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BIO 317 > 25 - Signaling to the Nucleus & Nuclear Hormone Receptor Signaling > Flashcards

25 - Signaling to the Nucleus & Nuclear Hormone Receptor Signaling Flashcards

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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)

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2
Q

What are the different types of tyrosine kinases?

A

RTKs, and nRTKs

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3
Q

What does nRTK stand for?

A

Non-receptor tyrosine kinase

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4
Q

What is the structure of an RTK?

A

Membrane-spawning proteins with an extracellular binding site

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5
Q

What is the structure of an nRTK?

A

Cytosolic proteins, usually coupled to transmembrane proteins

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6
Q

What are the substrates of RTKs?

A

Growth factors and hormones

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7
Q

What are the substrates of nRTKs?

A

Other proteins (protein-protein interactions)

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8
Q

How does an nRTK get activated?

A

When an associated receptor binds to a cytokine

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9
Q

Where are nRTKs found?

A

Associated to other receptors at their intracellular domain

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10
Q

What happens to nRTKs when its associated receptor binds to a cytokine?

A

They phosphorylate each other and the receptor

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11
Q

What is the purpose of nRTK phosphorylation?

A

It recruits other cytoplasmic factors to send the signal to the nucleus

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12
Q

True or false: the cytokine receptor has kinase activity

A

False: the associated nRTKs have kinase activity, not the receptor

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13
Q

What type of protein is JAK?

A

An nRTK

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14
Q

What molecules does JAK recruit?

A

STAT molecules

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15
Q

What happens when STAT molecules are recruited by JAK?

A

They get phosphorylated and dimerize

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16
Q

What happens when STAT molecules are phosphorylated and dimerized?

A

They move to the nucleus to act as transcription factors

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17
Q

What does the cytokine do to the cytokine receptor?

A

It brings the beta subunits close together to allow for JAK phosphorylation

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18
Q

What does JAK stand for?

A

Janus kinase

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19
Q

What does STAT stand for?

A

Signal transducer and activator of transcription

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20
Q

What does JAK phosphorylate?

A

Other JAKs, the receptor, and STATs

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21
Q

When do STATs get phosphorylated?

A

After docking on the pTyr sytes

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22
Q

How do STATs dimerize?

A

Via their SH2 domains

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23
Q

What do STATs do in the nucleus?

A

They bind to DNA to activate gene transcription

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24
Q

What determines the specific cytokine response element generated by the cell?

A

The different JAK, STAT, and receptor specificity

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25
Q

Why does STAT dissociate from the receptor and dimerize?

A

The amino acid sequences surrounding the pTyr on the receptor are less favored than the amino acid sequences surrounding the pTyr on STAT

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26
Q

What is the structure of JAK?

A

It has a kinase domain and a pseudokinase domain

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27
Q

What is a kinase domain (on JAK)?

A

The domain that can phosphorylate tyrosines

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28
Q

What is a pseudokinase domain (on JAK)?

A

The domain that is catalytically inactive, but has regulatory function

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29
Q

What is the J1 domain in JAK?

A

The kinase domain

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30
Q

What is the J2 domain in JAK?

A

The pseudokinase domain

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31
Q

What is the function of J1 in JAK?

A

Phosphorylate tyrosines

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32
Q

What is the function of J2 in JAK?

A

Regulate the activity of JAK

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33
Q

What is the hallmark of JAK kinases?

A

The combination of a kinase and pseudokinase domain next to each other

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34
Q

What defines the cellular response to cytokines and other growth factors?

A

The different combinations of receptors, JAKs, and STATs present in the cell

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35
Q

True or false: STAT molecules can only form dimers

A

False: they can also form trimers

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36
Q

What processes (3) utilize JAK signaling?

A

Hematopoiesis, cell proliferation, and immune function

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37
Q

What do receptor serine/threonine kinases do?

A

Activate transcription factors directly at the receptor

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38
Q

What is an example of a serine/threonine kinase?

A

TGF-beta receptor

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39
Q

What type of molecule is the TGF-beta receptor?

A

A serine/threonine kinase

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40
Q

What does TGF-beta stand for?

A

Transforming growth factor beta

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41
Q

What types of activities do serine/threonine kinases mediate?

A

Pleotropic activities (varied)

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42
Q

What are some functions (4) of serine/threonine kinases?

A
  1. Inhibit proliferation
  2. Induce ECM synthesis
  3. Bone formation
  4. Embryonic development (dorsal-ventral specification)
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43
Q

What are growth factors?

A

Proteins that play important roles in regulating cell differentiation, division, and movement

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44
Q

What do activating mutations of growth factor receptors commonly lead to?

A

Cancers

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45
Q

What does TGF-beta do?

A

Exerts anti-proliferative effects on target cells

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46
Q

True or false: TGF-beta plays widespread roles in only vertebrate development

A

False: it is also important in invertebrate development

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47
Q

What happens if there is a loss of TGF-beta receptors?

A

The cell gets transformed into a cancerous state

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48
Q

How is TGF-beta secreted?

A

As an inactive precursor

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49
Q

What happens to TGF-beta once it is secreted from the cell?

A

It undergoes proteolytic processing and attaches to the ECM

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50
Q

When is TGF-beta released from the ECM?

A

When it receives the appropriate signal

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51
Q

What type of signaling does TGF-beta induce?

A

Paracrine signaling

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52
Q

What receptor does TGF-beta first bind to?

A

A type II TGF-beta receptor

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53
Q

What happens when TGF-beta binds to a type II TGF-beta receptor?

A

It then phosphorylates and binds to a type I TGF-beta receptor

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54
Q

What happens when the type I TGF-beta receptor is phosphorylated?

A

It recruits and phosphorylates Smad proteins

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55
Q

When is the type I TGF-beta receptor phosphorylated?

A

When TGF-beta binds to a type II TGF-beta receptor

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56
Q

What do Smads do after being activated by type I TGF-beta receptors?

A

They oligomerize and move to the nucleus to activate gene transcription

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57
Q

What is the structure of the TGF-beta receptors in the cell membrane?

A

Dimers

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58
Q

When a TGF-beta is fully bound, how many individual receptors is it bound to?

A

4 (2 type I dimers, and 2 type II dimers)

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59
Q

What are Smurfs?

A

Smad inhibiting proteins

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60
Q

True or false: there are many kinds of Smads

A

True: they are a diverse family of proteins

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61
Q

True or false: Smads are always activating

A

False: there can also be inhibiting Smads to stop the signal

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62
Q

What defines the signaling response to TGF-beta?

A

Different combinatorics of type II and type I receptors, leading to different Smads

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63
Q

How do Smads regulate gene transcription?

A

By physical interaction with DNA binding transcription factors, such as CBP and p300

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64
Q

What types of molecules are Smads?

A

Transcription factors

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65
Q

What happens when Smads are phosphorylated?

A

Their nuclear localization signal is exposed, allowing them to be moved to the nucleus

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66
Q

What is Imp-beta?

A

A transport molecule

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67
Q

What does Imp-beta stand for?

A

Importin-beta

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68
Q

What does Imp-beta do?

A

Move activated Smads to the nucleus

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69
Q

When does Imp-beta bind to Smad?

A

When its nuclear localization signal is exposed through phosphorylation

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70
Q

What determines the activity of repressors to shut down Smad signaling?

A

TGF-beta

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71
Q

What feedback loop is controlled by TGF-beta?

A

A negative feedback of repressors to stop Smad signaling

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72
Q

How do repressors stop Smad from activating gene transcription?

A

They recruit histone deacetylases to condense the chromatin

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73
Q

What happens if TGF-beta receptors are overexpressed?

A

The cells transform into a cancerous state

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74
Q

What is the structure of the TGF-beta prepropeptide?

A

A signal peptide, a prodomain, and a mature peptide domain

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75
Q

What is another name for the prodomain of TGF-beta?

A

The latency-associated polypeptide for TGF-beta

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76
Q

What is the structure of the TGF-beta propeptide?

A

A prodomain, and a mature peptide domain

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77
Q

What happens to the prepropeptide of TGF-beta to turn it into the propeptide?

A

The signal peptide is cleaved?

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78
Q

What happens to process the propeptide of TGF-beta?

A

The prodomain is cleaved, and is noncovalently attached to the mature peptide domain

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79
Q

True or false: the TGF-beta complex with the prodomain can only be a heterodimer

A

False: it can also be a heterodimer

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80
Q

What holds two dimers of TGF-beta complex together?

A

Disulfide bonds

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81
Q

What is the structure of the latent TGF-beta complex?

A

Two mature peptides noncovalently linked to two prodomains, and held together with disulfide bonds

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82
Q

What can the latent TGF-beta complex associate with?

A

The ECM, or the plasma membrane

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83
Q

How does latent TGF-beta complex associate with the ECM?

A

Through LTBPs

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84
Q

What does LTBP stand for?

A

Latent TGF-beta binding protein

85
Q

What does LTBP do?

A

Associate the latent TGF-beta complex to the ECM

86
Q

How does latent TGF-beta complex associate with the plasma membrane?

A

Through GARPs

87
Q

What is the term for a latent TGF-beta complex associated with an LTBP?

A

An LLC

88
Q

What does LLC stand for?

A

Large latent complex

89
Q

What is an LLC?

A

A latent TGF-beta complex associated with an LTBP

90
Q

What does GARP stand for?

A

Glycoprotein-A repetitions predominant

91
Q

What does GARPs do?

A

Associate the latent TGF-beta complex to the plasma membrane

92
Q

What are cytonemes?

A

Extensions of the cell body

93
Q

What is the purpose of cytonemes?

A

They present TGF-beta receptors to the TGF-beta ligand complexes

94
Q

What bonds hold the prodomain to the mature peptide in the latent TGF-beta complex?

A

Noncovalent interactions

95
Q

How does the latent TGF-beta complex bind to TGF-beta receptors?

A

It releases the mature peptide from the noncovalently attached prodomains

96
Q

True or false: Smads have many roles in transcriptional regulation

A

True: they can be activators or repressors

97
Q

What is a self enabling mechanism?

A

Smads can promote gene expression, which can lead to translation of other Smads, which can then lead to other gene responses

98
Q

True or false: Smads cannot interact with other Smads

A

False: they can participate in self enabling mechanisms to lead to complex gene interactions

99
Q

What other signaling can be done through the TGF-beta receptor (besides Smad dependent pathways)?

A

Other pathways, or type II receptor dependent pathways

100
Q

What other effects can Smads have (besides transcriptional regulation)?

A

Chromatin remodeling, and miRNA processing regulation

101
Q

What hypes of signals do nuclear hormone receptors respond to?

A

Hydrophobic nuclear signaling molecules

102
Q

What are some examples of hydrophobic signaling molecules?

A

Cortisol, estradiol, testosterone, thyroxine, vitamin D, etc.

103
Q

What are some functions of hydrophobic signaling molecules?

A

Stress, pregnancy, metabolism, growth, development, differentiation, etc.

104
Q

How many nuclear receptors have been identified in humans?

A

48

105
Q

What happens when a ligand binds to a nuclear receptor?

A

It translocates to the nucleus and regulates gene transcription

106
Q

How do nuclear receptor ligands get into the cell?

A

They readily diffuse through the cell membrane

107
Q

Where are nuclear receptors found?

A

In the cytosol or in the nucleus

108
Q

What is the structure of a nuclear receptor?

A

A ligand binding domain, a hinge domain, a DNA binding domain, and a transcription activation domain

109
Q

How does a nuclear receptor stay in the cytosol when no ligand is present?

A

An inhibitor complex stays bound to the receptor

110
Q

How does a ligand get to a nuclear receptor in the nucleus?

A

It moves through the nuclear pore

111
Q

What happens when a hormone binds to a nuclear receptor (in terms of the domains)?

A

The inhibitory complex is released, exposing the DNA binding domain

112
Q

What domain is exposed in a nuclear receptor when a ligand binds?

A

The DNA binding domain, and nuclear localization signals

113
Q

What are the two schemes of nuclear translocation?

A

Release and binding

114
Q

What is the release scheme of nuclear translocation?

A

HSP bound to the nuclear receptor in the cytoplasm is released upon hormone binding, allowing the receptor to translocate to the nucleus

115
Q

What is the binding scheme of nuclear translocation?

A

HSP binds to the nuclear receptor upon hormone binding, allowing the receptor to translocate to the nucleus

116
Q

What does HSP stand for?

A

Heat shock protein

117
Q

In what state do nuclear receptors usually bind to the DNA?

A

As a dimer

118
Q

What did Chambon and Evans do?

A

Cloned multiple nuclear receptors

119
Q

What did Chambon and Evans find?

A

That nuclear receptors all had common motifs (close evolutionary past)

120
Q

What is an orphan receptor?

A

A receptor with an unknown ligand

121
Q

How were the ligands of orphan receptors identified?

A

By using chimeric receptors and reporter genes

122
Q

What was the chimeric gene used to identify ligands of orphan receptors?

A

The activation domain and DNA binding domain of GR, and the ligand binding domain of the orphan receptor

123
Q

What does GR stand for?

A

Glucocorticoid receptor

124
Q

What is the purpose of the GR activation and DNA binding domain in the chimeric receptor to study orphan receptors?

A

It can bind and activate a known gene (GR gene), which can be measured through a reporter like luciferase

125
Q

What is the problem with using chimeric receptors to study orphan receptors?

A

Still need to test a variety of ligands to see what the chimeric receptor will actually respond to

126
Q

What is often found in the ligand binding domain of nuclear receptors?

A

An NLS

127
Q

What does NLS stand for?

A

Nuclear localization signal

128
Q

What is meant by a “tiered effect” of steroid signaling?

A

Primary proteins are first synthesized, which then activate transcription of secondary proteins, and turn off transcription of their own proteins

129
Q

What do primary proteins do in a tiered steroid signaling?

A

Turn off transcription of their own genes, and act as cofactors to turn on transcription of other secondary genes

130
Q

What is a class I NR called?

A

A steroid hormone receptor

131
Q

What are the ligands of class I NR?

A

Androgen, estrogen, progesterone, glucocorticoids, and mineralocorticoids

132
Q

What does NR stand for?

A

Nuclear receptor

133
Q

What is the response element of class I NR?

A

IR3

134
Q

What does IR3 stand for?

A

Inverted repeat separated by 3 nucleotides

135
Q

What type of dimer is a class I NR?

A

Homodimer

136
Q

What is a class II NR called?

A

An RXR heterodimer

137
Q

What are the ligands of class II NR?

A

Fatty acids, cholesterol, vitamin D, steroids, etc.

138
Q

What is the response element of class II NR?

A

DRn, ERn, or IRn

139
Q

What does DRn stand for?

A

Direct repeat

140
Q

What does ERn stand for?

A

Everted repeat

141
Q

What does IRn stand for?

A

Inverted repeat

142
Q

What is an ERn?

A
143
Q

What is an DRn?

A

–>n–>

144
Q

What is an IRn?

A

–>n

145
Q

What is an IR3?

A

—>nnn

146
Q

What type of dimer is a class II NR?

A

Heterodimer

147
Q

What is a class III NR called?

A

An RXR homodimer

148
Q

What are the ligands of class III NR?

A

Retinoic acid, lipids

149
Q

What is the response element of class III NR?

A

DRn

150
Q

What type of dimer is a class III NR?

A

Homodimer

151
Q

What is a class IV NR called?

A

A monomeric receptor

152
Q

What are the ligands of class IV NR?

A

Melatonin, cholesterol

153
Q

What is the response element of class IV NR?

A

Single response element

154
Q

What type of dimer is a class IV NR?

A

Monomer

155
Q

What does the DNA binding site on an NR have specificity towards?

A

The specific type of repeat element on the DNA

156
Q

What is the variability rule?

A

The size of the spacer between the repeats (1-5 nt) determines which heterodimer can bind to the response element

157
Q

What is a response element?

A

The segment of DNA that a DNA binding protein can bind to

158
Q

True or false: the same sequence can lead to different heterodimer partners

A

True: the spacing between the repeats can dictate which heterodimer can bind to the DNA

159
Q

What is the basic structure of chromatin

A

The nucleosome

160
Q

What does the nucleosome look like?

A

Beads on a string

161
Q

What is a nucleosome?

A

DNA wrapped around histones, plus 200 nt of linker DNA

162
Q

How can a nucleosome be separated by other nucleosomes?

A

By using a nuclease to digest the linker DNA

163
Q

How can the DNA be released from the nucleosome?

A

By using high salt

164
Q

What is the structure of a histone?

A

An octomeric structure (dimers of H2A, H2B, H3, and H4)

165
Q

How is chromatin organized?

A

Into fibers of increasing size

166
Q

What is the 10 nm fiber?

A

DNA winds around histones to form beads

167
Q

What is the 30 nm fiber?

A

Nucleosomes comes together to form a thicker fiber

168
Q

What is the 300 nm fiber?

A

The 30 nm fiber forms loop domains that attach to proteins

169
Q

What is the 700 nm fiber?

A

The metaphase chromosome

170
Q

What is the purpose of organizing chromatin into fibers?

A

Have a high concentration of DNA in the nucleus

171
Q

What is chromatin?

A

A complex of DNA and protein found in the nucleus of eukaryotic cells

172
Q

What are histones?

A

Proteins responsible for the first level of DNA packing

173
Q

What are some possible post-translational modifications of histones?

A

Acetylation, methylation, ubiquitination, sumoylation, and phosphorylation

174
Q

What do the post-translational modifications of histone tails dictate?

A

How tight or loose the DNA wraps around the histones

175
Q

What post-translational modification occurs at lysines of histone tails?

A

Acetylation

176
Q

What enzyme acetylates histone tails?

A

HATs

177
Q

What does HAT stand for?

A

Histone acetyltransferase

178
Q

What enzyme deacetylates histone tails?

A

HDACs

179
Q

What does HDAC stand for?

A

Histone deacetylatase

180
Q

What does acetylation do to gene expression?

A

Increases gene expression

181
Q

What does deacetylation do to gene expression?

A

Silences gene expression

182
Q

What proteins does acetylation bring in?

A

Bromodomain proteins

183
Q

What brings in bromodomain proteins?

A

Acetylation

184
Q

What proteins does methylation bring in?

A

Chromodomain proteins

185
Q

What brings in chromodomain proteins?

A

Methylation

186
Q

What does methylation do to gene expression?

A

Silences gene expression

187
Q

What does demethylation do to gene expression?

A

Increases gene expression

188
Q

What is the ongoing research regarding the histone code?

A

How different combinations of post-translational modifications affects gene expression

189
Q

What can be said about the proteins that modify histones (in terms of cell signaling)?

A

They are downstream of signaling pathways

190
Q

What do barrier sequences do?

A

Separates the spread of heterochromatin from different genes in the DNA

191
Q

What is heterochromatin?

A

Highly bound chromatin

192
Q

What is euchromatin?

A

Loosely bound chromatin

193
Q

What do insulator sequences do?

A

Prevent enhancers and silencers from influencing other genes and promoters

194
Q

What type of protein is CBP?

A

A HAT

195
Q

How does CBP alter the DNA?

A

It opens the DNA to allow for transcription of a CRE/CREB regulated gene

196
Q

What are the theories of opening up DNA after histone modifications?

A
  1. The histone core disassembles and reassembles

2. The DNA slides along the histones

197
Q

What do pioneer factors do?

A

Bind to regions between nucleosomes and recruit histone modification and chromatin remodeling complexes

198
Q

What is needed to create an active enhancer (from the nucleosome)?

A

Pioneer factors need to recruit histone modification and chromatin remodeling complexes

199
Q

How can NR without ligands lead to negative regulation?

A

They can act as repressors by methylating the DNA or by inhibiting other complexes

200
Q

What does ligand binding to an NR do to the complexes recruited?

A

It can change the complex recruited, changing it from repression to activation

201
Q

True or false: coactivators for histone modifications are specific to one particular pathway

A

False: they are common to multiple pathways

202
Q

What is an example of coactivators for histone modifications?

A

CBP and p300

203
Q

How can CBP and p300 act as integration points for signaling?

A

They can be recruited by a variety of transcription factors

204
Q

How can CBP activity be modulated?

A

By various kinds of inputs (crosstalk)

205
Q

What is meant by “modularity” for transcription factors?

A

They can have multiple partners and bind to multiple genes

206
Q

What does ChIP stand for?

A

Chromatin immuno precipitation

207
Q

What is the purpose of ChIP?

A

Method to identify gene targets of specific transcription factors

208
Q

What are the steps (4) of ChIP?

A
  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

BIO 317 (27 decks)

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