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ANAT 262 > Nuclear lamins, pores and biocondensates 3 > Flashcards

Nuclear lamins, pores and biocondensates 3 Flashcards

1
Q

Describe theways of rna transport across npc

A

Rna polymerases make rna
Directio of rna transport

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2
Q

Describe rna pol 1 - rna transport across npc

A

Generate diff transcripts = rRNA (47s), NOT 5S rRNA tho

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3
Q

Describe rna pol 2- rna transport across npc

A

Mrna (hnrna=heterogenous nuclear rna)
SnRNA -small,involved in splicing

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4
Q

Describe rna pol 3 - rna transport across npc

A

5S rRNA
tRNA

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5
Q

Describe mRNA - rna DIRECTION transport across npc

A

Nucleus to cytoplasm - tap, ran independent
Bulk of mRNA exported by this way

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6
Q

Describe tRNA - rna DIRECTION transport across npc

A

Nucleus to cytoplasm
Exportin - importin beta fam so needs ran - dependent

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7
Q

Describe rRNA - rna DIRECTION transport across npc

A

Nucleus To cytoplasm
As part of large or small ribsoomal subunit
Crm1 (importing beta fam), requires ran

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8
Q

Describe snRNA - rna DIRECTION transport across npc

A

Nucleus to cytoplasm - after binding to proteins and modification in the cytoplasm
Cyt to nculeus requires ran

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9
Q

What is tap

A

Tip associated protein
Aka nxf1 - nuclear rna export factor 1

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10
Q

Describe whole process nuclear export mRNA

A

Pol 2
5prime cap
3prime poly a tail
Intron = has snRNp, nrs signal - binds splicing factors, contains nuclear retention signals
Some proteins removed before export, some remain bound and enter cytoplasm
Shuttle then, remove some proteins from transcript and other proteins binds, these proteins go back to nculeus *shuttling protein
mRNA always bound to protein

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11
Q

What is required for mrna nuclear transport

A

Signals
Energy
Transport factors

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12
Q

Describe signals needed for mRNA nuclear export

A

5’ cap
Poly a tail
Absence of introns = most important, bc get rid of nrs

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13
Q

Describe energfy needed for mRNA nuclear export

A

Rna helicases = involved in restructuring mRNA in nucelus and cytoplasm

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14
Q

Describe transport factors needed for mRNA nuclear export

A

Taps - nxf1 recognize mRNA
Rna helicases
Nucleoporins- like nup98

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15
Q

Describe nuclear export of unspliced or partially spliced hiv-1 mRNA

A

Rre = rev response element, restricted to virus mRNA
Rev protein, carries a nuclear export signal- nes
Unspliced viral mRNA - bound to splicing factors, have nrs
Unspliced viral mRNA bound to rev protein, recognizes rre, nes recognized by crm1, = allows incomplete spliced mRNA to get from nculeus to cytoplasm

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16
Q

What happens if inhibit all crm1

A

Cells die
(Accumulate virus rna in nculeus)
Mainly - crm1 needed for export ribosomal subunits

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17
Q

What is important for stress response - stress granules

A

Importin alpha
Importin beta fam members
Ddx3 (rna helicase)

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18
Q

What is important for protein disaggregation

A

Importin beta fam members

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19
Q

What is important for chaperone function

A

Importin alpha
Importin beta fam members

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20
Q

What promotes nup solubility maybe

A

Crm1

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21
Q
  • how to make stress granules - gen
A

Proteins in cytoplasm undergo liquid liquid phase sep = can make stress granules
Stres dependent
Transient
Usually disassemble

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22
Q

When can stress granules happen

A

Temp, ph change
Salt change
Oxidative stress
Hypoxia
Heart attacks

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23
Q

What is bad about stress granules

A

If stress chronic = biocondensates can transition to gel like or glass like condensate = cannot be dissasembled - amyloid fibrils = worst case, bc damages cell and permanent

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24
Q

Name disease relevance of stress granules

A

Neurodegeneration
Cancer
Viral infections

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25
Why make stress granules
Recruit pro apoptosis factors - pro death - when in grnaules = inactive so cells survive take many mRNAs floating in cytoplasm and put in stress granules = protect from degradation
26
What are stress granules
Assemble in cytoplasm Rna binding proteins, molecules involved in trafficking Importin alpha1 = important for assembling full sized sg, smaller sg = more prone to death when stress
27
What is located in stress granules
Hur - sg Marker, importin alpha too DNA marker (dapi), sg marker (g3bp1), oligo-dt(50)= detects poly a rna
28
Describe properties of stress granules - by using an ex
Dynamic granules bc formed by liquid liquid phase sep Mixing of proteins and rna can generate droplets Addition of more rna can produce hollow droplets - organization of biocondensates changes, add diff types rnas = change bioconjugates But when transition to more permanent structures = lose ability to fuse and divide = important for neurodegeneration
29
Describe how sg are key players in human dieseases
Bad in this situation, normally good tho Chemo drugs - stress cells, cancer cells make sgs = harder to kill, tumour micro environment, chemo —> sg assembly—>treatment resistance Persistent granules —> neurodegeneration Hiv interferes with sgs formation = cells more prone to death, impaired sg formation —> enhanced infectivity
30
What do nuclear transport receptors do
Limit pathological liquid liquid phase sep during neurodegeneration Prevent/reduce formation of permanent or persistent aggregates in cells
31
Describe transportin 1 - neurodegenration contyext
Member importin beta fam = work like chaperone that prevents formation of permanent aggregates - can remove proteins from permenant agggretaes = limit it
32
Name tdp43 and fus
Tap=43 = tar dna binding protein Fus - fused in sarcoma Involved in neuro degeneration
33
Describe tdp43 and fus
Rna binding proteins involved in several aspects of rna homeostasis - like splicing and mRNA export from nculeus and for diseases prodcueddd by dipeptide repeats
34
What happens when mutate tdp-43 and fus
Associated with als (amyotrophic lateral sclerosis) and ftd (fronto temporal dementia) Parkinson’s, Alzheimer’s Disease associated mutant proteins often prone to aggregation Can limit phenotype of disease
35
Describe post translational import of proteins into diff organelles - gen
Similar - trafficking to nculeus, peroxisomes and mito Similar processes
36
Describe post translational import of proteins into diff organelles - in cytoplasm
Fully synthesized polypeptides associated with chaperones in cytoplasm - hsp70
37
Describe post translational import of proteins into diff organelles - in organelles
In membrane = recognizes targeting sequences we have to move protein and receptor into organelle Chaperones - another chap, helps final folding of proteins and also its translocation
38
Describe transport into peroxisomes
One way = into peroxisomes from cytosol
39
What are peroxisomes
Bag of enzymes 0.2-1 micron diameter Single membrane surrounds peroxisomal matrix
40
What do peroxisomes do
Role in detoxification reactions - enzyme catalase oxidizes diff compounds and removes h2o2 (controls cellular redox status) Beta oxidation - degradation of long chain fatty acids Involved in synthesis of plasmalogens - generation of myelins
41
Name the 2 ways peroxisomes made
From scratch or by division
42
Describe peroxisomes biogenesis - scratch
Vesicles come from er or mito and fuse = pre peroxisome Needs to import proteins from cytoplasm to matrix to generate and mature peroxisome Then divide
43
Describe peroxisomes biogenesis - division
Just simple division Increase in size and divide in 2
44
Where are proteins in peroxisomes from
Proteins in peroxisomal matrix = have to be imported from cytoplasm - some from mito/er, some de novo
45
Name factors required for protein import into peroxisomes or mitochondrial matrix
Signals Energy Cellular import apparatus
46
Describe encoding of genes - peroxisomes
All membrane and matrix proteins encoded by nuclear genes
47
Describe protein import - peroxisomes
Protein import into peroxisomal matrix is post translational
48
Describe type of proteins - peroxisomes
Can import fully folded proteins - transported into peroxisomal matrix
49
Describe energy of protein import - peroxisomes
Protein import into peroxisomal matrix requires energy = ATP
50
Describe peroxins
MEDIATES trafficking Encoded by pex genes - mediate peroxisomal biogenesis and protein import
51
What mediates protein import into peroxisomal matrix
Transient translocon and involves phase sep at translocon Reside in peroxisomal membrane
52
Name the 2 types of targeting signals for peroxisomal matrix
Pts1 Pts2
53
Describe pts1
Skl - serine, lysine, leucine Needed at c term Never cleaved off 90% pts signals
54
Describe pts2
N term sometimes cleaved Mutation can convert pts to mts (goes to mito) in primary hyperoxaluria type 1
55
Describe targeting of pts1 containing proteins to peroxisomal matrix - step 1
Unfolded protein - with skl then folds and binds Skl receptor - pts1 receptor (PEX5) COMPlex docks at peroxisomal membrane
56
Describe targeting of pts1 containing proteins to peroxisomal matrix - step 2
Docking of complexes = No energy required Occurs at 4 degrees Celsius = cold
57
Describe targeting of pts1 containing proteins to peroxisomal matrix - step 3
Translocation Energy required Moved into matrix
58
Describe targeting of pts1 containing proteins to peroxisomal matrix - step 4
Skl dissociates and take recpetor back out to cytoplasm
59
Describe targeting of pts1 containing proteins to peroxisomal matrix - step 5
Energy requires to get Skl recpetor back out into cytoplasm
60
What do peroxisomal membranes contain
Transient translocon No pore/permanent holes Cargo with skl (pex5), binds to larger protein complex sitting in membrane = allows opening and cargo to enter matrix
61
Describe pex13
Membrane protein pex13 = has conserved yg region that forms mesh work in lipid bilateral Yg domains form hydrogels in vitro (yg = cytosine, glycine) = fill lumen of transient opening Hydrophobic = can only fit up to 2nm diameter
62
Describe pex5
Associates with pex13 and trans locates into matrix Partitions into yg domain meshwork Moves cargo across meshwork into peroxisomal lumen
63
Describe recycling of pex5
Ubiquitination and retrotranslocation Once cargo and pex5 in peroxisomal lumen = pex14 teams membrane protein Indy’s pex5 receptor and becomes ubiquinated pex10-12= ub ligase complex Pex1, pex6 aaa atpase in cytosol = pulls ubs and pulls pex5 out and into cytoplasm and then can get rid of ub and free to start another cycle PORES TRANSIENT AND. V SMALL, MOVEMENT OF CARRIER DEPENDENT ON REVERSIBLE UB OF CARRIER
64
Name types of peroxisomal disorders
Peroxisome biogenesis disorders Single peroxisomal protein defect
65
Describe peroxisomal biogenesis disorders
Zellwegersyndrome= mutation PEX5 Neonatal adrenoleukodystrophy Infantile Refsum disease Rhizomelic chondrodysplasia punctata
66
Describe single peroxisomal protein defects
X-linked adrenoleukodystrophy Hyperoxaluria type I Refsum disease Thiolase deficiency
67
Name human genes involved in peroxisomes biogenesis - specific diseases
Pex5 - cytosol/peroxisomal membrane = affects pts1 recpetor = causes zellweger syndrome, neonatal adrenoleukodystrophy Pex7 = cytosol/peroxisomal membrane, affects pts2 receptor, causes = rhizomelic Chondrodysplasia Punctata
68
Describe mitochondria -Gen
Transport one way to mito form cytosol 4 major compartments = inner membrane, outer membrane, inter membrane space, matrix Mito = produce energy by making atp and by electrochemical gradient across membrane Most proteins of mito = synthesized in cytoplasm, imported post translationally
69
Describe targeting sequence to mito Matrix
MTS = mito targeting sequence Length of 25-35 aas residues Amphipathic helix
70
Describe mito protein translocators
Protein has to be unfolded Bind receptors then interact with outer mito membrane In inner mito membrane = tim23 complex (translocation in inner mito membrane, diff kinda), Tim 22 complex, oxa complex (need this, oxidase assembly complex) In outer mito membrane = Tom complex, transporter
71
Describe transport factors - mito protein import
In inter membrane space - space between outer and inner mito membranes = Tiny Tim’s
72
Describe energy requirements for protein sorting to mito matrix
Cytoplasm = need atp bc need hsp70s Across inner mito membrane = need trans membrane potential - will be stuck in space between if no membrane potential In mito matrix = need atp bc hsp70s too (Tim - pull protein into matrix)
73
Describe sorting to inner mito membrane = 1st way, involving matrix space
Cytosol - Tom complex and through Tim complex Cleavage site = cleave signal sequence And get into matrix space To get to inner mito membrane = need second signal sequence and interacts with oxa complex in inner mito membrane = inserts protein here CAN ALSO put Proteins from mito - synthesized in mito into inner mito membrane
74
Describe sorting to inner mito membrane = 2nd way - only cytoplasm proteins
Tom in outer mito membrane Need inter membrane chaperones - tiny Tim’s to help keep protein in none aggregated state Tim 22 complex helps insert protein into inner mito membrane Only FOR PROTEINS COMING FROM CYTOPLASM Need atp in cytoplasm and electrochemical gradient across inner mito membrane (do not need atp in matrix tho)
75
Describe sorting to outer mito membrane
Tom complex —> inter membrane space has tiny Tim chaperones —> Sam (sorting and assembly machinery) complex in outer mito membrane = fully fold and release protein into outer mito membrane
76
Describe pathway components and energy requirements for matrix
Tom, tim23, chaperones Need atp, and electrochemical gradient
77
Describe pathway components and energy requirements for Inner membrane - multiple pathways
Tom, tim22 or tim23, chaperones, oxa translocase Atp, electrochemical gradient
78
Describe pathway components and energy requirements for Outer membrane
Tom, inter membrane chaperones, SAM Atp needed
79
Name abnormal mito protein import and human dieseases
Human deafness dystonia syndrome Proteins involved = ddp1/timm8a = mutation in a tiny tim
80
Describe human deafness dystonia syndrome
X linked recessive disorder Loss of function mutation Cannot move hand properly
81
Summarize = post translational protein import into diff organelles for nuclei nucleoplasm
In and out nculeus Size limit = active transport 45nm - if larger = use diff mechanism Diffusion = 8nm, 45 Kia All signals to get protein into nculeus permanent Gate = npc Proteins can be fully folded
82
Summarize = post translational protein import into diff organelles For peroxisomes - matrix
Many but not all signals to get proteins in are permanent Skl= permanent n term signals - may or may not be permanent Gate = flexible translocon, transiently active, 2kda size max Proteins can be fully folded
83
Summarize = post translational protein import into diff organelles For mito - matrix
Protein has to be fully folded Signal sequence removed and protein then folds Gate = Tim/tom

ANAT 262 (24 decks)

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