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MCB 2050 second half > The endomembrane system and ER > Flashcards

The endomembrane system and ER Flashcards

1
Q

which organelles make up the endo-membrane system

A
  • ER
  • Golgi
  • Endosomes
  • lysosome/vacuoles
  • secretory granules
  • plasma membrane
  • nucleus
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2
Q

Which organelles are excluded from the endomembrane system

A
  • peroxisomes
  • chloroplasts
  • mitochondria
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3
Q

what is the purpose of the endo-membrane system

A
  • “indirect communication” through exchanging (trafficking) materials between each organelle via small, membrane-bound transport vesicles
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4
Q

general vesicle transport: step 1

A

‘cargo’ containing vesicle buds off the donor membrane compartment

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5
Q

general vesicle transport step 2

A

nascent vesicle is transported through the cytosol to the recipient membrane compartment
- involves molecular motors and the cytoskeleton

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5
Q

general vesicle transport: step 2

A

nascent vesicle is transported through the cytosol to the recipient membrane compartment
- involves molecular motors and the cytoskeleton

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6
Q

general vesicle transport: step 3

A

the vesicle fuses with the proper recipient membrane and cargo proteins are incorporated into the recipient

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7
Q

general vesicle transport step 4

A

the entire process can occur on the reverse direction
- could be recycling of any ‘escaped’ proteins from the original donor

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8
Q

3 main proteins in the ER

A
  • soluble
  • transmembrane
  • resident protein of donor compartment
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9
Q

Biosynthetic trafficking pathway

A

ER to gogli to endosomes to lysosomes OR plama memb

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10
Q

constitutive secretory pathway

A

ER to Golgi to PM and/or released from cell
- cargo is ER-derived materials (that you make all the time)
- secretory transport vesicle membrane components are incorporated into the PM and vesicle lumen cargo is released

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11
Q

regulated secretion pathway

A

ER to Golgi to secretory granule to PM
- occurs in specialized cells (only occurs when your body tells you to
- ER-derived materials stored in secretory granules are release in response to a cellular signal
- materials released via exocytosis

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12
Q

endocytic trafficking pathway

A
  • opposite direction of secretory pathways
    PM to endosomes to lysosomes
  • incorporates materials from the PM and/or extracellular space destined for degradation
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13
Q

endoplasmic reticulum structure

A

lumen: aqueous space inside ER tubules and cisternae
tubules and cisternae: ER integral membrane proteins that regulate ER curvature - in constant flux

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14
Q

rough vs smooth ER

A

rough: mostly cisternae with bound ribosomes, involved in protein and membrane phospholipid synthesis
smooth: mostly curved tubules lacking ribosomes, involved in Ca2+ storage and hormone synthesis

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15
Q

ER subdomains

A
  • smooth ER
  • rough ER
  • Outer nuclear membrane
  • MAM and PAM
  • ER exit sites
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16
Q

fate of proteins synthesized on free ribosomes

A
  • remains in the cytosol
    or
  • targets to the proper intracellular destination
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17
Q

fate of proteins synthesized on RER ribosomes

A
  • remains in the RER or localizes to another ER subdomain
    or
  • targets from the ER to another post-ER compartment in the endomembrane system
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18
Q

co-translational translocation of a soluble protein into the RER lumen

A
  • insertion of a protein made on a free ribosome in the cytosol into the RER lumen
19
Q

what is an SRP

A

signal recognition particle
- a ribonucleoparticle that binds to the ribosome and stops protein translation
- the SRP and its receptor are both G-proteins
- SRP targets the entire ribosome + polypeptide complex to the surface of the ER where it binds to its receptor

20
Q

what is an SRP receptor

A
  • hetero-dimeric ER integral membrane protein complex
  • serves as a docking site for the incoming SRP
21
Q

what is a translocon

A

a structure in the ER membrane that feeds the nascent protein into the membrane
- polar molecule with +ve AAs on its lumen side and -ve AAs on the cytoplasmic side

22
Q

what causes displacement and return of the plug

A

displacement: when the signal sequence interacts with the interior of the translocon
return: release of the ribosome

23
Q

what is the main difference in translocation of a soluble vs. integral membrane protein across the ER membrane

A
  • soluble enters the lumen (goes all the way through translocon)
  • integral membrane have TMDs
24
Q

what makes Type 1 integral membrane proteins unique from the others

A

has a signal sequence
- has a stop-transfer anchor sequence like a soluble protein, no SAS

25
Q

what makes Type 2 integral membrane proteins unique from the others

A
  • has a signal anchor sequence
  • +ve residues before the SAS
26
Q

what makes Type 3 integral membrane proteins unique from the others

A
  • has a signal anchor sequence
  • +ve residues after the SAS
27
Q

Insertion of tail-anchored proteins

A
  • their hydrophobic alpha-helix is on the C-terminus
  • upon emergence from the ribosome, the alpha-helix is bound by Get3-ATP
  • when translation is complete, Get3-ATP binds with Get1/2-ATP, which hydrolyzes it to transfer the a-helix to a membrane-spanning channel
28
Q

what proteins and lipids are not synthesized at the ER

A
  • glycolipids synthesized at the Golgi
  • chloroplast and mitochondrial lipids
29
Q

different types of membrane proteins

A

integral membrane: different regions of the protein facing the cytosol and/or ER lumen
peripheral membrane: located on either the cytosolic OR lumen side of the membrane
membrane phospholipids: distributed unequally between cytosolic and lumen leaflets

30
Q

what steps are involved in the processing of a new protein in the ER lumen

A
  1. signal sequence cleavage: removal of the N-terminal signal sequence
  2. initial glycosylation: addition of a sugar side chain
  3. protein folding and assembly: fold into proper 3D confirmation by reticuloplasmins
  4. quality control: misfolded or improperly assembled proteins and recognized and fixed or degraded
31
Q

what is glycosylation

A

-addition of oligosaccharide chains to proteins
- the order of monomers in oligosaccharides impact the function of the glycosidicprotein

32
Q

what are functions of oligosaccharides on glycoproteins

A
  • assists in binding with other molecules
  • assists in protein folding
  • important for intracellular trafficking - targets proteins
33
Q

what is N-liked glycosylation

A
  • addition of specific short-chain sugars to the terminal amino group of an asparagine
    consists of 2 stages
    1. core glycosylation
    2. core modification
34
Q

what does the core oligosaccharide consist of

A

14 monomers total…
2 NAc
9 Mannose
3 glucose

35
Q

process of core glycosylation

A
  • various ER membrane-bound glycosyltransferases synthesize the core oligosaccharide
  • the core oligosaccharide is a branched chain consisting of 2 NAc, 9 mannose and 3 glucose
  • starting to build it on the dol phosphate, each enzyme adds a specific sugar to a specific position on the growing core oligosaccharide
  • in the final step, glycosyltransferase links the core sugar to a specific N residue on the protein
  • it is only transferred to luminal-facing N residue on the sequence N-x-S/T-
36
Q

process of core modification

A
  • after transfer to the nascent protein, the 14 sugar core oligosaccharide is gradually trimmed
  • the first 2 terminal glucose units are removed by glucosidase 1 and 2
  • the nascent protein is also folded by reticuloplasmins
  • during folding, glycoprotein is also subjected to ER quality control
  • mature protein is released and either retained in the ER or sent to the Golgi
37
Q

what is calnexin

A

a membrane-bound reticuloplasmin that mediates a glycoprotein’s final folding steps
- after glucosidase II removes the terminal (last) glucose unit from the core oligosaccharide the protein is released from calnexin

38
Q

what happens if the protein is misfoled when released from calnexin

A
  • the protein is recognized by GT (glucotransferase) monitoring enzyme - recognizes hydrophobic residues that are usually masked in correctly folded proteins
  • GT monitoring enzyme adds back a single glucose to the terminal end of the core
  • misfolded protein binds again to calnexin to redo the final step
  • entire process continues until the protein is properly folded OR it is degraded via the ERAD pathway
39
Q

how does the protein enter the ERAD pathway

A

if the protein is misfolded it is translocated out of the ER and into the cytosol via the translocon = retrotranslocation

40
Q

ER-associated degradation

A
  • in the cytosol, oligosaccharide chains are removed and misfolded protein is ubiquitinated
  • Ub-protein binds to the lid of the proteasome
  • the Ub chain is removed, the protein is threaded into the proteasome where it is degraded and its amino products can be reused
41
Q

what is a proteasome

A

a complex barrel-shaped subunit protein-degrading machine located in the cytosol (and nucleus)

42
Q

mono vs poly ubiquitin

A

mono-Ub: serves as a signal for membrane protein import into endosomal vesicles
poly-Ub: serves as a signal for ER protein degradation and most other cellular proteins destined for normal turnover via degradation by the proteasome

43
Q

unfolded protein response (UPR) pathways

A
  • occur when misfolded proteins accumulate in the ER in levels too high for the ERAD pathway
  • signalled by ER stress
  • mediated by protein sensors (PERK or ATF6)
  • posses ER lumen-facing stress-sensing domains that bind molecular chaperons (BiP)
  • BiP binding makes the sensors inactive in non-stress conditions
44
Q

PERK mediated UPR pathway

A
  • when misfolded proteins accumulate, BiP is released from PERK
  • PERK sensors dimerize and become active
  • cytosolic-facing kinase domains of the activated PERK dimer phosphorylate and inhibit the TF elF2a
  • protein synthesis in the cell decreases so that chaperons can focus on pre-existing misfolded proteins in the ER
  • ER stress is alleviated or cell death occurs
45
Q

ATF6-mediated UPR pathway

A
  • when misfolded proteins accumulate BiP is released from ATF6
  • active ATF6 moves from the ER to the Golgi
  • at the Golgi, the cytosolic-facing TF domain of ATF6 is cleaved off and targets to the nucleus
  • ATF6 TF domain up-regulates a number of genes encoding proteins for quality control of proteins
  • ER stress is alleviated or cell death occurs

MCB 2050 second half (6 decks)

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