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ANAT 365 - Cellular Trafficking > Vesicle Transport in Immunity > Flashcards

Vesicle Transport in Immunity Flashcards

1
Q

What are the two types of bacteria?

A

Gram positive and gram negative

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2
Q

Gram negative bacteria have _________ membrane(s) while gram positive bacteria have __________ membrane(s) with a thick peptidoglycan wall

A

Two; one

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3
Q

Transporters and _______________ machinery exist in both forms of bacteria

A

Secretion

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4
Q

Gram _______________ bacteria shed vesicles to help infect cells

A

Negative

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5
Q

What are some functions of gram negative bacteria in infecting cells?

A

Protect the bacteria by shedding vesicles
Facilitate infection when they contain virulence factors

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6
Q

How does bacteria infect the gut?

A

The lower pH of the stomach triggers the oligomerization of periplasmic proteins and their insertion into the outer membrane as a pore
Fusion with target cell membrane leads to depolarization and permeabilization of the cell
Bacteria can enter cell

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7
Q

Which transport machinery is present in gram negative and positive bacteria?

A

Sec and Tat transport machinery

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8
Q

What are the secretion systems of gram negative bacteria?

A

Type II, type III, type IV, type V/VI

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9
Q

Associate the following functions to the secretion system:
i. Secretes effector proteins, share similarity to components with flagellar apparatus
ii. Can transfer DNA and proteins
iii. Secretes toxins, small molecules, which disables host protein synthesis, leading to lethal infection
iv. Translocate portions of themselves

A

i. III
ii. IV
iii. II
iv. V/VI

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10
Q

Which degrading cells clear bacteria and develop immunity?

A

Macrophages and dendritic cells

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11
Q

Dendritic cells allow for the selection of antigens for presentation on class ________ MHC

A

II

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12
Q

Dendritic cells activate which cells to generate antibodies?

A

CD4+ T cells

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13
Q

Associate the following characteristics to MHC class I or MHC class II cells:
i. All somatic cells
ii. Dendritic cells, macrophages and B cells
iii. Peptides enter ER through TAP transporters
iv. Peptides are loaded on their proteins
v. Pathogens in the cytosol are degraded by proteases
vi. Pathogens in the endosome/phagosome are degraded by proteases
vii. Bind to CD4+ T cells
viii. Bind to cytotoxic CD8+ T cells

A

i. MHC class I
ii. MHC class II
iii. MHC class I
iv. MHC class II
v. MHC class I
vi. MHC class II
vii. MHC class II
viii. MHC class I

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14
Q

Bacterial infection by ______________ must be specifically induced

A

Phagocytosis

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15
Q

What is the zipper mechanism?

A

Surface proteins on bacteria bind to host cell proteins

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16
Q

What mechanism initiates upon bacterial secretion of effectors that activate actin and lipid remodeling events?

A

Trigger mechanism

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17
Q

What phenomenon is modulated by changes to PIP?

A

Signaling by the bacteria

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18
Q

Which PIPs are found in the phagosome?

A

Pi(4,5)P2 at the top, PI(3,4,5)P3 at the bottom and PI(3)P once internalized

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19
Q

Listeria uses the _____________ mechanism and shigella uses the _____________ mechanism

A

Zipper; trigger

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20
Q

What are some ways that bacterial effectors modulate actin?
i. Some are injected early to activate internalization
ii. Others are secreted later to enable closure through depolymerization
iii. Some evolved to evade internalization into macrophages, but allow entry into non-phagocytic cells
iv. Others are secreted once the bacteria has escaped the endosome

A

All of the above

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21
Q

Which bacteria replicate within their own specialized vacuolar compartment?

A

Salmonella and Legionella

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22
Q

True or false: Salmonella containing vacuole interact with other organelles

A

True

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23
Q

What does Salmonella do to prevent its compartment from becoming hydrolytic?

A

Recruitment of R-SNARE SipA and SNAREs Syntaxins 7, 8 and 13 to keep the bacteria from entering the late endosome
Salmonella effectors alter retromer and M6P transport

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24
Q

Which bacteria needs to escape the phagosome to replicate?

A

Shigella

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25
Q

Which protein is recruited to help the escape of Shigella?

A

Rab11-positive recycling endosomes

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26
Q

How does bacteria move within the cell?

A

Actin comet tails

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27
Q

What mechanism is used by the host cell to capture and kill cytosolic bacteria?

A

Xenphagy

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28
Q

Place the steps of bacteria homicide in order:
i. Galectins recruit NDP52
ii. Glycans recruit Galectins which sense damaged membrane and target them for degradation
iii. NDP52, optineurin and p62 interact with LC3 to incorporate cargo into autophagosome
iv. NDP52 recruits Ub E3 ligases
v. P62 binds to Traf6 and optineurin binds DUBs
vi. Phagosome rupture induced by bacteria exposes glycans

A

vi, ii, i, iv, v, iii

29
Q

What are the ways that infected cells die?

A

Apoptosis, necrosis, pyroptosis

30
Q

Fit the description to the type of death:
i. Dying cell expresses and releases specific cytokines to recruit immune cells to help
ii. Silent form of death
iii. Death from damage, loss of ATP, membrane rupture and inflammation

A

i. Pyroptosis
ii. Apoptosis
iii. Necrosis

31
Q

Bacterial ______________ around the _________________ block apoptotic machinery

A

Effectors; mitochondria

32
Q

Bacteria can activate ______-survival pathways

A

Pro

33
Q

Bacteriophage are viruses that affect the _______________ cells

A

Bacterial

34
Q

How are bacterial viruses formed?

A

Phage attaches to host bacteria and injects genetic material
DNA integrated into bacterial genome and replicated
Pro-phage is found in all daughter bacterial cells

35
Q

True or false: All phages are lytic and some phages are lysogenic

A

True

36
Q

What are some ways that bacteriophage can inject its DNA?

A

Evolution of a new receptor binding protein (RBP)
Gain access to masked receptors by integration of depolymerizing enzymes
Expression of multiple RBPs to increase flexibility

37
Q

Phages can be used as antibacterial treatments as opposed to _____________

A

Antibiotics

38
Q

True or false: There are more bacterial species that exist than phages

A

False, there are 10-100x more phages than bacterial species

39
Q

Place the following events of the life cycle of a virus in order:
i. Penetration
ii. Assembly
iii. Uncoating
iv. Release
v. Attachment
vi. Biosynthesis

A

v, i, iii, iv, ii, vi

40
Q

There are two types of viruses. What are they?

A

Enveloped and non-enveloped

41
Q

What are the differences between enveloped and non-enveloped viruses?

A

Enveloped viruses have a viral capsid enveloped in a membrane
Non-enveloped viruses only have capsids

42
Q

Which viruses are enveloped?

A

Influenza, HIV, Ebola, SARS-COV2

43
Q

What virus is non-enveloped?

A

Rotavirus

44
Q

How do animal viruses enter the host cell?

A

Endocytosis

45
Q

Internalization of the virus is _______________-mediated

A

Clathrin

46
Q

_______________ generally triggers viral uncoating and/or fusion of the virus with _______________ membrane

A

Acidity; endocytic

47
Q

True or false: There is only way for viruses to enter the cell

A

False, there are a variety of ways to enter the cell based on their features

48
Q

Rotavirus causes acute _________________ and caused the death of 453,000 children younger than 5 worldwide

A

Gastroenteritis

49
Q

How many ways can rotavirus enter the cell?

A

Two, clathrin and non-clathrin mediated endocytosis

50
Q

Rotavirus is released into cytosol with the help of which proteins?

A

Rab5, Rab7, Rab9, ESCRT, cathepsins

51
Q

Viral exit from endosome generally relies upon _________ transitions

A

pH

52
Q

How does pH mediate the exit of the virus from the endosome?

A

pH drop can open helical proteins in capsid proteins or activate viral proteases that cleave viral capsid proteins

53
Q

The cleaved proteins interact with the ______________ side of the acidified endosome and disrupt the membrane, allowing the _____________ to escape

A

Luminal; capsid

54
Q

Identify the following descriptions to the model of viral exit from the endosome:
i. Viral proteins directly embed into the membrane and generate a pore for viral escape
ii. Viral proteins coat the membrane and solubilize like a detergent

A

i. Pore formation
ii. Carpet model

55
Q

Which part of the non-enveloped virus exits the capsid and enters the pore?

A

RNA

56
Q

What are some features of an enveloped virus?

A

Spike protein receptor binding, E protein and M protein, lipid bilayer, N protein, ssRNA

57
Q

What are the two types of binding and entry of enveloped viruses?

A

Viral proteins withing the envelope bind to the cell surface proteins for entry; SNARE-type fusion machinery is found in the viral envelope
Viral fusion proteins can be active upon docking to cell surface receptors - fusion process occurs like SNARE pathway

58
Q

Link the following descriptions to the classes of viral fusion proteins:
i. Alpha-helical, require cleavage event to reveal fusogenic region
ii. Mix of alpha helix and beta sheets, no cleavage event
iii. Beta sheets, fusogenic region bound to another membrane protein that is cleaved

A

i. Class I
ii. Class III
iii. Class II

59
Q

Identify whether the events of SARS-COV2 pathway belong to endosomal or cell surface entry:
i. Cleavage of S2 by TMPRSS2
ii. ACE2 receptor binding
iii. Acidification of endosome
iv. Cathepsin L cleavage of S2

A

i. Cell surface
ii. Endosomal
iii. Endosomal
iv. Endosomal

60
Q

What happened to S1 spike protein?

A

It was cleaved during biogenesis in Golgi of previously infected cell

61
Q

Viral genome replication can occur in the ____________ or ______________

A

Cytosol; nucleus

62
Q

DNA viruses are replicated in the ______________, RNA viruses are replicated in the ________________

A

Nucleus; cytosol

63
Q

What are some ways that the viral genome goes through the nuclear pore?

A

Entire capsid can cross the nuclear pore or capsids disassemble the pore with just the genome entering the nuclear pore
Some viral genomes are transported and cross into the nucleus without capsids

64
Q

How do the viral genomes exit the nucleus?

A

Triggering apoptosis to exit the nucleus
Some viruses assemble in the nucleus and the capsids exit

65
Q

How does the virus become enveloped again?

A

Herpesvirus buds into the perinuclear space
Vesicles fuse with outer nuclear envelope and release capsid into cytosol
Capsid binds to Golgi and viral proteins are expressed in membrane of Golgi
Capsid is internalized

66
Q

Where do viruses that stayed in the perinuclear space go?

A

They enter the ER and exit to the Golgi

67
Q

What is apoptotic mimicry?

A

The exposure of phosphatidylserine as a marker of apoptosis on the virus’ membrane, allowing it to enter the host cell and cause an infection

68
Q

SV40 has a capsid protein that mimics the ____________ protein that binds phosphatidylserine receptors

A

GAS6

69
Q

Internalization of apoptotic fragments drives _________-inflammatory signaling

A

Anti

ANAT 365 - Cellular Trafficking (5 decks)

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