Genetics of Viruses Flashcards
1
Q
what does “obligate intracellular parasite” mean, and what does it describe?
A
viruses, cannot survive without living host cell
2
Q
what do viruses depend on host cells for?
A
- amino acids and nucleotides
- protein-synthesis machinery
- energy (ATP)
3
Q
what is the extracellular state of a virus, and its characteristics?
A
- virions
- metabolically inert
- no respiratory or biosynthetic functions
4
Q
who is MRS GREN?
A
8 characteristics of living organisms
- movement
- respiration (metabolism)
- sensitivity
- growth
- reproduction
- excretion
- nutrition
5
Q
what are the three arguments for viruses being living organisms?
A
- viruses can reproduce (in intracellular state)
- viruses can direct metabolic processes (in intracellular state)
- viral genomes can evolve (no single gene is shared by all viruses, viruses evolve w host and acquire their genes)
6
Q
what are two arguments for viruses being non-living?
A
- viruses are not cells
- do not have protoplasm or organelles - viruses lack some living organism characteristics
- no metabolism
- no nutrition needed
- cannot make energy (ATP)
- not sensitive
- no growth
- no excretion
7
Q
how do viruses challenge the cell theory?
A
- cells are smallest unit of life
- viruses have genetic material but no molecular machinery - cells arise from pre-existing
- can replicate but only in host cells - living organisms composed of cells
- viruses are acellular, no protoplasm or organelles
- metabolically inert, no resp or biosynthesis
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
9
Q
describe the structure of the viral genome
A
- dna OR rna
- single OR double stranded
- linear OR circular
10
Q
what are three types of viruses (classified by genetic material)?
((that u need to know))
A
- double-stranded DNA
- eg. T4 and lambda - negative sense single-stranded RNA
- genome is mRNA, immediately translated by host - single-stranded RNA-reverse transcriptase (RT) viruses
- reverse transcriptase (RNA to DNA) to produce DNA from viral RNA
11
Q
what are two types of essential proteins coded for by viral genomes?
A
- regulatory: regulate host gene action
- structural: eg capsid protein
12
Q
what is a capsid formed from?
A
capsomeres (identical protein subunits)
13
Q
what are viral envelopes, and what is its function?
A
facilitating viral entry
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)
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
16
Q
what are the five general steps of reproduction of an enveloped virus?
A
- adsorption (attach to host)
- penetration (viral nucleic acid enter host cytoplasm)
- synthesis & replication (new viral components made by host cell machinery)
- assembly (new viruses assembled)
- release (new viruses leave)
17
Q
what are examples of virulent and temperate phages?
A
virulent: T4 (lytic)
temperate: lambda (lysogenic)
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
describe the entire lytic cycle (reproductive cycle of a virulent phage): 5 steps
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
describe the entire lysogenic cycle (reproductive cycle of temperate phages with envt trigger): 4 steps
| 4th step is what happens when lysogenic to lytic
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
how can temperate phages reproduce (lysogenic to lytic)?
- capable of both
- envt trigger (eg. UV light, some chemicals) activates virus
- switch from lysogenic to lytic
28
state the three mechanisms for variation in viral genomes
1. mutation
2. recombination
3. reassortment
29
why are there higher rates of mutation (leading to genetic variation) in RNA viruses?
- 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
how do recombination and reassortment occur in viruses?
recombination:
- co-infection
- crossing over
reassortment:
- co-infection
- new packaged viruses produced with new allele combinations
31
define antigenic shift
sudden change in antigenicity of virus due to reassortment of genome with another viral genome
32
define antigenic drift
gradual accumulation of mutations in viral genomes that alters antigenicity
33
what are the factors that influence rate of viral genome mutation?
- single-stranded RNA cannot be proofread
- viral polymerases have low fidelity
- viral reverse transcriptase cannot correct misincorporation errors
34
what are reteroviruses?
viruses with RNA and reverse transcriptase enzyme that converts their viral RNA into DNA (eg. HIV)
35
# no of viruses involved, mechanism, rate, impact immunity, cross-species
compare antigenic shift and antigenic drift
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
what are the two surface glycoproteins found on the influenza virus?
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
what are the two matrix proteins enclosing the influenza nucleocapsid?
M1: monomers of matrix protein
M2: ion channel that lowers or maintains pH of endosome (transport vesicle)
38
what are the enzymes found in the influenza virus?
PB1, PB2, PA: forms RNA-dependent RNA polymerase (replicase)
NS1: regulates viral replication mechanisms
39
describe the entire reproductive process of influenza virus: 5 steps
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
what are the two surface glycoproteins on HIV?
- gp120: binds to CD4 receptors (macrophages, Th cells)
- gp41: helps fuse HIV envelope and host cell membrane
41
what are the three enzymes found in HIV?
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
describe the entire reproductive cycle of HIV: 5 steps
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
what is the difference btw the tail sheaths of virulent and temperate phages?
virulent (lytic); contractile
temperate (lysogenic): non-contractile
44
what is the difference between how influenza and HIV enter the cell?
influenza: receptor-mediated endocytosis
HIV: not that (checking)
