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BIOC 303 > 2.1 - Transmembrane Transport (Insertion into ER Membrane) > Flashcards

2.1 - Transmembrane Transport (Insertion into ER Membrane) Flashcards

1
Q

how is a protein inserted into the ER lumen/membrane?

A
  • ribosome docks onto ER membrane surface - injects polypeptide in the ER lumen as it is being synthesized - ER signal sequence cleaved off by signal peptidase
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2
Q

Type 1 ER protein

A

ER protein with one TM segment and an ER signal sequence (amino end in ER lumen)

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3
Q

Type 1 ER protein - topology

A

s18

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4
Q

Type 1 ER protein - hydropathy plot

A

s19

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5
Q

Type 2 ER protein

A

ER protein with one TM segment start-transfer sequence (amino end in cytosol)

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6
Q

Type 2 ER protein - topology

A

s20

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7
Q

Type 2 ER protein - hydropathy plot

A

s21

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8
Q

signal-anchor sequence

A

found in type 2 and 3 ER proteins

  • start-transfer sequence near N-term of protein that is a TMS recognized by SRP
  • positive is always facing the cytosol
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9
Q

why is the positive charge of the start-transfer sequence of type 2/3 ER proteins always towards the cytosol?

A

negatively charged lipids are present around the translocation channel

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10
Q

Type 3 ER

A

ER protein with one TM segment start-transfer sequence (amino end in ER lumen)

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11
Q

Type 3 ER protein - topology

A

s23

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12
Q

Type 3 ER protein - hydropathy plot -

A

probably same as type 2

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13
Q

Type 4 ER protein

A

multi-pass ER protein with a start transfer-sequence and a start-transfer sequence (can have multiple

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14
Q

positive-inside rule with alkaline phosphatase

A

1) hairpin loop inside = blue

2) hairpin loop outside = white

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15
Q

explain the charge gradient across the ER membrane at the translocon

A
  • cytoplasmic side of ER membrane (-)/basic
  • ER lumen side of ER membrane (+)/acidic
  • makes a charge gradient across the membrane, so harder to insert + residues across the membrane
  • expect that cytosolic loops will have more + charged residues
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16
Q

SecYEG

A

translocation channel/translocon of prokaryotes

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17
Q

Sec61aBg

A

translocation channel/translocon of eukaryotes

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18
Q

SecYEg

A

translocation channel/translocon of archaea

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19
Q

translocon

A

membrane channel in the ER membrane through which the polypeptide chain is transferred through

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20
Q

translocon structure

A

membrane channel protein made of 3 subunits

  • pore ring made of 6 isoleucines gated by a short helix when closed
  • SecY/Sec61 alpha
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21
Q

how can protein structure be determined experimentally?

A

X-ray diffraction of protein crystals

  • beam of X-ray (short wavelengths) directed across crystal
  • some X-rays are scattered in waves based on the structure and the diffraction pattern can be used to make an electron density map
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22
Q

SecYEG

Sec61aBg

A

???

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23
Q

what happens if you remove the plug from translocon

A

cell dies

- membrane loses impermeability to ions

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24
Q

what is the translocon pore ring made of

A

6 isoleucines (hydrophobic amino acid resides)

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25
Q

what is the function of the pore ring

A

forms a gasket around the polypeptide chain in transit so that it is ion tight

26
Q

what is the equivalent of the Sec61B subunit in bacterial translocon?

A

SecG

27
Q

what is the equivalent of the Sec61g subunit in bacterial translocon?

A

SecE

28
Q

what is the purpose of the seam opening of Sec complex

A

lateral opening along seam allows the translocating peptide chain to access the lipid bilayer

29
Q

how is the TMS released from the Sec complex

A

two halves of SecY/Sec61a opening

30
Q

describe secondary protein structure of porins

A

beta-barrel proteins

31
Q

why are porins not found in the IM of bacteria

A

???

32
Q

two modes of protein translocation (2)

A

1) co-translational translocation

2) post-translational translocation

33
Q

co-translational translocation

A

translocation during translation

34
Q

post-translational translocation

A

translation before translocation. Chaperone proteins maintains the proteins in a loosely folded state

35
Q

how does post-translational translocation work in bacteria?

A

SecA ATPase uses ATP to push the protein across the SecY complex (ratchet mech)

36
Q

how does post-translational translocation work in yeast?

A

BiP ATPase binds polypeptide chains as it emerges from the pore (pulling mechanism)

37
Q

what kind of translocation occurs across the ER membrane

A

co-translational translocation

38
Q

what does the translocator need to feed the polypeptide through the pore

A

accessory proteins (SecA ATPase in bact, BiP ATPase in euk)

39
Q

is yeast prokaryotic or eukaryotic

A

eukaryotic (has a nucleus)

40
Q

BiP ATPase function (2)

A
  • protein that pull proteins in post-translational translocation (yeast) across ER membrane
  • also acts as a chaperon
41
Q

OST complex location

A

oligosaccharide transferase complex

- located in ER lumen

42
Q

OST complex function

A

glycosylate proteins that are in the ER lumen

43
Q

what proportion of eukaryotic proteins are glycosylated

A

50%

44
Q

why are so few proteins in the cytosol are glycosylated

A

OST (oligosaccharide transferase) are only located in the ER lumen

45
Q

how does the carbohydrate layer of the ER useful for the cell

A

protects cells against mechanical and chemical damage

46
Q

how does glycosylation in ER lumen work

A

N-linked glycosylation - oligosaccharide transferred to Asn on polypeptide via oligosaccharide transferase

47
Q

what holds the preformed oligosaccharide in the ER lumen prior to it being used for glycosylation

A

dolichol (special lipid) holds preformed oligosaccharide (14 sugar units) in ER lumen via a high energy pyrophosphate bond

48
Q

where does O-linked glycosylation occur and what proportion is it performed in

A

In the Golgi

49
Q

what is O-linked glycosylation

A

preformed oligosaccharide linked to OH group of serine (S) or threonine (T)

50
Q

what are oligosaccharides used for

A

used as tags to mark the state of protein folding

51
Q

calnexin

A

ER chaperone protein

- binds to oligosaccharide on incompletely folded proteins and retains them in the ER until the protein is folded

52
Q

calreticulin

A

ER chaperone protein - binds to oligosaccharide on incompletely folded proteins and retains them in the ER until the protein is folded

53
Q

lectin

A

carbohydrate-binding proteins

54
Q

PDI

A

protein disulfide isomerase

- protein in the ER that helps the formation of S-S bonds

55
Q

where do disulfide bonds form

A

in the ER usually, the reducing environment makes it hard for S-S bonds to form in the cytosol

56
Q

GPI

A

glycophosphatidylinositol anchor

57
Q

GPI function

A

1) protein transportation
2) cell adhesion
3) cell wall synthesis
4) cell surface protection

58
Q

how is GPI added onto proteins?

A

ER protein, GPI-transamidase, cleaves off C-terminal transmembrane segment and attaches GPI anchor to C-terminus of protein

59
Q

what kind of proteins is GPI found on

A

plasma membrane proteins

60
Q

HA

A

influenza hemagglutinin - antigenic glycoprotein responsible for binding of virus to cell (target is sialic acid)

61
Q

why is trypanosoma brucei so potent

A

parasite that is able to cross blood brain barrier

  • VSG (variable surface glycoprotein) coat prevents the immune system from accessing the PM epitopes of the parasite
  • allows it to evade the immune system
  • antigenic variation allows it to avoid specific immune responses

BIOC 303 (14 decks)

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