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MIMM 324 > Lecture 3 > Flashcards

Lecture 3 Flashcards

1
Q

What are the functions of structural proteins?

A

-Protection of the genome
-delivery of the genome

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2
Q

What do structural proteins have to do?

A

Structural proteins have to:
-Assembly of a stable, protective shell
-specific recognition and packaging of the nucleic acid genome
-Interaction with hist cell membranes to form the envelope

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3
Q

What do structural proteins participate in: Delivery of the genome explained

A

in order to deliver the genome, the structural proteins have to
-bind to host cell receptors
-uncoat the genome
-fusion with cell membrane (for enveloped viruses)
-need to transport of the genome to the appropriate site in the cell in the nucleus

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4
Q

What is a capsid?

A

comes from the latin capsa=box
protein shell surrounding the genome

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5
Q

what is the nucleocapsid?

A

core
nucleic acid with capsid around it: protein assembly with the virion

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6
Q

what is an envelope?

A

viral membrane
host cell-derived lipid bilayer that surrounds viral particles

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7
Q

what is a virion?

A

infectious viral particle

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8
Q

Virus particles are homostable or metastable?

A

they are metastable
-they must exist in 2 states:
they must protect the genome aka stable
they must come apart upon infection aka unstable

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9
Q

True or false: energy is put into the virus particle during uncoating

A

false
True or false: energy in put into the virus particle during assembly so that it can release viral particles when they find the right cell

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10
Q

True or false: metastability is the potential energy used for dissasembly of the cell provide the proper signal

A

true
viral particles themselves have not attainted minimum free energy conformation they are sort of spring loaded

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11
Q

How is metastability acheaved?

A

Stable structure:
Created by symmetrical arrangement of many identical proteins to provide maximal contact

Unstable structure:
Structure is not usually permanently bonded together
use non-covalent bonds
can be taken apart or loosened on infection to release or expose the genome

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12
Q

How do we learn about viral structure?

A

-electron microscopy
-x-ray crystallography
-electron cryomicroscopy (cryoEM) and tomography
-Nuclear magnetic resonance spectroscopy aka NMR

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13
Q

Electron microscopy

A

-Biological materials have little inherent contrast - need to be stained
-Negative staining with electron-dense material (uranyl acetate, phosphotungstate), scatter electrons (1959)
-Resolution 50-75 Å (1 Å = 0.1 nm)
-you look at the scatter pattern
-Detailed structural interpretation is impossible

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14
Q

Cryo-EM

A

-Freeze viral particles in water
-Take a bunch of images
-3D reconstruction of viruses
you get better resolution and you can almost see the individual polypeptide chains

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15
Q

X-e=ray crystallography

A

-you make crystals
-bombard the crystal with x ray
-collect the diffraction pattern of those
-calculate the 3d structure of the protein or virion
excellent resolution

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16
Q

What did Watson and Crick discovered other than DNA structure?

A

symmetry in viruses!!!
- Identical protein subunits are distributed with helical
symmetry for rod-shaped viruses Platonic polyhedra symmetry for round viruses
- Platonic polyhedra symmetry for round viruses

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17
Q

what is a subunit?

A

single folded polypeptide chain

18
Q

what is a structural unit?

A

a protomer aka asymetric uni
unit from which capsids or nucleocapsids are built: one or more subunits

19
Q

What are the rules for “self assembly?”

A

Rule 1: Each subunit has ‘identical’ bonding contacts with its neighbors
Repeated interaction of chemically complementary surfaces at the subunit interfaces naturally leads to a symmetric arrangement

Rule 2: These bonding contacts are usually non-covalent
Reversible
Error-free assembly
Meta-stable
they kinda break apart and reassemble up until they get that good stable conformation

20
Q

True or false:All capsid proteins can self assemble into ‘virus- like particles’ (VLPs)

A

False: Many capsid proteins (aka they do not have viral genome)can self assemble into ‘virus-like particles’ (VLPs)
HBV and HPV vaccines are VLPs made in yeast

21
Q

Helical symmetry

A

-Coat protein molecules engage in identical, equivalent interactions with one another and with the viral genome
-Construction of a large, stable structure from a single protein subunit aka 1 capsid protein on RNA binds with other capsids

22
Q

How are viruses able to get round capsids?

A

• All round capsids have a precise number of proteins (multiples of 60 are common - 60, 180, 240, 960, etc)
• Spherical viruses come in may size, but capsid proteins are 20-60 kDa in size

23
Q

What did Caspar and Klug do?

A

-they knew from watson and cricks work that round capsids are icosahedrons aka no other platonic solids were used
-Capsid subunits tended to be arranged as hexamers and pentamers

24
Q

Icosahedral symmetry

A

icosahedron: solid with 20 faces, each an equilateral triangle
-allows the formation of a closed shell with smallest number (60) of identical subunits

25
Q

Simple icosahedral capsids

A

-made of 60 identical protein sub units
-the protein subunit is the structural unit
-interactions of all molecules with their neighbors are identical aka had to head and tail to tail all at the penton

26
Q

true or false: adeno associated virus 2 aka parvovirus is a helical virus

A

FALSE it is a simple icosahedral virus
25 nm
t=1
-60 copies of a single capsid protein

27
Q

How are larger virus particles built?

A

-by adding more subunits
-3 modes of subunit packing
-pentamers and hexamers
-bonding interactions are quasiequivalent: all engage to tailto tail and head to head

28
Q

What is quasiequivalence

A

-When a capsid contains more than 60 subunits, each occupies a quasiequivalent position to one another
-the non-covalent binding properties of subunits in different structural environments are similar but not identical

29
Q

true or false SV40 aka polyomavirus has 60 sububnits

A

-falseeeeeee àit is 50 nm
-t=6
-72 pentamers of VP1= 360 subunits

30
Q

what is triangulation number T?

A

the number of facets per triangular face of an icosahedron
-combining several triangular facets allows assembly of larger face from same structural unit

31
Q

true or false: mimivirus has a T of 1200

A

true

32
Q

large complex capsids

A

-distinct components with different symmetries
-presence of proteins devoted to specialized

  • e.g. Adenovirus (150 nm, T=25, 720 copies of viral protein II + 60 copies of protein III, fibers at the 12 vertices
33
Q

What physical components of tailed bacteriophages?

A

-head: icisahedral capsid
-contractile tail (attached to one fivefold access of the icosahedral capsid)
built with helical symettry
-baseplate
for attachment

34
Q

true or false: capsids can’t be covered by host membrane

A

FALSE
Capsids can be covered by host membranes (envelope)

35
Q

what is an envelope and how is it aquired?

A

-Envelope is a lipid bilayer derived from host cell
-Envelope acquired by budding of nucleocapsid through a cellular membrane
Can be any cell membrane (virus- specific)
-nucleocapsids inside the envelope may have helical or icosahedral symmetry.

36
Q

how do u aquire an envelope?

A

the virus gets replicated inside a cell including viral glycoproteins that’ll gp to the membrane of the cell
when the virus wants to get out it’ll bud off and I’ll become enveloped with that cell’s membrane that has the glycoproteins

37
Q

viral envelope glycoproteins

A

-integral membrane glycoproteins
-ectodomain: responsible for attachment, antigenic sites, fusion
-internal domain: responsible for assembly
-oligomeric: spikes like the one on sars cov

38
Q

true or false: envelopes can be structured or unstructured

A

true
• Unstructured envelopes
- Can vary in size and shape
(pleomorphic)
• Structured envelopes
- Sometimes the capsid can impart structure on the envelope

39
Q

true or false: envelopped viruses are all the same aka no exception

A

falseee there are exceptions like the poxvirus that is not icasehidral
the pandoravirus and the pithovirus have an apical pore probs important for the release of the virus

40
Q

what are a virions components?

A

-capsid
-core
-tegument
-enveloppe if envelopped
-enzymes
polymerases, integrases, associated proteins, proteases and etc
-activators of transcription-required for efficient infection
-cellular components-histones trna(HIV), lipids, host proteins and more

41
Q

what is a tegument?

A

space between nucleic acid and the enveloppe you can put random stuff in it or like an RT

MIMM 324 (26 decks)

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