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Mol. Cell > Midterm No. 3, Opus 4 > Flashcards

Midterm No. 3, Opus 4 Flashcards

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1
Q

Is the Notch signal pathway good for signal amplification?

A

No. It’s a high speed train to the nucleus, no room for amplification

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2
Q

What protein connects Notch signaling to Alzheimer’s?

A

Gamma-secretase

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3
Q

What are the two pathologies to look for when diagnosing Alzheimer’s?

A

Extracellular amyloid plaques and intracellular (in neurons) neurofibrillary tangles

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4
Q

How is Amyloid Precursor Protein (APP) normally recycled?

A

It’s a transmembrane protein (single TMD) in the plasma membrane. It’s normally clipped by alpha-secretase and gamma-secretase when its recycled

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5
Q

How are amyloid plaques formed?

A

APP is cut by beta-secretase and gamma-secretase. This causes a bit of APP’s TMD to be left in the fragment. That hydrophobic section causes aggregation, leading to amyloid plaque formation

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6
Q

(General) how do hydrophilic ligands activate intracellular signaling?

A

Via a cell surface receptor

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7
Q

(General) how do hydrophobic ligands activate intracellular signaling?

A

Via simple diffusion straight into the cell, then binding to an intracellular receptor

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8
Q

How do ligands get to nuclear receptors?

A

Hydrophobic ligands do simple diffusion across the plasma and nuclear membranes

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9
Q

What do nuclear receptors + their bound ligands act as?

A

Transcriptional regulators

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10
Q

How do signals for nuclear receptors travel through the bloodstream?

A

They are hydrophobic, so they have to be bound by carrier proteins

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11
Q

What is the role of heat shock proteins in NHRs (nuclear hormone receptors)?

A

They bind to the NHRs’ hydrophobic binding domains, prevent those hydrophobic residues from being exposed (which could be dangerous)

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12
Q

List the 3 domains present in NHRs

A
  1. Ligand binding domain
  2. DNA binding domain
  3. Transcription activating domain
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13
Q

What are NHRs?

A

Ligand-triggered transcription factors

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14
Q

Do NHRs directly affect gene expression?

A

Yes

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15
Q

Once active (ligand is bound), what can NHRs bind to?

A

Coactivator proteins

Examples include chromatin remodeling complexes, HDACs, mediator binding sites, etc

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16
Q

What’s the purpose of NHRs’ coactivator proteins?

A

To directly turn transcription on/off by directly interacting with the DNA

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17
Q

Why were Nobel’s dynamite factories good work environments for people with heart disease?

A

Because they were exposed to nitroglycerin, a vasodilators (esp for coronary arteries)

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18
Q

What is acetylcholine?

A

A water-soluble signal molecule, key neurotransmitter

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19
Q

What type of receptor does acetylcholine bind to in heart muscles, and what is its effect?

A

GPCR, decreases rate and force of contraction

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20
Q

What type of receptor does acetylcholine bind to in salivary glands, and what is its effect?

A

GPCR, increases cytoplasmic Ca2+ secretion

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21
Q

What type of receptor does acetylcholine bind to in skeletal muscles, and what is its effect?

A

Ligand-gated ion channels, stimulates contraction

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22
Q

What type of receptor does acetylcholine bind to in (most) smooth muscles, and what is its effect?

A

GPCR, stimulates muscle contraction

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23
Q

Why does acetylcholine cause vasodilation in smooth arterial muscles?

A

Acetylcholine binds to a GPCR in the endothelial cells

GPCR → PLC → Ca2+/Calmodulin → NO synthase

NO synthase catalyzes:
Arginine + O2(g) → Citrulline + NO(g)

NO(g) does simple diffusion across the epithelial plasma membrane and smooth arterial muscle plasma membrane, and binds to an intracellular receptor in the smooth muscle cell

The NO receptor is a guanylyl cyclase. It catalyzes GTP → cGMP + Pi. (same family as adenylyl cyclase)

cGMP activates PKG (protein kinase G), which uses its kinase activity to relax the muscle cell (specifically it activates myosin phosphatase)

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24
Q

What are the downstream intracellular effects of acetylcholine binding to a GPCR in endothelial cells?

A

GPCR → PLC → Ca2+/Calmodulin → NO synthase

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25
What does NO synthase catalyze?
Arginine + O2(g) → Citrulline + NO(g)
26
When cGMP levels are high, will smooth arterial muscle cells be relaxed or contracted?
Relaxed cGMP activates PKG, which activates myosin phosphatase to relax the cell
27
When cGMP levels are low, will smooth arterial muscle cells be relaxed or contracted?
Contracted No cGMP means PKG is inactive, myosin phosphatase can't be activated, muscle cell can't be relaxed
28
How does the acetylcholine-NO-vasodilation pathway turn off?
PDE1 (a phosphodiesterase) converts cGMP to GMP; this halts the path by removing the signal (cGMP), PKG cannot be activated without cGMP
29
How long is NO's half-life?
Very short, only 5-10 seconds
30
How long is cGMP's half-life
Very short due to PDE1
31
What is IC50?
Half of the maximal inhibitory concentration
32
You want a more potent/effective drug. Should IC50 be low or high?
Low
33
You want a less potent/effective drug. Should IC50 be low or high?
High
34
Your drug has a low IC50. How potent is it?
Very potent, very effective
35
Your drug has a high IC50. How potent is it?
Not very potent, low efffectiveness
36
Why is it important to run multiple IC50's to determine your drug's specificity?
To know if it works on the PDE you want To know if it works against other PDE's, may be helpful in determining potential side effects
37
Why is one of the symptoms of severe sepsis a massive crash in blood pressure?
Immune cells produce NO as part of their defense during sepsis. If the sepsis is too severe, so much NO will be produced that all arteries/veins/vessels will dilate, causing a mass crash in blood pressure
38
In most cells, where does actin gather?
Around the edges
39
In most cells, where are the microtubules?
The middle/majority of the cytoplasm
40
In most cells, where are the intermediate filaments?
They stabilize the nucleus
41
What is the cytoskeleton? (definition)
A system of filaments that enables cells to interact mechanically with each other and the environment
42
What are the functions of the cytoskeleton?
Maintain correct cell shape Physical robustness (not fragile) Creates internal structure Involved in motility/movement
43
Does the cytoskeleton function more like an ant trail or an interstate highway? Explain
Ant trail Highways exist in the same place once they’re built. Ant trails mostly maintain the same shape, but the individual ants are constantly moving. Many of these filaments are constantly and dynamically remodeling, even though they seem to be fairly stable.
44
Size of actin filaments
7-9 nm in diameter
45
How abundant are actin filaments?
Very 1-10% of total cell proteins
46
Size of intermediate filaments
10 nm in diameter
47
Size of microtubules
25 nm in diameter
48
What NTP is associated with actin?
ATP
49
What NTP is associated with intermediate filaments?
None!
50
What NTP is associated with microtubules?
GTP
51
Which of the 3 filament types (actin, IF, microtubules) are polar?
Actin and microtubules only IFs are not polar
52
Implications for IFs not being polarized?
Can't be associated with motors and motor proteins
53
How are the polymers of protein subunits that make up actin, IFs, and microtubules held together?
Weak non-covalent bonds
54
Bacterial homolog to actin
MreB
55
G-actin
Globular actin, individual monomers
56
F-actin
Filamentous actin
57
True or false: actin is an ATPase
True! G-actin monomers have a cleft in their centers where ATP binds! Hydrolysis happens!
58
Which process is faster: formation of the G-actin triad or the rest of the polymerization?
The rest of the polymerization
59
Which process is slower: formation of the G-actin triad or the rest of the polymerization?
Formation of the G-actin triad
60
Biochem in vitro outcome: low actin concentration
Whole population consists of monomers
61
Biochem in vitro outcome: increasing actin concentration
There's a point where filaments form. Monomer levels stay constant, additional actin is polymerized into filaments
62
Actin treadmilling
Actin is an ATPase. It hydrolyzes its actin-ATP while in filament form, then delplymerizes in it actin-ADP form. Actin can be lost and gained from both ends, but the critical concentrations are different enough that the + end predominantly gains / polymerizes and the - end predominantly loses / depolymerizes Treadmilling adds to the ant trail concept. A filament could stay the same size, but it’s not always made of the same subunits. The ratioin of monomers to polymers can remain stable even though the filaments are technically new
63
Based on biochem's concentration numbers: Low G-actin concentration
Gain at no end Loss at both ends (though mostly - end)
64
Based on biochem's concentration numbers: Medium G-actin concentration
Gain at + end Loss at - end
65
Based on biochem's concentration numbers: High G-actin concentration
Gain at both ends (though mostly +) Loss at no ends
66
Low G-actin concentration
Below critical concentration of both ends, both lose
67
High G-actin concentration
Above critical concentration of both ends, both gain
68
But! The actual concentration of actin in the cell is WAY over the critical concentration! From the numbers the biochemists generated from in vitro assays, we should expect almost all the cell’s actin to be polymerized, but it’s not! Why?
Profilin, cofilin, and thymosin-beta4 are actin-binding proteins. They maintain a pool of G-actin and keep things dynamic. They’re breaks on the system to make sure its not all polymerized
69
Profilin
Adenosine exchange factor (AEF) Adds monomeric actin-ATP to the + end
70
Cofilin
Breaks off chunks of filament at the - end
71
Thymosin-beta4
Sequesters monomeric ATP-actin Stockpiles then hands off to profilin at appropriate times
72
Formin FH2 domain
Acts as a molecular “rocking ratchet” Promotes long, linear filaments Acts in a dimer, binds to a actin dimers Sits on the + end, stacks actin dimers appropriately
73
Formin RBD (rho binding domain)
Small GTPase lipid-linked to the plasma membrane Ensures polymerization happens near the plasma membrane, lococalizes polymerization GTPase activity regulates the entire formin protein, regulates polymerization Blocks unregulated function FH2’s ratcheting+polymerization can occur only when Rho is bound to GTP (aka when Rho is active)
74
Formin FH1 domain
Recruits and binds to profilin-bound actin-ATP for FH2 Hands off the actin-ATP to be polymerized by FH2
75
Arp2/3 Complex
When the Arp2/3 complex is activated (by an activator protein, causes a conformational shape change), Arp2/3 is accessible for binding The Arp2/3 complex becomes the - end for the nucleated actin filament. Actin monomers are added to the + end The Arp2/3 complex is basically a regulated actin dimer. Its activator protein regulates filament nucleation/organization. Addition of 1 actin monomer (to activate the complex) yields a nucleating timer Arp2/3 complexes can also bind to the sides of pre-existing actin filaments (70 degree angle between filaments). This allows for networks of filaments fo form, haskmark networks, branching
76
What are Arp2 and Arp3?
Homologs to actin, structural/molecular cousins Actin related proteins
77
What does filament nucleation via an Arp2/3 complex demonstrate?
That nucleation of 3 actin monomers is key to filament polymerization
78
Why should you never eat death cap mushrooms?
Because they contain phalloidin, a protein that binds to actin filaments and prevents them from depolymerizing. (it’s convenient for cell biologists thought because it’ll label and fix actin filaments when combined with rhodamine)

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