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BIO230 Final > Week 7 > Flashcards

Week 7 Flashcards

1
Q

How do changes in gene expression lead to development?

A
  • cell types
  • tissues
  • organs
  • organisms
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2
Q

How do cells change during development?

A
  • numbers
  • shapes
  • functions
  • interactions
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3
Q

What happens if organisms lose control of interactions, shapes, cell numbers, and/or functions?

A
  • cells divide too much
  • cancer
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4
Q

How are cells and tissues organized spatially?

A
  • membrane trafficking
  • cytoskeletal networks
  • cell adhesion
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5
Q

What does a polar cell mean?

A
  • different at either end
  • apical domain
  • basolateral domain
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6
Q

What can a polarized cell do?

A
  • have different functions at different cell regions
  • define inside vs outside
  • transmit signals from one end to the other
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7
Q

What is membrane trafficking?

A

the processes that control the movement of proteins and lipids within the cell

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8
Q

What are the two main types of membrane transport?

A

exocytosis and endocytosis

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9
Q

How is membrane trafficking done?

A
  1. exocytosis directly to the target domain
  2. exocytosis to any domain then endocytosis followed by recycling to the target domain
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10
Q

What is a special characteristic of some trafficking routes?

A

polarized

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11
Q

Where are proteins organized for membrane trafficking?

A

at sorting stations

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12
Q

How are different trafficking routes balanced?

A

by retrieval pathways

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13
Q

How is the secretory pathway considered polar?

A

ER->Golgi->plasma membrane
- different beginning and end

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14
Q

How are proteins organized at sorting stations in the secretory pathway?

A

the sorting station is the trans-Golgi network

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15
Q

How are different routes balanced by retrieval pathways in the secretory pathway?

A

ER retrieval from Golgi

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16
Q

What is constitutive secretion?

A
  • the “default pathway” for the transport of proteins and lipids, occurring continuously without specific signals
  • present in all eukaryotic cells.
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17
Q

What is the role of clathrin-coated vesicles in constitutive secretion?

A
  • return membrane components back to the Golgi
  • shrinks the vesicle and helps concentrate the cargo for secretion
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18
Q

What is regulated secretion?

A
  • a process where vesicles containing cargo are fully formed but do not fuse with the plasma membrane until a specific signal is received
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19
Q

Give an example of regulated secretion.

A
  • the release of histamine from mast cells
  • The vesicles containing histamine remain in the cell until a signaling event triggers their fusion with the plasma membrane
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20
Q

What happens if a cell needs extra membrane material?

A

regulated secretion can deliver extra membrane material

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21
Q

When would a cell need extra membrane material?

A
  • cytokinesis (cell division)
  • phagocytosis (engulfing things)
  • plasma membrane repair
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22
Q

What is exocytosis?

A

the process by which cells transport materials out of the cell via vesicles that fuse with the plasma membrane

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23
Q

What is endocytosis?

A

the process by which substances are brought into the cell

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24
Q

How are proteins removed from the plasma membrane?

A

via endocytosis

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25
Q

Why are endocytosis trafficking routes considered polar?

A

plasma membrane->early endosome-> lysosome

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26
Q

What is considered the sorting station for proteins in the endocytosis pathway?

A

endosomes

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27
Q

How are different routes balanced by retrieval pathways in the endocytosis pathway?

A

re-secretion to the plasma membrane

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28
Q

What are the main options for endocytosed proteins?

A
  1. Recycling to the same domain of the plasma membrane.
  2. Transcytosis to the other domain of the plasma membrane.
  3. Degradation in the lysosome.
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29
Q

What role do LDL receptors play in cholesterol uptake?

A
  • bind to LDL particles, which contain cholesterol
  • the LDL-receptor complex is internalized into the cell via endocytosis
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30
Q

What happens to LDL after it is internalized by the cell?

A
  • LDL is transported to early endosomes (either be recycled back to the plasma membrane or directed to lysosomes for degradation)
  • releasing cholesterol
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31
Q

What is the fate of the LDL receptor after it has facilitated cholesterol uptake?

A
  • can be recycled back to the plasma membrane to participate in further rounds of cholesterol uptake
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32
Q

What is the role of clathrin in the endocytosis of LDL?

A

coats the budding vesicles that internalize the LDL-receptor complex

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33
Q

What are the types of membrane changes during vesicle trafficking?

A
  1. vesicle forms from the donor membrane into the cytoplasm
  2. vesicle fusion: vesicle merges with a target membrane
  3. vesicle forms from a donor membrane away from the cytoplasm
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34
Q

What type of vesicles does clathrin mediate the formation of?

A
  • clathrin-coated vesicles
  • involves transporting cargo into the cell from the plasma membrane into the cytoplasm
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35
Q

What are the different protein coats?

A
  1. COP1-coated vesicles: from Golgi to ER, between different Golgi cisterna
  2. COP2-Coated vesicles: from ER to Golgi
  3. Clatherin-Coated vesicles: from Golgi and plasma membrane to endosome
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36
Q

What are SNARE proteins?

A

a group of proteins that mediate the fusion of vesicles with their target membranes

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37
Q

What are the two main types of SNARE proteins involved in vesicle fusion?

A

t-SNAREs (target SNAREs) and v-SNAREs (vesicle SNAREs)

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38
Q

How do t-SNAREs and v-SNAREs interact during vesicle fusion?

A

must be on opposite membranes to interact, forming a complex that facilitates the fusion of the vesicle

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39
Q

What is the primary function of ESCRT proteins?

A

the formation of vesicles that transport proteins and lipids away from the cytoplasm (endocytosis)

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40
Q

How do ESCRT proteins contribute to vesicle formation?

A

assemble into large complexes that facilitate the budding of vesicles from the membrane

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41
Q

What is the role of ESCRT-0?

A
  • recognizes and binds to ubiquitinated proteins on the membrane
  • initiating the sorting process for cargo destined for degradation or recycling
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42
Q

What happens after ESCRT-0 binds to ubiquitinated proteins?

A

ESCRT-0 recruits ESCRT-I and ESCRT-II complexes, which further facilitate the invagination of the membrane and the budding off of vesicles

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43
Q

What is the significance of ubiquitin in the ESCRT pathway?

A

tags proteins for degradation and serves as a signal for ESCRT proteins to recognize and sort these proteins into vesicle

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44
Q

What is the relationship between ESCRT proteins and viruses?

A

Some viruses hijack the ESCRT machinery to facilitate their budding and release from host cells

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45
Q

What is the role of ESCRT-III?

A

creates the buding

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46
Q

What are phosphoinositides?

A

a class of lipids that are characterized by a glycerol backbone, a phosphate group, and an inositol sugar, which can be phosphorylated at various positions

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47
Q

How can phosphoinositides be modified?

A

can be phosphorylated on the inositol sugar at specific positions

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48
Q

What role do phosphoinositides play in cellular membranes?

A
  • Different types of phosphoinositides are found at various membrane domains and compartments
  • help to “label” different membrane domains and compartments
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49
Q

How are phosphoinositides named?

A

by their phosphoryl groups
PI(phosphorylation site positions)P(total number of phosphorylation sites)

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50
Q

What is the function of kinases and phosphatases in relation to phosphoinositides?

A

Kinases: phosphorylate phosphoinositides
Phosphatases: removes phosphate groups,
- interconversion of different PIPs.

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51
Q

What binds to phosphoinositides?

A

different proteins bind to different PIPs

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52
Q

What is the significance of PI(4,5)P2?

A

a specific phosphoinositide that targets clathrin coat assembly, p

53
Q

How are PI(4,5)P2, cargo, and clathrin bound?

A

by adaptor proteins

54
Q

What are Rab GTPases?

A

molecular switches that regulate vesicle trafficking

55
Q

What role do Rab GTPases play in vesicle targeting?

A

are molecular switches that direct vesicles to their appropriate target membranes by interacting with specific effector proteins

56
Q

What is Rab GEF responsible for?

A

the exchange of GDP for GTP
- turns on GTPase

57
Q

What is Rab GAP responsible for?

A
  • activates GTPase
  • GTP hydrolysis
  • turns GTPase off
58
Q

What is the significance of Rab5-GTP in endosomal trafficking?

A
  • crucial for the early endosome formation
  • can recruit PI 3-kinase, which helps in the membrane identity
59
Q

How do Rab GTPases interact with phosphoinositides (PIPs)?

A

can combine with specific PIPs to give membranes distinct identities, facilitating the correct targeting of vesicles

60
Q

How do Rab5-GTP, PI(3)P, and Rab5-GEF interact in vesicle trafficking?

A
  • Rab5-GEF activates Rab5 by converting it to Rab5-GTP.
  • Rab5-GTP recruits PI(3)P to the membrane, promoting the maturation of early endosomes and facilitating the fusion of vesicles with target membranes
  • more Rab5-GEF makes more active Rab5-GTP (positive feedback loop)
61
Q

How do Rabs and SNAREs work together in vesicle targeting and fusion?

A

Rabs help in the initial targeting of vesicles to their destination membranes, while SNAREs mediate the final fusion step

62
Q

What are the three main components of the cytoskeleton involved in cell polarity?

A

actin filaments, microtubules, and intermediate filaments

63
Q

How do polarized microtubules contribute to cell function?

A

transport vesicles and proteins to different ends of the cell

64
Q

What role does polarized actin play in cell behavior?

A

defines cell shape and behavior

65
Q

How do intermediate filaments contribute to cell polarity?

A

provide structural support and contribute to cell polarity

66
Q

What is the significance of dynamic rearrangements of the cytoskeleton in polarized cells?

A

allow cells to adapt their shape and function

67
Q

How does interphase crawling/migrating cell undergo dynamic rearrangements?

A

Not always:
- microtubules radiate from the cell center
- Actin enriched at the cell cortex

68
Q

How does mitosis undergo dynamic rearrangements?

A
  • microtubules form the mitotic spindle
  • actin at cell cortex disassembles
69
Q

How does cytokinesis undergo dynamic rearrangements?

A
  • microtubules keep cell components separate
  • actin forms the contractile ring
70
Q

What are polar tubulin dimers composed of?

A

1 α-tubulin and 1 β-tubulin bound by GTP

71
Q

What is the orientation of α-tubulin and β-tubulin in a polar tubulin dimer?

A

α-tubulin = minus-end
β-tubulin = plus-end.

72
Q

How do tubulin dimers assemble to form microtubules?

A
  • assemble head-to-tail to create polarized protofilaments
  • form a hollow microtubule structure of 13 protofilaments
73
Q

What is dynamic instability in microtubules?

A

rapid switching between growth and shrinkage of microtubules, primarily occurring at the ends where GTP caps are present or loss

74
Q

When are microtubules likely to grow or shrink?

A

Growth: GTP-bound heterodimers
Shrinkage: GDP-bound heterodimers

75
Q

What happens when the tubulin dimers have been in the protofilament for a while?

A

β-tubulin will cut GTP to GDP

76
Q

What are the two forms of tubulin heterodimers involved in microtubule dynamics?

A

D-form (GDP-bound) and T-form (GTP-bound

77
Q

How does GTP influence microtubule stability?

A

GTP-bound β-tubulin stabilizes the plus end of the microtubule, promoting growth
GDP-bound β-tubulin leads to instability and depolymerization (α-tubulin is ALWAYS bound by GTP)

78
Q

What is the role of the GTP cap in microtubule dynamics?

A
  • GTP cap at the plus end of a microtubule promotes polymerization and stability
  • when lost, the microtubule is more likely to undergo depolymerization
79
Q

What is the approximate rate of depolymerization at the exposed D-form heterodimer?

A

100 times faster at the exposed D-form heterodimer compared to the T-form

80
Q

What is γ-tubulin?

A

a protein that plays a crucial role in the nucleation and stabilization of microtubules at the minus ends

81
Q

Where is γ-tubulin typically found in animal cells?

A

found near centrioles

82
Q

What is the function of the γ-tubulin ring complex?

A

helps to nucleate microtubules by interacting with α-tubulin at the minus-end, stabilizing it and protecting it from depolymerization.

83
Q

How are different microtubule patterns created?

A

different patterns of nucleation

84
Q

Where do microtubules grow from?

A

γ-tubulin ring complexes located in the pericentriolar material (aren’t attached to centrosomes)

85
Q

Can γ-tubulin be found in plant cells?

A

Yes it is found on other microtubules
- γ-tubulin ring complex is attached to augmin, which is attached to a second microtubule

86
Q

What happens to microtubules in the absence of γ-tubulin?

A

microtubules may become unstable and more prone to depolymerization

87
Q

What role do microtubules play in vesicle transport?

A

serve as tracks along which vesicles and organelles are transported within the cell

88
Q

Which proteins are involved in the transport of vesicles along microtubules?

A

Microtubule-associated proteins (MAPs), kinesins, and dyneins

89
Q

How do kinesins and dyneins differ in their function?

A

Kinesins: transport vesicles and organelles towards the plus end of microtubules (away from the cell center)
Dyneins: move them towards the minus end (toward the cell center).

90
Q

What are some similarities between kinesins and dyneins?

A
  • both motors can hold onto vesicles or organelles with their other domain
  • both motors use ATP hydrolysis for energy
91
Q

What is a notable ability of Tilapia fish regarding their skin color?

A

can change their skin color through the action of microtubule motors, which transport pigment-containing vesicles

92
Q

How do kinesins and dyneins function in Tilapia fish color change?

A

Dark Tilapia: kinesins and dyneins compete for pigment-containing vesicles
Light Tilapia: kinesins are inhibited, causing the vesicles to move towards the minus ends near centrioles by dyneins

93
Q

What are the characteristics of actin monomers?

A
  • are asymmetric, which makes them polar
  • can bind and hydrolyze ATP
  • assemble into polarized actin filaments, typically forming two strands twisted together.
94
Q

How do actin filaments exhibit polarity?

A
  • a plus end and a minus end
  • The plus end is where actin monomers are added
  • the minus end is where they are removed
95
Q

What is treadmilling in the context of actin filaments?

A

the dynamic process where actin filaments maintain a constant length while monomers are added at the plus end and lost from the minus end

96
Q

What are the two subunits involved in treadmilling?

A

T-form: actin ATP-Bound
D-form: actin ADP-bound

97
Q

When is depolymerization faster for actin?

A

it’s much faster at an exposed D-form monomer

98
Q

What happens at the plus and minus end of actin?

A

Plus end: addition is fast - hydrolysis lags behind
Minus end: addition is slow - hydrolysis catches up

99
Q

What is the ARP2/3 complex?

A

a protein complex that nucleates actin filaments

100
Q

What do ARP2 and ARP3 have in common?

A

very similar structure to actin monomers

101
Q

How does the ARP2/3 complex contribute to actin filament dynamics?

A

nucleates the minus end of actin filaments and protects them from depolymerization
- plus-ends grow away from ARP2/3 complex

102
Q

How does the ARP2/3 complex interact with existing actin filaments?

A

can nucleate new actin filaments on pre-existing filaments

103
Q

What proteins regulate the activity of the ARP2/3 complex?

A

Nucleation-promoting factors (NPFs) activate the ARP2/3 complex by binding to it

104
Q

How are proteins released from ARP2/3?

A

they sever the minus end

105
Q

How do proteins shape the network of actin filaments?

A

they cap the plus-end

106
Q

What is the general structure of actin networks?

A

Polar (not perfect)
- generally minus in the middle of the cell
- generally positive at the edge of the cell

107
Q

What is the significance of focal adhesions in cell movement?

A

points where actin filaments anchor to the extracellular matrix via integrins

108
Q

What is the function of myosins in relation to actin filaments?

A

motor proteins that use ATP hydrolysis to generate force and movement along actin filaments
- actin and myosin contract to bring the lagging edge forward

109
Q

What is the significance of the lamellipodium and substratum in cell movement?

A

lamellipodium: the growing end
substratum: the floor

110
Q

How does a cell move forward?

A

the growing actin network pushes the cell leading edge forward

111
Q

What are integrins?

A

transmembrane proteins that facilitate cell-extracellular matrix (ECM) adhesion

112
Q

What is the structure of integrins?

A

heterodimers composed of two subunits, an alpha (α) and a beta (β) subunit

113
Q

What role do integrins play in cell migration?

A

anchor the cell (actin filaments) to the ECM, providing the necessary adhesion for cells to crawl and migrate

114
Q

What are the primary components involved in generating contractile forces in cells?

A

Actin and myosin

115
Q

How do myosins generate force?

A

use ATP hydrolysis for energy to “walk” towards the plus end of actin filaments

116
Q

What is the role of actin filaments in muscle contraction?

A

serve as tracks for myosin to pull against

117
Q

What are Rho family GTPases?

A

small GTP-binding proteins that act as molecular switches

118
Q

Name the main members of the Rho family GTPases.

A
  • Rho
  • Rac
  • Cdc42
119
Q

How do Rho family GTPases influence actin organization?

A

affects cell shape, cell polarity, and cell behavior

120
Q

What happens when Rho GTPases are over-activated?

A

leads to distinct patterns of actin organization, which can disrupt normal cell function and behavior

121
Q

What role does Rac-GTP play in cell movement?

A

Rac-GTP activation dominates at the leading edge of a cell

122
Q

What is the role of Rho-GTP in cell movement?

A

Rho-GTP activation at the back of the cell facilitates contraction and pulling of the cell’s rear

123
Q

What is the role of GEFs and GAPs in the function of Rho family GTPases?

A

GEFs: activate Rho GTPases by promoting the exchange of GDP for GTP
GAPs: inactivates them by accelerating GTP hydrolysis

124
Q

How do neutrophils exhibit polarity?

A

through the organization of their cytoskeleton, which allows them to have a leading edge that extends toward the target and a trailing edge that retracts

125
Q

How do bacteria influence the polarity of neutrophils?

A
  • can induce polarity in neutrophils through chemotactic signals
126
Q

What happens to neutrophils in the presence of a bacterium?

A
  • bacterium releases chemoattractant which binds to receptors in the neutrophils, which transmits a signal inside
  • Rac dominates, which results in the polymerization of actin to grows
  • Rho dominates, which results in actin-myosin contraction to bring the back end in
  • Rho and Rac inhibit each other to keep them separate
127
Q

What is symmetry breaking in the context of C. elegans?

A

refers to the process by which a fertilized egg transitions from a symmetrical state to an asymmetrical state
- creates an anterior and posterior end

128
Q

What triggers symmetry breaking in C. elegans?

A

the entry of sperm into the fertilized egg, which defines the posterior end

129
Q

How does sperm entry influence cytoskeletal polarization in C. elegans?

A

initiates events that lead to the polarization of the cytoskeleton:
- actin filaments are organized by a gradient of Rho-GTP activity
- microtubules are organized by centrosomes near where the sperm entered

BIO230 Final (5 decks)

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