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COB Molecular > Lec 2.1 Control of gene expression > Flashcards

Lec 2.1 Control of gene expression Flashcards

1
Q

What makes cells different?

A

Differentiation in cell depends on changes in gene expression

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2
Q

What two things does gene regulation require?

A

DNA and DNA binding proteins

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3
Q

What is a motif?

A

sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function.

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4
Q

What is the structure of a DNA transcription factor?

A

N-DNA binding module-Dimerization module-Activation module-Regulatory module-C

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5
Q

Do transcription factors have ALL modules?

A

No

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6
Q

What will a transcription factor have?

A

A DNA binding module, Activation module.

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7
Q

What is the evidence for Transcription Factors being modular? The experiment design.

A

Experimental design: place DNA in cell (yeast). Promoter and reporter gene. Have DNA binding protein made in yeast cell. Transcription Factor binds to promoter DNA and activates two modular domains- DNA binding and activation

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8
Q

What are the 4 DNA-binding domain structural motifs?(transcription factors)

A

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

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9
Q

What is the most common DNA-binding motif?

A

Helix-turn-helix

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10
Q

What is the structure of Helix-turn-helix? Where does it fit?

A

Two alpha helices and fits into major groove

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11
Q

What is the Zinc Finger domain? Where does it bind?

A

DNA binding motif that includes Zn atom. Binds to major groove of DNA

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12
Q

Where are Zinc finger domains found? What do they do to DNA?

A

Found in tandem clusters and stabilizes interaction with DNA

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13
Q

What is the structure of the Leucine zipper motif? What does it do to DNA?

A

2 alpha helical DNA binding domain. Grabs DNA like clothespin.

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14
Q

What holds the Leucine zipper motif together?

A

Interactions between hydrophobic AA side chains (leucines).

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15
Q

What is the structure of the helix-loop-helix domain?What does it do to DNA?

A

Short alpha chain connected with a longer alpha chain. Grabs DNA like a clothespin

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16
Q

What allows the helix-loop-helix domain to bind to DNA like the leucine zipper?

A

Flexibility of loop allows helix to fold back and cross second helix to bind to DNA

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17
Q

How many domains or modules does the helix-loop-helix domain have?What are they?

A
  1. Binding,Dimerization, activation
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18
Q

Do helix-loop-helix domains occur as only homodimers?

A

No. Both homodimers or heterodimers.

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19
Q

Hereditary spherocytosis (HS) results from what?

A

Zn Finger transcription factor mutation, which causes a mutation in KLF1 causing the weak cytoskeleton of red blood cells.

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20
Q

What is HS?

A

hemolytic anemia, fragile red blood cells that lyse and release hemoglobin

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21
Q

What does the cytoskeleton do for RBCs?

A

Durability and stability to RBCs. Allows to fit in tight capillary spaces.

22
Q

What are 4 ways to identify transcription factors?

A

EMSA, Affinity chromatography, Reporter assay, CHIP

23
Q

What does the EMSA (Electrophoretic mobility shift assay) do?

A

Used to detect protein complexes with nucleic acids.

24
Q

What does affinity chromatography do?

A

isolates DNA binding protein. Purification of seq specific binding proteins.

25
Q

What does CHIP stand for?

A

Chromatin immuno-precipitation

26
Q

What does CHIP do?

A

Allows identification of sites in the genome that a KNOWN regulatory protein binds to.

27
Q

How do gene activators work? 4 ways

A

By nucleosome remodeling, nucleosome removal, histone replacement, and histone modifications

28
Q

How does nucleosome remodeling work?

A

Opens access of transcription machinery to DNa

29
Q

How does nucleosome removal work?

A

Removal of histones makes the DNA naked

30
Q

How does histone replacement work?

A

Exchangement of histones allow greater access to nucleosomal DNA

31
Q

How does histone modification work?

A

Histone acetylation makes it easier to remove histones

32
Q

What does Competitive DNA binding mean, pertaining to gene repressor proteins when they inhibit transcription?

A

Activator and repressor compete for same binding site)

33
Q

What does masking the activation surface mean, pertaining to gene repressor proteins when they inhibit transcription?

A

Both have own binding sites but repressor will also bind to activator.

34
Q

What does Interaction with Transcription factors mean, pertaining to gene repressor proteins when they inhibit transcription?

A

Repressor binds to DNA and blocks assembly of transcription factors

35
Q

What does Recruitment of chromatin remodeling complexes mean, pertaining to gene repressor proteins when they inhibit transcription?

A

CRM returns the promoter to the pre-transcriptional nucleosome state

36
Q

What does recruitment of histone deacetylases mean, pertaining to gene repressor proteins when they inhibit transcription?

A

Recruitment of histone deacetylases make it harder to open up DNA

37
Q

What does recruitment of histone methyl transferase mean, pertaining to gene repressor proteins when they inhibit transcription?

A

Recruitment of histone methyl transferase means no expression.

38
Q

What does synthesis mean pertaining to how regulatory gene proteins are regulated?

A

If you make them or not

39
Q

What does Ligand binding mean pertaining to how regulatory gene proteins are regulated?

A

You can make the protein but you need a ligand as well

40
Q

What does covalent modification mean pertaining to how regulatory gene proteins are regulated?

A

phosphorylation.

41
Q

What does addition of a subunit mean pertaining to how regulatory gene proteins are regulated?

A

Just Addition of subunit.

42
Q

What does unmasking mean pertaining to how regulatory gene proteins are regulated?

A

ex. Make protein and its associated with inhibitor but we unmask it and thus activate it

43
Q

What does Nuclear entry mean pertaining to how regulatory gene proteins are regulated?

A

ex Inhibitory protein bound to the protein and cant get through the nucleus)

44
Q

What does proteolysis mean pertaining to how regulatory gene proteins are regulated?

A

If the reg protein gets cut to get into the nucleus

45
Q

What alpha globin chains are associated with embryo? Adult?

A

Embryo: Zeta. Adult: Alpha

46
Q

What beta globin chains are associated with fetal? Adult?

A

Fetal: epsilon,gamma. Adult: Delta, Beta.

47
Q

Essay: Differentiate two transcription factors

A

1.helix-loop-helix domain:Short alpha chain connected with a longer alpha chain. Grabs DNA like a clothespin. 2. Zinc finger: DNA binding motif that includes Zn atom. Binds to major groove of DNA. stabilizes interaction with DNA

48
Q

Describe one way in which transcription factors are identified

A

affinity chromatography, isolates DNA binding protein. Purification of seq specific binding proteins.

49
Q

Describe two ways in which repressor proteins inhibit transcription

A
  1. Competitive DNA binding. (activator and repressor compete for same binding site). 2. Recruitment of histone methyl transferase. (No expression)
50
Q

What are the 6 ways gene repressor proteins inhibit transcription?

A
  1. Competitive DNA binding. 2. Masking the activation surface. 3.Interaction with Transcription factors. 4.Recruitment of chromatin remodeling complexes. 5. Recruitment of histone deacetylases. 6. Recruitement of histone methyl transferase.
51
Q

What are the 7 ways regulatory gene proteins are regulated?

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

COB Molecular (36 decks)

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