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Biol 413: Cell Bio > Ch 15, 16, 19 (signaling, cytoskeleton, ECM) > Flashcards

Ch 15, 16, 19 (signaling, cytoskeleton, ECM) Flashcards

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1
Q

5 basic types of signaling (endocrine, paracrine, neuronal, contact-dependent, and autocrine)

A

contact-dependent: cell-cell specific; membrane-bound signal molecule
paracrine: short distane, local distribution; local mediator
autocrine: short distance, local distribution; local mediator (signaling cell = target cell)
synaptic: long distance, cell specific; neurotransmitter
endocrine: long distance, wide distribution; hormone

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2
Q

Describe the formation of signaling complexes by scaffolding proteins

A

Bring singaling proteins into close proximity, enhancing specificity and efficiency of the signal transmission by preventing unnecessary interactions between signaling molecules

so that their transient interactions in a crowded and heterogeneous environment of cytosol can be greatly facilitated

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3
Q

describe phosphorylation of receptor to allow docking of intracellular signals

A

phosphorylated tyrosine residues act as docking sites for intracellular signaling molecules, which in turn activate kinases and initiate signaling cascades

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4
Q

describe phospholipid modification to recruit intracellular signaling molecules

A
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5
Q

What are molecular switches and how do they work?

A
  • kinases and phosphatases
  • GTP-binding proteins
  • GEFs and GAPs
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6
Q

Kinase vs phosphatase

A

kinase- enzyme-adding phosphatate group (2 types: serine/threonine; tyrosine)
phosphatase- enzyme-removing phosphatase group

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7
Q

Ion channel- vs G-protein vs. enzyme-linked receptors

A

Ion channel : Ligand binding directly opens the ion channel, causing rapid changes in membrane potential.
G-protein coupled: Ligand binding activates a G protein which then interacts with downstream effector molecules to produce intracellular responses.
Enzyme-linked : Ligand binding activates the intrinsic enzymatic activity of the receptor or associated enzyme, leading to phosphorylation cascades.

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8
Q

what do enzymes activated by G-proteins trigger?

A

synthesis or release of second-messenger molecules that relay and amply the signal- cAMP/IP3/DAG/Ca2+

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9
Q

what do G-protein coupled receptors (Gas) activate?

A

adenylyl cyclase, which produces cAMP

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10
Q

What does cAMP do?

A

diffuses easily throughout the cell to interact with proteins in the cytosol, nucelus, and other organelles

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11
Q

What enzyme makes cAMP? what is a target of cAMP?

A

adenylyl cyclase
cAMP-dependent PKA

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12
Q

what is cAMP made of?

A

ATP

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13
Q

Order of GPCRs signaling leading to transcription of genes

A
  1. Activation of adenylyl cyclace
  2. binding of cAMP to PKA
  3. dissociation of PKA into catalytic and regulatory subunits
  4. binding of CREB to PKA
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14
Q

Explain what caffeine does

A

blocks cAMP phosphodiesterase –> levels of cAMP increase and accumulate, so keeps affecting pathway

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15
Q

phospholipase C reaction, products, and effects on a cell

A

products:
diacylglycerol activates protein kinase C
IP3 releases Ca2+ from ER

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16
Q

Diagram the structure and function of PKA, explain how mutations in different subunits affect its function

A
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17
Q

Describe calmodulin

A

When it binds to Ca2+, undergoes conformational change that allows it to bind CaM-kinase

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18
Q

What is CaMKII activated by?

A

calcium

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19
Q

what do CamKIIB knockout mice have?

A

memory impairment and fail to build nests

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20
Q

what do receptor tyrosine kinases activate?

A

Ras (active when GTP-bound; inactive when GDP-bound)

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21
Q

Why do cells use scaffolding proteins?

A

to ensure signal specificity between parallel pathways

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22
Q

Illustrate a Ras pathway and a MAP kinase cascade

A
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23
Q

Ways by which signal adaptation occurs and examples

A
  1. negative feedback
  2. delayed feed-forward
  3. receptor inactivation
  4. receptor sequestration (cholesterol)
  5. receptor destruction (receptor degraded in lysosome)
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24
Q

Describe the different signaling pathways that can lead to target specific gene transcription

A
  1. NFkB: stress and inflammatory stimulated pathways
  2. Wnt
  3. MAPK pathway
  4. PI3K/Akt/mTOR
  5. Notch pathway
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25
Q

how do cytokine receptors signal?

A

by associating with cytosolic tyrosine kinases
STAT (signal transducer and activators of transcription)

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26
Q

TGFB and Smad

A

TGFB- secreted signaling proteins
Smad- latent transcription regulators

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27
Q

wnt pathway proteins

A

Wnt- extracellular ligand
LRP- transmembrane receptor that binds wnt
Frizzled- transmembrane receptor that binds wnt
Dishevelled- cytosolic protein, recruited to activated frizzled
Axin, APC in complex with GSK3 and CK1- promote degradation of B-catenin
Groucho- transcriptional repressor

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28
Q

what does activation of frizzled and LRP do?

A

activates dishevelled and dismantles the axin-APC complex to stabilize B-catenin –> B-catenin enters nucleus and activates transcription by removing Groucho from DNA

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29
Q

Hedgehog signaling cascade pathway

A

primary cilium- membrane protrusion present in each vertebrate cell - senses env. and mediates signaling pathways
hedgehog- extracellular ligand
smoothened- transmembrane receptor present outside the cilium and enters the cilium upon pathway activation
patched- transmembrane receptor. inhibits smoothened
Gli 2- transcription factor inhibited by SuFu in absence of hedgehog
GLi3- transcription repressor modulated by Gpr161 in absence of hedgehog
SuFu- inhibits Gli2 and Gli3

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30
Q

receptors in plants vs animal cells

A
  • plants mainly have enzyme-coupled receptors
  • plant cells DONT use RTKs, steroid-hormone receptors, cAMP, and have few GPCRs
  • ethylene- gaseous hormone that regulates seed germination and fruit ripening
  • photochrome- light sensitive cytosolic serine/threonine kinase; mediates plant growth in response to light
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31
Q

ethylene signaling in plants

A

ethylene deactivates receptor –> deactivates CTR1 –> no degradation of EIN3 –> allows transcription

pathway turns on genes by relieving inhibition

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32
Q

What does binding of delta to Notch promote?

A

cleaves off Notch cytosolic tail –> moves into nucleus and regulates gene expression

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33
Q

what type of receptors do steroid hormones use?

A

intracellular receptors

nuclear receptor- bind steroid hormones and enter the nucleus to regulate gene transcription

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34
Q

cytoskeleton

A

network of protein filaments that extends throughout the cytoplasm

main functions:
support large cytoplasm volume
highly dynamic continously reorganized to fit the needs of the cell
large scale movement
muscle contraction
cell shape during development

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35
Q

Describe the role of the 3 types of cytoskeletal systems

A

actin filaments: cell motility, contraction
microtubules: mitotic spindles, cell polarity, intracellular transport
intermediate filaments: provide mechanical strength to cells; strongest of the 3; most abundant in an animal cell nucleus

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36
Q

proteins of the cytoskeletal system and their structure

A

actin filaments: protein actin, thin, 2-stranded helix
microtubules: tubulin; protein rigid hollow cylinder
intermediate filaments: fibrous intermediate filament protein; strong ropelike fibers

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37
Q

Describe, compare, and contrast the 3 types of cytoskeletal systems and how the filaments grow

A

actin filaments:
microtubules:

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38
Q

Explain what nucleation is

A

process of forming the actin oligomer needed for filmanet growth. Rate limiting step
(the time it takes to make the first short cluster. Need 3-monomer cluster)

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39
Q

Explain how the concentrations of cytoskeletal components monomers (for example actin) are maintained within the cell

A
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40
Q

Explain one simple way to generate cell polarity

A

proteins such as partitioning defective (PAR), and complexes such as Scribble, and Crumbs are responsible for polarity in epithelial cells

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41
Q

Why does so little of the actin polymerize into filaments?

A

cells keep sequestered to enable polarization as needed

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42
Q

cofilin

A
  • promotes actin depolymerization by introducing mechanical stress to the filament
  • binds actin-ADP preferentially (the one that is less stable)
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43
Q

myosin 2

A
  • present in muscles
  • dimer with 2 globular ATPase heads
  • one coiled-coil tail
  • binds actin to allow for skeletal muscle contraction
44
Q

actin filaments
myosin filaments

A

actin filaments- (thin filaments) are anchored to Z disc
myosin filaments (thick filaments)- overlap with minus end of actin

45
Q

Myofibrils

A

Contractile elements of muscle cells; extend the length of the cell

46
Q

What does Z disk do?

A

attaches 2 sarcomeres

47
Q

Sarcomere

A
  • Contractile unit of myofibril that shortens during muscle contraction
  • organized assemblies of actin and myosin filaments
48
Q

Diagram the myosin cycle, with ATP and ATP hydrolysis

A
49
Q

Explain muscle structure and how a muscle contracts

A

simultaneous shortening of all the cell’s sarcomeres due to sliding of actin filaments past the myosin filaments without change in length

ADD MORE??

50
Q

Explain how Ca2+ causes a muscle to contract, naming the key components

A

neurotransmitter signal causes release of Ca2+ from sarcoplasmic reticulum (specialized region of ER)
Ca2+ triggers actin-myosin contraction through binding of actin-associated proteins

51
Q

tropomyosin vs troponin

A

tropomyosin- rod-shaped protein that prevents binding of myosin to actin
troponin- calcium-sensitive complex that binds to tropomyosin. When Ca2+ levels rise, it moves tropomyosin so that myosin can bind to actin

52
Q

what happens when calcium binds to calmodulin?

A

activates myosin light chain kinase, which phosphorylates myosin, which allows interaction with actin and contraction

53
Q

Microtubules assembly

A
  • assembly and disassembly occurs only at the + end
  • dynamic instability- driven by GTP hydrolysis
  • catastrophe- microtobule shrinking when GTP hydrolysis is faster than addition of new tubulin subunits
  • rescue- adition of GTP-containing subunits to the shrinking end to resume growth
54
Q

Microtubule nucleation site

A

y-tubulin ring complex of the centrosome

microtubules only form out of these complexes

55
Q

centrosome vs centriole

A

centrosome: where microtubules are organized (a type of MTOC)
centriole- component of centrosome matrix (2 in centrosome)

56
Q

Why do cells need MTOC sites?

A
  • organization, efficiency
  • separate gamma ring from centrioles
  • make sure microtubules dont spontaneously assemble
  • not much free-tubulin in cell- when you need it, it will be ready to be made

microtubule-organizing center

57
Q

MAPs

A
  • bind microtubules and regulate their dynamics in cells
  • structure determines the spacing of microtubules within the cell
  • when bound to microtubule ends, can promote growth or disassembly
  • Kinesin-13, XMAP215

microtubule associated proteins

58
Q

Augmin

A
  • binds the side of an existing microtubule and recruits g-tubulin ring complex to nucleate a new microtubule branch (to branch microtubule off)
  • nucleates microtubule binding

a type of MAP

59
Q

Kinesin-13
XMAP215

A

Kinesin-13: binds to microtubule ends and pries them apart to increase catastrophe events (promotes disassembly)
XMAP215: binds free tubulin and delivers them to + end of microtubule, increasing polymerization rates (promotes microtubule assembly)

types of MAPs

60
Q

what can motor proteins do?

A
  • interact with microtubules to move cargo like organelles and macromolecules across long distances in cells
  • promote sliding microtubules one over another to generate specific microtubule arrengements
  • regulate microtubule dynamics
61
Q

kinesins

A
  • with microtubules, move cargo from - to + end (forward, with the growth of microtubules)
  • when ATP-bound: tightly bound; ADP-bound: loose
62
Q

what “drives” motor protein movement?

A

ATP hydrolysis

63
Q

dyneins

A
  • move from + to - end (back to the source)
  • movement occurs by linker swing, dynein-winch mechanism
64
Q

cilia vs flagella

A

cilia- can propel cells or sweep layers of liquid and particles along
flagella- enable cells to swim in liquid media

65
Q

axoneme

A
  • core structure of cilia/flagella
  • composed of microtubules and their associated proteins arranged in a distinct pattern
66
Q

what generates motion in cilia and flagella?

A

ciliary dynein bending

67
Q

keratins

A
  • most diverse intermediate filament family
  • found in skin, hair, nails, claws, and scales
68
Q

desmosome

A

cell-cell contact sites where intermediate filaments are anchored

69
Q

effect of mutated kertain expressed in the skin

A

epidermolysis bullosa simplex- causes blisters in response to slight mechanical stress

70
Q

amyotropic lateral sclerosis (ALS)

A

effect of abnormal accumulation of neurofilaments in soma and axons of motor neurons

71
Q

what happens when lamin is phosphorylated?

A

weakens the interaction between filmanets, causes the lamina to fall apart- important during cell division

72
Q

defect in lamin vs plectin

A

lamin- progeria: premature aging disorders
plectin: disease-combining features of epudermyosis bullosa simplex, ALS, and neurodegeneration

73
Q

plectin

A

an accessory protein that crosslinks filaments into bundles/connects them to microtubules, actin filaments

74
Q

Explain how Rho and Rac are involved in promoting cell movement

A

Rac activation- actin polymerization at cell periphery
Rho activation- stress fibers and focal adhesion formation

75
Q

Rac and Rho regulating cell movement

A

Rac dominates polymerization (protrusions)
Rho dominates actin-myosin contractions

they are antagonist to each other

76
Q

chemotaxis

A

movement of cells towards or away from a source of diffusible chemical

77
Q

Treadmilling

A

constant movement of actin monomers through the filament from + to - end

78
Q

why are intermediate filmanets not polar, but actin and microtubules are?

A

polarity: allows to have directionality. There is meaning to where it is headed. Made and dissassembled quickly- need to know where it starts
no polarity: just conntects to itself. No real meaning to being polar

79
Q

what drives extension of the actin protrusion?

A

Arp2/3

80
Q

Rac vs Rho, which is front and back of cell movement?

A

Rac: front
Rho: back

81
Q

what stimulates extension of filopodia?

A

Cdc42 polarization –> Par-3 –> Rac-GTP –> wave proteins –> Arp2/3

82
Q

How do cells have less contractility and stress fibers?

A

Rac-GTP –> PAK inhibits MHC and MLCK –> decreased myosin activity

83
Q

how are cells held together?

A

by interactions with ECM or cell-cell junctions

84
Q

Define cadherins and explain their role in cell-cell interactions

A
  • mediate cell-cell interactions (link cytoskeletons)
  • present in animal cells only
  • homophilic binding: adjacent cells bind to same or closely related type (more homo than hetero)
  • heterophilic binding: adjacent cells bind to different types
85
Q

how are cadherin intracellular domains linked to cytoskeleton?

A

at adherens junctions and desmosomes via adaptor proteins- including catenin

(cadherins link to actin through adaptor proteins)

86
Q

why are cells with cadherin mutations thought to be malignant?

A

cells become more motile, break off form original, and start tumor somewhere else

87
Q

how are transient cell-cell adhesions in bloodstream mediated?

A

by selectins

88
Q

how is calcium independent cell-cell adhesion mediated?

A

by members of immunoglobulin superfamily (IG)

89
Q

what do tight junctions do?

A
  • allow epithelial cells to limit solute diffusion (seals gaps between tissues to prevent leakage)
  • prevents proteins from migrating along side of the cell
  • claudins and occudins form the tight junctions
90
Q

Compare and contrast tight junctions and gap junctions

A
  • tight: create a watertight seal that prevents the movement of water and ions between cells.
  • Gap: allow the exchange of small molecules, ions, and second messengers between cells; couple cells both electrically and metabolically (gated channels); made from connexins
91
Q

how are astrocytes interconnected?

A

by gap junctions

92
Q

plasmodesmata and how they compare to tight or gap junctions

A
  • intercellular junctions in plants
  • perform similar roles as gap junctions: connecting adjacent cells to allow exchange of ions, small molecules BUT pass through the cell wall
93
Q

types of molecules that make up mammalian ECM

A
  1. proteoglycans and GAGs- large highly charged polysaccharides that can be linked to proteins (hyaluronan, perlecan; decorin, aggrecan)
  2. fibrous proteins- proteins of the collagen family (type 4 collagen; fibrillar collagen)
  3. glycoproteins- gp with conventional Asp-linked saccharides (laminin, nidogen, fibronectin)
94
Q

Proteoglycans vs GAGs

A

proteoglycans: proteins covalently linked to GAG chains
GAGs: glycosaminoglycans; unbranched polysaccharide disaccharide; negatively charged; form hydrated gels, resistant high compression pressures

95
Q

difference between proteoglycans and collagen

A

collagen assemble into long-triple stranded helical struces a-chains; resist stretch pressure

ADD MORE

96
Q

basal lamina & components

A
  • beneath epithelial cells, surrounds muscle, fat, and Schwann cells
  • role is to separate cells from the environment
  • nidogen, perlecan, laminin, type 4 collagen, integrin
97
Q

Explain the role of integrins in the cell and define their interacting partners

A
  • transmembrane laminin receptors that organize assembly of basal lamina
  • cells interact with ECM via transmembrane integrins
  • recruit intracellular signaling proteins at sites of cell-matrix to regulate cell division, growth, and survival
98
Q

molecular composition of the plant cell wall and compare to mammalian cell

A
  • a type of cellular matix (much stronger than animal cell ECM)
  • made of cellulose microfibrils and pectic polysaccharides
99
Q

NFKB IKK complex and Ikb

A

IKK: includes NEMO and is activated when TNFa binds to receptor
Ikb: binds NFkb and marks for degradation in absence of signal. Activated IKK promotes NFkb separation from Ikb

100
Q

Collagens are extremely rich in which amino acids?

A

glycine, proline

101
Q

In actin filmanet polymerization, what does the “lag phase” correspond to?

A

Nucleation

102
Q

Gq function

A

activates phospholipase C-B –> release of Ca2+

103
Q

what do arrestins do?

A

bind to phosphorylatd GPCRs to prevent GPCRs from interacting with G proteins

104
Q

how are enzyme-coupled receptors activated?

A

dimerization of 2 receptors from the binding of a signal

105
Q

what do tyrosine phosphatases do?

A

inactivate RTK receptors

106
Q

mTOR1 vs mTOR2

A

mTOR1: includes protein raptor; activated by Akt
mTOR2: helps activate Akt

Biol 413: Cell Bio (5 decks)

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