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75 Cards in this Set

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about half the total volume of the cell, site of protein degradation and synthesis and intermediary metabolism
membrane is responsible for about half the total area of membrane in a eukaryotic cell, also produces most of the lipid for the rest of the cell, a store for Ca2+, smooth ER can also make steroids, covalent addition of sugars to proteins
relative volumes occupied by organelles
mito 22%
Rough ER 9%
smooth ER 6%
nucleus 6%
the precursors of storage plastids, chromoplast, and chloroplast
nucleus topology
equivalent to the cytosol but topological different from other organelles, communication through nuclear pore complexes
organelles that contain their own DNA AND ribosomes
mito and plastid
topological relationships
1. nucleus and cytosol
2. endocytic and secretory organelles
3. mitochondria
4. plastids
sorting signals
aa sequence found on proteins that direct their delivery to locations outside the cytosol, two types, (1) signal sequences (found in gated transport and transmembrane transport) and (2) signal patches (seq. found separated from each other on the aa seq., found more so in lysosomes)
types of protein transport to and from compartements
1. gated transport-cytosol  nucleus
2. transmembrane transport- cytosol  mito, plastids, peroxisomes, ER
3. vesicular transport- ER, golgi, endosome, lysosome, cell surface, secretory vesicles all moving and transporting within topologically equivalent compartments
importance of signal sequences in transport
it is both necessary and sufficient for transport
replication of organelles
some, such as the ER, mito, plastids and peroxisomes, need presence of existing organelle to replicate from, info required for construction resides in both the organelle itself and the DNA that specifies the organelle’s proteins, cannot be made from scratch
nuclear envelope
double membrane, have ribosomes attached on cytosolic side and outer nuclear membrane
inner nuclear membrane
contains specific proteins that act as binding sites from chromatin and for the protein meshwork of the nuclear lamina that provides structural support for this membrane
outer nuclear membrane
continuous with the membrane of the ER, studded with ribosomes, proteins made here are transported into the space between the inner and outer nuclear membranes (perinuclear space, continuous w/ ER lumen)
nuclear pore complexes
aqueous pore that allows for transport of folded proteins, about 3000-4000 in mammalian cells, allows for passive diffusion of small molecules (5000 daltons or less) and active of larger ones, takes place in different parts of the complex, 9 nm diameter and 15 nm long, can allow active transport of molecules 26 nm in diameter
building blocks of nuclear pore complexes
1. column subunits-make up the bulk of the pore
2. annular subunits-extend spokes toward the center of the pore
3. luminal subunits-anchor the complex to the nuclear membrane
4. ring subunits-form the cytosolic and nuclear faces of the complex
also have fibrils that extend from the ring subunit, basket on the nuclear side, and a diaphragm that reduces the diameter of the pore to 9 nm
nuclear localization signals (NLSs)
signal sequences present on nuclear proteins, rich in (+) charged lysine and arginine
nuclear import receptors
bind to NLSs, bind to both the nucleoporin (with the cytosolic fibrils that have FG repeats) and NLS on the cargo protein, responsible for import
nuclear import adaptor protein
some cargo protein requires an adaptor protein to bind to a nuclear import receptor, recognize the NLS, nuclearporin and import receptor
nuclear export signals
analogous to NLSs, but for export
nuclear export receptors
analogous to nuclear import receptors, but for export
nuclear transport receptors (karyopherins)
gene family that encodes both the nuclear import and nuclear export receptors
GTPase essential in nuclear transport, found in both the nucleus and cytosol, required for both import and export
cytosolic GTPase-activating protein, triggers GTP hydrolysis, converts Ran-GTP to Ran-GDP,
nuclear guanine exchange factor, promotes the exchange of GDP for GTP, converts Ran-GDP to Ran-GTP
Ran binding protein
works with Ran-GAP to convert Ran-GTP into Ran-GDP
Ran and import
for import to occur, cargo binds to nuclear import receptor, enters nucleus and releases cargo by binding to Ran-GTP, Ran-GTP bound nuclear import receptor is then transported out of the nucleus, Ran-GTP is hydrolyzed to Ran-GDP and releases from the nuclear import receptor freeing it to bind to more cargo
Ran and export
for export to occur, nuclear export receptor must bind both Ran-GTP and the cargo, then allow it to leave the nucleus for the cytosol, Ran-GAP hydrolyzes Ran-GTP into Ran-GDP and releases both Ran-GDP and cargo
shuttling proteins
may contain both a nuclear localization and nuclear export signal, rate at which it is exported or imported determines its location
T-cell activation and the control of nuclear transport
in a resting T-cell, NF-AT is found in the cytosol in a phosphorylated state, when T-cells are activated, [Ca2+] INC in the cytosol, calcineurin binds to NF-AT dephosphorylating NF-AT exposing a nuclear import signal and blocking a nuclear export signal, NF-AT w/ calcineurin enters the nucleus and activates gene transcription of cytokines, DEC [Ca2+] release calcineurin and NF-AT is rephosphorylated exposing a export signal
mitochondrial proteins
first fully synthesized as precursor proteins in the cytosol and then translocated into mito by a posttranslational mechanism, most have signal sequence at their N terminus that is rapidly removed after import
signal sequence of mitochondria
found at the N terminus, has an affinity to form an alpha helix, where (+) charge residues are on one side and uncharged hydrophobics on the other
TOM complex
translocase of the outer mito membrane, one, functions across the outer mito membrane, import of all mito proteins, can help to insert transmembrane proteins into the outer membrane, has import receptor proteins that bind to the signal seq. on mito proteins
TIM complex
translocase of the inner mito membrane, two of them, functions across the inner mito membrane
TIM 23
bound to both the outer and inner mito membrane, transport of proteins into matrix space, also helps insert transmembrane proteins into the inner membrane
TIM 22
insertion of a subclass of inner membrane proteins including ADP, ATP and phosphate carrier proteins
OXA complex
also found on the inner mito membrane, mediates the insertion of inner membrane proteins that are synthesized within the mito or insert transmembrane proteins that have entered the matrix space through both TOM and TIM
hsp70 proteins and mito protein transport
help keep these proteins unfolded after synthesis and transport to the mito, is a cytosolic and mitochondrial hsp70
contact sites for mito protein transport
numerous sites where the inner and outer mito membrane are closely apposed, translocation occurs at or near these sites
ATPs role in mito protein transport
occurs at two sites, outside the mito is used to remove bound cytosolic hsp70, inside the matrix is responsible for removing bound mitochondrial hsp70 to allow for proper folding
H+ gradient and mito protein transport
necessary for proper translocation, found along the inner mito membrane, + inside the intermembrane space and – inside the matrix, used to drive ATP synthesis and drive the translocation of the targeting signals through the TIM complexes
thermal ratchet model of mito protein transport
the emerging chain slides back and forth by thermal motion, binding of hsp70 prevents backsliding, hand over hand method
cross-bridge ratchet model of mito protein transport
the hsp70 that binds to the protein undergoes conformational changes driven by ATP that pulls a segment of the polypeptide chain into the matrix, prevents backsliding
a chamber for the unfolded polypeptide chain that facilitates its folding by binding and releasing it through cycles of ATP hydrolysis
ways to form innermembrane proteins
1. OXA complex that binds to either mitochondrial genome proteins or imported proteins that reveal a second signal sequence after cleavage of the first that hides it
2. presence of a second signal sequence of the unfolded precursor protein that acts as a stop signal acting it to become embedded in the inner mito membrane
3. TIM22 complex, used in metabolite carrier proteins, used in specialization of multipass membrane proteins
ways to form intermembrane space proteins
formed by signal peptidases in the intermembrane space that cleave the protein from the signal sequence while still in the intermembrane space
import of proteins into ER
begins before the polypeptide chain is completely synthesized, it is a cotranslational process, protein is never released into the cytosol, never in danger of folding up before reaching the translocator in the ER membrane
membrane bound vs. free ribosomes
are structurally and functionally identical, only difference is the proteins they are making at any given time, common pool of ribosomal subunits in cytosol make both types
signal-recognition particle (SRP)
helps guide the ER signal sequence to the ER, cycles between the ER membrane and the cytosol and binds to the signal sequence and ribosome, complex particle consisting of six different polypeptide chains bound to a small RNA molecule, the signal sequence binding site is largely hydrophobic lined by Met, causes a pause in protein synthesis until it reaches the ER
SRP receptor
helps guide the ER signal sequence to the ER, found in the ER membrane, binds to the SRP-ribosome complex, brings it to a translocator, after translocation and translation continue, the SRP and SRP receptor are displaced
ER signal sequence
has eight or more nonpolar amino acids at its center
Sec61 complex
the ER translocator, forms a water-filled pore for the protein to translocate through, consists of three or four protein complexes, has a dynamic pore which opens only transiently when a ribosome with a growing polypeptide chain attaches to the ER membrane, has a binding site for the signal sequence as well to cause opening of the pore, opens in two directions (across the membrane to let the hydrophilic portions to cross the lipid bilayer and laterally to let hydrophobic portions of proteins partition into the bilayer)
different methods for ER translocation
does not always have to be co-translationally, can be imported after their synthesis
SecA ATPase
an ER translocation motor protein found in bacteria, uses ATP to push the protein through the transporter protein across the ER membrane
Sec62, 63, 71, 72 complex
found in eukaryotes, associated with the Sec61 complex, BiP (binding protein, similar to hsp70) binds to the polypeptide chain as it arises into the ER lumen and pulls it into the lumen in a method similar to hsp70 in the mitochondria
formation of single-pass transmembrane protein in ER
1. an additional hydrophobic segment found in the middle of the polypeptide chain stops the transfer process before the entire polypeptide is translocated (stop-transfer signal), causes the translocator to change shape, leads to N-terminus on the lumeneal side and C on the cytosolic side
2. an internal start sequence where the (-) charge is closer to the C-terminus, leads to C-terminus on the luminal side, more (+) charged end stays in the cytosol
3. an internal start sequence where the (-) charge is closer to the N-terminus, leads to N-terminus on the luminal side, more (+) charged end stays in the cytosol
multipass transmembrane proteins
have combinations of start-transfer and stop-transfer signals, start and stop transfer signals are determined by their location in a polypeptide chain, looks for these signals from the N-terminus to the C-terminus
ER retention signal
found on proteins in the ER that are resident there, four amino acids found at the C terminus
protein disulfide isomerase (PDI)
a resident ER protein, catalyzes the oxidation of free sulfhydryl (SH) groups on cysteines to form disulfide (S-S) bonds
a resident ER protein, helps bring proteins into the ER post-translationally, also uses ATP like hsp70, also helps in protein folding and making sure incorrectly folded proteins stay in the ER
compose most of the ER synthesized proteins, very few proteins in the cytosol are glycosylated (if they are it is normally with a single N-acetylglucosamine)
protein glycosylation
presence of a preformed precursor oligosaccharide (which is composed of N-acetylglucosamine, mannose and glucose w/ a total of 14 sugars) that is transferred en bloc to an NH2 group of an asparagine (said to be N-linked or asparagine-linked), may also bind to the OH group on serine, threonine or hydroxylysine (O-linked) in the golgi
oligosaccharyl transferase
catalyzes the transfer of the sugar group to a membrane-bound enzyme, active site only on the luminal side
lipid molecule, holds the precursor oligosaccharide in the ER membrane, transfers to the asparagine in one step, the sugars are added directly to the dolichol one by one, attached to dolichol through a pyrophosphate, about halfway through the process the sugar is flipped from the cytosoloic side to the luminal side after the (Man)5(GlcNAc)2 intermediate
calnexin and calreticulin
important in proper protein folding, bind to oligosaccharides on incompletely folded proteins and retain them in the ER, recognize an N-linked with only a single glucose, calnexin is bound to the ER membrane while calreticulin is soluble, ERp57 helps these two
glucosyl transferase
ER enzyme, keeps adding a glucose to oligosaccharides that are attached to unfolded proteins, an unfolded protein therefore undergoes glucose trimming (glucosidase) and glucose addition (glycosyl transferase) and maintains an affinitiy for calnexin and clareticulin until it folds properly
remove oligosaccharides from misfolded proteins in the cytosol
binds to misfolded proteins after deglycosylation and bring them to proteasomes where they are degraded
accessory exit proteins
help in removing misfolded proteins from the ER, Sec61 still used in removing the misfolded proteins
unfolded protein response
activated by an accumulation of misfolded proteins in the ER, leads to an INC in transcription of genes encoding ER chaperones and enzymes involved in ER protein degradation, steps include
1. misfolded proteins signal the need for more ER chaperons by activating a transmembrane kinase
2. activated kinase turns into an endoribonuclease
3. endoribonuclease cuts specific RNA molecules at two positions, removing an intron
4. two exons are ligated to form an active mRNA
5. mRNA is translated to make a gene regulatory protein
6. gene regulatory protein enters nucleus and activates genes encoding ER chaperones
7. chaperons are made in ER, where they help fold proteins
glycosylphosphatidylinosital (GPI) anchor
attached to the C terminus of some membrane proteins destined for the plasma membrane, forms in the lumen of the ER, cleavage of transmembrane portion and attachment to GPI anchor, important in the formation of lipid rafts
phosphatidylcholine (lecithin)
produced in the ER, main phospholipid used in membranes, formed from choline, two fatty acids and glycerol phosphate, catalyzed by enzymes in the ER but have active sites on the cytosolic face
mediates the rapid trasbilayer movement of newly formed phospholipids on the cytosolic side of the ER membrane, flip-flop action, can also be found on the cell membrane to make sure that both monolayers are populated evenly
specifically removes phsopholipids containing free amino groups (phosphotidylserine and phosphotidylethanolamine) from the extracellular leaflet and use the energy ATP hydrolysis to flip them directionally into the cytosolic side
phsopholipid exchange proteins
carrier protein used to transfer phospholipids from the ER membrane to mito and peroxisomes, water soluble, carry one phospholipid at a time