Lecture Notes Regulating Gene Expression Flashcards
1
Q
How is gene expression regulated in prokaryotes?
A
Prokaryotes make certain proteins only when they are needed
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
3
Q
Repressor protein bound at site where RNA wants to bind and prevents initiation of transcription
A
Negative regulation
4
Q
Activator protein enhances transcription
A
Positive regulation
5
Q
Regulating gene transcription allows E. coli to (blank) in an ever changing environment
A
Conserve energy
6
Q
(Blank) is the easiest sugar to metabolize
A
Glucose
7
Q
Lactose is (blank)
A
B-galactoside
8
Q
3 proteins needed for the uptake and metabolism of lactose
A
B-galactoside permease
B-galactosidase
B-galactoside transacetylase
9
Q
Carrier protein that moves lactose into the cell
A
B-Galactoside permease
10
Q
Hydrolyses lactose
A
B-galactosidase
11
Q
Transfers acetyl groups from acetyl coA to certain b galac
A
B-galactoside transacetylase
12
Q
(Blank) stimulates expression of B-Galactosidase
A
Lactose
13
Q
Lactose is a (blank)
A
Inducer
14
Q
Lactose increases or decreases mRNA
A
Increases
15
Q
E. coli makes (blank) first before proteins
A
MRNA
16
Q
Compounds that stimulate protein synthesis are called
A
Inducers
17
Q
(Blank) are made at a constant rate
A
Constitutive proteins
18
Q
2 ways to regulate metabolic pathways
A
- Regulation of enzyme activity
- regulation of enzyme concentration
19
Q
End product feeds back, inhibiting the activity of enzyme 1 only, quickly blocking pathway
A
Regulation of enzyme activity
20
Q
End product blocks the transcription of all 5 genes- no enzymes produced
A
Regulation of enzyme concentration
21
Q
Gene cluster with a single promoter
A
Operon
22
Q
A typical operon consists of:
A
A promoter
Two or more structural genes (z, y, and a)
An operator
23
Q
A short sequence between the promoter and the structural genes that binds regulatory proteins
A
Operator
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
25
Repressor binds operator sequence and blocks RNA poly from binding- no requirement and genes transcribe
Inducible system- lactose absent
26
Repressor protein has binding sequence for lactose - RNA polymerase binds to breakdown and metabolize lactose
Inducible system: lactose present
27
Trp operon is a (blank) system
Repressible
28
Trp operon- amino acid
Incorporated into proteins
29
The trp repressor binds the operator, and RNA synthesis is blocked
Tryptophan present
30
Repressor dissociates from the operator, and RNA synthesis proceeds
Absence of tryptophan
31
Metabolic substrate is a
Inducer
32
Regulatory protein is a
Repressor
33
Metabolic substrate interacts with a regulatory protein- repressor can't bind to operator and transcription proceeds
Inducible system
34
Control catabolic breakdown pathways
Inducible systems
35
Turned on when substrate is available
Catabolic pathways
36
Metabolic product is a
Co-repressor
37
A metabolic product binds to a regulatory protein, which then binds to the operator and blocks transcription
Repressible systems
38
Control anabolic (build) pathways
Repressible systems
39
Turned on until product concentration becomes excessive
Repressible systems
40
E. coli can use (blank) to increase transcription
Positive control
41
If glucose and lactose levels are both high, the (blank) is not transcribed efficiently
Lac operon
42
Efficient transcription requires (blank) to increase transcription
Binding of an activator protein to lac operon promoter
43
Example of activator protein
CAMP bund to CRP
44
Low glucose means CRP
Bound to promoter
45
High glucose means CRP
Not bound
46
A system or gene regulation in which presence of a preferred energy source represses other catabolic (break-down) pathways
Catabolite repression
47
RNA polymerases bind and are orientated at promoters so that (blank)
The correct DNA strand is transcribed
48
All promoters have (blank) that allow them to be recognized by RNA polymerase
Consensus sequences
49
Different classes of consensus sequences are recognized by regulatory proteins called
Sigma factors
50
Bind to RNA polymerase and direct it to certain promoters
Sigma factors
51
Genes for proteins with related functions may be at different locations in the genome, but share consensus sequences and can be recognized by
Sigma factors
52
Is active most of the time and binds to consensus sequences of housekeeping genes
Sigma factor 70
53
Genes normally expressed in actively growing cells
Housekeeping genes
54
How is gene expression regulated in eukaryotes?
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
55
Regulation- prokaryotic vs eukaryotic - BOTH
Use DNA protein interactions and negative/positive control to regulate gene expression
56
Beginning steps in initiation of eukaryotic transcription
TATA box in promoter bound by TFIID
57
Transcription initiation complex includes
TFIID- TFIIB- TFIIF- TFIIE- TFIIH
58
Binds to TATA box
TFIID
59
Binds both RNA polymerase and TFIID, and helps identify the transcription initiation site
TFIIB
60
Prevents nonspecific binding of the complex to DNA and helps recruit RNA polymerase to the complex
TFIIF
61
Similar to function of bacterial sigma factor
TFIIF
62
Binds to the promoter and stabilizes the denaturation of the DNA
TFIIE
63
Opens up the DNA for transcription
TFIIH
64
Transcription factor specificity does what
Plays an important role in cell differentiation
65
Regulatory sequences that bind transcription factors that activate transcription or increase rate of transcription
Enhancers
66
Bind transcription factors that repress transcription
Silencers
67
Structural motifs mediate (blank) which means what
DNA binding
| Fundamental to differentiation
68
What is a common structural motif?
Helix-turn-helix
69
For DNA recognition the structural motif must:
- 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
70
What does the lac repressor do and what is it often called?
Bonds DNA and inhibits ability of TF binding
| Dimer
71
Expression of transcription factors underlies (blank)
Cell differentiation
72
During development, cell differentiation is often mediated by
Changes in gene expression
73
All differentiated cells contain (blank)
Entire genome
74
The expression of just 3 TF is sufficient to transform (blank)
Fibroblast into a neuron
75
Coordinating gene expression
- separate genes unlike prokaryotes
| - same sequence of DNA in front of multiple genes
76
Process in which a multicellular organism undergoes a series of progressive changes that characterizes its life cycle
Development
77
Sets the fate of the cell
Determinaron
78
Determination
Sets the fate of the cell
79
The process by which different types of cells arise
Differentiation
80
Differentiation
The process by which different types of cells arise
81
Morphogenesis
Organization and spatial distribution of differentiated cells
82
Organization and spatial distribution of differentiated cells
Morphogenesis
83
Increase in body size by cell division and cell expansion
Growth
84
Growth
Increase in body size by cell division and cell expansion
85
Why do determination and differentiation occur?
Differential gene expression
86
Morphogenesis involves differential gene expression and the interplay of signals between cells:
- cell division
- cell expansion in plants
- cell movements are important in animals
87
Apoptosis is essential in
Organ development
88
Growth occurs by
Increasing the # of cells or enlargement of existing cells
89
Cell fates become progressively (blank) during development
More restricted
90
Cell fate determination is influenced by
Gene expression and the extracellular environment
91
Is determination before or after differentiation?
Determination
92
Changes in biochemistry, structure, and function that result in (blank)
Different cell types
93
Potential to differentiate into other cell types
Cell potency
94
Can differentiate to any cell type
Totipotent
95
Can develop into most cell types, but cannot form new embryos
Pluripotent
96
Can differentiate into several related cell types
Multipotent
97
Can produce only one cell type- their own
Unipotent
98
How does one egg cell produce so many different cell types?
2 processes for cell determination
- cytoplasmic segregation
- induction
99
Cytoplasmic segregation
Unequal cytokinesis
100
Induction
Cell to cell communication
101
Cytoplasmic segregation can determinate (blank)
Polarity and cell fate
102
Factors within a zygote or egg are not distributed evenly and end up in different daughter cells after division
Cytoplasmic segregation
103
Developing a "top" and "bottom"- can develop very early; yolk and other factors are distributed asymmetrically
Polarity
104
Top-nothing and bottom-small sea urchin = (blank) cut
Horizontal
105
Top and bottom- small sea urchins = (blank) cut
Vertical
106
The cytoskeleton contributes to
Asymmetric distribution of cytoplasmic determinants
107
Microtubules and microfilaments have (blank)
Polarity
108
Cytoskeletal elements can bind motor proteins that (blank)
Transport the cytoplasmic determinants
109
Communication from one cell to another can (blank)
Determine cell fates
110
Cells in a developing embryo influence one another's developmental fate via chemical signals and signal transduction mechanisms
Induction
111
What is the role of gene expression in development?
- 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
Inducers mediate signal transduction to (blank)
Dictate differential gene expression
113
Explain how inducers mediate signal transduction to dictate differential gene expression
- 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
B cell development is directed by
Signaling that causes differential gene expression
115
Inducer molecule signal mediates the expression of different genes which causes the cell to (blank)
Survive, perliforate, and proceed in development
116
2 things that happen after the receptor is bound
1) conformational change = receptor shape inside cell which changes to signal and is bound to Fit3 (chemical inducer)
2) phosphorylation
117
Differential gene transcription is a (blank)
Hallmark of cell differentiation
118
Process of transcription and differentiation in the formation of muscle cells
Mesoderm cells- myoblasts- muscle cell
| -event blocks behavior of cell when dividing in order to push differentiation forward
119
Differential gene expression drives (blank)
Development
120
How is gene expression linked to the way we look?
Pattern formation and morphogenesis
121
Creation of body form
Morphogenesis
122
The process that results in the spatial organization of tissues and organisms
Pattern formation
123
Morphogenesis involves
Cell division and differentiation, apoptosis
124
Pathways for apoptosis in C elegans
CED-9 to CED4 to CED-3 to apoptosis
125
Pathways for apoptosis in human neuron
BcL-2 to Apaf-1 to caspase-9 to caspase-3 to apoptosis
126
Dictate what differentiated cells become
Organ identity genes
127
The four organs in a flower are determined by the four groups of cells in the (blank)
Meristem
128
A protein called LEAFY controls (blank)
Transcription of organ identity genes
129
Plants with loss of function mutations of LEAFY (blank)
Do not produce flowers
130
Transgenic orange trees, expressing the LEAFY gene coupled to a strongly expressed promoter, (blank)
Flower and fruit years earlier than normal trees
131
Morphogen gradients provide (blank)
Positional information
132
The position of each cell is defined by (blank)
Concentration of morphogen
133
Describe example of specification of the vertebrate limb
Higher shh signaling drives differentiation of little finger vs thumb
134
What was discovered when scientists studied morphogens in fruit flies?
The head, thorax, and abdomen are each made of several fused segments and different body parts arise from these different segments
135
In fruit flies, when do segments appear?
early in development
136
In fruit flies, by the early larval stage what has already occurred?
cell fates already determined
137
When the embryo of fruit flies is first formed, what happens?
In the 1st 12 mitotic divisions, there is no cytokinesis, forming a multinucleate embyro and morphogens can diffuse easily in the embryo.
138
Steps of cell determination were studied using experimental genetics
- developmental mutations were identified
- mutants were compared with wild types to identify genes and proteins
- experiments confirmed gene and protein functions
139
Three gene classes of determination:
- Maternal effect genes
- Segmentation
- Hox
140
Set up the major axes of the egg
Maternal effect genes
141
Maternal effect genes
set up the major axes of the egg
142
Segmentation genes
determine boundaries and polarity of each segment
143
Determine boundaries and polarity of each segment
Segmentation genes
144
Determine which organ will be made at a given location
Hox genes
145
Hox genes
determine which organ will be made at a given location
146
transcribed in cells of the mother's ovary; the mRNAs are passed to the egg
maternal effect genes
147
(blank) and (blank) are genes that help determine the anterior-posterior axis of the embryo
Bicoid and nanos
148
subject to unequal distribution
maternal effect genes
149
What establishes the hunchback gradient?
Bicoid and nanos genes
150
Nanos (blank)
inhibits
151
Bicoid (blank)
stimulates
152
Mutations result in posterior structures being replaced by reversed anterior structures
Segmentation genes
153
3 classes of segmentation genes
gap, pair rule, segment polarity
154
organize broad areas; mutations result in omission of several body segments
Gap genes
155
divide embryo into units of two segments each; mutations result in every other segment missing
Pair rule genes
156
determine boundaries and anterior-posterior organization in individual segments
Segment polarity genes
157
Particular Hox gene encodes for
particular organ/body part
158
encode transcription factors that are expressed in different combinations along the length of the embryo
Hox genes
159
What determines cell fate in each segment of organism?
Hox genes
160
In Drosophilia, Hox genes determine (blank)
Segment identity
161
Hox genes have a 180 base pair sequence called the (blank)
Homeobox
162
The homebox encodes a 60 amino acid sequence called the (blank)
Homeodomain
163
The homeodomain binds to
specific DNA sequences in the promoters of target genes
164
Is differentiation reversible?
yes
165
A zygote is totipotent meaning it can
give rise to every cell type in organism
166
As development proceeds, cells become determined and lose their (blank)
totipotency
167
What is an example in which differentiated plant cells can be turned totipotent?
Carrot cloning
168
Nuclear transfer experiments show that genetic material from a single cell can be used to (blank) animals
clone
169
Initial cloning experiments show reversible nature of (blank)
differentiation
170
Cloning experiments indicated that
-no genetic info is lost as cell passes through developmental stages
171
Step 1 to cloning a mammal (Dolly)
took mammary epithelial cells and cultured them (#1 sheep)
172
Step 2 to cloning a mammal (Dolly)
harvested eggs from #2 sheet and eneucleated them
173
Step 3 to cloning a mammal (Dolly)
fused 1 mammary epithelial cell with 1 eneucleated egg
174
Step 4 to cloning a mammal (Dolly)
induced cells to divide- embryos
175
Step 5 to cloning a mammal (Dolly)
embryos implanted into 3rd sheep
176
What did the cloning of Dolly the sheep show?
fully differentiated cell from a mature animal can revert to totipotent
177
What are the benefits of cloning animals?
- increase # of valuable animals (ex- trangenic animals with genes with therapeutic properties)
- preservation of endangered species
- preservation of pets
178
What is one specific example involving a positive benefit from cloning an animal?
cow genetically engineered to make HGH in milk cloned to produce hormone for children with growth hormone deficiency
179
Rapidly dividing, undifferentiated cells that can differentiate into several cell types
Stem cells
180
Stem cells
rapidly dividing, undifferentiated cells that can differentiate into several cell types
181
In plants, stem cells are in the (blank)
meristems
182
In mammals, stem cells occur in tissues that require frequent (blank)
replacement (skin, blood, intestinal lining)
183
Two types of adult stem cells
Hematapoetic and mesencymal stem cells
184
Stem cell transplantation often occurs
after cancer
185
stem cell "healing" therapy
stem cells may be able to insert into the tissue and differentiate or induce tissue regeneration
186
Experiments show that damaged tissues can heal more effectively if (blank)
stem cells are injected into tissue
187
Using ESCs to obtain (blank)
pluripotent stem cells
188
ESCs (blank)
repair tissue, recover from disease, heart attack
189
ESCs can be (blank)
harvested from human embryos conceivied by in-vitro
190
2 problems with harvesting ESCs from embyros
- some people object to destruction of human embryos
| - stem cells could provoke an immune response in a recipient
