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World of Viruses > virus replication cycle > Flashcards

virus replication cycle Flashcards

1
Q

what are some of the ways the cell culture system has benefitted virology, vaccine development, and research?

A
  • vaccines against polio, measles, and rubella were derived using cell cultures
  • helped discover oncoviruses (viruses that can produce tumors)
  • helped discover reverse transcriptase in the study of RNA viruses
  • helped with the plaque assay and one-step growth experiment
  • helped us discover/learn the virus replication cycle using the one-step growth cycle
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2
Q

what are the 3 types of cell cultures?

A
  1. primary cell cultures
  2. diploid cell strains
  3. continuous (immortal) cell cultures
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3
Q

what are primary cell cultures?

A

cell cultures derived from live tissue/organs, therefore composed of multiple cell types
- have limited cell division capacity: 5-20 times

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4
Q

what are diploid cell cultures?

A
  • single cell type (usually epithelial or fibroblast cells
  • cell can divide up to 100 times
  • normal morphology and number of chromosomes
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5
Q

what are continuous cell cultures?

A
  • aka. immortal cell cultures, therefore cancer cells usually (derived from tumors, cells mutated by oncoviruses)
  • homogenous (uniform) cell type
  • immortal therefore infinite dividing capacity
  • cells can grow on eachother/pile up (don’t need contact with culture media to grow)
  • produce tumors when injected in lab animals
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6
Q

what are cytopathic effects (CPE)?

A

morphological alterations of a cell due to viral infection. can be:

  • cell death
  • cell rounding & detaching from surface
  • syncytium (large, multi-nucleus cell bodies formed from fusion)
  • alterations in morphology & number of chromosomes
  • inclusion bodies (aggregation of virions/viral proteins in a cell)
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7
Q

what are the major differences between animal cells and plant cells?

A
  • plant cells have a cell wall and animal cells don’t

- plant cells also have large storage vacuoles and chloroplasts, whereas animal cells don’t

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8
Q

what is the one-step growth cycle?

A

experiment done by Delbruck & Ellis which aimed to synchronously infect cells with viruses and monitor the virus growth at set intervals

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9
Q

what does a one-step growth cycle/synchronous infection of cells require?

A

a high multiplicity of infection (MOI) = 5- 10

  • MOI: # of infectious virions to # of cells
  • essentially requires 5-10 infectious virions/cell
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10
Q

what is the eclipse period of the one-step growth cycle?

A

time from inoculation to the appearance of the 1st intra-cellular virion

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11
Q

what is the latent period of the one-step growth cycle?

A

the time from inoculation to the appearance of the 1st extra-cellular virion (cell has lysed)

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12
Q

what is the burst size of the the one-step growth cycle?

A

the amount of virions produced in a single cell (before it lysed/”burst”)

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13
Q

what are the 5 steps of the viral replication cycle?

A
  1. attachment to cell
  2. entry and uncoating of virion
  3. biosynthesis (producing all the parts of virus for assembly; transcription & translation)
  4. assembly of virus
  5. egress (release)
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14
Q

what is the attachment step of the viral replication cycle?

A
  • collision between virion and cell that results in attachment when virion proteins (glycoproteins) bind to target cell receptors
  • attachment is strengthened as more receptors bind more virion proteins
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15
Q

what is are 2 examples of how naked viruses attach to target cells?

A
  1. they attach via surface features of the virion (ex. poliovirus has a depression surrounding each pentamer which is where the target cell receptor can fit in)
  2. attach via fibers on virion surface (ex. adenoviruses have fibers anchored at each penton base that have a depression in the homo-trimer of the fiber where the Car receptor (target cell receptor) can fit/attach
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16
Q

what are examples for how enveloped viruses attach to cells?

A

using glycoproteins

  • ex. influenza viruses use Hemagglutinin (homo-trimer)
  • ex. HIV has a surface glycoprotein HIV-1 which can bind to CD4 of T-Helper cells and macrophages (requires co-receptor ‘alpha-chemokine receptor’ for the T-cell strain of HIV to bind to the T-cell, and requires co-receptor ‘beta-chemokine receptor’ for the macrophage strain of HIV to bind to the macrophage)
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17
Q

what are the 3 basic mechanisms viruses use to enter a cell?

A
  1. drilling a hole through the plasma membrane and inserting genome
  2. fuse their envelope with the plasma membrane (requires neutral pH and fusion proteins to pull the membranes together)
  3. receptor-mediated endocytosis, followed by uncoating at nuclear or endosomal membrane (requires low pH environment like the endosome or lysosome)
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18
Q

Poliovirus is the best studied system for viral entry and unocating. How does it enter and uncoat?

A

creates hole in plasma membrane:

  1. attaches to Poliovirus receptor (Pvr)
  2. N-terminus of VP1 becomes exposed and inserts into target cell plasma membrane
  3. a pore is then formed in the membrane and viral RNA is inserted
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19
Q

how do paramyxoviruses enter the cell?

A

by fusing the membranes using fusion proteins:

  1. receptor binding occurs at plasma membrane
  2. fusion peptides are exposed, enabling membrane fusion
  3. uncoating then occurs after fusion of membranes, and genome is released into cytoplasm
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20
Q

what are the steps of receptor-mediated endocytosis?

A
  1. ligand-receptor binding & clathrin coated pit forms
  2. dynamin ring forms to cut clathrin-coated vesicle from membrane, and vesicle is endocytosed
  3. clathrin coat dissociates and vesicle fuses to early endosome and releases contents
  4. pH of endosome lowers, becoming late endosome which then fuses with the lysosome (lowest pH)
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21
Q

how do influenza viruses enter the cell?

A

using receptor-mediated endocytosis:

  1. Hemagglutinin attaches to sialic acid, resulting in endocytosis of influenza
  2. fusion peptide emerges from Hemagglutinin, inducing membrane fusion
  3. H+ gets pumped into endosome, lowering the pH so the matrix layer (nucleocapsid) is dismantled
  4. with no matrix layer, RNPs are released into cytosol and eventually imported into nucleus
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22
Q

how do adenoviruses (naked viruses) enter the cell?

A

using receptor-mediated endocytosis:

  1. adenovirus fiber binds to Car (cell receptor)
  2. the penton base of capsid interacts with integrin receptor, leading to endocytosis
  3. due to lowering of pH, the fibers dismantled in the endosome
  4. due to further lowering of the pH in the late endosome, the penton bases of the capsid dismantle (capsid still intact), and the broken virion is released into the cytosol
  5. virion uses microtubules of cell to get to nuclear pore, and viral genome is released into the nuclear pore complex
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23
Q

how to T-even bacteriophages enter the cell?

A

drilling hole in plasma membrane:

  1. tail fibers attach to LPS and OmpC (outer membrane protein C) of bacterial cell, which induces a conformational change in the phage’s baseplate causing the tail sheath to contract and expose tube needle
  2. tube needle drills through bacteria’s outer membrane
  3. phage lysozymes degrade peptidoglycan layer, so then genome is injected through the plasma membrane into the bacterial cell
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24
Q

how do plant viruses enter plant cells?

A
  • mechanical transmission through wounds in plant tissue
  • vertical transmission (from parent plant to offspring through the pollen or seeds)
  • vegetative propagation (virally infected plant was propagated)
  • insect vector transmisson (carrying virus and feed on
25
Q

what are the 3 broad categories of viruses based on genome expression strategies?

A
  1. DNA viruses
  2. RNA viruses
  3. Viruses that use reverse transcription (retroviruses)
26
Q

where do all 3 biosynthesis steps (translation, transcription, and genome replication) occur in the cell for RNA viruses?

A

all 3 steps occur in the cytoplasm

27
Q

where do all 3 biosynthesis steps (translation, transcription, and genome replication) occur in the cell for DNA viruses?

A

translation: cytoplasm
transcription: nucleus
genome replication: nucleus

28
Q

where do all 3 biosynthesis steps (translation, transcription, and genome replication) occur in the cell for Retroviruses?

A

translation: cytoplasm
transcription: nucleus
genome replication: nucleus

29
Q

Since DNA viruses can be large and have so many genes, their gene expression is ordered. What are the gene expression ‘stages’?

A
  1. immediately early genes
  2. early genes
  3. late genes
  4. for some viruses, even very late genes
30
Q

what are immediately early (IE) genes?

A

genes expressed right after infection. the function of IE proteins is to:

  • render cells into S phase (for DNA replication)
  • inhibit host defence and biosynthesis of host cell genes
  • induce expression or next set of genes in cascade
31
Q

what is an example of an immediately early gene and it’s function?

A

adenoviruses IE proteins bind p53 (tumor suppressor protein), which blocks p53-mediated apoptosis and forces the cell to enter S phase

32
Q

what are early (E) genes?

A

genes for the enzymes and accessory factors required for genome replication

33
Q

what are late (L) genes?

A

structural proteins required for virion assembly

34
Q

what cells do DNA viruses infect?

A

they infect cells that are either dividing (ie. stem cells in bone marrow) OR they force quiescent cells into S phase

35
Q

why do DNA viruses have the potential to be oncogenic?

A

because in order to force quiescent cells into S phase they shut down the cell’s ability to trigger apoptosis
(ex. Herpesvirus, adenoviruses)

36
Q

what must RNA viruses associate with during biosynthesis?

A

a type of intra-cellular membrane (ER, endosome, vesicle, mitochondria, chloroplast, etc)

37
Q

what do RNA viruses require that they must encode themselves for transcription & replication?

A

RNA-dependent RNA polymerase (RdRP)

38
Q

what makes +ssRNA viruses unique compared to -ssRNA viruses?

A

for +ssRNA viruses, the genomic RNA serves as the FIRST mRNA

39
Q

how do +ssRNA viruses replicate?

A

genomic RNA is translated (since it acts as mRNA) and produces replicase, which contains the conserved domains methyl transferase (MTR), helicase (HEL), and RdRP to generate complimentary RNA (-ssRNA) and then use that as the template to generate +ssRNA genomes for packaging (all using replicase enzymes)

40
Q

what form does the -ssRNA genome exist as, and why?

A

exists as a RNP (ribonucleoprotein) which must first be transcribed before translation occurs because -ssRNA is the antisense/complimentary strand of RNA and therefore can’t be translated directly like +ssRNA can

41
Q

what type of virus (genome) is influenza virus?

A

-ssRNA

42
Q

how do influenza viruses transcribe & replicate?

A

RNP (contains NLS) enters the nucleus, where it will replicate and transcribe. splicing of the transcripts made from some genome segments is required. RNP also functions as a helicase and binds ssRNA

43
Q

how do retroviruses & para-retroviruses transcribe & replicate?

A
  • reverse transcription in cytoplasm using reverse transcriptase (RTase) starts when virion enters host cell
  • the viral complimentary DNA (provirus) is integrated into the host cell genome so the cellular replication components (DNA dependent RNA polymerase 2) can produce viral mRNAs and genomic RNAs
44
Q

what is reverse transcription?

A

creating DNA genome from RNA genome

45
Q

what type of genome does retroviruses have?

A

ssRNA

46
Q

what are the steps that enveloped viruses use to assemble and exit the cell?

A
  1. form individual structural units of capsid
  2. spontaneous assembly of structural units into capsid shell
  3. selective packaging of viral genome and other virion components
  4. creating envelope from a host cell membrane
  5. exit infected cell
47
Q

what are the steps that naked viruses use to assemble and exit the cell?

A
  1. form individual structural units of capsid
  2. spontaneous assembly of structural units into capsid shell
  3. selective packaging of viral genome and other virion components
  4. exit infected cell (usually through lysis)
48
Q

how are structural units assembled?

A

spontaenously due to interactions between capsid protein subunits that are dictated by primary AA sequence

49
Q

what viruses assemble capsid & package genome in the cytoplasm?

A

most viruses except for one group of RNA viruses and Poxviridae viruses

50
Q

what viruses assemble capsid & package genome in the nucleus?

A

DNA viruses, retroviruses

51
Q

what are the 3 main ways structural units can be assembled?

A
  1. assembled from individual proteins (ex. adenoviruses, formation of penton requires fiber protein and penton base protein)
  2. assembly from a polyprotein (ex. polio viruses, proteolytic cleavage is used for protein components to fit toegther)
  3. chaperone-assisted assembly (ex. adenoviruses, utilize chaperone to form individual proteins into trimers)
52
Q

how are capsid shells assembled for RNA viruses?

A

genome RNA is involved in virion assembly (true for TMV and many other +ssRNA viruses due to helical symmetry)

53
Q

how are capsid shells assembled for DNA viruses?

A

for large DNA viruses and bacteriophages (with DNA genomes), a procapsid (shell) is formed first, followed by a collapse of scaffold protein structures, and the DNA genome is inserted (requires ATP)

54
Q

how does the capsid & genome packaging of TMV assemble?

A

using double disc structural units
- the origin of assembly is a hairpin structure formed near the 3’ end of the RNA genome, and the genome threads through as the double discs build up

55
Q

how do naked viruses exit the cell (egress)?

A

ex. poliovirus, adenoviruses

lyses the infected cell

56
Q

how do enveloped viruses exit the cell (egress)?

A

in most cases, source of envelope is plasma membrane so they will bud off at plasma membrane

57
Q

what does tissue tropism mean?

A

its a viruses’ preference for a certain type(s) of tissue or cell in host

58
Q

what is a susceptible cell?

A

cells that allow attachment & entry of viruses due to presence of suitable receptors, but may not support viral replication

59
Q

what is a permissive cell?

A

cells that permit replication of a virus because they possess what the virus needs to replicate (may or may not be susceptible though)

World of Viruses (5 decks)

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