Lecture 2 Flashcards
What is the one thing all viruses have in common?
Symmetry in structure
Issue DNA viruses must overcome?
DNA viruses must overcome issue with very stable double stranded DNA, its stiffness. Cells need to use tricks to condense it
Advantage RNA viruses have over DNA viruses in structure?
RNA is mostly single stranded and can fold back to stem loops, easily condensed.
Disadvantage RNA viruses have against DNA viruses?
RNA is much less stable, leading to upper limit for RNA viral genomes. Only dsDNA is stable enough for very complex viruses.
How are RNA viruses genomes condensed?
Complex secondary structures formed with e.g. catalytic activity (ribozymes), a branched polymer; important for assembly.
Why is symmetry used by viruses?
Genetic economy (minimalism). Requires less energy. Building blocks are interchangeable. Size of container vs coding length = more genes require larger container, which would require more genes etc... nucleic acid is 6 times heavier than the protein it encodes Recyclability of building blocks.
Summary: symmetry is a good way to ‘reuse’ building blocks to reduce complexity of genome so that it is small enough to fit in the container it encodes.
First virus to be shown to have structural symmetry?
Tobacco Mosaic Virus.
Shown to have 2D, helical, rod-like particles.
What other viruses shows 2D symmetry?
Bacteriophage M13 (ssDNA) shows 2D symmetry, but not as stiff as TMV. More flexibility. The virus that infects E. coli.
Ebola virus also displays helical symmetry.
What part of the virus resembles icosahedral symmetry?
The Capsid
What rotation orders correspond to what degree of rotation?
Order 2: 180 degrees
Order 3: 120 degrees
Order 4: 90 degrees
What order of rotational symmetry does an equilateral triangle have
Order 3
What is icosahedral symmetry?
6 axes of 5-fold symmetry.
10 axes of 3-fold symmetry.
15 axes of 2-fold symmetry
What is the Caspar and Klug theory of quasi-equivalence?
How larger, more complex viruses assemble their capsid.
Icosahedral symmetry only accounts for at most 60 subunits in capsid.
Viruses with larger capsids use quasi-equivalence, using four triangles to make one even larger triangles, etc…
What does quasi-equivalence mean in terms of subunits meeting?
The corners of the larger ‘triangle’ has 5 subunits meeting, whereas the corners of the smaller triangles have 6 subunits.
What does quasi-equivalence mean in terms of subunits meeting?
The corners of the larger ‘triangle’ has 5 subunits meeting, whereas the corners of the smaller triangles have 6 subunits. Visible under a microscope as pentamers and hexamers.
How many subunits does a T=1 virus have?
60 subunits. Smallest option. 12 pentagonal clusters = 60 protein subunits.
How many subunits does T=3 virus have?
180 protein subunits.
12 pentagonal clusters and 20 hexagonal clusters.
What are T numbers?
Classify different ways in which surface lattices can be constructed. T number is the number of subdivisions of an icosahedral face and is given in terms of the h and k steps you move along along the axes labelled h and k.
T = h^2 + hk + k^2
What complications arise with larger T numbers?
Exists multiple ways to construct, which are mirror images of one another. Particle has handedness which happens unless k=0 or k=h.
How large can viruses get by using CK theory?
Limit up to T=60.
What is the T number of Mimivirus?
T= 900-1200
Mistaken for bacterium.
How do bacteriophages display symmetry?
Icosahedral symmetry in their head and helical symmetry in their tails
Alternative to CK theory?
Viral Tiling Theory
Quasiequivalent but not triangular (e.g. kite or rhomb)
More than one type of tiling (Penrose tiling) (e.g kite and rhomb)
Example of T=3? 1
Pariacotovirus:
One prototile: triangle with three decorated vertices. b r g
Matching rules: Blue vertices must meet blue ones, red vertices must have green on both side, vice versa.
Vertex atlas: Two vertex stars - (b,b,b,b,b and r,g,r,g,r,g).
Example of T=3? 2
Bacteriophage MS2:
Two rhombus prototile: one tile with blue and red, other with green at ends.
Matching rules: Blue meets blue, red meets green.
Vertex atlas: Three stars (b,b,b,b,b, r,g,r,g,r,g, and b,b,r,g,g,r).
Example of T=3? 3
Poliovirus:
One prototile: kite with blue decoration where two long edges meet and red and green at other vertices meet long edges.
Matching rules: blue meets blue, red meets green.
Vertex atlas: Three stars (b,b,b,b,b, r,g,r,g,r,g and r,g,r,g).
What is non-quasiequivalence?
Viruses whose number of subunits do not match CK theory: HPV, SV40 - icosahedral but not quasi equivalent.
Due to more than one tile -> Penrose type tilings.
Sale layout as T=7(d) CK virus but with pentamers instead of hexamers.
Other non-quasiequivalent viruses?
Geminivirus (ssDNA).
Twinned T=1 icosahedra, fused together at one pentameric vertices. Consists of 110 capsid protein subunits and one molecule of ss(+) sense DNA of ~2.7kb.
What experimental techniques are are used to study virus structure?
X-Ray (early work done by e.g. Crick Watson Klug).
NMR (complicated for whole virus but used for individual protein subunits).
Cryo-EM (single particle analysis and tomography).
TEM (whole virus).
What interaction is observed by using Cryo-EM?
MS2 bacteriophage infecting male E coli (F-pilus).
