EXAM 1 Intro to Virology Flashcards
are viruses large or small? what is the size range?
small, ranging from 20-300nm in diameter
what are viruses typically composed of?
nucleic acid (genetic material) and a protein sheath which carries the nucleic acids
what is the virion?
the entire viral construction outside the cell
what is responsible for the vast range of viruses? about how many mammalian viruses are there?
variations in virus size, nucleic acid, protein sheath, virion, etc.
there are about 320,000 mammalian viruses
viruses lack ___, and cannot ___ on their own
- organelles
- replicate (obligate intracellular parasites)
how is it that viruses can replicate?
they enter a host cell and then have the potential to replicate rapidly and exponentially
are viruses considered to be living organisms? why or why not?
generally no, because they are dependent on other organisms for replication (ie. although they carry genetic material, they cannot carry out translation on their own)
what is infection heredity/ horizontal gene transfer?
viruses pass genetic material into cells (bacterial or otherwise) that is then passed into the genome
what is the capsid?
- the outer protein sheath of the virus
- provides predominant structure
what are the general shapes that capsids can have?
- icosahedral (spherical)
- helical (cylindrical)
- complex (combination of the two)
what are the 3 basic functions of the capsid?
- protect the genetic material of the virus
- aid entry into the cell in terms of attachment and/or penetration of the cellular membrane
- package viral enzymes used in viral replication
T or F:
the capsid is a single, uniform structure
false
it is composed of a collection of individual repeating subunits
describe viral size relative to capsid structure/subunits
the amount of information is smaller to make many identical subunits rather than one relatively large capsid structure; thus, the virus has less genetic information to lug around/replicate
describe helical viruses
they are composed of multiple protein subunits packed into a helical arrangement with the genetic material coiled into a helix inside it.
ex. tobacco mosaic virus
describe icosahedral viruses
composed of repeating subunits called capsomeres, which are composed of 5-6 individual protein structures, which are called protomers
what is the difference between enveloped and naked viruses?
- enveloped viruses have part of the host cell’s lipid membrane attached to the outside of the virus
- naked viruses consist only of the capsid surrounding the genetic material
the viral envelope is derived from what?
generally from the plasma membrane, but can come from nuclear and cytoplasmic membranes
what are “spikes” or “envelope proteins” that are found on viral envelopes?
- viral glycoproteins embedded in the envelope
- function to help viruses attach to host cell membranes
- can also act as specific antigens for the immune system
what is the “tegument” or “matrix protein”?
- a layer of proteins between the capsid and envelope of enveloped viruses
- serve to attach the envelope to the capsid and can be involved with delivering viral genetic material/replication enzymes into cells
- it is amorphous but polar (has an outside and an inside)
can viruses have either DNA or RNA as their genetic component?
yes
this is a large part of the classification of viruses
can both DNA and RNA viruses be single or double stranded?
yes
name the types of “sense” that RNA virses can be
- positive-sense
- negative-sense
- double stranded
- ambisense (both positive and negative sense RNA on the same strand)
- **sense refers to the reading (translation) direction of the genetic material
describe positive sense RNA
indicates that it may be directly translated into viral proteins (5’ to 3’)
aka mRNA
describe negative sense RNA
forms a complementary strand which could then be translated into viral proteins (3’ to 5’)
negative sense viruses often carry an RNA dependent polymerase within the virion
what is the baltimore system of classification?
viruses are grouped according to genetic material present in the virion
describe groups I - VII of the baltimore classification system
*be able to draw this out*
what is the first step the virus must take in order to get its genetic material into a cell?
it must penetrate the plasma membrane of the cell
do viruses have the capacity for locomotion?
- no
- they must rely on collision to reach cells
- this depends on the concentration of cells vs. the concentration of virions in a given space
how do viruses attach to cells?
- they attach via glycoproteins located on either the envelope (enveloped virus) or the capsid (naked virus)
- their targets are typically glycoproteins found on the cell surface
describe the receptors that viruses target on cell surfaces
- viruses have evolved to target a plethora of different receptors on cell surfaces
- these receptors generally have other “jobs” aside from attaching viruses (ex. cell/immune signaling are common targets)
- viruses can also require a co-receptor to enter a cell (ex. HIV-1 and CD4 with CCR5/CSCR4 chemokine receptors)
T or F
the attachment of any one spike to a receptor is equally as strong as the attachment of multiple spikes
false
the greater the number of attached spikes, the stronger the attachment
once the virus attaches to the cell surface, what is the next step?
it penetrates the cell
once inside the host cell, it is mostly off the radar of the immune system (called the eclipse phase)
so, if antibodies are going to interfere with the virus, they are generally going to prevent attachment
what are the two different pathways that enveloped viruses follow to get into the host cell?
- direct fusion: HIV-1, herpesvirus, paramyxoviruses
- viropexis: influenza, rubella, rabies
- both of these involve the envelope interacting with the cell membrane and the release of the capsid into the cytoplasm
describe direct fusion
involes a viral attachment protein mediated fusion of the viral envelope and plasma membrane, and results in the capsid directly entering the cell
the viral envelope stays at the plasma membrane, leaving the capsid and genetic material (nucleocapsid) free to enter the cytoplasm
describe viropexis
- receptor mediated endocytosis
- effectively when a virus binds its receptors on the cell surface, they are internalized, dragging the viral capsid along with them
describe naked capsid penetration
- effectively, these viruses enter the cell trhough viropexis, but must disrupt the endosomal vesicle because they have no envelope to fuse with it
- typically the low pH conditions in vesicles can activate viral proteins which lyse the vesicles
- some viruses rely on the low pH to disrupt their capsid, release their genetic material, and activate viral transcription enzymes
what is uncoating?
strategy that viruses employ to get inside cells, or rather to get their genetic material into the cell
in other words, the capside stays outside, while the core proteins enter the cell
what is a bacteriophage?
infecting bacterial cell that directly injects its genetic material out through its tail, through the plasma membrane and directly into the cell
once inside the host cell, enveloped viruses find themselves inside low pH endosomal vesicles. what is the result?
causes fusion and release of the nucleocapsid into the cytoplasm
so the viral envelope does enter the cell, but fuses with an endosomal vesicle, not the plasma membrane directly
describe transcription of viral genetic material
- the main event for the virus is replication, and to do this, it must generate viral mRNA in order to hijack the translation machinery of the cell and replicate its protein components
- the way in which each individual virus does this depends on the genetic material it has
- remember that whatever the virus has initially, it must get to sense mRNA (positive RNA)
name the 8 steps of the viral life-cycle
- attachment
- penetration (endocytosis)
- uncoating
- DNA replication
- RNA transcription
- protein translation
- assembly of virions
- cell lysis
what is viral assembly?
- the insertion of individual viral genomes into individual capsids
- sometimes called “encapsidation”
- this process is generally step-wise and is regulated by energetically favorable interactions between the viral genetic material and the capsid proteins
what is the “packaging site”?
viral genomes are spliced/modified prior to cytoplasmic to prepare them to enter the capsids, and there is usually a specific site on the viral genome that codes for proteins intended to intitiate assembly (called the packaging sites)
what do helper proteins do?
- viral capsids contain helper proteins that guide the viral genome into the capsid through a specialized pore structure, packing it neatly inside
- this can occur at a specific phase during capsid assembly or as a discrete process after capsids are assembled
the protein capsid is assembled in such a way as to favor what?
the incorporation of viral genomes
what is viral egression?
once progeny virions are assembled, they must get out of the cell (viral egression)
how are progeny virions released from non-enveloped viruses, like bacteriophages?
the cell is directly lysed by viral enzymes, releasing the progeny virions
this is direct, but does not allow for further replication because it kills the host cell
how do many naked human viruses typically trigger apoptosis and release progeny virions?
- through disruption of protein synthesis and/or normal cell cycle functioning
- they also make proteins that delay this process until they are assembled
- in other words, they keep the cell alive long enough to complete replication and assembly, then allow the cell to die, releasing them
how do enveloped viruses release progeny virions?
- they need to acquire some host membrane once assembled in their capsids and therefore tend to proceed down the normal protein secretion pathways of the cell, acquiring a membrane at various points in transit
- some will take a bit of nuclear membrane (herpesviruses), some organelle membranes (poxyviruses), and most of the others take a bit of the plasma membrane on their way out
- they are then expelled by either exocytosis or by budding from the plasma membrane
- this generally doesn’t kill the cell, with the esception of HIV-1
what happens to the progeny virions that have been released from host cells?
they are accessible to the immune system (aka they are “visible” again)
what do viral attachment proteins do?
they generally determine which species a virus will infect and in which cells/tissues those species will be affected
they often determine host range and/or tissue specificity
what can happen if viral attachment proteins are mutated?
it can cause many things:
a virus that won’t bind anything
a virus that will bind to different cells (tissues)
a virus that can affect other species
often the immune system produces antibodies to viral attachment proteins. why are they often not effective?
many viruses keep their viral attachment proteins up in small clefts that are too small for antibodies to easily access
