BIOC20 - Lecture 2 Exam Study Guide
What are capsids? - ANSWER They package viral genomes and transmit them to a new
host cell
What is a nucleocapsid? - ANSWER It is a capsid with an enclosed genome
What is a virion? - ANSWER A complete, infectious virus particle, possibly including an
envelope
What is an envelope? - ANSWER A lipid bilayer that encapsulates a viral capsid
What microscopy methods are used to study virions? - ANSWER Virions are studied by
electron microscopy and X-ray diffraction
What is negative staining? - ANSWER It is when viruses do not absorb the stain and
appear lighter against a dark stained background
What is positive staining? - ANSWER It is when viruses absorb the stain and the target
areas you are looking for are stained (proteins, nucleic acids, lipids)
Why are positive and negative staining sub-optimal? - ANSWER They both can lead to
damaged tissues leading to unwanted staining of artifacts
What is cryoelectron microscopy? - ANSWER It uses liquid nitrogen to flash freeze
samples allowing for extremely well preserved structures (tissues and viruses) in
samples
How are images made from CryoEM? - ANSWER Data from many images are merged
using a computer program giving the true image of the structure
What is crystallization and X-ray diffraction? - ANSWER This can only be used if the virus
can be crystallized, if this is possible then the crystalline structure causes a beam of
incident X-rays to diffract into many specific directions.
What are the pros and cons to crystallization and X-ray diffraction? - ANSWER Pros:
extremely high res images
Cons: Cannot be focused so a computer program is required to analyze diffraction
patterns to create an image
Why can viruses spontaneously self-assemble into simple, symmetric packages? -
ANSWER Viruses are composed of many copies of identical subunits increasing genetic
economy
What is genetic economy? - ANSWER It allows viruses with a very small genome to be
extremely efficient while building solid capsids; there is 2 ways to do so..
, i) they make subunits that are versatile, and can be repeated and used to create one
dome
ii) express numerous proteins that interact together and form one dome
What gives capsids their symmetry? - ANSWER Identical subunits
What does capsid "shape" refer to? - ANSWER The geometry of the capsid outline -
spherical, cubic, tubular, etc.
What does capsid "symmetry" refer to? - ANSWER The rotational and translational
operations that describe it - twofold axis, threefold axis, etc.
What are the 3 kinds of capsid symmetry that are possible? - ANSWER Geometric
principles have demonstrated that closed shells of identical subunits can have..
- tetrahedral; polygon w/ 4 identical triangular faces
- cubic; 6 identical square faces
- icosahedral; 20 triangular faces
Where does the name icosahedral come from? - ANSWER Greek language - eikosi = 20
What kinds of capsids HAVE NOT been described for viruses? - ANSWER Tetrahedral
and cubic
What are the possible icosahedral capsid rotational axis'? - ANSWER Fivefold, threefold
and twofold
What are the characteristics of a twofold rotational axis? - ANSWER It contains 30 oval
midpoints of the triangular edges. It takes two 180 degree rotations to bring it back to its
original shape
What are the characteristics of a threefold rotational axis? - ANSWER It contains 20
triangular faces. It takes three 120 degree turns to bring it back to its original shape
What are the characteristics of a fivefold rotational axis? - ANSWER It contains 12
pentagon vertices. It takes five 72 degree rotations to bring it back to its original shape
Describe the parvovirus genome. - ANSWER 5kb ssDNA, 20nm diameter
Describe the capsid proteins for the parvovirus. - ANSWER It has 60 copies of 520 amino
acid capsid proteins - approx. 1/3 of its coding capacity
What kind of shape does the parvovirus capsid have? - ANSWER Icosahedral - it
contains 20 triangualr faces, made up of 60 proteins which means each triangular face
is made up of three subunits (proteins)
What are capsids? - ANSWER They package viral genomes and transmit them to a new
host cell
What is a nucleocapsid? - ANSWER It is a capsid with an enclosed genome
What is a virion? - ANSWER A complete, infectious virus particle, possibly including an
envelope
What is an envelope? - ANSWER A lipid bilayer that encapsulates a viral capsid
What microscopy methods are used to study virions? - ANSWER Virions are studied by
electron microscopy and X-ray diffraction
What is negative staining? - ANSWER It is when viruses do not absorb the stain and
appear lighter against a dark stained background
What is positive staining? - ANSWER It is when viruses absorb the stain and the target
areas you are looking for are stained (proteins, nucleic acids, lipids)
Why are positive and negative staining sub-optimal? - ANSWER They both can lead to
damaged tissues leading to unwanted staining of artifacts
What is cryoelectron microscopy? - ANSWER It uses liquid nitrogen to flash freeze
samples allowing for extremely well preserved structures (tissues and viruses) in
samples
How are images made from CryoEM? - ANSWER Data from many images are merged
using a computer program giving the true image of the structure
What is crystallization and X-ray diffraction? - ANSWER This can only be used if the virus
can be crystallized, if this is possible then the crystalline structure causes a beam of
incident X-rays to diffract into many specific directions.
What are the pros and cons to crystallization and X-ray diffraction? - ANSWER Pros:
extremely high res images
Cons: Cannot be focused so a computer program is required to analyze diffraction
patterns to create an image
Why can viruses spontaneously self-assemble into simple, symmetric packages? -
ANSWER Viruses are composed of many copies of identical subunits increasing genetic
economy
What is genetic economy? - ANSWER It allows viruses with a very small genome to be
extremely efficient while building solid capsids; there is 2 ways to do so..
, i) they make subunits that are versatile, and can be repeated and used to create one
dome
ii) express numerous proteins that interact together and form one dome
What gives capsids their symmetry? - ANSWER Identical subunits
What does capsid "shape" refer to? - ANSWER The geometry of the capsid outline -
spherical, cubic, tubular, etc.
What does capsid "symmetry" refer to? - ANSWER The rotational and translational
operations that describe it - twofold axis, threefold axis, etc.
What are the 3 kinds of capsid symmetry that are possible? - ANSWER Geometric
principles have demonstrated that closed shells of identical subunits can have..
- tetrahedral; polygon w/ 4 identical triangular faces
- cubic; 6 identical square faces
- icosahedral; 20 triangular faces
Where does the name icosahedral come from? - ANSWER Greek language - eikosi = 20
What kinds of capsids HAVE NOT been described for viruses? - ANSWER Tetrahedral
and cubic
What are the possible icosahedral capsid rotational axis'? - ANSWER Fivefold, threefold
and twofold
What are the characteristics of a twofold rotational axis? - ANSWER It contains 30 oval
midpoints of the triangular edges. It takes two 180 degree rotations to bring it back to its
original shape
What are the characteristics of a threefold rotational axis? - ANSWER It contains 20
triangular faces. It takes three 120 degree turns to bring it back to its original shape
What are the characteristics of a fivefold rotational axis? - ANSWER It contains 12
pentagon vertices. It takes five 72 degree rotations to bring it back to its original shape
Describe the parvovirus genome. - ANSWER 5kb ssDNA, 20nm diameter
Describe the capsid proteins for the parvovirus. - ANSWER It has 60 copies of 520 amino
acid capsid proteins - approx. 1/3 of its coding capacity
What kind of shape does the parvovirus capsid have? - ANSWER Icosahedral - it
contains 20 triangualr faces, made up of 60 proteins which means each triangular face
is made up of three subunits (proteins)
