Exam IV Flashcards
1
Q
What is signal transduction?
A
The conversion of an extracellular input to an intracellular output
2
Q
Cells are exposed to many extracellular stimuli. What does this mean for the cell?
A
The combination of inputs a cell receives can dictate its fate (Lives, proliferates, differentiates, dies, etc.)
3
Q
Cell signaling enables transmission from _____ to _____.
A
outside of the cell; nucleus
4
Q
Cell signaling turns on and off [slowly/quickly] while gene expression turns on and off [slowly/quickly].
A
quickly; slowly
5
Q
Between cell signaling and gene expression, which is more energetically costly?
A
Gene expression (Transcription and translation)
Cell signaling is energetically cheap because there’s no protein synthesis
6
Q
What are the principal mechanisms of state change?
A
- Binding/dissociation
- Post-translational modification
- Conformational change
- Localization
7
Q
For Src kinase, what is the input signal?
A
A phosphatase that removes the pTyr527 modiification
8
Q
For Src kinase, what is the output signal?
A
An active kinase domain that phosphorylates downstream proteins
9
Q
How does buried surface area relate to protein-protein interactions?
A
A larger buried SA means stronger binding interaction
10
Q
True or false? The end goal of binding interactions in signaling pathways is to be as avid (high affinity) and specific (high specificity) as possible, so as we look back at the evolution of signaling pathways, we see a trend in this direction.
A
False.
Some organisms may have signaling pathways that are more promiscuous or have lower specificity to allow for flexibility in responding to a range of signals.
11
Q
How is the Kd of an interaction matched to the physiological concentration of the molecules involved?
A
Increasing the local concentration of a biomolecule can increase the likelihood of binding
12
Q
What is allosteric regulation?
A
A state change to a protein caused by binding of a ligand outside of the active site
13
Q
Membrane localization can dramatically [decrease/increase] the relative concentration of signaling molecules.
A
increase
14
Q
What is the logic behind post-translational modifications?
A
- Fast
- Energetically cheap
- Usually reversible
- Combinatorial
15
Q
What chemical effects do post-translational modifications have?
A
Changes size, shape, charge of amino acid side chains, hydrophobicity, and hydrophilicity
16
Q
Name five post-translational modifications aside from phosphorylation.
A
- Glycosylation (Sugar)
- S-palmitoylation (Lipids)
- Isomerization (Proline residues)
- Ubiquitinatin/sumoylation (Proteins)
- Degradation
17
Q
What are five effects of post-translational modification on cell signaling?
A
- Change conformation
- Promote binding
- Prevent binding
- Change subcellular localization
- Change proteolytic stability
18
Q
In signal pathway diagrams, a double negative means what?
A
Positive
19
Q
What is the difference between coherent and incoherent feedforward?
A
Coherent: Two pathways lead to the same output
Incoherent: One pathway leads to the output and the other represses it
20
Q
How does half life relate to the duration of cell signaling?
A
The concentration of components with longer half lives take longer to fall after synthesis rate drops
21
Q
How does the concentration of signaling components with short half lives change?
A
It changes rapidly when the synthesis rate increases or decreases
22
Q
The speed of response and duration of signaling depend on what?
A
The rate of synthesis and degradation of signaling molecules
23
Q
Maximum output is determined by what?
A
The amount of signaling protein
24
Q
How do coherent feedforward motifs with an “AND” gate sense sustained input?
A
Both the slow AND fast paths must occur at the same time to produce output
25
Describe the three desensitization adaptations in cell signaling.
1. Receptor sequestration: Receptor is sent into an endosome but recycles back to the membrane
2. Receptor down-regulation: Receptor is sent to an endosome, then to a lysocome to be degraded. New synthesis is required to restore receptors.
3. Receptor inactivation, inactivation of signaling protein, production of inhibitoary protein: Inhibition
26
What are the four ways extracellular signals can act over short or long distances?
1. Contact-dependent
2. Paracrine: Releasing signaling molecules that bind to surrounding cells
3. Synaptic
4. Endocrine: Cell targets a distant cell through the bloodstream
27
What are the common classes of hormones?
1. Amine (Norephinephrine)
2. Peptide (Oxytocin)
3. Protein (Human growth hormone)
4. Steroid (Testosterone, progesterone)
27
[Hydrophobic/hydrophilic] molecules can pass through the cell membrane to intracellular receptors.
Hydrophobic
27
[Hydrophobic/hydrophilic] molecules can't pass through the cell membrane and need ______ to relay the information.
Hydrophilic; cell-surface receptors
27
Define an antagonist.
A ligand that blocks the actions of the agonist by competitively binding to the receptor
28
What are the four major classes of receptors?
1. GPCRs
2. Enzyme-linked
3. Ion-channel
4. Intracellular
28
Define an agonist.
A ligand that activates a receptor
29
Describe how GPCRs work.
Ligand binds to receptor, causing a conformational change. This creates a binding pocket in the receptor inside of the cell for the next protein.
30
Describe how enzyme-linked receptors work.
Inactive: Two parts of the receptor are unbound
Active: Ligand binds, bringing the two parts together and activating the receptor
31
Describe how ion-channel receptors work.
Inactive: Channel is closed
Active: Ligand binds, opening the channel and allowing ions to flow through
32
Describe how intracellular receptors work.
Ligand goes through the cell membrane and into the cytoplasm, binding to an intracellular receptor.
33
Briefly describe what happens when a GPCR is activated.
Alpha subunit in trimeric G protein is activated, releasing the beta and gamma subunits to go and activate other proteins
34
Drugs aimed at specific [receptor class] are among the most effective and common pharmaceuticals.
GPCRs
35
True or false. GPCRs are highly specific and recognize only a limited amount of ligands.
False.
GPCRs recognize an enormous diversity of ligands with very different physical natures.
36
How many transmembrane domains do GPCRs have?
Seven
37
Describe the transmembrane domains in GPCRs.
1. 24-25 aa long
2. Hydrophobic
3. Alpha-helical
38
What part of the transmembrane domains in GPCRs is especially important for activating the alpha subunit?
The intracellular loop between helices 5 and 6
39
What is the effect of conformational changes in the extracellular ligand binding domain in GPCRs?
It also causes conformational changes in the intracellular GEF domain through the transmembrane helices (Think marionette puppets)
40
What are G proteins?
Signaling proteins that bind guanine nucleotides and function as molecular switches
41
When are GTP-binding proteins active and inactive?
Active: Bound to GTP
Inactive: Bound to GDP or nothing
42
The presence of what molecule induces the conformational change in G-proteins?
Gamma-phosphate
(Without it, it's GDP-bound. With it, it's GTP-bound and active.)
43
What are the two major types of G-proteins?
Monomeric and heterotrimeric
44
Where are trimeric G-proteins in the cell?
Attached to the plasma membrane
45
GDP is bound to the alpha subunit. Is the G-protein active or inactive?
Inactive
46
How are G-proteins attached to the plasma membrane?
The alpha and gamma units are linked to the membrane by covalently attached fatty acid and isoprenoid units, respectively.
47
What kind of enzyme is the alpha unit of a G protein?
GTPase (Hydrolases that bind GTP and hydrolyze it to GDP)
48
What are the two domains of the alpha subunit in G proteins?
1. Ras domain (Forms one face of binding pocket)
2. Alpha helical domain (Forms the other side of the guanine nucleotide binding pocket)
49
What are the three major types of G proteins?
1. Gs
2. Gi
3. Gq
50
What is the function of the G-protein Gs?
Activates adenylyl cyclase and activates Ca2+ channels
51
What is the function of the G-protein Gi?
Inhibits adenylyl cyclase
52
What is the function of the G-protein Gq?
Activates phospholipase C-beta
53
Describe the four steps of the activation of a G-protein by an activated GPCR.
1. Ligand binds to GPCR, causing a conformational change that allows the G protein to bind to it.
2. Binding of the G protein alters the G protein's conformation, and the AH domain of the alpha subunit moves out, letting GDP escape.
3. GTP binding to the alpha subunit closes the binding pocket, causing a conformational change that releases the beta-gamma subunit.
4. The freed up alpha and beta-gamma subunits can now regulate downstream effector molecules.
54
A GPCR stays active as long as what?
As long as ligand is bound, allowing it to activate many G proteins
55
Describe the four steps in which GPCR signaling activates adenylyl cyclase in response to epinephrine.
1. Epinephrine binds GPCR
2. Conformational change in GPCR accelerates the exchange of GDP to GTP, activating the Gs-alpha subunit.
3. GTP-bound Gs-alpha subunit binds and activates adenylyl cyclase
4. Activated adenylyl cyclase converts ATP to cAMP, a second messenger
56
cAMP is hydrolyzed by ____ to form 5'-AMP.
phosphodiesterases (PDEs)
57
What are three hormone-induced responses mediated by cyclic AMP?
1. Adrenaline causes glycogen breakdown in muscles
2. Glucagon causes glycogen breakdown in the liver
3. Adrenaline, ACTH, glucagon, and TSH causes triglyceride breakdown in fat
58
How does cAMP allosterically activate protein kinase A?
cAMP binds to the two regulatory subunits of PKA, releasing the two catalytic subunits, which are now active.
59
Protein kinase A is dependent on what molecule for activation?
cAMP
60
What kind of kinase is protein kinase A?
Serine/threonine protein kinase
61
Describe the subunits of protein kinase A in the absence of cAMP.
The catalytic subunits are bound to regulatory subunits, which inhibit catalytic activity.
62
What is the immediate response to the activation of protein kinase A?
Phosphorylation of many proteins
63
What does CRE stand for?
cAMP response element
64
What does CREB stand for?
cAMP response element binding protein
65
What does CBP stand for?
CREB-binding protein
66
Describe the role that CRE, CREB, and CBP play in activating gene transcription.
1. Activated protein kinase A phosphorylates an inactive CREB, activating it
2. CBP can now bind to an active CREB
3. CBP-CREB complex binds to CRE on the DNA upstream from the now activated target gene, leading to transcription
67
Active adenylyl cyclase produces cAMP, activating protein kinase A.
How does this lead to increased glycogen breakdown?
PKA phosphorylates and activates glycogen phosphorylase kinase, which phosphorylates and activates glycogen phosphorylase, leading to glycogen breakdown.
68
Active adenylyl cyclase produces cAMP, activating protein kinase A.
How does this lead to increased gluconeogenesis?
PKA phosphorylates CREB, a transcription activator, leading to increased PEPCK transcription and increased gluconeogenesis
69
What affect does Gi-alpha have on adenylyl cyclase?
An inhibitory hormone binds to the receptor, activating the inhibitory G protein, which turns adenylyl cyclase off (No cAMP production)
70
What is the function of cAMP phosphodiesterase (PDE)?
It resets cAMP signaling by catalyzing a hydrolysis reaction to convert cAMP into AMP
71
What are two bacterial toxins that hijack G-protein signaling?
Cholera and pertussis (Whooping cough)
72
How does cholera affect G-protein signaling?
It locks Gs-alpha in an active state.
The A1 subunit of cholera catalyzes the ADP-ribosylation of Gs-alpha, making it unable to hydrolyze GTP.
This leads to increased cAMP levels.
73
How does pertussis affect G-protein signaling?
It locks Gi-alpha in an inactive state.
A pertussis subunit catalyzes the ADP-ribosylation of Gi-alpha, making it unable to interact with GEFs.
This leads to elevated cAMP levels and overactive PKA.
74
What is the function of phospholipases?
They hydrolyze membrane phospholipids at different positions in the molecule
75
Where do phospholipase C's cleave?
The phosphodiester bond between the glycerol backbone and phosphate head group
76
What happens when phospholipase C-beta cleaves PIP2? What is produced?
PIP2 is cleaved into the secondary messengers diacylglycerol and IP3.
Diacylglycerol is still attached to the membrane and activates protein kinase C.
IP3 releases Ca2+ from the ER. Ca2+ also activates PKC.
77
How does IP3 release Ca2+ from the ER?
IP3 is very water soluble and diffuses through the cytoplasm to the ER membrane, where it stimulates an IP3-gated calcium channel
78
What two molecules are required to activate protein kinase C?
Diacylglycerol and calcium
(C is for calcium)
79
Why is PKC recruited to the membrane?
Diacylglycerol is required to activate PKC, and it's bound to the membrane.
80
What is the function of the C1 and C2 domains in protein kinase C?
They keep PKC inhibited.
81
What does an activated Gq activate?
Phospholipase C-beta
82
Diacylglycerol is the precursor for what two molecules?
Arachidonic acid and prostaglandins (PGs)
83
What do "EF hand" domains bind to?
Ca2+
84
What is the function of calmodulin (CaM)?
It's a major mediator of Ca2+ signaling.
85
How does calmodulin work?
When calcium-bound, it forms a barbell shape. The exposed central helix has an affinity for target proteins and will wrap around them.
86
How does GPCR kinase (GRK) desensitize GPCRs?
GRKs phosphoylates GPCR on multiple sites.
Arrestin binds to phosphorylated GPCR, desensitizing GPCR.
87
What are enzyme-coupled receptors?
Transmembrane proteins with single membrane spanning domains
88
How are enzyme-coupled receptors activated?
Substrate binding causes dimerization (Two domains coming together). These dimers are active.
89
Name the five types of enzyme-coupled receptors.
1. Receptor tyrosine kinases (RTKs)
2. Tyrosine kinase-associated receptors
3. Receptor serine/threonine kinases
4. Receptor guanylyl cyclases
5. Receptor tyrosine phosphatases
90
What is the function of receptor tyrosine kinases (RTKs)?
Phosphorylate on specific tyrosines (Growth factor receptors)
91
What is the function of tyrosine kinase-associated receptors?
Non-covalent association with intracellular tyrosine kinases (Cytokine receptors)
92
What is the function of receptor serine/threonine kinases?
Phosphorylate specific serines or threonines (TBF-beta receptors)
93
What is the function of receptor guanylyl cyclases?
Synthesize cGMP
94
What is the function of receptor tyrosine phosphatases?
Remove phosphate from tyrosines
95
What is the most abundant type of enzyme-coupled receptor?
Receptor tyrosine kinases (RTKs)
96
For receptor tyrosine kinases, is the tyrosine kinase domain inside or outside the cell?
Inside
97
How many times do RTKs span the membrane?
Once
97
True or false? RTKs are dimers in the absense of a ligand.
False. They're monomers when inactive and dimers when active.
97
What do RTKs regulate?
Cell proliferation, growth, differentiation, migration, and fate
98
What are four mechanisms of dimerization for RTKs?
1. Ligand is a dimer and simutaneously binds to two receptors.
2. A monomeric ligand binds to two receptors, bringing them together.
3. Two ligands bind to two receptors and bring them together.
4. The ligand is already a dimer and induces a conformational change, activating the kinase activity.
99
Describe the inactive state of RTKs.
RTKs are monomers anchored in the plasma membrane by a single transmembrane domain (Except insulin receptor, which has two)
100
What happens when a ligand binds to a RTK?
The receptor monomers dimerize, activating the tyrosine kinase activity of one/both monomers.
101
What are the two mechanisms by which dimerization of RTKs activates tyrosine kinase activity?
1. Cross phosphorylation: Activated tyr kinase domains phosphorylate each other
2. Conformational changes in the domain in response to ligand binding lead to one tyr domain (Activator) activating the other (Receiver). The receiver phosphorylates both subunits.
102
What occurs once the internal domains of the RTK are phosphorylated?
The domains serve as docking sites for signaling proteins
103
Describe the structure of SH2 domains.
Central beta-sheet separating two alpha-helices
One binding site on each side of the beta-sheet. One for amino acid side chain (specificity) and one for phosphotyrosine.
104
Describe the structure of PTB domains.
Two orthogonal beta-sheets form a sandwich, capped by a C-terminal alpha-helix
105
A single RTK can have many phosphorylation sites that recruit what?
SH2 or PTB domain-containing proteins
106
What is the function of adapter proteins in relation to RTKs?
Adaptors have binding domains that scaffold multiple proteins, bringing them closer
107
What is Grb2?
An adaptor that binds to RTKs
Composed of a central SH2 domain surrounded by two SH3 domains
108
What do SH3 domains bind to?
Proline-rich regions
109
Describe the structure of SH3 domains.
Contain two binding groves. One binds to proline and the other to hydrophobic amino acid.
110
PTB binds preferentially to what motif?
NPxpY
x = Any amino acid
pY = Phosphotyrosine
111
What are the common recognition motifs for SH3 domains?
Polyproline type II (PPII) heclies
PxxP sequences
112
How do RTKs become oncogenic?
They can mutate, becoming dimerized and active without the ligand. The external domain can be truncated, which also activates the receptor without the ligand.
113
Src protein kinases are all [cytosolic/extracellular] tyrosine kinases.
cytosolic
114
What happens when SH2 and SH3 domains bind to Src?
It locks Src in its catalytically inactive "off state."
115
When Src is inactive and bound to SH2 and SH3, how can it become active?
1. Removal of pTyr527 by a phosphatase
2. Competitive binding of SH2 and SH3 by other proteins
116
After Src tyrosine kinase is activated, what does it do?
It phosphorylates the RTK on other sites, creating more SH2 recruitment sites for other proteins in other pathways to bind.
117
An abnormally activated Src leads to ____.
cancer
118
What is the function of phospholipase C-gamma?
Same as phospholipase C-beta
Cleaves PIP2 to make two secondary messengers (Diacylglycerol and IP3), allowing RTks to increase cytoplasmic Ca2+ and activate protein kinase C.
119
What are the major differences between phospholipase C-gamma and phospholipase C-beta?
Differences are in the binding domains in the C-terminus
PLC-gamma has tyrosine residues phosphorylated by the activated RTK
120
What are mitogens?
Signaling molecules that induce cell proliferation by triggering mitosis
121
Describe the signaling pathway from RTK to Ras
1. Grb2 adaptor protein recognizes a phosphorylated tyrosine on the RTK via its SH2 domain
2. Grb2 recruits Sos via its two SH3 domains
3. Sos stimulates guanine nucleotide exchange, activating Ras (Requires GTP)
122
What is the function of Sos?
It's recruited by Grb2 and catalyzes the exchange of GTP for GDP in Ras
123
What are Ras proteins?
Small/monomeric G proteins that function as binary switches
124
How do GTPase activating proteins (GAPs) affect Ras?
They reduce Ras activation by increasing its ability to hydrolyze GTP.
125
How do guanine exchange factors (GEFs) affect Ras?
They accelerate Ras activation by promoting the exchange of GTP for the bound GDP.
126
Why is it important that Ras is turned off?
Oncogenic forms of Ras have mutations that interfere with its ability to interact with Ras-GAP, meaning it's mostly in the active state and continuously signaling the cell to divide
127
Phosphorylation of ___, ___, and ___ leads to the transcription of genes involved in cell proliferation.
Myc; Jun; Fos
128
What are the three intermediates in the MAP kinase cascade?
Raf, Mek, Erk
129
What two peptide hormones maintain blood glucose homeostasis?
Insulin and glucagon
130
When and where is insulin produced? What does it trigger?
It's produced by beta-cells in the pancreas in response to high blood glucose levels.
It triggers glucose uptake and glycogenesis.
131
When and where is glucagon produced? What does it trigger?
It's produced by the pancreas in reponse to low blood glucose levels.
It triggers glycogenolysis (breakdown of glycogen to glucose).
132
How is insulin produced?
1. Preproinsulin is translated and sent into the rough ER
2. Clevage of signal peptide and introduction of 3 disulfide bonds makes proinsulin
3. In the Golgi, cleavage by an endopeptidase and exoprotease makes insulin
133
Insulin is stored as a _____, but released to the blood as a _____.
hexamer; monomer
134
Insulin is anabolic. What does this mean?
Insulin signals the building of macromolecules, cells, and tissues
135
How is the insulin receptor different from most RTKs?
It's a "dimer" prior to insulin binding
136
Describe the structure of an insulin receptor.
1. Heterotetrameric protein
2. External alpha-subunit linked to internal beta-subunit by disulfide bond
3. Two of these monomers are linked by disulfide bonds so that the receptor is already dimeric without insulin
137
How does the structure of insulin receptors change before and after binding insulin?
Unbound: Beta-subunits are too far apart to cross-phosphorylate each other
Bound: Conformational changes in the extracellular domains bring the kinase domains closer together
138
What do insulin receptors bind?
Insulin, insulin-like growth factor I (IGF-I), and IGF II
139
How does insulin receptor substrate 1 (IRS1) interact with the insulin receptor?
IRS1 binds to the phosphotyrosine, and the kinase on the receptor further phosphorylates multiple tyrosine residues in IRS1
140
The Pleckstrin homology (PH) domain on IRS1 bind to what?
Phosphotidylinositols (PIP3)
141
How is insulin receptor substrate (IRS) recruited to the insulin receptor?
IRS is recruited by its PTB domain to the phosphotyrosines on IR.
142
What do adaptor proteins do?
They link proteins together through protein binding domains (Ex. SH3) to make larger signaling complexes
143
What are docking proteins?
Proteins that contain:
1. An N-terminal motif/domain for direct membrane association
2. Many tyrosine phosphorylation sites for effector recruitment
144
What do scaffolding proteins do?
They interact with multiple members of a signaling pathway and tether them into a signaling complex
145
The phosphatidylinositide 3-kinase (PI3K) pathway is key to what?
Cellular growth and survival
This pathway is one of the most commonly altered in human tumors
146
What is the difference between IP3 and PIP3?
IP3 stimulates release of Ca2+ from ER
PIP3 recruits proteins to the membrane
147
What does PI 3-kinase convert?
It converts the membrane phospholipid PIP2 to PIP3
148
What is the function of PIP3?
PIP3 serves as a docking site for proteins with PH domains
149
How is Akt (protein kinase B) activated?
1. Recruitment to plasma membrane via PIP3
2. Phosphorylation by protein kinase PDK1
150
After activation, what does Akt do?
It phosphorylates downstream proteins on ser/thr
151
What is the overall effect of Akt?
1. Stimulates glucose transport, glycolysis, and glycogen synthesis
2. Stimulates cell proliferation
3. Stimulates protein synthesis
4. Inhibits apoptosis
152
What is PTEN, and what is its function?
It's a lipid phosphatase that dephosphorylates PIP3 to yield PIP2.
It's a tumor suppressor.
153
Name the six steps of the PI 3-kinase pathway.
1. Growth factor or insulin binds to an RTK and activates PI 3-kinase
2. PI 3-kinase phosphorylates, converting PIP2 into PIP3
3. PIP3 serves as a recognition site for PDK1 and other kinases with PH domains like Akt
4 . PDK1 phosphorylates Akt when it's docked at the membrane, activating it
5. Akt phosphorylates many other proteins
6. PTEN dephosphorylates PIP3, inactivating the pathway
154
What is the function of rapamycin?
It functions like an adaptor, bringing a mechanistic target of rapamycin (mTOR) close to FKBP-12, which inhibits its kinase activity.
155
What are the differences between mTOR C1 and mTOR C2?
mTOR C1:
1. Complexed with Raptor
2. Sensitive to rapamycin
3. Regulated indirectly by Akt
4. Stimulates cell growth and protein synthesis
mTOR C2:
1. Complexed with Rictor
2. Insensitive to rapamycin
3. Regulates Akt by serine phosphorylation
4. Regulates cytoskeleton and cell metabolism
156
What is Bad? How is it inihibited?
Bad is a pro-apoptotic protein.
It's phosphorylated and inhibited by Akt (Prevents the initiation of apoptosis)
157
What are cytokines?
Small proteins that act as signaling (endocrine, paracrine, or autocrine) molecules used in immune response
158
Describe the structure of cytokine receptors.
They transverse the membrane once, function as dimers, and are closely linke to intracellular tyrosine kinases
159
Activated cytokine receptors activate what pathway?
JAK-STAT pathway
160
What does STAT stand for?
Signal transducer and activator of transcription
161
What are the five steps in the Jak/STAT pathway?
1. When inactive, STATs are in the cytosol as monomers
2. STATs are recruited via their SH2 domains to the phosphorylated cytokine receptor
3. A Jak phosphorylates the STAT, causing it to come off of the receptor.
4. The SH2 domain on STAT recognizes the phosphotyrosine on another STAT, and they dimerize
5. Dimerization of STAT leads to its nuclear localization, DNA binding, and regulation of transcription
162
Signaling through the TGF-beta superfamily requires __ types of receptors.
2
(Type I and type II receptors)
163
Type I and type II TGF-beta receptors are always present as ______, which come together to form _______.
homodimers; heterotetramers
164
TGF-beta receptors as composed of ___ different subunits. The receptor is a ___.
2; tetramer (2 Type I and 2 type II)
165
How does the TGF-beta receptor complex form?
Type II receptor dimer binds to ligand first and then forms a complex with the type I receptor dimer
166
After ligand binding, how does the TGF-beta receptor activate its activity?
Type II subunit phosphorylates a site on the type I subunit to activate its kinase activity
167
What does the type I subunit in the TGF-beta receptor do upon activation?
It phosphorylates latent transcription factors AKA Smads
168
What is the function of SARA?
It's a scaffolding protein that binds to PI(3)P in the membrane, stimulating the phosphorylation of SMAD2/3
169
What happens when TGF-beta receptors are internalized via the clathrin-mediated pathway?
Activation is promoted
170
What happens when TGF-beta receptors are internalized via the caveolin-mediated pathway?
Endosomes are enriched in SMAD7, which recruits SMURF to ubiquitinate the receptor, leading to degradation.
171
Does TGF-beta promote or suppress tumor formation?
Depends.
Normally, it's a tumor suppressor. As tumors start spreading, they become TGF-beta resistant. In tumors, TGF-beta is oncogenic.
172
What are ANPs?
Hormones secreted by the heart in response to high blood pressure
173
What is the function of ANPs?
They relax smooth muscle cells in blood vessels and stimulate the excretion of Na+ and H2O.
They regulate salt and water balance, and thus blood pressure.
174
Describe the structure of ANP receptors.
They have a kinase homology domain (KHD) and a guanylyl cyclase domain on the cytosolic side of the membrane
175
How does the kinase homology domain work?
Upon ANP binding, conformational change leads to ATP binding and activation of the guanylyl cyclase domain
Dephosphorylation leads to desensitization
176
Receptor guanylyl cyclases make ___, which activates ___.
cGMP; PKG
177
What is the effect of activating PKG?
It inhibits the ER IP3-gated Ca2+ channel by phosphorylating it.
Less Ca2+, less smooth muscle contraction (Smooth muscle relaxation)
178
What is nitric oxide (NO)?
A highly reactive and toxic, free radical gas with a short half-life (5 sec)
179
What is the function of NO?
It functions as a signal molecule when at low concentrations.
It functions as a killer at high concentrations.
180
NO is synthesized in cells by what?
Nitric oxide synthases (NOS)
181
Name the three types of NOS.
1. Neuronal constitutive NOS (nNOS)
2. Endothelial constitutive NOS (eNOS)
3. Induced NOS (iNOS)
182
Where does nNOS function?
Nervous system
183
Where does eNOS function?
Vascular system
184
What is the function of iNOS?
Kills microbes, viruses, and surrounding cell
185
What is the pathway of NO signaling in vasodilation? (6 steps)
1. Acetylcholine binds to GPCR on endothelial cells, activating Gq
2. Ca2+/calmodulin binds eNOS to activate it, leading to NO synthesis
3. NO acts as a paracrine mediator to influence nearby cells
4. NO binds to intracellular guanylyl cyclase and activates it, making cGMP
5. cGMP activates PKG
6. PKG phosphorylates IP3-gated calcium channel, inhibiting it and relaxing the smooth muscle
186
What are the subunits of guanylyl cyclase?
1. Regulartory (Heme containing)
2. Catalytic (Heterodimer)
187
Transport via ion channels is always [active/passive].
passive (In the direction of the concentration gradient)
188
How do voltage-gated channels work?
They respond to a voltage change across the membrane
189
What do ligand-gated extracellular ligand channels bind to?
Neurotransmitters
190
What do ligand-gated intracellular ligand channels bind to?
Ions, second messengers, nucleotides
191
How do mechanically-gated channels work?
They're linked to the cytoskeleton and respond to mechanical stress
192
Signaling across synaptic junctions is controlled by what kind of channels?
Ligand-gated
193
Acetylcholine binds to which two classes of receptors?
1. GPCRs to activate Gi or Gq (Muscarinic acetylcholine receptors)
2. Ion channels (Nicotinic acetylcholine receptors)
194
Describe the structure of the nicotinic acetylcholine receptor.
Five subunits (transmembrane alpha helix) form a channel
195
How does the nicotinic acetylcholine receptor work?
The channel opens when two molecules of acetylcholine bind to the extracellular surface of the receptor
The pore opens, allowing Na+ to move across the membrane
Acetylcholine is rapidly degraded or removed, and the channel closes
196
With acetylcholine bound, the nicotinic acetylcholine receptor stays open. True or false?
False. The receptor flickers between open and closed states until acetylcholine is degraded or removed.
197
Steroid receptors are ____ receptors.
nuclear
198
Nuclear receptors have [short/long]-term effects on the body. Why?
long
The ligands have long half-lives.
199
Steroid hormones are terpenoid compounds derived from _____.
cholesterol
200
List the five steps in which steroid hormones are derived from cholesterol.
1. Isoprene building blocks (5C)
2. Squalene (30C)
3. Cholesterol (27C)
4. Androgens
5. Estrogens
201
Testosterone is converted to estradiol via which molecule?
Aromatase (Androgens to estrogens)
202
Steroid hormones enter the cell via [active/passive] diffusion.
passive
203
Ligands for type I nuclear receptors bind with [low/high] specificity and [low/high] affinity.
high; high
204
Type II nueclear receptors bind many compounds with [low/high] affinity and [low/high] specificity.
low; low
205
What are selective receptor modulators (SRMs)?
Ligands for specific nuclear receptors (Tissue-specific regulators)
206
What are the two types of SRMs?
SERMs: Selective ER modulators (Birth control agonist, chemotherapy)
SARMs: Selective AR modulators (Steroid abuse agonist, chemotherapy)
207
What is the difference between type I and type II nuclear receptors in terms of binding?
Type I bind to inverted repeats as homodimers.
Type II bind to direct repeats as heterodimers with RXR (Retenoid X receptor)
208
How many nuclear receptors are there in humans?
48
209
How to nuclear receptors bind to DNA?
Via zinc fingers
Alpha helix of zinc fingers insert into major groove of DNA to make sequence-specific contacts
210
What are enhancers?
Short segments of DNA that bind transcription factors that activate genes
211
Nuclear receptors typically bind to what?
Short sequences of DNA (Hormone response elements; HREs) that function as enhancers
212
Respone elements for steroid receptors are ______.
palindromes (inverted repeats)
213
DNA binding sites for type II RXR heterodimeric receptors are [inverted/direct] repeats.
direct
214
What are the three steps in signaling through the steroid (type I) nuclear receptor?
1. Inactive receptor in the cytoplasm is bound to heat shock protein complex
2. Binding to hormone causes receptor to dissociate from HSP
3. Receptor dimer translocates to nucleus to bind to HREs, increasing gene transcription
215
Nuclear receptors for non-steroid hormones bind to DNA as _______.
heterodimers (One being RXR)
216
What happens when type II nuclear receptors bind to DNA?
They bind in a co-repressor complex in the absense of ligand, silencing the gene
217
Nuclear receptors regulate gene transcription directly or indirectly?
Both directly and indirectly
218
What are latent transcription factors?
Proteins that go into the nucleus to activate gene expression only after they've been activated
219
What's a zymogen?
A protein that's produced in an inactive state and needs to be activated by protease degradation
220
Wnt signaling leads to what?
Dephosphorylation of the protein to be degraded
221
NF-kappaB signaling leads to what?
Phosphorylation of the protein to be degraded
222
What are Wnts?
Ligands that act as paracrine mediators to control development and contribute to cancer formation
223
What do Wnt ligands bind to?
Frizzled receptors
224
Describe the structure of Frizzled receptors.
They transverse the membrane 7 times and resemble GPCRs
225
Activation of Frizzled involves which co-receptor?
LRP (LDL-receptor-related protein)
226
What is the function of the Wnt pathway?
Regulates the proteolysis of beta-catenin, which functions in cell adhesion and gene regulation
227
When inactive, beta-catenin is in the cytoplasm in a "degradation" complex with which four other proteins?
1. Axin: Scaffold protein
2. APC: Scaffold protein
3. GSK3: Ser/thr kinase
4. CK1: Ser/thr kinase
228
What marks beta-catenin for degradation?
Phosphorylation of beta-catenin by CK1 and by GSK3
229
Wnt responsive genes are kept inactive by what complex?
Groucho co-repressor bound to LEF1/TCF activators
230
List the steps of how Wnt signaling is activated.
1. Wnt ligands bring together Frizzled and LRP receptors
2. This activates the Dishevelled (Dsh) protein
3. Dsh recruits GSK1 and CK1 to the receptor complex
4. LRP gets phosphorylated
5. Axin is brought to the receptor
All this disrupts the degradation complex. Beta-catenin won't be degraded.
231
Where does unphosphorylated beta-catenin go?
It goes to the nucleus, kicking off Groucho and binding to LEF1/TCF
Wnt target genes are transcribed
232
What is Myc?
A transcription factor that promotes cell growth and proliferation
Target gene for beta-catenin
233
What is Apc?
Tumor suppressor gene
234
How do colonic crypts form?
In cells that lack Apc, beta-catenin remains high even without Wnt, leading to uncontrolled cell growth.
235
What are the six hallmarks of cancer?
1. Evading apoptosis
2. Self-sufficiency in growth signals
3. Insensitivity to anti-growth signals
4. Sustained angiogenesis
5. Limitless replicative potential
6. Tissue invasion and metastasis
236
Is a single abnormal cell enough cause cancer?
Yes
237
Is a single mutation enough to cause cancer?
No
238
Cancer increases exponentially as a function of ___.
age
239
Cancer is usually caused by [dominant/recessive] mutations.
recessive
240
What is the difference between dominant and recessive mutations in cancer?
Dominant: Gain of function enables oncogene to promote cell transformation
Recessive: Loss of function in BOTH gene copies eliminates tumor suppressor gene, promoting cell transformation
241
All gain-of-mutation, dominant mutations that convert proto-oncogenes to oncogenes increase what to promote cell transformation?
The activity or amount of protein
242
How does the p53 pathway relate to cancer?
It regulates reponses to stress and DNA damage
243
How does the Rb pathway relate to cancer?
It initiates cell division
244
How does the RTK/Ras/PI3K pathway relate to cancer?
It transmits signals for cell growth from the exterior of the cell to the nucleus
245
Mutations in what protein are devastating with regard to oncogenesis?
p53 (Guardian of the genome)
246
Mutations in TP53 are found in most cancers. Why?
p53 is critical. It serves as an "antenna," altering the cell to any dangerous situations
247
Most p53 mutations are in the binding domain, so p53 can still bind to DNA as a tetramer. Why does this matter?
Because p53 functions as a tetramer, mutation of only one allele of TP53 permits cancer
