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Biology 416 VIROLOGY > Structure > Flashcards

Structure Flashcards

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1
Q

What is a subunit (protein subunit)?

A

Single folded polypeptide chain

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2
Q

What is a structural unit?

A

Unit from which capsids or nucleocapsids are built

May compromise one protein subunit or multiple different protein subunits

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3
Q

What is a capsid?

A

The protein shell surrounding the nucleic acid genome

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4
Q

What is a nucleocapsid?

A

The nucleic acid-protein assembly packed within the virion

Used when this assembly is a discrete substructure of a particle

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5
Q

What is an evelope?

A

The host cell-derived lipid bilayer carrying viral glycoproteins

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6
Q

What is a virion?

A

The infectious virus particle

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7
Q

What is a metastable structure?

A

A structure has not attained the lowest free energy state

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8
Q

What is resolution?

A

The minimal size of an object that can be distinguished by microscopy or other methods of structural analysis

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9
Q

What is helical symmetry?

A

The symmetry of regular wound structures defined by the relationship P = u x p

P = pitch of the helix
u = the number of structural units per turn
p = the axil rise per unit
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10
Q

What is icosahedral symmetry?

A

The symmetry of an icosahedron the solid with 20 faces and 12 vertices related by axes of two three and five fold rotational symmetry

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11
Q

What is a glycoprotein?

A

a protein carrying covalently linked sugar chains (oligosaccharides)

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12
Q

What is an integral membrane protein?

A

Proteins that are embedded in a lipid bilayer with external and internal domains connected by one or more membrane-spanning domains

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13
Q

What are membrane-spanning domains?

A

A segment of an integral membrane protein that spans the lipid bilayer

Often alpha-helical

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14
Q

What are the two main functions of virion proteins of the viral genome?

A

Protection

Delivery

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15
Q

Why are virus particles considered “metastable”?

A

Because they need to be strong enough to protect the viral genome and labile enough to be released or uncoated inside the host cell

Has to be stable AND unstable

  • stable = protects viral genome
  • unstable = delivery/uncoating

Self-assembly —>
Uncoating

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16
Q

As individual proteins assemble to form a large capsid, their surface charge and polarity is ____ while their contact region is ____. This leads to a __ in the energy of the capsid system and provides the driving force for capsid ___

A

Minimized

Maximized

Decrease

Self-assembly

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17
Q

What is the smallest thing scientists can see when using X-ray crystallography?

A

Atoms

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18
Q

What structure(s) was determined by X-ray crystallography?

A

DNA, Penicillin, Vitamin B-12, Insulin, Hemoglobin

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19
Q

What limitations does X-ray crystallography have?

A

Requires proteins to be packed together in a stable organized structure

Some proteins are too flippy to line up in a crystal

Requires the formation and creation of crystals

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20
Q

What does Cryo-electron microscopy (Cryo-EM) use as a energy source?

A

Uses electrons rather than light as energy source

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21
Q

How does Cryo-EM assemble pictures?

A

Computer algorithms assemble multiple pictures of sample into one composite 3D image

22
Q

How are proteins in Cryo-EM orientated?

A

proteins in sample can be in multiple orientations

23
Q

Where are proteins kept in Cryo-EM?

A

Thin layer of liquid and frozen

24
Q

An icosahedron comprises _ equilateral triangular faces related by _, __, and __ axis of rotational symmetry.

A

20; 5; 3; 2

25
Q

What do h and k represent in the Triangulation equation?

A

0 and/or any positive integer

26
Q

What does a virus need to be alive?

A

Genetic material and a capsid

27
Q

What is the difference between capsid and nucleocapsid?

A

Nucleocapsid is the same structure as a capsid, but an envelope is present

28
Q

What are the bonding interactions in the virus capsid?

A

Non-covalent

If it was covalent, it will be stronger

29
Q

What are the steps in X-ray crystallography workflow?

A

Step 1: crystal
x-rays
Step 2: Diffraction pattern
phrases
Step 3: Electron density map and atomic model
fitting in between
Atomic model back to diffraction pattern is called refinement

30
Q

What is a chimera?

A

composed of more than one organism/species

31
Q

How has Cryo-EM improved resolution over time?

A

Lower resolution = better

X-ray crystallography had a higher resolution than Cryo-EM

32
Q

What is the Cryo-EM structure of Zika virus?

A

Frozen, hydrated ZIKV
- Black boxes: smooth, mature virus particles

Icosahedral symmetry
- Black triangle: 5-fold, 3-fold, 2-fold

33
Q

How do viruses build protective coats (capsids)?

A

Helical symmetry

Icosahedral symmetry

Complex symmetry

34
Q

Which viruses have helical symmetry?

A

Tobacco Mosaic Virus (TMV)

Vesicular stomatitis virus (VSV, Cryo-EM)

Nucleocapsid (N) protein bound to RNA (decamer; x-ray crystl.

35
Q

How to know whether it is helical or icosahedral symmetry?

A

Helical symmetry as it is wrapping around the genomes

36
Q

How to know whether capsid or nucleocapsid?

A

Nucleocapsids are substructures found within

Capsids are substructures of a whole particle

37
Q

What are simple icosahedral capsids?

A

60 identical protein subunits

Identical interactions between subunits

38
Q

How do we build larger virus particles with icosahedral symmetry?

A

Add more subunits

Bonding interactions:
Quasiequivalent

39
Q

What is Quasiequivalent?

A

Similar but not identical

Capsid > 60 subunits

Noncovalent binding properties of subunits

40
Q

What is a triangulation number (T)?

A

Number of facets per triangular face of an icosahedron

Determines size of capsid
- capsids with T>1 have a 6-fold axis of symmetry

41
Q

How to find amount of viral capsids?

A

60 * T (T determines size)

units = proteins

42
Q

What are enveloped viruses?

A

Host derived lipid bilayer

43
Q

How are the envelope in viruses acquired?

A

Through budding of nucleocapsid through cell membrane

44
Q

What kind of symmetry do nucleocapsids have?

A

May have icosahedral or helical symmetry

45
Q

What is the external domain of the integral membrane glycoprotein for?

A

Binding to cell receptors, sugars

46
Q

What is the internal domain of the integral membrane glycoprotein for?

A

Essential for virus assembly

47
Q

Where are viral envelope glycoproteins located?

A

Perpendicular or parallel to lipid membrane

48
Q

What makes complex virus particles complex?

A

Head is icosahedral and tail is helical

49
Q

Describe Bacteriophage T4.

A 
Complex virus
--------------------------------
Head: Icosahedral symmetry
- dsDNA genome
- T= 13 (End)
- T = 20 (Midsection)

Tail: Helical symmetry
- injection of viral genome into host cells

50
Q

Describe Mimivirus.

A

Icosahedral symmetry

Dense coat of long fibers

Unique “starfish”-shaped structure

51
Q

Describe Pithovirus/Pandoravirus.

A

Pithovirus siberium
- isolated from permafrost soil sample in Siberia

Amphora (vase-like) shape

Protruding “cork”

52
Q

What are some nonstructural components in virus particles?

A

Enzymes

  • polymerases, integrases
  • capping enzymes
  • topoisomerases
  • proteases

Other viral proteins

  • non-enzymatic
  • important for viral replication

Cellular components
- tRNAs, lipids, histones, glycoproteins, antiviral proteins

Biology 416 VIROLOGY (7 decks)

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