Ch.15, Part 1 - Cell Compartments Flashcards
- Mem-Enclosed Organelles - Protein Sorting
Where in the cell are steroid hormones synthesized, organic molecules (e.g. alcohol) detoxed, and Ca2+ stored for signaling?
SER
Describe the key functions of endosomes.
Endosomes:
- Series of compartments thru wh materials pass before endocytosed into lysosomes.
- Sort ingested molecules and recycle some of them back to pmem.
Peroxisomes break down lipids and toxic molecules thru ________.
Peroxisomes break down lipids and toxic molecules thru oxidation.
T/F: Synth of virtually all proteins begins on free ribosomes.
True
Synth of virtually all proteins begins on free ribosomes.
- Exception: a few mito/chloro proteins are synthd on ribos w/i organelle itself.
Proteins w a _________ are directed to certain organelles, otherwise remain in cytosol.
Proteins w a sorting signal are directed to certain organelles, otherwise remain in cytosol.
Endocytosis of water-soluble proteins occurs via diff mechanisms in diff organelles. Describe the pathway for proteins moving fr the cytosol into the nucleus.
Cytosol → nucleus: xprtd thru nuclear pores.
- Pores function as selective gates that actively transport specific macros but also allow free diffusion of smaller molecules
Endocytosis of water-soluble proteins occurs via diff mechanisms in diff organelles. Describe the pathway for proteins moving fr the cytosol into ER/mito/chloro.
Cytosol → ER/mito/chloro: xprtd across mem via protein translocators in mem.
- Unlike xprt thru nuclear pores, xprtd protein typ must unfold → snake across mem thru translocator.
- Bac: similar protein translocators in pmem → export proteins fr cytosol.
Unlike xprt thru nuclear pores, xprt fr cytosol to ER/mito/chloro typ reqs the protein to _____ and snake across mem thru _________.
Unlike xprt thru nuclear pores, xprt fr cytosol to ER/ mito/chloro typ reqs the protein to unfold and snake across mem thru translocators.
Endocytosis of water-soluble proteins occurs via diff mechanisms in diff organelles. Describe the pathway for proteins moving fr the ER to its target/other endomem compartments.
ER → target, also b/w endomem compartments: proteins ferried by transport vesicles, wh pinch off fr mem of one compartment → fuse w mem of second compartment.
- Transport vesicles deliver soluble cargo proteins, as well as proteins/lipids that are part of vesicle mem.
Sorting signals are a continuous stretch of ~ ____ AAs long that are _____ (often/always) cleaved off after sorting.
Sorting signals are a continuous stretch of ~ 15-60 AAs long that are often (not always) cleaved off after sorting.
What would happen if a sorting signal (signal seq) was deleted fr an ER protein?
Sorting signals can be added/removed/shuffled → change nature of protein.
- E.g. signal seq deleted fr ER protein → converted into a cytosolic protein.
T/F: wrt sorting signals, the specific AA seq matters more than the physical properties of the AAs w/i the signal seq.
False
Physical props (hydrophobicity) matter more than AA seq, i.e. can swap one hphobic AA for another and still retain proper sorting.
The nuclear envelope is formed fr two concentric bilayers. Describe the general struc/func of ea.
Nuclear envelope - formed fr two concentric bilayers:
-
Inner mem contains some proteins that act as binding sites for chromos, others provide anchorage for nuclear lamina.
- Nuclear lamina - fine meshwork of protein filaments; lines inner face of inner mem; struc support.
- Outer mem closely resembles and is continuous w ER.
The __________ a finely woven meshwork of protein filaments that lines _____ (inner/outer) face of the ______ (inner/outer) nuclear mem and provides structural support.
The nuclear lamina a finely woven meshwork of protein filaments that lines inner face of inner nuclear mem and provides structural support.
Nuclear pores are a complex of ~30 proteins characterized by extensive _______ regions wh fill the _______ (inside/outside/center) of the channel.
Nuclear pores are a complex of ~30 proteins characterized by extensive unstructured regions (intrinsically disordered seqs) wh fill the center of the channel.
- Unstruc regions consist of short, repeated AA seqs wh bind one/an when pore is empty and form loose gel thru wh small, water-soluble molecules can pass freely and nonselectively.
Nuclear pores are a complex of ~30 proteins characterized by extensive unstructured regions (intrinsically disordered seqs) wh fill the center of the channel. How does this soft, tangled meshwork of proteins influence the function of nuclear pores?
Unstructured regions (disordered seqs) form soft, tangled meshwork that fill center of channel → prevent passage of large molecules while allowing small, water-soluble molecules to pass freely and nonselectively.
- Unstruc regions consist of short, repeated AA seqs wh bind one/an when poor is empty and form loose gel thru wh small, water-soluble molecules can easy traverse.
- Larger molecules pass via import receptors, wh penetrate pore by interrupting interactions b/w repeated AA seqs of unstruc regions → open local passageway, bumping fr one repeat seq to next → delivers cargo into nucleus → empty receptor returns to cytosol via nuclear pore for reuse.
T/F: Nuclear pores allow small, water-soluble molecules to pass freely and nonselectively.
True
T/F: Nuclear pores allow small, water-soluble molecules to pass freely and nonselectively.
In order for large molecules/macromolecules to pass thru nuclear pores, they must display an appropriate __________.
In order for large molecules/macromolecules to pass thru nuclear pores, they must display an appropriate sorting signal (signal seq).
- Nuclear localization signal - signal seq that directs protein fr cytosol into nucleus; typ 1-2 short seqs w several positively charged lysines (lys; K) or arginines (arg; R).
Nuclear localization signals are signal seqs that direct protein fr ______ into ______; typ 1-2 short seqs w several ________ (pos/neg) charged lysines (Lys; K) or arginines (Arg; R).
Nuclear localization signals are signal seqs that direct protein fr cytosol into nucleus; typ 1-2 short seqs w several positively lysines (lys; K) or arginines (arg; R).
Cytosolic proteins containing nuclear localization signals are recognized by ____________, wh interact w __________that extend fr the rim of the pore.
Cytosolic proteins containing nuclear localization signals are recognized by nuclear import receptors, wh interact w cytosolic fibrils that extend fr the rim of the pore.
- Similar export receptors/mechanism.
- Larger molecules pass via import receptors, wh penetrate pore by interrupting interactions b/w repeated AA seqs of unstruc regions → open local passageway, bumping fr one repeat seq to next → delivers cargo into nucleus → empty receptor returns to cytosol via nuclear pore for reuse.
Describe how larger molecules traverse nuclear pores via import receptors.
Larger molecules pass via import receptors, wh penetrate pore by interrupting interactions b/w repeated AA seqs of unstruc regions → open local passageway, bumping fr one repeat seq to next → delivers cargo into nucleus → empty receptor returns to cytosol via nuclear pore for reuse.
- Recall: when pore empty, unstruc regions (repeat AA seqs) bind w ea/o → form loose gel thru wh small, water-soluble molecules pass freely/nonselectively.
Import of nuclear proteins reqs energy via ___ hydrolysis, mediated by ____ - a monomeric GTPase.
Import of nuclear proteins reqs energy via GTP hydrolysis, mediated by Ran - a monomeric GTPase.
Import of nuclear proteins reqs energy via GTP hydrolysis, mediated by Ran - a monomeric GTPase. Describe this nuclear xprt mechanism.
Nuclear xprt via GTP hydrolysis mechanism:
- Nuclear import receptor binds protein w nuclear localization signal in cytosol → enters nucleus thru pore.
- Ran-GTP binds import receptor → releases protein → import-Ran-GTP complex leaves nucleus thru pore.
- Accessory protein in cytosol triggers Ran to hydrolyze terminal P of GTP → Ran-GDP dissocs fr import receptor → import receptor ready to bind next protein.
- Similar cycle for nuclear export receptors.
Describe the importation of mito/chloro proteins; incl how they traverse both mems, whether they unfold, if/when signal seqs are removed, and chaperone involvement.
Importation of mito/chloro proteins:
- Typ have signal seq at N-terminus.
- Xlctd simult across both inner/outer mems at specialized sites whr the two mems conn.
- Protein unfolds as it is transported.
- Signal seq removed after xlctn complete.
- Chaperone proteins inside mito/chloro help pull protein across and fold once inside.
-
Subseq xprt typ reqs further sorting signals, wh are often only exposed after first signal seq removed.
- E.g. insertion of xmem proteins into inner mem is guided by signal seqs that start/stop xfr process across mem.
Mito precursor proteins contain a signal seq at N-terminus → bind to import receptors → bind import receptor protein and protein xlctr in outer and inner mems → unfolds → xlctd into mito matrix; pulled and refolded by chaperone proteins → signal seq cleaved.
Once inside mito matrix, how are proteins distributed (xlctd) to other areas of mito, e.g. outer mem?
Subseq xprt typ reqs further sorting signals, wh are often only exposed after first signal seq removed.
- E.g. insertion of xmem proteins into inner mem is guided by signal seqs that start/stop xfr process across mem.
Proteins destined for wh locations first enter ER fr cytosol?
Proteins destined for endomem compartments (e.g. mem/lumen of Golgi/endos/lysos; pmem) all first enter ER fr cytosol.
- ER signal seq - 8+ hphobic AAs; involved in both initial xprt fr cytosol to ER and xlctn across ER mem.
Many ribos bind to ea mRNA, forming a polyribosome. After co-xl protein synth finishes, what happens to ribosomes in this complex?
After co-xl protein synth, ribosomal subunits are released fr polyribosome and join common pool in cytosol.
What two protein components help guide ER signal seqs to ER mem?
Two protein components help guide ER signal seqs to ER mem:
- Signal-recognition particle (SRP) - cytosolic; binds both the free ribo (w mRNA) and ER signal seq (N-terminus of growing polyp).
- SRP receptor - embedded in ER mem; recogs SRP.
Describe the co-translational protein transport mechanism.
SRP mechanism:
- SRP binds ribo/ER signal seq → xl slows (doesn’t stop completely) → SRP binds SRP receptor on ER → SRP released
- Receptor passes ribo to protein xlctr in ER mem → (ER signal seq opens xlctr channel) → xl recommences.
- Polyp is threaded thru xlctr channel as a large loop → protein released after C-terminus passes thru channel.
- Signal seq is cleaved → xlctr channel closes.
- ER signal seq is removed by xmem signal peptidase w active site on noncytosolic (lumen) side of ER mem → rapidly degraded in bilayer.
In co-translational transport and subseq protein synth on ER mem-bound ribosomes, when is the protein released, and what happens to the signal seq?
SRP mechanism:
- SRP binds ribo/ER signal seq → xl slows (doesn’t stop completely) → SRP binds SRP receptor on ER → SRP released → receptor passes ribo to protein xlctr in ER mem → (ER signal seq opens xlctr channel) → xl recommences → polyp threaded thru xlctr channel as a large loop…
-
Protein is released after C-terminus passes thru channel → signal seq cleaved → xlctr channel closes.
- ER signal seq is removed by xmem signal peptidase w active site on noncytosolic (lumen) side of ER mem → rapidly degraded in bilayer.
In co-translational transport and subseq protein synth on ER mem-bound ribosomes, on wh side of the mem are AAs added to the growing polyp chain?
AAs are added to the growing polyp chain exposed on cytosolic side of mem while the signal seq at N-terminus remains bound in translocator→ growth of polyp pushes chain thru xlctr channel as a loop.
_______ signals det the arrangement of xmem proteins in the lipid bilayer.
Start/stop signals det the arrangement of xmem proteins in the lipid bilayer.
For single-pass xmem proteins, on wh side of the mem are the N- and C-termini.
Single-pass xmem proteins have defined orientation in mem: N-terminus on lumenal side; C-terminus on cytosolic side.
- Recall: once inserted, xmem protein doesn’t change orientation, wh is retained thru/o any subsequent vesicle budding and fusion events.
Multi-pass xmem proteins are unique in that an internal ____________ seq—rather than signal seq at N-terminus—starts protein xfr.
Multi-pass xmem proteins are unique in that an internal start-xfr seq—rather than signal seq at N-terminus—starts protein xfr.
- Also contains internal stop-xfr seq (like single-pass xmem proteins) wh anchors protein in mem.
For multi-pass xmem proteins, hphobic signal seqs are thought to work in pairs. Explain.
Multi-pass xmem proteins: Hphobic signal seqs are thought to work in pairs:
- An internal start-xfr seq initiates xlctn → continues until stop-xfr seq → the two hphobic seqs are then released into bilayer, where they remain as mem-spanning α helices.
- Complex multipass proteins contain many hphobic mem-spanning α helices → req additional pairs of start- and stop-xfr seqs: one seq reinitiates xlctn further down polyp, the other stops xlctn and causes polyp release, etc.
- I.e. multipass mem proteins are stitched into bilayer as they are synthd; like a sewing machine.
Single-pass xmem proteins have a defined orientation: N-terminus on lumenal side; C-terminus on cytosolic side. Do multi-pass xmem proteins also have a defined orientation.
Multi-pass xmem proteins always have N-terminus on cytosolic side, but C-terminus orientation deps on # of passes.
- Single-pass orientation arises fr fact that an ER signal seq at N-terminus starts protein xfr, and this signal seq is later cleaved → releasing new N-terminus in lumen.
- Multi-pass xmem proteins start xfr not fr an ER signal seq at N-terminus, but an internal start-xfr seq → N-terminus always on cytosolic side; C-terminus deps on # of passes.
- Double-check this.
Predict the mem orientation of a protein that is synthd w an uncleaved, internal signal seq but does not contain a stop-xfr seq.
The internal signal seq functions as a mem
anchor; bc there is no stop-xfr seq, h/e, the C-terminal
end of the protein continues to be translocated into
the ER lumen → N-terminal domain in cytosol, followed by a single xmem segment, and a C-terminal domain in
the ER lumen.
Predict the mem orientation of a protein that is synthd w an N-terminal cleaved signal seq followed by a stop-xfr seq, followed by a start-xfr seq.
The N-terminal signal seq initiates xlctn of the N-terminal domain of the protein until xlctn is stopped by the stop-xfr seq. A cytosolic domain is synthd until start-xfr seq initiates xlctn again. The C-terminal domain of the protein is xlctd into the lumen of the ER. The resulting protein therefore spans the mem twice. Both its N- and C-terminal domains are in ER lumen, and a loop domain b/w the two xmem regions is exposed in the cytosol.
What arrangement of signal seqs would enable the insertion of a multipass protein w an odd # of xmem segments?
It would need a cleaved signal seq, followed by
an internal stop-xfr seq, followed by pairs of
start- and stop-transfer seqs
