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bioc2002 > Protein trafficking > Flashcards

Protein trafficking Flashcards

1
Q

how do proteins get to a location?

A

sorting signal

if no sorting signal then stays in cytosol

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2
Q

how do proteins get to a location?

A

sorting signal

if no sorting signal then stays in cytosol

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3
Q

types of sorting signal?

A

patch- AAs make patch in 3d form

sequence- AAs at the end of a chain

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4
Q

what type of sequence codes for nuclear import?

A

K/R rich

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5
Q

what type of sequence codes for mitochondrial import

A

Amphipathic/ alpha helix

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6
Q

what type of sequence codes for ER import

A

hydrophobic AAs

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7
Q

what size protein can fit through the nuclear pore

A
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8
Q

where can a signalling sequence be recognised

A

membrane bound receptor or soluble receptor

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9
Q

where do proteins get synthesised

A

in cytosol ( ribosomes)

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10
Q

how do proteins know to go to the nucleus

A

nuclear localisation signal

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11
Q

what makes up the nuclear pore complex

A

nucleoporin proteins in a basket arrangement

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12
Q

what size proteins can fit through the nuclear pore?

A

50kD or 5kD ask someone

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13
Q

what are the nuclear import receptors

A

importin part of karyopherin family

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14
Q

what is ran GTP

A

small GTP binding protein

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15
Q

what is ran GTP

A

smole GTP binding protein

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16
Q

what does exportin recognise on the inner membrane?

A

L rich domain

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17
Q

what does exportin recognise on the inner membrane?

A

L rich domain

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18
Q

types of sorting signal?

A

patch- AAs make patch in 3d form

sequence- AAs at the end of a chain

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19
Q

what type of sequence codes for nuclear import?

A

K/R rich

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20
Q

what type of sequence codes for mitochondrial import

A

Amphipathic/ alpha helix

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21
Q

explain protein import to the mitochondria

A

ATPase Hsp70 in cytosol binds to protein being transported to stop folding proteins signal sequence binds to TOM (Translocon of the Outer Membrane)
protein goes through TOM then TIM (Translocon of the Inner Membrane)
in TIM localisation sequence cleaved by protease, mt Hsp70 binds
Hsp60 also binds helps translocation

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22
Q

when is the only time a chemical gradient is needed for protein trafficking

A

across the inner mitochondrial membrane.

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23
Q

where can a signalling sequence be recognised

A

membrane bound receptor or soluble receptor

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24
Q

where do proteins get synthesised

A

in cytosol ( ribosomes)

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25
Q

how do proteins know to go to the nucleus

A

nuclear localisation signal

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26
Q

what makes up the nuclear pore complex

A

nucleoporin proteins in a basket arrangement

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27
Q

what size proteins can fit through the nuclear pore?

A

50kD or 5kD ask someone

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28
Q

what are the nuclear import receptors

A

importin part of karyopherin family

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29
Q

how does the importin work

A 
soluble receptor (importin) makes contact with F G (gphenylalanine glycine repeats) importin binds to the protein and takes it through nuclear pore complex
importin and protein dissociat when inside the nucleus
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30
Q

what is ran GTP

A

smole GTP binding protein

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31
Q

what is the soluble receptor that helps in the export of proteins from the nucleus

A

EXPORTIN
part of karyopherin family
nuclear export receptor

32
Q

what does exportin recognise on the inner membrane?

A

L rich domain

33
Q

explain the Ran-GTP cycle

A

maintans balance between import and export
Ran GDP in cytosol
enters nucleus
interacts with Ran-Guanine nucleotide exchange factor (Ran-GEF) swaps GDP for GTP.
Ran GEF bound to chromatin
Ran-GTP leaves nucleus
hydrolysed by Ran-GAF (ran guanine nucleotide activating factor)
Ran GaP free in cytosol
gradient of Ran GTP to Ran GDP assists import export

34
Q

explain nuclear import

A

protein with NLF binds to importin
importin contacts FG repeats in nuclear pore complex and takes target protein through the pore
in nucleus Ran GTP binds to importin- displaces the protein being taken to the nucleus
importin moves out of the nucleus
Ran GAP hydrolyses Ran GTP to Ran GDP.
Ran GDP has lower affinity for importin so dissociates.

35
Q

nuclear export

A

protein with nuclear export signal binds exportin WITH RAN GTP
travels through the membrane binds Ran GAP hydrolyses Ran GTP to Ran GDP which falls off exportin.
exportin goes back through the pore and repeat

36
Q

why and how are proteins unfolded

A

protein channel much smaller than nuclear pore have to be unfolded to fit
to keep the protein unfolded other proteins bind only folds in mt

37
Q

explain protein import to the mitochondria

A

proteins signal sequence binds to TOM (Translocon of the Outer Membrane)
protein goes through TOM then TIM (Translocon of the Inner Membrane)

38
Q

when is the only time a chemical gradient is needed for protein trafficking

A

across the inner mitochondrial membrane.

39
Q

How do proteins get to Outer mt Memebrane

A

example Porin
binds to TOM kept unfolded in intermembrane space by chaperone
goes through SAM (Sorting and Association Material) (in outer membrane)
SAM helps the protein fold and it diffuses away in the membrane

40
Q

How does an Inner Mt Membrane protein reach the Inner membrane

A

Protein goes through TOM
goes through TIM
signal sequence cleaved
reveals stop transfer sequence -hydrophobic
stays in the membrane
protein becomes membrane spanning of the inner membrane

41
Q

how does a protein get to the inter membrane space/ inner membrane
attatch to innermembrane with a domain in the inter membrane cells

A

Goes through TOM
through TIM- signal sequence cleaved uncovers second signal sequence and enters matrix
recognised OXA complex (complex in inner membrane mediates movement of proteins made in mt) and the second signal (hydrophobic) moves laterally in the inner membrane

42
Q

how does a protein get to the inter membrane space

A

Goes through TOM
through TIM- signal sequence cleaved uncovers second signal sequence and enters matrix
recognised OXA complex (complex in inner membrane mediates movement of proteins made in mt) and the second signal (hydrophobic) moves laterally in the inner membrane
the rest of the protein is cleaved becomes membrane of inter membrane space

43
Q

what is a signal sequence

A

N terminus
positively charged AA (one or more)
followed by 6-12 hydrophobic AAs

44
Q

what is the SRP

A 
Signal recognition particle
in cytosol
has a region that binds to signal sequence and region that binds to ribosome 
complex brought to ribosome
complex of 6 proteins and 1 RNA
45
Q

what is the SRP R

A

receptor for SRP recognises SRP+ protein (+ ribosome) on ER membrane- goes through Sec 61- translocon of ER membrane

46
Q

How do proteins get synthesised into ER directly

cotranslation?

A

nascent protein plus ribosome binds to SRP brings chain to ribosome which binds SRP R in ER membrane
SRP and SRP R dissociate-
ribosome translates directly into ER
energy comes from hydrolysis of GTP to power the assembly of translocon and chain complex
ribosome translates protein directly into the ER leaving the signal sequence in the membrane which is cleaved

47
Q

post translational movement to the ER

A

similar to mt
Hsp70 keeps it unfolded
protein directed to Sec62,62,71,72 complex goes through sec 61 channel
Hsp70 or BiP used to pull protein through/stop sliding back
the signal sequence on the protein enters Sec61 and is cleaved by signal peptidases

48
Q

membrane protein of ER

A

signal into Sec61, cleaved stop sequence remains in membrane difusses laterally
(multiple membrane spanning unit proteins have several stop sequences which remain in the membrane)

49
Q

glycosylation in ER

A

along with translocation is glycosylation
on asparagine residues

N-X-S
N-X-T
oligosacharyl transferase transfers oligosaccharide to the N residue
utilised to see how far through the translocation process a protein has gone
like a ER tag

50
Q

where do disulphide bridges form

A

ER

51
Q

explain the rocess of vesicles fusing

A

1) trans snare complex formed
2) membranes fuse
3) contents released
4) cis snare formed
5) N-ethylmaleimide-sensitive factor (NSF) ( an AAA ATPase)- undoes snare complex dissociates- Alpha snap= accessory to NSF

52
Q

where can a protein go from the ER

A

endosome, Golgi, lysosome, cell membrane, vesicle

53
Q

function of ER

A

proteins are glycosylated and folded

54
Q

explain vesicular transport

A

once the protein has entered the ER it never crosses another membrane
protein coat causes the membrane to bud ( mechanical force)
coat promotes membrane budding
the proteins that go inside the vesicle are specific for the coat
membrane receptors that end up in vesicle act as receptor for target protein.
each coat has a GTP binding domain
snare proteins for assembly/ dissasembly

55
Q

soluble secreted protein

A

COPII
cis golgi
medial, trans golgi
constutive secretion- regardless of external factors

56
Q

COPI

A

cis GOLGI to ER

57
Q

Clathrin

A

trans GOLGI TO ENDOSOME
Plasma membrane to endosome
golgi to lysosme, melanosome or platelet vesicle

58
Q

ER to Cis GOLGI

A

COPII +
COAT: SEC23/24, SEC13/31, SEC16
GTPase:Sar1

59
Q

cis GOLGI to ER

A

COPI
Coat:coatomers conatining COP
GTPase:ARF

60
Q

trans GOLGI TO ENDOSOME

A

either

1) Clathrin + AP1+ ARF
2) Clathrin + GGA+ ARF

61
Q

Plasma membrane to endosome

A

Clathrin + AP2+ ARF

62
Q

golgi to lysosme, melanosome or platelet vesicle

A

AP3 + ARF

63
Q

what do GTPases do

A

control coat recruitment

64
Q

direct fusion

A

happens between late endosome/lysosme
the 2 compartments fuse to make a hybrid organelle
lysosme specific properties removed in vesicle to switch back

65
Q

Endocytosis

A

Clathrin coated vesicle at plasma membrane
binds to adapter e.g AP2
clathrin deforms membrane
dynein pinches off vesicle
once vesicle is forme coat dissociates almost immediately

66
Q

what makes sure vesicle binding is specific?

A

SNAREs
specificity of snares V snares and T snares
need bundle of 4 alpha helices
tetanous toxin cleaves snares
Rab GTP binds to Rab effector on target membrane brings the two together.
leads to the assembly of snares

67
Q

explain the rocess of vesicles fusing

A

1) trans snare complex formed
2) membranes fuse
3) contents released
4) cis snare formed

68
Q

How do soluble proteins get to the ER

A

constantly lost and brought back
COPII always takes some soluble ER proteins with it to Cis Golgi
KDEL sequence- ER localisation system
cis GOLGI has recognition for KDEL R
COPI takes KDEL + KDEL R back to ER
ER protein only binds KDEL R in Golgi because it is more acidic there because

69
Q

how do transmembrane proteins get back to ER

A

Retrieval signal KKXX
CopII takes it to Golgi
CopII brings it back

70
Q

how does a plasma membrane protein reach its target

A

COPII coated vesicles take what will be a plasma membrane protein to the cis golgi
protein associates with cis golgi membrane
moves to medial then trans golgi
packaged from trans golgi- constitutive secretion

71
Q

soluble secreted protein

A

COPII
cis golgi
medial, trans golgi
constutive secretion

72
Q

regulated secretion

A

COPII
golgi
regulated secreted vesicle
need a signal to be released

73
Q

what are the two theories for moving through the golgi

A

1) vesicular theory- movement of proteins through golgi via vesicles
2)cisternal maturation- cisterna matures and takes on role of neighbouring part . vesicles transfer the characteristic molecules back to new part taking its role
2=favoured

74
Q

getting proteins to the lysosome

A

lysosome hydralase precursor from ER
phosphate added to manose-> manose-6-phosphate
manose-6-phosphate R in late golgi drawn into clathrin coated vesicle with MP6 receptor in it
vesicle uncoats and taken to late endosome which is kept acidic by ATPase pump causes the dissociation of MP6 and MP6 R

75
Q

O-linked glycosylation

A

sugar added to -OH group of S T

catalysed by a series of glycosyl transferase enzymes in golgi

76
Q

without adding mannose 6 P

A

mucolipidosis type II

poor growth/skeletal problems

77
Q

endocytosis

A

LDL through LDLR

and EGF

bioc2002 (4 decks)

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