Lecture 2: virus architecture

Question 1

functions of structural proteins

Answer 1

protection of the genome and delivery of viral genome

Question 2

how are viral genomes protected

Answer 2

• capsid
• recognition/packaging of nucleic acid genome
• interaction with host cell membranes to form viral envelope

Question 3

stable protective coat around virus

Answer 3

capsid

Question 4

possible structures of a virus

Answer 4

viral envelope around, naked, spherical and helical

Question 5

how is the viral genome delivered

Answer 5

• binds to host cell receptors- very specific (capsid has viral receptors)
• uncoating of the genome
• fusion with cell membrane (now in the cell)
• transport of genome to appropriate cellular site

Question 6

cellular site for RNA and DNA

Answer 6

RNA- cytoplasm

DNA- nucleus

Question 7

single, viral-encoded protein

Answer 7

subunit

Question 8

basic unit of capsid, one or multiple protein subunits

Answer 8

structural unit

Question 9

surface structures as seen in EM

Answer 9

morphological unit (capsomere)

Question 10

protein shell around nucleic acid

Answer 10

capsid

Question 11

nucleic acid: capsid protein assembly

Answer 11

nucleocapsid

Question 12

lipid bilayer carrying glycoprotein

obtain from host

Answer 12

envelope

Question 13

complete infectious viral particle

Answer 13

virion

Question 14

describe virion structure

Answer 14

genome- nucleic acid core

capsid- surrounds genome; viral encoded

envelope- from host cell

complete or infectious

Question 15

how is a virus metastable

Answer 15

-stable when protecting genome before infection

• unstable when allowing infection
  - virus recognizes receptor and triggers endocytosis into host, uncoating its genome

-change of pH and binding to receptor causes uncoating virus particle

Question 16

how can a virus be stable and unstable

Answer 16

stable
-symmetrical arrangement of identical subunits

unstable
-structure not permanently bonded

• virus particles aren’t at min free energy level; stored potential energy = spring-loaded
• potential energy used for disassembly if cell provides proper signal

Question 17

nucleocapsid inside the envelope may have __________ symmetry

Answer 17

helical or icosahedral

Question 18

describe viral envelopes

Answer 18

• host lipid membrane (viral encoded proteins)

- flexible shape (helical- ebola, bullet shape- rabies, pleomorphic- herpes)

Question 19

saggy and baggy viral envelope

Answer 19

pleomorphic

Question 20

examples of (-)ssRNA and helical capsids

Answer 20

• Paramyxoviridae (measles and mumps)
• Rhabdoviridae (rabies)
• Orthomyxoviridae (influenza)
• Filoviridae (ebola)

Question 21

must be present on virus to be infectious

Answer 21

glycoproteins

Question 22

describe viral envelope glycoproteins

Answer 22

integral mem glycoproteins
ectodomain- attachment, antigenic sites, fusion
internal domain- assembly
oligomeric- spikes
perpendicular (no symmetry) or parallel (symmetry)

Question 23

describe helical and icosahedral nucleocapsids

Answer 23

helical- unstructured envelopes

icosahedral- structured envelopes

Question 24

largest known virus

Answer 24

pandoravirus 1000x500 nm

Question 25

• negative staining (50-75 A resolution, stain background, shape, capsomeres)
• some distortions

Answer 25

EM

Question 26

• rapid freeing
• specimen preserved
• lower contrast
• improved resolution (8-20 A)
• computer reconstruction
• secondary structure (surface features)

Answer 26

cyro-EM

Question 27

• naked virions (crystalized, bombard with x-rays)
• highest resolution (2-3 A)- shortest wavelength; atomic level
• measure diffraction patterns
• computer generated images (put back together)

Answer 27

x-ray diffraction

Question 28

were the first to see viruses put together

Answer 28

watson and crick

Question 29

watson and cricks rules for building virions

Answer 29

• virions either spherical or rod- shaped
• many copies of similar proteins
• repeated interactions

rule 1- identical bonding contacts b/t subunits
rule 2- bonds usually non-covalent

Question 30

describe icosahedral symmetry

Answer 30

closed shell/identical subunits

• tetrahedron (4 triangular faces)
• cube (6 square faces)

icosahedron (20 triangular faces)

• most economical w/ least amt of subunits used
• 12 vertices (black pentagons soccer ball)
• 20 triangular faces

smallest # of subunits

• 60 identical subunits
• small viruses (parvovirus)

axis’s
-five fold, two fold, three fold

Question 31

characteristics of capsids

Answer 31

icosahedral symmetry

Question 32

equivalence vs quasi equivalence

Answer 32

simplest = equivalent

• parvovirus: singel structure proteins, 60 copies = 60 subunits
• poliovirus: three structural proteins, 60 copies = 180 subunits, least economical

multiple = quasi equivalent
-norwalk virus: single structure, 180 copies = 180 subunits, most economical

multiple of 60 copies***

Question 33

cluster of 3 subunits

Answer 33

facet

Question 34

triangulation number equation

Answer 34

T = h^2 + hk + k^2

Question 35

number of “jumps” between pentamers

Answer 35

triangulation number

Question 36

number of structural units/faces

Answer 36

T

Question 37

total number of subunits

Answer 37

60T (smallest is T=1)

Question 38

permissible T values

Answer 38

1, 3, 4, 7, 13, 16, 25…

12 pentamers + # of hexamers

Question 39

describe helical structure

Answer 39

elongated tube
-identical subunits, wind around a groove, # of nucleotides/subunit varies

naked capsid (rigid)

enveloped capsid (flexible)

ex: TMV

Question 40

helical structure equation

Answer 40

P= u X p

P=pitch of helix (height per turn)
u=# subunits per turn
p= displacement b/t subunits