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Cells and Immunity > Intracellular traficking > Flashcards

Intracellular traficking Flashcards

1
Q

What is the total cell volume of the cytosol?

A

50-60%

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2
Q

What is the total cell volume of the mitochondria?

A

20%

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3
Q

What is the total cell volume of the rough ER cisternae

A

6%

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4
Q

What is the total cell volume of the nucleus?

A

6%

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5
Q

What is the total cell volume of the peroxisomes?

A

1%

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6
Q

What is the total cell volume of the lysosomes?

A

1%

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7
Q

What is the total cell volume of the endosomes?

A

1%

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8
Q

What are the advantages of compartmentalisation?

A

Reactions confined to particular regions of the cell.

Reactions don’t interfere with each other.

Greater efficiency through more organised reactions/processes.

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9
Q

What problems arrise from compartmentalisiation

A

Need to deliver all components to correct compartment - targeting

Need to have mechanisms to specifically move components around the cell

Need to be able to move components in and out of compartments

Need to maintain organelle, compartment and cell integrity.

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10
Q

What is needed to get proteins and other cellular constituents to the correct compartment?

A

Specific targeting sequences

Specific recognition mechanisms

Specific delivery mechanisms

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11
Q

What are common mechanism for intracellular trafficking?

A

Protein recognition and specific protein-protein interactions

G protein cycles

cf. Cell signalling

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12
Q

What are targeting sequences?

A

Cellular postcode

short sequences of amino acids within the sequence of the protein which tell the machinery where the protein should go

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13
Q

What are the types of targeting sequences?

A

Signal sequence

Transmembrane domains

Organelle specific uptake sequences

Nuclear localisation sequences

Various protein and lipid binding domains.

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14
Q

For proteins going to the endoplasmic reticulum where is the usual signal location within protein?

A

N-terminal

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15
Q

For proteins going to the mitochondrion where is the usual signal location within protein?

A

N-terminal

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16
Q

For proteins going to the chloroplast where is the usual signal location within protein?

A

N-terminal

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17
Q

For proteins going to the peroxisome where is the usual signal location within protein?

A

C-terminal

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18
Q

For proteins going to the nucleus where is the usual signal location within protein?

A

internal but need to end up on outside of protein once folded

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19
Q

For proteins going to the endoplasmic reticulum what is the usual nature of the signal?

A

“core” of 6-12 mostly hydrophobic amino acids often preceeded by one or more basic amino acid

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20
Q

For proteins going to the mitochondrion what is the usual nature of the signal?

A

3-5 nonconsecutive Arg or Lys residues often with Ser, Thr, and small hydrophobic amino acid residues and
poor in Glu and Asp residues

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21
Q

For proteins going to the chloroplast what is the usual nature of the signal?

A

No common sequence motifs
Generally rich in Thr, Ser and small hydrophobic amino acid residues
Poor in Glu and Asp residues

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22
Q

For proteins going to the peroxisome what is the usual nature of the signal?

A

Usually Ser-Lys-Leu at extreme C-terminus

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23
Q

For proteins going to the nucleus what is the usual nature of the signal?

A

One cluster of 5 basic amino acids, or two smaller clusters of basic residues separated by ~10 amino acids

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24
Q

For proteins going to the endoplasmic reticulum, is the signal removed?

A

Yes

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25
Q

For proteins going to the mitochondrion, is the signal removed?

A

Yes

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26
Q

For proteins going to the chloroplast, is the signal removed?

A

Yes

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27
Q

For proteins going to the peroxisome, is the signal removed?

A

No

28
Q

For proteins going to the nucleus, is the signal removed?

A

No

29
Q

What is the structure of the nuclear pore complex?

A

On the cytoplasmic side it is a ring structure with filaments that project into the cytosol
On the inner side of the nucleus is a basket filament structure with a terminal ring

30
Q

What is the proposed mechanism for nuclear import?

A

Cargo protein with a nuclear localisation sequence
Protein is recognised by importins
Cargo importin complex together with GDP ran is recognised by the cytosolic side and transported into nucleus
Once there RCC1 protein cause exchange of GDP on ran and allows GDP to bind.
Changing shape of ran protein to be active causing release of cargo into nucleus separating it from the importins.
The ran GDP importin complex is recognised by the basket on nuclear side of the pore and transported back into the cytosol

31
Q

What do G proteins act as?

A

Molecular switches

32
Q

What is the on state for a G protein?

A

GTP on state

33
Q

What is the off state for a G protein?

A

GDP off state

34
Q

What is the proposed mechanism for nuclear export of a protein?

A

Cargo protein has NES (nuclear exclusion sequence) on surface.
GDP ran activated by RCC1.
Interacts with exportin changing the shape of it so it recognises the NES on cargo
Cargo complex recognised by basket side of pore and is transported through pore.
Once in cytosol a GTPase activating protein for ran hydrolyses GTP.
Change causes confirmation of exportin so it realeases the cargo protein.
Exportin and ran both recognised by nuclear pore and imported back into nucleus

35
Q

What defines an NLS (nuclear localisation sequence)?

A

High in basic amino acids

36
Q

What defines an NES (nuclear exclusion sequence)?

A

Rich in leucine

37
Q

What are peroxisomes?

A

Small organelles 0.2-1 mm in dia

Lack DNA

Single membrane

Enlarged by addition of protein and lipid

Enzyme contents vary but all enzymes present use molecular oxygen to oxidise substrates forming H2O2 (Catalase breaks this down to H2O)

Abundant in liver cells

38
Q

How is a protein taken into a peroxisome?

A

protein interacts with iron molecules (heme) and forms tetramer.
Transport protein interacts with SKL uptake targeting sequence in the cytosol.
Complex is recognised by receptor pore channel on surface of peroxisome called the pex14p receptor.

39
Q

How is the signal sequence removed after targetting for proteins destined for the mitochondria (and chloroplast)?

A

removed by proteases

40
Q

Where does import of proteins occur for the mitochondria (and chloroplast)?

A

sites of close contact between inner and outermembranes

41
Q

What are chaperones?

A

bind and maintain unfolded state of newly synthesised proteins

ATP dependent process

42
Q

What are Hsc70 (heat shock 70 protein) and mitochondrial import stimulating factor?

A

Chaperones

43
Q

How is a protein imported into the mitochondrial matrix?

A

Newly synthesised precursor protein has N terminal mitochondrial matrix targetting sequence.
A chaperone attaches.
Either Hsc70 which can interact with transmembrane proteins Tom 20 and 22.
Or MSF which can interact with transmembrane protein Tom 70 and Tom 37, and once interacted with outer surface it would then get passed down to Tom 20 and Tom 22.
Tom 20 and Tom 22 complex along with protein interacts with Tom 40 which the protein is fed through into the intermembrane space.
On inner membrane Tim 44, Tim 23/17 form a channel that allows protein to be poked through to the inner matrix.
On inside the protein binds with another chaperone so that it doesn’t begin to fold until its all in the matrix

44
Q

When are heat shock proteins made in higher amounts?

A

When cells are stressed and allows them to deal with proteins that could have potentially become unfolded due to temp stresses

45
Q

Does the delivery of proteins from the RER into the ER occur once the proteins are made or during it?

A

During it

It is a cotranslational process

46
Q

What is a microsome?

A

a fragment of endoplasmic reticulum

47
Q

How are proteins targeted for secretion transported?

A

mRNA starts translating protein with the signal sequence
This sequence is recognised by the signal recognition particle (SRP).
SRP binds to ribosome and nascent section of protein preventing further translation until ribosome docks to surface of ER.
Once SRP ribosome complex attach to SRP receptor the translocon opens and ribosome docks onto it.
Newly synthesised part of protein pushes into translocon, releasing SRP and ribosome continues to make more of the protein pushing into the lumen of the ER.
Once signal sequence is in it is cleaved off.
Inside lumen the chaperone proteins interact to help keep it not start to fold until all the protein is produced
Once protein is complete it is released into lumen and chaperone proteins disengage.

48
Q

What is the KDEL sequence?

A

Lys-Arsp-Glu-Leu
secreted
Golgi to ER
COP I vesicle type

49
Q

What does a COP I vesicle type mean?

A

Golgi to ER

50
Q

What does a clathrinn vesicle type mean?

A

plasma membrane to endosome

51
Q

What does a COP II vesicle type mean?

A

ER to Golgi

52
Q

What is Brefeldin A?

A

Fungal metabolite

Blocks transport from ER to Golgi

53
Q

What are the small GTP binding proteins for clathrinn?

A

ARF

54
Q

What are the small GTP binding proteins for COP I?

A

ARF

55
Q

What are the small GTP binding proteins for COP II?

A

Sar1

56
Q

What structure does Clathrin have?

A

Triskelion
3 heavy chains
3 light chains
each heavy chain has a binding site for assembly particles

57
Q

What does Dynamin do?

A

GTPase

binds to neck of forming vesicle to aid budding

58
Q

What are key proteins for vesicle fusion to occur?

A

SNARE, SNAP, and Rab proteins

59
Q

Using SNARE, SNAP, and Rab proteins how does a vesicle fuse?

A

V SNAREs on vesicle interact with T SNAREs on membrane by winding together allowing vesicle to fuse.
SNAP unwinds SNARE proteins
Rab is a G protein on surface that acts as an identifier and binds to effector protein to aid in stabilisation.

60
Q

How do lipids help to specify comparments?

A

phosphorolated lipids only found in certain areas

61
Q

What are membraneless organelles

A

distinct compartments within a cell not enclosed by a lipid membrane

62
Q

What are examples of membraneless organelles

A

Nucleolus and nuclear speckles in nucleus

P bodies and P granules in cytosol

63
Q

what did Randy Schekman do?

A

Discover set of genes required for vesicle traffic

Using yeast as a model system

64
Q

What did James Rothman do?

A

unravelled protein machinery that allows vesicles to fuse with their targets to permit transfer of cargo.

65
Q

What did Thomas Sudhof do?

A

revealed how signals instruct vesicles to release their cargo with precision.

Cells and Immunity (3 decks)

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