viral structures Flashcards
what is a virion?
a complete infectious particle
what is a capsid?
viral container/shell
what is a nucleocapsid?
when the capsid is intertwined with the genome
i.e. the capsid contains elements of the genome
what is the envelope? describe it
when there is a lipid bilayer membrane enclosing the capsid
host-derived from when the virus exits the cell; gives the virus an advantage when infecting hosts
contains viral proteins – this is how the virus will interact with receptors!
the viral envelope glycoproteins are newly synthesized and then embedded into the host membrane where it will wait for virus which will take it as it leaves host cell
what other interactions do capsid proteins assist with aside from protecting the genome and delivering it?
with cellular components for transport to intracellular sites of assembly
with cellular components to ensure an efficient infectious cycle
with the host immune system
- in rare cases, capsid proteins are enough to induce immune response
how was the viral structure first observed?
was first observed thru electron microscopy
SOME viruses are smaller than ribosomes, some larger… but they’re smaller than other organelles
uses negative staining with electron-dense materials (to absorb electrons), giving a contrasted image
- allows you to see elements of the structure, such as the envelope
the downside of electron and microscopy is that it tends to destroy certain structural elements
- can’t appreciate fine details
describe x-ray crystallography in regards to how it’s used to observe viruses
technique depends on the ability of viral proteins/virion to crystallize
even more detailed than cryo-electron microscopy
darker areas are canyons
areas that interact with receptors for attachment
describe cryo-electron microscopy in regards to how it’s used to observe viruses
main method used now because it doesn’t damage the virus
no stain, so the structure is preserved
instead, flash freeze samples and image at very cold temperatures – the freezing provides the contrast
- can see more details!
use of computers to reconstruct images
describe nuclear magnetic resonance spectroscopy (NMR) in regards to how it’s used to observe viruses
used if your protein does not crystallize
depends on the radiation emitted from a nucleus in a magnetic field - to obtain key info on how the proteins behave
radiation emitted are measured by spectra
inherent property of certain nuclei to have a magnetic moment
we can see how proteins behave in 3D – NOT the whole virion
- a limitation as we are exclusively looking at specific proteins
list the different methods of observing viral structures in order from least detailed to most detailed
electron microscopy
cryo-electron microscopy
x-ray and NMR
cryo-electron microscopy’s resolution could surpass x-ray and NMR one day
note that all the other techniques aside from NMR, gives full virion structures!
- NMR only gives viral proteins
describe the protein composition of viruses
virions are made from many copies of few proteins
lacks a variety of proteins because they do not have enough power/size to accommodate multiple proteins
how is the virus able to fit in so many proteins onto its capsid?
with such a small area, it take thousands of proteins to make the shell
all these proteins are able to compactly form a shell due to symmetry
protein subunits on the surface are identical and the contacts (between subunits) will be identical as well
what are the 2 types of symmetry present in viruses?
helical symmetry
- for rod shaped viruses
e.g. tobacco mosaic virus
polyhedral symmetry
- for round viruses
e.g. simian virus 40
what are the 2 rules of symmetry (for all types) that provides the basis for assembly
each subunits had identical bonding contacts with neighbouring subunits
- achieves higher level of symmetry
bonds between subunits are mostly via non-covalent
- makes it easy to break apart for when the genome needs to be exposed!
how is gardasil a HPV vaccine when it has no elements of the HPV genome?
the shell of HPV is synthesized using synthetic yeast systems and coat proteins for hepatitis B virus and human papilloma virus which self-assembles into shells
this shell is enough to illicit an immune response (immunogenic)
describe the structure of helical symmetry
nucleic acid found in the middle and is surrounded by proteins
- like a shawarma stick
the protein subunits interacts with other identical protein subunits in an identical manner
nucleocapsid
- the subunits also interact with the viral genome that’s found in the middle
- they can be composed one type of protein or multiple types
in more complex structures, nucleoproteins will associate with viral genomes… this is the case for ebola
what are some viruses that exhibit helical symmetry
measles virus
vesicular stomatitis virus
ebola virus
what proteins form the nucleocapsid of the ebola virus?
VP30, VP24, VP35
describe the structure of polyhedral symmetry
round or spherical capsids
regardless of the irregularly shaped proteins, viral capsids are able to appear round/spherical due to symmetry
it was observed that round capsids have a defined number of proteins
- proteins are often in multiples of 60
- number of subunits were 60, 180, 240, 960…
this is how viruses are so round and efficient
describe the structure of icosahedral symmetry (a type of polyhedral)
polyhedral solid with 20 faces
- each of the faces is an equilateral triangle (it’s symmetrical)
accommodates genomes and efficiently protects them
allows formations of a closed shell with a minimum of 60 identical subunit (3 subunits per face x 20 trimers)
what are the rules for the axis of symmetry present in icosahedrons? what are the exceptions?
“5 fold axis of symmetry” found at the vertex
- 5 proteins attached to one vertex
“3 fold axis of symmetry” found at the face
- 3 proteins on a face
“2 fold axis of symmetry” found at the edge
- 2 proteins attached to an edge
rules tend to be less upheld as the virus becomes bigger
this is to accommodate more proteins… rules are still there - just not as strict
referred to as quasi-equivalence
- the extent of similarity between these structurally unique environments occupied by the chemically identical subunits in the virus capsid
- a virus is called quasi-equivalent if it is almost perfectly symmetrical - these are bigger viruses
describe capsid assembly using poliovirus as an example
made on a string
proteins will fold with interactions (generally non-covalent)
once joined together, 3CDpro, a protease cuts the string, creating a protamer (5S unit)
5 protamers assemble into a pentamer
12 pentamers form the capsid
