Control of Gene Expression I Flashcards
(150 cards)
1
Q
What is the primary function of an organism’s DNA?
A
To encode all of the RNA and protein molecules required to construct its cells.
2
Q
Do different cell types in a multicellular organism contain the same DNA?
A
Yes, different cell types contain the same genome.
3
Q
What is the main reason for the differences between cell types in a multicellular organism?
A
They synthesize and accumulate different sets of RNA and protein molecules.
4
Q
What classic experiments demonstrated that differentiated cells do not lose important DNA sequences?
A
Experiments with frogs injecting a differentiated cell nucleus into an enucleated egg.
5
Q
What do RNA and protein products allow cells to do?
A
Differentiate and perform specialized functions.
6
Q
What are the two types of genes present in humans?
A
- About 20,000 protein-coding genes
- An estimated 5000 noncoding RNA genes.
7
Q
What is the significance of the mRNA content in identifying cell types?
A
Each cell type produces a characteristic set of mRNAs, allowing for accurate identification.
8
Q
What external factor can cause a cell to change its gene expression?
A
Extracellular cues such as hormones.
9
Q
What happens to protein production in liver cells when exposed to glucocorticoids?
A
Production of a set of proteins is dramatically increased.
10
Q
What is one example of a protein that is specifically expressed in red blood cells?
A
Hemoglobin.
11
Q
What method can be used to visualize the differences in protein expression between two tissues?
A
2D PAGE
(two-dimentional polyacrylamide gel electrophoresis)
12
Q
What is one conclusion drawn from detailed DNA sequencing of genomes in different tissues?
A
Changes in gene expression during development do not generally involve changes in DNA sequence.
13
Q
What is the role of tyrosine aminotransferase in liver cells?
A
It breaks down tyrosine in food.
14
Q
What do post-translational modifications affect in proteins?
A
The final pattern of protein production.
15
Q
Which technique provides detailed information about protein identity and modifications?
A
Mass spectrometry.
16
Q
What is one reason for the differences in protein levels between cell types?
A
Different levels of expression of common genes.
17
Q
What is the role of tyrosine aminotransferase in gene expression?
A
It is an enzyme whose production can be regulated by glucocorticoids in different cell types.
Fat cells reduce the production of this enzyme in response to glucocorticoids.
18
Q
How do different cell types respond to the same extracellular signal?
A
They can respond very differently, reflecting cell specialization.
Some cell types do not respond to glucocorticoids at all.
19
Q
At which steps can gene expression be regulated in the pathway from DNA to protein?
A
Gene expression can be regulated at seven steps:
* Transcriptional control
* RNA-processing control
* RNA transport and localization control
* Translational control
* mRNA degradation control
* Protein degradation control
* Protein activity control.
20
Q
What is transcriptional control?
A
It regulates when and how often a gene is transcribed.
It is a crucial control point for gene expression.
21
Q
What is RNA-processing control?
A
It regulates the splicing and processing of RNA transcripts.
22
Q
What does RNA transport and localization control involve?
A
It involves selecting which completed mRNAs are exported from the nucleus to the cytosol and determining their localization.
23
Q
What is translational control?
A
It regulates which mRNAs in the cytoplasm are translated by ribosomes.
24
Q
What is mRNA degradation control?
A
It selectively destabilizes certain mRNA molecules in the cytoplasm.
25
What is protein degradation control?
It selectively degrades specific protein molecules.
26
What does protein activity control involve?
It involves activating, inactivating, or localizing specific protein molecules.
27
Why is transcriptional control considered paramount for many genes?
It prevents the synthesis of superfluous intermediates.
28
What are transcription regulators?
Proteins that recognize specific sequences of DNA to control transcription.
## Footnote
They bind to cis-regulatory sequences.
29
What are cis-regulatory sequences?
DNA sequences that must be on the same chromosome as the genes they control.
30
How do transcription regulators interact with DNA?
They recognize and bind to specific cis-regulatory sequences using their structural motifs.
31
What is the major groove in DNA?
A wider region of the double helix where most transcription regulators make contacts.
32
What is molecular recognition in transcription regulation?
It relies on an exact fit between the surfaces of transcription regulators and DNA.
33
What are the structural motifs commonly found in transcription regulators?
They include helix-turn-helix, homeodomain, and leucine zipper motifs.
34
What is the function of the recognition helix in DNA-binding proteins?
It fits into the major groove of DNA and helps recognize specific DNA sequences.
35
What are homeotic selector genes?
Genes that code for transcription regulators involved in development, particularly in Drosophila.
36
What is the significance of the major groove in DNA?
It contains unique patterns that allow transcription regulators to distinguish between base pairs.
37
What does the leucine zipper motif consist of?
Two α helices joined to form a short coiled-coil
## Footnote
This motif allows proteins to bind DNA as dimers.
38
How do leucine zipper proteins bind to DNA?
As dimers with two long α helices held together by hydrophobic amino acid side chains
## Footnote
Often involving leucines extending from each helix.
39
What role does S-adenosyl methionine play in certain transcription regulators?
It is needed for the protein to bind DNA
## Footnote
This small molecule regulates the activity of the DNA-binding protein.
40
What are zinc fingers?
Zinc-coordinated DNA-binding motifs that have a simple structure where a zinc atom holds an α helix and a β sheet together
## Footnote
They often cluster to create a continuous stretch of α helices along the DNA major groove.
41
Describe the helix-loop-helix motif.
A short α helix connected by a loop to a longer α helix
## Footnote
This structure allows binding to DNA and interaction with another protein.
42
What is the significance of dimerization in transcription regulators?
It increases both the affinity and specificity for DNA
## Footnote
Dimerization doubles the length of recognized cis-regulatory sequences.
43
How does cooperative binding differ from noncooperative binding in transcription regulators?
Cooperative binding shows an all-or-none phenomenon
## Footnote
Binding is more pronounced at certain concentrations, leading to a S-shaped curve.
44
What factors contribute to the lower affinity of transcription regulators for DNA in nucleosomes?
Cis-regulatory sequences may face inward or be altered in conformation
## Footnote
These factors make them less accessible to transcription regulators.
45
What is 'nucleosome breathing'?
The transient exposure of DNA at the end of a nucleosome
## Footnote
This allows transcription regulators to bind despite the tight wrapping of DNA around histones.
46
What happens when a transcription regulator binds to exposed DNA in a nucleosome?
It can prevent the DNA from tightly rewrapping around the nucleosome core
## Footnote
This can facilitate the binding of additional transcription regulators.
47
What is the effect of passing replication forks on transcription regulators?
They provide additional windows of opportunity for transcription regulators to bind to DNA
## Footnote
Replication forks temporarily displace histones.
48
What are transcription regulators?
Proteins that recognize short stretches of double-helical DNA called cis-regulatory sequences, determining which genes are transcribed.
49
What is the role of pioneer factors?
They are transcription regulators that can bind to nucleosomes and are often the first proteins to bind DNA when a gene becomes transcriptionally active.
50
How do transcription regulators interact with nucleosomes?
Some can bind with nearly the same affinity on nucleosomes as they do on naked DNA, especially if their cis-regulatory sequences are exposed.
51
What is the significance of nucleosome remodeling complexes?
They are attracted by pioneer factors and alter chromatin structure, facilitating the binding of additional transcription regulators.
52
What is the relationship between binding affinity and the duration of transcription regulator binding?
Higher affinity results in longer binding durations on DNA.
53
Fill in the blank: Transcription regulators can weakly bind to any DNA sequence, which allows them to _______.
scan for their target.
54
How do most transcription regulators bind to DNA?
As homodimers or heterodimers.
55
What is the significance of structural motifs in transcription regulators?
They are used to recognize DNA sequences.
56
What is a characteristic feature of transcription regulator binding?
They typically work in groups and bind to DNA cooperatively.
57
What happens to transcription regulators when they do not find a matching cis-regulatory sequence?
They dissociate within seconds.
58
What is the effect of a transcription regulator binding to a cis-regulatory sequence on nucleosome stability?
It typically destabilizes the nucleosome.
59
What is the dynamic nature of transcription regulators in the cell?
They are constantly moving, binding, and dissociating from DNA.
60
What are transcription regulators?
Proteins that bind to cis-regulatory sequences in the genome to influence gene transcription.
61
How do transcription regulators switch genes on and off?
By binding to specific DNA sequences and either blocking or facilitating RNA polymerase access to the promoter.
62
What is an operon?
A cluster of genes transcribed from a single promoter as one long mRNA molecule.
63
What is the function of the tryptophan repressor?
It switches off the tryptophan operon when tryptophan is abundant.
64
What happens to the tryptophan operon when tryptophan concentrations are low?
The operon is transcribed, producing enzymes for tryptophan biosynthesis.
65
What is the tryptophan operator?
A cis-regulatory sequence within the promoter recognized by the tryptophan repressor.
66
How does the tryptophan repressor function as an allosteric protein?
It changes shape upon binding tryptophan, allowing it to bind tightly to the operator sequence.
67
What role do transcription activators play?
They switch genes on by enhancing the binding of RNA polymerase to the promoter.
68
What is the role of CAP in the lac operon?
It acts as an activator that requires cAMP to bind DNA and activate transcription.
69
What two conditions must be met for the lac operon to be expressed?
* Glucose must be absent
* Lactose must be present
70
What is the function of the Lac repressor?
It shuts off the lac operon in the absence of lactose.
71
What is DNA looping in bacterial gene regulation?
A process where cis-regulatory sequences located far from the gene interact with RNA polymerase via looped DNA.
72
What is the difference between transcription regulation in bacteria and eukaryotes?
Eukaryotic regulation involves more proteins and longer DNA sequences, while bacterial regulation is simpler.
73
What are the two main types of transcription regulators?
* Repressors
* Activators
74
What is the primary function of cis-regulatory sequences?
To specify the time and place of gene transcription.
75
How do activator proteins increase transcription initiation rates?
By providing favorable interactions that help attract RNA polymerase to the promoter.
76
What is the significance of the Lac operon in genetics?
It provides insights into how transcription is controlled and integrates multiple signals.
77
What is the structural motif commonly used by transcription regulators to bind DNA?
Helix-turn-helix
78
What occurs when the intracellular concentration of tryptophan drops?
The tryptophan repressor dissociates from DNA, allowing transcription of the operon.
79
True or False: Activator proteins can act as repressors depending on the placement of their binding site.
True
80
What is the role of allolactose in the lac operon?
It binds to the Lac repressor, causing a conformational change that releases the repressor from the operator.
81
What is the overall purpose of transcription regulators in gene expression?
To control the expression of genes based on environmental and cellular conditions.
82
What is the main difference between transcription regulation in eukaryotes and bacteria?
Eukaryotes involve many more proteins and longer DNA stretches, with indirect interactions between transcription regulators and RNA polymerase.
83
What are cis-regulatory sequences?
Sequences that specify the time and place for gene transcription by being read by transcription regulators.
84
What roles do positive transcription regulators (activators) and negative regulators (repressors) play?
Activators help RNA polymerase to begin transcription, while repressors block transcription.
85
How do transcription regulators interact with RNA polymerase in eukaryotes?
Interactions are almost always indirect, involving intermediate proteins like histones and the Mediator complex.
86
What is the gene control region?
The entire expanse of DNA that regulates and initiates transcription of a eukaryotic gene, including the promoter and cis-regulatory sequences.
87
How many general transcription factors are required by RNA polymerase II?
Five general transcription factors, with 27 subunits in total.
88
What is the significance of the TATA box?
It is a DNA recognition sequence for the general transcription factor TFIID.
89
What is the function of coactivators and co-repressors?
Coactivators activate transcription, while co-repressors repress it, and they typically do not bind DNA directly.
90
True or False: Eukaryotic transcription regulators often function alone.
False. They usually assemble in groups at cis-regulatory sequences.
91
What is DNA looping and why is it important in eukaryotic transcription?
DNA looping allows regulatory proteins to interact with each other and control RNA polymerase at the promoter.
92
Fill in the blank: Eukaryotic transcription activators promote transcription by _______.
triggering changes to the chromatin structure of the promoters.
93
What are the main mechanisms by which eukaryotic transcription activators alter chromatin structure?
*Covalent histone modifications*
*Nucleosome remodeling*
*Nucleosome removal*
*Histone replacement*
94
What is the role of the Mediator protein complex in transcription?
It serves as a bridge between DNA-bound transcription activators, RNA polymerase, and general transcription factors.
95
How do activator proteins increase the rate of transcription initiation?
By attracting and positioning RNA polymerase II at the promoter and releasing it for transcription.
96
What is a biomolecular condensate in the context of transcription regulation?
A phase transition that forms a structure holding together the components needed to initiate transcription.
97
What is the role of chromatin remodeling complexes in transcription?
They alter chromatin structure to increase DNA accessibility for transcription machinery.
98
Fill in the blank: The recruitment of additional proteins to the promoter is often triggered by _______.
local chromatin changes directed by transcription regulators.
99
How does alternative RNA splicing complicate the definition of a gene?
It allows for different RNA products from a single gene, affecting its functional interpretation.
100
What type of modifications are triggered by a transcription activator?
Histone tail modifications
## Footnote
These modifications attract additional proteins to the promoter, including a chromatin remodeling complex and a general transcription factor.
101
What is the role of RNA polymerase II during transcription?
Transcribes through a gene and modifies histones ahead of it
## Footnote
This process includes acetylation and deacetylation, which helps maintain transcription efficiency.
102
What happens to histones just ahead of the RNA polymerase during transcription?
They are acetylated and then rapidly deacetylated and methylated
## Footnote
This modification leaves behind nucleosomes resistant to transcription.
103
What can trigger the release of a paused RNA polymerase?
Binding of a new transcription activator to the gene's control region
## Footnote
This can involve chromatin remodeling or signaling through coactivators.
104
What is transcriptional synergy?
The joint effect of multiple transcription activators working together
## Footnote
This results in a transcription rate that exceeds the sum of their individual contributions.
105
What is the significance of condensate formation during transcription initiation?
It increases the efficiency of transcription initiation
## Footnote
Condensates hold proteins in proximity, facilitating rapid exchanges during transcription.
106
How do eukaryotic transcription repressors inhibit transcription?
By using various mechanisms without directly competing with RNA polymerase, like packing of DNA into heterochromatin (for inhibition of large regions of the genome).
Or by competiting DNA binding (binding to the same site as the activator), masking of the activation surface (repressor binds to activator), direct interaction with the genral transcription factors, recruitment of chromatin remodeling complexes, recruitment of histone deacetylases, or recruitment of histone methyl transferase.
## Footnote
These mechanisms ensure efficient repression and can quickly reverse the repressed state.
107
What is the role of histone methyl transferase proteins?
They bind to methylated histones
## Footnote
Histone methylation plays a crucial role in gene regulation and chromatin structure.
108
How can a repressor protein prevent transcription?
By outcompeting activator proteins for binding to the same regulatory DNA sequence
## Footnote
This is one of several mechanisms through which repressors can inhibit gene expression.
109
What is one way a repressor can quench an activator?
By blocking the recruitment of its coactivators
## Footnote
This interaction can prevent the activator from functioning properly.
110
What does a repressor attract to remove histone acetylation?
A histone deacetylase.
Removal of acetyl groups results in a more condensed chromatin and results in decreaded transcription.
## Footnote
Histone acetylation is often necessary for transcription initiation.
111
How do insulator sequences function to prevent gene interference?
By forming loops of chromatin mediated by specialized proteins, which brings genes and control regions in close proximity.
Insulators restrict the range of activators/repressors, so that they dont affect nearby genes.
## Footnote
This keeps a gene and its control region in proximity while preventing control region cross-talk.
112
What is the role of barrier sequences in gene regulation?
Prevent the spread of heterochromatin into genes that need to be expressed
## Footnote
This ensures that essential genes remain active.
113
How do insulators and barrier sequences contribute to the genome organization?
They help divide the genome into independent domains of gene regulation and chromatin structure
## Footnote
This organization is crucial for proper gene expression.
114
How does the complexity of eukaryotic gene regulation compare to prokaryotic?
Eukaryotic regulation is much more complex due to larger genome size and variety of cell types
## Footnote
This complexity requires multiple transcription regulators for each gene.
115
What determines the time and place of gene transcription in eukaryotes?
The particular spectrum of transcription regulators present in the cell
## Footnote
These regulators bind to the control region of the gene to modulate its expression.
116
What is the significance of cell memory in multicellular organisms?
Cell memory allows cells to maintain their differentiated state through many generations.
## Footnote
This is crucial for the formation of organized tissues.
117
What is the function of the Drosophila Even-skipped (Eve) gene?
The Eve gene is crucial for proper Drosophila embryo development; its mutation can lead to embryo failure.
## Footnote
Eve is expressed in seven stripes along the embryo.
118
What is the structure of the Eve gene control region?
The Eve gene control region is approximately 20,000 nucleotide pairs long and consists of multiple regulatory modules.
## Footnote
Each module specifies a stripe of Eve expression.
119
What happens when a regulatory module is removed from the Eve gene?
The regulatory module can still direct expression in the correct position when placed in front of a reporter gene.
## Footnote
This demonstrates the modular nature of the regulatory region.
120
Which transcription regulators activate and repress the Eve gene?
Activators: Bicoid, Hunchback; Repressors: Krüppel, Giant.
## Footnote
The balance of these proteins determines Eve expression in stripe 2.
121
What is meant by combinatorial control in transcription regulation?
Combinatorial control refers to the use of different combinations of transcription regulators to control gene expression.
## Footnote
This allows for precise spatial and temporal gene expression.
122
What is the importance of the stripe 2 element in the Eve gene?
The stripe 2 element autonomously specifies its expression when isolated.
## Footnote
It reads positional information from transcription regulators.
123
How do transcription regulators respond to extracellular signals?
Transcription regulators are activated by signals that pass through the plasma membrane to generate responses in different cell types.
## Footnote
This process is crucial for multicellular organism development.
124
What is the role of enhancers in mammalian gene regulation?
Enhancers are modular regions that regulate genes, such as the α-globin gene involved in hemoglobin synthesis.
## Footnote
They interact with transcription factors to influence gene expression.
125
What determines the final level of transcription across the stripe in the Eve gene?
The interaction and competition between activators and repressors determine the transcription level.
## Footnote
This includes complex mechanisms involving coactivators and co-repressors.
126
List two ways in which transcription regulators can be activated.
* Ligand binding
* Covalent modification
## Footnote
Other methods include protein complex formation and unmasking of activation domains.
127
What is the role of a DNA-binding protein in transcription regulation?
Formation of a complex with a separate protein that has a transcription-activating domain.
## Footnote
This complex is crucial for activating transcription of specific genes.
128
How can an activation domain be unmasked?
By the phosphorylation of an inhibitor protein.
## Footnote
Phosphorylation can lead to the activation of transcription factors that were previously inhibited.
129
What stimulates nuclear entry of regulatory proteins?
Removal of an inhibitory protein that prevents entry into the nucleus.
## Footnote
This is a critical step for the activation of gene expression.
130
What is the significance of the five modules in the α-globin regulatory region?
Each module can independently act as an enhancer to specify production of α-globin, but only in erythroid cells.
## Footnote
Erythroid cells express the necessary transcription regulators for this function.
131
What is combinatorial gene control?
The process by which combinations of transcription regulators control the expression of individual genes and contribute to the specification of multiple cell types.
## Footnote
This allows for a high level of complexity in gene regulation.
132
What is the role of master transcription regulators?
They specify cell types by controlling the expression of many genes.
## Footnote
Examples include MyoD for muscle cells and transcription factors like Oct4, Sox2, and Klf4 in pluripotent cells.
133
What happens when transcription regulators are expressed artificially?
They can convert one type of differentiated cell into another.
## Footnote
For example, liver cells can be converted into neuronal cells by expressing neuron-specific transcription regulators.
134
What is a key feature of specialized cell types in response to environmental changes?
They must rapidly turn some genes on and off.
## Footnote
This allows them to adapt and respond to signals from other cells.
135
How does the human glucocorticoid receptor protein control gene expression?
It forms a complex with a glucocorticoid steroid hormone to bind to its cis-regulatory sequences.
## Footnote
This mechanism is activated during stress conditions like starvation or intense physical activity.
136
What are the three master transcription regulators in embryonic stem cells?
Klf4, Oct4, Sox2
## Footnote
These regulators play a crucial role in maintaining pluripotency in embryonic stem cells.
137
What is the role of the glucocorticoid receptor in liver cells?
Stimulates liver cells to increase glucose production
## Footnote
This occurs through the expression of genes coding for metabolic enzymes.
138
What happens to the expression of glucocorticoid-regulated genes when the hormone is absent?
The expression drops to its normal level
## Footnote
This reflects the transient nature of the glucocorticoid receptor's effect.
139
What is cell memory?
The property that allows differentiated cells to maintain their identity
## Footnote
This is crucial for ensuring that progeny cells remain of the same type.
140
What is a positive feedback loop in the context of transcription regulation?
A mechanism where a master transcription regulator activates its own gene transcription
## Footnote
This helps maintain cell identity through divisions.
141
What is the significance of feedback loops in transcription circuits?
They allow cells to maintain stable gene expression and respond to signals
## Footnote
Positive feedback loops create memory, while negative feedback helps regulate levels.
142
What type of circuit can respond to prolonged input signals while disregarding brief ones?
Feed-forward loop
## Footnote
This mechanism allows the cell to filter out noise and respond to significant signals.
143
How do transcription regulators interact to create complex circuits?
They can be combined to perform different types of operations
## Footnote
This resembles electronic circuits that process information.
144
What is one potential outcome of a delay in a feedback loop?
Spontaneous oscillations in gene expression
## Footnote
This can occur if feedback mechanisms do not respond instantaneously.
145
What is the relationship between transcription regulators and gene transcription in differentiated cells?
Transcription regulators ensure only appropriate genes are expressed
## Footnote
This is essential for maintaining the specialized functions of different cell types.
146
What is indicated by the presence of multiple transcription regulators in a circuit?
Increased complexity of circuit behaviors
## Footnote
This allows for more sophisticated control of gene expression.
147
What is the primary function of the transcription regulators in a higher eukaryotic organism?
To control the transcription of specific genes in different cell types
## Footnote
This ensures cellular diversity and specialization.
148
What is one of the simplest mechanisms for producing cell memory?
Direct or indirect positive feedback loops
149
What do transcription circuits enable a cell to perform?
Many types of logic operations
150
What drives highly sophisticated programs of embryonic development?
Simple transcription circuits combined into large regulatory networks
