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Biology Unit 3 > Lecture Notes Regulating Gene Expression > Flashcards

Lecture Notes Regulating Gene Expression Flashcards

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1
Q

How is gene expression regulated in prokaryotes?

A

Prokaryotes make certain proteins only when they are needed

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2
Q

To shut off the supply of a protein, the cell can

A

1) downregulate mRNA transcription (most effective)
2) hydrolyze mRNA, preventing translation
3) prevent mRNA translation at the ribosome
4) hydrolyze the protein after it is made
5) inhibit the proteins function

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3
Q

Repressor protein bound at site where RNA wants to bind and prevents initiation of transcription

A

Negative regulation

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4
Q

Activator protein enhances transcription

A

Positive regulation

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5
Q

Regulating gene transcription allows E. coli to (blank) in an ever changing environment

A

Conserve energy

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6
Q

(Blank) is the easiest sugar to metabolize

A

Glucose

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7
Q

Lactose is (blank)

A

B-galactoside

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8
Q

3 proteins needed for the uptake and metabolism of lactose

A

B-galactoside permease
B-galactosidase
B-galactoside transacetylase

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9
Q

Carrier protein that moves lactose into the cell

A

B-Galactoside permease

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10
Q

Hydrolyses lactose

A

B-galactosidase

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11
Q

Transfers acetyl groups from acetyl coA to certain b galac

A

B-galactoside transacetylase

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12
Q

(Blank) stimulates expression of B-Galactosidase

A

Lactose

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13
Q

Lactose is a (blank)

A

Inducer

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14
Q

Lactose increases or decreases mRNA

A

Increases

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15
Q

E. coli makes (blank) first before proteins

A

MRNA

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16
Q

Compounds that stimulate protein synthesis are called

A

Inducers

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17
Q

(Blank) are made at a constant rate

A

Constitutive proteins

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18
Q

2 ways to regulate metabolic pathways

A
  • Regulation of enzyme activity

- regulation of enzyme concentration

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19
Q

End product feeds back, inhibiting the activity of enzyme 1 only, quickly blocking pathway

A

Regulation of enzyme activity

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20
Q

End product blocks the transcription of all 5 genes- no enzymes produced

A

Regulation of enzyme concentration

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21
Q

Gene cluster with a single promoter

A

Operon

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22
Q

A typical operon consists of:

A

A promoter
Two or more structural genes (z, y, and a)
An operator

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23
Q

A short sequence between the promoter and the structural genes that binds regulatory proteins

A

Operator

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24
Q

Three ways to control operon transcription

A

1) an inducible operon regulated by a repressor protein
2) a repressible operon regulated by an activator protein
3) an operon regulated by an activator protein

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25
Q

Repressor binds operator sequence and blocks RNA poly from binding- no requirement and genes transcribe

A

Inducible system- lactose absent

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26
Q

Repressor protein has binding sequence for lactose - RNA polymerase binds to breakdown and metabolize lactose

A

Inducible system: lactose present

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27
Q

Trp operon is a (blank) system

A

Repressible

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28
Q

Trp operon- amino acid

A

Incorporated into proteins

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29
Q

The trp repressor binds the operator, and RNA synthesis is blocked

A

Tryptophan present

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30
Q

Repressor dissociates from the operator, and RNA synthesis proceeds

A

Absence of tryptophan

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31
Q

Metabolic substrate is a

A

Inducer

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32
Q

Regulatory protein is a

A

Repressor

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33
Q

Metabolic substrate interacts with a regulatory protein- repressor can’t bind to operator and transcription proceeds

A

Inducible system

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34
Q

Control catabolic breakdown pathways

A

Inducible systems

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35
Q

Turned on when substrate is available

A

Catabolic pathways

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36
Q

Metabolic product is a

A

Co-repressor

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37
Q

A metabolic product binds to a regulatory protein, which then binds to the operator and blocks transcription

A

Repressible systems

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38
Q

Control anabolic (build) pathways

A

Repressible systems

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39
Q

Turned on until product concentration becomes excessive

A

Repressible systems

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40
Q

E. coli can use (blank) to increase transcription

A

Positive control

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41
Q

If glucose and lactose levels are both high, the (blank) is not transcribed efficiently

A

Lac operon

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42
Q

Efficient transcription requires (blank) to increase transcription

A

Binding of an activator protein to lac operon promoter

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43
Q

Example of activator protein

A

CAMP bund to CRP

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44
Q

Low glucose means CRP

A

Bound to promoter

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45
Q

High glucose means CRP

A

Not bound

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46
Q

A system or gene regulation in which presence of a preferred energy source represses other catabolic (break-down) pathways

A

Catabolite repression

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47
Q

RNA polymerases bind and are orientated at promoters so that (blank)

A

The correct DNA strand is transcribed

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48
Q

All promoters have (blank) that allow them to be recognized by RNA polymerase

A

Consensus sequences

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49
Q

Different classes of consensus sequences are recognized by regulatory proteins called

A

Sigma factors

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50
Q

Bind to RNA polymerase and direct it to certain promoters

A

Sigma factors

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51
Q

Genes for proteins with related functions may be at different locations in the genome, but share consensus sequences and can be recognized by

A

Sigma factors

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52
Q

Is active most of the time and binds to consensus sequences of housekeeping genes

A

Sigma factor 70

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53
Q

Genes normally expressed in actively growing cells

A

Housekeeping genes

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54
Q

How is gene expression regulated in eukaryotes?

A

1) remodeling chromatin- epigenetics
2) transcriptional control
3) processing control
4) transport control
5) mRNA stability control
6) translational control of protein synthesis
7) posttranslational control of protein activity
8) protein degradation

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55
Q

Regulation- prokaryotic vs eukaryotic - BOTH

A

Use DNA protein interactions and negative/positive control to regulate gene expression

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56
Q

Beginning steps in initiation of eukaryotic transcription

A

TATA box in promoter bound by TFIID

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57
Q

Transcription initiation complex includes

A

TFIID- TFIIB- TFIIF- TFIIE- TFIIH

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58
Q

Binds to TATA box

A

TFIID

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59
Q

Binds both RNA polymerase and TFIID, and helps identify the transcription initiation site

A

TFIIB

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60
Q

Prevents nonspecific binding of the complex to DNA and helps recruit RNA polymerase to the complex

A

TFIIF

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61
Q

Similar to function of bacterial sigma factor

A

TFIIF

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62
Q

Binds to the promoter and stabilizes the denaturation of the DNA

A

TFIIE

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63
Q

Opens up the DNA for transcription

A

TFIIH

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64
Q

Transcription factor specificity does what

A

Plays an important role in cell differentiation

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65
Q

Regulatory sequences that bind transcription factors that activate transcription or increase rate of transcription

A

Enhancers

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66
Q

Bind transcription factors that repress transcription

A

Silencers

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67
Q

Structural motifs mediate (blank) which means what

A

DNA binding

Fundamental to differentiation

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68
Q

What is a common structural motif?

A

Helix-turn-helix

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69
Q

For DNA recognition the structural motif must:

A
  • fit into a major or minor groove
  • have amino acids that can project with interior of double helix
  • have amino acids that can bond with interior bases
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70
Q

What does the lac repressor do and what is it often called?

A

Bonds DNA and inhibits ability of TF binding

Dimer

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71
Q

Expression of transcription factors underlies (blank)

A

Cell differentiation

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72
Q

During development, cell differentiation is often mediated by

A

Changes in gene expression

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73
Q

All differentiated cells contain (blank)

A

Entire genome

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74
Q

The expression of just 3 TF is sufficient to transform (blank)

A

Fibroblast into a neuron

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75
Q

Coordinating gene expression

A
  • separate genes unlike prokaryotes

- same sequence of DNA in front of multiple genes

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76
Q

Process in which a multicellular organism undergoes a series of progressive changes that characterizes its life cycle

A

Development

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77
Q

Sets the fate of the cell

A

Determinaron

78
Q

Determination

A

Sets the fate of the cell

79
Q

The process by which different types of cells arise

A

Differentiation

80
Q

Differentiation

A

The process by which different types of cells arise

81
Q

Morphogenesis

A

Organization and spatial distribution of differentiated cells

82
Q

Organization and spatial distribution of differentiated cells

A

Morphogenesis

83
Q

Increase in body size by cell division and cell expansion

A

Growth

84
Q

Growth

A

Increase in body size by cell division and cell expansion

85
Q

Why do determination and differentiation occur?

A

Differential gene expression

86
Q

Morphogenesis involves differential gene expression and the interplay of signals between cells:

A
  • cell division
  • cell expansion in plants
  • cell movements are important in animals
87
Q

Apoptosis is essential in

A

Organ development

88
Q

Growth occurs by

A

Increasing the # of cells or enlargement of existing cells

89
Q

Cell fates become progressively (blank) during development

A

More restricted

90
Q

Cell fate determination is influenced by

A

Gene expression and the extracellular environment

91
Q

Is determination before or after differentiation?

A

Determination

92
Q

Changes in biochemistry, structure, and function that result in (blank)

A

Different cell types

93
Q

Potential to differentiate into other cell types

A

Cell potency

94
Q

Can differentiate to any cell type

A

Totipotent

95
Q

Can develop into most cell types, but cannot form new embryos

A

Pluripotent

96
Q

Can differentiate into several related cell types

A

Multipotent

97
Q

Can produce only one cell type- their own

A

Unipotent

98
Q

How does one egg cell produce so many different cell types?

A

2 processes for cell determination

  • cytoplasmic segregation
  • induction
99
Q

Cytoplasmic segregation

A

Unequal cytokinesis

100
Q

Induction

A

Cell to cell communication

101
Q

Cytoplasmic segregation can determinate (blank)

A

Polarity and cell fate

102
Q

Factors within a zygote or egg are not distributed evenly and end up in different daughter cells after division

A

Cytoplasmic segregation

103
Q

Developing a “top” and “bottom”- can develop very early; yolk and other factors are distributed asymmetrically

A

Polarity

104
Q

Top-nothing and bottom-small sea urchin = (blank) cut

A

Horizontal

105
Q

Top and bottom- small sea urchins = (blank) cut

A

Vertical

106
Q

The cytoskeleton contributes to

A

Asymmetric distribution of cytoplasmic determinants

107
Q

Microtubules and microfilaments have (blank)

A

Polarity

108
Q

Cytoskeletal elements can bind motor proteins that (blank)

A

Transport the cytoplasmic determinants

109
Q

Communication from one cell to another can (blank)

A

Determine cell fates

110
Q

Cells in a developing embryo influence one another’s developmental fate via chemical signals and signal transduction mechanisms

A

Induction

111
Q

What is the role of gene expression in development?

A
  • all cells in an organism have the same genes, but each cell expresses only certain ones
  • the mechanisms that control gene expression during cell fate determination and differentiation
112
Q

Inducers mediate signal transduction to (blank)

A

Dictate differential gene expression

113
Q

Explain how inducers mediate signal transduction to dictate differential gene expression

A
  • inducer molecules bound by receptors on surface of cell
  • bound receptor creates a signaling cascade internally that sends TFs into nucleus to cause gene expression and bind DNA
114
Q

B cell development is directed by

A

Signaling that causes differential gene expression

115
Q

Inducer molecule signal mediates the expression of different genes which causes the cell to (blank)

A

Survive, perliforate, and proceed in development

116
Q

2 things that happen after the receptor is bound

A

1) conformational change = receptor shape inside cell which changes to signal and is bound to Fit3 (chemical inducer)
2) phosphorylation

117
Q

Differential gene transcription is a (blank)

A

Hallmark of cell differentiation

118
Q

Process of transcription and differentiation in the formation of muscle cells

A

Mesoderm cells- myoblasts- muscle cell

-event blocks behavior of cell when dividing in order to push differentiation forward

119
Q

Differential gene expression drives (blank)

A

Development

120
Q

How is gene expression linked to the way we look?

A

Pattern formation and morphogenesis

121
Q

Creation of body form

A

Morphogenesis

122
Q

The process that results in the spatial organization of tissues and organisms

A

Pattern formation

123
Q

Morphogenesis involves

A

Cell division and differentiation, apoptosis

124
Q

Pathways for apoptosis in C elegans

A

CED-9 to CED4 to CED-3 to apoptosis

125
Q

Pathways for apoptosis in human neuron

A

BcL-2 to Apaf-1 to caspase-9 to caspase-3 to apoptosis

126
Q

Dictate what differentiated cells become

A

Organ identity genes

127
Q

The four organs in a flower are determined by the four groups of cells in the (blank)

A

Meristem

128
Q

A protein called LEAFY controls (blank)

A

Transcription of organ identity genes

129
Q

Plants with loss of function mutations of LEAFY (blank)

A

Do not produce flowers

130
Q

Transgenic orange trees, expressing the LEAFY gene coupled to a strongly expressed promoter, (blank)

A

Flower and fruit years earlier than normal trees

131
Q

Morphogen gradients provide (blank)

A

Positional information

132
Q

The position of each cell is defined by (blank)

A

Concentration of morphogen

133
Q

Describe example of specification of the vertebrate limb

A

Higher shh signaling drives differentiation of little finger vs thumb

134
Q

What was discovered when scientists studied morphogens in fruit flies?

A

The head, thorax, and abdomen are each made of several fused segments and different body parts arise from these different segments

135
Q

In fruit flies, when do segments appear?

A

early in development

136
Q

In fruit flies, by the early larval stage what has already occurred?

A

cell fates already determined

137
Q

When the embryo of fruit flies is first formed, what happens?

A

In the 1st 12 mitotic divisions, there is no cytokinesis, forming a multinucleate embyro and morphogens can diffuse easily in the embryo.

138
Q

Steps of cell determination were studied using experimental genetics

A
  • developmental mutations were identified
  • mutants were compared with wild types to identify genes and proteins
  • experiments confirmed gene and protein functions
139
Q

Three gene classes of determination:

A
  • Maternal effect genes
  • Segmentation
  • Hox
140
Q

Set up the major axes of the egg

A

Maternal effect genes

141
Q

Maternal effect genes

A

set up the major axes of the egg

142
Q

Segmentation genes

A

determine boundaries and polarity of each segment

143
Q

Determine boundaries and polarity of each segment

A

Segmentation genes

144
Q

Determine which organ will be made at a given location

A

Hox genes

145
Q

Hox genes

A

determine which organ will be made at a given location

146
Q

transcribed in cells of the mother’s ovary; the mRNAs are passed to the egg

A

maternal effect genes

147
Q

(blank) and (blank) are genes that help determine the anterior-posterior axis of the embryo

A

Bicoid and nanos

148
Q

subject to unequal distribution

A

maternal effect genes

149
Q

What establishes the hunchback gradient?

A

Bicoid and nanos genes

150
Q

Nanos (blank)

A

inhibits

151
Q

Bicoid (blank)

A

stimulates

152
Q

Mutations result in posterior structures being replaced by reversed anterior structures

A

Segmentation genes

153
Q

3 classes of segmentation genes

A

gap, pair rule, segment polarity

154
Q

organize broad areas; mutations result in omission of several body segments

A

Gap genes

155
Q

divide embryo into units of two segments each; mutations result in every other segment missing

A

Pair rule genes

156
Q

determine boundaries and anterior-posterior organization in individual segments

A

Segment polarity genes

157
Q

Particular Hox gene encodes for

A

particular organ/body part

158
Q

encode transcription factors that are expressed in different combinations along the length of the embryo

A

Hox genes

159
Q

What determines cell fate in each segment of organism?

A

Hox genes

160
Q

In Drosophilia, Hox genes determine (blank)

A

Segment identity

161
Q

Hox genes have a 180 base pair sequence called the (blank)

A

Homeobox

162
Q

The homebox encodes a 60 amino acid sequence called the (blank)

A

Homeodomain

163
Q

The homeodomain binds to

A

specific DNA sequences in the promoters of target genes

164
Q

Is differentiation reversible?

A

yes

165
Q

A zygote is totipotent meaning it can

A

give rise to every cell type in organism

166
Q

As development proceeds, cells become determined and lose their (blank)

A

totipotency

167
Q

What is an example in which differentiated plant cells can be turned totipotent?

A

Carrot cloning

168
Q

Nuclear transfer experiments show that genetic material from a single cell can be used to (blank) animals

A

clone

169
Q

Initial cloning experiments show reversible nature of (blank)

A

differentiation

170
Q

Cloning experiments indicated that

A

-no genetic info is lost as cell passes through developmental stages

171
Q

Step 1 to cloning a mammal (Dolly)

A

took mammary epithelial cells and cultured them (#1 sheep)

172
Q

Step 2 to cloning a mammal (Dolly)

A

harvested eggs from #2 sheet and eneucleated them

173
Q

Step 3 to cloning a mammal (Dolly)

A

fused 1 mammary epithelial cell with 1 eneucleated egg

174
Q

Step 4 to cloning a mammal (Dolly)

A

induced cells to divide- embryos

175
Q

Step 5 to cloning a mammal (Dolly)

A

embryos implanted into 3rd sheep

176
Q

What did the cloning of Dolly the sheep show?

A

fully differentiated cell from a mature animal can revert to totipotent

177
Q

What are the benefits of cloning animals?

A
  • increase # of valuable animals (ex- trangenic animals with genes with therapeutic properties)
  • preservation of endangered species
  • preservation of pets
178
Q

What is one specific example involving a positive benefit from cloning an animal?

A

cow genetically engineered to make HGH in milk cloned to produce hormone for children with growth hormone deficiency

179
Q

Rapidly dividing, undifferentiated cells that can differentiate into several cell types

A

Stem cells

180
Q

Stem cells

A

rapidly dividing, undifferentiated cells that can differentiate into several cell types

181
Q

In plants, stem cells are in the (blank)

A

meristems

182
Q

In mammals, stem cells occur in tissues that require frequent (blank)

A

replacement (skin, blood, intestinal lining)

183
Q

Two types of adult stem cells

A

Hematapoetic and mesencymal stem cells

184
Q

Stem cell transplantation often occurs

A

after cancer

185
Q

stem cell “healing” therapy

A

stem cells may be able to insert into the tissue and differentiate or induce tissue regeneration

186
Q

Experiments show that damaged tissues can heal more effectively if (blank)

A

stem cells are injected into tissue

187
Q

Using ESCs to obtain (blank)

A

pluripotent stem cells

188
Q

ESCs (blank)

A

repair tissue, recover from disease, heart attack

189
Q

ESCs can be (blank)

A

harvested from human embryos conceivied by in-vitro

190
Q

2 problems with harvesting ESCs from embyros

A
  • some people object to destruction of human embryos

- stem cells could provoke an immune response in a recipient

Biology Unit 3 (5 decks)

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