Term
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Definition
| Contains the dna for all the proteins expressed in the cell, where mRNA is made, histones, and chromatin |
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Term
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Definition
-Where rRNA is made and ribosomes assembled, no histones, and no chromatin.
-Ribosomal proteins are shipped in and combined w/rRNA to make ribosomes. The ribosomes are then shipped out.
-snoRNA help catalyze ribosomal assembly in the nucleolus |
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Term
Nuclear Lamina
-What happens if the NL has defects? |
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Definition
Net looking thing on the inside of the nuclear envelope, denser chromatin here, made up of lamins.
-Regulates genes by acting as a sink for TF. The TFs get stuck and can't effect DNA
-Defects lead to premature aging and MS |
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Term
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Definition
-Connection for: actin in the cytoplasm, nuclear envelope, nuclear lamina, and chromatin
-Chromatin binds via BAF |
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Term
| LINC and BAF in cell division |
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Definition
| -They will make up vesicles and cover up the chromosomes. |
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Term
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Definition
-8 total proteins, 2 of each type
-Limits the access of TF to dna
-Can be modified. Transcription mainly regulated by methylation and acetlylation
-Modified on the N terminus |
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Term
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Definition
-Some modifications can swap out different types of histones in the nucleosome
-For example: H2A and H2B can be swapped out for H2X and H2X, which binds protein less tightly. |
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Term
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Definition
-Can be random or specific
-Will be random in areas that no transcription takes place
-Will be specific in transcriptional start and regulatory sites. |
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Term
| Chromatin modification propagation |
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Definition
| -Modification will be propagated a long distance via reader and writer complexes |
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Term
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Definition
-Transports 1000 molecules per second
-Passively transports molecules below 25-40 kDa
-Made up of 30 proteins
-Always open, like Dennys. |
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Term
| Main components of a nuclear pore |
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Definition
-Cytoplasmic fibrils, central core, nuclear basket
-Nucleoporins that contain binding sites for transported proteins |
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Term
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Definition
1) Cargo binds to importin via NLS (nuclear localizing signal, AA)
2) Complex loosely binds to nucleoporins and makes its way inside the nucleus
3) The complex disassociates once RAN binds to importin
4) Equilibrium is never reached and flow is always into the nucleus.
-Export works the same way, but the cargo has an NES and binds to the ran/exportin complex |
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Term
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Definition
-A small GTPase
-Active when in the GTP state, inactive when in the GDP state
-GEF activates, GAP inactivates
-For nuclear transport, GEF is inside the nucleus to active RAN and help it to bind to importin/exportin, and GAP is outside the nucleus to inactivate and release RAN |
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Term
| How does the cell know what proteins go to the ER and which do not? |
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Definition
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Term
| What is the pore that allows proteins to pass through the membrane of the ER? |
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Definition
| It's the Sec61 complex (translocon pore) |
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Term
| Translational protein translocation |
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Definition
1) A signal sequence emerges out of the ribosome and binds the SRP (signal recognition protein)
2) SRP binds to a SRP receptor on the ER surface
3) The signal sequence binds to the Sec61 translocon and the SRP falls off
4) The protein is translated into the ER and falls off as the ribosome falls apart |
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Term
| Post-translational protein translocation |
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Definition
-Uses a molecular Ratchet System
-Chaperone proteins bind to the protein to keep them from folding
-BiP (binding protein) binds to the protein in a GDP bound state as it enters the ER
-As more of the protein jiggles through the pore, more BiP binds.
-When GDP-BiP becomes GTP-BiP the protein is released |
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Term
| Transmembrane translocation |
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Definition
| -There's a gate in the translocon that opens up and lets the protein slip out the side into the lipid monolayer |
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Term
| Folding proteins in the ER |
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Definition
-The ER has lots of chaperone proteins and is highly reducing, this slows folding
-Unfolded response: too many unfolded proteins will signal the nucleus to make more chaperone proteins
-Incorrect response: incorrect folding results in proteins being shipped back through the translocon and degraded. |
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Term
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Definition
-E1 receives a Ub via ATP
-E1 transfers Ub to E2, no ATP needed
-E3 act as an adaptor to move the Ub from E2 to a specific protein
-E4 then makes chains of Ub on the protein
-Protein is degraded in the core of a proteasome |
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Term
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Definition
-Sar1 is a small GTPase, in it's GTP state it binds to the membrane via a lipid tail
-The Sar 1 can now bind to COP-II (or other coat proteins)
-Cargo is concentrated either by interaction with the coat proteins, or adapter transmembrane proteins |
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Term
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Definition
-The small GTPase must be hyrdolyzed to GDP.
-The coat machinery will then fall off
-A GAP is not needed in this case |
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Term
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Definition
-Fusion and docking are separate steps
-Things can be docked for a long time without being fused, Ca triggers fusion in this case
-Hemi-fusion takes lots of energy |
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Term
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Definition
-V-snare on the vesicle meets up with the T-snare on the target.
-The two complex with snap-25.
-A great amount of energy is released and the membrane are forced close enough to fuse |
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Term
1) What takes apart the snare complex?
2) What prevents t-snares from interacting with v-snares? |
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Definition
1) alpha snap and NSF
2) sec1 binds to t-snares. This is what allows vesicles to be docked but not fused. |
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Term
| What drives vesicle specificity? |
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Definition
-NOT the snares, they help, but are a redundant system
-The docking machinery drives the specificity |
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Term
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Definition
-Tethering proteins on the vesicle and target bind
-Only happens if the vesicle has the correct Rab in the GTP state
-Rab is hydrolyzed by GAPs in the target membrane |
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Term
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Definition
| Vesicle budding, transport, tethering, and fusion. |
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Term
| Cis and trans faces of the Golgi |
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Definition
-Vesicles arrive from the ER at the Cis face
-Vesicles leave the golgi from the trans face |
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Term
| Types of protein modifications that take place in the golgi |
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Definition
-N-linked glycosylation: starts in the ER, branched structures
-O-linked glycosylation: starts in the golgi, unbranched
-sulfation
-phosphorylation |
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Term
| Two models for intragolgi transport |
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Definition
-Vesicle: vesicles of substrate move between the cisternae, this is not the correct model
-Maturation model: enzymes move between the cisternae |
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Term
| Types of endocytotic pathways |
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Definition
Clathrin dependent-coated pits
Macropinocytosis-fluid uptake, no vesicles
Phagocytosis-intake of large particles
Caveolae-little caves |
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Term
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Definition
-Like COP in that it sculpts the membrane in vesicles
-Forms coats and then falls off after budding
-Different from COP in that with Clathrin the cargo recruits the coat. In COP, COP froms the coat and then recruits cargo |
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Term
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Definition
| -Interact side to side and end to end, forming coils and creating pits in the cell membrane |
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Term
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Definition
-A GTPase that drives budding in the GTP bound state
-Works by constricting around the membrane |
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Term
| How do you degrade non-lumenal proteins? |
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Definition
| -Need multi-vesicular bodies |
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