Book Notes Regulating Gene Expression Flashcards
1
Q
What is the major control point for gene expression?
A
Promoter
2
Q
Sequence of DNA adjacent to the coding region of a gene where proteins bind and control the rate of transcription
A
Promoter
3
Q
Study of heritable changes in gene expression that do not involve changes in DNA sequence
A
Epigenetics
4
Q
Prokaryotic cell can (blank) supply of unneeded protein
A
Shut off
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
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
7
Q
Bind to promoter region and determine which genes are activated
A
Repressor proteins and activator proteins
8
Q
Binding of a repressor protein prevents transcription
A
Negative regulation
9
Q
Activator protein binds DNA to stimulate transcription
A
Positive regulation
10
Q
Regulating gene transcription (blank)
A
Conserves energy
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
12
Q
Carrier protein in the bacterial plasma membrane that moves sugar into cell
A
B-Galactoside permease
13
Q
Enzyme that hydrolyses lactose to glucose and galactose
A
B-Galactosidase
14
Q
Transfers acetyl groups from acetyl CoA to certain B-galactosides
A
B-galactoside transacetylase
15
Q
Addition of lactose increase or decreases?
A
Increase
16
Q
MRNA levels dramatically (blank) during lag period after lactose added to medium
A
Increase
17
Q
Stimulate synthesis of a protein
A
Inducers
18
Q
Proteins produced
A
Inducible proteins
19
Q
Proteins made all the time at constant rate
A
Constitutive proteins
20
Q
Encode 3 enzymes for processing lactose in E. coli and specify the amino acid sequences of protein molecules
A
Structural genes
21
Q
Cluster of genes with single promoter
A
Operan
22
Q
Encodes 3 lactose- metabolizing enzymes in E. coli
A
Lac operon
23
Q
Short stretch of DNA that lies between promoter and structural genes
A
Operator
24
Q
What binds with regulatory proteins?
A
Operator
25
Operator-repressor interactions control transcription in the (blank)
Lac and trp operons
26
When repressor is bound, transcription of (blank) blocked
Operon
27
Repressor protein has 2 binding sites -
operator/inducer
28
Prevents binding of RNA poly to promoter and operon not transcribed
Absense of inducer
29
Change in 3D structure prevents repressor from binding to operator and RNA polymerase binds
Presence of inducer
30
Binds to the repressor, the repressor changes shape and binds to the operator, inhibiting transcription
Co-repressor
31
Inducible systems control (blank)
Catabolic pathways
32
Repressible systems control (blank)
Anabolic pathways
33
Catabolic pathways
Turned on only when substrate available
34
Anabolic pathways
Turned on until excessive
35
Protein synthesis can be controlled by (blank)
Increasing promoter efficiency
36
Positive control to increase transcription through presence of (blank)
Activator protein
37
Efficient transcription of the lac operon requires (blank)
Binding of an activator protein to its promoter
38
Cyclic cAMP binds to activator protein called cAMP receptor protein producing what
A conformational change in CRP that allows it to bind to lac promoter
39
Efficiency reduced with abundant glucose because cAMP levels (blank) and (blank occurs)
Decrease
| CRP does not bind
40
System of gene regulation in which the presence of the preferred energy source represses other catabolic pathways
Catabolite repression
41
Promoters share blank that allow them to be recognized by the RNA polymerase and other proteins
Consensus sequences
42
Short stretch of DNA that appears, with little variation, in many different genes
Consensus sequences
43
All the genes that are normally expressed in actively growing cells
Housekeeping genes
44
Proteins in prokaryotic cells that bind to RNA poly and direct it to specific classes of promoters
Sigma factors
45
(Blank) is active most of the time and binds to consensus sequences of housekeeping genes
Sigma-70 factor
46
Both prokaryotes and eukaryotes are similar in regulation of gene transcription in that:
Both use DNA protein interactions and negative/positive control
47
Promoter contains
TATA box and regulatory sequences
48
Regulatory proteins that help control transcription
Transcription factors
49
Help with initiating transcription by assembling on chromosome
General transcription factors
50
What are the general transcription factors?
TFIID- TFIIB- TFIIF- TFIIE- TFIIH
51
Specific transcription factors play and important role in (blank)
Cell differentiation
52
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
TFIID
53
Binds both DNA polymerase and TFIID and helps identify the transcription initiation site
TFIIB
54
Prevents nonspecific binding of the complex to DNA and helps recruit RNA polymerase to the complex
TFIIF
55
Similar to sigma factor
TFIIF
56
Binds to the promoter and stabilizes the denaturation of DNA
TFIIE
57
Opens up DNA for transcription
TFIIH
58
Steps of initiation of transcription in eukaryotes
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
59
Bind transcription factors that either activate transcription or increase the rate
Enhancers
60
Bind factors that repress transcription
Silencers
61
When transcription factors bind to enhancers or silencers, they interact with RNA polymerase complex, causing the DNA to
Bend
62
Consist of different combinations of structural elements (protein conformations)
Structural motifs
63
An intact DNA double helix can be recognized by a protein motif whose structure:
- 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
64
Repressors can inhibit transcription by
- prevention of binding of transcriptional activators to DNA
- interaction with other DNA-binding proteins to decrease rate of transcription
65
The expression of transcription factors underlies (blank)
Cell differentiation
66
All differentiation cells contain (blank) and their specific characteristics arise from (blank)
Entire genome
| Differential gene expression
67
Providing new, functional cells to patients who have disease that involve the degeneration of certain cell types
Cellular therapy
68
Manipulated expression of transcription factors in cells to change them into neurons
Fibroblasts
69
Expressin of genes can be coordinated if they share (blank) that bind the same (blank)
Regulatory sequences
| Transcription factors
70
To coordinate expression, each gene has a specific regulatory sequence near its promoter called the (blank)
Stress response element
71
Transcription factor binds to stress response element and stimulates
MRNA synthesis
72
Actively dividing, unspecialized cells that have the potential to produce different cell types depending on the signals they receive from the body
Stem cells
73
Inject stem cells into damaged tissues, where they will (blank)
differentiate and form new, healthy tissues
74
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
Development
75
development involves distinct but (blank) processes
overlapping
76
sets the developmental fate of the cell
determination
77
different types of cells arise, leading to cells with specific structures and functions
differentiation
78
organization and spatial distribution of differentiated cells into the multicellular body and its organs
morphogenesis
79
increase in size of the body and its organs by cell division and cell enlargement
growth
80
involves differential gene expression and the interplay of signals between cells
morphogenesis
81
4 things involved in morphogenesis
- cell division
- cell expansion
- cell movements
- apoptosis
82
growth
cell enlargement
83
cell fates become progressively more (blank) during development
restricted
84
each undifferentiated cell will become part of a particular type of tissue
cell fate
85
amphibians- donor tissue = early embryo
adopts fate from surroundings/extracellular environ
86
amphibians- donor tissue = older embryo
continues on original path
87
determination is a (blank), the final realization of that is (blank)
commitment/ differentiation
88
cell's potential to differentiate into other cell types
potency
89
any cell type including embryonic
totipotent
90
most cell types not embryonic
pluripotent
91
several different, related cell types
multipotent
92
produce only own cell type
unipotent
93
What 2 things determine cell fate?
- cytoplasmic segregation
| - induction
94
cytoplasmic segregation
unequal cytokinesis
95
induction
cell to cell communication
96
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
cytoplasmic segregation
97
a factor is actively produced and secreted by certain cells to induce other cells to become determined
induction
98
Cytoplasmic segregation can determine (blank) and (blank)
polarity and cell fate
99
distinct "top" and "bottom" ends of an organism/structure
polarity
100
sea urchin polarity example- horizontal cut
bottom small sea urchin and top none
101
sea urchin polarity example- vertical cut
2 small sea urchins from both halves
102
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
cytoplasmic determinants
103
microtubules and microfilaments have (blank) and cytoskeleton can bind (blank)
polarity/ motor proteins
104
inducers passing from one cell to another can determine (blank)
cell fates
105
signaling events by which cells in a developing organism communicate and influence one another's developmental fate
inducers
106
example of inducer
development of lens in the vertebrate eye
107
How does an inducer work in the vertebrate eye?
surface tissue begins to develop into a lens when it receives a signal from the optic vesicle
108
inducers trigger sequences of (blank) in the responding cells
gene expression
109
induction leads to
the activation or inactivation of specific sets of genes through signal transduction cascades
110
simplify- differential gene expression
induction leads to the activation or inactivation of specific sets of genes through signal transduction cascades
111
What is the role of gene expression in development?
each cell expresses only selected genes
112
Cell fate determination involves signal transduction pathways that lead to (blank)
differentiatial gene expression
113
How do signal transduction pathways lead to differential gene expression?
inducer molecule binds to its specific receptor on the surface of a cell, stp leads to activation
114
lower concentraton of inducer =
no gene expression activated
115
Differential gene transcription is a (blank) of cell differentiation
hallmark
116
Example of differential gene transcription involving blood cells
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
Example of differential gene transcription involving muscle precursor cells
- 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
MyoD role as transcription factor in relation to muscle tissue
MyoD activated in stem cells that repair muscle tissue as it gets damaged
119
MyoD stands for
myoblast determining gene
120
the process that results in the spatial organization of a tissue or organism
pattern formation
121
What is pattern formation linked to?
morphogenesis
| -creation of body form involving apoptosis
122
Multiple proteins interact to determine (blank)
developmental programmed cell death
123
Example of apoptosis used for development
human hands and feet
124
Namatode worm programmed cell death example
- 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
Human development example of proteins interacting to determine developmental programmed cell death
proteaseases called caspases and Bcl2 and Apafl binding
126
undifferentiated, rapidly dividing cells in plants
meristems
127
Encode proteins that act in combination to produce specific whorl features
organ identity genes
128
encode transcription factors that are active as dimers
organ identity genes
129
proteins with 2 polypeptide subunits
dimers
130
replacement of one organ for another
homeotic mutation
131
transcription of the floral organ identity genes controlled by (blank)
LEAFY protein
132
Morphogen gradients provide (blank)
positional information
133
diffuses from one cell or group of cells to surrounding cells, setting up a concentration gradient
morphogen
134
2 requirements of morphogen
- signal must directly affect target cells
| - different concentrations of signal must cause different effects
135
Vertebrate limb positioning example
- 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
High SHH means
little finger
137
Low SHH means
thumb
138
A cascade of transcription factors establishes (blank) in the fruit fly
body segmentation
139
When are the fates determined in fruit flies?
by time larva appears
140
the first 12 cycles of nuclear division are not accompanied by cytokinesis and therefore a
multinucleate embryo forms
141
events leading to cell fate determination
- developmental mutations identified
- mutant compared with wild time flies
- experiments confirming roles
142
Cascade of gene expression occurs with what 3 types of genes?
- maternal effect genes
- segmentation genes
- hox genes
143
Maternal effect genes
set up the major axes of egg
144
Segmentation genes
determine the boundaries and polarity of each segment
145
Hox genes
determine which organ will be made at a given location
146
set up the major axes
maternal effect genes
147
determine the boundaries and polarity of each segment
segmentation genes
148
determine which organ will be made at a given location
hox genes
149
unevenly distirbuted cytoplasmic determinants = products of
specific maternal effect genes
150
2 genes called (blank) and (blank) determine anterior-posterior axis
Bicoid and Nanos
151
actions of Bicoid and Nanos establish a gradient of another protein called
hunchback
152
The # and polarity of the Drosophilia larval segments are determined by the (blank)
segmentation genes
153
3 types of segmentation genes
- gap
- pair rule
- segment polarity
154
organize broad areas along the anterior-posterior axis
gap genes
155
divide the embryo into units of 2 segments each
pair rule genes
156
determine the boundaries of anterior-posterior organization of the individual segments
segment polarity genes
157
mutations in gap genes =
gaps are mutations
158
mutations in pair rule genes =
embryos miss every other
159
mutations in segment polarity genes =
segments in which posterior structures are replaced by reversed anterior structures
160
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
Hox genes
161
where are Hox genes located?
2 clusters on chromosome 3
162
a mutation in a Hox gene can result in one organ being replaced by another
homeotic genes
163
common 180 base pair sequence
homeobox
164
60 amino acid sequence
homeodomain
165
recognizes and binds to a specific DNA sequence in the promoters of its target genes
homeodomain
166
Determined cells differentiate into (blank)
specialized cells
167
Plant cells can be totipotent shown by
carrot cloning
168
Nuclear transfer allows
cloning of animals
169
humans totipotency permits (blank) and (blank)
genetic screening and certain assisted reproductive technologies
170
frog experiment leads to what 2 important conclusions
- genomic equivalence- no info lost from nuclei of cells
| - cytoplasmic environ around cell nucleus can modify its fate
171
Wilmut did what
cloned 1st mammal by somatic cell nuclear transfer
172
Dolly showed that
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
reasons to clone animals
- expansion of the #s of valuable animals
- preservation of endangered species
- preservation of pets
174
multipotent stem cells differentiate in response to (blank)
environmental signals
175
rapidly dividing, undifferentiated cells that can differentiate into diverse cell tyeps
stem cells
176
in plants, stem cells are in (blank)
meristem
177
2 types of multipotent stem cells
Hematopoietic (red and white blood)
| Mesenchymal (produce bone and connective tissues)
178
hematopoietic stem cells proliferate in the bone marrow in response to (blank)
growth factors
179
hematoipoietic stem cell transplantation
stem cells harvested and injected back into patient after cancer treatment
180
hollow sphere of cells
blastocyst
181
differentiate into most cell types but cannot give rise to complete organisms
pluripotent
182
can be removed from the blastocyst and grown in laboratory culture almost indefinitely
embryonic stem cells (ESC)
183
What does ESC stand for?
embryonic stem cells
184
mouse experiments done with ESC show
cells' developmental potential and the roles of environmental signals
185
problems with embryos grown in lab and used to tissue damage
- objection to destruction of human embryos
| - stem cells/tissues provoke immune response
186
Where did they make pluripotent stem cells from skin cells?
Japan
187
Explain how to make pluripotent stem cells from skin cells
- isolated genes and inserted into skin cells
| - altered skin cells
188
induced pluripotent stem cells (IPS cells) means
immune response avoided
