Viral Classification1-Au Coin Flashcards
What is the significance of viruses not being able to be filtered?
hard to associate a disease with the causative virus b/c you can’t filter it out & isolate it!
also makes it harder to sterilize things.
What does it mean that viruses are obligate intracellular parasites?
they have to be inside the host cells to replicate b/c they need to borrow the machinery!
T/F Although, viruses struggle to replicate apart from host machinery, they can make their own proteins.
False. They need the machinery of a host cell to make energy or any proteins.
They are also not technically alive.
Are viruses made of RNA or DNA?
they can be made of either, but not both at once
RNA–>DNA with reverse transcriptase one option.
T/F Viruses have a naked capsid or enveloped morphology.
True. Can have a viral membrane (received from host cell plasma membrane or organelle membrane).
Viruses must be ______ to endure in nature. What is its ideal host?
infectious
a naive host! So it doesn’t have to try so hard in mutating etc to evade the host mechanisms.
Viruses have been optimized by ______ and _____ to infect humans and other hosts.
mutation
selection.
T/F Viruses must encode any required processes not provided by the cell.
True.
How do viral components come together once they have been produced in a host cell?
they natural self assemble b/c they have a high affinity for each other…
What are the 2 main types of viruses?
Naked Capsid (nonenveloped) Enveloped Viruses
Which is bigger-DNA or RNA?
DNA is bigger! 200kB
RNA usu <30KB
What are the positive viral structural proteins?
they are what make the capsids to surround the viral genome
What do the glycoproteins & membrane from the host cell do?
they give you an envelope for your virus!
What are the components of the basic virion-non-enveloped?
DNA/RNA + structural proteins + enzymes & nucleic acid binding proteins = nucleocapsid
What are some examples of naked capsid viruses?
papilloma virus
adenovirus
poliovirus
What are the components of an enveloped virus?
DNA/RNA + Structural Proteins + Enzymes & Nucleic Acid binding proteins + Glycoproteins & Host membrane =Enveloped VIrus
What are some examples of enveloped viruses?
herpes virus
retroviruses
What are some ways to classify viruses based on their structure?
size
morphology
nucleic acid
What are some ways to classify viruses based on their biochemical characteristics?
structure & mode of replication
What are some ways to classify viruses based on the diseases they cause?
encephalitis
hepatitis
What are some ways to classify viruses based on their means of transmission?
arbovirus-spread by insects
What does it mean to classify viruses based on tropism?
tissue or organ
**adenovirus & enterovirus
Which Hep viruses are DNA & which are RNA?
DNA: just Hep A
the rest are RNA!
Adenovirus was first isolated in the _____.
adenoids
Arboviruses are spread by what?
arthropods
insects with an exoskeleton
the picornavirus is named based off of what?
its structural characteristics…it is small!
The retrovirus is named based off of what characteristic?
biochemical characteristic
the presence of reverse transcriptase
What’s the deal with reovirus?
has respiratory, enteric effects
o for orphan-b/c it was first discovered when they didn’t know what it did!
What’s the worst way to name a virus?
by location-residents will raise objections
What are the 2 main classifications of DNA viruses?
enveloped
naked capsid
Give 3 examples of enveloped DNA viruses.
Pox
Herpes
Hepadna
What are some examples of Naked Capsid DNA viruses?
Polyoma
Papilloma
Adeno
Parvo
What is an example of a virus that causes the common cold?
adenovirus
What is an example of a hepadna virus?
Hep B
What are the 4 main categories of RNA viruses?
+RNA
-RNA
+/-RNA
+RNA via DNA
What are the 2 main types of +RNA viruses?
Nonenveloped & Enveloped
What does it mean to be + strand RNA?
an example of this is messenger RNA
it means that you could put that RNA in a cell & it would be infectious as opposed to -RNA that couldn’t make proteins on its own
What are 2 examples of non enveloped +RNA viruses?
Picorna
Calici
What are 3 examples of enveloped +RNA viruses?
Toga-ex: rubella
Flavi
Corona
What are the units used to measure viruses? What is the largest virus? Note: the only one that can be seen under a light microscope?
nanometers (10^-9)
Poxviruses (300nm)
What makes larger virions larger?
they have a larger genome & are more complex
Give a good definition of a virion.
nucleic acid genome packaged into a protein coat (capsid or ribonucleocapsid) or a membrane/envelope
What is the tegument layer of a virion?
it is b/w the capsid & the envelope & has viral proteins that help with viral replication
What is a bacteriophage?
virus that infects bacteria
How big is a human cell?
30-100 micrometers
What are the 2 main types of naked capsid virus structures?
Icosahedral nucleocapsid (DNA or RNA) Helical Ribonucleocapsid (RNA)
What does the icosahedral nucleocapsid look like?
polygonal structure with DNA or RNA in the center
can be enveloped in host membrane to make an enveloped virus
What does the helical ribonucleocapsid look like?
helical shape of RNA
proteins are bound to the RNA=ribonucleocapsid
can also be enveloped in host membrane
T/F Both enteric viruses & polio virus are enveloped.
False. They are typically naked capsid viruses.
What is the function of the VAP-viral attachment protein?
this is on the surface of the capsid or envelope of the virus & it attaches to the target cell
Glycoproteins on the surface of viruses can be VAPs & are antigenic. What are the antibodies that bind these proteins called?
neutralizing antibodies
HIV CD4 T helper cells gp120 molecule How do these all relate to the virus terminology we have learned?
HIV: virus Note: becomes inactivated when its envelope dries out.
gp120: VAP
CD4: target receptor
T helper cells: target cell
What’s the deal with the polio virus?
enteric virus
RNA genome
protein capsid
fecal-oral route to spread
Which is more durable–protein capsid or envelope of a virus?
capsid WAY more durable! It can handle pH changes, drying, detergents etc.
Rigid structure.
That is why you need enteric viruses to be capsid.
Envelopes are delicate!
What is contained in a viral envelope?
think about what is contained in a cell membrane
lipids, proteins, glycoproteins
Enveloped viruses are mainly transmitted via what b/c of their delicate structure?
body fluids!
maintained only in aqueous solutions
Most helical capsids are +/- strand RNA/DNA viruses.
Helical Rods
negative strand RNA viruses
Note: these ribonucleoproteins self assemble. Don’t need ATP!
T/F Although ribonucleoproteins self assemble, icosahedral capsids require ATP to form.
False. They also self assemble.
Simple icosahedrons like picornaviruses are made of __capsomers each with ____fold symmetry.
12
five-fold symmetry-pentameric!
Describe the structure of the icosahedral capsid–broken down into units.
Little Proteins (3)–>1 protomer
5 protomers–>1 pentamer capsomere
12 pentamers–>1 mature virion!
How do you get a bigger virus with an icosahedral virion shape?
add more structural proteins in between the pentamers
What is the term to VAPs that bind to red blood cells? What do they do?
hemagglutinins
it causes RBCs to clump together-agglutinate!
Give an example of hemagglutinins with a virus?
H1N1 virus has hemagglutinins as its VAP
it causes RBCs to clump
What causes the spikes on viruses? They are immunodominant. What does this mean?
glycoproteins
immunodominant-antibodies will be made against them.
T/F All negative strand RNA viruses are naked capsid.
False. they are all enveloped.
Influenza A is an RNA virus. Is it negative or positive strand? What type of genome does it have?
negative strand RNA virus
segmented genome
separate genes code for separate proteins
What is the tegument layer?
b/w the envelope & nucleocapsid
has enzymes & proteins that facilitate viral infection
help with viral replication
What are the basics of the phases of viral replication?
virus must recognize target cell, attach and penetrate the plasma membrane, uncoat its genome into cytoplasm and in many cases deliver genome to the nucleus
genome replication and viral macromolecular synthesis followed by viral assembly and release
latency is when extracellular infectious virus is not detected but viral genomes can be detected
What is the burst size?
the number of infectious particles from a single cell
Which virus has its own DNA polymerase-it is that large?!
Herpes virus
How do viruses often come in the host cell?
mainly via receptor-mediated endocytosis
could also be fusion of viral membrane & host membrane
After the capsid of the virus has been removed-where do the DNA viruses go? Where do the RNA viruses go?
DNA viruses go to the nucleus.
RNA viruses stay in the cytoplasm.
What are several ways to exit a host cell if you are a virus?
budding-host may survive
exocytosis-host may survive
lysis-kills host
Describe the process of viral replication
Recognition: VAP (usu a glycoprotein or viral protein on capsid only viruses) finds a target cell & binds a receptor.
Penetration via receptor-mediated endocytosis (esp when you don’t have a membrane).
Can also come in via fusion of viral membrane w/ cell membrane. Virus could lose membrane at that point. Could lose it in the endosome
Uncoating: the capsid shell needs to go. Genome moves. DNA to nucleus; RNA in the cytoplasm.
Need to make mRNA (+ strand RNA) to make viral proteins.
Also need to replicate for new viral genomes.
Release: Non-envelope: leave by lysis
Enveloped viruses: Exocytosis via secretory pathway
Budding & release can be a way of the virus to leave-gentle exit.
The host cell could survive if the virus leaves via budding & release or exocytosis.
T/F Viruses can bind to any target.
False. they have a host range. their VAP needs to match the target receptor.
What is tissue tropism w/ respect to viruses?
the susceptible target cells-which tissues etc.
What are VAPs usu?
specific glycoproteins of enveloped viruses
T/F VAPs can only be glycoproteins.
False. They can be proteins, carbs, glycoproteins or glycolipids.
Can VAPs be found on non enveloped viruses?
Yes, can be proteins on capsids.
HA of influenza A binds to what?
sialic acid receptors of lung tissue
In general, naked capsids enter the host cell how?
receptor mediated endocytosis
In general, enveloped viruses enter the host cell how?
by fusion of their membranes
What is the optimal pH for fusion proteins?
varies
could be neutral or acidic
What is the exception to the rule that DNA genomes go to the nucleus of the host for replication?
poxviruses
DNA but remain in the cytoplasm
What is the exception to the rule that RNA genomes replicate in the cytoplasm?
influenza (orthomyxoviruses) are neg. sense RNA viruses that replicate in the nucleus
retroviruses also replicate in the nucleus
What’s the deal with synctia?
this is a form of immune evasion
virus spreads from cell to cell
What do most DNA viruses use to make their enzymes & mRNA?
host DNA-dependent RNA pol II
What are 2 things that mRNAs need?
3’ poly A tail-keeps it from being degraded; signal for it to leave the nucleus
5’methylated cap-binds it to ribosomes
T/F Virus must encode enzymes for transcription.
True.
How does mRNA production & replication happen for viral double stranded DNA?
transcription: use host machinery in nucleus, translated by host cell ribosomes into proteins
replication: semiconservative, rolling circular & linear
How does single stranded DNA viruses accomplish transcription & replication in a host cell?
transcription: SSDNA–>DSDNA, transcribed by host machinery
replication: replicated by DSDNA viruses
Pos stranded RNA viruses accomplish transcription & replication in host cell how?
Transcription: already acts like mRNA & can bind ribosomes. Makes a polyprotein. Cleaved into individual proteins. Makes RNA dep RNA pol as one of its first proteins.
Replication: + RNA strands turned into - RNA strands w/ the RNA dep RNA pol. Then a bunch more + RNA strands are made.
Neg stranded RNA viruses accomplish transcription in the host cell. How?
transcription: transcribed into mRNA by the RNA dep RNA pol that is carried in by the virion
How is double stranded RNA used to make mRNA?
DSRNA’s neg strand is used to make mRNA with the RNA polymerase that is in the capsid.
How do retroviruses work?
Retroviruses are (+) RNA that are converted to complementary DNA (cDNA) by reverse transcriptase carried in the virion. cDNA integrates into the host chromosome, and the host makes mRNAs, proteins, and full-length RNA genome copies.
What is the name of the drugs that target the herpes viruses? How do they work?
acyclovir
nucleoside analogs
gets incorporated into the genome
causes chain termination-no more addition of extra nucleotides
works on viral polymerase, but not the host polymerase, so has awesome specificity!
What are some examples of double stranded DNA viruses?
polyoma papilloma adeno herpes pox
What are some examples of single stranded DNA viruses?
parvo
What are some examples of + strand RNA viruses?
picorna noro toga flavi corona
What are some examples of neg strand RNA viruses?
rhabdo paramyxo orthomyxo bunya filo
DSRNA example?
Reovirus
T/F Some complex DNA viruses encode their own transcription factors to regulate the expression of viral genes.
True.
T/F Viral DNA pol (encoded by DNA viruses) make fewer errors than host DNA pol.
False. More errors. no proofreading.
Note: these are only coded for by large DNA genomes
DNA polymerases from viruses can be targeted by what?
antiviral nucleotide analogs
Viral DNA replication begins where?
at an origin
different origins for lytic & latent replication. Lytic-make a lot more!
Describe the process of DNA viral replication.
VAP & receptor. First!
Fusion @ membrane.
Capsid delivered into cytoplasm.
Capsid is degraded @ the nuclear pore.
DNA genome is inserted into the nucleus.
Have early & late genes that are made (not all made at once).
Icosahedral Capsids filled with DNA genome in the nucleus.
Capsids bud out of nucleus & acquire tegument proteins in cytoplasm & acquire envelope as bud thru viral glycoprotein modified Golgi membranes.
Virus released by exocytosis or cell lysis.
So…with DNA viral replication there are immediate early, early, and late phase transcription & translation. Describe how this works.
IE: these proteins promote cell takeover
E: DNA Dependent DNA polymerase
**Genome replicated.
Late: structural proteins for viral capsid & glycoproteins
Late proteins go back into nucleus & assemble around DNA genome to make virus.
T/F RNA dependent RNA polymerase has a fast & high mutation rate.
True.
Describe briefly how RNA virus replication occurs.
- Bind cell surface (ex: rabies virus)
- receptor mediated endocytosis, endosome delivers virus into cytoplasm. Neg sense RNA genome.
- virion has the RNA dependent RNA pol–>makes mRNA from the neg strand RNA
- Genome replicated & formed in a nucleocapsid
- Virus buds from cell
Why is it that viral mRNA is often preferentially translated?
some viruses block cellular mRNA from leaving the nucleus
can down regulate the translation of host mRNA
T/FSome viral proteins require post-translational modifications such as phosphorylation and glycosylation
True
When does viral budding occur? Which types of viruses often bud?
after the association of the nucleocapsid with the intracellular portion of viral glycoproteins
**RNA viruses bud
If a virus doesn’t bud…how might they acquire their envelope?
budding into ER or Golgi Apparatus
When is ATP needed for viral assembly?
Almost never! When Herpes Virus DNA is inserted into its capsid.
Mutated viruses can have which 3 results?
- no change in phenotype
- detrimental effects
- enhance pathogenecity & produce drug resistance
Mutations to essential genes causes what?
Mutations to less serious genes causes what?
Essential genes-lethal! Noninfectious virus
Less Serious Genes-Attenuated Mutants, less serious disease.
How might new virus strains be produced?
via intermolecular exchange b/w viruses or virus & host–called recombination
What’s the deal with reassortment?
viruses with segmented genomes can be shuffled in the presence of other genes
