1
Q
How does virus get released? What does each one do? (3)
A
- Lysis: eg T4 = holin makes holes in membrane, t4 lysozyme dissolves cell wall
- Budding: eg flu = viral genome/structural proteins congregate at budding site
Curvature forms
Excised out via neruaminidase when bud is mature
Virus is free - Cell-to-cell release
2
Q
How does cell-to-cell release occur? In what for ex?
A
- In plant viruses
- Plasmodesmata occrus: channel communication between plant cells and virus can be released
3
Q
How do viruses exist as living?
A
- Possess own genetic material (nucleic acids)
- Reproduce offspring
- Catalyze biochemical rxns, encode enzymes
4
Q
How do viruses exist as non-living?
A
- Acellular structures
- No metabolism
- Depend on host to reproduce
5
Q
Non-eveloped vs enveloped viruses?
A
- Enveloped have outer lipid bi-layer
- Non-enveloped have a capsid (more resistant)
6
Q
How do viruses infect and multiply?
A
- Need host cell: eukaryotes and prokaryotes/archaeal
- Animal cells: plasma membrane, plant & bacterial cells: membrane and cell wall
- Cell barriers must be navigated to infect
7
Q
What are the 5 steps of viruses entering a host cell?
A
- Attachment to surface
- Entry/breach of host cell barrier
- Synthesis of viral components in host
- Assembly of viral progeny
- Release of viral progeny through barrier
8
Q
How does attachment of virus occur?
A
- Interaction between specific molecules present on the virus and host cell surface
- Host cell molecule = receptor
- Virus molecule = receptor-binding protein
9
Q
Where is the receptor-binding protein for viruses found?
A
- On capsid on non-enveloped viruses
- On envelope of enveloped viruses
- Protein interacts with receptor on host cell
10
Q
What can a receptor on a host cell be? What virus doesn’t have a discovered receptor?
A
- Protein molecule, carb molecule
- Can be unique to one virus or for multiple
- Can have co-receptor
- Virus receptor may not be present in all hosts or on all tissues
- This determines the tissue tropism of virus
-*Plant viruses
11
Q
What is tissue tropism?
A
- Capacity for virus to infect, replicate, and cause disease to certain parts of the host
- Like certain tissues, organs, or cell types
12
Q
How can viruses enter the host cell?
A
- Actively: fusion, endocytosis, direct injection
- Passively: enter damaged cell
13
Q
How does a virus enter by fusion?
A
- Used by mainly enveloped (eg HIV)
- Spikes/proteins bind to receptors on surface
- Lipid bilayer of envelope fuses with host cell membrane
- Caspid w/ genetic material is released into cytoplasm
14
Q
How does a virus enter by endocytosis?
A
- Used by enveloped and non-enveloped (eg Flu)
- Spikes/proteins bind to receptor
- Receptor-mediated endocytosis triggered/engulfed
- Increased acidity allows for capsid to escape and enter cytoplasm
15
Q
How does a virus enter passively?
A
- Most plant viruses
- Wound gets created by environmetal element like animal or weather
- Leads to damaged cell wall and plasma membrane
- Virus enters cell, genome injected from capsid
16
Q
How does a virus enter through direct injection?
A
- eg T4 bacteriophage
- tail comes in contact with cell wall
- small pore created
- hi pressure environment, genome released into cell
17
Q
How does a viral genome synthesize?
A
- replicate to make copies for progeny
- transcribe into mRNA
- translate mRNA into viral proteins
18
Q
How does replication of viral genome occur?
A
- depends on type and configuration of DNA
- occurs in nucleus or cytoplasm of eukaryotic host
- in cytoplasm of prokaryotic host
19
Q
How does transcription of viral genome occur?
A
- depends on type and configuration of genome
- occurs at viral genome replication site
20
Q
How does translation of viral genome occur?
A
- viruses hijack host cell translation machinery
- like host cell mRNA
- occurs in cytoplasm
- 2 proteins made: structural and non-structural
21
Q
How are viral progeny assembled?
A
- compelx, regulated process
- occurs in cytoplasm, nucleus, or plasma membrane
- structural proteins interact with each other sequentially
- then interact with viral genom to assemble viral progeny with help of non-structural proteins
- then released
22
Q
What are DNA viruses?
A
- have DNA genome
- most bacterial and archaeal viruses
- 1/2 of human, fungal, algal viruses
- few plant viruses
- *might be largest group of known viruses
23
Q
How does viral DNA genome exsist?
A
- double stranded
- single stranded
- linear
- circular
24
Q
Central dogma of life? DNA viruses also follow this
A
- DNA dependent DNA polymerase (from host or viral) recognizes DNA that needs to be copied
- DNA to mRNA via transcription (w/ DNA dependent RNA polymerase from host)
- mRNA to protein via translation (w/ ribosome from host)
- DNA replicates
25
How are DNA virus genes expressed sequentially?
immediate early genes (transcription factors)--> early intermediate genes (DNA polymerase) --> late genes (structural/non-structural)
26
What are the critical components of DNA replication?
- topoisomerase (unwinds)
- helicase (replication fork formed)
- primase (RNA primer)
- 3' end of primer (DNA synthesis primed
- nucleotides (building blocks)
- polymerase (new DNA strand synthesized
- ligase (joins it all)
27
Differences in DNA replication in virus?
- primase might or might not be required
- 3' end of primer can be RNA or DNA
- nucleotides always come from host
- rest comes from host or virus
28
Linear dsDNA genome replication
?
29
General issue of linear dsDNA replication?
- RNA primers removed after replication is complete
- left with truncated 5' ends
- ends can be filled by eukaryotes but not viruses
30
How do viruses overcome the issue of linear dsDNA replication?
- form concatemers and close ends via covalent bonding after DNA replication
- circularize the linear dsDNA before replication
- use viral protein as primer for DNA replication
31
What is a concameter? How is it formed?
- long dsDNA molecule with 2 or more dsDNA genoms in a row
- genomes are joined via successive homologous recombination
- cleaved by endonuclease into individual genomes
- packed into viral progeny
- next replication cycle continues
32
How are ends closed by covalent bonding?
- closed ends are nicked by helicase (host)
- 3' forms hairpin and is primer for RNA primer independent replication
- DNA polymerase uses 3' end as primer and same strand as template
- DNA synthesis begins
- 2 genome concatemer formed --> cleaved into individual genomes
33
How to circularize linear dsDNA? also known as what?
- truncated ends are ligated
- outer DNA strands nicked by helicase and free 3' end formed
- DNA polymerase uses 3' end as primer and same strand as template
- DNA synthesis begins
- RNA primer independent replication
- other outer end of DNA is displaced
- RNA primer formed on displaced strand
- DNA polymerase uses 3' end as primer and displaced strand as template
- RNA primer DEPENDENT replication
- 2 genome concatemer --> cleaved into genomes
- *rolling-circle replication
34
How to use viral protein as a primer?
- viral protein forms complex with DNA polymerase
- complex binds to 3' end of bottom DNA
- uses it as template, DNA synthesis starts
- top strand is displaced and circularized
- complex binds to 3' of circle and uses itself as a template for DNA synthesis
35
What is linear ssDNA genome replication? eg
- Palindromic ends form hairpins
- 3' end used as primer
- RNA primer independet replication starts (self as template)
- bottom strand nicked, free 3' end
- replication resumes using upper hairpin as template
- dsDNA intermediate formed
- hairpins formed at one end of each strand
- replication resumes --> top strand displaced and incorporated as genome into viral progeny
- bottom strand continues cycle with RNA primer independent replication/using self as primer
36
What is circular dsDNA genome replication? eg
- helicase nicks strands
- 2 replication forks formed
- RNA primer dependent replication in both direction
- leading and lagging strands like with linear dsRNA rep.
- offspring genomes are catenated
- decatenated by topoisomerase
- incorporated into viral progeny
- bidirectional genom replication occurs
37
Circular ssDNA genome replication? eg
- DNA polymerase converts ssDNA into dsDNA
- outer strand replicates as in circular dsDNA rep.
- displaced strand circularized by ligation
- incorporated into viral progeny
- inner strand continues to replicate
38
What are the DNA virus transcription and genome replication sites?
- Eukaryotic = nucleus for most DNA viruses, cytoplasm for a few
- Prokaryotic = cytoplasm for all viruses
39
What are some viruses with an RNA genome?
influenza, ebola, hepatitis C, HIV, covid
40
what are configurations of RNA genome viruses?
ss, ds, linear (one fragment or several), circular
41
what is the RNA virus transcription and genome replication site in eukaryotic and prokaryotic cells?
- in cytoplasm of both
- in nucleus of some eukaryotic cells, eg influenza
42
what two polarities does ssRNA genome exsist in?
pos and neg sense strands
43
dogma of +ssRNA viruses? RdRp?
- occurs in two steps of translation and replication
- virus synthesizes RdRp in host cell
- virus enters cell and releases genome which becomes mRNA and can start synthesizing proteins immediately
44
dogma of -ssRNA? RdRP?
- 3 steps of transcription into mRNA and then translation and replication
- RdRp carried in capsid
45
how does gene expression work for RNA viruses?
- whole RNA genome can act as one gene to encode for a polyprotein (one large protein)
- OR individual genes can each encode for a protein or multiple proteins
46
How does +ssRNA virus gene expression work?
- polyprotein gets synthesized
- gets cleaved into individual proteins
- first is done by host protease and than by viral proteases
- one of the products is RdRp
47
What mechanisms does -ssRNA virus gene expression use?
- alternative initiation
- ribosomal frameshifting
- alternative splicing
48
what is alternative initiation?
- codon is read with AUG so a protein is made
- but there's another AUG in the middle of codon if read differently (frameshift)
- another protein is made
49
what is ribosomal frameshifting?
- ribosome skips a nucleotide
- so one protein is made and then anotehr protein
50
what is alternative splicing?
- introns are spliced out since they are redundant and don't code for anything
- exons get put together
- but exon might be skipped, resulting in a different protein
51
How does linear ssRNA genome replication occur?
- RdRp primes itself at the 3' end
- strand made from 5' to 3' like DNA
- occurs continuously in one direction
- in -ssRNA a +ssRNA intermediate is formed
- in +ssRNA a -ssRNA intermediate is formed
52
dogma of dsRNA virus?
- RdRp in capsid
- neg strand transcribed into pos dsRNA
- acts as mRNA and makes proteins
- pos strand and RdRP put into capsid
- pos strand becomes neg strand to make dsRNA
(transcription and replication occur while dsRNA is still insdie the capsid)
53
When does reverse transcripatase get used? what kind of viruses use it? ex?
- since +ssRNA isn't used as mRNA although they contain it
- used by retroviruses like HIV
54
What type of activity occurs with reverse transcriptive enzyme?
- RdDp activity
- DdDp activity without proofreading
- RNase H activity
55
What is RdDp? DdDp?
- RNA dependent DNA polymerase
- DNA dependent ...
56
What occurs with reverse transcription of RNA viruses?
- two copies of +ssRNA in capsid
- these have direct repeats at each end and a PPT
- Rnase degrades the RNA part of the RNA/DNA hybrid
- except fo PPT which is removed and binds to the other strand and starts synthesizing with 3' end as priming end
- results in dsDNA which is slightly longer
- this can lead to translation of the mRNA into protein
57
How is reverse transcription used for DNA viruses?
- for viruses with an incomplete genome
- DNA repair machinery repairs the incomplete DNA virus to become a complete circle (or cccDNA)
- cccDNA is template to make new rcDNA
- can undergo same dogma of dsDNA
- dsDNA gets packaged into a capsid alongside rev. trans. which acts on the ssRNA to turn it into dsRNA
58
What are the 3 types of viral infections in animal host cells?
acute, persistent, and transformative
59
characteristics of acute infection?
- short incubation period of 12-48 hours
- large number of viral progeny
- host cell dies
- clinical symptoms
- virus can be cleared from host
60
characteristics of persistent infection? 2 specific types?
- long incubation period of days to months
- can persist for life
- host cells survive
- latent and chronic
61
characteristics of latent infection?
- only genome and few viral proteins are present
- no viral progeny
- no clinical symptoms
- can be reactivated into acute infection via stimulus like stress or hormonal changes
62
characteristics of chronic infection?
- active replication
- few viral progeny
- clinical symptoms are present
63
characteristics of transformative infection?
- infected cells become cancerous
- viral oncogenes
- viral oncoproteins inactivate host tumor suppressor proteins AND hyperactive host proto-oncogenes
- leads to uncontrolled cell division and cancer
64
what are the types of viral infections in bacteria and archaeal host cells?
- lytic infection
- lysogenic infection
65
lytic infection? life cycle?
- phage DNA injects DNA into host cytoplasm
- new phages synthesized and released after cell lyses
- new phages bind to other cells
- host cells die
66
lysogenic infection? life cycle?
- bacteria can become dormant due to nutrient deprivation
- can become reactivated into lytic infection via change in growth conditions or exposure to UV
- phage DNA gets integrated into host chromosome and is copied when cell divides (becomes prophage)
- temperate phage can become virulent
- doesn't kill host cells
67
what are the five modes of virus transmission (between) hosts?
- aerosol: respiratory droplets
- faecal-oral: contaminated food or water
- bodily fluid
- zoonotic transmission: infected animal contact
- vector transmission: insect bites
68
how do viruses transmit within the host?
- replication at the site of exposure and then move to other tissues
- direct entry into bloodstream and then spread to target tissue
- viral progeny can release into blood and infect other tissues like the brain
69
what are the 5 types of viral diseases in humans? (infection is different from disease)
- airborne
- food and water borne
- direct contact
- zoonotic
- arthropod borne
70
flu?
- airborne
- acute
- caused by influenza virus A or B
- secondary bacterial infection can lead to pneumonia
71
covid-19?
- airborne
- acute
- caused by SARS Cov 2
- fluid build up in lungs
72
mumps?
- airborne
- acute
- caused by mumps virus
- enlarged salivary glands
- childhood disease
73
measles and rubella?
- airborne
- acute
- caused by measles and rubella virus
- rash
74
viral gastroenteritis?
- food and water borne
- acute
- caused by rotavirus or noravirus
- "stomach flu"
75
poliomyelitis?
- food and water borne
- acute phase (mild symptoms) --> chronic (spreads to CNS/paralysis)
- caused by polio virus
76
viral hepatitis?
- food and water borne
- acute
- caused by hepatitis A and E
- liver is inflamed
77
AIDS?
- direct contact
- caused by HIV
- acute (T immune cells infected) --> aymptomatic phase (continues to replicate in tissue) --> chronic (weak immune system)
78
cold sores/genital herpes?
- direct contact
- latent phase: virus in nerve cells
- acute phase: virus can reactivate
- caused by herpes simplex virus 1 and 2
79
warts and cervical cancer?
- direct contact
- caused by HPV
- transformative
80
zoonotic diseases? examples?
- high mortality rate
- acute
- examples
- ebola: vascular system damage, transmission through eating or handling animals
- rabies: infection of skeletal muscle cells and CNS, transmission through bites
- avian flu: pneumonia and acute respiratory syndrome, transmission through poultry
81
arthropod borne diseases?
- acute infections
- mosquitos
- fever
- examples: chikungunya, dengue, west nile, zika
82
how to prevent vs treat viral infection?
- prevent through surveillance and vaccines
- treat through antivirals, antibodies, and anrisera
83
factors that drive virus emergence?
- ecological changes
- human demographics & behavior
- international travel & trade
- virus change and adaptation
83
what does WHO do?
- global alert and response
- for epidemics, pandemics, public health emergenices
- assess risk
- coordinate responses like travel advisory, containment, and mitigation
84
what is targetted for antiviral intervention/how to treat with antiviral durgs?
- inhibit any of the 5 steps of the virus life cycle
- interfere with functioning of a component of that step
- selective toxicity to host
85
vaccine?
- prep whole or part of microbe that induces protective adaptive immunity in host
- provides adaptive immunity
- viral vaccines contain whole virus or receptor bind protein
86
adaptive immunity?
- neutralizing anitbodies and memory cells circulate in bloodstream
- memory cells can make the antibodies again
87
what do vaccine induced antibodies do?
- block virus attachment
88
4 types of viral vaccine preparations? how it's done?
- inactivated whole virus (dead strain) = heat or chemicals
- attenuated whole virus (live virus but can't cause disease) = culture in unfavorable conditions or mutations
- viral mRNA or protein (receptor binding protein) = mRNA in lipid nanoparticles or protein complexed with inert material
- vector with viral gene (receptor binding protein) = cloned in non-replicating virus
89
viral vaccine formulation and dose?
- some require combo of mutiple doses to maintain neutralizing antibodies and response
- different stages might develop different antibodies
- some vaccines make multiple viruses in the same does
90
success rate of vaccines?
- some are eradicated (e.g. smallpox, poliovirus)
- global burden is decreased in others (e.g. measles, flu)
91
important components at each step of virus life cycle?
- assembly: receptor binding protein and receptor
- entry: fusion and endocytosis components
- synthesis/genome replication: RNA/DNA polymerase and nucleotides
- synthesis & assembly/polyprotein processing: proteases
- release: proteins
92
how does amantadine work as anti-influenza virus?
inhibits release of influenza virus from capsid from endosome
93
how does ribavirin work as anti hepatitis C or acyclovir as anti-herpesvirus)? (genome replication)
- nucleotide or nucleoside analogues are used (w/ out phosphate)
- elongation step during RNA or DNA synthesis is interrupted
- b/c polymerase adds the wrong building block (drug) --> added to genome --> can't add another one so elongation stops
94
how does maviret work as anti-hepatitis C drug? (polyprotein processing)
- +ss RNA genome acts as mRNA to make poly proteins
- needs to be cleaved by protease
- so protesase is targetted and polyprotein isn't cleaved
95
how does tamiflu work as anti-influenza virus?
inhibits budding which prevents viral progeny from being released
96
passive immunization?
- neutrailizing antibody produced
- different classes can be produced
- stops spread of progeny to bloodstream
97
MICROBIO
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