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MCB 2210 Cellular Biology > BLOCK 3 > Flashcards

BLOCK 3 Flashcards

1
Q

cytoskeleton

A

group of several different types of filamentous protein polymers

can form stable structures but is dynamic

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2
Q

accessory proteins

A

control the assembly and function of cytoskeleton

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3
Q

cytoskeleton properties

A

polar (not symmetric)

some structures are long lived, others are transient

can resist external forces and generate pushing or contractile ones

polymers can grow and shrink as subunits are assembled or disassembled

can rapidly reorganize in response to environment

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4
Q

functions of cytoskeleton

A

cell morphogenesis

cell organization

cell division

cell adhesion

cell motility

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5
Q

4 polymers in cytoskeletons

A

actin filaments (F-actin)
microtubules
intermediate filaments
septins

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6
Q

what drives cell dynamics?

A

actin and microtubule cytoskeletons

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7
Q

actin

A

most abundant protein in eukaryotic cells

1-20% of total proteins in cells

sequence has been conserved through evolution (actin is 80% identical in human and ameoba)

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8
Q

actin in simple eukaryotes

A

one gene

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9
Q

actin in mammals

A

several actin genes that produce multiple types of actin

a-actin in muscle
b-actin and y-actin in non muscle cells

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10
Q

actin filaments

A

G-actin monomers bind ATP and compose F-actin helical polymers

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11
Q

G-actin monomer

A

separated into two lobes by a cleft that binds ATP or ADP and Mg2+

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12
Q

F-actin

A

helical polymer of G-actin subunits held together by non-covalent interactions

all oriented in the same direction – polar

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13
Q

Barbed end of actin

A

+ end; elongates up to 10x faster than the pointed end

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14
Q

pointed end of actin

A
  • end; elongates slower than barbed end
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15
Q

polymerization of actin in vitro

A

salts and G-actin

reversible

different than in the cell

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16
Q

ways of monitoring actin polymerization

A

measuring the scattering of light (F-actin scatters more than G-actin)

pyrene-actin and spectrophotometry

visualizing filaments by fluorescence and EM

conducting sedimentation analysis (F-actin sediments more rapidly because larger than G-actin)

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17
Q

pyrene-actin and spectrophotometry

A

attach fluorescent tag (pyrene) to actin which fluoresces more brightly when incorporated into AF-actin than in G-actin

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18
Q

first step in actin polymerization

A

nucleation

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19
Q

nucleation of actin

A

formation of a stable seed “nucleus” of three actin monomers which can elongate to form a filament

lag phase because is slow since actin dimers are unstable

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20
Q

how to eliminate lag phase

A

add nucleating factors or actin filaments

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21
Q

second step in polymerization

A

elongation

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22
Q

elongation of actin

A

subunits add onto nuclei leading to growth. fast phase

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23
Q

third step in actin polymerization

A

steady state

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24
Q

steady state in actin

A

no net increase or decrease in amount of polymerized actin. elongation is balanced by shrinkage

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25
Q

critical concentration in actin

A

G-actin concentration in equilibrium with F-actin concentration

concentration of G actin at steady state

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26
Q

CC in actin in vitro

A

0.2uM

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27
Q

if the free subunit concentration is above CC

A

subunits will add onto the ends of filaments

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28
Q

if the free subunit concentration is below CC

A

subunits will be lost from the ends of filaments

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29
Q

how to demonstrate kinetics of actin filament ends

A

mix G-actin and F-actin with myosin S1 fragment to mark filament polarity. Newly assembled filaments are much longer at the plus end

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30
Q

ATP hydrolysis & CC

A

each actin monomer has an ATP that is hydrolyzed to ADP after its assembly into the polymer

ATP hydrolysis causes a conformational change that destabilizes the interactions within the filament

in the presence of ATP the two ends of an actin filament have different critical concentrations

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31
Q

CC+

A

0.12uM

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32
Q

CC-

A

0.6uM

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33
Q

at free actin concentrations >0.6uM

A

filaments grow at both ends

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34
Q

free actin concentrations <0.12uM

A

actin will shrink at both ends

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35
Q

free actin concentrations between 0.12uM and 0.6uM

A

filaments grow at + end and shrink at - end

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36
Q

actin treadmilling

A

in the presence of ATP, actin will polymerize until the monomer concentration falls between the CCs of the two ends and will be treadmilling at steady state

leads to flux of actin subunits through the filament

not in equilibrium because requires ATP hydrolysis

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37
Q

total actin concentration in cells

A

200uM

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38
Q

G-actin in cells

A

80uM

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39
Q

F-actin in cells

A

120uM

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40
Q

actin binding proteins (ABPs)

A

regulates assembly and disassembly of actin

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41
Q

actin sequestering proteins

A

maintains actin in monomer form by binding to monomers and preventing them from polymerizing

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42
Q

Thymosin B4

A

primary monomer sequestering protein

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43
Q

profilin

A

monomer binding protein that promotes G-actin to exchange ADP for ATP

binds + end of G-actin to inhibit initial nucleation but promotes actin polymerization onto existing filaments

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44
Q

thymosin B4 + profilin

A

compete to control growth of actin filaments

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45
Q

cofilin

A

interacts with and severs ADP-actin filaments leading to enhanced - end depolymerization of growth from new + ends

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46
Q

actin nucleating proteins (nucleators)

A

accelerate the initial kinetics of polymerization

and control cell shape, movement, and division during health and disease

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47
Q

formin

A

nucleators that quickly generate long unbranched filaments

dimerizes and facilitates barbed (+) end growth while remaining attached to the (+) end

humans have 15

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48
Q

Tandem actin monomer binding proteins

A

nucleate unbranched filaments

remain at (-) end during filament assembly

> 7 in humans

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49
Q

ARP 2/3 complex

A

only actin nucleator that generates branched filaments

works with WASP family proteins to activate nucleation activity

causes formation of new actin filaments that is capped at its pointed (-) end by ARP2/3 but is free to elongate at barbed (+) end

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50
Q

phalloidin

A

prevents filament depolymerization (further polymerization is not affected)

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51
Q

cytochalasin

A

binds to + end of filaments and caps them; prevents elongation

CC shifts to - end and filaments eventually depolymerize

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52
Q

cytochalasin effects

A

blocks locomotion and cytokinesis; reversible

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53
Q

latrunculin

A

binds to actin monomers and prevents polymerization by sequestering them

causes rapid disassembly of actin filaments

reversible

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54
Q

microtubules

A

polymer of tubulin subunits in a cylindrical filament 24nm in diameter

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55
Q

subunit of microtubules

A

tubulin heterodimers

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56
Q

tubulin heterodimers

A

a-tubulin and b-tubulin

ab dimers do not come apart under physiological conditions

mammals have many a and b tubulin genes

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57
Q

protofilaments

A

has plus end and minus end

composed of stacked tubulin heterodimers

13 interact laterally to create a barrel for a microtubule

intrinsic polarity

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58
Q

cryo-EM

A

proteins frozen in liquid nitrogen vapor instead of the conventional fixation and heavy metal staining

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59
Q

ab tubulin heterodimers bind

A

GTP/GDP

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60
Q

B-tubulin ___ hydrolyze GTP to GDP

A

can

can also exchange GTP for GDP

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61
Q

A-tubulin ___ hydrolyze GTP to GDP

A

cannot

irreversibly binds to GTP

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62
Q

minus end (slow growing) of microtubule

A

ringed with a-tubulin

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63
Q

plus end (fast growing) of microtubule

A

ringed with b-tubulin

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64
Q

MTOC / centrosome

A

inside the cell the minus ends of microtubules are usually capped and embedded here

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65
Q

microtubule dynamics in vitro

A

polymerization of pure tubulin initiated by raising temperature to 37 degrees and depolymerization at 4 degrees

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66
Q

tubulin polymerization monitoring

A

measuring scattering of light (polymer scatters more than monomer or dimer)

attach fluorescent tag (rhodamine or fluorescein) to tubulin

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67
Q

microtubule assembly kinetics

A

similar to actin

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68
Q

at tubulin concentrations below CC

A

polymerization does not take place

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69
Q

tubulin concentrations above CC

A

polymerization is induced and microtubules assemble until free tubulin concentration falls to CC and steady state is reached

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70
Q

elongation of MT

A

GTP bound ab-tubulin heterodimers add onto + ends of MTs

B-tubulin hydrolyzes GTP to GDP after it is incorporated into the MT

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71
Q

the growing (+) end of the microtubule will contain

A

GTP B-tubulin

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72
Q

the bulk of the microtubule will contain

A

GDP B-tubulin

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73
Q

GTP cap

A

GTP b-tubulin on + end of mirotubule

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74
Q

how can the GTP cap be lost?

A

dissociation of GTP subunits from the MT end or by GTP hydrolysis

loss of GTP cap destabilizes the polymer

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75
Q

why does loss of the GTP cap destabilize the polymer?

A

GTP tubulin more readily makes lateral interactions with other protofilaments that maintain cylindrical structure of the end

if the MTs have a GDP cap these connections are weakened and the protofilaments tend to splay apart

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76
Q

protofilament splaying

A

destabilizes the MT and leads to depolymerization or shrinkage

off rate of GDP tubulin is high and disassembly of the MT can be rapid and can result in complete disassembly of that MT

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77
Q

catastrophe

A

complete disassembly of MT after loss of GDP cap

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78
Q

rescue

A

MT regrowth after catastrophe

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79
Q

individual microtubules have dynamic instability

A

rapidly change length

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80
Q

dynamic instability

A

alternation between growing and shrinking states occur randomly and is due to the conversions between a GTP and a GDP cap at the plus end

at steady state, total amount of polymer in bulk solution of MT is constant but any individual MT can be either elongating or shortening

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81
Q

total tubulin concentration in cells

A

10-20uM

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82
Q

cc of tubulin in cells

A

0.03uM

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83
Q

why do microtubules not form randomly in cells if polymerization is highly favored from their Ccs?

A

kinetic barrier of nucleation

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84
Q

microtubule-associated proteins (MAPs)

A

aids microtubule assembly

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85
Q

microtubule organizing center (MTOC)

A

nucleates and organizes cellular microtubules

MTs radiate from here

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86
Q

centrosome

A

MTOC in interphase cells

consists of a pair of centrioles surrounded by a pericentriolar material

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87
Q

MTs in interphase cells

A

minus end of the MT is embedded in the centrosome and plus end faces the cytosol

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88
Q

taxol

A

binds MTs and stabilizes the polymer, preventing disassembly

blocks MT dependent processes (mitotic spindle assembly)

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89
Q

colchicine

A

binds to tubulin dimer so when it polymerizes, further polymerization is prevented on the MT end

promotes formation of a GDP gap and MT destabilization

reversible

90
Q

nocodazole

A

binds to tubulin subunits and triggers depolymerization

reversible

91
Q

pericentriolar material (PCM)

A

MT minus ends embedded here

92
Q

y-TURC

A

protein complex of y-tubulin and other proteins; anchors MTs at the centrosome

nucleates assembly of pure tubulin

93
Q

y-tubulin

A

nucleates microtubules at the centrosome

conserved in all eukaryotes and is distinct from ab-tubulin

does not polymerize itself but exists in a protein complex called y-TURC

94
Q

ABPs

A

control assembly, disassembly, organization, and movement of actin filaments

95
Q

formins

A

bind monomers and filaments

96
Q

ARP2/3 complex

A

binds monomers and filaments

97
Q

Thymosin b4

A

binds monomers

98
Q

profilin

A

binds monomers

99
Q

latrunculin

A

actin; depolymerizes by binding actin subunits

100
Q

cytochalasin B

A

actin; depolymerizes by capping filament plus ends

101
Q

phalloidin

A

actin; stabilizes by binding along filaments

102
Q

taxol

A

MT; stabilizes by binding along filaments

103
Q

nocodazole

A

MT; depolymerizes by binding tubulin subunits

104
Q

colchicine

A

MT; depolymerizes by capping filament ends

105
Q

Actin binding proteins (ABPs)

A

control assembly, disassembly, organization, movement of actin filaments

106
Q

capping proteins

A

stabilize filaments by binding to their ends

stabilized bc prevents addition or loss of subunits from ends

107
Q

CapZ

A

capping protein; caps the + end of filaments

108
Q

tropomodulin

A

caps - end of actin filaments

109
Q

stabilizing proteins

A

bind along length of filaments

110
Q

tropomyosin

A

binds subunits along filaments and stabilizes polymerized state

111
Q

severing/depolymerizing proteins

A

disassemble actin filaments and higher order structures

112
Q

cofilin

A

enhances rate of actin depoly by severing actin filaments and creating more (-) ends

113
Q

gelsolin

A

severs actin filaments and breaks them into short fragments but remains bound to (+) end (activated by calcium)

114
Q

cross-linking proteins

A

have two actin-binding domains separated by spacer domains to produce assemblies of different types

115
Q

filamin and spectrin

A

cross linking proteins with longer, more flexible spacers

arrange filaments in gel-like networks

116
Q

fimbrin, vilin, fascin

A

cross linking proteins with shorter, more rigid spacers

organize filaments into aligned bundles (and lead to tight bundles)

117
Q

a-actinin

A

crosslinks filaments into bundles that are arranged into parallel and antiparallel arrays for contraction

118
Q

membrane-actin linker proteins

A

attach actin cytoskeleton to the plasma membrane

interactions between integral membrane proteins and actin filaments

119
Q

ERM proteins

A

act as linker between F-actin and integral membrane proteins

120
Q

spectrin

A

connects actin to membrane proteins

121
Q

dystrophin

A

links cortical actin to muscle cell membranes via dystroglycan complex

122
Q

cell cortex

A

actin-rich layer beneath plasma membrane

gives mechanical strength and allows surface movments

123
Q

spectrin-based membrane skeleton

A

lies immediately adjacent to plasma membrane

124
Q

ezrin

A

links bundled actin to the membrane in microvilli

125
Q

hereditary spherocytic anemias

A

mutations in genes encoding proteins of RBC membrane skeleton (spectrin, ankyrin, band 4.1)

rupture easily

126
Q

muscular dystrophies

A

genetic; weakening of skeletal muscle

127
Q

Duchenne muscular dystrophy (DMD)

A

dystrophin is messed up; plasma membrane of muscle cells weaken and eventually rupture

128
Q

Microtubule associated proteins (MAPs)

A

control assembly, disassembly, organization, and movement of microtubules

129
Q

tubulin oligomer binding proteins

A

stathmin can bind and sequester tubulin heterodimers or oligomers and promote catastrophe and depoly

130
Q

nucleating proteins

A

y-TURC nucleates MT assembly at centrosome

131
Q

end binding proteins

A

+TIPS bind to the (+) end of MTs

132
Q

+TIPS

A

EB1

CLIP-170

133
Q

EB1

A

+TIP that regulates (+) end dynamics and can link MTs to organelles

134
Q

CLIP-170

A

+TIP that mediates interaction of chromosomes and membranes with (+) end

135
Q

severing proteins

A

severs MTs and promotes depoly at (-) ends

katanin

136
Q

katanin

A

severing protein

137
Q

depolymerizing proteins

A

a subset of kinesins promote MT depolymierzation at (+) end by binding to and inducing protofilament curling

138
Q

kin13

A

depolymerizing protein

promotes depolymerization of GTP-tubulin and does not involve hydrolysis of GTP cap

139
Q

polymer-binding MAPs

A

stabilize MTs by binding to their sides

enhance assembly by stabilizing nuclei

organize MTs into bundles

mediate Mt interactions with other proteins

140
Q

polymer-binding MAPs domains

A

MT binding domain

projection domain

141
Q

MT binding domain of polymer-binding MAPs domains

A

binds several tubulin dimers at once and helps stabilize polymer

142
Q

projection domain of polymer-binding MAPs domains

A

interacts with MTs or other structures such as IF

143
Q

Tau

A

organize MTs in neuronal axons and dendrites

144
Q

MAP2

A

organize MTs in neuronal axons and dendrites; spacing bw MTs is greater than in Tau expressing cells

145
Q

Tau aggregation in an insoluble form

A

involved in Alzheimer’s disease pathogenesis

146
Q

myosin motor proteins

A

move along actin filaments by coupling the energy from ATP hydrolysis to conformational changes

mechanochemical enzymes

147
Q

most myosins are ____ end directed motors

A

(+)

148
Q

myosin composition

A

heavy and light chains

149
Q

heavy chain of myosin

A

head, neck, and tail domains

150
Q

head (motor) domain of myosin

A

actin binding and ATPase activities

151
Q

neck domain of myosin

A

regulatory function, site of attachment for regulatory and essential light chains or calmodulin

152
Q

tail domain of myosin

A

differ depending on properties

153
Q

myosin II

A

first described as motor protein in muscle that powers contraction

2 heavy and 2 light chains

tails mediate polymerization of myosin II into bipolar thick filaments

154
Q

actin filament sliding assay

A

motor function of myosin is demonstrated by filament sliding assays

myosin molecules stuck to glass, add actin filaments

155
Q

ATP hydrolysis is coupled to myosin ____

A

motility

156
Q

myosin ATPase activity is _____

A

actin-activated

157
Q

myosin-actin cross-bridge cycle: rigor state

A

ATP binding site is empty and myosin is tightly bound to actin

0

158
Q

myosin-actin cross-bridge cycle: ATP binding

A

when ATP binds to myosin, ATP binding cleft closes, opens actin binding cleft and weakens interaction with actin

1

159
Q

myosin-actin cross-bridge cycle: ATP hydrolysis

A

after detaching from actin filament ATP is hydrolyzed to ADP and pi

conformational change and causes head to move to new position before rebinding the filament

2-3

160
Q

myosin-actin cross-bridge cycle: Pi release

A

pi released and myosin head changes

POWER STROKE

exerts force on actin filament causing it to move

restoring to rigor conformation

4

161
Q

myosin-actin cross-bridge cycle: ADP release

A

after ADP is released, myosin remains in rigor state and ATP exchange releases the head from actin

5

162
Q

myosin I

A

shorter tail domains, single-headed, do not assemble into filaments

163
Q

myosin I tails

A

mediate movement of filaments past one another

attach to and move vesicles or organelles

164
Q

Myosin V

A

dimers; vesicle transport

165
Q

which myosins have conserved head domains with variable tail regions?

A

III, IV, VI-XV

166
Q

myosin VI

A

moves towards (-) end of F-actin

167
Q

myosin V dimrs

A

walk along F-actin

processive movement: one head always in contact with the actin

168
Q

myosin VI mutation

A

deafness in mice

169
Q

myosin VII mutations

A

deafness and blindness in humans

170
Q

two classes of MT motor proteins

A

kinesins and dyneins

171
Q

kinesins

A

MT-activated mechanochemical ATPases

172
Q

3 classes of kinesins

A

Kin-N
Kin-C
Kin-I

differ in location of motor domain in primary sequence of protein

173
Q

Kin N kinesins

A

motor domain at N-terminus

+ end directed

174
Q

Kin C kinesins

A

C terminal motor domain

(-) end directed

175
Q

Kin I kinesins

A

internal motor domain

do not move along MTs but bind MT ends and promote protofilament peeling

176
Q

conventional kinesin

A

two heavy chains, two light chains

motor head at N term of heavy chain

neck domain

a-helical coiled-coil tail domain

kinesin light chains mediate interaction of kinesin with membrane vesicles

177
Q

microtubule gliding assay

A

demonstrates motor function of kinesin

178
Q

kinesin cross bridge cycle

A

similar to myosin

179
Q

processive motility of kinesin motor proteins

A

movement over long distances without dissociating

important for vesicle and organelle transport

180
Q

dyneins

A

enzymes that couple the energy from ATP hydrolysis to (-) end directed movement along MTs

2-3 heavy chains

181
Q

two types of dyneins

A

cytoplasmic

ciliary/flagellar

182
Q

dynactin complex

A

links dynein to cargo

critical for cytoplasmic dynein

mediates attachment of dynein to vesicles and organelles

183
Q

charcot-marie-tooth disease and kidney diseases

A

kinesin deficiencies

184
Q

chronic infections of respiratory tract due to nonfunctioning cilia

A

dynein deficiencies

185
Q

ALS

A

mutation in dynactin complex

186
Q

where are the microtubule + ends

A

edge of cell

187
Q

where are the - ends in MT

A

in centrosomes

188
Q

are kinesins or dyneins important for melanosome localization in high cAMP?

A

kinesins

189
Q

are kinesins or dyneins important for melanosome localization in low cAMP?

A

dyneins

190
Q

what will melanosome organization look like if you treat cells with taxol?

A

MTs stabilized and grow at plus ends

191
Q

actin functions

A

membrane protrusion
cell adhesion
endocytosis and trafficking
cytokinesis

192
Q

actin functions: membrane protrusion

A

lamellipodia and filopodia

193
Q

actin functions: cell adhesion

A

stress fibers and focal adhesions

194
Q

actin functions: endocytosis and trafficking

A

clathrin pits and endosomes

195
Q

microtubule functions

A

organelle positioning

anterograde transport

retrograde transport

mitosis

196
Q

microtubule functions: organelle positioning

A

ER and golgi

197
Q

microtubule functions: anterograde transport

A

ER to golgi to plasma membrane

198
Q

microtubule functions: retrograde transport

A

Endosome to golgi to ER

199
Q

lamellipodia and filopodia

A

membrane protrusions that move adhere to substrate

have stress fibers that function in cell adhesion and contraction

200
Q

fibroblast

A

cell of connective tissue

201
Q

lamellipodia

A

thin sheet like structures of fibroblast

202
Q

filopodia

A

thin needle-like projections or spikes on fibroblast

203
Q

what happens when you microinject cells with fluorescently labeled actin?

A

actin is incorporated into filaments at extreme leading edge and polymerization takes place there

204
Q

what drives membrane protrusion?

A

assembly of actin filaments

205
Q

retrograde flow

A

after actin filaments are nucleated, the network of filaments moves backward to interior of cell

cofilin is the major depolymerizing activity behind the leading edge

206
Q

actin filament orientation

A

(+) ends facing membrane in the direction of protrusion

207
Q

lamellipodia actin filament organization

A

branched

208
Q

filopodia actin filament organization

A

parallel bundles

209
Q

stress fibers

A

long bundles of actin filaments that lie along the lower surface of the cell

ends terminate at focal adhesions

210
Q

focal adhesions

A

transmembrane structures that attach cell to underlying substrates

211
Q

how are dynamic actin specializations triggered to form?

A

small G protein class: Rho GTPases

212
Q

Rho-family GTPases

A

Rho
Rac
CDC42

213
Q

Guanine nucleotide dissociation inhibitors (GDIs)

A

stabilize inactive GDP-bound form

214
Q

WASP family proteins interacting with Rho-family GTPases

A

WASP proteins are actiavted by small GTPases to assemble actin in membrane protrusions

usually is autoinhibited but Cdc42-GTP binding relieves the autoinhibition

crucial for signaling cascades to activate WASP / formins

215
Q

microinjection of Rac-GTP

A

formation of lamellipodia and membrane ruffles

216
Q

microinjection of Cdc42-GTP

A

formation of filopodia

217
Q

microinjection of Rho-GTP

A

formation of stress fibers

218
Q

what does actin cytoskeleton direct?

A

endocytosis endosome trafficking, endosome rocketing, and membrane sorting

219
Q

what does branched actin assembly facilitate?

A

endocytic internalization

220
Q

what does MT cytoskeleton direct?

A

organelle positioning, membrane transport, secretory pathway

221
Q

how does golgi positioning depend on MT?

A

golgi is usually near the centrosome

MT position golgi near ER

222
Q

stress fibers contract in response to phosphorylation of non-muscle myosin II light chain by MLCK

A

know it

MCB 2210 Cellular Biology (3 decks)

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