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BQ II > T.15 GENETIC DEPENDENT MECHANISM > Flashcards

T.15 GENETIC DEPENDENT MECHANISM Flashcards

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1
Q

What determines the global profile of gene expression in a cell?

A

Only a set of genes is expressed at a time in a cell; thus, the gene expression profile depends on cell type and conditions, controlled by gene expression regulation.

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2
Q

What does DNA encode and what is the first step of protein synthesis?

A

DNA encodes genes with coding and non-coding regions (promoter + introns); the first step of protein synthesis is making an RNA copy of the transcribable gene regions.

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3
Q

How is the primary RNA processed after transcription?

A

Primary RNA is processed to remove non-coding regions, generating mRNA that serves as the template for protein synthesis.

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4
Q

What are the three main mechanisms controlling protein synthesis?

A
  1. Genetic control via transcription factors and histone modifiers. 2. Genetic control via RNAs like miRNA. 3. Epigenetic regulation via DNA methylation.
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5
Q

What is Control 1 in gene expression regulation?

A

Genetic control where genes encode transcription factors that bind promoters and recruit histone-modifying enzymes to induce or block transcription.

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6
Q

What is Control 2 in gene expression regulation?

A

Genetic control where genes encode RNAs (e.g. miRNA) that bind to mRNA to regulate its stability and prevent translation.

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7
Q

What is Control 3 in gene expression regulation?

A

Epigenetic regulation where gene transcription is blocked by methylation accumulation in parts of the gene.

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8
Q

What do genetic and epigenetic regulation depend on?

A

Genetic control depends on DNA sequence; epigenetic regulation is DNA-sequence independent.

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9
Q

What are the two categories of DNA sequences involved in transcription regulation?

A

Proximal regions (close to the TSS) and distal regions (far from the TSS).

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10
Q

What is the function of the proximal promoter?

A

Contains the basal promoter region to which the basal transcription machinery (initiation sequence, GTFs, RNA pol II) binds.

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11
Q

What are the two ways the basal promoter can function?

A

Indirectly by encoding initiation recognition sequences, or directly via the TATA box.

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12
Q

Why can’t the proximal promoter serve as a regulatory mechanism?

A

Because it encodes constitutive genes expressed all the time and provides binding sites for GTFs like RNA pol II.

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13
Q

Where can the distal promoter be located?

A

It may be within the promoter, outside the promoter, or even outside the gene, as long as it’s far from the TSS.

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14
Q

What do distal regulatory sequences encode?

A

Response elements containing binding sites for multiple transcription factors that regulate gene expression.

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15
Q

What is the role of transcription factors at distal regions?

A

They bind to enzymes at the promoter, enhancing or inhibiting transcription depending on the stimulus and gene.

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16
Q

What are silencers and enhancers in transcription regulation?

A

Silencers recruit TFs for positive regulation; enhancers recruit TFs for negative regulation of transcription.

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17
Q

How do distal elements interact with the transcription machinery despite being far from TSS?

A

DNA is wrapped around histones, allowing distal elements to contact the basal machinery in 3D space.

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18
Q

What is the role of insulators in transcription regulation?

A

They isolate enhancers and silencers to affect specific gene expression outcomes.

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19
Q

What gene expression outcomes are possible with and without insulators?

A

No insulator: both genes expressed; insulator between genes: only gene 1 or gene 2 expressed.

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20
Q

What are the main functions of transcription factors?

A

Activation in response to stimuli, DNA sequence recognition and binding, recruitment of regulatory enzymes.

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21
Q

How do transcription factors bind DNA?

A

Through DNA-binding motifs; the binding is non-covalent and dynamic.

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22
Q

What is the structure of transcription factors?

A

They form homo- or heterodimers with DNA-binding domains, enzyme-binding domains, and nuclear localization domains (NLDs).

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23
Q

What determines whether a TF activates or inhibits transcription?

A

The enzyme it binds to (coactivator or corepressor) determines whether it acts as activator or inhibitor.

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24
Q

Can the same TF regulate multiple genes?

A

Yes, a TF can modulate different genes even encoding proteins with opposite functions depending on stimuli.

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25
What is an example of TF modulating different genes?
STAT3 can activate Myc (promotes proliferation) or p2lwaf1 (inhibits proliferation) depending on stimuli.
26
How long are TFs active?
They are active for a limited time, regulated by mechanisms affecting stability, nuclear import/export, DNA-binding, and dimerization.
27
What are the five main mechanisms regulating TF activity?
1. TF abundance, 2. nuclear import, 3. DNA-binding, 4. dimerization, 5. interaction with co-regulators.
28
How is TF abundance modulated?
Stimulus increases TF protein levels; after stimulus, TF is degraded via proteasome-mediated ubiquitination (e.g., c-Myc).
29
How is TF nuclear import regulated?
TFs remain inactive in cytosol by binding to inhibitory subunits that mask the NLS until activated by stimulus (e.g., NFkB).
30
What happens to transcription factors (TFs) in the absence of stimulus?
TFs are inactive as monomers in the cytosol.
31
What happens to TFs in response to a stimulus?
The TF is activated.
32
What is an example of a TF that uses DNA-binding activity as a control mechanism?
STAT.
33
What happens upon stimulus to activate STAT?
Receptors of STAT are activated.
34
What does JAK kinase do upon STAT receptor activation?
JAK kinase binds to the active receptor and phosphorylates the transcription factor.
35
What results from STAT phosphorylation by JAK?
STAT dimerizes and is imported into the nucleus.
36
What happens after STAT enters the nucleus?
STAT dimer binds to target genes and regulates gene expression.
37
How is STAT activity turned off after stimulus ends?
PISA, a STAT inhibitor, binds to the STAT DNA-binding domain, preventing DNA binding and detaining transcription.
38
What transcription factor can dimerize with both c-Myc and Mad?
Max.
39
What do Max/Myc and Max/Mad heterodimers bind to?
The same DNA sequence: E-box.
40
What determines whether Max binds c-Myc or Mad?
The respective abundance of c-Myc or Mad.
41
What happens in response to a stimulus regarding Max and c-Myc?
c-Myc levels increase and Max dimerizes with c-Myc.
42
What does the Max/c-Myc heterodimer do?
It recruits coactivators and induces expression of proliferative target genes.
43
What happens when the stimulus ends with regard to Max dimers?
c-Myc levels decrease, Mad levels increase, and Max dimerizes with Mad.
44
What does the Max/Mad heterodimer do?
It recruits a corepressor, repressing expression of target genes and blocking proliferation.
45
What happens to nuclear receptors in the absence of ligands?
They remain inactive.
46
How do nuclear receptor ligands activate transcription?
By binding to the receptor, triggering activation.
47
What type of molecules are nuclear receptor ligands?
Lipid-soluble hormones that diffuse through membranes.
48
What maintains steroid receptors inactive without ligand?
Heat-shock proteins (HSP).
49
What happens when steroid hormones bind nuclear receptors?
They dissociate the receptor from HSP, activating it.
50
What can nuclear receptors do once active and in the nucleus?
Homodimerize to bind specific response elements in target genes or heterodimerize with RXR.
51
What happens when nuclear receptors heterodimerize with RXR?
They bind DNA as inactive TFs, but ligand-bound RXR heterodimers become active TFs.
52
What is epigenetic control?
Changes that affect chromatin packaging and expression without changing DNA sequence.
53
What are the three types of epigenetic control?
Histone modification, RNA interference (non-coding RNA), and DNA methylation.
54
What effect do histone tail modifications have?
They change chromatin condensation and regulate transcription.
55
What do chromatin remodeling complexes do?
Move nucleosomes away from original DNA positions to allow TF binding; ATP-dependent.
56
What is the role of HAT (Histone Acetyl Transferase)?
It acetylates histone tails, removing positive charges and allowing transcription.
57
What is the role of HDACs (Histone Deacetylases)?
They remove acetyl groups from histone tails, inhibiting transcription.
58
How does histone acetylation affect chromatin?
It opens (decondenses) chromatin, promoting transcription.
59
What types of histone modifications can create protein binding sites?
Acetylation, phosphorylation, methylation, ubiquitylation.
60
What are some domains that recognize modified histones?
Chromodomains and bromodomains.
61
What does the "histone code" refer to?
A unique combination of post-translational modifications that define gene expression patterns.
62
Can histone modifications influence each other?
Yes, a modification can inhibit or enhance another on the same or adjacent histones.
63
How do non-histone proteins affect histone modifications?
Post-translational modifications of TFs can recruit histone modifiers like HATs or HDACs.
64
What is an example of TF modification affecting transcription?
Modification of NFKB creates binding sites for either repressors or activators.
65
What is DNA methylation?
Addition of methyl groups to cytosines by methyltransferases, condensing chromatin.
66
What does DNA hypermethylation do?
It condenses chromatin, preventing transcription.
67
What does DNA hypomethylation do?
It decondenses chromatin, allowing transcription.
68
What enzyme maintains methylation patterns after DNA replication?
DNA methyltransferase 1.
69
What enzymes methylate new regions of DNA during life?
DNAMT3A and DNAMT3B.
70
Can DNA methylation be reversed?
No, methylation is irreversible.
71
What is the effect of hypermethylation over time on gene expression?
The gene becomes silenced due to chromatin condensation.
72
What role does methylation play in tissue specificity?
It determines which genes are expressed in each cell type.
73
What is gene silencing through methylation?
The process where hypermethylation suppresses gene expression in differentiated cells.
74
What are siRNA and miRNA?
Small, non-coding RNAs from viruses or cellular processes involved in RNA interference.
75
What enzyme produces siRNA from dsRNA?
Dicer cleaves both ends of dsRNA, producing siRNA.
76
What complex binds siRNA to mediate gene silencing?
RISC (RNA-induced silencing complex).
77
What does RISC do upon binding siRNA?
It unwinds and degrades the sense strand, allowing the short strand to bind complementary mRNA.
78
What happens when siRNA binds mRNA?
RISC degrades the target mRNA strand, preventing its translation and function.
79
What is micro RNA (miRNA)?
A type of RNA involved in post-transcriptional regulation of gene expression.
80
Where can miRNAs originate from?
They can originate from genes or from introns during RNA splicing.
81
What structural feature allows miRNA to form hairpins?
Auto-complementary sequences within the RNA.
82
What happens to pre-miRNA in the cytosol?
It is recognized by Dicer, which cleaves its ends to form double-stranded RNA.
83
What does the Dicer enzyme do to pre-miRNA?
It cleaves its ends to produce a double-stranded RNA.
84
What happens after Dicer processes miRNA?
RISC complex recognizes the double-stranded RNA and unwinds it.
85
What happens if miRNA is fully complementary to its mRNA target?
The mRNA is degraded.
86
What happens if miRNA is not fully complementary to its mRNA target?
Translation is inhibited; no protein is synthesized.
87
What does miRNA regulation depend on?
The degree of sequence complementarity between miRNA and the target mRNA.
88
What is the first step in the molecular mechanism of gene expression regulation (A)?
A transcription factor binds as a dimer to a specific site on the gene promoter.
89
What does the transcription factor recruit in step A?
A histone modifier (HAT).
90
What does the recruited HAT enzyme do?
It acetylates the histone tails of the nucleosome and surrounding ones.
91
What effect does histone acetylation have in step A?
It causes chromatin to decondense.
92
What do modified histone tails create?
Binding sites for histone modifiers or chromatin remodelers.
93
What do chromatin remodelers do after histone modification?
They move nucleosomes away, making DNA more accessible to transcription factors.
94
What is the overall result of step A in gene expression regulation?
Increased accessibility to DNA for transcription factors and continuation of gene activation.
95
What happens in step B of gene expression regulation?
A transcription factor recruits a remodeler to move the nucleosome.
96
What does nucleosome repositioning allow in step B?
It exposes a TF binding site for another transcription factor to bind.
97
What happens after the second transcription factor binds in step B?
It recruits a histone modifier to acetylate histone tails, continuing the activation process.
98
What is the function of specific regulatory transcription factors?
They recognize promoter sequences and initiate gene regulation.
99
What is the role of HMG proteins in gene expression regulation?
They induce DNA bending.
100
Which proteins are involved in gene expression regulation?
Specific transcription factors, HMG, histone modifiers, chromatin remodelers, nucleosomes, basal machinery, and mediator.
101
What constitutes the basal transcriptional machinery?
RNA polymerase, general transcription factors (GTF), and the mediator.
102
What is the mediator complex?
A large protein complex that connects basal transcriptional machinery with transcription factors and histone modifiers.

BQ II (17 decks)

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