Virology Midterm

248 flashcards

What is a virus?: An infectious agent that requires a host cell to reproduce
What is a virion?: A complete infectious virus particle outside a cell
What is the typical size range of many viruses?: About 20 to 300 nanometers with exceptions
Are viruses cellular organisms?: No they are acellular
What does obligate intracellular parasite mean?: Must use a living host cell to reproduce
What is a virus genome made of?: DNA or RNA
What virus was used to control rabbit populations?: Myxoma virus
What enzyme was first discovered through studies of retroviruses?: Reverse transcriptase
What is a bacteriophage?: A virus that infects bacteria
What is a host range?: The hosts a virus can infect
What technique visualizes virus particles at high resolution?: Electron microscopy
What technique can determine three dimensional virion structure?: Cryo electron microscopy
What is negative stain electron microscopy useful for?: Viewing virus particle shape and surface
What separates proteins mainly by molecular mass?: SDS PAGE
What separates viral nucleic acids by size?: Gel electrophoresis
What assay measures infectious virus particles?: Plaque assay
What units report a plaque assay result?: Plaque forming units per milliliter
What does a plaque represent?: A region of infected or destroyed cells caused by infectious virus
What method detects protein protein interactions?: Co immunoprecipitation
What method locates viral proteins inside cells?: Immunofluorescence microscopy
What approach tests the function of a viral gene?: Mutagenesis followed by phenotype analysis
What does PCR amplify?: DNA
What is RT PCR used for?: Converting RNA to DNA before amplification
What is a virus titer?: Amount or concentration of virus in a sample
What does an infectivity assay measure?: Virus capable of causing infection
What is a temperature sensitive mutant?: A mutant functional at permissive temperature but not restrictive temperature
What is the permissive temperature?: Temperature allowing a conditional mutant to function
What is the nonpermissive temperature?: Temperature at which a conditional mutant loses function
What is rate zonal centrifugation based on?: Different sedimentation rates
What is isopycnic centrifugation based on?: Different buoyant densities
What is a capsid?: Protein shell enclosing the viral genome
What is a nucleocapsid?: Viral genome together with its capsid or associated nucleoproteins
What is a viral envelope?: Lipid membrane surrounding some virions
Where do most viral envelopes originate?: Host cell membranes
What is helical symmetry?: Capsid proteins arranged in a spiral around the genome
What is icosahedral symmetry?: Capsid architecture based on twenty triangular faces
How many faces does an icosahedron have?: 20
How many vertices does an icosahedron have?: 12
What shape is rabies virus?: Bullet shaped
What shape are filoviruses such as Ebola virus?: Filamentous or thread shaped
What virus has rod shaped nucleocapsids?: Baculovirus
What virus group can have an internal membrane beneath the capsid?: Iridoviruses
What does a positively charged viral protein often bind?: Negatively charged nucleic acid
What does an isoelectric point of 11 suggest at physiological pH?: The protein has a net positive charge
What does myristylation often help a viral protein do?: Associate with membranes
What is a nuclear localization signal?: A protein sequence directing import into the nucleus
Which amino acids are common in nuclear localization signals?: Lysine and arginine
Are enveloped viruses common among bacteriophages?: No most known bacteriophages are nonenveloped
What is a capsomere?: A visible morphological subunit of a capsid
What is the function of viral surface proteins?: Often mediate receptor binding and entry
What is a segmented viral genome?: A genome divided into separate nucleic acid molecules
What is an ambisense genome?: A genome with both positive and negative coding orientations
What is horizontal transmission?: Spread between individuals in the same generation
What is vertical transmission?: Spread from parent to offspring
What is a vector?: An organism that carries a pathogen between hosts
What is a reservoir host?: A host population maintaining a virus in nature
What is tissue tropism?: Preference for infecting particular cell or tissue types
What helps determine host range and tissue tropism?: Receptor availability and intracellular permissiveness
How can plant viruses enter through intact plant defenses?: Wounds or feeding vectors that breach the cell wall
What insects commonly transmit plant viruses?: Aphids and other sap feeding insects
Which influenza viruses are commonly carried by wild birds?: Avian influenza viruses
What are occlusion bodies?: Protective protein structures enclosing some insect virus virions
What virus group commonly makes occlusion bodies?: Baculoviruses
Why might insect vectored viruses spare the insect?: Maintaining vector survival can support transmission
Do viruses always evolve toward lower virulence?: No virulence can increase or decrease
What is virulence?: Degree of disease severity caused by a pathogen
What is zoonotic transmission?: Transmission from animals to humans
What is a mechanical vector?: A carrier that transports virus without viral replication inside it
What is the first step of virus entry?: Attachment to a host cell receptor
What does influenza virus bind on host cells?: Sialic acid
What is the primary receptor for HIV 1?: CD4
What coreceptors can HIV 1 use?: CCR5 or CXCR4
What is receptor mediated endocytosis?: Uptake after receptor binding into a cellular vesicle
What protein forms many coated pits?: Clathrin
How do enveloped viruses deliver their nucleocapsids into cells?: Membrane fusion or endocytic uptake followed by fusion
How can naked viruses enter cells?: Endocytosis followed by membrane penetration or disruption
What is uncoating?: Release of the viral genome from protective viral structures
What cellular tracks support long range virus transport?: Microtubules
What motor carries cargo toward the nucleus on microtubules?: Dynein
What motor usually carries cargo toward the cell periphery?: Kinesin
What happens as a virus recruits additional receptors?: Attachment can become stronger and effectively irreversible
What can trigger viral membrane fusion?: Receptor binding or low endosomal pH
What is the role of a fusion protein?: Merges viral and cellular membranes
What is an endosome?: Membrane bound compartment formed during endocytosis
What is a permissive cell?: A cell supporting completion of viral replication
What is viral transcription?: Synthesis of viral mRNA from a nucleic acid template
What is translation?: Synthesis of proteins from mRNA by ribosomes
What do most viruses use to translate proteins?: Host cell ribosomes and translation machinery
What does positive sense RNA mean?: RNA has the same coding sense as mRNA
Can Class IV positive sense RNA act directly as mRNA?: Yes
Can Class VI retroviral RNA function immediately as mRNA after entry?: No it first undergoes reverse transcription
What must negative sense RNA viruses make before translation?: Positive sense mRNA
What is the TATA box associated with?: Transcription promoter
What does an enhancer do?: Increases transcription by binding regulatory factors
What do transcription factors do?: Regulate transcription by binding DNA control sequences
What does AATAAA signal in DNA?: Polyadenylation of the RNA transcript
What is the function of the five prime mRNA cap?: Supports stability nuclear export and translation initiation
What is the function of a poly A tail?: Helps mRNA stability and translation
What is RNA splicing?: Removal of introns and joining of exons
What is an intron?: Sequence removed from a primary RNA transcript
What is an exon?: Sequence retained in mature spliced RNA
Which viruses are most likely to use host splicing machinery?: Viruses transcribing RNA in the nucleus
Which viruses are least likely to have splice dependent genes?: Viruses transcribing entirely in the cytoplasm
What is an open reading frame?: Nucleotide sequence that can encode a protein
What is a polyprotein?: Large protein later cleaved into multiple proteins
What is an IRES?: Internal ribosome entry site enabling cap independent translation
What is leaky scanning?: Ribosome bypasses one start codon and initiates downstream
What is ribosomal frameshifting?: Ribosome changes reading frame during translation
What is glycosylation?: Addition of sugar groups to proteins
What is acylation?: Addition of fatty acyl groups to proteins
What is phosphorylation?: Addition of phosphate groups to alter protein properties
What is proteolytic cleavage?: Cutting a protein into smaller functional products
What is N linked glycosylation attached to?: Asparagine
What is O linked glycosylation attached to?: Serine or threonine
Where does much viral glycoprotein processing occur?: Rough ER and Golgi
What directs proteins into the nucleus?: Nuclear localization signal and importins
What helps proteins and RNA leave the nucleus?: Nuclear export signal and exportins
What is the function of HIV Rev?: Promotes nuclear export of specific viral RNAs
What does reverse transcriptase synthesize from RNA?: DNA
What two polymerase activities does reverse transcriptase have?: RNA dependent DNA polymerase and DNA dependent DNA polymerase
How does influenza obtain caps for viral mRNAs?: Cap snatching from host mRNAs
What is a monocistronic mRNA?: mRNA with one main protein coding region
What is a polycistronic mRNA?: mRNA with multiple protein coding regions
Where does eukaryotic transcription usually occur?: Nucleus
Where does eukaryotic translation occur?: Cytoplasm
Why can bacteria transcribe and translate simultaneously?: They lack a nucleus separating the processes
What is the Shine Dalgarno sequence?: Bacterial ribosome binding sequence
What is the bacterial promoter minus ten region called?: Pribnow box
What is the function of bacterial sigma factor?: Helps RNA polymerase recognize promoters
What is a typical bacterial ribosome size?: 70S with 30S and 50S subunits
What is a typical eukaryotic cytoplasmic ribosome size?: 80S with 40S and 60S subunits
What is the main movement mechanism of baculovirus nucleocapsids after entry?: Actin based transport toward the nucleus
Why is there one ssDNA Baltimore class but two ssRNA classes?: RNA viruses have distinct positive and negative sense pathways
Where do most DNA viruses replicate genomes?: Nucleus
Where do most RNA viruses replicate genomes?: Cytoplasm
Which DNA virus group replicates in cytoplasm?: Poxviruses
Which negative sense RNA virus replicates in nucleus?: Influenza virus
Where does retroviral reverse transcription usually occur?: Cytoplasm
Where is retroviral DNA transcribed to RNA?: Nucleus
What is the function of a replication origin?: Specific site where genome copying begins
What is a primer?: Starting group providing a free hydroxyl for polymerase extension
What types of primers can DNA viruses use?: RNA primers protein primers or self priming DNA
Do all RNA viruses require a separate primer?: No many initiate RNA synthesis de novo
What virus uses self priming DNA ends?: Parvovirus
What DNA virus uses a protein primer?: Adenovirus
What RNA virus group uses a protein primer?: Picornaviruses
What primes initial reverse transcription in retroviruses?: Host transfer RNA
What does helicase do?: Unwinds double stranded nucleic acid
What does primase do?: Synthesizes short RNA primers
What does DNA ligase do?: Joins DNA fragments
What are Okazaki fragments?: Short DNA pieces made on the lagging strand
What is semiconservative DNA replication?: Each daughter duplex has one old strand and one new strand
What is conservative dsRNA replication?: Parental dsRNA remains intact while a new duplex forms
What virus family can use conservative dsRNA replication?: Reoviridae
What is a DNA dependent DNA polymerase?: Enzyme copying DNA from a DNA template
What is an RNA dependent RNA polymerase?: Enzyme copying RNA from an RNA template
What is a reverse transcriptase?: RNA dependent DNA polymerase that also copies DNA
Why do cytoplasmic DNA viruses encode polymerase?: Suitable host DNA replication enzymes are not available there
What DNA viruses often use host DNA polymerase?: Small nuclear DNA viruses
What DNA viruses often encode their own DNA polymerase?: Large DNA viruses such as herpesviruses
How do ssDNA viruses replicate?: First convert ssDNA to dsDNA then copy genomes
How do Class IV positive RNA viruses replicate?: Positive RNA to negative RNA intermediate to positive RNA
How do Class V negative RNA viruses replicate?: Negative RNA to positive RNA intermediate to negative RNA
Where must RNA dependent RNA polymerase recognize RNA templates?: At their three prime ends
What is rolling circle replication also called?: Sigma replication
What is theta replication?: Replication of circular DNA through a theta shaped intermediate
What is a concatemer?: Long DNA molecule containing linked copies of a genome
What viral DNA replication mechanism can produce concatemers?: Rolling circle replication
How does adenovirus copy its DNA?: Protein primed strand displacement
What is reverse transcription?: Synthesis of DNA from an RNA template
Which Baltimore classes use reverse transcription?: Class VI and Class VII
What is the genome of a Class VI retrovirus?: Positive sense single stranded RNA
What is the genome of a Class VII pararetrovirus?: Double stranded DNA with reverse transcription in its cycle
How do helical nucleocapsids assemble?: Coat proteins assemble along the viral genome
How do many icosahedral nucleocapsids assemble?: Empty procapsid forms before genome packaging
What is a procapsid?: Immature empty capsid shell
What is a prohead?: Immature head of a tailed bacteriophage
What is a packaging signal?: Viral genome sequence recognized for encapsidation
What is a portal protein complex?: Capsid opening used to package viral DNA
What are scaffolding proteins?: Temporary proteins guiding capsid construction
What is self assembly?: Virion components spontaneously assemble under suitable conditions
Which simple virus is a classic self assembly example?: Tobacco mosaic virus
What is directed assembly?: Assembly requiring additional factors and cellular conditions
Which viruses commonly require directed assembly?: Herpesviruses and tailed bacteriophages
Why is tightly packed viral nucleic acid challenging?: Negative phosphate charges repel one another
What helps neutralize genome phosphate charge?: Positively charged basic proteins or cations
Where do most enveloped viruses obtain their membranes?: Host cell membranes during budding
What is de novo viral membrane formation?: Virus directed formation of a new membrane
What virus group can form membranes de novo?: Poxviruses
What virus group has internal membranes under its capsid?: Iridoviruses
What do viral matrix proteins do?: Link nucleocapsid and envelope proteins during budding
What viral protein commonly contacts the cytoplasmic tail of envelope glycoproteins?: Matrix protein
What are ESCRT proteins?: Host proteins helping pinch off budding virions
What are viral late domains?: Protein motifs that recruit budding machinery such as ESCRT
Where does influenza typically bud from epithelial cells?: Apical surface
Where does vesicular stomatitis virus typically bud?: Basolateral surface
What influenza enzyme helps release budding virions?: Neuraminidase
What is lysis?: Cell rupture releasing virions
What is exocytosis?: Vesicle fusion releasing virions outside the cell
What is extrusion in filamentous phages?: Virion exit through cell surface without lysis
What is burst size?: Number of infectious virions released per lysed cell
What cellular spaces are topologically equivalent to extracellular space?: Lumens of ER and Golgi and other secretory compartments
What is virion maturation?: Structural changes that produce an infectious particle
What helps plant viruses spread cell to cell?: Plasmodesmata and viral movement proteins
What is a productive infection?: Infection producing new infectious virions
What is a nonproductive infection?: Infection not producing new infectious virions
What is a latent infection?: Viral genome persists without ongoing production of virions
What is an abortive infection?: Replication fails without establishing latency
What is a defective virus?: Virus lacking a function required for complete replication
What is a helper virus?: Virus supplying missing functions to a defective virus
What is a persistent infection?: Infection lasting a long time
What is lysogeny?: Latent phage infection involving a temperate phage
What is a prophage?: Phage genome maintained in a bacterial host
What can reactivate latent herpesvirus?: Changes such as immune suppression or UV exposure
What is an example of viral latency in neurons?: Herpes simplex virus
What can varicella zoster reactivation cause?: Shingles
What is innate immunity?: Rapid defense not requiring antigen specific memory
What is adaptive immunity?: Antigen specific defense with immunological memory
What does complement do against viruses?: Coats targets or damages membranes and enhances immunity
What do type I interferons do?: Induce antiviral defenses in nearby cells
What do natural killer cells do?: Kill infected or abnormal cells
What does APOBEC3 do?: Can introduce mutations during viral reverse transcription
What does tetherin also called BST 2 do?: Tethers budding enveloped virions to the cell surface
What HIV protein counteracts tetherin?: Vpu
What is antibody neutralization?: Antibody binding that prevents virus infectivity
How can antibodies neutralize viruses?: Block attachment entry fusion or uncoating
What cells secrete antibodies?: Plasma cells derived from B cells
What is the main role of CD4 helper T cells?: Coordinate and activate immune responses
What is the main role of CD8 cytotoxic T cells?: Kill infected cells displaying viral peptides
What does MHC class I present?: Peptides to CD8 T cells
What does immunological memory do?: Supports faster stronger responses upon reexposure
What is RNA interference?: Sequence specific destruction of target RNA
What does Dicer do?: Cuts double stranded RNA into siRNAs
What does RISC do?: Uses small RNA to recognize and cleave matching mRNA
What is apoptosis?: Programmed cell death
What are caspases?: Proteases that execute apoptosis
How can viruses evade interferon defenses?: Block interferon production or signaling
How can viruses evade CD8 T cells?: Reduce MHC class I antigen presentation
How can viruses evade apoptosis?: Encode proteins that inhibit cell death pathways
What are defective interfering particles?: Defective viral particles that reduce helper virus production
How do plant viruses move between neighboring cells?: Through plasmodesmata using movement proteins
How can viruses spread long distances in animals?: Through blood or nerves
How can viruses spread long distances in plants?: Through phloem
What is an asymptomatic infection?: Infection without noticeable disease
What is an incubation period?: Time between infection and first symptoms or signs
What factors affect severity of viral disease?: Virus virulence and dose plus host immunity and health
Can host immune responses cause tissue damage?: Yes immune responses can contribute to symptoms
What is an epitope?: Specific antigen region recognized by immune receptors