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BIO 317 > 22 - Signaling and Gene Regulation & Control of Gene Transcription > Flashcards

22 - Signaling and Gene Regulation & Control of Gene Transcription Flashcards

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1
Q

What is the major takeaway of cell signaling?

A

Signaling pathways lead to changes in gene expression

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2
Q

True or false: almost all cells in an organism are genetically identical

A

True: they all have the same DNA

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3
Q

What produces differences between cell types?

A

Differences in gene expression

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4
Q

What is differential gene expression?

A

The expression of different genes by cells within the same genome

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5
Q

True or false: gene expression only refers to translation

A

False: it includes everything from chromatin remodeling to protein degradation

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6
Q

Which steps (6) can gene expression be controlled?

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport and localization control
  4. Translation control
  5. mRNA degradation control
  6. Protein activity control
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7
Q

What characteristics describe signaling that alters protein function/activation state?

A

More rapid, less energy, more quickly reversible

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8
Q

What characteristics describe signaling that alters protein levels?

A

Less rapid, more energy, less quickly reversible

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9
Q

What is an example of translational control?

A

ERK signaling being compartmentalized within the cell

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10
Q

What scaffold localizes ERK at the golgi?

A

Sef

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11
Q

What is a polysome?

A

mRNA transcript with multiple ribosomes on it

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12
Q

What does MNK1 do?

A

It phosphorylates eIF-4E to initiate protein synthesis

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13
Q

How is MNK1 activated?

A

Through phosphorylation by ERK and p38

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14
Q

What happens when 4E-BP1 is phosphorylated?

A

It releases eIF4E, which can help form the initiation complex

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15
Q

What does MNK stand for?

A

MAP kinase interacting kinase

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16
Q

How is 4E activated?

A

Through phosphorylation by MNK

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17
Q

What is needed for 4E to initiate protein synthesis?

A
  1. It needs to be phosphorylated by MNK (through p38/ERK)

2. It needs to be localized by being released from p4E-BP1

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18
Q

What does 4E-BP1 stand for?

A

4E binding protein 1

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19
Q

What phosphorylates 4E-BP1?

A

the mTORC1

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20
Q

What does mTORC1 stand for?

A

mTOR complex 1

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21
Q

How is mTOR activated?

A

Through phosphorylation by Akt

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22
Q

What is cap-dependent mRNA translation?

A

A 5’ cap is needed on the mRNA to form the proper rings for translation

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23
Q

What does IRES stand for?

A

Internal ribosome entry site

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24
Q

What can inhibit TOR?

A

Cancer cells, viruses, and stress

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25
Q

What happens if mTOR is inhibited?

A

4E-BP1 cannot be phosphorylated, so it remains bound to 4E

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26
Q

What is another name for eIF-4E?

A

4E

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27
Q

What happens in cap-independent mRNA translation?

A

4E cannot bind to the IRES at the mRNA

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28
Q

How come 4E cannot bind to the IRES in cap-independent mRNA translation?

A

It is not released from 4E-BP1, since mTOR is inhibited

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29
Q

Which translation process uses IRESes?

A

Cap-independent mRNA translation

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30
Q

What type of translation do viruses typically use?

A

Cap-independent mRNA translation

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31
Q

How come viruses typically uses cap-independent mRNA translation?

A

They usually do not have the capping proteins to go through cap-dependent mRNA translation

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32
Q

What proteins are produced (in a healthy cell) from a cap-independent mRNA translation process?

A

Proteins that respond to stress (hypoxia, etc.)

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33
Q

What are TSC1 and TSC2?

A

Tumor suppressor genes

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34
Q

Where are TSC1 and TSC2 found?

A

Upstream of mTOR

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35
Q

What do TSC1 and TSC2 do?

A

Influence and slow down cell growth

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36
Q

How are TSC1 and TSC2 regulated?

A

By phosphorylation due to many different effectors

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37
Q

What is the significance of TSC1 and TSC2 having many phosphorylation sites?

A

It can be phosphorylated by a variety of effectors

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38
Q

How can mRNA be targeted to subcellular locations?

A

Through complexes bound to motor proteins

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39
Q

How is localized translation of mRNA achieved at mushroom bodies?

A

Through transport of mRNA to that specific location

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40
Q

How can localization and translation of mRNA lead to axon growth?

A

Different factors can stimulate mRNA translation to promote filopodial extension or withdrawal

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41
Q

How is axon turning mediated?

A

Through specific translation at the growth cone, leading to filopodial extension or withdrawal

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42
Q

How does local translation affect the post-synaptic density?

A

By altering the function and stabilization of the synapse

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43
Q

True or false: all proteins are made in the cell body

A

False: some mRNA can be transported to be locally translated elsewhere

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44
Q

How can signaling (4 ways) be controlled in the nucleus?

A
  1. Transcriptional (initiation, elongation, termination)
  2. RNA processing (capping, splicing, poly-A tail)
  3. mRNA export
  4. Surveillance (degradation)
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45
Q

What do gene regulatory proteins do?

A

Bind to regulatory sequences to influence transcription

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46
Q

What do general transcription factors do?

A

Bind close to the TATA box to promote RNA polymerase II binding

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47
Q

What is the shape of DNA?

A

3D (not linear)

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48
Q

Why is DNA having a 3D structure important?

A

It is important for the DNA to fold in order to transcribe gene properly

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49
Q

What is an enhancer?

A

A DNA region that activators can bind to to promote gene transcription

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50
Q

What is an activator?

A

A protein that binds to an enhancer region to promote gene transcription

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51
Q

What is a mediator?

A

A protein that brings together the general transcription factors and the activators to regulate gene expression

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52
Q

What are DNA-bending proteins?

A

Proteins that help DNA bend into 3D shapes to allow for gene transcription

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53
Q

Which parts of transcription are usually the downstream signaling target?

A

The enhancers (gene regulatory proteins)

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54
Q

What is the structure of cohesin?

A

A ring-type structure

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55
Q

What does cohesion do?

A

Keep the DNA looped together to mediate proper gene expression

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56
Q

What was the first discovered DNA binding factors for transcription?

A

CRE

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57
Q

What does CRE stand for?

A

cAMP response element

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58
Q

What question led to the discovery of CRE?

A

How does cAMP signaling regulate transcription of cAMP-responsive genes?

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59
Q

What are some common reporter assays used in molecular biology?

A

CAT reporters, and luciferase reporters

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60
Q

What does CAT reporter stand for?

A

Chloramphenicol acetyltransferase reporter

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61
Q

How does a CAT reporter work?

A

Higher amounts of CAT leads to higher amounts of acetylated products

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62
Q

How does a luciferase reporter work?

A

Higher amounts of luciferase lead to stronger glows when D-luciferin (substrate) is added

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63
Q

What is the importance of the SST gene?

A

It was known to be stimulated by cAMP

64
Q

What does SST stand for?

A

Somatostatin gene

65
Q

What was the experimental procedure using CAT and SST?

A

Parts of SST were cleaved, and the luminescence was recorded

66
Q

What was the result of the experiments using CAT and SST?

A

There was a significant increase up to a deletion of 48 bp

67
Q

What was the conclusion of the experiments using CAT and SST?

A

There was a DNA region somewhere in the identified 23 bp that was responsive to cAMP (CRE)

68
Q

What question was asked about the 23 bp found using the CAT reporter?

A

Are these 23 bp necessary and sufficient to activate a cAMP response?

69
Q

Are the 23 bp necessary and sufficient to activate a cAMP response (in the CRE experiments)?

A

Yes: it makes other genes cAMP responsive if added upstream

70
Q

What is CRE?

A

A DNA segment that is responsive to cAMP

71
Q

What is the structure of CRE?

A

An eight bp palindromic sequence (TGACGTCA)

72
Q

What do native genes that respond to cAMP have in common?

A

They all have the CRE sequence

73
Q

Where is the CRE usually found?

A

Within 100 bp of the TATA box

74
Q

What happens if the CRE is moved upstream (more than 100 bp)?

A

It becomes less active

75
Q

What question was asked after discovering CRE?

A

What binds to CRE?

76
Q

How was CREB discovered?

A

Through an affinity column with CRE

77
Q

What was the experimental procedure to discover CREB?

A
  1. Create an affinity column with CRE on beads
  2. Run cell extract over it
  3. Purify whatever binds
78
Q

What is CREB?

A

The binding protein that binds to CRE

79
Q

What does CREB stand for?

A

CRE binding protein

80
Q

What domains are found on CREB?

A

A DNA binding domain, and an activation domain

81
Q

What does the DNA binding domain on CREB do?

A

Form dimeric leucine zippers

82
Q

What is the importance of the palindromic CRE sequence?

A

Needs dimeric CREB to bind and recognize to each strand of the DNA through the leucine zipper

83
Q

What does the activation domain on CREB do?

A

Contains Ser133 that needs to be phosphorylated for CREB to function

84
Q

What phosphorylates Ser133 on CREB?

A

PKA

85
Q

How does CREB bind to CRE?

A

Through a leucine zipper motif

86
Q

What protein negatively regulated CREB?

A

PP-1

87
Q

What is PP-1?

A

A phosphatase that dephosphorylated CREB

88
Q

What is the rate limiting step of transcription due to cAMP?

A

PKA entering the nucleus

89
Q

How does attenuation of the CREB signal work?

A

Through dephosphorylation by PP-1

90
Q

True or false: CREB can only be activated by PKA

A

False: it can also be phosphorylated by CaM-KII and MAPK

91
Q

True or false: CREB activation occurs at a constant rate

A

False: it can happen slowly or quickly

92
Q

What pathway mediates fast activation of CREB?

A

The CaMKII pathway

93
Q

What pathway mediates slow activation of CREB?

A

The MAPK/rsk pathway

94
Q

What is the feedforward mechanism of CREB?

A

Calmodulin can activate both the CamKII and the MAPK/rsk pathway, leading to activation of CREB

95
Q

What is the significance of the feedforward mechanism of CREB?

A

This leads to branched timing of impact (quick and sustained gene changes)

96
Q

What is another name for MAPK?

A

ERK

97
Q

What is another name for ERK?

A

MAPK

98
Q

True or false: CRE is an enhancer

A

True: it is a segment of DNA where an activator can bind to stimulate gene expression

99
Q

True or false: CREB is a specific transcription factor

A

True: it is an activator that binds to CRE to stimulate gene expression

100
Q

What does CBP stand for?

A

CREB binding protein

101
Q

What does CBP do?

A

Binds CREB to the basal transcription complex

102
Q

What is the purpose of KID/KIX/Q2 domains?

A

Allow for transcription factors to bind to each other to allow for gene transcription

103
Q

What is the first level of transcriptional control in cAMP signaling?

A

PKA phosphorylates CREB

104
Q

What is the second level of transcriptional control in cAMP signaling?

A

CBP has histone acetylation activity to open up the chromatin

105
Q

True or false: transcription complexes only have binding functions

A

False: they can also have activation aspects as well as binding

106
Q

What are miRNAs?

A

Short RNA sequences derived from a primary transcript

107
Q

Where are miRNAs created?

A

From a specific gene in the genome

108
Q

What is the function of miRNAs?

A

Down-regulate cytoplasmic mRNAs through translational repression and mRNA decay (regulation)

109
Q

What are siRNAs?

A

Short RNA sequences derived from longer double stranded RNAs

110
Q

What does duplex mean?

A

Double stranded RNA

111
Q

Where are siRNAs created?

A

From viruses or other endogenous sources

112
Q

What is the function of siRNAs?

A

Target RNAs for cleavage in the cytoplasm (defense)

113
Q

What does rasiRNA stand for?

A

Repeat-associated small interfering RNAs

114
Q

What are rasiRNAs?

A

Short sequences derived from repetitive regions (centromeres and transposon regions)

115
Q

What are the different types of rasiRNAs?

A

hcRNAs (yeast) and piRNAs (mammals)

116
Q

What base pairing does miRNA have?

A

Incomplete base pairing

117
Q

What base pairing does siRNA have?

A

Perfect matching

118
Q

What process does miRNA mediate?

A

Inhibition of translation

119
Q

What process does siRNA mediate?

A

Cleavage

120
Q

What are argonautes?

A

Proteins that make up the RISC complex

121
Q

What is the RISC complex?

A

The complex of protein and RNA responsible for RNAi

122
Q

What is the structure of the RISC complex?

A

Argonaute proteins and miRNA or siRNA

123
Q

What does RISC stand for?

A

RNA induced silencing complex

124
Q

How are RISCs loaded with miRNA created?

A

By processing of the pre-miRNA in the nucleus, and loading it onto the argonaute protein

125
Q

How are RISCs loaded with siRNA created?

A

By cutting dsRNA with dicer proteins, and loading it onto the argonaute protein

126
Q

What do dicers do?

A

Cut foreign dsRNA to create siRNA

127
Q

What does dsRNA stand for?

A

Double stranded RNA

128
Q

What is thought to be the origin of siRNA?

A

Defense against dsRNA viruses

129
Q

What is RNA silencing?

A

The process of small RNAs inhibiting gene expression in a variety of ways

130
Q

What does RNAi stand for?

A

RNA interference

131
Q

What is the relationship between RNAi and RNA silencing?

A

RNAi is a branch of RNA silencing

132
Q

What parts of RNA silencing are not part of RNAi?

A

RNA silencing at the DNA and chromatin level

133
Q

How does the RISC complex work?

A

It scans mRNA with the miRNA or siRNA to find and interfere with that particular mRNA

134
Q

How are miRNAs created?

A

From single stranded precursor RNAs that fold back on themselves (with complementary sequences)

135
Q

What roles (6) do miRNAs play?

A
  1. Regulatory role in development
  2. Patterning of the nervous system
  3. Control of cell proliferation and cell death
  4. Leaf and flower development in plants
  5. Differentiation of various cell types
  6. Development of cancer
136
Q

True or false: miRNAs are general throughout the body

A

False: there are specific to different tissues in the body

137
Q

In what part of the genome are miRNAs coded for?

A

In both introns and exons

138
Q

True or false: miRNAs are only found in coding RNAs

A

False: they can also be found in noncoding RNAs

139
Q

What is non-extensive base pairing?

A

Only a few of the base pairs match in the RISC and the target mRNA

140
Q

Which small RNA uses non-extensive base pairing?

A

miRNA

141
Q

What is the outcome of non-extensive base pairing?

A

Repression

142
Q

What is extensive base pairing?

A

All of the base pairs match in the RISC and the target mRNA

143
Q

Which small RNA uses extensive base pairing?

A

siRNA

144
Q

What is the outcome of extensive base pairing?

A

Degradation

145
Q

Which type of base pairing leads to a change in the argonaute conformation?

A

Extensive base pairing

146
Q

Which type of base pairing does not lead to a change in the argonaute conformation?

A

Non-extensive base pairing

147
Q

How can RNAi be used to study gene function?

A

It can be used to knockout the gene, and see the effect of removing this gene

148
Q

True or false: RNAi received a Nobel Prize

A

True: it received the Nobel Prize in 2006 in Physiology/Medicine

149
Q

How can researchers use siRNA to their advantage?

A

They can introduce siRNA to allow for degradation of a specific mRNA, thus knocking out the gene that mRNA translates for

150
Q

How does miRNA relate to cell signaling?

A

Cell signaling can lead to regulation of miRNAs

151
Q

What is an example of a cell signaling pathway regulating miRNA?

A

The MAPK pathway can turn on or turn off specific miRNAs, thus impacting protein levels

152
Q

How are miRNAs and Ras signaling connected?

A

Through multiple feedback and feedforward loops

153
Q

How can miRNAs be used in a feedback loop?

A

They can inhibit proteins that inhibit effectors of the pathway that leads to expression of the miRNA

154
Q

How are miRNAs and the ECM connected?

A

Signaling through the ECM can lead to miRNAs that lead to changing and readjusting the ECM

155
Q

How are miRNAs and the glucose pathway connected?

A

miRNAs can target insulin mediators (both kinases and phosphatases) to influence glucose levels

156
Q

What effectors can miRNAs target in the glucose pathway?

A

Both kinases and phosphatases

157
Q

How come miRNAs can be described as dial systems?

A

They can tune gene regulation up or down, depending on the signaling pathways

BIO 317 (27 decks)

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