Endomembrane System Part 1 Flashcards
1
Q
what is the endoplasmic reticulum a starting point for
A
both secretory and biosynthetic pathways
2
Q
what is the ER the site of
A
protein and lipid synthesis
protein folding
processing/quality control
3
Q
what is the ER
A
highly complex network of membrane-enclosed, rod-like tubules and sheet like cisternae
4
Q
what organelle has the largest surface area
A
ER
5
Q
what is the lumen
A
aqueous space inside ER tubules and cisternae
6
Q
what do tubules and cisternae shapes get mediated by
A
reticulons
7
Q
what are cisternae
A
flattened sacs
8
Q
what are in constant flux
A
ER tubules and cisternae - undergo bending, growth/shrinkage, fusion, fission
9
Q
what does the ER consist of
A
multiple subdomains
10
Q
classic examples of subdomains in the ER
A
rough ER
smooth ER
11
Q
what does the RER consist of
A
mostly cisternae with bound ribosomes
12
Q
what is the RER involved in
A
protein and membrane phospholipid synthesis
13
Q
what does the SER mostly consist of
A
curved tubules lacking ribosomes
14
Q
what is the SER involved in
A
Ca2+ storage
hormone synthesis
15
Q
how many other ER subdomains are there
A
> 20
16
Q
nuclear envelope
A
outer nuclear membrane continuous with RER, contains Nups and attached ribosomes
17
Q
what is the Mitochondria-Associated membrane (MAM)
A
ER region that makes direct contact with mitochondria involved in membrane protein and lipid exchange
18
Q
what is the plasma membrane-associated membrane (PAM)
A
ER region that makes direct contact with the plasma membrane involved in membrane protein and lipid exchange
19
Q
what are ER exit sites (ERES)
A
ER regions where transport vesicles bud off enroute to Golgi (where vesicles are made)
20
Q
what are free ribosomes in the cytoplasm the fate of
A
nascent, properly folded soluble or membrane bound protein in the cytoplasm
21
Q
what are the 2 possible fates of free ribosomes in the cytoplasm
A
- remain in cytoplasm
- targets (post translationally) to proper intracellular compartment
22
Q
what are ER ‘membrane bound’ ribosomes the fate of
A
nascent, properly folded soluble or membrane protein in RER
23
Q
3 possible fates of ER ‘membrane bound’ ribosomes
A
- remains in RER or localizes to another ER subdomain
- localizes to other ER derived organelles
- targets from ER onto another compartment in endomembrane system
24
Q
co-translational translocation of soluble protein in RER lumen
A
protein targeting to and across ER membrane
25
signal sequence in co-translational translocation
stretch of 8-15 hydrophobic amino acids - RER targeting signal
26
signal recognition particle (SRP)
ribonucleoprotein particle consists of 6 proteins and 1 small RNA
27
SRP receptor
hetero-dimeric ER integral membrane protein complex
28
what do the cytoplasmic-facing domains of SRP receptor serve as
docking site for incoming SRP
29
what is the Sec61 translocon
multi-protein complex consisting of several ER integral membrane protein subunits (a, B, y)
30
what is the shape of sec61 translocon
hourglass shaped aqueous channel
31
what does the hourglass-shaped translocon channel of Sec 61 contain
pore ring
32
what is the pore ring in the Sec61 translocon
ring of 6 hydrophobic amino acids located at the narrowest diameter of channel
33
what does the pore ring in the Sec61 translocon serve as
a gate to seal channel to ions/small molecules to help maintain ER compartmentalization
34
what is the Sec61 translocon channel also blocked by
short alpha-helix plug
35
what is the short alpha-helix plug in the Sec61 translocon
second gate-keeping mechanism
36
how does the alpha-helix plug in Sec61 translocon get away from channel
during protein translocation the growing polypeptide forces the plug away from channel
37
what is signal peptidase
ER integral membrane protein (protease) associated with translocon
38
where does signal peptidase face
the catalytic domain of signal peptidase faces the ER lumen
39
what do reticuloplasmins (ER molecular chaperones) do
bind to nascent proteins and mediate proper protein folding and oligomeric assembly
40
what do reticuloplasmins prevent
protein aggregation
41
examples of reticuloplasmins
BiP
calnexin
calreticulin
42
membrane protein topology
number of membrane-spanning domains and orientation
43
what is transmembrane domain
typically alpha-helix of 16-25 hydrophobic amino acids
44
how is the typical TMD favourable
energetically favourable with hydrophobic interior of phospholipid bilayer
45
what do ER integral membranes with multiple TMDs lack (Type IV)
N-terminal sequence
46
what do multi-spanning ER membrane proteins (Type IV) contain
both internal SA sequences and internal STA sequences
47
what is Type 1 membrane protein
nascent polypeptide-ribosome complex targets to and associated with translocon
48
what is the comparison between orientations with Type I and Type II membrane proteins
opposite orientations
49
does the type II membrane protein have a N-terminal signal sequence
no
50
what does Type II membrane protein possess
internal signal anchor (SA) sequence
51
comparison between orientations with type III membrane protein
same orientation as type I, but like type II, possess internal signal - anchor SA sequence
52
what is the positive outside rule
positively charged residues adjacent to TMD determine orientation of TMD/membrane protein
53
where are most membrane proteins and lipids synthesized
at ER
54
where do glycolipids get synthesized
golgi
55
how are nascent ER membrane proteins and lipids distributed and/or orientated in lipid bilayer
asymmetrically
56
integral membrane proteins
different regions of protein located on either cytoplasmic or exoplasmic
57
peripheral membrane proteins
located on either cytoplasmic or lumenal side of ER membrane
58
membrane phospholipids
distributed unequally between cytoplasmic and exoplasmic leaflets of ER membrane bilayer
59
where is protein and lipid asymmetry established
ER and are maintained throughout the rest of the endomembrane system
60
what are the 4 final steps in cotranslational-translocation pathway
1. signal sequence cleavage
2. initial stages of glycolysation
3. protein folding and assembly
4. protein quality control
61
what does signal sequence cleavage entail
removal of N-terminal signal sequence by signal peptidase
62
what are the initial stages of glycolysation
covalent addition of unique carbohydrate side chains carb side chains to specific amino acids of nascent protein
63
what occurs during protein folding and assembly
nascent protein folded into proper 3D conformation and oligomeric assembly by molecular chaperones/reticuloplasmins
64
what are most proteins synthesized in ER
glycoproteins
65
what are glycoproteins
linked to one or more oligosaccharides
66
what are the benefits of glycolysation
sugar groups aid in proteins proper folding and serve as binding sites for other macromolecules that interact
67
what is the most common form of glycosylation
N-linked glycosylation
68
what is N-linked glycosylation
addition of specific short chains of sugar monomers to terminal amino group of asparagine
69
2 staged of N-linked glycosylation
core glycosylation
core modification
70
in core glycosylation, what occurs
various membrane bound glycosyltransferases synthesize core oligosaccharide
71
what does core glycosylation begin with
addition of first sugar to dolichol phosphate
72
what is the final step of core glycosylation
transfer of core oligosaccharide from dolichol lipid carrier to nascent soluble/membrane protein while being synthesized
73
in core glycosylation, where does core oligosaccharide get transferred to
luminal-facing portions of nascent ER proteins with specific amino acid motif
74
what is the specific amino acid motif in proteins where the core oligosaccharide gets transferred to
-N-x-S/T
75
what does tunicamycin do
blocks the first step of N-linked glycosylation, preventing proper folding of nascent ER proteins
76
how does tunicamycin block N-linked glycosylation
inhibits glycosyltransferase action
77
what is core modification
the second stage of N-linked glycosylation
78
what occurs during core modification
attached 14-sugar oligosaccharides are sequentially trimmed and modified
79
what gets removed during core modification and by what
2 of 3 terminal glucose units by ER lumenal glucosidases
80
in core modification, what is the removal and re-addition of the last glucose unit import for
proper protein folding/assembly
81
what does protein disulfide isomerase (PDI) do in core modification
catalyzes formation of intra/intermolecular disulphide bonds
82
what else do core oligosaccharides added to the nascent protein during N-linked glycosylation contribute to
proper protein folding/assembly and stability
protein quality control
83
what does ER lumen mannosidase do with ER protein quality control
removes one mannose unit if protein is properly folded/assembled
84
what recognizes the protein if it is misfiled/misassembled
UGGT monitering enzyme (glucosyltransferase)
85
what does the UGGT monitoring enzyme serve as
protein conformation sensing protein - usually recognizes hydrophobic residues masked inside correctly folded protein
86
what does UGGT monitoring enzyme do
adds back single glucose unit to oligosaccharide core, which then binds to reticuloplasmins to try again
87
how long does ER protein quality control process continue
until protein is properly folded, or misfolded proteins are eventually degraded
88
what does the ER-Associated degradation dislocation ERAD do
takes misfolded proteins that cannot be fixed and degrades them
89
what does the ERAD pathway involve
AAA ATPase p97
90
what is AAA ATPase p97
ER membrane protein utilizes ATP hydrolysis to pull misfolded proteins across ER membrane into cytosol
91
during ER protein degradation, what occurs in cytoplasm
oligosaccharide chains removed and misfolded protein poly-ubiquitinated
92
what does it mean for the protein to be poly-ubiquitinated
protein linked to chain of repeating (poly) ubiquitin units
93
ubiquitin (UB)
small (76 amino acids) protein involved in diverse cellular functions
94
mono-UB
serves as signal for targeting membrane proteins into intralumenal vesicles of late endosomes/multivesicular bodies
95
poly-UB
serves as signal for protein degradation and for most other cellular proteins destined for normal turnover
96
what does poly-UB protein get degraded by
proteasome
97
what is a proteasome
barrel shaped multisubunit protein-degrading machine located in cytoplasm (and nucleus)
98
what signals Unfolded Protein Response UPR pathways
under certain conditions, misfolded/misassembled proteins can accumulate into ER in high levels and overload ERAD which results in ER stress
99
what is each UPR pathway mediated by
unique protein sensor - ER integral membrane spanning proteins
100
examples of unique protein sensors that mediate UPRs
Ire1
PERK
ATF6
101
what do both PERK and ATF6 possess
ER lumenal-facing stress sensing domains
102
form of PERK and ATF6 sensors in non stress conditions
inactive by binding to BiP
103
what is eIF2a
cytosolic protein translation factor required for initiation of protein synthesis - participates in rmRNA binding
104
ERES-derived transport vesicles
move properly-folded proteins out of ER to Golgi and/or other compartments in endomembrane system
