exam 3 Flashcards
1
Q
what is the notably pathways that the secretory vesicles take
A
they start in the ER and work their way to secretion (the extracellular space) or a lysosome (have to pass through the Golgi in all cases)
2
Q
what is the notable pathway of the endocytic vesicles
A
they come from the extracellular space, go though early then late endosomes, and then go to the lysosome (recycling)
3
Q
what is the notable pathway of the retrieval vesicles
A
all pathways start secretion in an endosome, and then
– they can be recycled in an early endosome and given back to the extracellular space (recycled)
– passed through the Golgi apparatus and then given to the ER,
– they can also just remain in the Golgi
4
Q
what is the notable pathway of the autophagy vesicles
A
comes from cytosol and goes into the lysosome
5
Q
why do we need different coats on vesicles with different destinations
A
so other molecules can identify and singles to either direct or let in the vesicle, and load them correctly.
6
Q
what does a Cathrin coat (triskelion) on a vesicle do
A
it forms the outer layer and drives the formation of a vesicle
7
Q
what do the light and heavy chains do on the coat of a vesicle
A
– the light chains help generate a force for membrane budding via actin filaments,
– the heavy (N-term domains) chains protrude inward and bind to the adaptor proteins in the second layer of the coated vesicle
8
Q
What do adaptor proteins do
A
they select cargo into clathrin-coated vesicles
both the outer layer and the second layer interact with membrane lipids and membrane-bound cargo receptors
9
Q
why does the clathrin triskelion fall off after the vescile buds off
A
it is no longer needed, and it needs to expose the receptors and surface receptors in the vesicle
10
Q
what do phosphoinositides do
A
mark organelles and membrane domains
11
Q
what molecule gets phosphorylated and de-phosphorylated at various positions in their inositol sugar ring, and what does it form
A
phosphoinositol, and becomes phosphoinositides or phosphatidylinositol phosphates
(the head groups of these are recognized by adaptor proteins that can tell them apart)
12
Q
What do the phosphatidylinositol phosphates (PIPs) do and where
A
they are located in several different membranes and membrane domains, and they usually have specific vesicle transport events
13
Q
What do cytoplasmic proteins regulate
A
the pinching off and uncoating of coated vesicles
– done so by making a spiral at the neck of each bud
– a GTPase domain within it regulates the rate of which it pinches of and seals it off
14
Q
how do the vesicles rapidly lose their clathrin coat, and what is the key
A
lose it via chaperone proteins in the cytoplasm, and the key is through ATPase and Hsc70 taking off the diphosphates
15
Q
what do rab proteins do
A
they guide transport vesicles to their target membrane
16
Q
What do rab proteins (like Rab-GDP) contain that allows them to dock and fuse to the membrane
A
they carry a vesicle that has a v-snare that attaches to a trans-snare complex which brings into the membrane, the actual rab gets releases in the cytosol (they don’t leave the cell along with everything else)
17
Q
how do proteins typically leave the ER
A
in COPII-Coated transport vesicles
18
Q
why do we have COPII in our vesicles
A
adaptor proteins on the second layer of coating interact with the n-termini of cargo receptor proteins, the c-termini interact with the exit signals in soluble cargo proteins
19
Q
why don’t mistakes happen when the COPII coated vesicles leave
A
there are three layers that the mistake would have to get through, and the top two are mediating transport
20
Q
the retrieval pathway to the ER uses what
A
sorting signals like lys-asp-glu-leu (KDEL) getting bound to a c-term signal and either brings it back to the ER or continues to the early tubular cluster late parts of the Golgi apparatus
21
Q
why is having signals for escaped membrane ER resident proteins with a KKXX sequence unrelaible
A
because there are only two amino acids that need to be there, the last two can be anything, and then get sent back to the ER if they also have a COPI-coated vesicle
22
Q
Why does the Golgi apparatus consist of an ordered series of compartments
A
a protein made in the ER needs to be modified, so the vesicles travel through the Golgi to do so
23
Q
What are the three pathways of secreation from the trans Golgi network
A
- Signal-mediated diversion to lysosomes (via endosomes)
- Signal-mediated diversion to secretory vesicles (for regulated secretion)
- constitutive secretory pathway
24
Q
Signal-mediated diversion to lysosomes (via endosomes)
A
involves a mannose 6-phosphate receptor, which sorts lysosomal hydrolases in the trans-Golgi network
25
Why aren't hydrolyses harmful in ER, but cause dissociation in the endosomes
the endosomes have an acidic environment that activates hydrolyses, but the ER and Golgi do not have the environment (additionally, hydrolyses get tagged and carried out in the ER and Golgi)
26
Pathway two: Signal-mediated diversion to secretory vesicles (for regulated secretion)
elect cargos are stored in secretory vesicles in specialized cells until an extracellular signal arrives, similar to insulin and neurotransmitter response
27
pathway three: constitutive secretory pathway
operates to deliver proteins and others to cell surfaces constitutively in un-polarized cells. in polarized ell, a specific signal needs to direct them to specific domains
28
Is the formation of secretory vesicles a regulated or constitutive process and how
regulated,
1) secretory proteins aggregate in the trans-Golgi network. the immature secretory vesicles contain clathrin coats
2) similar to insulin-secreting cells, anti-clathrin antibodies conjugated to gold particles are used to locate clathrin molecules
29
Why is it important in nerve cells to recycle synaptic vesicles in the presynaptic plasma membrane
they can't make enough in the endocytic vesicles to keep up with the amount of signals that fire
30
What can direct proteins from the trans Golgi network to the appropriate domain of the plasma membrane
Polarized cells
31
Is direct sorting in the trans Golgi network or the indirect sorting via early endosome operated (transcytosis)
indirect likely and the vesicle path first goes to the basolateral membrane to the the apical plasma membrane so that contact with the outside doesn't happen first
done so by endosomes
32
Vesicle formation needs ___ filaments, but vesicle traffic needs _____
actin filaments, microtubules
33
Cells use what to import selected extracellular macromolecules
apolipoprotein B (a type of receptor- mediate Endocyte) and it mediates the binding of LDL to cell surface LDL receptors in the plasma membranes
34
specific proteins are retrieved from___ and then returned to the plasma membrane
early endosomes
35
how do early endosomes get recruited to continue forward or return back to the plasma membrane
LDL receptors bind to the AP2 adaptor protein, which recruits clathrin to initiate endocytosis, which, after fusion, will determine the location
36
why do hydrolyses only function in acidic conditions
it leads to a carbon dissociation in molecules
37
What is phagocytosis
the extracellular. surrounds (engulfs) a molecule like a bacterium as it ender the cell and then escorts it to the lysosome
38
what is endocytosis
an active process that is mediated by receptors, which then gets delivered to early and then late endosomes, which then get delivered to lysosomes
also done with extracellular material
39
what is macropinocytosis
usually done with fluids, membranes and particles attach to the plasma membrane and get delivered to late endsomes
40
what is autophagy
engulfed cytosol and organelles (from inside the cell already) form around molecules like mitochondria and then get delivered straight to the lysosome
41
what are the different pathways to deliver to lysosomes
phagocytosis, endocytosis, macropinocytosis, autophagy, and Direct Transport via the Golgi Apparatus
42
How can specizialed phagocytic cells ingest large particles
a large vesicle can be formed by white blood cells like macrophages and neutrophils to ingest microorganisms or dead cells--
43
how is pseudopod ( a dynamic projection of the cell membrane and cytoplasm that allows a cell to move or engulf particles) formation and extension driven
usually driven by actin polymerization and reorganization
44
what is necessary for the ingestment of large particles
- antibodies on the target (usually a bacteria),
- Fc receptors on the surface of a phagocytic cell (to bring in the target into the plasma membrane
- PI(4,5)P2 stimulates actin polymerization and PI(3,4,5)P3 depolymerize actins at the base
45
what happens to vesicles of unknown origins
they fuse and grow to form a double membrane-enclosed (induction) autophagosome, which gets fused with a lysosome
46
What happens to damaged mitochondria
They will get ubiquitylated on the outer membrane, which gets by a receptor on an autophagosome membrane
47
What does the cytoskeleton determine
cellular organization and polarity
48
in intestinal epithelial cells what do bundled actin filament do
support microvilli at the apical surface-- a band is also made below the microvillus which connects filaments via cell to cell adherians
49
in intestinal epithelial cells how are microtubules found
they run vertically from the top to the bottom and provide global coordiantion of organelles and vesicle transport
50
in intestinal epithelial cells how are intermediate filaments bound
they are anchored to desmosomes (cell to cell connection) and hemidesmosomes ( attach to extracellular matrix)
51
Why does actin have a dynamic and stable structures have importance for the cell
they help determine the shape of the cell surface and are necessary for whole cell locomotion (muscle) and drive the pinching of one cell into two
52
what are the properties of actin filaments
its parts are made of a plus and minus end and they are assembled in a head to tail manner to form a right-handed helix
typically a faster growing plus end and a slower growing minus end
53
which actin protein nucleates assembly and remains associated with the growing plus end
formin
54
which actin filament nucleates assembly to form a branched network and remains associated with the minus end
Arp 2/3 complex
55
which actin filament binds NPF which binds monomers and concentrates them at sites of filament assembly
Profilin
56
how do ARP 2 and ARP 3 which attach to actin filaments not become apart of a actin filament
they have a plus end similar to actin but their minus is not similar
57
what do the ARP 2 and ARP 3 complexes do?
they form an inactive complex and a nucleating probing factor will then bind to the complex which then facilitates nucleating actin filament growth at the plus end
usually acts most efficiently when bound to a pre-existing actin filament
58
what does Dimeric formin do
it associates with the plus end of actin filaments and facilitates the addition of a NEW actin monomer; each formin monomer has a binding site for a monomeric actin
59
what does formin and profilin do
formins facilitate the addition of actin molecules to the GROWING plus end when profilin is bound (polymerization), formins have a binding site to recruit profilin
forming also contains whisker-like domains that have several binding sites for profiling actin complexes
60
what do nucleation promoting factors (NPFs) do
bind profilin which leads to the nucleation of branched actin filaments (by ARP2/3) but also the elongation of new filaments
61
what is myosin 2 made of
it has two heavy change and four light chains (light chains bind to the head and regulate it) which form thick myosin filaments, there is also a neck or hinge region
62
what does myosin 2 do
in its head, it can hydrolyze ATP to walk toward the plus end of an actin filament (while the actin filament itself goes to the minus end as its getting pushed in that direction)
63
What does the sliding of myosin 2 along actin filaments do
it causes muscles to contract
when a sarcomere contracts the myosin filament slides toward the plus end of actin filaments
64
what is in a sacromere
2 Z-discs (light bands) and a M line (dark band)
z-disks attachment sites for the plus end of actin filaments
M-line is the location of proteins that link adjacent myosin 2 filaments
65
what is tropomodiun (in a z-disk, light band)
a protein that caps and stabilizes the minus ends of actin filaments
66
what is nebulin
a protein that binds actin filaments to influence their length
67
what is titin
it extends from z disc and associates with myosin thick elements as molecular spring and ruler (helps the engagement of myosin with actin)
68
why does myosin walk with a single head
one needs to be moving and attached to titin to find the actual actin
69
what mineral concentration needs to rise in order to initiate muscle contraction
Ca2+
70
what is tropomyosin
it is locked on an actin filament by the binding of troponin T and I (inhibitory domains) to tropomyosin in the absence of Ca2+
71
troponin T and I vs troponin C
T and I are inhibitory domains that lock onto tropomyosin, while C binds calcium and causes troponin I and tropomyosin to release their hold on actin (causing a muscle contraction)
72
what are microtubules structure
long, hollow cylinders that are made of the protein tubulin and are 25nM, much more rigid than actin filaments, and are made of 13 protofilaments
73
what do microtubules do
they form the mitotic spindles and cilia, they also determine the position of organelles and direct intracellular vesicle transport. they also attach a centrosome and are usually long and straight
in protozoans they form the framework upon which the entire cell is built
74
what is the subunit of microtubules
a heterodimer
GTP with an alpha-tubulin embedded deep or tightly
GTP or GDP can be associated with beta-tubulin (can polymerize)
75
what are the qualities of the beta and alpha subunits of microtubules
beta is at the plus end and ends to grow and shrink more rapidly
the alpha is a the minus end
76
How many Gamma (Y)-tubulin subunits are there in a microtubules and what does it do
13 subunits, and they make a ring that nucleates (starts the formation of ) microtubules
77
when gamma tubulin starts nucleating in the centrioles, does the plus end or the minus end of microtubules leave the centrosome
plus and goes outward
78
what is a gamma-TuRc
an alpha-beta-tubulin dimer that nucleates assembly of microtubules and remains associated with the minus end of a microtubule
79
what is kinesin-13
a microtubule-associated protein (MAP) that induces catastrophe and disassembly in microtubules-- prys apart plus ends (depolymerization)
80
what is XMAP13
a microtubule-associated protein (MAP) that stabilizes plus ends and promotes rapid microtubule growth-- binds tubulin dimers and delivers them to the plus end (polymerization)
81
what do microtubule plus-end-binding proteins modulate
microtubule dynamics and attachments
they help mediate if microtubules should grow or shrink due to the frequency of catastrophes
82
what do kinesins do to microtubules
they walk to the plus end via their nucleotide-binding motor heads and carry organelles or vesicles on their long coil tails
83
leading and lagging heads of kinesin properties
the lagging head leaves the tubulin binding site (via ATP hydrolysis) and passes the leading head (binding of ATP to this site pulls the rear head forward) and rebinds to the next binding site
84
what do dyneins do to microtubules
they also move along microtubules via minus-end directed movement, typically used for organelles and vesicle trafficking and position the centrosome and nucleus during cell migration.
85
dynein properties
is a two-headed molecule that contains two heavy chains that have a motor head that has domains for ATP binding and hydrolysis
the heads are connected by long linkers which have intermediate and light chains bound to it
86
where do dyneins walk are what are they mediated by
to the minus end of microtubules and are mediated by dynactin
87
what is dynactin
mediates the attachment of dynein to a membrane-enclosed vesicle or organelle ,
it is a large protein complex and includes proteins that bind to dynein and form an actin-like filament made of ARP1
88
What is an intermediate filament
a rope like fiber with a diameter of 10nm, they provide support/ shape,
help with meshwork -- anchorage sites for chromosomes and nuclear pores
and cell-to-cell connections
89
what is the structure of an intermediate filament
a monomer pairs to another monomer to make a dimer, and the dimers then algin to make a tetramer (antiparallel) and then 8 tetramers pack together to make a staggard filament
90
why is the tetramer in a intermediate filament staggard
-- help equalize the polarity of the plus and minus ends, making a non-polar unit
-- makes symmetry
-- can help make higher-ordered structures and allows for longitudinal interactions
91
what do linker proteins do
connect cytoskeletal filaments and bridge the nuclear envelope
92
what is a SUN protein
a linker protein that connects to the nuclear lamina or chromosomes (inside nucleus and membrane)
93
what is a KASH protein
a linker protein in the outer nuclear envelope that connects to the cytoplasmic cytoskeleton by binding microtubule motor proteins, plectin, or actin filaments
(envelope and cytoplasm)
94
What do adhesion junction include
all four types of junctions and involving actin and intermediate filaments
95
what are the two major ways animal cells are bound together
-- in epithelial tissue, cytoskeletons link from cell to cell through adhesion junctions
-- in cell-matrix junctions attach epithelial tissue to the connective tissue
96
tight junctions function
seals the gap between epithelial cells and a fence between plasma membrane domains -- allows for glucose to diffuse only by na+ transporters
97
adherens junction function
connects actin filament bundles in one cell with that in the next, these filaments get tethered by adaptor proteins to cadherins
98
desmosome function
connects intermediate filaments in one cell to those in the next cell (indirect connection) , helps give mechanical strength
99
gap junction function
allows the passage of small water-soluble molecules from cell to cell (not macromolecules)
made of 6 connexon subunits
100
hemidesmosome function
anchors intermediate filaments in the cell to the extracellular matrix also connects epithelial cells to the basal lamina
101
actin-linked cell-matrix junction function
anchors actin filaments in cell to extracellular matrix
102
what links the cytoskeleton form cell to cell or to extracellular matrix with the help of adaptor proteins
transmembrane adhesion proteins (like a z-3adaptor protein and linking to a amino acid)
103
how do cadherins mediate homophilic adhesion
the n-term of one cadherin bind to a another n-term in a cadherin in another cell -- at the edge it is filled with Ca2+ to limit flexing
104
why do cadherins attach to actin filaments
they are small filaments so they are easy to grab
105
does myosin two walk upwards or downwards if actin filaments are being pulled down by non-muscle myosin 2
upwards
106
what does the domain in alpha-catenin do when stretched by tension
it exposes a binding site for vinculin which in-tern recruits more actin filaments
107
what is huluwa (zebrafish embryo example)
a protein that is located on the plasma membrane that is essential for the organizer and body axis formation
108
what can the folding of epithelial sheets do
make a epithelial tube which helps with vertebrate development
109
why do tight junctions contain strands of transmembrane adhesion proteins
it allows for the termini to both be on the cytoplasmic side where they can interact with adaptor proteins (like actin filaments so they can move)
110
how are gap junction made one-on-one from two different cells
they use signals to trigger the other cell to make a gap junction in the same spot
111
what do selectins mediate
transient cell-cell adhesion in the stream (a white blood cell will roll on an endothelial cell and get let in by integrin-dependent adhesion and emigration)
112
what do lectin domains of selectins on endothelial cells bind too in blood vessels
specific oligosaccharides of glycoproteins or glycolipids with low affinity
113
what does integrins on white blood cells bind too
specific Ig-family proteins (ICAM) on the surface of endothelial cells that enable white blood cells to stop and leave the blood stream
114
what is ICAM
intercellular cell adhesion molecule (ICAM) is expressed on endothelial cells and some other cell types; it binds heterophilically to integrin on white blood cells
115
what is NCAM
neural cell adhesion molecule (NCAM)
expression in neurons and many other cell types
mediated homophilic binding (fine tining compared to cadherins)
116
what is nectin*
expressed in many cell types, and often found at adherens junctions where it interacts with cadherins to establish and strengthen specific cell-cell interactions during tissue formation.
117
what is integrin
transmembrane heterodimers that link the extracellular matrix to the cytoplasm
its N-term is extracellular and binds to sequences in fibronectin or other matrix proteins
118
what does beta-integrins c-term bind to
adaptor proteins that interact with actin filaments directly-- like talin
talin also brings vincilins, which attach to more actin filaments
119
in hemidesmosomes, what do integrin filaments do
anchors the cell to outside the basal lamina, and attaches to keratin intimate filaments inside via adaptor proteins BP230 and plectin
120
What happens when a integrin switches between an active and inactive confirmation
inactive (no tension) are small and compact
active (tension), they are elongated and attach to actin filaments as they are near the cell membrane and have a lot of them.
121
how do integrins get activated
thrombin binds to its receptor which sends a signal that activates Rap1
Rap1 kicks GDP out and GTP goes in triggering the recruitment of talin and Kindlin
talin and kindlin then activate B-integrin
122
tension across cell-matrix junction stimulates what
the recruitment of vinculin and other proteins by talin, this strengthens the attachment of the junction to the cytoskeleton
123
what is the advantage of having so many signaling steps in a cell signaling pathway
regulation, and multiple pathways
124
what are the four main types of cell signaling
contact-dependant,
paracrine
synaptic
endocrine
125
What are the three major classes of cell-surface receptor proteins
- Neurotransmitter ion-channel coupled receptors
-g-protein coupled receptors
-enzyme coupled receptors
126
What are the two main ways that signals get relaid in cells
by phosphorylation and dephosphorylation by protein kinases and ATP (not always) , or signaling by GTP binding
127
What do other small molecules like cyclic amp Ca2+ and diacylglycerol (via diffusion) act as in intracellular signaling
secondary messengers
128
What are the five ways cells can adjust their sensitivity to a signal (usually termination)
negative feedback, delayed feedforward, receptor inactivation (via phosphorylation and ubiquitination of the receptor proteins) , receptor sequestration (reversible), and receptor destruction (irreversible)
129
what is a commmon feature for the five ways of signal termination and why
the receptor starts on the outside of the cell holding a ligand, likely to receive the signal to do one of the pathways
130
What do trimeric G-protein coupled receptors do
when it gets bound by a signaling molecule, GPCRs act like a GEF and induce an alpha subunit to release GDP to GTP
this activates the alpha and beta-gamma subunits, which in turn get a response
131
What does Cyclic AMP do with relation to serotonin
it is found to put you to sleep,
sense serotonin is a neurotransmitter and a ligand for a GPCR, when cells are fed with serotonin the cell shows a 20x increase in cyclic AMP for 20 seconds
132
which subunit of trimeric protein (Gs) activates adenylyl cyclase
the alpha subunit
133
What is CREB
a protein that recruites a transcription co-activator CBP
it gets activated when PKA gets activated Via cAMP levels rising
134
what does IP3 increase
Ca2+
135
what does diacylglycerol do and how does it get activated
it recruites PKC to the cyctosolic face (which is phosphorlated)
136
What does Nitric oxide gas do
It mediates signaling between cells
the role of it is to relax smooth muscles in a blood vessel wall
it usually increases as Ca2+ levels rise, causing it to be made from arginine
137
what does smell and vision depend on
GPCRs (g-coupled protein receptors)
-- relies on Na+, cAMP-gated cation channels, and cAMP
138
what are the major cytoskeletal filaments in the cilia
microtubules
139
what does the odorant (via olfactory neuron) receptor from ancestral and domestic mosquitoes show us about mosquitos
Different receptors allow for different mosquitoes to smell and find food
140
how do you activate tyrosine kinases (RTKs)
they have a single protein that comes in and dimerizes two trans autophosphorylation kinase domains
141
what are the advantages of having ligand dimers
- specificity
- affinity
- allosteric effects
- stability
- cooperative interactions
142
what causes the dimerization of RTKs
the binding of EGF (epidermal growth factors), and then that causes the receiver and activator to trans- autophosphorylate multiple tyrosines in the c-term of both
143
what are the two receptors involved in the dimerization of RTKs
EGFR, epidermal growth factor receptor, and ...?
144
what binds to phosphorylated tyrosines in enzyme coupled receptors
proteins with SH2 domains -- usually in a protein with a PDGF (platelet-derived growth factor with 5 phosphorylation docking sites )
145
What mediates sigaling by most RTKs
a monomeric GTPase known as adaptor protein Grb2 which recognized a specific phosphorylated tyrosine on the activated receptor through its SH2 domain
SH3 will then recruit other factors
146
what does SH3 recruit once simulated by SH2 and Grb2
SOS, a ras -GEF, and sos will end up activating ras GEF by stimulating the replacement of GDP on by GTP on ras
147
what does ras recruit once GTP makes it active
a MAP kinase signaling molecule,
ras recruits Raf and activates it
Raf activates Mek
Mek activates Erk
Erk phosphates a variety of target proteins
148
How does a growth cone collapse the cytoskeleton via the Rho family and GTPases
it couples cell-surface receptors to the cytoskeleton,
RhoA-GTP ultimately induces the collapse via phosphotyrosines and the binding of a cell surface ephrin a1 protein (see figure 15-52)
149
When unspecified epithelial cells become a neural cell what happens to the surrounding cell
the one cell (the winner) will strongly express delta and inhibits is neighbors from developing into a neural cell-- the delta ligand will interact with the surface of neighboring cells in a contact dependent manner
150
What are nuclear receptors
ligand-modulated transcription regulators
some extracellular signal molecules that bind to intracellular receptors-- mostly all of them are small and hydrophobic, like testosterone or the hydroxylated form of vitamin D3
151
do nuclear receptors like the orphan nuclear receptors have a long or short signaling pathway and what does it require
short
it requires a DNA-binding domain, a ligand-binding domain, a ligand, and coactivators
152
how does the circadian clock function to control gene expression
by negative feedback loops using the time gene and protein, the Per gene and protein, and mRNAs.
the per and tim proteins make a dimer phosphorylation, which regulates the formation and degradation (at night)
153
what are the 3 plant clocks made of
TOC1, CCA1, and LHY
154
when does LHY and CCA1 get expressed
when light hits the plant LHY and CCA1 gets expressed and activate other morning genes
they are redundant genes to each other and are both expressed in the morning
155
when does TOC1 get expressed
it gets repressed by LHY and CCA1 during the day, but at night it doesn't and allows for the transcript levels of this gene to rise (evening gene)
