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

Lecture 1 Exam 3 Flashcards

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
Q

HS can be mutated in zinc finger protein gene called what?

A

Klf1 (Kruppel-like factor 1)

26
Q

What protein binds to promoters of all genes in EMS and turns them on?

A

KLF1 zinc finger protein (3 zinc finger domains)

27
Q

What is the critical amino acids for KLF1 DNA binding motif?

A

RER- (Arg-Glu-Arg) wild type DNA binding motif

HS would have RDR- (Arg-Asp-Arg) mutant form- no transcription

28
Q

Normal KLF1 binds to DNA and leads to what?

A

Leads to transcription KLF1 mRNA

29
Q

In HS, KLF1 Zn finger domain 2 binds to what and causes what?

A

Binds to the opposite strand change in binding so no transcription leading to no RNA-no protein.

30
Q

What does EMSA stand for?

A

Electrophoretic mobility shift assay

31
Q

What does EMSA detect?

A

Detection of sequence-specific DNA binding proteins.

32
Q

What are the steps in identification of transcription factors II?

A
  • 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
Q

What are the steps in identification of transcription factors III?

A
  • Affinity chromatography
  • Isolate DNA binding protein
  • Purification of sequence specific binding proteins
34
Q

What does CHIP stand for?

A

Chromatin Immuno-Precipitation

35
Q

What does CHIP do?

A

This technique allows identification of the site in the genome that a known regulatory protein binds to. It is done in living cells.

36
Q

At the end of CHIP what can be used to identify a sequence?

A

PCR product at end can be used to identify sequence

37
Q

What is a gene control region?

A

DNA region involved in regulating and initiating transcription of a gene

38
Q

A gene control region includes what?

A

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
Q

Where do RNA polymerase and general transcription factors assemble where?

A

At the promoter

40
Q

Where do other gene regulatory proteins (activators or repressors) bind to?

A

Regulatory sequences which can be adjacent, far upstream or in introns downstream of the promoter

41
Q

What serves as an intermediary between gene regulatory proteins and RNA polymerase II?

42
Q

Gene activator proteins modify DNA- Local chromatin structure in 4 ways, name those 4 ways.

A

Nucleosome remodeling
Nucleosome removal
Histone replacement
Histone modification (e.g. histone acetylation)

43
Q

Nucleosome remodeling and histone removal favors transcription how?

A

By increasing accessibility of DNA to proteins.

44
Q

What are the ways in which gene repressor proteins inhibit transcription?

A

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
Q

Describe competitive DNA binding (in which gene repressor protein inhibits transcription)

A

Activator and repressor compete for the same binding site.

46
Q

Describe masking the activation surface (in which gene repressor protein inhibits transcription)

A

both proteins bind to DNA but the repressor binds to the activation domain of the activator protein

47
Q

Describe direct interaction with the general transcription factors (in which gene repressor protein inhibits transcription)

A

The repressor binds to DNA and blocks assembly of general transcription factors

48
Q

Describe recruitment of chromatin remodeling complexes (in which gene repressor protein inhibits transcription)

A

The repressor recruits a chromatin remodeling complex which returns the promoter to the pre-transcriptional nucleosome state

49
Q

Describe Recruitment of histone deacetylases (in which gene repressor protein inhibits transcription)

A

The repressor attracts a histone deacetylase to the promoter-harder to remove deacetylated histones and open up DNA

50
Q

Describe Recruitment of histone methyl transferase (in which gene repressor protein inhibits transcription)

A

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
Q

Depending on the composition of complexes, proteins can be either _____ or ______.

A

activating or repressing

52
Q

How are gene regulatory proteins controlled? Name the 7 ways.

A
  1. Synthesis
  2. Ligand binding
  3. Covalent modification phosphorylation
  4. Addition of subunit
  5. Unmasking
  6. Nuclear entry
  7. Proteolysis
53
Q

What are the alpha globin like chains?

A

Zeta and alpha

54
Q

What are the B globin like chains?

A

Epsilon, gamma, delta and beta

55
Q

The alpha globin chain zeta is found where?

56
Q

The alpha globin chain alpha is found where?

57
Q

The B-globin like chain epsilon is found where?

58
Q

The B-globin like chain gamma is found where?

59
Q

The B-globin like chain delta is found where?

60
Q

The B-globin like chain beta is found where?

61
Q

How are beta globin genes arranged?

A

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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