Ch 15, 16, 19 (signaling, cytoskeleton, ECM) Flashcards
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
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
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
4
Q
describe phospholipid modification to recruit intracellular signaling molecules
A
5
Q
What are molecular switches and how do they work?
A
- kinases and phosphatases
- GTP-binding proteins
- GEFs and GAPs
6
Q
Kinase vs phosphatase
A
kinase- enzyme-adding phosphatate group (2 types: serine/threonine; tyrosine)
phosphatase- enzyme-removing phosphatase group
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.
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+
9
Q
what do G-protein coupled receptors (Gas) activate?
A
adenylyl cyclase, which produces cAMP
10
Q
What does cAMP do?
A
diffuses easily throughout the cell to interact with proteins in the cytosol, nucelus, and other organelles
11
Q
What enzyme makes cAMP? what is a target of cAMP?
A
adenylyl cyclase
cAMP-dependent PKA
12
Q
what is cAMP made of?
A
ATP
13
Q
Order of GPCRs signaling leading to transcription of genes
A
- Activation of adenylyl cyclace
- binding of cAMP to PKA
- dissociation of PKA into catalytic and regulatory subunits
- binding of CREB to PKA
14
Q
Explain what caffeine does
A
blocks cAMP phosphodiesterase –> levels of cAMP increase and accumulate, so keeps affecting pathway
15
Q
phospholipase C reaction, products, and effects on a cell
A
products:
diacylglycerol activates protein kinase C
IP3 releases Ca2+ from ER
16
Q
Diagram the structure and function of PKA, explain how mutations in different subunits affect its function
A
17
Q
Describe calmodulin
A
When it binds to Ca2+, undergoes conformational change that allows it to bind CaM-kinase
18
Q
What is CaMKII activated by?
A
calcium
19
Q
what do CamKIIB knockout mice have?
A
memory impairment and fail to build nests
20
Q
what do receptor tyrosine kinases activate?
A
Ras (active when GTP-bound; inactive when GDP-bound)
21
Q
Why do cells use scaffolding proteins?
A
to ensure signal specificity between parallel pathways
22
Q
Illustrate a Ras pathway and a MAP kinase cascade
A
23
Q
Ways by which signal adaptation occurs and examples
A
- negative feedback
- delayed feed-forward
- receptor inactivation
- receptor sequestration (cholesterol)
- receptor destruction (receptor degraded in lysosome)
24
Q
Describe the different signaling pathways that can lead to target specific gene transcription
A
- NFkB: stress and inflammatory stimulated pathways
- Wnt
- MAPK pathway
- PI3K/Akt/mTOR
- Notch pathway
25
how do cytokine receptors signal?
by associating with cytosolic tyrosine kinases
STAT (signal transducer and activators of transcription)
26
TGFB and Smad
TGFB- secreted signaling proteins
Smad- latent transcription regulators
27
wnt pathway proteins
**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
28
what does activation of frizzled and LRP do?
activates dishevelled and dismantles the axin-APC complex to stabilize B-catenin --> B-catenin enters nucleus and activates transcription by removing Groucho from DNA
29
Hedgehog signaling cascade pathway
**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
30
receptors in plants vs animal cells
* 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
31
ethylene signaling in plants
ethylene deactivates receptor --> deactivates CTR1 --> no degradation of EIN3 --> allows transcription
## Footnote
pathway turns on genes by relieving inhibition
32
What does binding of delta to Notch promote?
cleaves off Notch cytosolic tail --> moves into nucleus and regulates gene expression
33
what type of receptors do steroid hormones use?
intracellular receptors
nuclear receptor- bind steroid hormones and enter the nucleus to regulate gene transcription
34
cytoskeleton
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
35
Describe the role of the 3 types of cytoskeletal systems
**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
36
proteins of the cytoskeletal system and their structure
**actin filaments**: protein actin, thin, 2-stranded helix
**microtubules**: tubulin; protein rigid hollow cylinder
**intermediate filaments**: fibrous intermediate filament protein; strong ropelike fibers
37
Describe, compare, and contrast the 3 types of cytoskeletal systems and how the filaments grow
actin filaments:
microtubules:
38
Explain what nucleation is
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)
39
Explain how the concentrations of cytoskeletal components monomers (for example actin) are maintained within the cell
40
Explain one simple way to generate cell polarity
proteins such as partitioning defective (PAR), and complexes such as Scribble, and Crumbs are responsible for polarity in epithelial cells
41
Why does so little of the actin polymerize into filaments?
cells keep sequestered to enable polarization as needed
42
cofilin
* promotes actin depolymerization by introducing mechanical stress to the filament
* binds actin-ADP preferentially (the one that is less stable)
43
myosin 2
* present in muscles
* dimer with 2 globular ATPase heads
* one coiled-coil tail
* binds actin to allow for skeletal muscle contraction
44
actin filaments
myosin filaments
**actin filaments-** (thin filaments) are anchored to Z disc
**myosin filaments** (thick filaments)- overlap with minus end of actin
45
Myofibrils
Contractile elements of muscle cells; extend the length of the cell
46
What does Z disk do?
attaches 2 sarcomeres
47
Sarcomere
* Contractile unit of myofibril that shortens during muscle contraction
* organized assemblies of actin and myosin filaments
48
Diagram the myosin cycle, with ATP and ATP hydrolysis
49
Explain muscle structure and how a muscle contracts
simultaneous shortening of all the cell's sarcomeres due to sliding of actin filaments past the myosin filaments without change in length
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50
Explain how Ca2+ causes a muscle to contract, naming the key components
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
tropomyosin vs troponin
**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
what happens when calcium binds to calmodulin?
activates myosin light chain kinase, which phosphorylates myosin, which allows interaction with actin and contraction
53
Microtubules assembly
* 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
Microtubule nucleation site
y-tubulin ring complex of the centrosome
## Footnote
microtubules only form out of these complexes
55
centrosome vs centriole
centrosome: where microtubules are organized (a type of MTOC)
centriole- component of centrosome matrix (2 in centrosome)
56
Why do cells need MTOC sites?
* 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
## Footnote
microtubule-organizing center
57
MAPs
* 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
## Footnote
microtubule associated proteins
58
Augmin
* 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
## Footnote
a type of MAP
59
Kinesin-13
XMAP215
**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)
## Footnote
types of MAPs
60
what can motor proteins do?
* 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
kinesins
* with microtubules, move cargo from - to + end (forward, with the growth of microtubules)
* when ATP-bound: tightly bound; ADP-bound: loose
62
what "drives" motor protein movement?
ATP hydrolysis
63
dyneins
* move from + to - end (back to the source)
* movement occurs by linker swing, dynein-winch mechanism
64
cilia vs flagella
**cilia**- can propel cells or sweep layers of liquid and particles along
**flagella**- enable cells to swim in liquid media
65
axoneme
* core structure of cilia/flagella
* composed of microtubules and their associated proteins arranged in a distinct pattern
66
what generates motion in cilia and flagella?
ciliary dynein bending
67
keratins
* most diverse intermediate filament family
* found in skin, hair, nails, claws, and scales
68
desmosome
cell-cell contact sites where intermediate filaments are anchored
69
effect of mutated kertain expressed in the skin
epidermolysis bullosa simplex- causes blisters in response to slight mechanical stress
70
amyotropic lateral sclerosis (ALS)
effect of abnormal accumulation of neurofilaments in soma and axons of motor neurons
71
what happens when lamin is phosphorylated?
weakens the interaction between filmanets, causes the lamina to fall apart- important during cell division
72
defect in lamin vs plectin
**lamin**- progeria: premature aging disorders
**plectin**: disease-combining features of epudermyosis bullosa simplex, ALS, and neurodegeneration
73
plectin
an accessory protein that crosslinks filaments into bundles/connects them to microtubules, actin filaments
74
Explain how Rho and Rac are involved in promoting cell movement
Rac activation- actin polymerization at cell periphery
Rho activation- stress fibers and focal adhesion formation
75
Rac and Rho regulating cell movement
Rac dominates polymerization (protrusions)
Rho dominates actin-myosin contractions
| they are antagonist to each other
76
chemotaxis
movement of cells towards or away from a source of diffusible chemical
77
Treadmilling
constant movement of actin monomers through the filament from + to - end
78
why are intermediate filmanets not polar, but actin and microtubules are?
**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
what drives extension of the actin protrusion?
Arp2/3
80
Rac vs Rho, which is front and back of cell movement?
Rac: front
Rho: back
81
what stimulates extension of filopodia?
Cdc42 polarization --> Par-3 --> Rac-GTP --> wave proteins --> Arp2/3
82
How do cells have less contractility and stress fibers?
Rac-GTP --> PAK inhibits MHC and MLCK --> decreased myosin activity
83
how are cells held together?
by interactions with ECM or cell-cell junctions
84
Define cadherins and explain their role in cell-cell interactions
* 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
how are cadherin intracellular domains linked to cytoskeleton?
at adherens junctions and desmosomes via adaptor proteins- including catenin
(cadherins link to actin through adaptor proteins)
86
why are cells with cadherin mutations thought to be malignant?
cells become more motile, break off form original, and start tumor somewhere else
87
how are transient cell-cell adhesions in bloodstream mediated?
by selectins
88
how is calcium independent cell-cell adhesion mediated?
by members of immunoglobulin superfamily (IG)
89
what do tight junctions do?
* 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
Compare and contrast tight junctions and gap junctions
* **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
how are astrocytes interconnected?
by gap junctions
92
plasmodesmata and how they compare to tight or gap junctions
* 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
types of molecules that make up mammalian ECM
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
Proteoglycans vs GAGs
**proteoglycans**: proteins covalently linked to GAG chains
**GAGs**: glycosaminoglycans; unbranched polysaccharide disaccharide; negatively charged; form hydrated gels, resistant high compression pressures
95
difference between proteoglycans and collagen
collagen assemble into long-triple stranded helical struces a-chains; resist stretch pressure
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96
basal lamina & components
* 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
Explain the role of integrins in the cell and define their interacting partners
* 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
molecular composition of the plant cell wall and compare to mammalian cell
* a type of cellular matix (much stronger than animal cell ECM)
* made of cellulose microfibrils and pectic polysaccharides
99
NFKB IKK complex and Ikb
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
Collagens are extremely rich in which amino acids?
glycine, proline
101
In actin filmanet polymerization, what does the “lag phase” correspond to?
Nucleation
102
Gq function
activates phospholipase C-B --> release of Ca2+
103
what do arrestins do?
bind to phosphorylatd GPCRs to prevent GPCRs from interacting with G proteins
104
how are enzyme-coupled receptors activated?
dimerization of 2 receptors from the binding of a signal
105
what do tyrosine phosphatases do?
inactivate RTK receptors
106
mTOR1 vs mTOR2
**mTOR1**: includes protein raptor; activated by Akt
**mTOR2**: helps activate Akt
