Lecture 2 Flashcards
What is a phage?
A virus that infects bacteria
What is the model virus for E.Coli?
How is it transmitted?
How many genes does it encode?
MS2 (Male Specific 2)
Sexually transmitted virus through male F-pilus
4 and only one is structural
What do all virus capsids have in common?
Symmetry
Icosahedral (3D): 12 vertices with 5 traingles meeting at each vertex (20 triangles in total)
Helical (2D): Clyinderical shape
How do viruses overcome the rapid degradation of nucliec acids outside of the cell?
Protective container around the nucleic acid; The Capsid
What is the difference between DNA and RNA?
DNA: Double helix which is very stable. Requires histones for folding due to the stiffness of the helix.
RNA: Mostly single stranded and flexible. With the strand moving randomly. Can base pair randomly and form stem loops. Is both an information store and can have its own catalytic activity.
Why do viruses use symmetry?
- Genetic economy (Minimal amount of gene products if all capsid proteins the same)
- Assembly more simple (Building blocks interchangeable)
- Minimum energy (=most stable)
- Size of the container vs coding length
- If coded a gene for entire capsid without repeated building block then the gene would be too big to fit in
- Multiple functions for many viral components
Why are icosahedral structures non-crystal forming?
Why are they used?
Cannot be packed into a lattice
Largest symmetry for a single particle
What is the formula for the pitch of a helix?
P=µ * p
Pitch=Subunits per turn * axial rise per subunit
Ouline the capsid structure of M13
How is M13 similar to MS2?
Positive COOH group of g8p binds to negative phosphate backbone of DNA with negative NH2 group of g8p left on exterior face. Ends are capped with g6p, g7p g9p and g3p. Forms flexible helical structure.
M13 also infects F-plius of male E.Coli
What are the monomers of a capsid?
What is the structure of the monomer?
Capsomeres
Hexamers of identical proteins
How many axes of different fold symmetries does an icosahedral have?
6 axes of 5-fold
10 axes of 3-fold
15 axes of 2-fold
What does caspar klug quasi-equivalence show?
The local environment around each protein looks approximately the same. The triangles aren’t icosahedrally symmetrical but can still be made from same building block and are all still triangles. Instead of forming pentamers at the vertex some will form hexamers at the vertices of the smaller triangles.
What type of lattice is used for Caspar-Klug theory?
Hexagonal
Mid point of hexagon is corner of the triangle
How do you form the triangles using a hexagonal lattice?
Go between middle of hexagons in h direction for H steps and then change direction by 60º and go in the k direction for K steps.
The starting point is one corner of the triangle and the end point after both k and h directions is the second corner. This can be used to find final corner and make a triangle.
What is the T number?
The number of subdivisions of an icosahedral face (Number of small triangles per large triangle)
T=h2+kh+k2
How can the T number be used to calculate the number of protein subunits? and the number of hexamers?
60T protein subunits (20T faces with 3 proteins in each)
10 (T-1) hexamers
What types of handedness exist?
How does each arise?
Dextro arises when K>H
Laevo arises when K<h>
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Can this model been seen in real life?
Yes; although the theory is predictive, viruses following the predicted surface lattices have been seen.
How does CK theory improve the limit on the number of protein subunits?
Mathematically only 60 possible
But quasi-equivalence means that 60T subunits possible
Which type of viruses uses both helical and icosahedral symmetry?
Bacteriophage
- Helical in tail
- Icosahedral in head
Which viruses have been shown to not follow caspar-krug theory?
Cervical cancer, HPV and human papilloma virus
What theory was developed for non-casper-klug viruses?
The Viral Tiling Theory
Quasiequivalent but not triangular
OR
Non-quasiequivalent (different shaped building blocks)
Discuss the capsid of the Pariacotovirus
One prototile; triangular with three different vertices.
One vertice (blue) matches with itself to form the pentamers (b,b,b,b,b)
Other two vertices (green and red) are mixed at the hexamers (r,g,r,g,r,g)
Discuss the capsid of the Bacteriophage MS2
Two rhombus prototiles; one with blue and red vertices and one with both green vertices
Blue meets with blue, (b,b,b,b,b) and red meets with green (r,g,r,g,r,g) (b,b,r,g,g,r)
Discuss the capsid of the Poliovirus
One prototile; kite with blue at the vertex of the long edges and green/red at the vertex of short and long edges
Blue meets blue (b,b,b,b,b), red meets green (r,g,r,g,r,g)(r,g,r,g).
How are MS2 and poliovirus similar?
Both are still quasiequivalent but not caspar-klug becuase non-triangular building blocks are used
How are some viruses icosahedral without following CK theory?
Non-quasiequivalent; have different shaped subunits
Same layout as as a CK-virus with the same T number but with all pentamers
How is the capsid structure of the geminivirus different?
Twinned T=1 icosahedrals; loss of one of the vertices on both particles and then fused together
Which is the largest virus?
Why is its structure different?
Pithovirus : 2.5 microns with 500 genes
More bacterial in structure; just sack with apical pore to release genetic material
Why can dsDNA viruses have larger genomes?
What is the outcome?
DNA more stable; RNA would break if too big
Allows for more proteins with more complex and less symmetrical structure
What experimental techniques can be used to visualise viruses?
X-ray crystallography
NMR
Cyro-EM
TEM
(NOT optic microscopy because can’t resolve)
How does cyro-EM work?
Freezes particle to minimise radiation damage and fix in natural environment
3D reconstruction made by icosahedral averaging
