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H2 Biology > Genetics of Viruses > Flashcards

Genetics of Viruses Flashcards

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1
Q

what does “obligate intracellular parasite” mean, and what does it describe?

A

viruses, cannot survive without living host cell

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2
Q

what do viruses depend on host cells for?

A
  • amino acids and nucleotides
  • protein-synthesis machinery
  • energy (ATP)
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3
Q

what is the extracellular state of a virus, and its characteristics?

A
  • virions
  • metabolically inert
  • no respiratory or biosynthetic functions
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4
Q

who is MRS GREN?

A

8 characteristics of living organisms
- movement
- respiration (metabolism)
- sensitivity
- growth
- reproduction
- excretion
- nutrition

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5
Q

what are the three arguments for viruses being living organisms?

A
  1. viruses can reproduce (in intracellular state)
  2. viruses can direct metabolic processes (in intracellular state)
  3. viral genomes can evolve (no single gene is shared by all viruses, viruses evolve w host and acquire their genes)
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6
Q

what are two arguments for viruses being non-living?

A
  1. viruses are not cells
    - do not have protoplasm or organelles
  2. viruses lack some living organism characteristics
    - no metabolism
    - no nutrition needed
    - cannot make energy (ATP)
    - not sensitive
    - no growth
    - no excretion
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7
Q

how do viruses challenge the cell theory?

A
  1. cells are smallest unit of life
    - viruses have genetic material but no molecular machinery
  2. cells arise from pre-existing
    - can replicate but only in host cells
  3. living organisms composed of cells
    - viruses are acellular, no protoplasm or organelles
    - metabolically inert, no resp or biosynthesis
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8
Q

what is the basic structure of a virus?

A

in all viruses:
- genome (DNA or RNA)
- capsid (protein coat)

in some viruses:
- envelope
- enzymes

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9
Q

describe the structure of the viral genome

A
  • dna OR rna
  • single OR double stranded
  • linear OR circular
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10
Q

what are three types of viruses (classified by genetic material)?

((that u need to know))

A
  1. double-stranded DNA
    - eg. T4 and lambda
  2. negative sense single-stranded RNA
    - genome is mRNA, immediately translated by host
  3. single-stranded RNA-reverse transcriptase (RT) viruses
    - reverse transcriptase (RNA to DNA) to produce DNA from viral RNA
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11
Q

what are two types of essential proteins coded for by viral genomes?

A
  • regulatory: regulate host gene action
  • structural: eg capsid protein
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12
Q

what is a capsid formed from?

A

capsomeres (identical protein subunits)

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13
Q

what are viral envelopes, and what is its function?

A

facilitating viral entry

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14
Q

what is the function of lysozyme, and which viruses contain it?

A
  • penetrate bacterial cell wall, viral nucleic acid enters
  • lyses host cell to release new virus later
  • bacteriophages (T4 and lambda)
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15
Q

what if the function of neuraminidase, and what virus contains it?

A
  • breaks down glycosidic bonds of glycoproteins/lipids of animal cell connective tissue
  • aid in virus liberation
  • influenza
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16
Q

what are the five general steps of reproduction of an enveloped virus?

A
  1. adsorption (attach to host)
  2. penetration (viral nucleic acid enter host cytoplasm)
  3. synthesis & replication (new viral components made by host cell machinery)
  4. assembly (new viruses assembled)
  5. release (new viruses leave)
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17
Q

what are examples of virulent and temperate phages?

A

virulent: T4 (lytic)
temperate: lambda (lysogenic)

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18
Q

describe the structure of a T4 phage

A
  • head (with double-stranded DNA)
  • tail (tail sheath, multiple tail fibres, base plate)
19
Q

what is the function of tail fibre(s) in a virus, and what type of virus has how many each?

A
  • allows phage to adsorb onto surface of bacterial host by binding to specific receptors on cell surface
  • virulent / lytic / T4: multiple
  • temperate / lysogenic / lambda: one
20
Q

what is the function of a tail sheath in viruses, and in which viruses is it found?

A
  • surrounds central tube
  • contracts during penetration, thrusts central tube through host cell wall and membrane
  • found in virulent bacteriophages
21
Q

what is the function of a base plate in viruses?

A
  • contacts host cell surface
  • undergoes conformational change
  • allows DNA to be extruded from head, through central tube into host cell
22
Q

what are the types of nucleic acids found in T4, lambda, influenza, HIV?

A
  • T4 AND lambda: double-stranded DNA
  • influenza: eight segments of negative sense single-strand RNA
  • HIV: two identical positive-sense single-stranded RNA (RT)
23
Q

what are the reproductive cycles of virulent and temperate phages respectively?

A

lytic and lysogenic

24
Q

what is the structure of the head of lambda bacteriophage?

A

5’-terminus of each DNA strand is single-stranded tail of 12 nucleotides long
important in prophage formation

25
Q

describe the entire lytic cycle (reproductive cycle of a virulent phage): 5 steps

A
  1. adsorption
    - multiple tail fibres attach to specific receptors on bacteria host cell surface
    - base plate makes contact
  2. penetration
    - sheath undergoes conformational changes, contracts
    - central tube pierces cell wall and membrane of host
    - phage uses lysozyme to hydrolyse peptidoglycan cell wall for insertion
    - DNA extruded through tail tube, capsid left outside
  3. synthesis and replication
    - host cell machinery taken over
    - host cell DNA RNA protein synthesis stopped
    - DNA polymerase replicates viral DNA (raw materials from host DNA degradation)
    - viral mRNA synthesised by host RNA polymerase, made into enzymes by host machinery
  4. assembly
    - viral proteins assembled to form phage heads, tails, tail fibres –> complete bacteriophage
  5. release
    - host cell lysed by lysozyme
    - water enters cell by osmosis, cell swells and bursts
26
Q

describe the entire lysogenic cycle (reproductive cycle of temperate phages with envt trigger): 4 steps

4th step is what happens when lysogenic to lytic

A
  1. adsorption
    - single tail fibre attaches to specific receptor on host cell surface
    - base plate contacts cell surface
  2. penetration
    - DNA extruded from head through tail tube into host cell
    - capsid left outside host
  3. prophage formation
    - prophage insertion: phage circularises and inserts itself into specific site on chromosome
    - forms prophage
    - viral DNA replicated with chromosome each time host cell divides, passed on to daughter cells
  4. lysogenic to lytic
    - when envt trigger, lysogenic to lytic
    - lysis genes activated, viral genome exised from chromosome
27
Q

how can temperate phages reproduce (lysogenic to lytic)?

A
  • capable of both
  • envt trigger (eg. UV light, some chemicals) activates virus
  • switch from lysogenic to lytic
28
Q

state the three mechanisms for variation in viral genomes

A
  1. mutation
  2. recombination
  3. reassortment
29
Q

why are there higher rates of mutation (leading to genetic variation) in RNA viruses?

A
  • no proofreading mechanisms in single-stranded RNA w/o complementary strand
  • RNA viruses experience much higher rates of mutations
  • reverse transcriptase (in HIV) has very low fidelity
  • causes antigenic drift
30
Q

how do recombination and reassortment occur in viruses?

A

recombination:
- co-infection
- crossing over

reassortment:
- co-infection
- new packaged viruses produced with new allele combinations

31
Q

define antigenic shift

A

sudden change in antigenicity of virus due to reassortment of genome with another viral genome

32
Q

define antigenic drift

A

gradual accumulation of mutations in viral genomes that alters antigenicity

33
Q

what are the factors that influence rate of viral genome mutation?

A
  • single-stranded RNA cannot be proofread
  • viral polymerases have low fidelity
  • viral reverse transcriptase cannot correct misincorporation errors
34
Q

what are reteroviruses?

A

viruses with RNA and reverse transcriptase enzyme that converts their viral RNA into DNA (eg. HIV)

35
Q

no of viruses involved, mechanism, rate, impact immunity, cross-species

compare antigenic shift and antigenic drift

A

no of viruses: shift has 2, drift has 1
mechanism: shift by recombination or reassortment, drift by mutation
rate: shift rare, drift often
immunity: shift no pre-existing immunity, drift may have some
cross-species: shift may infect new species, drift cannot

36
Q

what are the two surface glycoproteins found on the influenza virus?

A

haemagglutinin (HA):
- binds to receptors containing sialic acid
- attach virus to host cell membrane receptor

neuraminidase (NA):
- hydrolyses mucus so virus enters cells of respiratory tract
- facilitates budding by cleaving receptors containing sialic acid

37
Q

what are the two matrix proteins enclosing the influenza nucleocapsid?

A

M1: monomers of matrix protein
M2: ion channel that lowers or maintains pH of endosome (transport vesicle)

38
Q

what are the enzymes found in the influenza virus?

A

PB1, PB2, PA: forms RNA-dependent RNA polymerase (replicase)
NS1: regulates viral replication mechanisms

39
Q

describe the entire reproductive process of influenza virus: 5 steps

A
  1. adsorption
    - HA binds to receptors containing sialic acid
  2. penetration
    - virus taken into host by receptor-mediated endocytosis in endosome
    - endosome fuses with lysosome, lowering pH
    - low pH triggers conformational changes in HA
    - viral envelope and endosome membrane fuses
    - eight viral segments of influenza genome released into host
  3. synthesis and replication
    - viral replicase (RNA-dependent RNA polymerase) converts negative sense RNA into positive sense
    - + sense RNA is template for synthesis of full-length negative viral RNA for new viruses
    - + sense RNA used as mRNA, translated by host cell to form viral proteins for new virus
  4. assembly
    - eight - sense RNA and enzymes packaged (glycoprotein joins during budding out)
  5. release
    - budded out
    - gains HA, NA, M2
    - NA cleaves sialic acid residues on cellular receptor btw new virus and host cell
40
Q

what are the two surface glycoproteins on HIV?

A
  • gp120: binds to CD4 receptors (macrophages, Th cells)
  • gp41: helps fuse HIV envelope and host cell membrane
41
Q

what are the three enzymes found in HIV?

A
  1. reverse transcriptase (viral RNA to DNA)
  2. integrase (incorporate DNA into host genome)
  3. protease (cleaves viral plp into functional proteins during viral maturation)
42
Q

describe the entire reproductive cycle of HIV: 5 steps

A
  1. adsorption / attachment
    - gp120 binds to CD4
  2. penetration
    - gp120 conformational change, binds to coreceptor
    - coreceptor is CXCR4 on Th, CCR5 on macrophages
    - gp41 pulls virus close to host, coreceptor allows entry of gp120-CD4 complex
    - HIV envelope fuses with host cell membrane, releasing viral contents
  3. synthesis
    - reverse transcriptase: viral RNA to DNA –> double-stranded DNA molecule
    - DNA passes through nuclear pore into nucleus
    - latent provirus made: integrase allows viral DNA to integrate into host genome
    - proviral DNA turns to RNA by host RNA polymerase –> viral proteins synthesised (to be cleaved)
    - viral surface glycoproteins incorporated into host cell membrane
  4. assembly
    - HIV proteins and RNA genome assembly near cell membrane: 2 single-stranded RNA with RT, integrase, protease
  5. release
    - glycoprotein studded membrane envelope gained when virus released
    - buds off
    - viral maturation: HIV protease cleaves single long chain into functional proteins
    - mature HIV formed
43
Q

what is the difference btw the tail sheaths of virulent and temperate phages?

A

virulent (lytic); contractile
temperate (lysogenic): non-contractile

44
Q

what is the difference between how influenza and HIV enter the cell?

A

influenza: receptor-mediated endocytosis

HIV: not that (checking)

H2 Biology (24 decks)

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