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BIOC 303 > 2.3 Vesicular Transport > Flashcards

2.3 Vesicular Transport Flashcards

1
Q

vesicular transport

A

mediate exchange of components between compartments

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2
Q

clathrin

A

mediate endocytosis from plasma membrane to endosome to lysosome (bring nutrients in for cell)

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3
Q

COPI

A

mediate vesicular transport from Golgi to ER

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4
Q

COPII

A

mediate vesicular transport from ER to Golgi

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5
Q

anterograde pathway

A

ER to Golgi, mediated by COPII vesicles

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6
Q

retrograde pathway

A

Golgi to ER, mediated by COPI vesicles

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7
Q

LDL receptor

A

bring in LDL particles (contains nutrients such as cholesterol) into the cell

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8
Q

Stage 1: LDL Receptor Cycle (4 steps)

A

Vesicle formation

1) cargo (LDL) binds to cargo receptor (LDL receptor) on exterior of PM
2) adaptor proteins and Arf bind to cytosolic side of the cargo receptor (forms binding site)
3) coat assembly - clathrin binds to binding site of AP+Arf
4) vesicle forms

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9
Q

Arf

A

small monomeric GTPase that forms a binding site for clathrin with adaptor proteins (AP) during endocytosis

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10
Q

how is a clathrin coat formation possible (special characteristic of clathrin)

A

clathrin self polymerizing

- forms a triskelion that spontaneously self-assembles into polyhedral cage

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11
Q

Stage 2: LDL Receptor Cycle (5 steps)

A

Fission and Uncoating

1) dynamin assembles as ring around bund
2) GTPase domain of dynamin regulates pinching off of vesicle
3) non-cytosolic leaflets of membrane to fuse together
4) dynamic recruits other proteins to budding vesicle to bend patch of bilayer
5) Arf GTPase: vesicle rapidly loses clathrin coat

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12
Q

Rab

A

large and diverse subfamily of small monomeric GTPase

  • recognizes naked vesicle
  • important for vesicle trafficking
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13
Q

how is it ensured that the endocytosis vesicle is transported to the right location

A

depends on the type of Rab that is recruited (specific Rabs for different organelle targets)

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14
Q

Rab structure

A

small, has:

  • GTPase (GDP in free state)
  • amphipathic helix
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15
Q

Binding Mechanism for Rab

A

1) Free Rab (GDP form) recognized by Rab-GEF on donor membrane)
2) GDP phosphorylated to GTP
3) Rab becomes membrane bound (amphipathic helix inserts into the outer membrane)

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16
Q

how are Rabs selectively distributed at the membrane

A

PiP (inositol lipids)

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17
Q

where are the kinases and phosphatases for converting PiP located

A

on the cytosolic side of the organelle (some are integral and some are peripheral membrane proteins)

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18
Q

Stage 3: LDL Receptor Cycle

A

Recruitment of Rab GTPase to the vesicle

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19
Q

Stage 4: LDL Receptor Cycle (4 steps)

A

1) tethering - membrane Rab proteins on the vesicle binds to the Rab effectors on target membrane
2) docking - complementary SNAREs on the vesicle and target membrane pair together as vesicle approaches the membrane. A force is applied
3) fusion - as the SNAREs twist together, the two bilayers fuse together (separate layers>stalk>hemifusion>fusion pore)
4) synaptotagmin finishes process

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20
Q

synaptotagmin

A

activated by Ca2+, binds to SNARE complex and causes fusion clamp to tighten further and creates additional disturbance in lipid bilayer and finishes the vesicle fusion process

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21
Q

tetanus

A

neurotoxin that cleave SNARE proteins in nerve terminals (very, very toxic, LD50=1 ng/kg)

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22
Q

botulism

A

neurotoxin that cleave SNARE proteins in nerve terminals

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23
Q

Stage 5: LDL Receptor Cycle (4 steps)

A

Recycling of SNAREs

1) SNAREs are separated by NSF and a-SNAP
- NSF (wrench): ATPase that hydrolyzes ATP to catalyze dissociation of SNARE pairs
- a-SNAP (socket): soluble NSF attachment protein

NOTE: like a wrench system

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24
Q

what is needed to dissociate SNARE pairs

A

1) NSF
2) a-SNAP
3) ATP

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25
Q

what is defective 34

A

accumulation in cytosol

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26
Q

what is defective 34

A

accumulation in ER

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27
Q

what is defective 34

A

accumulation in ER to Golgi transport vesicles (COP1, COP2, VTC, KDEL)

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28
Q

what is defective 34

A

accumulation in Golgi (Golgi, Secretory Vesicles)

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29
Q

what is defective 34

A

accumulation in secretory vesicles

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30
Q

VTC

A

vesicular tubular cluster

- mediates transport from ER to to Golgi

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31
Q

homotypic fusion

A

fusion of membranes from same compartment, forms vesicular tubular clusters

32
Q

VTC steps (4)

A

1) vesicles bud off from ER exit sites and shed COPII coat
2) homotypic fusion of vesicles to form vesicular tubular clusters
3) vesicular tubular clusters move along microtubules with help of motor proteins
4) bud off process of COPI coated transport vesicles that carry back resident ER proteins and cargo receptors

33
Q

describe the mechanism for COPII vesicle formations

A

very similar process to clathrin coat/assembly and disassembly

34
Q

homotypic fusion steps (3)

A

1) NSF with ATP unwinds the SNARE bundles on the vesicles
2) SNAREs bundle together and pull the vesicles together
3) vesicle membrane fusion

35
Q

how are proteins packaged into vesicles (general)

A

selective process

1) proteins recognized by receptors
2) receptors recognized by adaptor proteins
3) adaptor proteins are recognized by COPII
4) coat assembly

36
Q

why is the retrograde pathway important (from Golgi to ER)

A
  • sometimes proteins with exit proteins (resident ER proteins) sometimes randomly enter the vesicle and needs to be returned
37
Q

what are the ER retrieval signals and the proteins that are associated with them?

A

1) KKXX @ C-term: for resident ER membrane proteins

2) KDEL: soluble ER protein

38
Q

KKXX

A

ER retrieval signal for ER membrane proteins that have been accidently taken away by COPII vesicles during anterograde transport
- binds directly to COPI coats

39
Q

KDEL

A

ER retrieval signal for soluble ER proteins that have been accidently taken away by COPII vesicles during anterograde transport

40
Q

what do ER resident proteins bind to?

A

KDEL receptor on cis-Golgi network with their KDEL ER signal sequence

41
Q

how is the affinity of the KDEL receptor for KDEL sequence regulated

A

pH

  • binds protein with KDEL sequence at low pH (Golgi)
  • releases protein with KDEL sequence at high pH (ER)
42
Q

how is the pH regulation of the KDEL sequence to KDEL receptor useful

A

prevents the KDEL sequence from interacting with the KDEL receptor in the ER where the binding is not necessary

43
Q

describe the faces of the Golgi stack

A

cis face (entry) and trans face (exit)

44
Q

what are the Golgi called and how are they different from each other?

A

cisterna, contain characteristic set of processing enzymes

45
Q

how are the resident ER proteins associated with the Golgi apparatus and why is this desired?

A

Golgi resident proteins are all membrane bound. This makes retrieval easier because it can be regulated via the COPII mechanism

46
Q

what are the characteristics of the constitutive secretory pathway

A

unregulated membrane fusion

- can release the newly synthesized soluble proteins right away to environment

47
Q

what are the characteristics of the regulated secretory pathway

A

requires a signal (hormone/neurotransmitter)

- triggers secretion of the secretory proteins that are being stored in secretory vesicles

48
Q

how are lysosome proteins regulated

A

by pH. synthesized as proenzyme and requires an acidic environment for activation (pH 4.5-5.0)

49
Q

how is the environment of the lysosome acidic

A

vacuolar H+ ATPase uses ATP to pump H+ into lysosome

50
Q

why does the membrane of the lysosome not just break down to it’s own enzymes?

A

the membrane is highly glycosylated to protect itself from its own proteases and lipases

51
Q

M6P targeting steps

A

1) lysozyme proenzyme with a mannose is brought to the cis Golgi network
2) P-GLcNAc is added
3) M6P signal is uncovered

52
Q

M6P targeting steps

A

1) lysozyme proenzyme with a mannose is brought to the cis Golgi network
2) P-GLcNAc is added onto mannose residue with GlcNAc phosphotransferase
3) M6P signal is uncovered (GlcNAc removed via GlcNAc hydrolase
4) M6P binds to M6P receptor at the trans Golgi network
5) receptor-dependent transport to early endosome
6) acidic pH dissociates the proenzyme from the M6P receptor
7) phosphate is removed from the lysosomal proenzyme
8) M6P receptor is recycled and brought back to the trans Golgi network

53
Q

describe lysosomal storage disease

A

GlcNAc phosphotransferase in the cis Golgi network is defective

  • lysosomal hydrolases are not tagged in the cis Golgi network and then not recognized by the M6P receptors in the trans Golgi network
  • hydrolases are secreted at the cell surface instead of getting transported to lysosomes
  • lysosome has no lysosomal hydrolases so the lysosomal substrates accumulate in the lysosome
54
Q

P-GlcNAc definition

A

GlcNAc phosphotransferase

- adds GlcNAc-phosphate to mannose residues onto lysosomal proenzymes

55
Q

I cells

A

inclusion cells, undigested substrates accumulate in lysosomes

56
Q

what is the default secretory pathway

A

Golgi to extracellular space

57
Q

what are the 3 pathways for bringing materials to the lysosome

A

1) intracellular traffic
2) autophagy
3) phagocytosis

58
Q

describe intracellular traffic pathway of delivery of materials to lysosomes

A

1) macromolecules taken up from extracellular space via endocytosis
2) endosomes mature to lysosomes

59
Q

describe autophagy pathway of delivery of materials to lysosomes

A

degradation pathway of parts of cells

1) formation of autophagosome (double membrane forms around whatever)
2) autophagosome fuses with lysosome/late endosome
3) thing digested and metabolites are derived

60
Q

describe phagocytosis pathway of delivery of materials to lysosomes

A

digestion of large particles and microorganisms

1) macrophages and neutrophils engulf objects to form phagosome
2) phagosome fuses with lysosome
3) thing digested

61
Q

how are late endosomes formed

A

endocytosis

62
Q

how are endo-lysosomes formed

A

late endosomes fuse with pre-existing lysosomes

63
Q

how are lysosomes formed

A

endo-lysosomes fuse with each other

64
Q

how are components in early endosomes digested (4)

A

1) early endosome with stuff inside
2) sequestration (formation of invaginating buds) to form internal vesicles
3) multivesicular bodies fuse with late endosomal compartment
4) further acidification of late endosome activates the lysosomal enzymes

65
Q

shape/charge of PC

A

cylindrical, neutral

66
Q

shape/charge of PE

A

conical, neutral

67
Q

shape/charge of SM

A

cylindrical, neutral

68
Q

shape/charge of PS

A

cylindrical, negative

69
Q

shape/charge of PI

A

cylindrical, negative

70
Q

what are lipid-packing defects and where do they arise from

A

when the lipids aren’t stacked nicely with each other

  • shape of lipids not cylindrical (PE and DAG are conical)
  • unsaturated double bonds introduces kinks
71
Q

shape/charge of DAG

A

conical, neutral

72
Q

describe the packing of lipids in the ER and what can this be attributed to

A

loose packing

  • unsaturated phospholipids
  • low sterols
73
Q

describe the packing of lipids in the PM and what can this be attributed to

A

tight packing

  • saturated lipids
  • high sterols
74
Q

how are electrostatics related to packing defects

A

generally less packing defects = high electrostatics

75
Q

how can the electrostatics of different membrane territories in the cell explained

A

by the degree of packing defects in the membrane (more defects = less electrostatics)

BIOC 303 (14 decks)

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