Post-translational translocation of non-secretory proteins across membranes could occur in which organelles?
mitochondria
chloroplasts
nuclei
Golgi
ER
peroxisomes
lysosomes
Select the correct sequential steps for cotranslational translocation (signal hypothesis):
ER signal sequence is translated at free ribosome
Sequence allows ribosome to bind to a translocator on RER
Pore is formed and polypeptide is translated through to the RER lumen
Signal peptidase cleaves signal sequence
Protein is released into the ER lumen
The discovery of cotranslational translocation involved:
Secretory proteins translated in vitro were smaller than those in vivo. Microsomes from ER added to in vitro proteins resulted in larger size.
Secretory proteins were the same size in vitro and in vivo.
Secretory proteins translated in vitro were larger than those in vivo. Microsomes from ER added to in vitro proteins resulted in correct size.
Signal sequences:
vary greatly but have 6+ hydrophobic aa string at N terminus
vary greatly but have 8+ hydrophobic aa string at N terminus
vary greatly but have 6+ hydrophobic aa string at C terminus
vary greatly but have 8+ hydrophobic aa string at C terminus
Signal recognition particle can bind to signal sequences of multiple shapes and sizes because:
Hydrophilic pocket lined with methionine, which has inflexible side chains.
Hydrophobic pocket lined with methionine, which has flexible side chains.
Hydrophobic pocket lined with methionine, which has inflexible side chains.
Select the steps for SRP function:
SRP binds to small ribosomal subunit
SRP binds to large ribosomal subunit.
Binding pocket fits around nascent chain exit site and binds to ER signal sequence.
Translational pause domain positions at interface between ribosomal subunits.
SRP binds to SRP-R.
Mechanism possibly related to GDP binding sites near SRP-R.
SRP released, translation continues embedded in ER.
ER signal sequence binds to hydrophobic site on inside of locator, opening the channel.
Polypeptide extruded into ER, peptidase cleaves signal.
ER signal sequence is checked:
One time. SRP.
Two times. SRP, SRP-R.
Three times. SRP, SRP-R, signal peptidase.
Translocator for secreted proteins in ER is called:
Sec 59.
Sec 51.
Sec 61.
Sec 63.
Sec 61 has opening in side for:
Integration of TMDs.
Cleaved signal sequence to diffuse into membrane.
Ribosome to insert peptide from side.
Hydrophobic influence in Sec 61 pore.
A type I TMD has:
N terminus in ER lumen.
C terminus in ER lumen.
A type II TMD has:
For 1 pass TMDs, orientation is determined by:
Location of (+) charge, always goes to cytosol
Location of (+) charge, always goes to ER lumen
Location of 3 aa repeat, always goes to cytosol
Location of 3 aa repeat, always goes to ER lumen
In two TMD insertion, the signal is cleaved.
In multiple TMD insertion:
There is an internal start-transfer sequence and C-terminus stop-transfer sequence.
There is an N-terminus start-transfer sequence and a C-terminus stop-transfer sequence.
There is an internal start-transfer sequence and internal stop-transfer sequence.
There is an N-terminus start-transfer sequence and an internal stop-transfer sequence.
Many ER resident proteins stay in the ER because:
They have an ER retention signal.
They are too small to be absorbed into vesicles.
They are anchored on a special receptor called ER-R.
PDI is:
Protein disulfide isomerase.
Protein disulfur isomerase.
Protein disulfide isomerate.
Protein disulfur isomerate.
PDI's function is:
Formation of disulfide bonds between sulfhydryls of cysteins.
Formation of disulfide bonds between sulfhydryls of nucleotides.
Binding to unfolded proteins to prevent aggregation.
Binding to unfolded proteins to facilitate aggregation.
BiP is:
Binding Protein.
Binder Protein.
Binding in Protein.
BiP functions by:
Binding to unfolded proteins and preventing aggregation.
Binding to unfolded proteins and promoting aggregation.
Forming disulfide bonds between sulfhydryls of cysteins.
Forming disulfide bonds between sulfhydryls of nucleotides.
BiP and PDI aid in:
Secretory pathway in the Golgi.
Secretory pathway in the ER.
Proper folding of proteins.
Aggregation of proteins.
Glycosylation aids in:
Folding proteins.
Protecting against degradation.
Cell communication.
Sorting.
Which is more common at 90%?
N-linked glycosylation.
O-linked glycosylation.
N-linked glycosylation occurs by attaching sugar residues to:
Amide nitrogen of asparagine.
Amide nitrogen of cysteine.
Amide nitrogen of serine.
OST is:
oligosaccharyl transferase.
oligosaccglycol transferase.
oligoseryl transferase.
OST transfers what structure to the target side chain during N-linked glycosylation?
14 sugar compound of GlcNAc, mannose, glucose.
14 sugar compound of GlcNAc, mannose.
16 sugar compound of GlcNAc, mannose, glucose.
16 sugar compound of GlcNAc, mannose.
OST glycosylates:
All asparagines.
Only asparagines within a specific sequence (Asn - X - Ser/Thr).
Initial sugars that form the basis of all N-linked glycosylations are:
2 GlcNAc, 3 Man
3 GlcNAc, 2 Man
2 Glu, 3 GlcNAc
3 Glu, 2 GlcNAc
2 Man, 3 Glu
3 Man, 2 Glu
OST aids in glycosylation of cytosolic proteins.
Dolichol:
Holds sugar structure awaiting transfer by OST.
Builds sugar structure awaiting transfer by OST.
Facilitates ATP hydrolysis of OST.
Holds energy for sugar transfer in pyrophosphate bond.
Uses ATP to transfer sugar.
Uses GTP to transfer sugar.
OST:
Is associated with every Sec 61 translocator and each has a dolichol anchor nearby.
Is associated with some Sec 61 translocators and each has a dolichol anchor nearby.
Is associated with all Sec 61 translocators but not dolichols.
OST catalyzes the addition of sugar groups:
During translation of the target protein.
After the signal peptide is cleaved.
The instant translation finishes.
Which sugar combination is associated with entrance into the Golgi?
8 Man, 2 GlcNAc
6 Man, 2 GlcNAc
2 Man, 8 GlcNAc
2 Man, 6 GlcNAc
O-linked glycosylation:
Makes up about 90% of glycosylation events.
Makes up about 10% of glycosylation events.
Involves attachment of sugar to hydroxyl group of serine.
Involves attachment of sugar to hydroxyl group of threonine.
Synthesis of precursor oligosaccharide begins:
In membrane layer.
Cytosolic face.
ER lumen face.
Is very hydrophobic, spans bilayer 3+ times.
Is very hydrophilic, spans bilayer 3+ times.
Is very hydrophobic, spans bilayer 2 times.
Is very hydrophilic, spans bilayer 2 times.
Synthesis on dolichol:
Is en bloc.
Is one sugar at a time.
Dolichol's pyrophosphate bond is located:
In the membrane.
Within dolichol.
Between dolichol and the sugar group.
In the sugar group.
On the end of the sugar group.
During flip of dolichol, (Glc)3(Man)9(GlcNAc)2 turns into (GlcNAc)2(Man)5.
ER chaperones require:
K+
Ca2+
H+
Mg2+
Calnexin & calreticulin:
Prevent unproperly folded proteins from leaving the ER.
Keep ER resident proteins critical for proper folding inside the ER.
Are the only proteins needed for proper management of proteins in the ER.
Calnexin is membrane bound.
Calreticulin is membrane bound.
Select the proper steps for calnexin function:
Calnexin recognizes a single glucose after glucose trimming.
Calnexin recognizes a double glucose after glucose trimming.
ER resident glucosidase removes final glucose(s) off of protein.
Calreticulin recognizes absence of glucose and binds.
If proper folding occurs, protein is bound by glucosyl transferase.
Inproperly folded proteins have sugars added back onto their N-linked oligo to go back through cycle.
If proper folding fails:
Protein goes through retrotranslocation.
Protein possibly goes back through Sec61.
N-glycanase removes oligosaccharide chains en bloc in ER.
Oligosaccharide chains removed in cytosol.
Ubiquitin marks proteins for degradation by recognizing certain sequences that should not be exposed in properly-folded proteins.
Lysosome breaks down ubiquitin-marked proteins.
Proteaomse processes ubiquitin-marked proteins.
Consider proteins that take too long to fold:
They are processed in the same manner as proteins that are incorrectly folded once recognized.
They have an organic timer mediated by mannosidase.
Calnexin cycle resets the mannose timer.
Proteins that fold properly keep all their mannoses.
Unfolded protein response involves:
Accumulation of unfolded proteins in ER.
Activation by high proteasome activity.
Increased transcription of genes involving ER chaperones, retrotranslocation proteins, protein-folding proteins.
Involve IRE1.
IRE1:
is a transmembrane protein kinase.
is an ER chaperone catalyst.
autophosphorylates.
dimerizes.
trimerizes.
has endoribonuclease domain that edits a specific mRNA in cytosol.
affects activation of genes in nucleus through mRNA editing.
enters the nucleus after signaling to affect gene transcription.
____ controls coat assembly.
GTP binding protein.
Sar1.
Sec61.
ATP binding protein.
ATPase.
GEF is:
guanine nucleotide exchange factor.
guanine export factor.
Sar1 is associated with COPI vesicles.
Sec12:
is an ER membrane protein.
is a cytosolic protein.
is a type of GEF.
binds Sar1-GDP and catalyzes release of GDP and binding of GTP.
binds Sar1-GTP and catalyzes hydrolysation and subsequent release of GDP.
is involved with COPI vesicles.
is involved with COPII vesicles.
Select the correct steps for COPII coat assembly:
Sar1-GTP serves as a binding site for Sec23 & 24.
Sec23 & 24 select cargo.
Sec13 & 31 proteins form second layer to COPII structure.
Sec16 increases coat polymerization efficacy.
Sec17 increases coat polymerization efficacy.
Sec23 promotes GTP hydrolysis of Sar1-ATP.
Sec23 promotes GTP hydrolysis of Sar1-GTP.
Sar1-GDP is released from vesicle membrane, allowing coat to rapidly dissemble.
t-SNARE is exposed on surface, allowing fusing process to begin.
v-SNARE is exposed on surface, allowing fusing process to begin.
Rab-GDP is active in the cytosol.
Rab-GTP is free in the cytosol.
Select the correct steps for vesicle fusion:
Vesicle binding is mediated by Rab GTPase.
Cytosolic Rab-GDP converted to Rab-GTP by GEF.
Rab-GTP binds to Rab effector on target membrane.
t-SNARE and v-SNARE become close enough to interact and "hook."
NSF with an alpha-SNAP binds the SNAREs.
NSF catalyzes hydrolysis of ATP, forming energy needed to dissociate SNARE complexes.
Rab protein hydrolyzes its bound GTP releasing Rab effector.
Rab-GDP is released into cytosol for next cycle.
Studies with VSVG-GFP revealed:
Some vesicles detached from the ER directly fused with the Golgi if the travel distance was short.
COPII vesicles traveled toward the Golgi when originally thought COPII did retrograde transport back to the ER.
If Golgi was several micrometers away, vesicles en route to Golgi fused prior to Golgi contact, forming cis-Golgi network.
Retrograde vesicles budded off the Golgi toward the ER.
trans-Golgi network formed after trans-Golgi pushed out of Golgi from cisternal maturation.
Purpose of retrograde transport to ER:
Return t-SNARE.
Return v-SNARE.
Return membrane to ER.
Retrieve ER resident proteins.
Bring proteins back for new modifications before packaging to PM.
Retrograde transport to ER from Golgi involves COPI while retrograde transport from Golgi to Golgi involves COPII.
COPI coat proteins are composed of:
6 large cytosolic polypeptide complexes (coatomers).
4 large cytosolic polypeptide complexes (coatomers).
Coatomers with alpha and beta subunits.
Whole coatomers, no subunits.
COPI vesicles are controlled by:
Sec12, a GEF.
ARF (ADP ribosylation factor).
Sar1, a GTP-binding factor.
Select the proper steps for COPI formation:
ARF-GDP is weakly tethered to the Golgi membrane by a weak covalent protein mod on N-terminus.
ARF-GTP is strongly tethered to the Golgi membrane by a strong covalent protein mod on N-terminus.
GEF on Golgi catalyzes formation of ARF-GTP. ARF now strongly tethered to Golgi membrane.
Tight association of ARF-GTP serves as foundation for coatomer formation on COPI vesicles.
Coat dissembles and Rab mediates binding to target membrane.
SNARES facilitate fusion to target membrane.
Yeast COPI mutants showed protein accumulation in ER. This was because...
Mutant COPI vesicles lacked the ability to perform vesicle transport of proteins to the Golgi apparatus.
Mutant COPI vesicles successfully formed vesicles, but the mutation made them immediately fuse back with the ER so transport did not occur.
Mutant COPI vesicles could not bring back proteins necessary for anterograde transport to continue.
Mutant COPI vesicles fused readily with COPII vesicles, interrupting the transport chain.
Because ER resident proteins are so abundant...
They easily get trapped in outgoing vesicles.
Retrograde transport is necessary to maintain presence of ER resident proteins in the ER.
Specialized receptors prevent ER resident proteins from getting entrapped in outgoing vesicles.
ER resident proteins are mostly free in the ER lumen, so outgoing vesicles usually do not trap ER resident proteins, and the cell can replace readily those that do.
Soluble ER resident proteins are targeted back to the ER...
By an ER retention signal (KDEL) that passes directly to the membrane, causing a COPI vesicle to form.
By an ER retention signal (KDEL) that binds to a special KDEL Receptor in low pHs, allowing retrograde transport.
By an ER retention signal (KDEL) that binds to a special KDEL Receptor in high pHs, allowing retrograde transport.
By an ER retention signal (KDEL) that binds to KDEL Receptor on COPII vesicles, essentially redirecting the vesicle to the ER before fusion with the Golgi.
What special signal targets KDEL receptor back to the ER?
KKXX signal on C terminus.
KKXX signal on N terminus.
KDEL signal on C terminus.
KDEL signal on N terminus.
3 Man, 2 Glu on C terminus.
3 Man, 2 Glu on N terminus.
KDEL Receptor binds to KDEL to:
Take back ER resident proteins.
Forward modified proteins to the next part of the Golgi.
KDEL binds at:
low pH.
high pH.
KDEL is released from KDEL-R at:
ER has a ____ pH compared to the Golgi.
lower
higher
KKXX binds to:
outer phospholipids of COPI vesicles.
alpha and beta subunits of COPI vesicles.
special KDEL-R receptor on COPI vesicles.
KDEL-R.
It's been observed that yeast mutants that lack COPI alpha and beta subunits:
still have successful retrograde transport of KDEL-signal proteins.
have proteins that need to be transported back to the ER remaining in the Golgi.
send KDEL-marked proteins to lysosomes.
lack the problem of having ER-resident proteins being erroneously sent to the Golgi.
Forward movement of proteins through the Golgi involves vesicles.
Backward movement of Golgi enzymes involves vesicles.
In cisternal maturation, trans becomes medial and medial becomes cis.
Scale-covered algae:
had cell-wall glycoproteins assembled in the Golgi that were 20X larger than any observed vesicle.
had cell-wall glycoproteins that were small enough to fit inside vesicles.
had cell-wall glycoproteins that were about as large as vesicles, spurring additional research into cisternal maturation.
Collagen synthesis by fibroblasts:
involves precollagen, a precusor too large for vesicles.
involves precollagen aggregates, which have never been seen in vesicles.
provides evidence for cisternal maturation.
provides evidence for anterograde vesicular transport in the Golgi.
provides evidence that retrograde Golgi transport of enzymes occurs.
involves trimming of precollagen, the pieces of which are transported backwards via vesicles in the Golgi.
involves COPII vesicles to bring enzymes in the Golgi forward as cisternal maturation occurs.
Enzymes move retrograde in the Golgi via:
COPI vesicles.
COPII vesicles.
They don't. They move back in the same compartment via cisternal maturation.
The Golgi does what to secreted proteins during processing?
en bloc modifications to the oligosaccharides, where a protein's modification is processed separately and one exchange occurs before exportation.
sequential modifications to the oligosaccharides, where each product is another enzyme's substrate.
varies different proteins' oligosaccharides.
uniforms different proteins' oligosaccharides.
A soluble protein sent to the Golgi can only be secreted.
Select the correct steps for processing of lysosomal enzymes by the Golgi:
Lysosomal proteins come to the Golgi with (Man)8(GlcNAc)2 oligosaccharide.
Lysosomal proteins come to the Golgi with (Man)3(GlcNAc)2 oligosaccharide.
2 cis Golgi residents form the M6P.
2 medial Golgi residents form the M6P.
M6P is an oligosaccharide.
N-acetylglucosamine phosphotransferase binds to lysosomal protein signal.
N-acetylglucosamine phosphotransferase catalyzes addition of phosphorylated GlcNAc group to carbon 6 of mannose on enzyme oligosaccharide.
GlcNAc phosphotransferase can mistakenly add M6P to secretory proteins.
Phosphodiesterase removes GlcNAc, leaving a phosphate.
Phosphodiesterase removes phosphate, leaving the oligosaccharide.
Select the possible destinations of proteins from the t-Golgi network.
PM via constitutive secretion.
PM via selective secretion.
PM via regulated secretion.
Lysosome via late endosome.
Lysosome directly.
PM directly.
ER via retrograde transport.
ER directly.
Regulated secretion:
involves release of a protein after a stimulus.
involves constant and direct secretion of a protein.
involves storing a protein in a vesicle for long term storage.
involves sending a protein directly to the PM.
involves nothing.
During protein-storing vesicle formation:
Proteins in vesicles from t-Golgi network aggregate before fusing with the target storage vesicle.
Proteins in vesicles fuse directly to the target storage vesicle without aggregation.
Studies show mammalian secretory cells contain:
Chromogranin.
Chromogranin A.
Chromogranin B.
Chromogranin I.
Chromogranin II.
The Chromogranin proteins in mammalian cells
aggregate only in storage vesicles.
aggregate in the t-Golgi network, but only with a pH of 6.5 and 1mM Ca2+.
aggregate in the t-Golgi network, but only with a pH of 5.5 and 1mM Ca2+.
may be basis for sorting secretory proteins either into regulated or constitutive secretion.
is not involved in sorting secretory proteins into regulated or constitutive secretion.
Proteins that do not associate with a Chromogranin aggregation:
will not be secreted.
will only be secreted from a storage vesicle.
will be carried to the PM for constitutive secretion.
Chromogranin aggregations do not bind with secretory proteins.
Proproteins of constitutive secreted proteins:
undergo proteolytic cleavage to form a mature, active protein.
undergo proteolytic cleavage in the t-Golgi network.
in mammalian cells are probably processed by furin.
in mammalian cells are probably processed by endoprotease PC2.
are cleaved once, at C-terminal dibasic sequence.
are cleaved once, at N-terminal dibasic sequence.
PC2 and PC3
are exoproteases.
act on proproteins for constitutive secreted proteins.
can help form insulin from proinsulin.
Insulin:
is cleaved to form N-terminal B chain and C-terminal A chain connected by disulfide bonds.
is a constitutive secreted protein.
probably has processing done by carboxypeptidase, which removes 2 basic aa residues.
Proteolytic processing is common because
keeps harmful enzymes from acting anywhere except its target organelle.
Peptides that are too large need to be contained in proproteins.
ex. enkephalins would not be synthesizable without proteolytic processing.
SNARE complex is stable because:
long alpha helices that coil to form a four alpha helix bundle.
long alpha helices that coil to form a two alpha helix bundle.
Hydrophobic residues at central core.
Hydrophilic residues at central core.
Alignment of aas of opposite charge forming favorable electrostatic interaction.
Clathrin:
mediates COPI and COPII vesicles.
mediates lysosomal enzyme transport vesicles.
are diskelions.
have three limbs.
polymerize to form polygonal lattice.
associates with AP complexes when monomer.
associates with AP complexes when polymerized.
Type of APs:
AP1, helps with t-Golgi network to endosome transport.
AP1, helps with PM to endosome transport.
AP2, helps with PM to endosome transport.
AP2, helps with endosome to t-Golgi network transport.
AP3, helps with t-Golgi network to lysosome transport.
AP3, helps with t-Golgi network to endosome transport.
AP1 interacts with:
KDEL.
KKXX.
YXXo.
DXLL.
DFGXo.
GGA is:
a new type of AP.
AP1.
AP2.
AP3.
a clathrin GTPase.
AP3:
can help deliver proteins to melanosomes in skin cells.
can help mediate protein transport to specialized compartments.
may not need clathrin for its vesicles to function.
helps vesicles bypass the late endosome.
GGA interacts with:
Clathrin is needed for GGA vesicles.
All lysosomal vesicles utilize ARF GTPase to initiate coat assembly.
Dynamin is necessary for Clathrin coated vesicles to form.
Dynamin polymerizes around the neck of the vesicle bud and hydrolyzes ATP.
Dynamin:
hydrolyzes ATP.
hydrolyzes GTP.
helps COPI and COPII vesicles form.
works via conformational change that pinches vesicles.
Hsc70:
is a constitutive expressed molecular chaperone.
does not exist.
uses ATP hydrolysis.
uses GTP hydrolysis.
allows v-SNARE exposure and binding via Rab effector action.
allows t-SNARE exposure.
ARF hydrolyzes to have conformational change that regulates timing of clathrin depolymerization.
Select correct steps for transport of lysosomal enzymes to the lysosome:
M6P receptor binds in TGN.
pH must be 5.5 for M6P receptor to function.
ARF allows for coat assembly.
M6P receptor has YXXF.
M6P receptor has YXXo.
Dynamin does its thang.
Vesicle is uncoated via Hsc70.
Rab-GTP binds with Rab effector to facilitate SNARE interactions.
M6P receptor dissociates at lysosomal pH, and a phosphatase breaks up M6P.
Some M6P is then transferred to cell surface.
M6P is present at cell surface:
because it is sent there from the ER.
to release lysosomal enzymes into the ECM.
to retrieve lysosomal enzymes that were missorted.
Microphages can ingest:
25% of own volume per hour.
5% of PM per minute.
Phagocytosis:
is actin-mediated.
involves pseudopodia that surround target particle.
requires substances to transmit signals to inside of the cell.
is used by almost all cell types.
Fab regions:
recognize and bind infection organisms.
aid in pseudopodia development.
bind to other cells to mark as friendly.
Fc receptors allow phagocytic immune cells to target cells marked by Fab.
Receptor-mediated endocytosis:
involves clathrin-coated pits.
mostly utilizes AP1.
mostly utilizes AP2.
mostly utilizes AP3.
requires GTP hydrolysis to occur.
requires that receptors be recycled.
involves receptors that are freshly made from the Golgi.
The rate-limiting step of ligand internalization is:
number of receptors.
GTP concentration.
ATP concentration.
clathrin abundancy.
Ligands for receptor-mediated endocytosis include:
H2O
cholesterol carriers
erroneously sorted lysosomal proteins
protein hormones
transferrin
iron-binding proteins
Functions of cholesterol include:
maintain membrane fluidity.
fatty acid conversion.
synthesis of steroids.
killing heart tissue.
Water-soluble carriers for lipids called:
lipoproteins.
lipocholesterols.
lipocarriers.
McDonald's.
HDLs contain:
high levels of protein.
high levels of lipids.
high levels of cholesterol.
LDLs contain more ___ relative to HDLs.
proteins.
fats.
cholesterol.
Shell of LDL/HDLs composed of:
apolipoproteins.
polioproteins.
cholesterol-containing phospholipid monolayer.
cholesterol-containing phospholipid bilayer.
cholesterol-containing phospholipid trilayer.
LDL/HDL shell is amphipathic because:
outer hydrophilic surface.
inner hydrophilic surface.
outer hydrophobic surface.
inner hydrophobic surface.
LDL:
is the major cholesterol carrier.
carries more cholesterol than HDL.
has hydrophobic core with about 1500 esterified chol. molecules.
has only one apolipoprotein called apoA-100.
LDL-R:
has one TMD.
has two TMDs.
has long terminal N exoplasmic segment with ligand binding arm.
has long terminal C exoplasmic segment with ligand binding arm.
has binding arm with 7 cysteine-rich repeats of 40aa each.
has binding arm with 5 cysteine-rich repeats of 30aa each.
has YXXP signal.
has NPXY signal.
binds to AP-1.
binds to AP-2.
Select proper steps for LDL intake:
Neutral pH of cell surface allows apoB binding to LDL-R binding arm.
NPXY signal grabs AP-1 to form clathrin coat.
NPXY signal grabs AP-2 to form clathrin coat.
Dynamin hydrolyses GTP to pinch off vesicle.
Vesicle is shed with Hsc70's help. ARF-GTP to ARF-GDP.
Rab interaction allows for SNARE complex formation at pH of 5 at endosome.
At acidic endosome, histidine on LDL-R beta-propeller becomes (+).
Ligand binding arm now binds to LDL-R beta propeller.
LDL is released.
In lysosome, LDL:
has apoB hydrolyzed by protease.
has cholesterol esters exposed to cholestryl esterases.
Microvilli are composed of:
actin
MTs
intermediate filaments
Aggregations of small soluble subunits of cytoskeleton fibers are:
polymers.
protofilaments.
complete structures.
monomers.
dimers.
held together by strong covalent bonds, allowing for strength of the cytoskeleton.
held together by weak non-covalent bonds, allowing flexibility.
Protofilaments:
must avoid breaking from mere thermal motion.
form lateral connections with adjacent protofilaments.
assemble/disassemble only at the ends.
can assemble/disassemble in the middle.
of intermediate filaments form alpha helix coiled coils.
of actin and MTs are formed from globular monomers.
Microfilaments:
are the thinnest structures.
measure at 7 nm in width.
support the shape of the cell.
are made of actin monomers that form 3 chains that twist around each other.
G-actin:
has ATP binding site in cleft (facing (-) end) in center.
has a distinct polarity +/-.
has polarity due to electroactive aa side chains.
The plus end of an actin subunit polymer:
is positively charged.
is barbed.
is pointed.
breaks down and builds up rapidly.
changes rather slowly.
A lag is seen at the beginning of actin subunit interaction because:
nucleation must occur, which is a slow process.
subunits at the plus end are competing for space.
ATP hydrolysis takes time to occur.
Adding a nucleated actin segment:
worsens lag time.
eliminates lag time.
doesn't have an effect.
Catalysts of nucleation:
allow nucleation to occur quicker.
allow structures to build anywhere.
target structures to areas needed by the cell.
Actin nucleation is often regulated:
by external signals.
by genes.
by evil scientists.
Nucleation catalyzation can occur from:
ARF.
ARP2/3.
Formin.
Furin.
Formins:
help catalyze nucleation.
capture 2 actin molecules to begin nucleation.
dimerize.
continue to associate with actin at the plus end.
dissociate after nucleation.
ARP2/3:
is structurally similar to actin.
has a different plus end compared to actin.
allows actin monomers to bind at plus end.
remains bound to (-) end of actin polymer.
needs an activating factor to free it from accessory proteins that hold its active site out of orientation.
is most efficient at a 70 degree angle to preformed actin filament.
is associated with leading edge of migrating cells to allow cellular direction change.
Actin can hydrolyze its bound ATP:
anytime at the same rate.
quicker when in a filament.
quicker as a monomer.
never.
Actin-ADP is:
more likely to exist in a filament.
more likely to exist as a monomer.
more likely to dissociate from the filament.
less likely to dissociate from the filament.
If the rate of adding subunits to an actin filament is faster than the rate of ATP hydrolysis:
Now the filament has an ATP cap.
Now the filament has an ADP cap.
But, if the rate of subunit addition is low:
ADP hydrolysis occurs faster, allowing an ADP cap to form.
The world explodes.
Treadmilling:
makes me tired.
involves net addition at the minus end and net loss at the plus end simultaneously.
involves net addition at the plus end and net loss at the minus end simultaneously.
During treadmilling, the filament is changing length.
Thymosin:
binds to actin subunits, preventing binding to (+) or (-) end.
this is because thymosin blocks the area of the protein that hooks on to the filament.
thymosin blocks ATP binding site.
Profilin:
decreases rate of elongation.
binds to plus side of actin monomer.
favors hydrolysation of ATP to ADP.
is thought to bind to some formins to "stage" for action on the polymer.
Regulation of thymosin and profilin affect overall actin filament formation.
Cofilin:
binds filaments forcing tight twisting in the structure.
helps add monomers to the plus end of the filament.
weakens the contacts between subunits.
makes actin-ADP dissociation easier.
makes actin-ATP association easier.
binds preferentially to actin-ADP units.
destroys new filaments moreso than old ones.
has effects blocked by tropomyosin.
increases rate of disassembly.
Capping proteins stabilize ends of filaments.
Capping proteins are made where actin must be stable for long periods of time, like muscle cells.
Microfilaments are necessary for:
cytokinesis.
cleavage furrow.
Microtubules are the thickest of the cytoskeletal structures at 30nm.
MTs are hollow and built from:
11 parallel protofilaments.
13 parallel protofilaments.
15 parallel protofilaments.
An MTOC:
is a microtubule organizing center.
is a centrosome in mammalian cells.
is on each end of a MT.
MTs determine the position of cytoplasmic organelles including vesicles.
MTs direct movement of chromosomes during cell division.
Tubulin:
is a heterodimer.
is composed of 3 globular proteins, alpha, beta, gamma subunits.
has its globular proteins held together via noncovalent bonds.
has alpha and beta subunits.
has two nucleotide binding domains for GTP (alpha, beta).
GTP is bound at the intersection between the alpha and beta subunits, and can be hydrolyzed.
GTP is bound to the beta subunit, and can be hydrolyzed by the beta subunit itself.
Alpha subunit is a GTPase.
What kind of contacts occur between tubulin subunits?
lateral
longitudinal
these contacts allow MTs to be stiff
MT alpha subunits are exposed at the minus end.
MT beta subunits exposed at minus end.
MT elongation involves:
tubulin-GTP binding to the plus end.
tubulin-GTP hydrolysis to tubulin-GDP while part of the filament.
tubulin-GDP causes curvature to form, weakening MT structure.
GTP caps can be formed if polymerization is faster than GTP hydrolyzation.
Dynamic instability has:
shrinking phase called catastrophe.
growing phase called rescue.
MT are nucleated at centrosomes.
A centrosome:
has a pair of centrioles.
is composed of fibrous centrosome matrix.
has about 50 gamma tubulins.
divides during interphase to aid with mitosis.
has many proteins in the matrix, that catalyze addition of tubulins.
Gamma tubulin:
is more abundant than alpha and beta units.
is involved in nucleation.
Gamma tubulin ring complex (gamma TuRC):
is formed from gamma tubulin and other proteins.
allows nucleation to occur.
binds the plus end of tubulin subunits to its minus end.
caps the minus end of the MTs.
Stathmins:
bind to tubulin subunits to prevent binding to the polymer.
facilitate tubulin binding to the polymer.
cap the end of the MT to prevent subunit binding.
MAPs (MT associated proteins):
prevent binding of subunits to the polymer.
bind to the polymer to stabilize.
bind to subunits to prevent interaction with the polymer.
Kinesin 13:
has motor activity.
attaches to the end of the MT to create a stabilizing cap.
pries apart the end of a MT.
does not interact with the end of the MT.
XMAP215
allows anaphase to occur.
can stabilize MT ends.
can be phosphorylated to be deactivated.
is not a MAP.
TIPs:
are plus end tracking proteins.
are plus end tubulin proteins.
can attach and stabilize the growing MT to different locations in the call.
accumulate and remain attached at the plus end.
Intermediate filaments:
are about 10 nm in width.
are the thickest filaments.
are required for correct cell functioning.
can have varied compositions.
are constructed only from a particular protein subunit.
can be constructed from keratin, vimentin, lamins, etc.
IMs can attach to cell junction proteins.
IMs are:
strong.
weak.
brittle.
bendable.
easy to break.
difficult to break.
Why are IMs unique?
different monomers.
assemble in nonpolar fashion.
IM structure:
two monomers form coiled-coil dimer.
each monomer has globular domain at each N & C terminus.
monomers have small, short alpha helical structure.
10 protofilaments made up of pentamers form intermediate filament.
8 protofilaments made up of tetramers form intermediate filament.
Strong lateral connections give IFs rope-like character.
IFs:
outer skin layer made of keratin that functions as a barrier.
support and anchor structures to maintain shape.
line the outside of the lining of the nuclear envelope.
provide strength to long axons of neurons.
Different cytoskeletal filaments have different motor proteins.
Myosin moves on:
actin, toward (+)
actin, toward (-)
MT, toward (+)
MT, toward (-)
Myosin:
is a large family of 37+ motor proteins.
typically refers to myosin II.
are all (-) end-directed.
is a two-headed dimer.
has alpha helices that form a coiled-coil tail.
has two small chains.
Coiled coils of myosin:
have heptad (7) aa repeat sequence.
have hydrophobic side chain interactions on 1st and 4th amino acids.
have hydrophobic side chain interactions on 2nd and 4th amino acids.
hydrophobic side chains weakly bind to form a superhelix.
Myosin thick filaments:
are formed by bundles of myosin motor proteins that form a polar contractile unit.
have a bare zone in the middle of the filament that has no myosin.
has myosin going one way on one side and another way on the opposite side.
myosin III is used to make myosin thick filaments.
Muscle contraction occurs because:
myosin shortens.
myosin and actin slide past each other.
myosin and actin shorten.
myosin filaments slide past each other.
Long thin muscle fibers:
are actually very large single cells.
are several cells lined up on a filament.
have majority of cytoplasm made up of myofibrils.
have most of cytoplasm filled with mitochondria.
have contractile units called sarcomeres.
Sarcomeres:
are arrays of parallel and overlapping thick (myosin) and thin (actin) filaments.
span from Z disc to Z disc.
have capZ proteins that cap and stabilize myosin heads.
have capZ proteins that cap and stabilize actin heads.
span from Z disc to capZ to Z disc to capZ.
Tropomodulin:
caps actin on (-) end.
caps actin on (+) end.
caps myosin on (-) end.
caps myosin on (+) end.
Straitions seen in sarcomeres are:
dark bands of actin.
dark bands of myosin.
light bands of actin.
light bands of myosin.
Thick filaments during contraction:
walk towards Z disc.
walk towards bare zone.
are driven by ~300 myosin heads that each have.
are driven by ~30 myosin heads that each have.
Sarcomere shortens __% of length in __ time.
10%, 1/50th second
20%, 1/50th second
10% 1/100th second
20%, 1/100th second
Z disc caps (+) and (-) ends of actin.
M line is another descriptor of the "bare zone."
M-line contains:
myosin heads.
myosin coiled-coil tails.
actin filaments.
actin coiled-coil tails.
Nebulin:
binds to actin and spans the length of it. Acts like a molecular ruler.
binds to myosin and spans the length of it. Acts like molecular ruler.
binds to actin and connects end to Z disc. Acts like molecular spring.
binds to myosin and connects end to Z disc. Acts like molecular spring.
Which accessory protein binds to myosin and acts like a spring that spans from M line to the Z disk?
Titin
Nebulin
Troponin is complex of 3 polypeptides essential for beginning muscle ____________ made up of __________.
muscle contraction; Trop I, Trop T, Trop C.
muscle contraction; Trop I, Trop T, Trop R.
muscle relaxation; Trop I, Trop T, Trop C.
muscle relaxation; Trop I, Trop T, Trop R.
Tropomysin binds:
along the groove of actin helix.
along the groove of myosin helix.
In absence of Ca2+, Troponin I binds to Troponin T to make I-T complex.
Troponin IT complex formation:
pulls tropomyosin out of groove.
allows tropomyosin back into the groove.
hydrolyzes tropomyosin.
phosphorylates tropomyosin.
Which troponin binds to tropomyosin:
I
T
C
Muscle contraction steps:
SR releases Ca2+ which binds to Troponin C.
Tropomyosin moves out of its groove.
Myosin head can now bind to actin after ATP binding.
Myosin head can now bind to actin after GTP binding.
Binding and hydrolysis of ATP/GTP causes conformational change in converter domain.
Swinging of lever arm causes head to move along actin.
Let's start with contraction just ended:
Myosin is attached to actin microfilament without a nucleotide.
Head is at 45 degree angle to filament.
Head is at 60 degree angle to filament.
ATP quickly binds and causes a conformational change in lever arm.
Myosin dissociates from actin.
As Ca2+ is taken up into SR by calcium P pump, Troponin I & T form IT complex.
ATPase myosin activity cleaves ATP to ADP and Pi.
Conformational change causes lever arm to swing 90 relative to filament, binds to actin.
Inorganic phosphate released, causing lever arm to return to 45 degree angle (the power stroke).
Myosin head loses ADP.
Rigor mortis:
begins a few hours after death and dissapates 48-60 hours after death.
is caused by a lack of ATP.
involves myosin being "stuck" in position.
dissipates after thermal energy causes myosin to break down.
ends when enzymes involved in degradation break down myosin heads.
is sped up by cold.
Kinesin:
is a motor protein.
mostly move vesicles and organelles toward the (-) end of MTs.
commonly refers to Kinesin II.
has a heavy chain on N terminus, the motor domain.
is involved in superfamily of at least 14 members.
Which region of kinesin has conformational changes during ATP binding and hydrolysis?
binder domain.
linker region.
either motor head domain.
alpha helical tail.
Kinesin C terminus holds cargo.
Has a similar function and a similar sequence to myosin II.
Select the steps of mechanochemical kinesin cycle:
Heads work in walking motion fueled by ATP.
Kinesin is typically bound to ADP, which will bind weakly to MT once contact made.
Kinesin-ADP becomes Kinesin-ATP.
Kinesin ATP will bind weakly to MT. Conformational change of ATP binding causes lagging strand to zip forward 8nm.
ATP hydrolyzed at on new lagging head.
New leading strand releases ADP and binds ATP with MT.
Lagging strand propelled forward.
Cool note. MT bound tightly by kinesin ATP, just like myosin II binds tightly to actin without nucleotide.
Dynein:
moves vesicles and organelles towards the center of the cell.
is involved in separation of chromatids during anaphase.
includes cytoplasmic dynein with 2 large head motor domains and 2 light domains.
includes complex axonemal dynein with 3 large heads and many light chains.
are the slowest motor proteins.
Dynein function:
large motor head in a ring at C terminal domain.
has 6 AAA domains, 4 of which retain ATPase activity with one primary.
has tail that carries cargo.
has long coiled-coil stalk that binds MT.
ATP hydrolysis causes attachment of stalk to MT.
release of ADP and Pi leads to the large power stroke conformational change.
8nm steps toward (-) of MT.
Kinesin directs vesicles and organelles to cell exterior.
Cdc42 yields large number of filopodia made of MTs.
Rac, Rho, cdc42 are small G proteins that alter actin skeleton.
Taxol kills rapidly dividing cells by stabilizing MTs.
