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82 Cards in this Set
- Front
- Back
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What are the two universal functions of viral genomes
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1. encode proteins required by the virus
2. Template for viral genome production |
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All viruses must ________ _______ required by the virus and provide a _______ for viral genome production
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encode proteins
template |
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What are some of the strategies for making mRNA?
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*multiple sub genomic mRNA
*alternative splicing *RNA Editing *Nested transcription *coding on both strands *polyprotein synthesis *leaky scanning *TLN Termination suppression *Ribosomal frameshifting *IRES |
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In terms of decoding information what is
What is multiple subgenomic mRNA? |
One genome produces several short mRNAs
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In terms of decoding information what is RNA editing
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single nucleotide inserted to mRNA
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In terms of decoding information what is mRNA splicing?
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one transcript is "cut and pasted" to produce multiple mRNA encoding different proteins
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In terms of decoding information what is nested transcription
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multiple transcription star sites makes overlappig mRNAs
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In terms of decoding information what is Coding on both strands?
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mRNA produced from two genome strands
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In terms of decoding information what is polyprotein synthesis?
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single translation initiation for one viral protein which is proteolytically cleaved
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In terms of decoding information what is leaky scanning?
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multiple AUG on single mRNA produces different proteins from same reading frame
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In terms of decoding information what is translation termination suppression?
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proteins end at different stop codons
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In terms of decoding information what is ribosomal frameshifting?
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translation of the same mRNA changes reading frame and produces different proteins
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In terms of decoding information what is IRES?
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The internal ribosome entry site on mRNA (no 5'cap needed for translation intiation)
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How is the size of viral genome limited?
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The capsid limits size, but icosahedral capsids can be quite large.
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How much of the Herpesvirus genome is devoted to capsid creation?
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75%
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Why are RNA genomes so small?
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RNA is less stable and
RNA polymerases have no proofreading |
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What are some threats to virus?
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Temperature, pH, radiation, proteolytic and nucleolytic enzymes
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All virus coats have at least ____ protein coat called _____________
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one
nucleocapsid (or just capsid) |
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What is a capsid made of?
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one or more proteins in regular & repetitive interactions resulting in regular structure.
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How is capsid symmetry determined?
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by spatial patterns resulting from interactions of proteins making up the capsid
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Most Eukaryotic viruses have what shape?
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helical or isocahedral
(but some are more complex) |
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Describe helical structures
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Rodlike or filamentous structures
Expands to any size genome open structure |
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Give an example of a virus with helical structure
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Tobacco Mosaic Virus
Paramyxo- Rhabdoviruses |
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Describe icosahedral symmetry
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20 faces, 12 vertices (2,3,5 fold axes of rotational symmetry)
Not expandable - "closed" |
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What is poliovirus' capsid made of?
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60 copies of 4 proteins
VP1, VP2, VP3, VP4 |
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Describe orientation of poliovirus' capsid proteins
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5 VP1 proteins cluster around 5 fold axes
VP2 and VP3 alternate at 3 fold axes VP4 on inner surface - in contact with RNA genome |
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Describe Adenovirus capsid
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Complex
Hexons and pentons with long fibers at 12 vertices |
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Describe Herpes' complex structure
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3 major structures with viral proteins
-Nucleocapsid surrounding DNA -Tegument covers nucleocapsid -Envelope surrounds tegument |
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What are the 3 mechanisms for packaging the genome?
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1. Direct contact with shell
2. Cellular DNA binding proteins 3. Specialized viral nucleic acid binding proteins |
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In terms of packaging the genome, describe what happens in "direct contact with shell"
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-Capsid proteins interact w/genome
-Genome may/may not be ordered within shell |
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In terms of packaging the genome, describe cellular DNA binding proteins
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-Cellular histones bind, form nucleosomes
-No need to encode DNA binding proteins -DNA enters celling looking like cellular DNA |
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In terms of packaging the genome, describe specialized viral nucleic acid binding proteins
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-Viral enoded proteins bind to nucleic acid genome
-positively charged - helps overcome negative charges from phosphates -Nucleocapsid proteins in (-0) RNA viruses, retroviruses |
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How are viral envelopes derived?
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-Derived from cellular membranes
-Viral proteins embedded in membrane -often viral proteins have post translational modifications |
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Helical viruses with envelopes all have ______ genomes
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(-)RNA
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What are some of the other viral particle components besides genome?
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Virion enzymes
other viral proteins nongenomic nucleic acids cellular macromolecules |
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Give an example of virion enzymes and what they do
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the catalyze virus specific reactions
examples: RNA dependant polemerase or reverse transcriptase integrase, porteases, cap-dependent nuclease and viral mRNA capping protein |
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What are some of the cellular macromolecules packaged in with the genome
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histones, tRNA, chaperon
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Some viruses need a single extracellular protein for attachment called a _________ others need an additional _________ called a __________
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receptor protein coreceptor
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Cells with the proper receptor are ________ to infection
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susceptible
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For a productive infection, cell must be both ________ and ___________.
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susceptible permissive
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How is host range determined
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by the receptor
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Give example of host range determination
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poliovirus infects primates but not mice, although mice make homologous protein to polio receptor it is different enough that polio cannot get in. Some primate cells produce the right receptor but no production due to lack of another protein.
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What is tropism
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the specificity of virus for cell or tissue type determined in part by receptors
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What are tools used to identify a viral receptors
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monoclonal antibodies, cDNA,
recombinant virus w/drug resistant gene or report gene (GFP) |
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How does one ID a receptor using drug resistant gene?
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First find a permissive cell with no receptor. Using cDNA library to find receptor gene, add recombinant virus w/drug resistant gene to cells, and grow in presence of drug. Living cells (resistant to drug) are infected - have receptor
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How does one ID a receptor using GFP?
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First find a permissive cell with no receptor. Using cDNA library to find receptor gene, add recombinant vius with GFP reporter gene. Cells that fluresce are infected and therefore have recepter
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How does one ID a receptor using mAB?
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First find a permissive cell with no receptor. Using cDNA library to find receptor gene, add antibody specific to receptor (AB could have reporter gene attached) cells with AB have receptor gene.
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What are the limitations on the experimental techniques on ID receptors?
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May identify a closely related protein
Some viruses require a coreceptor for infection |
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How does one prove that a protein is in fact the receptor?
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If ID w/ mAB then clone DNA, transfor non-susceptible cell line and demonstrate binding to cell surface.
If ID w/cloned DNA, demonstrate binding of mAB to cell surface and mAB blocks viral infection. |
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What is receptor for HIV-1?
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CD-4 receptor on T-helper cells plus chemokine receptors
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What is the major barrieer to virus entry?
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the plasma membrane
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How do viruses exploit cellular mechanisms for uptake of macromolecules?
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By using endocytosis and phagocytosis - non-specific
Receptor Mediated Endocytosis (RME) - specific depends on interaction with specific receptors |
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How do enveloped viruses enter cells?
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Fusion of viral membrane w/plasma membrane and passage through endocytic pathway
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How do nonenveloped viruses enter cells?
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Disrupting endosomal membrane (proteins in coat will physically interact of membrane) pore formation in membrane via lysosome/caveolae
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Describe the uncoating at plasma membrane by a enveloped virus
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viral glycoproteins bind cell receptors
Fusion protein F catalyzes membrane fusion (hydrophobic region inserts into cell membrane when cleaved by host protease when virus is near cell) Viral nucleocapsid is then released into cytoplasm |
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Describe process of entering cell via RME
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Virus binds to receptor and enters cell via endosomes. AFter endocytosis, endosomes become acidic (protons pumped into the lumen of endosme as part of the normal function of endosome) This acidic environment catalyzes membrane fusion of viral and cellular membranes, proteolysis of viral proteins and uncoating of genome
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Describe the uncoating in cytoplasm by ribosomes
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RME -> low pH -> changes in spike glycoprotein of envelope -> fusion
fusion of membranes releases capsid to cytoplasm ribosome directly bind to C protein, disassemble capsid, allowing translation of RNA |
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How does a nonenveloped virus, such adenovirus, enter a cell?
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-virus enters cell via RME
-particle transported inside endosome toward nucleus and structural proteins are remvoed sequentially in endosome -endosomal membrane disrupted by free capsid proteins -remaining capsid docks with nuclear pore complex and viral DNA importaed to nucleus |
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How does pore formation by viral proteins, such as in poliovirus, happen?
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-receptor is Ig-like Pvr
-after binding to Pvr, many changes to capsid --VP1 capsid protein becomes more hydrophobic, VP4 is lost --VP1 interacts with membrane and forms a pore --+RNA enters cytoplasm either before or afer endocytosis |
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What type DNA and coat does adenovirus have
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dsDNA, multiportein coated icosahedral capsid
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What type of genome does poliovirus require?
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Ig-like Pvr
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Where do viruses replicate?
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some in cytoplasm, others in nucleus
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How do viruses that must replicate in nucleus get into the nucleus?
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proteins with nuclear localization signals (NLS) are recognized and translocated across Nuclear Pore Complex (NPC) If genome is smaller than 26nm and has NLS it can enter nucleus
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If a genomic complex is too large to enter thru pore, how does genome get in?
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-Some virus capsids bind NPC import DNA
-Only when cells divide can the retroviral DNA get integrated -mitotic nuclear membrane breakdown seems required |
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How does influenze virus get replicated in nucleus?
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-naked RNA not translocated, only with viral protein
-the NP (nuclear pore)protein associated with RNA has NLS (Nuclear localization signals) |
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What are the requirements of Viral RNA genomes
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-genome must be copied from end to end with no loss of information (gneome synthesis)
-genome must allow synthesis of mRNA that can be efficiently trnaslated by cell |
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How was Polio 3Dpol originally identified?
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By the ability to synthesize RNA from an RNA template in the presence of a cellular transcriptional inhibitor, amantidine
- Amantidine inhibits cellular RNA pol - PV Pol still funcitons after treatment with amantidine |
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RNA-dependent RNA synthesis requires what conditions?
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-begins at specific locations
-requires viral accessory proteins -sometimes requires host cell proteins |
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All nucleic acid polymerases share ________ and __________ similarities
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sequence structural
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Where are many RNA dependent polymerases found that makes them difficult to identify?
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Membrane associated
- therefore very difficult to purify - identified based on sequence homology |
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What is difference between Naked RNA or Nucleocapsid RNA in terms of template?
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(-) strand viruses usally have proteins bound to RNA which keeps RNA ss and are not replicated when naked
(+) RNA viruses are usually naked and frequently tranlated immediately on entry and replication doesn't depend on nucleocapsid proteins bound to genome |
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What is the purpose of secondary structures of RNA?
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Can be recognized specifically by proteins involved in RNA synthesis, translation and assemby
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General strategies of translation of (-)RNA viruses (what are the possibilities and what would be the results)
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-produce full length (+) strand as template to make (-) strand
- antitermination gives full length (+) so can be used for genome synthesis -Produce mRNA for protein synthesis - not full length so cannnot be template for genomic, if segmented = 1-2 mRNA/segmnent, if not = multiple mRNAs produced from single genome |
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General strategies of translation of (+)RNA viruses (what are the possibilities and what would be the results)
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-function as mRNA
(+)mRNA is template to produce full length (-)RNA so can be used as templete ofr (+) genome synthesis or for subgenomic mRNA synthesis |
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General strategies of translation of ambisense RNA viruses (what are the possibilities and what would be the results)
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Genomic RNA is template for some mRNA synthesis. Full length copy RNA (antigenome RNA is template for some mRNA)
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General strategies of translation of dsRNA viruses (what are the possibilities and what would be the results)
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mRNA can be translated or used as template for full length (-) strand -> ds genome
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Viral RNA Polymerase is composed of __________________
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3 proteins:
PB1, PB2 and PA |
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In influenza infections, there are two types of RNA made in infected cells. These are?
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-capped, polyA, subgenomic mRNA
-Full length (+) and (-) genomic RNA |
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When influenza first infects a cell what type translation initially occurs?
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Initially only mRNAs are produced, after NP made, enters nucleus, and RNA synth switches to (+) and (-) genome synthesis
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What is Cap snatching?
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Cellular mRNA cleaved a few nucleotides after 5' Cap, then 5' Cap is used as primer for mRNA sythesis
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Describe influenza's cap snatching activity
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-Cellular mRNA cleaved a few nuc. after 5'Cap
-5' Cap used as primer for mRNA synthesis -G is added to complementay C in genome then extension of mRNA and polyAdenylation -if no NP, RNA Pol terminates slightly before end of genome -PB1 & PB2 resonsible for mRNA synthesis - |
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Describe influenza's mRNA synthesis
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-Cap snatching
-RNA Pol activated by specific viral sequences -PB1 binds 5' virus genome sequence -PB2 binds cell mRNA cap -PB1 binds 3' genome end -once cap is cleaved initiationand elongation occurs -just before 5' end reached, polyA tail aded to mRNA -termination |
