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131 Cards in this Set

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What are the 5 major groups of negative strand RNA viruses?
Rhabdoviridae
Paramyxoviridae
Orthomyxoviridae
Bunyaviridae
Reoviridae
What is the prototype of Rhabdoviridae?
VSV (Vesicular Stomatitus Virion-an arbovirus)
Give an example of Rhabdoviridae.
Rabies!
What is the nucleocapsid composed of?
The nucleoprotein (N) is wrapped around the RNA
What are characteristics of VSV?
~11000 nt
no cap or poly(A) tail
helical nucleocapsid ("bullet-shaped")
Proteins: N, P, M, G, L
How are the poly(A) tails added?
by the transcriptase "stuttering"

transcriptase proceeds to end of gene and stutters on a stretch of U residues to add poly(A)
Describe the VSV replication cycle.
1. Receptor Mediated
Endocystosis
2. Transcription of negative stranded mRNA into positive sense mRNA. (Sequential Transcription)
3.
What is the function of the N protein?
The N protein is wrapped around RNA to form a protected helical nucleocapsid.

Full-length negative-sense strand is only generated when levels of N protein become high enough in the cell so that newly synthesized positive-sense RNA can associate with it. This association prevents the rocking-polyadenylation-cleavage-reinitiation process used in the generation of mRNA and allows the formation of full-length template.
What is the function of the P protein?
Part of the polymerase complex
What is the cause of the different ratios of the N, P, M, G, and L proteins?
Reinitiation at each gene junction is only about 60% efficient.
What is the function of the M protein?
Interacts with lipid envelope and virus core.
Blocks cell nuclear-cytoplasmic transport functions.
Shuts off host transcription and translation.
What is the function of the G protein?
G protein spikes (transmembran glycoprotein) bind to virus receptor on host cells and is also responsible for membrane fusion.
What is the function of the L protein?
Part of the polymerase complex
What is the function of the polymerase complex (L and P proteins)in VSV?
Cap mRNA, generate mRNA, polyadenylate positive-sense viral mRNA, and replicate the viral genome.
What is the prototype of Paramyxoviridae?
Sendai
What is the prototype of Orthomyxoviridae?
Influenza
What is the prototype of Bunyaviridae?
LaCrosse
What is the prototype of Reoviridae?
Reovirus
What are viruses with monopartite genomes?
Viruses with monopartite genomes contain a single piece of virion negative-sense RNA.
What is a multipartite genome?
Many groups of negative-sense RNA viruses have segmented genomes.
Viral genes are encoded in separate RNA fragments, ranging from 2-8 fragments.
What is an RNA-dependent transcriptase and what does it do?
An enzyme synthesizing RNA (usually mRNA) using Watson-crick base-paring rules and RNA as a template.

This is how negative-sense RNA viruses transcribe their RNA into translatable mRNA.
The cell has no mechanism for transcription of mRNA from an RNA template.
What families of viruses have monopartite genomes?
Rhabdoviridae, Paramyxoviridae, Filiviridae, and Bornaviridae
(4)
What are zoonoses?
Diseases of other vertebrates transmissible to humans.
What is the common function of the L and P proteins of VSV?
The L and P proteins function together to cap mRNA, generate mRNA, polyadenylate positive-sense viral mRNA, and replicate the viral genome.

JUST CHECKING!
REMEMBER THE FUNDAMENTALS!!!!
What are the four subgroups of the paramyxoviridae family?
Paramyxoviruses
Rubulaviruses
Morbilliviruses
Pneunoviruses
What are some characteristics of paramyxoviridae?
~15 kb genomes
Spherical with helicial RNP core
Fusion protien (F)
Hemagglutinin (HN)
Encodes 6 genes
What is different about the P/L complex in paramyxoviruses?
The P/L polymerase complex inserts extra non-coded G residues in the middle of some P transcripts (stuttering mechanism); this gives rise to additional proteins encoded in different reading frames.
What is the function of HN (hemagglutinin) in paramyxoviridae?
Binds to receptors and also has neurominidase activity required for proper virus release.
What type of diseases are caused by paramyxoviridae?
parainfluenza, mumps, measles, RSV
What are some characteristics of Filoviridae?
~19 kb genome
Semicircular shape
Gene orginization similar to rhabdo and paramyxoviruses
What are some examples of Filoviridae?
Marburg and Ebola viruses which cause hemorrhagic fevers
What are some characteristics of Bornaviridae?
~9 kb genome
Gene organization similar to other mononegavirales
Encodes 6 genes (envelope proteins, structural proteins, and a viral polymerase)
Causes a variety of neurological symptoms in many vertebrate animals
What makes Bornaviridae different from most monogeavirales?
it replicates in the nucleus and some mRNAs are spliced
What is the prototype of Orthomyxoviridae?
Influenza viruses (A, B, and C serotypes)
What is antigenic drift?
Gradual accumulation of MUTATIONS in HA and NA surface proteins can overcome immunity to previous strain
What is antigenic shift?
REASSORTMENT of genome segments in cells infected with TWO diferent viruses can cause major changes in surface proteins

Creation of new "hybrid" viruses
What are some characteristics of influenza?
~14 kb genome
Roughly spherical virion
8 separate genome segments in the form of helical RNPs
2 distinct surface proteins: neuraminidase (NA) and hemagglutinin (HA)
What is the function of neuraminidase?
destroys receptor binding sites on surface of infected cells so virus can bud out properly

Neuraminidase has functions that aid in the efficiency of virus release from cells. Neuraminidase cleaves terminal sialic acid residues from carbohydrate moieties on the surfaces of infected cells. This promotes the release of progeny viruses from infected cells. Neuraminidase also cleaves sialic acid residues from viral proteins, preventing aggregation of viruses. Administration of chemical inhibitors of neuraminidase is a treatment that limits the severity and spread of viral infections.
What is the function of hemagglutinin?
Receptor recognition and fusion activity
Why does the flu virus use the nucleus?
Both transcription and replication take place in the host cell nucleus.

1) the flu replicase cannot cap mRNA
2) Influenza A virus uses the intramolecular splicing machinery of the host cell's nucleus.
What is cap stealing?
Flu replicase cannot cap mRNA; therefore each flu virus mRNA generated has to use a cellular mRNA cap as a "primer" Synthesis of each flu virus mRNA begins with a short stretch of cellular mRNA with its 5' methylated cap.
Form of intermolecular splicing
What are some similarities between Orthomyxovirus and Paramyxovirus?
RNA genome is single stranded, negative sense
Helical nucleocapsid
Virion-associated transcriptase
Buds from the cell surface
Neuraminidase and Hemagglutinin
What are some differences between Orthomyxovirus and Paramyxovirus?
Orthomyxovirus mRNA can be spliced
Orthomyxoviruses have a segmented genome.
Orthomyxoviruses require a nucleus for replication
Orthomyxovirus mRNA requires cellular caps (cap stealing)
What are some characteristics of the Bunyaviridae family?
One of the largest known virus family with five distinct genus subgroups and >300 distinct serotypes
Most are arboviruses
What are some characteristics of bunyavirus?
3 genome segment (L, M, S)
What does the L segment in buynaviruses code for?
Polymerase
What does the M segment in bunyaviruses code for?
Surface proteins G1 and G2 and NSm protein.
What does the S segment in bunyaviruses code for?
N protein (helical RNPs) and NS protein from alternate reading frames.
In bunyaviruses, where does cap stealing occur?
the cytoplasm
What are ambisense genomes?
Genomes that containe both positive- and negative-sense genes.
The term ambisense refers to the fact that the open reading frames defining the two proteins are oriented in opposite directions in the genome RNA
Which bunyaviruses have ambisenes genomes?
Phleboviruses and Tospoviruses
What is the prototype of Arenaviridae?
lymphochoriomeningitis virus (LCMV)
What are the main carriers of Arenaviridae?
Rodents
What are some characteristics of Arenavirus?
Two genome segments (helical RNPs)
Viral mRNAs have caps (probably derived from host mRNAs and no poly(A)
Has ambisense coding strategy.
What is the prototype of reoviridae?
Reovirus "Respiratory orphan virus"
What are some characteristics of Reovirus?
nonenveloped
2 or 3 concentric icosahedral protein shells
10 dsRNA segments
Positive sense strand of genome segments and transcripts have a 5' end cap but no poly(A)
Minus sense has neither
What replicates HDV genome?
all viral RNA synthesis in HDV is carried by host cell RNA pol II and produces a capped and polyadenylated subgenomic RNA.
How does linearization and circulation of the HDV genome occur?
catalyzed by ribozyme activity of viral RNAs
What viruses belong to the mononegavirales group?
Rhabdoviridae
Paramyxoviridae
Filoviridae
Bornaviridae
There are 4 main groups
What are some unique properties of HDV genome?
Small covalently-closed circular ssRNA of negative sense with a high base-pairing content
Genome encodes only a single nucleocapsid protein from the + sense antigenome
HDV particles are enveloped with three membrane glycoproteins derived from HBV
What is the function of short delta antigen?
required for replication
What is the function of long delta antigen?
suppresses replication and promotes assembly.
What are some characteristics of viriods?
Found only in plants
small covalently-closed circular ssRNA that is highly base-paired
RNA is replicated by cellular RNA polymerases and genome has ribozyme activity
Encodes no protein-therefore viriods are NOT VIRUSES!
What are the five main domains of viriods?
Left-hand terminal domain
Pathogenic domain
Conserved central domain
Variable domain
Right-hand terminal domain
What are the three ways to classify retroviridae?
Seven groups based on Genetic Relatedness
Three groups based on Pathogenesis
Two groups based on Gene Numbers
What are the three groups of retroviridae based on Pathogenesis?
Oncornaviruses
Lentiviruses
Spumaviruses
How do oncornaviruses cause cancer?
They stimulate infected cell replication, but the process is usually slow and infection is inapparent.
What does GAG stand for?
group specifc antigen
What does the Pol gene of retroviruses consist of?
Reverse transcriptase, protease, and integrase which are all associated with capsid core.
How are the core enzymes (reverse transcriptase, protease, and integrase) derived?
By cleavage of the Gag-pol precursor before release of mature particles.

All are derived by a pattern of proteolytic cleavage from precursor proteins. This maturational cleavage occurs only following encapsidation of the viral genome and release of the virion from the infected cell.
What are the three essential "genes" of all retroviruses?
gag, pol, and env protein

They are required for the early stages of retrovirus infection.
What does LTRs stand for?
long terminal repeat sequences
Describe the retroviruse genome map.
5' cap:R:U5:(PB):(leader):gag:prot:pol:int:env:(PP):U3:R:polyAn;3'
What is PB?
PB is the primer binding site for the cellular tRNA primer that initiates reverse transcription.
What is the function of the leader sequence?
The leader contains genome packaging and mRNA splicing signals
What is PP?
A short polypurine tract also used for reverse transcription (generation of DNA from virion RNA).
What is a provirus?
Viral DNA

The double stranded cDNA produced by reverse transcriptase as the 1st step in infection by a retrovirus.

Serves as a cellular gene whose sole function is to replicate virus by transcription.
What is the function of the Env protein?
important in receptor recognition, and all retrovirus-infected cells express some Env protein on the cell's surface.

Always translated from a spliced mRNA
What are the two mechanisms for generation of the Gag-Pol precursor?
1) Suppression of a stop codon between the gag and pol genes.
2) Ribosomal frameshifting (slipping). Some viruses encode the gag and pol genes in two different reading frames, and the generation of the Gag-Pol precursor requires and unusual ribosomal slipping mechanism.
What is the purpose of the untranslated sequences of retroviruses?
the untranslated terminal sequences contain control elements required for generating provirus and synthesis of viral genomes and mRNAs.
What are the steps of retrovirus replication?
1) Receptor-mediated membran fusion or penetration
2) Reverse transcriptase and RNAse-H
3) Integration of cDNA into genome
4) Transcription
5) Translation of viral protein
6) Protease mediates virion maturation after budding
6 Steps
What is the function of RNase-H?
It is a part of the reverse transcriptase enzyme.

It degrades RNA strand of short RNA/DNA duplex.
What is the LTR sequence composed of?
U3, R, and U5

control regions for viral RNA transcription
What happens to unspliced full length transcripts of retroviruses?
They are exported to the cytoplasm and either translated into gag and gag-pol proteins or assembled with nucleocapsid proteins.
What is done with the pol II transcripts (gag-pro-pol) that are spliced?
They produce env mRNA , tax, rex, vif, and other viral genes SPECIFIC to different retroviruses.
What are the three mechanisms by which the oncornaviruses transform host cells (cause loss of growth regulation)?
1) action of a v-onc gene
2) alteration of normal cellular control via LTR activiation of a normal c-onc gene
3) increased release of growth-promoting cytokines from infected cell that alters normal growth control of non-infected cells.
What is the significance of the v-onc gene?
The presence of a v-onc gene in a retrovirus is often correlated with the ability of the virus to rapidly cause tumors in infected animals.
What is the function of integrase?
Integrase mediates the transport of cDNA through the nuclear pore
What is the function of LTRs?
LTR serves both as a promoter and as a polyadenylation/transcription stop signal.
What are the five classes of cell growth regulators?
1) growth hormones
2) receptors for extracellular growth signals
3) G proteins, which act as transducers of extracellular signals by interaction with receptors and binding of GTP
4) protein kinases that regulate the action of other proteins and enzymes by phosphorylation of serine/threonin or tyrosine residues;
5) specific transcription factors that either turn on or turn off critical genes.
What is the receptor for HIV and where is it located?
The CD4 receptor is present on some lymphoid cells (macrophages, helper T cells) and a few other cell types.
What are some co-receptors for HIV?
CCR5 on macrophages

CXCX4 on T cells
What is the function of LTRs?
LTR serves both as a promoter and as a polyadenylation/transcription stop signal.
What are the five classes of cell growth regulators?
1) growth hormones
2) receptors for extracellular growth signals
3) G proteins, which act as transducers of extracellular signals by interaction with receptors and binding of GTP
4) protein kinases that regulate the action of other proteins and enzymes by phosphorylation of serine/threonin or tyrosine residues;
5) specific transcription factors that either turn on or turn off critical genes.
What is the receptor for HIV and where is it located?
The CD4 receptor is present on some lymphoid cells (macrophages, helper T cells) and a few other cell types.
What are some co-receptors for HIV?
CCR5 on macrophages

CXCX4 on T cells
What are retroelements or retroids?
sequences that use reverse transcriptase to propagate

These include retroviruses, retrotransposons, retroposons, and retrointrons.
What are some examples of Hepadnaviruses?
Hepatitus B and cauliflower mosaic virus of plants
What are some characteristics of Hepatitis B?
Enveloped virion
Icosahedral core
Contains Reverse transcriptase
Three membrane associated proteins
Linear 3.2 kb DNA genome is partially double stranded
Overlap between 5'end of plus and 3' end of minus strands maintains genome as a circle.
Encodes 4 ORFs
What are the 4 ORFs the Hepatitis B virus encodes?
Core, polymerase, and S overlap; mRNAs have different start sites but have a common polyadenylation site (no splicing)
What are some characteristics of Cauliflower Mosaic Virus?
8 kb
dsRNA with three ss breaks
Six proteins are encoded.
What are the groups DNA viruses are divided into?
Small genomes, Medium genomes, Large genomes.
What are some examples of small genome DNA viruses?
papovaviruses, parvoviruses
What are some examples of medium genome DNA viruses?
adenoviruses, T-odd bacteriophages
What are some examples of large genome DNA viruses?
herpesviruses, T-even bacteriophages
What are the two families of papovavirus?
polyomaviruses and papillomaviruses
What is an example of a polyomavirus?
SV40
What are some characteristics of papovaviruses in general?
Naked icosahedral capsids; covalently closed circular genomes.
Remain associated with hosts for long periods.
Can cause cell transformation and sometimes tumors.
What are some characteristics of SV40?
Three capsid proteins
Host histones associate with its 5.2 kb genome.
Has a control region with an ORI, early promoter, and late promoter.
What is significant about the T antigen?
useful for DNA replication and transcription.

Binds to Rb and p53 which activates cell division
Binds to ORI to activate DNA replication
Shuts off early transcription
Activates late transcription
Describe the replication cycle of SV40.
The T antigen binds to the Origin of Replication (melts, separates DNA strands). The HOST polymerase complex synthesizes viral DNA (with leading and lagging strands). HOST topoisomerase and reolvases separate interlocked circles. Replicated DNA associates with HOST histones before encapsidation.
What does the early transcript of SV40 code for?
The T antigen, which is used for viral replication.
What are some characteristics of the papilolomavirus genome?
Nonenveloped
Circular
dsDNA
7.2 kb
Contains a control region (LCR) with promoter/enhancer/replication origin like SV40
Extensive mRNA splicing occurs.
What are some characteristics of Parvoviridae?
nonenveloped
icosahedral
~5 kb ssDNA
Give an example of parvoviridae.
AAV (Adeno-associated virus)
What is Adeno-associated virus?
a well known defective parvovirus that relies on co-infection with adenovirus or herpes virus as a helper to stimulate host cell division.
What is the role of the rep protein in parvoviruses?
The Rep protein is required for DNA synthesis (makes specific nicks in hairpin loops). Rep is also required for integration.
What are some characteristics of Adenoviridae?
non-enveloped
Icosahedral
Abortive infection can lead to cell transformation
Linear ds genome ~30 kb
Inverted terminal repeat sequences that serve as origins for replication.
Core protein acts like histones to condese genome in chromatin-like structure.
What is the function of the E1A proteins of adenoviruses?
The E1A family of proteins stimulate cell replication by blocking host p53 and Rb
What is the function of the E1B proteins of adenoviruses?
The E1B proteins block cell apoptosis.
What are the three subgroups of Herpesviridae?
They are grouped based on relatedness: Alpha, Beta, Gamma
What are some characteristics of the Herpesvirus genome?
Complex
Icosahedral capsid
Tegument layer
Enveloped
Linear dsDNA (Circular in INFECTED cells)
Few mRNAs are spliced, and most encode a single ORF.
2 Repeat and 2 Unique regions
Where does HSV-1 infect?
HSV-1 tends to favor lip and facial area on initial infection and establishes latent infectionin trigeminal ganglion.
Where does HSV-2 infect?
HSV-2 favors genital mucosa and becomes latent in sciatic nerve ganglia.
Where does HSV-1 infect?
HSV-1 tends to favor lip and facial area on initial infection and establishes latent infectionin trigeminal ganglion.
Where does HSV-2 infect?
HSV-2 favors genital mucosa and becomes latent in sciatic nerve ganglia.
What are some characteristics of Poxviridae?
Largest known genome (160 to ~200 kb)
dsDNA with unique "closed ends" (hairpin loops) and relatively long inverted terminal repeats
Replicates in the cytoplasm of infected cells (rare for DNA viruses)
What are types of vaccines currently being used?
1) Live attenuated virus
2) Killed virus vaccine (chemically inactivated virulent virus)
3) Subunit vaccine (purified viral protein)
What types of vaccines are exploratory?
1) Recombinant virus (heterologous avirulent virus as carrier)
2) DNA vaccine (injection/transfection of encoding DNA fragment)
3) Ingestible peptide vaccines (transgenic plants)
What is variolation against smallpox?
Deliberate infection with "dried scabs" from recovering individuals
What are interferons?
IFN's are very potent, species specific, and bind to specific receptors found on most cells; binding leads to activation of >=100 genes which render cells resistant to virus infection.
IFN's also have anti-tumor activity (inhibit cell growth)