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MCB2050 > Unit 3: Endomembrane System and ER > Flashcards

Unit 3: Endomembrane System and ER Flashcards

1
Q

What is the Endomembrane System?

A
  • dynamic, coordinated network of all cell’s organells and related structures except peroxisomes, chloroplasts and mitochondria
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2
Q

What does the Endomembrane System do?

A
  • exchange/ traffic lots of materials between organelles
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3
Q

What does the cell use to traffick things in the Endomembrane System?

A
  • small membrane bound vesicles
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4
Q

What organelles does the Endomembrane System consist of?

A
  • Endoplasmic Reticulum
  • Golgi
  • Endosome
  • Lysosomes/Vacuoles
  • Secretory granules
  • Plasma membrane
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5
Q

How are the organelles of the endomembrane system structurally and functionally different?

A
  • particular set of proteins
  • unique set of activities
  • compartmentalization and functional diversity
  • conserved in eukaryotes
  • dynamic structures
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6
Q

Step One Vesicle Transport

A
  • cargo containing vesicle buds of donor membrane
  • vesicle COAT proteins selects which donor membrane and lumenal cargo proteins can enter the nascent transport vesicle
  • and regulate vesicle formation and budding
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7
Q

Step Two Vesicle Transport

A
  • nascent vesicle tranported through cytosol to recipient membrane compartment
  • vesicle RECEPTOR proteins regulate the intracellular trafficking of the vesicle to the proper recipient of the mebrane
  • involves molecur motors and cytoskeleton highways
  • motor proteins direct vesicle movement within the cell by linking to vesicle surface and to cytoskeleton elements
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8
Q

Step Three Vesicle Transport

A
  • vesicle FUSES with proper recipient membrane compartment
  • RECEPTOR proteins also regulate veiscle recipient membrane fusion
  • vesicle donor membrane and lumenal cargo proteins incorporated into recipient compartment
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9
Q

Step Four Vesicle Transport

A
  • entire process of budding and fusion is repeated and can occur in the reverse direction
  • other receptor proteins regulate RECYCLING of any proteins that escaped to recipient compartment and bring back to donor membrane compartment
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10
Q

Trafficking Pathway: Biosynthetic Pathway

A
  • ER to
  • Golgi to
  • Endosome to
  • lysosome/vacuole OR plasma membrane
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11
Q

Trafficking Pathway: Secretory Pathway: Constitutive Secretion

A
  • ER derived materials continually to Golgi to PM
  • may release to extracellular space
  • Secretory transport vesicle membrane componenets are incorporated into PM
  • and vesicle lumenal cargo released into extracellular space
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12
Q

Trafficking Pathway: Secretory Pathway: Regulated Secretion

A
  • occurs only in SPECIALIZED cells
  • ER derived materials from Golgi stored in Secretory GRANULES
  • in RESPONSE to cellular SIGNAL
  • granules fuse with PM and
  • release (exocytosis) lumenal cargo into extracellular space
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13
Q

Neurotransmitter release by nerve cells is what trafficking pathway?

A
  • Regulated secretion of the secretory pathway
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14
Q

Trafficking Pathway: Endocytic pathway

A
  • operates in opposite direction to secretory pathway
  • moves INTO the cell
  • materials from PM destined for DEGRADATION
  • and extracellular space incorporated into the cell (endocytosis)
  • transported into the endosomes and lysosomes (vacuoles)
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15
Q

What organelle is the starting point for the secretory and biosynthetic pathways?

A

Endoplasmic reticulum

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16
Q

Which organelle has the largest surface area? Describe the organelle.

A

Endoplasmic reticulum

  • it is highly complex network of membrane-enclosed
  • rod-like tubules
  • and sheet-like cisternae
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17
Q

Two shapes of the ER structure?

A

ER tubules and cisternae

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18
Q

What mediates shape of the ER tubules and cisternae?

A
  • reticulons
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19
Q

What are reticulons?

A
  • unique ER integral membrane proteins
  • hair pin V shaped secondary structure
  • regulate curvature of the ER membrane (lipid bilayer)
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20
Q

Are ER tubules and cisternae static?

A
  • No, they are highly dynamic and are in constant flux

- undergo constant bending, fusion, fission etc

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21
Q

Two classic subdomains of the endoplasmic reticulum.

A
  • Rough ER and

- Smooth ER

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22
Q

Structure and role of the RER

A
  • mostly cisternae with bound ribosomes

- involved in protein and membrane phospholipid synthesis

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23
Q

Structure and role of the SER

A
  • mostly curved tubules lacking ribosomes

- involved in Ca2+ storage and hormone synthesis

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24
Q

3 examples of ER subdomains other than the 2 classic

A
  • outer nuclear membrane
  • mitochondria and plasma membrane- associated membranes (MAM and PAM)
  • ER Exit Sites (ERES)
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25
Q

What are the two main sites for protein synthesis?

A
  1. free ribosomes in cytosol

2. RER - ER ‘membrane-bound’ ribosomes

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26
Q

What is the fate of the nascent protein in the cytosol (synthesized in free ribosome in cytosol?

A
  • from the free ribosome in the cytosol
  • fate is to remain in the cytosol
    OR
  • target (postranslationally) to proper intracellular destination (i.e. mitochondria, chloroplasts, nucleus)

*recall all translation of mRNA begins on a free ribosome in the cyotosol - moves to RER using cotranslational translocation

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27
Q

What is the fate of nascent soluble or membrane protein (synthesized in the RER)?

A
  • to remain in the RER
  • or localize laterally in ER or other ER subdomain
  • OR
  • target (transport vesicles) from ER to another post-ER compartment in endomembrane system (golgi, endosome, lysosome, PM)
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28
Q

Step One: Cotranslational translocation of soluble protein into RER lumen
- Where is the signal sequence located and what is it?

A
  • on N-terminus of nascent polypeptide
  • stretch of 8-15 hydrophobic acids
  • serve as ER targeting signal
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29
Q

Step One: Cotranslational translocation of soluble protein into RER lumen
- What recognizes the signal sequence? What is it?

A

SRP - signal recognition particle

- ribonucleotide consisting 6 proteins and 1 small RNA

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30
Q

Step One: Cotranslational translocation of soluble protein into RER lumen
What does the SRP do?

A

SRP binds to the ribosome and stops protein translation

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31
Q

Step Two: Cotranslational translocation of soluble protein into RER lumen
- What targets the entire complex?

A
  • SRP targets complex (ribosome, stalled polypeptide, mRNA) at surface of ER
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32
Q

Step Two: Cotranslational translocation of soluble protein into RER lumen
What does the SRP bind to

A

SRP receptor

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33
Q

What is the SRP receptor

A

hetero-dimeric ER integral membrane protein complex

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34
Q

Step Two: Cotranslational translocation of soluble protein into RER lumen
What is the docking site?

A
  • cytosolic facing domains of SRP receptor (docking site for SRP)
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35
Q

Step Three: Cotranslational translocation of soluble protein into RER lumen
When the SRP released from SRP receptor, what occurs simultaneously?

A
  • ribosome binds the translocon (Sec61) on the cytosolic side
36
Q

Step Three: Cotranslational translocation of soluble protein into RER lumen
What does SRP release require?

A

GTP hydrolysis

- conformational change in SRP and SRP receptor

37
Q

Step Three: Cotranslational translocation of soluble protein into RER lumen
What does ribosome to translocon binding induce?

A

continuation of protein translation

38
Q

Step Three: Cotranslational translocation of soluble protein into RER lumen
What is the interaction within the interior of translocon?

A
  • signal sequence interacts with interior
  • results in conformational change in translocon subunits
  • opening/widening of pore ring and displacement of plug
39
Q

Step Four: Cotranslational translocation of soluble protein into RER lumen
What happens to the signal sequence as it enters the lumen

A
  • cleaved by signal peptidase
40
Q

What is the signal peptidase?

A

ER integral membrane protein (protease) located next to translocon
- catalytic domain faces ER lumen

41
Q

Step Four: Cotranslational translocation of soluble protein into RER lumen
What happens to the cleaved nascent protein as it enters the lumen?

A
  • glycosylated and begins to be properly folded by reticuloplasmiins
42
Q

What is a reticuloplasmin?

A

Chaperones at operates in the ER

- bind to nascent proteins and mediate their proper folding and oligomeric assembly

43
Q

Step Four: Cotranslational translocation of soluble protein into RER lumen
What happens after protein translation and translocation is terminated?

A
  • ribosome is released from translocon

- ribosome returns to cytosol for another round of protein import

44
Q

Step Four: Cotranslational translocation of soluble protein into RER lumen
What does the release of the ribosome lead to?

A
  • closing of translocon pore ring

- return of the plug

45
Q

What are the two mechanisms of maintaining membrane asymmetry?

A
  • lipid composition

- modification and orientation of integral membrane proteins

46
Q

How are integral membrane proteins modified and oriented?

A
  • lumenal domains of IMP
  • – remains in the lumen of endomembrane compartments; glycosylated
  • – forms extracellular domain on exoplasic face of PM
  • cytoplasmic domain always in cytoplasm
47
Q

What is the main difference in translocation and translation of soluble protein into the ER membrane and insertion of integral membrane protein into ER lumen?

A

mechanistic differences resulting in mature protein being inserted/anchored into the ER membrane

48
Q

Step One: co-translational insertion of an integral membrane protein into RER

A
  • term enters translocon
  • 1st/only TMD enters translocon interior
  • hydrophobic TMD interacts with hydrophobic pore ring stops anything further translocation of nascent protein through translocon
49
Q

What is the TMD?

A

trans membrane domain

  • typically alpha helical
  • hydrophobic 16-25 a.a.
  • serves as stop-transfer sequence (stop transferring protein through bilayer) of translocon
50
Q

Step Two (Nlumen-Ccytosol): co-translational insertion of an integral membrane protein into RER

A
  • interaction TMD with hydrophobic pore ring blocks translocation and signalss the translocon to open laterally
  • TMD segment of protein released laterally into membrane lipid bilayer
51
Q

Step Three (Nlumen-Ccytosol): co-translational insertion of an integral membrane protein into RER

A

Synthesis of cytosolic facing C terminus resumes

52
Q

Step Two (Ncytosol-Clumen): co-translational insertion of an integral membrane protein into RER

A
  • translocon’s interior interacts with protein TMD to stop translocation
  • several +ve charged amino acid residues located upstream (N term) of TMD
53
Q

What is the positive outside rule? (Step 3 of Ncytosol-Clumen)

A
  • nascent membrane protein TMD reoriented (reversed) by translocon so that positively charged residues face cytosol
  • reoriented TMD segment is released laterally into membrane bilayer
54
Q

Why is a reorientation necessary?

A

Positively charged amino acids determine topology of all membrane proteins
Therefore, translocon +ve on ER side and +ve amino acids are near N terminus, it must be flipped so that it is in the cytosol.

55
Q

Step Four (Ncytosol-Clumen): co-translational insertion of an integral membrane protein into RER

A
  • synthesis of proteins C terminus resumes

C term is now in the lumen

56
Q

How are membranes synthesized?

A
  • not de novo

- they come from pre-existing

57
Q

Where are most membrane proteins and lipids synthesized?

A

ER

- ER membrane proteins andl ipids can be trafficked to other membranes

58
Q

How are ER membrane proteins distributed and oriented in the lipid bilayer?

A
  • asymmetric
59
Q

3 examples of protein asymmetry in the ER membrane?

A
  • integral membrane proteins (regions face cytosol/lumen)
  • peripheral membrane proteins
  • membrane phospholipids (distributed unequally between leaflets)
60
Q

Where is protein and lipid assembly established?

A

ER and is maintained throughout rest of endomembrane system.

61
Q

What are the final 4 steps to co-translational translocation pathway in the ER lumen?

A
  1. signal sequence cleavage (always done) N-term cut
  2. Initial stages of glycosylation
  3. Protein folding and assembly
  4. Quality control
62
Q

What is the most common glycosylation?

A

N-linked glycosylation

adding it to the amino group of asparagine (N)

63
Q

Two stages of N-linked glycosylation.

A
  • core glycosylation (just adding it)

- core modification (modifiying oligosaccharide)

64
Q

Protein Glycosylation: 1st step - core glycosylation

What synthesizes the core oligosaccharide

A

ER membrane bound glycosyltransferases

65
Q

Protein Glycosylation: 1st step - core glycosylation

What is the final step?

A

glycosyltransferase linking core oligosaccharide to specific N reidue on soluble or integral protein that is still being synthesized

66
Q

Protein Glycosylation: 1st step - core glycosylation

Oligosaccharide ist transferred to which side of the synthesizing membrane?

A

only transferred to lumenal facing N residue part of sequence
- N-x-S/T-

67
Q

Protein Glycosylation: 2nd step: core modification

What happens after the nascent protein has a sugar oligosacch. attahed?

A
  • gradually trimmed and modified
68
Q

Protein Glycosylation: 2nd step: core modification

What trims the oligosaccharide?

A
  • glucosidase I and II (ER lumenal soluble proteins)

- trims 2 out of 3 glucoses

69
Q

Protein Glycosylation: 2nd step: core modification

How is the glycoprotein modified?

A
  • proper folding

- ER quality control - proper attachments

70
Q

What is the name of the reticuloplasmin that mediates the final steps of glycoprotein final folding?

A

calnexin

- nascent glycoprotein binds to calnexin

71
Q

For quality control, what removes the last glucose from the core oligosaccharide?

A

Glucosidase II

-released after from calnexin

72
Q

What happens if protein released from calnexin is misfolded?

A

it is recognized by GT monitoring enzyme

73
Q

What is GT monitoring enzyme and what does it do?

A
  • ER lumenal glucosyltransferase tat recognizes the hydrophobic residues that are masked by attached sugars
  • adds back single glucose residue at terminal end of trimmed core
74
Q

UGGT?

A

recognizes misfolded protein in ER lumen

75
Q

What happens to misfolded proteins?

A
  • ERAD pathway for degredation

- retrotranslocation from ER lumen to cytosol

76
Q

What binds misfolded proteins as a signal molecule for ER protein degredation?

A

Poly-Ub

for ERprotein degredation and othe proteins for normal turnover

77
Q

What is the complex for degredation? (organelle?)

A

proteasome

- proteasome is a complex barrel shaped multisubunit protein located in the cytosol and nucleus

78
Q

What happens when too many misfolded proteins accumulate in the ER?

A
  • very high levels in ER of misfolded proteins means

ER stress

79
Q

What does ER stress signal?

A

unfolded protein response (UPR)

80
Q

What is the role of ER integral membrane proteins in UPR pathway?

A
  • mediate UPR as protein sensors

- possess ER lumenal stress sensing domains that bind to molecular chaperones in the ER lumen

81
Q

2 examples of protein sensors in UPR?

A

PERK

ATF6

82
Q

In non-stress conditions PERK and ATF6 sensors are ____ due to ____

A

inactive

due to binding to BiP (molecular chaperones)

83
Q

What are the similarities between ATF6 and PERK?

A
  • bip is released to activate
84
Q

What happens in PERK?

A
  • PERK dimierize and active
  • cytosolic facng domain phophorylate and inhibit protein translation factor e eIF2a
  • therefore, protein synthesis decrease
  • slows down so available molecular chaperones can focus on preexisting proteins
  • ER stress alleviated
85
Q

What happens ATF6?

A

UPR pathway

  • active ATF6 moves from ER to Golgi (via transport vesicles)
  • at golgi - cytosolic facing
  • transcription factor domain of ATF6 is cleaved off and targets nucleus
  • ATF6 transcription factordomain upregulates number of genes encoding
86
Q

What is upregulated in the ATF6 pathway?

A
  • ATF6 transcription factor domain upregulates
  • ER molecular chaperones (proper folding)
  • ER export components (assis in moving out of ER)
  • ERAD components (assist in degrading misfolded proteins)

MCB2050 (10 decks)

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