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Biology Unit 3 > Book Notes Regulating Gene Expression > Flashcards

Book Notes Regulating Gene Expression Flashcards

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1
Q

What is the major control point for gene expression?

A

Promoter

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2
Q

Sequence of DNA adjacent to the coding region of a gene where proteins bind and control the rate of transcription

A

Promoter

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3
Q

Study of heritable changes in gene expression that do not involve changes in DNA sequence

A

Epigenetics

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4
Q

Prokaryotic cell can (blank) supply of unneeded protein

A

Shut off

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5
Q

5 steps for gene expression regulation in prokaryotes in relation to shutting off the supply of an unneeded protein

A

1) downregulate the transcription of mRNA doe that protein
2) hydrolyze the mRNA after it is made, thereby preventing translation
3) prevent translation of mRNA at ribosome
4) hydrolyze protein after it is made
5) inhibit function of protein

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6
Q

What is the most important step in the process of regulation of gene expression in prokaryotes?

A

Downregulate the transcription of mRNA for the unneeded protein

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7
Q

Bind to promoter region and determine which genes are activated

A

Repressor proteins and activator proteins

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8
Q

Binding of a repressor protein prevents transcription

A

Negative regulation

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9
Q

Activator protein binds DNA to stimulate transcription

A

Positive regulation

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10
Q

Regulating gene transcription (blank)

A

Conserves energy

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11
Q

What are the 3 proteins that are involved in the initial uptake and metabolism of lactose by E. coli?

A
  • B-Galactoside permease
  • B-Galactosidase
  • B-Galactoside-transacetylase
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12
Q

Carrier protein in the bacterial plasma membrane that moves sugar into cell

A

B-Galactoside permease

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13
Q

Enzyme that hydrolyses lactose to glucose and galactose

A

B-Galactosidase

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14
Q

Transfers acetyl groups from acetyl CoA to certain B-galactosides

A

B-galactoside transacetylase

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15
Q

Addition of lactose increase or decreases?

A

Increase

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16
Q

MRNA levels dramatically (blank) during lag period after lactose added to medium

A

Increase

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17
Q

Stimulate synthesis of a protein

A

Inducers

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18
Q

Proteins produced

A

Inducible proteins

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19
Q

Proteins made all the time at constant rate

A

Constitutive proteins

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20
Q

Encode 3 enzymes for processing lactose in E. coli and specify the amino acid sequences of protein molecules

A

Structural genes

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21
Q

Cluster of genes with single promoter

A

Operan

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22
Q

Encodes 3 lactose- metabolizing enzymes in E. coli

A

Lac operon

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23
Q

Short stretch of DNA that lies between promoter and structural genes

A

Operator

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24
Q

What binds with regulatory proteins?

A

Operator

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25
Q

Operator-repressor interactions control transcription in the (blank)

A

Lac and trp operons

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26
Q

When repressor is bound, transcription of (blank) blocked

A

Operon

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27
Q

Repressor protein has 2 binding sites -

A

operator/inducer

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28
Q

Prevents binding of RNA poly to promoter and operon not transcribed

A

Absense of inducer

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29
Q

Change in 3D structure prevents repressor from binding to operator and RNA polymerase binds

A

Presence of inducer

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30
Q

Binds to the repressor, the repressor changes shape and binds to the operator, inhibiting transcription

A

Co-repressor

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31
Q

Inducible systems control (blank)

A

Catabolic pathways

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32
Q

Repressible systems control (blank)

A

Anabolic pathways

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33
Q

Catabolic pathways

A

Turned on only when substrate available

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34
Q

Anabolic pathways

A

Turned on until excessive

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35
Q

Protein synthesis can be controlled by (blank)

A

Increasing promoter efficiency

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36
Q

Positive control to increase transcription through presence of (blank)

A

Activator protein

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37
Q

Efficient transcription of the lac operon requires (blank)

A

Binding of an activator protein to its promoter

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38
Q

Cyclic cAMP binds to activator protein called cAMP receptor protein producing what

A

A conformational change in CRP that allows it to bind to lac promoter

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39
Q

Efficiency reduced with abundant glucose because cAMP levels (blank) and (blank occurs)

A

Decrease

CRP does not bind

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40
Q

System of gene regulation in which the presence of the preferred energy source represses other catabolic pathways

A

Catabolite repression

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41
Q

Promoters share blank that allow them to be recognized by the RNA polymerase and other proteins

A

Consensus sequences

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42
Q

Short stretch of DNA that appears, with little variation, in many different genes

A

Consensus sequences

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43
Q

All the genes that are normally expressed in actively growing cells

A

Housekeeping genes

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44
Q

Proteins in prokaryotic cells that bind to RNA poly and direct it to specific classes of promoters

A

Sigma factors

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45
Q

(Blank) is active most of the time and binds to consensus sequences of housekeeping genes

A

Sigma-70 factor

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46
Q

Both prokaryotes and eukaryotes are similar in regulation of gene transcription in that:

A

Both use DNA protein interactions and negative/positive control

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47
Q

Promoter contains

A

TATA box and regulatory sequences

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48
Q

Regulatory proteins that help control transcription

A

Transcription factors

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49
Q

Help with initiating transcription by assembling on chromosome

A

General transcription factors

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50
Q

What are the general transcription factors?

A

TFIID- TFIIB- TFIIF- TFIIE- TFIIH

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51
Q

Specific transcription factors play and important role in (blank)

A

Cell differentiation

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52
Q

Binds to TATA box and changes both its own shape and DNA creating a new surface that attracts the binding of other GtF to form an initiation complex

A

TFIID

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53
Q

Binds both DNA polymerase and TFIID and helps identify the transcription initiation site

A

TFIIB

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54
Q

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

A

TFIIF

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55
Q

Similar to sigma factor

A

TFIIF

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56
Q

Binds to the promoter and stabilizes the denaturation of DNA

A

TFIIE

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57
Q

Opens up DNA for transcription

A

TFIIH

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58
Q

Steps of initiation of transcription in eukaryotes

A

1) TFIID binds to promoter at TATA
2) another transcription factor joins
3) RNA polymerase II binds after several tfs
4) more tfs
5) RNA polymerase ready to transcribe

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59
Q

Bind transcription factors that either activate transcription or increase the rate

A

Enhancers

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60
Q

Bind factors that repress transcription

A

Silencers

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61
Q

When transcription factors bind to enhancers or silencers, they interact with RNA polymerase complex, causing the DNA to

A

Bend

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62
Q

Consist of different combinations of structural elements (protein conformations)

A

Structural motifs

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63
Q

An intact DNA double helix can be recognized by a protein motif whose structure:

A
  • fits into major/minor groove
  • has amino acid that can project into the interior of double helix
  • has amino acids that can form hydrogen bonds with the interior bases
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64
Q

Repressors can inhibit transcription by

A
  • prevention of binding of transcriptional activators to DNA
  • interaction with other DNA-binding proteins to decrease rate of transcription
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65
Q

The expression of transcription factors underlies (blank)

A

Cell differentiation

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66
Q

All differentiation cells contain (blank) and their specific characteristics arise from (blank)

A

Entire genome

Differential gene expression

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67
Q

Providing new, functional cells to patients who have disease that involve the degeneration of certain cell types

A

Cellular therapy

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68
Q

Manipulated expression of transcription factors in cells to change them into neurons

A

Fibroblasts

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69
Q

Expressin of genes can be coordinated if they share (blank) that bind the same (blank)

A

Regulatory sequences

Transcription factors

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70
Q

To coordinate expression, each gene has a specific regulatory sequence near its promoter called the (blank)

A

Stress response element

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71
Q

Transcription factor binds to stress response element and stimulates

A

MRNA synthesis

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72
Q

Actively dividing, unspecialized cells that have the potential to produce different cell types depending on the signals they receive from the body

A

Stem cells

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73
Q

Inject stem cells into damaged tissues, where they will (blank)

A

differentiate and form new, healthy tissues

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74
Q

process by which a multicellular organism, beginning with a single cell, goes through a series of changes, taking on the successive forms that characterize its life cycle

A

Development

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75
Q

development involves distinct but (blank) processes

A

overlapping

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76
Q

sets the developmental fate of the cell

A

determination

77
Q

different types of cells arise, leading to cells with specific structures and functions

A

differentiation

78
Q

organization and spatial distribution of differentiated cells into the multicellular body and its organs

A

morphogenesis

79
Q

increase in size of the body and its organs by cell division and cell enlargement

A

growth

80
Q

involves differential gene expression and the interplay of signals between cells

A

morphogenesis

81
Q

4 things involved in morphogenesis

A
  • cell division
  • cell expansion
  • cell movements
  • apoptosis
82
Q

growth

A

cell enlargement

83
Q

cell fates become progressively more (blank) during development

A

restricted

84
Q

each undifferentiated cell will become part of a particular type of tissue

A

cell fate

85
Q

amphibians- donor tissue = early embryo

A

adopts fate from surroundings/extracellular environ

86
Q

amphibians- donor tissue = older embryo

A

continues on original path

87
Q

determination is a (blank), the final realization of that is (blank)

A

commitment/ differentiation

88
Q

cell’s potential to differentiate into other cell types

A

potency

89
Q

any cell type including embryonic

A

totipotent

90
Q

most cell types not embryonic

A

pluripotent

91
Q

several different, related cell types

A

multipotent

92
Q

produce only own cell type

A

unipotent

93
Q

What 2 things determine cell fate?

A
  • cytoplasmic segregation

- induction

94
Q

cytoplasmic segregation

A

unequal cytokinesis

95
Q

induction

A

cell to cell communication

96
Q

a factor within an egg, zygote, or precurser cell may be unequally distributed in the cytoplasm. After cell division, the factor ends up in some daughter cells or regions of cells, but not others

A

cytoplasmic segregation

97
Q

a factor is actively produced and secreted by certain cells to induce other cells to become determined

A

induction

98
Q

Cytoplasmic segregation can determine (blank) and (blank)

A

polarity and cell fate

99
Q

distinct “top” and “bottom” ends of an organism/structure

A

polarity

100
Q

sea urchin polarity example- horizontal cut

A

bottom small sea urchin and top none

101
Q

sea urchin polarity example- vertical cut

A

2 small sea urchins from both halves

102
Q

Distributed unequally in the egg cytoplasm and include specific proteins, small regulatory RNAs, and mRNAs, and they play roles in directing the embryonic development of many organisms

A

cytoplasmic determinants

103
Q

microtubules and microfilaments have (blank) and cytoskeleton can bind (blank)

A

polarity/ motor proteins

104
Q

inducers passing from one cell to another can determine (blank)

A

cell fates

105
Q

signaling events by which cells in a developing organism communicate and influence one another’s developmental fate

A

inducers

106
Q

example of inducer

A

development of lens in the vertebrate eye

107
Q

How does an inducer work in the vertebrate eye?

A

surface tissue begins to develop into a lens when it receives a signal from the optic vesicle

108
Q

inducers trigger sequences of (blank) in the responding cells

A

gene expression

109
Q

induction leads to

A

the activation or inactivation of specific sets of genes through signal transduction cascades

110
Q

simplify- differential gene expression

A

induction leads to the activation or inactivation of specific sets of genes through signal transduction cascades

111
Q

What is the role of gene expression in development?

A

each cell expresses only selected genes

112
Q

Cell fate determination involves signal transduction pathways that lead to (blank)

A

differentiatial gene expression

113
Q

How do signal transduction pathways lead to differential gene expression?

A

inducer molecule binds to its specific receptor on the surface of a cell, stp leads to activation

114
Q

lower concentraton of inducer =

A

no gene expression activated

115
Q

Differential gene transcription is a (blank) of cell differentiation

A

hallmark

116
Q

Example of differential gene transcription involving blood cells

A

B-globin expressed in red blood cells and present, not expressed in neurons shown through nucleic acid hybridization- probe for B-globin gene can be applied to DNA from brain cells and immature red blood cells, mRNA only finds in red blood cells

117
Q

Example of differential gene transcription involving muscle precursor cells

A
  • cells stop dividing and cell signaling activates the gene for a transcription factor called MyoD
  • gene for p21 activated (inhibits CDKs) and cell cycle stops
118
Q

MyoD role as transcription factor in relation to muscle tissue

A

MyoD activated in stem cells that repair muscle tissue as it gets damaged

119
Q

MyoD stands for

A

myoblast determining gene

120
Q

the process that results in the spatial organization of a tissue or organism

A

pattern formation

121
Q

What is pattern formation linked to?

A

morphogenesis

-creation of body form involving apoptosis

122
Q

Multiple proteins interact to determine (blank)

A

developmental programmed cell death

123
Q

Example of apoptosis used for development

A

human hands and feet

124
Q

Namatode worm programmed cell death example

A
  • sequential activation of 2 proteins called CED-4 and CED-3 appear to control programmed cell death
  • CED-9 binds CED-4 and prevents II from activating CED-3; if cell receives signal for apoptosis, CED-9 releases CED-4 which activates CED-3 protease
125
Q

Human development example of proteins interacting to determine developmental programmed cell death

A

proteaseases called caspases and Bcl2 and Apafl binding

126
Q

undifferentiated, rapidly dividing cells in plants

A

meristems

127
Q

Encode proteins that act in combination to produce specific whorl features

A

organ identity genes

128
Q

encode transcription factors that are active as dimers

A

organ identity genes

129
Q

proteins with 2 polypeptide subunits

A

dimers

130
Q

replacement of one organ for another

A

homeotic mutation

131
Q

transcription of the floral organ identity genes controlled by (blank)

A

LEAFY protein

132
Q

Morphogen gradients provide (blank)

A

positional information

133
Q

diffuses from one cell or group of cells to surrounding cells, setting up a concentration gradient

A

morphogen

134
Q

2 requirements of morphogen

A
  • signal must directly affect target cells

- different concentrations of signal must cause different effects

135
Q

Vertebrate limb positioning example

A
  • group of cells at posterior base of limb bud at cell wall = 2PA
  • cells of 2PA secrete a protein morphogen called sonic hedgehog (SHH)
  • SHH forms a gradient that determines the posterior/anterior axis
136
Q

High SHH means

A

little finger

137
Q

Low SHH means

A

thumb

138
Q

A cascade of transcription factors establishes (blank) in the fruit fly

A

body segmentation

139
Q

When are the fates determined in fruit flies?

A

by time larva appears

140
Q

the first 12 cycles of nuclear division are not accompanied by cytokinesis and therefore a

A

multinucleate embryo forms

141
Q

events leading to cell fate determination

A
  • developmental mutations identified
  • mutant compared with wild time flies
  • experiments confirming roles
142
Q

Cascade of gene expression occurs with what 3 types of genes?

A
  • maternal effect genes
  • segmentation genes
  • hox genes
143
Q

Maternal effect genes

A

set up the major axes of egg

144
Q

Segmentation genes

A

determine the boundaries and polarity of each segment

145
Q

Hox genes

A

determine which organ will be made at a given location

146
Q

set up the major axes

A

maternal effect genes

147
Q

determine the boundaries and polarity of each segment

A

segmentation genes

148
Q

determine which organ will be made at a given location

A

hox genes

149
Q

unevenly distirbuted cytoplasmic determinants = products of

A

specific maternal effect genes

150
Q

2 genes called (blank) and (blank) determine anterior-posterior axis

A

Bicoid and Nanos

151
Q

actions of Bicoid and Nanos establish a gradient of another protein called

A

hunchback

152
Q

The # and polarity of the Drosophilia larval segments are determined by the (blank)

A

segmentation genes

153
Q

3 types of segmentation genes

A
  • gap
  • pair rule
  • segment polarity
154
Q

organize broad areas along the anterior-posterior axis

A

gap genes

155
Q

divide the embryo into units of 2 segments each

A

pair rule genes

156
Q

determine the boundaries of anterior-posterior organization of the individual segments

A

segment polarity genes

157
Q

mutations in gap genes =

A

gaps are mutations

158
Q

mutations in pair rule genes =

A

embryos miss every other

159
Q

mutations in segment polarity genes =

A

segments in which posterior structures are replaced by reversed anterior structures

160
Q

encode a family of transcription factors that are expressed in different combinations along the length of the embryo, and help determine cell fate within each segment

A

Hox genes

161
Q

where are Hox genes located?

A

2 clusters on chromosome 3

162
Q

a mutation in a Hox gene can result in one organ being replaced by another

A

homeotic genes

163
Q

common 180 base pair sequence

A

homeobox

164
Q

60 amino acid sequence

A

homeodomain

165
Q

recognizes and binds to a specific DNA sequence in the promoters of its target genes

A

homeodomain

166
Q

Determined cells differentiate into (blank)

A

specialized cells

167
Q

Plant cells can be totipotent shown by

A

carrot cloning

168
Q

Nuclear transfer allows

A

cloning of animals

169
Q

humans totipotency permits (blank) and (blank)

A

genetic screening and certain assisted reproductive technologies

170
Q

frog experiment leads to what 2 important conclusions

A
  • genomic equivalence- no info lost from nuclei of cells

- cytoplasmic environ around cell nucleus can modify its fate

171
Q

Wilmut did what

A

cloned 1st mammal by somatic cell nuclear transfer

172
Q

Dolly showed that

A

fully differentiated cell from a mature organism can revert to a totipotent state, and that this cell can be used to create a new animal

173
Q

reasons to clone animals

A
  • expansion of the #s of valuable animals
  • preservation of endangered species
  • preservation of pets
174
Q

multipotent stem cells differentiate in response to (blank)

A

environmental signals

175
Q

rapidly dividing, undifferentiated cells that can differentiate into diverse cell tyeps

A

stem cells

176
Q

in plants, stem cells are in (blank)

A

meristem

177
Q

2 types of multipotent stem cells

A

Hematopoietic (red and white blood)

Mesenchymal (produce bone and connective tissues)

178
Q

hematopoietic stem cells proliferate in the bone marrow in response to (blank)

A

growth factors

179
Q

hematoipoietic stem cell transplantation

A

stem cells harvested and injected back into patient after cancer treatment

180
Q

hollow sphere of cells

A

blastocyst

181
Q

differentiate into most cell types but cannot give rise to complete organisms

A

pluripotent

182
Q

can be removed from the blastocyst and grown in laboratory culture almost indefinitely

A

embryonic stem cells (ESC)

183
Q

What does ESC stand for?

A

embryonic stem cells

184
Q

mouse experiments done with ESC show

A

cells’ developmental potential and the roles of environmental signals

185
Q

problems with embryos grown in lab and used to tissue damage

A
  • objection to destruction of human embryos

- stem cells/tissues provoke immune response

186
Q

Where did they make pluripotent stem cells from skin cells?

A

Japan

187
Q

Explain how to make pluripotent stem cells from skin cells

A
  • isolated genes and inserted into skin cells

- altered skin cells

188
Q

induced pluripotent stem cells (IPS cells) means

A

immune response avoided

Biology Unit 3 (5 decks)

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