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Molecular and cell biology > Membrane trafficking > Flashcards

Membrane trafficking Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Why do eukaryotes need membrane trafficking?

A

compartmentalisation allows more complexity
enzymes can modify subsets of proteins in certain environments
sequential modifications require exposure to distinct sets of enzymes
important in retrieval of proteins back to resident compartment

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2
Q

Secretory/ exocytic pathway

A

ER
golgi
PM/endosome/lysosome

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3
Q

Endocytic pathway

A

cell surface
endosome
golgi/ER/lysosome

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4
Q

How are proteins modified in the ER/golgi?

A

glycosylation
proteolytic cleaving

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5
Q

What happens in the ER lumen?

A

addition of pre-formed oligosaccharide to an aspargine amino acid in a consensus sequence

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6
Q

What happens in the golgi?

A

further sugars are added and structure can be further branched
oligosaccharide group is trimmed

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7
Q

What is the purpose for glycosylation?

A

to assist folding for trafficking and sorting inside the cell
to assist interactions with the ECM and with other proteins/sugars on other cells

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8
Q

Advantages of yeast as a model organism

A

amenable for genetic studies as they can grow as haploid or diploid
entire genome sequence is fully known and annotated
cheap and easy to grow large quantities
limited gene diversity + fundamental pathways conserved

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9
Q

Disadvantages of yeast as a model organism

A

limited cell to cell contact so uninformative about multicellularity
small so high resolution imaging of intracellular compartments difficult
cell wall which can preclude some studies

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10
Q

What was the rationale for the Novick and Scheckman experiment?

A

if proteins couldn’t be secreted the cell would increase density as vesicles accumulate

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11
Q

Novick and Schekman experiment

A

cells were analyses for their ability to secrete enzymes at permissive and restrictive temps
defined secretory mutants as those that failed to export active invertase and acid phosphatase
23 genes identified to be required to ensure protein transport from ER to membrane

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11
Q

Novick and Schekman experiment

A

cells were analyses for their ability to secrete enzymes at permissive and restrictive temps
defined secretory mutants as those that failed to export active invertase and acid phosphatase
23 genes identified to be required to ensure protein transport from ER to membrane

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12
Q

What does alpha factor have to do with the secretory pathway?

A

it is glycosylated and proteolytically cleaved at different stages
this helps us to follow it progress

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13
Q

What are the limitations of Novick and Schekman’s experiment?

A

only considered secretion to plasma membrane
defects in transport to endosome or vacuole would not be identified
redundantly functioning genes would not be identified as there isn’t much of this in yeast

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14
Q

Endocytosis

A

process through which the plasma membrane invaginates into the cell resulting in the production of a vesicle that is then able to fuse with endosomes and enter the endo-lysosomal system

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15
Q

What is endocytosis important for?

A

retrieval of molecules that form part of the secretory vesicle for recycling
downregulation of signals
remodelling cell surface lipid and protein composition

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16
Q

Stages in the endocytic pathway

A

plasma membrane → endocytic vesicle → early endosome → late endosome or recycling to the plasma membrane → golgi or vacuole

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17
Q

What is the major function of a lysosome/vacuole in endocytosis?

A

degradation of extracellular material taken up by endocytosis and certain intracellular components by a process termed autophagy

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18
Q

Carboxypeptidase Y

A

normally transported to lysosomes having been trafficked through ER and golgi
glycosylated and proteolytically cleaved at different stages which helps us follow its progress

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19
Q

How are vacuolar mutants classed?

A

depending on what stage at which they appear to block the route to the vacuole

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20
Q

What are the 4 possible destinations from the late golgi?

A

plasma membrane
early endosome
late endosome
vacuole

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21
Q

CPY transport

A

synthesised in prepro form and transported through to ER to the golgi where it is recognised by Vsp10 receptor
dissociates from Vsp10 at late endosome and trasnported to vacuoles where it is cleaved to generate mature form
Vsp10 retrieved to late golgi through specific aromatic signal in its protein sequence

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22
Q

What does the transport of CPY require?

A

cytoplasmic factors clathrin
2 adaptors called Gga1 and Gga2

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23
Q

Nuclear pores

A

consists of multiple copies of 30 different nucleoporins
each complex is made of 8 subunits with a central plug
contains DNA, nuclear pore proteins and tight junctions

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24
Q

Examples of substances moved across the nuclear envelope by pore complexes

A

transporting histones from the cytoplasm for packaging of new DNA
ribosomal units formed in the nucleus being transported into the cytoplasm

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25
Q

What amino acids are rich in nuclear transport recognition sites?

A

Lys
Arg
Pro

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26
Q

What is required for mRNA transport?

A

ATP hydrolysis
as it is inhibited by cooling to 4 degrees

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27
Q

What happens in the absence of ATP in protein transport?

A

the protein binds to the pore complex but remains outside the nucleus

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28
Q

Why must ribosomes be so closely associated with the ER membrane?

A

newly made proteins can be translocated into organelles co or post translationally
the majority are co-translationally translocated

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29
Q

How is a soluble protein destined for secretion synthesised co-translationally?

A

Signal sequence on growing polypeptide chain → cleavage of signal peptide → (through signal peptidase) NH2 → mature polypeptide chain in the ER lumen

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30
Q

How is the ER lumen adapted for protein synthesis and modification?

A

ER lumen is rich in chaperones and protein disulphide isomerases which allows the formation of sulfide linkages within proteins

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31
Q

How are membrane proteins inserted into the ER?

A

signal sequence that starts the transfer is recognised by sec61, the translocator → fed through but encounters a stop transfer sequence, usually a hydrophobic part of the protein -> means it is anchored to the ER → so the rest of the protein is exposed to the cytoplasm

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32
Q

BiP

A

chaperone in ER that associates with a newly synthesised protein and ensures it fold properly via complex quality conrol mechanisms in the ER

33
Q

What is the unfolded protein response?

A

translation is closed down and the synthesis of chaperones is upregulated due to quality control becoming swamped
cell can recover but apoptotic pathways will be activated if overwhelmed

34
Q

How do mitochondria, chloroplasts and bacteria move proteins post-translationally?

A

N terminal sequence is recognised by the TOM complex → the protein translocates through TOM and TIM23 → translocates through TIM23 into matrix of mitochondria → signal is cleaved off

35
Q

Anterograde transport

A

through the secretory pathway

36
Q

Retrograde transport

A

backwards (opposite of secretory)

37
Q

Essential components for transport vesicle formation

A

GTPase
adaptor proteins
coat proteins

38
Q

GEFs

A

guanine nucleotide exchange factors
allow the exchange of GDP for GTP to activate GTPase

39
Q

GAPs

A

GTPase activating proteins

40
Q

Ran GTPase

A

if cargo needs to enter nucleus it binds to nuclear receptors
when cargo dissociates and exits nucleus it encouters GAP
GAP hydrolyses GTP to GDP so cargo dissociates from receptors, so they can pick up more cargo

41
Q

COPII coated vesicles

A

formed at the exit sites of the ER and are a paradigm for transport vesicle formation

42
Q

COPII GTPase

A

called Sar 1 and is a member of the Arf family
adaptor is a sec protein and so is the coat protein

43
Q

What is the role of Sec24 in vesicular transport?

A

component of Sec24 recognises signal on cargo receptor which allows it to be recruited into a COPII vesicle

44
Q

What allows recruitment of the adaptor complex?

A

when Sar1 is converted from GDP into GTP form by GEF

45
Q

How are ER resident proteins excluded from the bud during COPII vesicle formation?

A

done by having a high SA:V ratio of the bud
so they don’t become trapped

46
Q

What is the purpose of COPII vesicle coating?

A

adaptor complex allows coat to be recruited
acts as a physical structure to stabilise the buds to make sure they form correctly
form a structural scaffold

47
Q

What occurs after the bud is formed in vesicular transport?

A

pinches off to create a coated vesicle crowded with receptors and cargo
this helps with exclusion of ER proteins to prevent their escape

48
Q

Smooth microsomes after centrifugation

A

have a low density and stop sedimenting and float at low sucrose concentration

49
Q

Rough microsomes after centrifugation

A

have a high density and stop sedimenting and float at high sucrose concentration

50
Q

How can ER be isolates from cells and used for reconsitution?

A

homogenization to break and vesiculate ER to create rough and smooth microsomes
put in tube with gradient of increasing sucrose concentration
centrifuge to seperate rough and smooth microsomes

51
Q

What acts as a GAP for Sar1?

A

Sec23

52
Q

When is secretion of vesicles blocked?

A

when coated vesicles cannot fuse with the target and deliver cargo
if they have a bulky coat it must be removed after the vesicle buds

53
Q

When is GAP activity enhanced?

A

following recruitment of the Sec13/31 coat
so the forming of the coat is coupled to this
leads to inactivation of GTPase Sar1
causes coat to dissassemble

54
Q

When Sar1 is in its active form

A

leads to formation of coat

55
Q

When Sar1 is in its inactive form

A

leads to dissassembly of coat
this cycling is necessary as they can’t function properly if activated all the time

56
Q

GDP mutants

A

will sequester GEFs so GTP dependent reactions will be suppressed

57
Q

GTPase mutants

A

cannot hydrolyse GTP so these normally have dominant negative effects

58
Q

What does expression of Sar1GDP cause?

A

inhibition of COPII formation

59
Q

COPII

A

GTPase- Sar1
coat- COPII
cargo- newly synthesised

60
Q

COPI

A

GTPase- Arf1
coat- COPI
cargo- retrieved & newly synthesised proteins

61
Q

Clathrin (TGN)

A

GTPase- Arf1
coat- clathrin
cargo- lysosomal proteins and regulated secretory proteins

62
Q

Clathrin (PM)

A

GTPase- ?
coat- clathrin
cargo- endocytosed material

63
Q

Trans goli network

A

major sorting station where a decision is made as to whether something will go straight to the mebrane or to the endosomal pathway

64
Q

Adaptor proteins

A

recognise and select cargo ensuring specificity
link coat to the membrane
recognise motifs in the cytoplasmic domains of membrane proteins
needed for all coated vesicles

65
Q

AP2

A

major clathrin adaptor
recognises a variety of peptide motifs and apendages
the beta 2 subunit is able to bind clathrin and the smaller subunits recognise the signals in transmembrane proteins

66
Q

Rough ER function

A

protein synthesis

67
Q

Smooth ER

A

sites of lipid synthesis and has roles in calcium storage

68
Q

How do advances in microscopy allow us to understand structure and function of membranes?

A

electron microscopy- size and exclusion of ribosomes, visualisation of protein tethers
live cell imaging- dynamics

69
Q

CLEM

A

correlative light and electron microscopy allows localisation of fluorescently labelled proteins to membrane contact sites

70
Q

Structure of membrane contact sites

A

ribosomes are excluded from contact sites
membranes are very close at 10-80nm
ER contacts can be short or long lived

71
Q

Tethers of membrane contact sites

A

protein-protein
protein-lipid
distance is usually around 30nm
inhibition of membrane fusion

72
Q

Membrane contact sites provide platforms for:

A

calcium mobilisation
lipid transfer
signalling
organelle division

73
Q

Sarcoplasmic reticulum

A

specialised ER for handling Ca2+ transients required for muscle contraction

74
Q

Contact sites in the ER

A

non-vesicular transfer of lipids
unidirectional

75
Q

LTPs

A

lipid transfer proteins
use concentration gradients of lipids to promote lipid transfer

76
Q

Neimann pick disease

A

affects spleen, liver, lungs, bone marrow, brain
happens when sphingomyelin accumulates in lysosomes

77
Q

How do MSCs participate in cell signalling?

A

ER tubule interacting with a later endosome
endosomes can drag sections of the ER

78
Q

Other functions of MSCs

A

regulating movement of EGFR into MVB
also involved in organelle fusion

79
Q

TDP-43

A

pathologically linked to ALS which regulates ER-mitochondria contacts

80
Q

Hereditary spastic paraplegia

A

disease associated mutations linked to REEP1 which leads to disruptions of ER mitochondria contacts

Molecular and cell biology (8 decks)

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