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BIOC0007 > Part 3 - protein trafficking and translocation > Flashcards

Part 3 - protein trafficking and translocation Flashcards

1
Q

How does a protein know where to go?

A

Signal sequence - exposed AA sequence at the end of a pp chain.
Signal patch - separate AA sequences until protein folds

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2
Q

Signal sequence in nuclar import?

A

Positive amino acids - arginine and lysine

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3
Q

Nuclear protein import proteins:

A 
NLS
Importin (karyopherin)
FG-repeats
Ran-GTP
Ran-GDP
Ran-GEF
Ran-GAP
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4
Q

Where is the Ran-GTP concentration higher?

A

In the nucleus

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5
Q

What does Ran-GEF do?

A

Converts Ran-GDP into Ran-GTP

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6
Q

What does Ran-GAP do?

A

Converts Ran-GTP into Ran-GDP

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7
Q

Signal sequence in mitochondrial import?

A

Amphipathic alpha helix - one end is hydrophilic, one end is hydrophobic

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8
Q

Is the protein folded or unfolded in mitochondrial import?

A

UNFOLDED!

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9
Q

How does it stay unfolded?

A

Hsp70

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10
Q

Basic process of mitochondrial import?

A

Protein is passed to TOM, which passes it to TIM, which passes it into the mitochondria.

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11
Q

What is required for translocation across the IMM?

A

Electrochemical gradient

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12
Q

What are the 2 potential mechanisms of Hsp70?

A

Binds to protein and pulls it into the matrix

Or binds to emerging protein and stops it from sliding back

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13
Q

What does Hsp60 do?

A

Helps the protein to be folded (after translocation)

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14
Q

How is a protein inserted into the OMM?

A

SAM - protein is passed to TOM, which then passes it on to SAM where the protein is folded into its mature structure.

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15
Q

What does a signal peptidase do when a protein is targeted for the IMM?

A

It cleaves the signal sequence, exposing a hydrophobic sequence (so it stays in the membrane)

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16
Q

How is a protein of the IMM moved to a different place in the membrane????

A

Via TOM and TIM-23 (into the matrix), signal sequence is cleaved. OXA complex then recognises a second sequence, leading to insertion into the IMM.

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17
Q

How does an IMS protein originate?

A

It is inserted intot he IMM by TOM and TIM, the hydrophobic sequence is then cleaved off by a protease in the IMS.

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18
Q

What does TIM-22 do?

A

integration of proteins into the IMM (post-TOM) - requires electrochemical gradient (and chaperones).

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19
Q

What is the difference between TIM-22 and TIM-23?

A

TIM-22 is involved in the insertion of proteins into the IMM, whereas TIM-23 inserts them into the matrix.

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20
Q

What is the signal sequence for ER translocation?

A

One positively charged/hydrophilic amino acid followed by a string of hydrophobic amino acids.

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21
Q

What is involved in ER protein transport?

A

A carrier - sec61

A receptor SRPR

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22
Q

What does SRP stand for?

A

Signal recognition particle

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23
Q

What is co-translational import?

A

SRP binds to the signal sequence (pause in translation). SRP binds to SRPR which brings the nescent chain to be inserted into the ER via sec61 (translation resumes in the ER).

24
Q

What happens once the nascent chain/ribosome have been released?

A

SRP and SRPR are released from the ribosome, SRPR moves along the membrane and SRP binds on and off. They are both both recycled: SRP binds to a new polypeptide chain and SRPR binds to another ribosome/SRP complex.

25
Q

In the translocation of a soluble protein, what happens once sec61has delivered it into the ER?

A

The signal sequence is cleaved, and a folded, mature, active form remains.

26
Q

What is a stop and start transfer sequence?

A

Involves hydrophobic regions - they stay in the membrane. The protein moves sideways, peptidase cleaves the signal and the protein becomes part of the membrane.

27
Q

What enzyme is involved in N-linked glycosylation?

A

Oligosaccharide transferase - it transfers sugars from the membrane-associated oligosaccharide onto an asparagine (N) residue.

28
Q

What AA sequence is recognised by OST?

A

NXS or NXT (X=any amino acid except glycine)

29
Q

What three types of ER translocation are there?

A

co-translational
post-translational
SRP-dependent/independent

30
Q

4 facts about the SRP Pathway?

A

Co-translational
GTP-dependent
SRP-dependent
N-terminal is cleaved or uncleaved

31
Q

Sec62/63 pathway?

A

SRP-independent
ATP-dependent
Co- or post-translational
Sec complex and BiP (an ATPase, acts like Hsp70)

32
Q

TRC 40 Pathway?

A

Post-translational
ATP-dependent
GPI added during PTM
C terminal membrane domain anchor

33
Q

What are two roles of chaperone proteins?

A

They help pps to be glycosylated and folded. They help mark incorrectly folded proteins for degradation.

34
Q

Where is the site of disulphide bond formation?

A

ER (oxidising environment)

35
Q

What is ERAAD and what happens?

A

ER-associated degradation. Incorrectly folded proteins get taken out of the ER by an unknown transporter to be degraded. This is done by polyubiquitination - marks the proteins for degradation to be taken to the proteosome.

36
Q

Are proteins folded or unfolded in ER import?

37
Q

3 methods to study protein translocation across a membrane?

A

Transfection approach - does an AA sequence act as a signal?
Biochemical approach - does a protein co-purify with a particular organelle?
Genetic approach - yeast as a model organism

38
Q

Where do proteins go once they’ve passed through the ER?

39
Q

What are the three pathway-types?

A

Retrograde/recylcing
Biosynthetic
Endocytic

40
Q

Two types of signal to direct proteins to the correct place?

A 
AA sequences (signal sequences/patches)
Protein modifications
41
Q

What is COPII? What are its associated proteins? What os the associated GTPase?

A

Transport from ER to Golgi.
Sec31/13/23/24/16
Sar1

42
Q

What is COPI? What are its associated proteins? What os the associated GTPase?

A

Forms a coated vesicle for transport from the Golgi to the ER. ARF.

43
Q

What is clathrin? What are its associated proteins? What os the associated GTPase?

A

Trans-Golgi to endosome, Plasma membrane to endosome, Golgi to lysosome. Clathrin AP1/2/3, ARF

44
Q

What are the 4 key processes of coat assembly?

A

1) Coat assembly and cargo selection
2) Bud formation
3) Vesicle formation
4) Uncoating

45
Q

Explain the process of vesicle fusion in 4 steps?

A

1) Vesicle docking - Rab-GTPase interacts with Rab-effector on the target membrane (tethering).
2) The SNAREs interact
3) Trans-SNARE complex forms, 1 alpha helix from v-SNARE, 3 from t-SNARE.
4) Cis-complex forms (on the same membrane). NSF and alpha-SNAP. ATP hydrolysis to break apart the cis-SNARE complex in order to recycle the SNAREs.

46
Q

What is KDEL a signal for?

A

Soluble ER-resident proteins. This sequence is at the C-terminus. Via COPI and COPII.

47
Q

How does the vesicle know to let go of the ER proteins?

A

The golgi is more acidic than the neutral ER so the soluble proteins are released in the ER (and bind in the golgi).

48
Q

What is the signal for ER-membrane resident proteins?

A

KKXX - a retrieval signal at the C terminus.

49
Q

What is O-linked glycosylation?

A

Sugars are added to the OH groups of Ser/Thr. Catalysed by glycosyl transferase enzymes.

50
Q

What are the 2 proposed mechanisms for Golgi organisation?

A

1) Vesicular transport

2) cisternal maturation

51
Q

What is the lysosome described as?

A

A bag of enzymes. The most acidic organelle in the cell.

52
Q

What sugar is added in the cis-Golgi?

A

Mannose-6-Phosphate

53
Q

What is NPXY a signal for?

A

LDL in plasma membrane - endocytosis signal. (AP2, clathrin coated pits). LDL is initially in the early endosome (acidic) which converts to an acidic lysosome where the LDL is degraded.

54
Q

What is the signal for EGF-R endocytosis?

A

YXX-(any hydrophobic amino acid) - cell proliferation

55
Q

How is an EGF signal switched off?

A

Ubiquitin tag. Endosome buds inwards forming a multi-vesicular body.

BIOC0007 (2 decks)

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