Ch 12 Pt 1 Flashcards
Nucleus (Intracellular Compartments)
DNA and RNA synthesis
Protects DNA
Two Membranes - envelope/Protect (compartments preform certain tasks -> organelles)
Ribosomes (Intracellular Compartments)
Protein synthesis
Made of Ribosomal RNA + Proteins
Cytoplasm (Intracellular Compartments)
Intermediary Metabolism (making and breaking down)
Protein synthesis (translation)
Consists of cytosol (fluid) and organelles (membrane bound, are suspended)
Endoplasmic Reticulum (Intracellular Compartments)
Smooth (Lack ribosomes, Ca2+ storage, lipid syntheses)
Rough (associates with ribosomes, protein syntheses)
Golgi Apparatus (Intracellular Compartments)
Protein modification (ex. modify with sugar) and sorting
Processing Center
Endosome (Intracellular Compartments)
Endocytosed material pass through organelles (endosomes) before reaching the lysosome (for degradation)
Sorting and Recycling
Lysosome (Intracellular Compartments)
Intracellular digestion
very acidic (via V type pumps)
Mitochondria (Intracellular Compartments)
Aerobic respiration
energy powerhouse
Peroxisome (Intracellular Compartments)
Oxidative reactions
Breakdown of long chain fatty acids
(detoxification reactions)
Compartments said to be ____ if they can communicate with one another without having to cross a membrane
topologically equivalent
topologically equivalent with extracellular space
(color = equivalence, lumen of compartments are same, due to formation via invagenation)
Endosomes
Secretory Vesicles
Golgi Apparatus
Lysosome
ER
Peroxisomes
(Other - Nucleolus and cytosol)
Eukaryotic cells are elaborately subdivided into a variety of
functionally distinct membrane-bound compartments
(separate biological processes)
___ requires the correct sorting of proteins to the appropriate destinations.
Biogenesis of organelles and the differentiated function of each compartment
(recognition tags - surface markers)
Most organelles can not be constructed __
de novo (from scratch).
At least one distinct protein from existing organelle membrane is needed to make new organelle.
Protein Traffic within eukaryotic cell
Gated transport - two way, cytosol to nucleolus
Transmembrane transport - unidirectional
Vesicular transport - two way
Gated transport
proteins and RNA move between cytosol and Nucleus through nuclear pore complexes
cytosol and nucleus ARE topologically equivalent
Protein translocation (Transmembrane transport):
Transport of specific proteins across the membrane from cytosol into a space that is topologically DISTINCT
Vesicular Transport
Movement of cargo from one topologically equivalent space to another. (Transport from ER to Golgi apparatus.)
Transported proteins do not cross a membrane.
How know where to go with vesicular transport
selectivity of cargo into vesical,
right cargo and right vesicle
Transported proteins do not cross a membrane (thus right cargo in right vesicle)
Regardless of their final destinations all proteins begin synthesis on
cytoplasmic ribosomes (polysomes)
polysomes
cytoplasmic ribosomes
Targeting information resides in ___ within the polypeptide.
“sorting signals” (localization sequences)
Signal sequences are often recognized by
complementary sorting receptors
Types of Sorting Signals
Signal Peptides
Signal Patches
Signal Peptides
is a specific ___
direct ___
specific 15-60 stretch of amino acids that dictate targeting. at N end
direct proteins from the cytosol to appropriate compartment (ER, mitochondria, chloroplasts, peroxisomes).
Signal Patches
is a specific ___
direct ___
specific 3-D arrangement of amino acids on surface of a folded protein that is organized into a signal recognition structure. (once folded, makes patch which is recognized)
direct enzymes and proteins to correct compartments (Golgi to lysosome transport).
Nuclear Structure
- Nuclear Envelope
- inner nuclear membrane
- outer nuclear membrane
- perinuclear space
- nuclear pore complex
- nuclear lamina
Nuclear Envelope composed of
two membranes that are continuous
Inner nuclear membrane
Binds to chromosomes (DNA)
Nuclear lamina (support filaments - provides overall structural stability of the nucleus)
Outer nuclear membrane
Studded with ribosomes (makes proteins that only function in perinuclear space, lumen of ER)
Synthesized proteins are transported into the
perinuclear space (continuous with the lumen of the ER)
Nuclear pore complex (anatomy pic in overall membrane)
Nucleo-cytoplasmic Exchange allows for the
bidirectional movement of proteins and RNA’s into and out of the nucleus at relatively high volume and with high rates of exchange.
Nucleo-cytoplasmic Exchange occurs through
“gated-pores”:
Nuclear Pore Complexes (NPC’s) - composed of nucleoporins (different proteins) - can expand, can get in bigger material (ex. ribosomal) - is a big complex
Typical mammalian cell contains ___ NPCs
3000-4000
Each NPC can transport up to ___ macromolecules/second
1000
(both directions at the same time!)
Each NPC contains ____ passages
aqueous passages, small water soluble molecules diffuse passively
size is what determines specificity
Proteins larger than ___ CAN NOT enter by passive diffusion (via NPCs)
60,000 daltons
Folding of NPCs
never completely folded, unstructured, but never gets lagged, rarely made of polar acids, so no patch to make for degradation.
NPC structure (TEM)
2- area looks like basket
1- disordered, tangled region
Ran GTP Cycle: Nuclear Transport
Ran GDP - crosses from cytosol to Nuc. ranGEF - drops GDP, new GTP binds, exports out of nuc to cytosol, Ran GAP, dephospolates. cycle repeats
Nuclear Import (steps to go from cytosol to nucleus)
Importin (receptor) binds to cargo (protein).
protein has positive charged amino acids, may form a patch. - recognized by importin
- Importin binds to FG repeats in unstructured domain of channel nucleoporins.
weak interactions - referred to as “random walk”
do all protines/cargo directory binds to importins
no, some need adaptors
Nuclear import (2d half/steps to go from nucleus to cytosol)
- Binding of cargo and receptor to Ran-GTP promotes (conf. change) release of cargo from receptor
- Importin + Ran GTP move through NPC
- Ran GAP: Hydrolysis of Ran-GTP, Ran-GDP dissociates from receptor
- Empty receptor (importin), ready for another round
(even without cargo the nuclear import receptor can move through complex)
Nuclear Export (steps)
- In nucleus, Ran-GTP promotes cargo (with nuc. export signal) binding to export receptor (exportin, recognizes signal). (making trimer complex)
- Ran-GAP binds, promotes GTP hydrolysis. Export receptor releases both its cargo and Ran-GDP
- Export receptor returned to nucleus
A coronavirus infects cell and blocks its nuclear pore complex (in yellow) with its ___ proteins (in pink).
By blocking the NPC, viruses __
ORF6
By blocking the NPC, viruses prevent the nucleus from exporting RNA strands. Thus the cell starts making the virus’s proteins/transcripts
Theory of how got mitochondria
endosymbiosis
archaea engulfed a bacteria
Similarities between Mitochondria and Bacteria
Both contain their own genomes (circular DNA)
Mitochondrial replication: Binary fission (also bacteria do)
Mitochondrial inner membrane
resembles plasma membrane of bacterial cell
Mitochondria have ribosomes (they make their own proteins/ have the ability to like bacteria)
Paramecium bursaria are
hosts for zoochlorellae, green algae, that reside within the cytoplasm.
The relationship appears to be symbiotic. The endosymbiont (algae) gains protection and possibly some essential nutrients from the host cytoplasm. and the cell gains a food source (that is not contained in food vacuole but still is around and later consumed when needed, cell also can make sugar via photosynthesis).
Functions of Mitochondria
Site of ATP synthesis
Energy in H+ gradient powers ATP synthesis (powerhouse of the cell)
Site of Fatty Acid Degradation (β oxidation)
Occurs in mitochondrial matrix
Leigh syndrome
Mutations in __
affect ___ causing ___
Mutations in one of several different mitochondrial genes can cause Leigh syndrome.
Mutations affect proteins required for complexes in Electron Transport Chain (Failure of oxidative metabolism) - Less ATP (heart brain, mussels have high energy demand)
Progressive neurological deterioration: Failure to thrive, loss of mental and movement abilities, respiratory failure (early childhood) prognosis 2-3 years
Hyperintense lesions found in basal ganglia (area of brain that helps control movement)
Structure of Mitochondria
- outer membrane
- cristae space
- inner membrane
- intermembrane space
- matrix space
All mitochondrial compartments contain proteins derived from polypeptides synthesized by the cell.
Mechanisms must exist for the import and sorting of proteins into the various compartments
Mitochodrial Signal sequence
Directs translocation of most mitochondrial proteins to the matrix.
Signal Peptide, usually at the N-terminus.
- Comprised of polar and non-polar aa’s arranged in an amphipathic helix.
once folded - one side is charged (pos, basic) and the other side is non charged
Protein Translocators
Multisubunit complexes mediate protein movement across mitochondrial membranes
Mitochondrial precursor proteins are translocated into mitochondria by a post translational mechanism
Include tom & sam (in cyctosol) and TIM and OXA in intramembrane/matrix space
TOM complex
between cytosol and intermembrane space
(Outer membrane): Import of all nucleus encoded mitochondrial proteins
translocation channel - allows polypeptide to move through
receptors - allow association with signal sequence
SAM complex
between cytosol and intermembrane space
Help fold beta barrel proteins
found in outer membrane (both bacteria and mitochondria - similarity)
TIM Complexes
(Inner Membrane) between intramembrane space and matrix space
TIM 22/TIM 23 - translocator in intermembrane
OXA complex
Insertion of inner membrane proteins synthesized within mitochondria (resident proteins)
Mitochondrial Precursor Proteins
Hsp70s -chaperone (associate by hydrophobic sequence) - prevent precursor proteins from aggregating or folding up before reaching TOM complex
Protein Import into Mitochondrial Matrix
Protein Import into Mitochondrial Matrix ENERGY
ATP hydrolysis (1. Outside mitochondria - chaperones to keep unfolded, 3. Matrix space - chaperones in microconidia. associate with TIM, “motor” pulling through)
Membrane potential across IM (2. signal sequence pas pos charge, attracted to neg charge in matrix space, pulling peptide sequence through TIM)
Insertion of Porins
porins are transported unfolded from TOM complex to IM space, bind to chaperons.
Bind to SAM complex (OM) - helps insertion and folding of porins.
Transport to IM
TIM than TOM
N terminal signal sequence enters matrix space
Stop-transfer sequence: prevents translocation across IM - is hydrophobic - retained in lipid bilayer
Proteins imported to IM space
IM is aq environment, not need stop transfer sequence.
enzyme cleaves hydrophobic sequence
second enzyme in IM space
one more step from transport to IM
Peroxisomes
Catalyze formation of plasmalogens (phospoholipids in mylen)
Lipid catabolism (breaks down large fatty acids)
Break down toxic substances (utilize oxygen) detoxification -
rat liver cell - puts oxygen in containers use when needed but protect rest
Peroxidation
detoxification of alcohol
ethanol to catalase (in peroxisomes)- peroxide to more toxic acetaldehyde, more quicky removed (because toxic)
About 25% of ethanol we drink is oxidized to acetaldehyde this way
Excess H2O2 is converted to water and oxygen
Import into Peroxisomes
Energy required (ATP hydrolysis)
Signal sequence (S-K-L, very specific) at C terminus of peroxisomal protein-recognized by soluble receptor in cytosol (Pex 5 (also capable of expanding))
Proteins can remain folded during import
