

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26
Q

describe the folding structure of the HIV-1 viral RNA genome

A

intrinsically folds into a lariat-like structure = important for downstream events

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27
Q

what are the 5 stages of the HIV-1 retroviral replication cycle?

A

entry
reverse transcription
integration
of viral genome
gene expression
viral particle assembly & release

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28
Q

what cells does HIV-1 target?

A

CD4+ T cells (sometimes macrophages)

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29
Q

describe the entry of HIV-1 into a host target cell

A

HIV Env spikes consist of gp120 and gp41

gp120 interacts with the CD4+ TCR on the host cell to ensure correct orientation of the virus

gp120-CD4+ TCR interaction induces a conformational change - exposes a chemokine co-receptor, either CCR5 of CXCR4 to bind with gp120 (CoR binding)

CoR Binding induces a further conformation change - exposes gp41 which inserts itself into the CD4+ T cell membrane, anchors the HIV-1 cell membrane with the host cell membrane through interlocking mechanism

viral core containing viral RNA genome, proteins and capsid shell is released into the cytoplasm of the CD4+ host cell

30
Q

what is CoR binding?

A

the binding of CD4+ T cell chemokine co-receptor - either CCR5 or CXCR4 - binding to gp120 on HIV

induces a further conformational change that exposes gp41

31
Q

what changes occur in gp41 to ensure the interlocking mechanisms for viral entry?

A

gp41 hepat repeat regions HR1 & 2 undergo a structural rearrangement - form a 6-helix bundle = interlocks and allows for fusion of viral & host membranes

32
Q

describe virus movement from the cytoplasm to nucleus (reverse transcription stage)

A

HIV-1 viral core with capsid shell enters host cell cytoplasm - uses host cell mechanisms like microtubules for directional active transport from the cytoplasm to the nucleus

specific residues on capsid proteins interact with nuclear pore complex proteins on the nuclear membrane

viral core (with RNA genome & proteins) then loses its capsid shell and enters the host cell nucleus via a nuclear pore complex

viral RNA genome undergoes reverse transcription by reverse transcriptase - ssRNA to dsRNA which is then integrated into the chromosomal host cell dsDNA genome by integrase = viral dsRNA becomes pro-viral DNA

pro-viral dsDNA can now be used as a template - transcribed alongside host cell DNA into ssRNA transcripts, translated into viral proteins

33
Q

function of integrase?

A

integrates dsDNA of viral genome into host cell dsDNA genome - ensures stable incorporation of pro-viral DNA

34
Q

function of reverse transcriptase?

A

reverse transcribes viral ssRNA genome into dsDNA

35
Q

what are nuclear pore complexes?

A

made up of proteins, on nuclear membrane - mediate movement from cytoplasm to nucleus and vice versa

36
Q

describe the structure of reverse transcriptase

A

multifunctional enzyme with two subunits - p66 and p51

p51 has a structural role, p66 contains the catalytic subunit for reverse transcription activity

contains three domains - palm, thumb and fingers

thumb and fingers are structural support
pal contains the catalytic site which binds nucleic acids for polymerisation to occur

37
Q

what two subunits make up reverse transcriptase?

A

p51
p66

38
Q

what does p66 do?

A

has the catalytic subunit which enables reverse transcription activity

39
Q

what does p51 do?

A

has a structural role

40
Q

list the three distinct enzymatic activities of reverse transcriptase

A

RNA dependent RNA polymerase
RNAse H
DNA dependent DNA polymerase

41
Q

how does reverse transcriptase facilitate RNA dependent RNA polymerase?

A

RT catalyses RNA dependent RNA polymerase for the addition of complementary dNTPs using ssRNA as a template to form ssDNA/ cDNA

42
Q

how does reverse transcriptase facilitate RNAse H?

A

RT has RNAse H activity, cleaves the RNA primer from the RNA-DNA duplex

43
Q

how does reverse transcriptase facilitate DNA dependent DNA polymerase?

A

RT catalyses DNA dependent DNA polymerase for the addition of complementary dNTPs to the ssDNA/ cDNA template

to produce a dsDNA duplex

44
Q

describe the process of reverse transcription of the viral ssRNA genome

A

RNA primer synthesised complementary to the viral RNA genome - binds

reverse transcriptase catalyses RNA dependent RNA polymerase to add complementary dTNPs along the ssRNA viral template in a sequence speciifc manner - cDNA/ ssRNA produced

RNA-DNA duplex is formed - RNAse H activity of RT cleaves RNA primer

DNA dependent DNA polymerase is then catalysed by RT - catalyses the addition of complementary dNTPs to the cDNA/ ssDNA template

forms a dsDNA duplex that can be integrated into host cell ds chromosomal DNA as proviral DNA

45
Q

describe the process of viral genome integration

A

integrase co-factors identify a target sequence on host cell genomic DNA - identified via specific sequences/ motifs, is transcriptionally active

integrase binds to both ends of viral dsDNA - cellular proteins then bind to integrase to guide the viral dsDNA towards the target site

integrase induces ds breaks in host cell genomic DNA - takes advantage of/ mimics host cell DNA repair mechanisms to integrate viral dsDNA into the host cell genome as proviral DNA
- ensures complementary nucleotide sequences and joining between the viral dsDNA ends and broken host dsDNA end

proviral DNA is now a permanent part of host cell genetic material (stabilised, integrated structure) - will be used as a template for the transcription, translation and production of viral proteins

46
Q

what mediates the selective transcription of just integrated proviral DNA?

A

Tat-TAR interactions

47
Q

describe gene expression of pro-viral DNA

A

integrated proviral DNA has all the elements needed for transcription - has regulatory elements like TAR and binding site for transcription factors to initiate transcription

Tat-TAR interactions ensure selective transcription of just proviral DNA

Tat (regulatory protein) binds to TAR (regulatory element) and enhances the selectivity, productivity and efficiency of just proviral DNA transcription from the promoter region

48
Q

how are different viral proteins generated from one proviral RNA transcript?

A

through differential splicing of mRNA transcript produced from proviral DNA

different RNA transcripts = different viral proteins upon translation

splicing from 5’ to 3’ end - creates an open reading frame needed to make new proteins

49
Q

what regulatory interactions are crucial in the nuclear export of unspliced retrovirus RNA

A

high specificity of Rev-RRE interactions

Rev and Cm1 (shuttling protein) interactions, Cm1 and nuclear pore interactions

50
Q

what’s the importance of Rev-RRE selectivity?

A

allows selective export of unspliced/ singly spliced viral RNA transcripts - these contain the full-length genome, important to not lose any genetic information for viral replication

RNA transcripts with conformational flexibility to fold into lariat-structures, Rev selectively recognises this and binds to RRE = facilitates nuclear export

51
Q

describe the nuclear export of unspliced retroviral RNA

A

Rev protein binds to RRE with high selectivity - recognises the specific lariat-structure unspliced/singly spliced viral RNA transcripts fold into

Rev interacts with Cm1 - a shuttling protein which interacts with a specific nuclear pore = allows Rev and unspliced viral RNA to leave nucleus via nuclear pore into cytoplasm
- viral hijacks cellular machinery, ensures viral RNA export is prioritised over host cell’s

52
Q

how do viral RNA transcripts fold into lariat-like structures?

A

RNA transcripts experience energy changes - gives them conformational flexibility to intrinsically fold into lariat structure

53
Q

what is Cm1?

A

shuttling protein - interacts with nuclear pore (interactions have specificity) to allow the nuclear export of Rev with unspliced/ singly spliced viral RNA

54
Q

describe the process of assembly and release of HIV-1 retrovirus (viral RNA)

A

unspliced HIV-1 RNA in the cytoplasm is translated into two polyproteins - Gag and Gag-Pol
- Gag = contains capsid, nucleocapsid and matrix proteins, responsible for assembly of capsid proteins
- Gag-Pol = contains enzymes for viral replication - integrase, reverse transcriptase and protease

polyproteins use ER/ endoplasmic reticulum processes and hijack cellular microtubule active transport - polyproteins transported from cytoplasm to plasma membrane

assemble viral components into nascent virions/ viral particles - contain the viral RNA genome, enzymes, proteins and other parts

55
Q

what does the Gag polyprotein (from assembly and release of virions) contain?

A

capsid, matrix and nucleocapsid proteins - Gag is responsible for the capsid proteins

56
Q

what does the Gag-Pol polyprotein (from assembly and release of virions) contain?

A

contains enzymes for viral replication - integrase, reverse transcriptase and protease

57
Q

what are the four steps involved in assembly and transport of the retrovirus?

A

dimerization of two unspliced RNA molecules/ transcripts

synthesis of Gag and Gag-Pol polyproteins & myristylation

protease activity releasing individual proteins from Gag & Gag-Pol proteins

virus hijacks host cell ESCRT machinery to organise its viral components

58
Q

describe the dimerization of two unspliced RNA molecules/ transcripts

A

RNA molecules undergo modifications in the Golgi which induces conformational changes - facilitates the formation of the kissing loop complex

two complementary regions of two ssRNA viral genomes brought together in close proximity, interact, and form stable base pairs - facilitated by reverse transcriptase

facilitates packing two ssRNA genomes in the same capsid for one virion

59
Q

what is a kissing loop complex?

A

forms from the interaction of two complementary regions from two ssRNA genomes/ molecules - brought into close proximity, interact and form stable base pairs

60
Q

what facilitates formation of the kissing loop complex?

A

reverse transcriptase

61
Q

why is the kissing loop complex useful?

A

facilitates packaging two ssRNA strands/ molecules into one capsid - one virion

62
Q

describe the myristylation of Gag and Gag-Pol polyproteins

A

Gag and Gag-Pol polyproteins from the unspliced viral RNA transcript - directional transport from the nucleus to cytoplasm to plasma membrane is due to myristylation

addition of myristoyl groups on specific amino acids residues of the polyproteins directs them to the plasma membrane

myristoyl groups anchor into the plasma membrane lipid bilayer

63
Q

what is the use of myristylation?

A

addition of myristoyl groups on specific amino acids resides

  • directs Gag & Gag-Pol proteins to plasma membrane for virion assembly and release
  • myristoyl groups anchor into the plasma membrane lipid bilayer
64
Q

describe how Gag and Gag-Pol polyproteins produce individual proteins

A

cleaved by protease - Gag produces capsid proteins (capsid, nucleocapsid and matrix proteins), and Gag-Pol produces viral enzymes

65
Q

what is the purpose of the capsid proteins produced following cleavage of the Gag polyprotein (for virion assembly and release)?

A

capsid proteins have specific orientations and locations where they bind the viral genome - organised by hijacked ESCRT machinery to come around the viral core components and form a capsid protein shell

viral core contains viral ssRNAs in kissing loop complex formation, viral enzymes, proteins and other parts

66
Q

what is the use of hijacking ESCRT machinery for viral replication?

A

viral hijacking of ESCRT machinery helps with membrane abscission of host cell plasma membrane and virion cell membrane once it starts budding off

67
Q

what is the normal function of ESCRT machinery?

A

traffics proteins for the cytokinesis of two daughter cells following cell division - acts as an endosomal sorting complex

68
Q

why is the immature virion less infective?

A

wrong orientation and conformation/ structural arrangement of proteins

69
Q

what mediates immature virion maturation?

A

protease from within the virion itself

70
Q

describe the maturation of an immature virion

A

protease cleaves certain proteins in immature virion - induces a structural rearrangement

leads to correct orientation and conformational arrangement of viral proteins for viral infectivity - viral proteins will properly interact with target host cell

Microbiology & Immunity (37 decks)

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