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Molecular Exam 3 Lecture 1 (Control of Gene Expression) > Lecture 1 Exam 3 > Flashcards

Lecture 1 Exam 3 Flashcards

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1
Q

What are common proteins?

A

Housekeeping proteins- ex; glucose metabolism

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2
Q

What is an example of specifically limited proteins?

A

Hemoglobin

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3
Q

What are the other factors post transcription include?

A

Alternative splicing (dystrophin gene), post translational modification.

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4
Q

What are the steps of control of gene expression? (6)

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport and localization control
  4. Translation control
  5. mRNA degradation control
  6. Protein activity control
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5
Q

Gene regulation requires what two things?

A
  1. Short stretches of DNA of defined sequence

2. Gene regulatory proteins

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6
Q

What are short stretches of DNA of defined sequence?

A

Recognition sites for DNA binding proteins.

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7
Q

What are gene regulatory proteins?

A

Transcription factors that will bind and activate gene

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8
Q

Recognition sequences for regulatory proteins ___?

A

TGATAG

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9
Q

____ gives preferred nucleotide at each position.

A

Size letter

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10
Q

Recognition sequences can be ___ or____to first exon

A

Can be PROXIMAL or DISTAL to first exon

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11
Q

Proteins recognize and bind to bases in what groove?

A

Major groove

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12
Q

A gene regulatory protein recognizes what?

A

A specific DNA sequence

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13
Q

The surface of the ___is extensively complementary to the surface of the ____ region to which it binds.

A

Protein; DNA

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14
Q

Gene regulatory proteins read the outside of what?

A

The DNA helix

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15
Q

What are the 4 parts of a DNA transcription factor?

Sequence specific transcription factors are modular

A

DNA binding module, dimerization module, activation module and regulatory module

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16
Q

In the Yeast cell experiment what are the two plasmids for the evidence for transcription factors being modular?

A
  1. The DNA target in a plasmid

2. The binding proteins (GAL4) made by plasmids.

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17
Q

What are the 4 DNA binding domain structural motifs?

A

Helix-turn-helix
Zinc finger motif
Leucine zipper
Helix-loop-helix

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18
Q

Describe helix-turn-helix.

A
  • Simplest most common DNA binding motif
  • Two alpha helices connected by short chain of amino acids that make the turn- turned at fixed angle
  • Longer helix=recognition module-DNA binding module-fits into major groove
  • Side chains of amino acids recognize DNA motif
  • Symmetric dimers: Bind DNA dimers
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19
Q

What are the DNA binding domain structural motifs that have alpha chains?

A

Helix-Turn-helix
Leucine Zipper
Helix-loop-helix

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20
Q

Describe zinc finger domain.

A
  • Shown is C2H2 type (Cys-His)
  • DNA binding motif includes Zn atom
  • Binds to major groove of DNA
  • Zn finger domains found in tandem clusters
  • 3 Zn finger domains in above figure one protein
  • Stabilized interaction with DNA
  • Multiple contact points
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21
Q

Describe Leucine zipper motif.

A
  • Two alpha helical DNA binding domain
  • Grabs DNA like clothespin
  • Activation domain overlaps dimer domain
  • Interactions between hydrophobic amino acid side chains (leucines)
  • Dimerizes through leucine zipper region
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22
Q

Describe Helix-loop-helix domain.

A
  • Consists of a short alpha chain connected by a loop to a second longer alpha chain
  • Occur as homodimers and heterodimers
  • Three domains or modules to this protein: DNA binding domain, dimerization domain, activation domain
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23
Q

What are the three domains or modules to the helix-loop-helix domain?

A

DNA binging domain, dimerization domain and activation domain.

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24
Q

What is an example of a Zn finger transcription factor mutation leading to disease?

A

Hereditary spherocytosis (HS)

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25
HS can be mutated in zinc finger protein gene called what?
Klf1 (Kruppel-like factor 1)
26
What protein binds to promoters of all genes in EMS and turns them on?
KLF1 zinc finger protein (3 zinc finger domains)
27
What is the critical amino acids for KLF1 DNA binding motif?
RER- (Arg-Glu-Arg) wild type DNA binding motif | HS would have RDR- (Arg-Asp-Arg) mutant form- no transcription
28
Normal KLF1 binds to DNA and leads to what?
Leads to transcription KLF1 mRNA
29
In HS, KLF1 Zn finger domain 2 binds to what and causes what?
Binds to the opposite strand change in binding so no transcription leading to no RNA-no protein.
30
What does EMSA stand for?
Electrophoretic mobility shift assay
31
What does EMSA detect?
Detection of sequence-specific DNA binding proteins.
32
What are the steps in identification of transcription factors II?
- Use radioactive DNA from known promoter - Mix radioactive DNA fragment with protein extract from cell - Run Electrophoretic gel - Proteins with DNA attached migrate according to size - See shift of radioactive band when protein is bound to DNA - Isolate protein to identify
33
What are the steps in identification of transcription factors III?
- Affinity chromatography - Isolate DNA binding protein - Purification of sequence specific binding proteins
34
What does CHIP stand for?
Chromatin Immuno-Precipitation
35
What does CHIP do?
This technique allows identification of the site in the genome that a known regulatory protein binds to. It is done in living cells.
36
At the end of CHIP what can be used to identify a sequence?
PCR product at end can be used to identify sequence
37
What is a gene control region?
DNA region involved in regulating and initiating transcription of a gene
38
A gene control region includes what?
Includes the promoter: where transcription factors and RNA polymerase II assembles and Regulatory sequences to which regulatory proteins bind to control rate of assembly process at the promoter
39
Where do RNA polymerase and general transcription factors assemble where?
At the promoter
40
Where do other gene regulatory proteins (activators or repressors) bind to?
Regulatory sequences which can be adjacent, far upstream or in introns downstream of the promoter
41
What serves as an intermediary between gene regulatory proteins and RNA polymerase II?
Mediator
42
Gene activator proteins modify DNA- Local chromatin structure in 4 ways, name those 4 ways.
Nucleosome remodeling Nucleosome removal Histone replacement Histone modification (e.g. histone acetylation)
43
Nucleosome remodeling and histone removal favors transcription how?
By increasing accessibility of DNA to proteins.
44
What are the ways in which gene repressor proteins inhibit transcription?
Competitive DNA binding Masking the activation surface Direct interaction with the general transcription factors Recruitment of Chromatin remodeling complexes Recruitment of histone deacetylases Recruitment of histone methyl transferase
45
Describe competitive DNA binding (in which gene repressor protein inhibits transcription)
Activator and repressor compete for the same binding site.
46
Describe masking the activation surface (in which gene repressor protein inhibits transcription)
both proteins bind to DNA but the repressor binds to the activation domain of the activator protein
47
Describe direct interaction with the general transcription factors (in which gene repressor protein inhibits transcription)
The repressor binds to DNA and blocks assembly of general transcription factors
48
Describe recruitment of chromatin remodeling complexes (in which gene repressor protein inhibits transcription)
The repressor recruits a chromatin remodeling complex which returns the promoter to the pre-transcriptional nucleosome state
49
Describe Recruitment of histone deacetylases (in which gene repressor protein inhibits transcription)
The repressor attracts a histone deacetylase to the promoter-harder to remove deacetylated histones and open up DNA
50
Describe Recruitment of histone methyl transferase (in which gene repressor protein inhibits transcription)
The repressor attracts a histone methyl transferase which methylates histones These methylated histones are bound to proteins which act to maintain chromatin in a transcriptionally silent form.
51
Depending on the composition of complexes, proteins can be either _____ or ______.
activating or repressing
52
How are gene regulatory proteins controlled? Name the 7 ways.
1. Synthesis 2. Ligand binding 3. Covalent modification phosphorylation 4. Addition of subunit 5. Unmasking 6. Nuclear entry 7. Proteolysis
53
What are the alpha globin like chains?
Zeta and alpha
54
What are the B globin like chains?
Epsilon, gamma, delta and beta
55
The alpha globin chain zeta is found where?
Embryo
56
The alpha globin chain alpha is found where?
Adult
57
The B-globin like chain epsilon is found where?
Embryo
58
The B-globin like chain gamma is found where?
Fetus
59
The B-globin like chain delta is found where?
adult
60
The B-globin like chain beta is found where?
Adult
61
How are beta globin genes arranged?
In linear fashion Ordered in the 5 to 3 direction in the same sequence of activation and expression during embryonic, fetal and adult development

Molecular Exam 3 Lecture 1 (Control of Gene Expression) (1 decks)

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