Term
| communication btw Nuc and cytoplasm occurs.. |
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Definition
| gated transport- nuclear pore complexes |
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Term
| mitochondrial protein communication |
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Definition
| (mitochondrial) membrane-bound transporters |
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Term
| proteins for secretion or membrane insertion |
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Definition
vesicular transport- budded vesicles
ER, golgi, endosomes, lysosomes, vesicles and PM
*both directions |
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Term
| ER lumen- nuclear envelope lumen |
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Definition
continuous with extracellular space (think evolution)
outer nuc membrane and ER membrane are contiguous |
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Term
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Definition
transcription occurs in nucleus, translation occurs in cytoplasm
*proteins needed for transcription need to be in nucleus |
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Term
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Definition
Nuclear Localization Signal
1-2 patches rich in Lysines(+) and Arginines(+) <-basic aa's
internal sequences- never cleaved (important in NE breakdown and reassembly of mitosis) |
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Term
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Definition
Leu-X-Leu-X-Leu-2X-Leu
*Hydrophobic |
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Term
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Definition
| protein remains in cytoplasm |
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Term
| 3 key concepts about nuclear pore(&#) |
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Definition
1-protein is completely translated
2-protein is folded
3-pore is aqueous
*3000-4000NPC per nuc |
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Term
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Definition
| nucleus contains chromosomal territories(between pores)- and nucleolus(DNA for rRNA) |
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Term
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Definition
anchored to inner nuc membrane and NPC's
anchored by interaction with membrane proteins and lipid modification and insertion |
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Term
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Definition
passive diffusion of molecules <9 nm (20kDa)
larger requires energy, is temp dependent, directional and selective |
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Term
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Definition
inside nucleus is 'basket'
cytosolic side has fibrils
octagonal array (with or without plug) |
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Term
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Definition
| structure is conserved, size differs |
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Term
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Definition
| under stress from fusion- membrane proteins at fusion 'anchor' other nuc pore proteins |
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Term
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Definition
| mutational analysis (gene knockout shows dif assembly steps) |
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Term
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Definition
# a factor of 8 (8, 16, or 32 per pore)
columnar- pore wall
annular- pore spokes
lumenal-NE anchor
ring-cyto and nucleo |
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Term
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Definition
| have FG(phenylalanine-glycine) hydrophobic repeats forming 'oily' microdomains. Interact with signal receptors recognizing NLS) |
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Term
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Definition
ß-binds cargo protein (necessary for all import)
∂-has own NLS, links cargo to ß
ß-90kDa
∂-55kDa
have hydrophobic patches interact with FG's- drives movement through pore |
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Term
| directionality of nuclear import |
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Definition
karyopherins bind ran proteins-
Ran-GTP exits nuc down gradient
Ran-GDP enters nuc down gradient
binding with ran-GTP loses ability to hold cargo(in nuc)
ran-GDP allows cargo binding(does NOT drive import) |
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Term
| Ran concentration gradients are kept up by.. |
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Definition
Ran-GAP (GTPase Activating) turns ran-GTP to Ran-GDP --> present in cytosol
*Ran-GDP moved to nuc by NTF2(down grad)
Ran-GEF (guanine nucleotide exchange factor,RCC1) turns ran-GDP to ran-GTP--> in nucleus(associated with chromatin) |
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Term
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Definition
| Nucleoporins- provide selectivity of pore |
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Term
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Definition
binds ran-GTP--> activating to bind outgoing cargo
moves down grad into cytosol
ran-GAP makes ran-GDP (release cargo)
also associates with FG repeats on fibrils |
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Term
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Definition
| constantly dock and shuttle without cargo as well |
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Term
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Definition
| nuclear export signal- exportins bind Leucine-rich hydrophobic regions |
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Term
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Definition
importinß- binds ran-GTP to move out
importin∂-needs to bind exportin to move out(has own NES) -binding promoted by Ran-GTP binding |
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Term
| import as response to environmental cues |
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Definition
NF-κB is in cytoplasm and inhibited by I-κB
activation phosphorylates I-κB (degraded)
NF-κB exposes NLS and moves into nuc, to induce transcription |
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Term
| export of transcription factors after environmental stimulus |
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Definition
new I-κB is made and has own NLS- imported
binds NF-κB
NES exposed, exported via exportin
now is OFF and in cytoplasm |
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Term
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Definition
nuclear factor of Activated T-cells
transcription factor in cytokine and immune response |
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Term
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Definition
| calcineurin activated by high Ca++ in T cell, dephosphorylates NF-AT exposing NLS, import (with calcineurin piggy back)--> transcription |
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Term
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Definition
| ATP and protein kinase phosphorylate, deactivating |
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Term
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Definition
| cyclosporin A inhibits calcineurin, blocking swelling pain, fever (cytokine production) |
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Term
| FG Nups specificity and location |
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Definition
can promote certian import vs. export
are also in specific domains |
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Term
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Definition
| blocks import of things that could degrade virus while trying to integrate own DNA |
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Term
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Definition
unidirectional-out of nuc
saturatable-M.M. specific binding. experimental saturation with tRNA slows tRNA export but not other RNA (means transport system is different-different receptors) |
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Term
| only exportation of good mRNA |
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Definition
7-methylguanosine is put on 5' end before transcription is finished (not needed)
splicing and poly-A tail important |
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Term
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Definition
dynamic membrane processes(fusion and fission)-
generates some of own proteins-different coding system |
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Term
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Definition
| binds spliced mRNA (has associated splicing factors) and binds FG repeats |
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Term
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Definition
outside nuc pore, anchored to cytoplasmic fibrils
1-binds mRNA by 5' end
2-'pulls' mRNA through pore
3-strips off associated proteins |
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Term
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Definition
matrix- enzymes for pyruvate/fatty acid oxidation
inner membrane- e- transport proteins, ATP synthesis
outer membrane- porins, lipid synthesis |
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Term
| nuclear-encoded proteins for mitochondria |
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Definition
20-50aa
sequence independent
amphipathic (hydrophobic vs philic patches)
unfolded
chaperoned by hsp60/70 bind hydrophobic areas
always at N-term
helix with amphipathic faces |
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Term
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Definition
70-cytosolic, keeps from folding
60-mitochondrial, bind/stabilize hydrophobic patches inside
signal sequence often cleaved by matrix signal peptidase after import
hsp70- needs ATP to remove |
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Term
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Definition
| need- proximity, coupled translocators, signal recognition |
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Term
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Definition
upper half mitochondrial import receptor- has groove to fit signal sequence(hydrophobic part)
TranslocaseOuterMembrane |
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Term
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Definition
| second half import receptor- binds basic part of signal (+ hydrophilic face) |
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Term
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Definition
import pore of outer mitochondrial membrane
no directionality- just a hydrophilic pore |
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Term
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Definition
spans both membranes, keeps in close proximity to TOMs
functions in transport through inner membrane
(TranslocaseInnerMembrane) |
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Term
| energy/directionality mitochondrial import |
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Definition
| if anchor is put on protein far from signal sequence, protein gets stuck- something is 'pulling' it in |
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Term
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Definition
| mitochondrial signal sequences have positive charge, may be attracted to negative charge of inside inner membrane |
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Term
| Brownian-Ratchet (thermal) |
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Definition
| hydrophobic patch is exposed by thermal motion- hsp binds and protein cannot move back through |
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Term
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Definition
| binding of hsp induces conformational change that 'pulls' protein into mitochondria |
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Term
| inner mitochondrial hsp60 |
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Definition
CHAPERONIN- barrel-like, hydrophobic sequences at rim, interacts with hydrophobic regions of protein
ATP makes GroES cap bind- stretches, dephosphorylation causes relaxation- cycles until protein is folded correctly with no hydrophobic regions expose |
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Term
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Definition
decrease in hsp70 results in neurofibrillary tangles
binds to Tau protein blocking phosphorylation-> no blockage= tangles |
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Term
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Definition
not double membrane crossing-
accepts proteins from TOM |
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Term
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Definition
translocase of matrix proteins OUT-
or can insert into inner membrane |
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Term
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Definition
can deposit proteins IN outer membrane
necessary for proteins to be deposited IN inner membrane |
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Term
| inner membrane spanning proteins |
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Definition
have sequence recognized by TIM22- deposit into inner membrane(specializes in multi-pass)
or matrix peptidase cleaves sequence- exposing signal for inner membrane spanning |
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Term
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Definition
need TOM to get TOM, need TOM to get TIM, need TIM to get TIM-
need mitochondria to get mitochrondria= endosymbiosis |
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Term
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Definition
single membrane
no DNA
all proteins nuclear encoded
*use molecular oxygen to degrade (oxidize) bad things
*breaks down peroxide=peroxidase
ßoxidation of fatty acids ->2C subunits and acetylCoA |
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Term
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Definition
PTS1-- recognized by pex5
nuclear encoded
3 aa
S(erine), K(basic-Lysine), L(eucine)
at C term
PTS2- complex, N-term, cleaved, rare, recognized by pex7
same translocase protein |
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Term
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Definition
1-receptor and cargo transported together
2-folded and large complexes can enter
differences-pex5 must be exported
SKL not cleaved |
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Term
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Definition
| synthesize glycocalyx, protein modification & quality control, sterol and lipid synthesis, membrane transport, Ca store, ribosome associated |
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Term
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Definition
| can assemble on one mRNA in cytosol- no signal, cytosolic protein |
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Term
| microsomes (rough or not) |
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Definition
regular microsomes were less dense- longer protein (no cleavage of signal sequence)
'rough' microsomes had proteins INSIDE lumen- shorter(sequence cleaved), denser |
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Term
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Definition
translation not finished at beginning of import
signal sequence targets for ER |
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Term
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Definition
sequence independent-
same signal entire secretory pathway
6-20 hydrophobic, flanked by positive
typically N-term(unless membrane passing) |
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Term
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Definition
signal recognition protein of ER transport-
7S RNA and 6 proteins-
C-term domain has hydrophobic methionines- binder receptor pocket |
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Term
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Definition
GTPase- for regulation
binds signal sequence early in translation
->halts translation by inserting into ribosome until recruited to ER membrane |
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Term
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Definition
also GTPase- binds receptor
continues translation
releases SRP- keeps ribosome and protein |
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Term
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Definition
ER translocon channel
binds- signal sequence induces channel to open |
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Term
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Definition
bi-directional
brownian ratchet(with BiP instead of hsp70), rRNA 'pushes' protein through
energy dependent |
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Term
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Definition
| folded over protein into sec61- cleavage for soluble protein (ER lumen) |
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Term
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Definition
1) n-term start, stop-transfer in middle= c term in cytosol
2) internal start (polarity + toward cytosol) allows N-term in cytosol ->no cleavage
3) same as two with polarity reversed= c-term cytosol |
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Term
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Definition
| one start-transfer one stop-transfer sequences- one revered polarity (both term to one side) |
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Term
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Definition
NH2 of asparagine side chain is glycosylated (NX S/T)
added by oligosaccharyl transferase(OST)
occurs 10/12 residues emerging from sec61
*don't want fully formed protein escaping glycosylation-OST near sec61, 90% efficient |
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Term
| oligosaccharide for glycosylation |
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Definition
preformed- 14 sugar complex,
2 N-acetylglucosamines
9 mannose
3 glucose at end
formed and held by dolicholphosphate |
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Term
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Definition
1) dolichol- in ER membrane (22 5C lipid)
sugars added 1-by-1, n-acetylglucosamine first via high energy pyrophosphate
2) starts in cytosol-> flippase at 5 mannose
-finishes in lumen
3)OST uses high energy phosphate bond to transfer to polypeptide
4) modification |
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Term
| functions of glycosylation |
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Definition
promotes proper folding
identification |
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Term
| modification of glycosylation |
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Definition
| glucosidase does first trimming in ER usually, some mannosidase in ER-> continues in golgi (addition and trimming) |
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Term
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Definition
GlycosylPhosphatidyl-Inositol
starts on cytosolic leaf (on inositol head group with GPI proteins) and is flipped- transferred 'en masse' to proteins for linkage
can be moved to PM and cleaved= signal |
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Term
| disulfide modification during translation |
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Definition
| ER lumen- oxidizing=disulfide bonds (antibodies) |
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Term
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Definition
protein disulfide isomerase-
disulfide bond formation on CH2-SH cysteine R groups
*also moves disulfide bonds from one place to another on same protein until the most stable conformation is reached |
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Term
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Definition
regenerated by Ero1P in ER membrane
Ero1P regenerated by interaction with FAD |
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Term
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Definition
*chaperones(LectinATPase)-mediate glycosylated folding with in membrane calnexin and calreticulin (ERp57 associated)
*terminal glucose needed |
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Term
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Definition
1) glucosidase I and II trim 2 glucoses
2) terminal glucose binds calnexin or calreticulin (Ca++ dependent)
3) glucosidase III cleaves terminal glucose- release
-> further trimming in ER-> Golgi |
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Term
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Definition
protein gets re-'glucosed' by UGGT
-> sent back to try again |
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Term
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Definition
| aggreagates activate kinase(Ire1p- BiP associated)=> endonuclease processes mRNA(in cytosol)-> encodes trancription factors(Hac1)-> (NLS) back to nucleus-> induces trancription/translation of ATPase chaperones fix folding |
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Term
| not folded correct in nuc- 2nd mammalian mechanism |
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Definition
ATF6- in membrane
aggregates transduce signal for cleavage on cytosolic side, ATF6 becomes a signal to stimulate transcription |
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Term
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Definition
| phosphorylates general translation machinery-> slowing down 'swampage' of ER while aggregates form so it doesn't clog |
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Term
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Definition
ERAD- ER AssociatedDegradation
proteins in ER too long will trim more mannose- could signal retrotranslocation to cytosol for degradation |
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Term
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Definition
ERAD- (p97 and Sec61, and cytosolic hsp70's pull out of ER)
polypeptide Ubiquitin attached(E3 Ub. Ligase)- targets for degradation by proteasome |
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Term
| endo and exocytic pathways |
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Definition
| different levels or each- proteins targeted for different places |
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Term
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Definition
need donor and receptor, signal and signal receptor
membrane budding-Clathrin, COPI, COPII |
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Term
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Definition
| from golgi/PM-> Endosome (ENDOCYTIC, maybe Exo) |
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Term
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Definition
| golgi<->golgi, or golgi-> ER (EXOCYTIC) |
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Term
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Definition
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Term
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Definition
6 peptide triskelion (3 heavy, 3 light)
self assemble into basket-like (with 5 or 6 sided) 'pits' of honeycomb
link into membrane, cause deformation |
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Term
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Definition
| uses GTP hydrolysis to move phospholipids of membrane deformation caused by clathrin close enough together to cause fusion and release of vesicle |
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Term
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Definition
clathrin will have adaptor complex bound to receptor crossing membrane- receptor binds cargo specifically
other cargo non-specific, whatever is in lumen
adaptors and membrane-bound proteins need to interact with coat proteins to reach destination |
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Term
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Definition
vesicle require ATP for 'decoating', clathrin will be reused
HSc70-ATP chaperone fuxns with Auxilin to decoat |
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Term
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Definition
COatProteins- exocytosis
II- bowtie complex of Sec's, self associate to deform membrane
(*can drive SAR1-GTP hydrolysis, weak)
COPI- bidirectional, uses ARF with Golgi based GEF |
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Term
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Definition
ARF acts with COPI-> ADP-Robosylation factor
SAR acts with COPII-> secretion-associated and Ras-related
GDP associated phosphorylated (by GEF) exposes lipophilic tail- associates with membrane near GEF(therefore GEF location=specificity of vesicle origin, ARF-GEF's and SAR-GEF's) |
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Term
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Definition
| impedes ARF acting GEF- no Golgi vesicles |
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Term
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Definition
donor membrane has RAB-GEF, phosphorylation GDP causes exposure hydrophobic tail-
inserted into membrane
associates with v-SNARE
facilitate docking and specificity of destination
after fusion- GTP hydrolyzed, Rab recycled |
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Term
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Definition
| Rab interacts with Rab receptor on acceptor membrane (dif Rab and receptor for every compartment) |
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Term
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Definition
| giantin(golgi), TRAPP(golgi sub-compartments), Exocyst(PM) |
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Term
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Definition
decoating also exposes v(vesicle)-SNAREs
interact with t(target)-SNAREs
∂helices(4) to bring membranes together to push out water and fuse
-specific like Rabs
*peripheral tSNAREs (neuronal) alsways 3t:1v generate fusion complex |
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Term
| bulk flow- problems and answers |
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Definition
ER proteins can be wrongfully moved to golgi
ER signal at c-term (KDEL- with BiP, or KKXX for membrane)
KKXX binds to COPI
KDEL receptors in golgi-bind KDEL and COPI
KDEL receptors bind COPII in ER
*may act differently and preferentially bind according to pH |
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Term
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Definition
bad proteins trafficked there-
modified to M6P- in golgi->
post-translational signal |
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Term
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Definition
protein binds n-acetylglucosamine phosphotransferase
transfers GlcNAc-P to terminal mannose
GlcNAc is cleaved leaving phosphorylated terminal mannose (M6P) |
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Term
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Definition
receptor is membrane bound- attaches protein to clathrin and v-SNARE's
low pH in lysosome releases protein from receptor, dephosphorylated and now in lysosome |
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Term
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Definition
defective GlcNAc phosphotransferase
=lysosome enzymes not targeted- can cause trouble in cell (secreted in blood but need low pH to function) |
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Term
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Definition
defective GlcNAc phosphotransferase
=lysosome enzymes not targeted- can cause trouble in cell (secreted in blood but need low pH to function) |
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Term
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Definition
defective GlcNAc phosphotransferase
=lysosome enzymes not targeted- can cause trouble in cell (secreted in blood but need low pH to function) |
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