25 - Signaling to the Nucleus & Nuclear Hormone Receptor Signaling Flashcards
(208 cards)
1
Q
What is the difference between signaling through nuclear receptors (as opposed to cell surface receptors)?
A
Nuclear receptors do not go through cytoplasmic factors (no intermediates)
2
Q
What are the different types of tyrosine kinases?
A
RTKs, and nRTKs
3
Q
What does nRTK stand for?
A
Non-receptor tyrosine kinase
4
Q
What is the structure of an RTK?
A
Membrane-spawning proteins with an extracellular binding site
5
Q
What is the structure of an nRTK?
A
Cytosolic proteins, usually coupled to transmembrane proteins
6
Q
What are the substrates of RTKs?
A
Growth factors and hormones
7
Q
What are the substrates of nRTKs?
A
Other proteins (protein-protein interactions)
8
Q
How does an nRTK get activated?
A
When an associated receptor binds to a cytokine
9
Q
Where are nRTKs found?
A
Associated to other receptors at their intracellular domain
10
Q
What happens to nRTKs when its associated receptor binds to a cytokine?
A
They phosphorylate each other and the receptor
11
Q
What is the purpose of nRTK phosphorylation?
A
It recruits other cytoplasmic factors to send the signal to the nucleus
12
Q
True or false: the cytokine receptor has kinase activity
A
False: the associated nRTKs have kinase activity, not the receptor
13
Q
What type of protein is JAK?
A
An nRTK
14
Q
What molecules does JAK recruit?
A
STAT molecules
15
Q
What happens when STAT molecules are recruited by JAK?
A
They get phosphorylated and dimerize
16
Q
What happens when STAT molecules are phosphorylated and dimerized?
A
They move to the nucleus to act as transcription factors
17
Q
What does the cytokine do to the cytokine receptor?
A
It brings the beta subunits close together to allow for JAK phosphorylation
18
Q
What does JAK stand for?
A
Janus kinase
19
Q
What does STAT stand for?
A
Signal transducer and activator of transcription
20
Q
What does JAK phosphorylate?
A
Other JAKs, the receptor, and STATs
21
Q
When do STATs get phosphorylated?
A
After docking on the pTyr sytes
22
Q
How do STATs dimerize?
A
Via their SH2 domains
23
Q
What do STATs do in the nucleus?
A
They bind to DNA to activate gene transcription
24
Q
What determines the specific cytokine response element generated by the cell?
A
The different JAK, STAT, and receptor specificity
25
Why does STAT dissociate from the receptor and dimerize?
The amino acid sequences surrounding the pTyr on the receptor are less favored than the amino acid sequences surrounding the pTyr on STAT
26
What is the structure of JAK?
It has a kinase domain and a pseudokinase domain
27
What is a kinase domain (on JAK)?
The domain that can phosphorylate tyrosines
28
What is a pseudokinase domain (on JAK)?
The domain that is catalytically inactive, but has regulatory function
29
What is the J1 domain in JAK?
The kinase domain
30
What is the J2 domain in JAK?
The pseudokinase domain
31
What is the function of J1 in JAK?
Phosphorylate tyrosines
32
What is the function of J2 in JAK?
Regulate the activity of JAK
33
What is the hallmark of JAK kinases?
The combination of a kinase and pseudokinase domain next to each other
34
What defines the cellular response to cytokines and other growth factors?
The different combinations of receptors, JAKs, and STATs present in the cell
35
True or false: STAT molecules can only form dimers
False: they can also form trimers
36
What processes (3) utilize JAK signaling?
Hematopoiesis, cell proliferation, and immune function
37
What do receptor serine/threonine kinases do?
Activate transcription factors directly at the receptor
38
What is an example of a serine/threonine kinase?
TGF-beta receptor
39
What type of molecule is the TGF-beta receptor?
A serine/threonine kinase
40
What does TGF-beta stand for?
Transforming growth factor beta
41
What types of activities do serine/threonine kinases mediate?
Pleotropic activities (varied)
42
What are some functions (4) of serine/threonine kinases?
1. Inhibit proliferation
2. Induce ECM synthesis
3. Bone formation
4. Embryonic development (dorsal-ventral specification)
43
What are growth factors?
Proteins that play important roles in regulating cell differentiation, division, and movement
44
What do activating mutations of growth factor receptors commonly lead to?
Cancers
45
What does TGF-beta do?
Exerts anti-proliferative effects on target cells
46
True or false: TGF-beta plays widespread roles in only vertebrate development
False: it is also important in invertebrate development
47
What happens if there is a loss of TGF-beta receptors?
The cell gets transformed into a cancerous state
48
How is TGF-beta secreted?
As an inactive precursor
49
What happens to TGF-beta once it is secreted from the cell?
It undergoes proteolytic processing and attaches to the ECM
50
When is TGF-beta released from the ECM?
When it receives the appropriate signal
51
What type of signaling does TGF-beta induce?
Paracrine signaling
52
What receptor does TGF-beta first bind to?
A type II TGF-beta receptor
53
What happens when TGF-beta binds to a type II TGF-beta receptor?
It then phosphorylates and binds to a type I TGF-beta receptor
54
What happens when the type I TGF-beta receptor is phosphorylated?
It recruits and phosphorylates Smad proteins
55
When is the type I TGF-beta receptor phosphorylated?
When TGF-beta binds to a type II TGF-beta receptor
56
What do Smads do after being activated by type I TGF-beta receptors?
They oligomerize and move to the nucleus to activate gene transcription
57
What is the structure of the TGF-beta receptors in the cell membrane?
Dimers
58
When a TGF-beta is fully bound, how many individual receptors is it bound to?
4 (2 type I dimers, and 2 type II dimers)
59
What are Smurfs?
Smad inhibiting proteins
60
True or false: there are many kinds of Smads
True: they are a diverse family of proteins
61
True or false: Smads are always activating
False: there can also be inhibiting Smads to stop the signal
62
What defines the signaling response to TGF-beta?
Different combinatorics of type II and type I receptors, leading to different Smads
63
How do Smads regulate gene transcription?
By physical interaction with DNA binding transcription factors, such as CBP and p300
64
What types of molecules are Smads?
Transcription factors
65
What happens when Smads are phosphorylated?
Their nuclear localization signal is exposed, allowing them to be moved to the nucleus
66
What is Imp-beta?
A transport molecule
67
What does Imp-beta stand for?
Importin-beta
68
What does Imp-beta do?
Move activated Smads to the nucleus
69
When does Imp-beta bind to Smad?
When its nuclear localization signal is exposed through phosphorylation
70
What determines the activity of repressors to shut down Smad signaling?
TGF-beta
71
What feedback loop is controlled by TGF-beta?
A negative feedback of repressors to stop Smad signaling
72
How do repressors stop Smad from activating gene transcription?
They recruit histone deacetylases to condense the chromatin
73
What happens if TGF-beta receptors are overexpressed?
The cells transform into a cancerous state
74
What is the structure of the TGF-beta prepropeptide?
A signal peptide, a prodomain, and a mature peptide domain
75
What is another name for the prodomain of TGF-beta?
The latency-associated polypeptide for TGF-beta
76
What is the structure of the TGF-beta propeptide?
A prodomain, and a mature peptide domain
77
What happens to the prepropeptide of TGF-beta to turn it into the propeptide?
The signal peptide is cleaved?
78
What happens to process the propeptide of TGF-beta?
The prodomain is cleaved, and is noncovalently attached to the mature peptide domain
79
True or false: the TGF-beta complex with the prodomain can only be a heterodimer
False: it can also be a heterodimer
80
What holds two dimers of TGF-beta complex together?
Disulfide bonds
81
What is the structure of the latent TGF-beta complex?
Two mature peptides noncovalently linked to two prodomains, and held together with disulfide bonds
82
What can the latent TGF-beta complex associate with?
The ECM, or the plasma membrane
83
How does latent TGF-beta complex associate with the ECM?
Through LTBPs
84
What does LTBP stand for?
Latent TGF-beta binding protein
85
What does LTBP do?
Associate the latent TGF-beta complex to the ECM
86
How does latent TGF-beta complex associate with the plasma membrane?
Through GARPs
87
What is the term for a latent TGF-beta complex associated with an LTBP?
An LLC
88
What does LLC stand for?
Large latent complex
89
What is an LLC?
A latent TGF-beta complex associated with an LTBP
90
What does GARP stand for?
Glycoprotein-A repetitions predominant
91
What does GARPs do?
Associate the latent TGF-beta complex to the plasma membrane
92
What are cytonemes?
Extensions of the cell body
93
What is the purpose of cytonemes?
They present TGF-beta receptors to the TGF-beta ligand complexes
94
What bonds hold the prodomain to the mature peptide in the latent TGF-beta complex?
Noncovalent interactions
95
How does the latent TGF-beta complex bind to TGF-beta receptors?
It releases the mature peptide from the noncovalently attached prodomains
96
True or false: Smads have many roles in transcriptional regulation
True: they can be activators or repressors
97
What is a self enabling mechanism?
Smads can promote gene expression, which can lead to translation of other Smads, which can then lead to other gene responses
98
True or false: Smads cannot interact with other Smads
False: they can participate in self enabling mechanisms to lead to complex gene interactions
99
What other signaling can be done through the TGF-beta receptor (besides Smad dependent pathways)?
Other pathways, or type II receptor dependent pathways
100
What other effects can Smads have (besides transcriptional regulation)?
Chromatin remodeling, and miRNA processing regulation
101
What hypes of signals do nuclear hormone receptors respond to?
Hydrophobic nuclear signaling molecules
102
What are some examples of hydrophobic signaling molecules?
Cortisol, estradiol, testosterone, thyroxine, vitamin D, etc.
103
What are some functions of hydrophobic signaling molecules?
Stress, pregnancy, metabolism, growth, development, differentiation, etc.
104
How many nuclear receptors have been identified in humans?
48
105
What happens when a ligand binds to a nuclear receptor?
It translocates to the nucleus and regulates gene transcription
106
How do nuclear receptor ligands get into the cell?
They readily diffuse through the cell membrane
107
Where are nuclear receptors found?
In the cytosol or in the nucleus
108
What is the structure of a nuclear receptor?
A ligand binding domain, a hinge domain, a DNA binding domain, and a transcription activation domain
109
How does a nuclear receptor stay in the cytosol when no ligand is present?
An inhibitor complex stays bound to the receptor
110
How does a ligand get to a nuclear receptor in the nucleus?
It moves through the nuclear pore
111
What happens when a hormone binds to a nuclear receptor (in terms of the domains)?
The inhibitory complex is released, exposing the DNA binding domain
112
What domain is exposed in a nuclear receptor when a ligand binds?
The DNA binding domain, and nuclear localization signals
113
What are the two schemes of nuclear translocation?
Release and binding
114
What is the release scheme of nuclear translocation?
HSP bound to the nuclear receptor in the cytoplasm is released upon hormone binding, allowing the receptor to translocate to the nucleus
115
What is the binding scheme of nuclear translocation?
HSP binds to the nuclear receptor upon hormone binding, allowing the receptor to translocate to the nucleus
116
What does HSP stand for?
Heat shock protein
117
In what state do nuclear receptors usually bind to the DNA?
As a dimer
118
What did Chambon and Evans do?
Cloned multiple nuclear receptors
119
What did Chambon and Evans find?
That nuclear receptors all had common motifs (close evolutionary past)
120
What is an orphan receptor?
A receptor with an unknown ligand
121
How were the ligands of orphan receptors identified?
By using chimeric receptors and reporter genes
122
What was the chimeric gene used to identify ligands of orphan receptors?
The activation domain and DNA binding domain of GR, and the ligand binding domain of the orphan receptor
123
What does GR stand for?
Glucocorticoid receptor
124
What is the purpose of the GR activation and DNA binding domain in the chimeric receptor to study orphan receptors?
It can bind and activate a known gene (GR gene), which can be measured through a reporter like luciferase
125
What is the problem with using chimeric receptors to study orphan receptors?
Still need to test a variety of ligands to see what the chimeric receptor will actually respond to
126
What is often found in the ligand binding domain of nuclear receptors?
An NLS
127
What does NLS stand for?
Nuclear localization signal
128
What is meant by a "tiered effect" of steroid signaling?
Primary proteins are first synthesized, which then activate transcription of secondary proteins, and turn off transcription of their own proteins
129
What do primary proteins do in a tiered steroid signaling?
Turn off transcription of their own genes, and act as cofactors to turn on transcription of other secondary genes
130
What is a class I NR called?
A steroid hormone receptor
131
What are the ligands of class I NR?
Androgen, estrogen, progesterone, glucocorticoids, and mineralocorticoids
132
What does NR stand for?
Nuclear receptor
133
What is the response element of class I NR?
IR3
134
What does IR3 stand for?
Inverted repeat separated by 3 nucleotides
135
What type of dimer is a class I NR?
Homodimer
136
What is a class II NR called?
An RXR heterodimer
137
What are the ligands of class II NR?
Fatty acids, cholesterol, vitamin D, steroids, etc.
138
What is the response element of class II NR?
DRn, ERn, or IRn
139
What does DRn stand for?
Direct repeat
140
What does ERn stand for?
Everted repeat
141
What does IRn stand for?
Inverted repeat
142
What is an ERn?
143
What is an DRn?
-->n-->
144
What is an IRn?
-->n
145
What is an IR3?
--->nnn
146
What type of dimer is a class II NR?
Heterodimer
147
What is a class III NR called?
An RXR homodimer
148
What are the ligands of class III NR?
Retinoic acid, lipids
149
What is the response element of class III NR?
DRn
150
What type of dimer is a class III NR?
Homodimer
151
What is a class IV NR called?
A monomeric receptor
152
What are the ligands of class IV NR?
Melatonin, cholesterol
153
What is the response element of class IV NR?
Single response element
154
What type of dimer is a class IV NR?
Monomer
155
What does the DNA binding site on an NR have specificity towards?
The specific type of repeat element on the DNA
156
What is the variability rule?
The size of the spacer between the repeats (1-5 nt) determines which heterodimer can bind to the response element
157
What is a response element?
The segment of DNA that a DNA binding protein can bind to
158
True or false: the same sequence can lead to different heterodimer partners
True: the spacing between the repeats can dictate which heterodimer can bind to the DNA
159
What is the basic structure of chromatin
The nucleosome
160
What does the nucleosome look like?
Beads on a string
161
What is a nucleosome?
DNA wrapped around histones, plus 200 nt of linker DNA
162
How can a nucleosome be separated by other nucleosomes?
By using a nuclease to digest the linker DNA
163
How can the DNA be released from the nucleosome?
By using high salt
164
What is the structure of a histone?
An octomeric structure (dimers of H2A, H2B, H3, and H4)
165
How is chromatin organized?
Into fibers of increasing size
166
What is the 10 nm fiber?
DNA winds around histones to form beads
167
What is the 30 nm fiber?
Nucleosomes comes together to form a thicker fiber
168
What is the 300 nm fiber?
The 30 nm fiber forms loop domains that attach to proteins
169
What is the 700 nm fiber?
The metaphase chromosome
170
What is the purpose of organizing chromatin into fibers?
Have a high concentration of DNA in the nucleus
171
What is chromatin?
A complex of DNA and protein found in the nucleus of eukaryotic cells
172
What are histones?
Proteins responsible for the first level of DNA packing
173
What are some possible post-translational modifications of histones?
Acetylation, methylation, ubiquitination, sumoylation, and phosphorylation
174
What do the post-translational modifications of histone tails dictate?
How tight or loose the DNA wraps around the histones
175
What post-translational modification occurs at lysines of histone tails?
Acetylation
176
What enzyme acetylates histone tails?
HATs
177
What does HAT stand for?
Histone acetyltransferase
178
What enzyme deacetylates histone tails?
HDACs
179
What does HDAC stand for?
Histone deacetylatase
180
What does acetylation do to gene expression?
Increases gene expression
181
What does deacetylation do to gene expression?
Silences gene expression
182
What proteins does acetylation bring in?
Bromodomain proteins
183
What brings in bromodomain proteins?
Acetylation
184
What proteins does methylation bring in?
Chromodomain proteins
185
What brings in chromodomain proteins?
Methylation
186
What does methylation do to gene expression?
Silences gene expression
187
What does demethylation do to gene expression?
Increases gene expression
188
What is the ongoing research regarding the histone code?
How different combinations of post-translational modifications affects gene expression
189
What can be said about the proteins that modify histones (in terms of cell signaling)?
They are downstream of signaling pathways
190
What do barrier sequences do?
Separates the spread of heterochromatin from different genes in the DNA
191
What is heterochromatin?
Highly bound chromatin
192
What is euchromatin?
Loosely bound chromatin
193
What do insulator sequences do?
Prevent enhancers and silencers from influencing other genes and promoters
194
What type of protein is CBP?
A HAT
195
How does CBP alter the DNA?
It opens the DNA to allow for transcription of a CRE/CREB regulated gene
196
What are the theories of opening up DNA after histone modifications?
1. The histone core disassembles and reassembles
| 2. The DNA slides along the histones
197
What do pioneer factors do?
Bind to regions between nucleosomes and recruit histone modification and chromatin remodeling complexes
198
What is needed to create an active enhancer (from the nucleosome)?
Pioneer factors need to recruit histone modification and chromatin remodeling complexes
199
How can NR without ligands lead to negative regulation?
They can act as repressors by methylating the DNA or by inhibiting other complexes
200
What does ligand binding to an NR do to the complexes recruited?
It can change the complex recruited, changing it from repression to activation
201
True or false: coactivators for histone modifications are specific to one particular pathway
False: they are common to multiple pathways
202
What is an example of coactivators for histone modifications?
CBP and p300
203
How can CBP and p300 act as integration points for signaling?
They can be recruited by a variety of transcription factors
204
How can CBP activity be modulated?
By various kinds of inputs (crosstalk)
205
What is meant by "modularity" for transcription factors?
They can have multiple partners and bind to multiple genes
206
What does ChIP stand for?
Chromatin immuno precipitation
207
What is the purpose of ChIP?
Method to identify gene targets of specific transcription factors
208
What are the steps (4) of ChIP?
1. Bind transcription factor to DNA
2. Digest DNA with restriction enzyme
3. Bind antibody against transcription factor to isolate complex
4. Analyze the gene sequences
