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Molecular Biology > Control of Gene Expression 1: Transcriptional Controls > Flashcards

Control of Gene Expression 1: Transcriptional Controls Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Different cells contain the same genes but express different what?

A

sets of protein; gene expression is different in different cells

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2
Q

What is an example of a “housekeeping protein”?

A

glucose metabolism

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3
Q

Hemoglobin is an example of what type of protein?

A

specifically limited protein

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4
Q

True or false?

Typical human cells express 30-60% of its 25,000 genes but level of gene expression varies

A

true

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5
Q

Alternative splicing (dystrophin gene) and post translational modification are other factors that occur when?

A

after transcription

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6
Q

What two things does gene regulation require?

A
  1. short stretches of DNA of defined sequence -recognition sites for DNA binding proteins
  2. gene regulatory proteins - transcription factors
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7
Q

True or False?

Recognition sequences can only be proximal to first exon

A

false; can be proximal or distal to first exon

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8
Q

In regards to DNA motif recognition, regulatory proteins associate with what?

A

major groove in DNA - presents a specific face for each of the specific base pairs

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9
Q

True or false?

The surface of the protein is extensively complementary to the surface of the DNA region to which it binds

A

true

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10
Q

A series of contacts between the regulatory protein and DNA is made which involves how many possible configurations?

A

4 configurations of base pairs

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11
Q

A typical gene regulatory protein-DNA interaction ivolves how many interactions?

A

10-20

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12
Q

The parts of a DNA transcription factor can be modular. What are some of these modules?

A

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

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13
Q

What is the simplest, most common DNA binding motif?

A

helix-turn-helix

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14
Q

Describe the structure of the helix-turn-helix domain

A

two alpha helices are connected by short chain of amino acids that make the “turn” at a fixed angle

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15
Q

The longer helix in the helix-turn-helix domain is what type of module?

A

recognition module - DNA binding module that fits into major groove

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16
Q

This DNA binding motif binds to the major groove of DNA and includes a Zn atom and when the amino acid sequence is drawn out, the structure looks like a finger.

A

Zinc finger domain

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17
Q

Are Zn Finger domains found in tandem clusters? If so, why?

A

yes; stabilizes interaction with DNA and provides multiple contact points

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18
Q

This motif has a dimerization domain, activation domain and DNA binding domain and has a two alpha helical structure with leucine side arms.

A

Leucine zipper motif

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19
Q

Where do interactions occur in the leucine zipper motif?

A

between hydrophobic amino acid (leucine) side chains

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20
Q

In the leucine zipper motif there is a leucine residue every __ amino acids down one side of the alpha helix in the dimerization domain

A

7

note: this forms zipper structure

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21
Q

In the leucine zipper motif, which domain does the activation domain overlap?

A

dimer domain

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22
Q

Describe the structure of the helix-loop-helix domain

A

consists of a short alpha chain connected by a loop to a second longer alpha chain

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23
Q

True or false?

the helix-loop-helix domain can only occur as a homodimer.

A

false; can occur as homodimer or heterodimer

24
Q

How many modules are there in the helix-loop-helix domain? What are they?

A

3; DNA binding domain, dimerization domain, activation domain

25
Q

What is hereditary spherocytosis (HS)?

A

a hemolytic anemia characterized by spherical and fragile RBCs that lyse and release hemoglobin

26
Q

What is the clinical presentation of hereditary spherocytosis?

A

hemolysis, anemia, splenomegaly

note: presentation ranges from mild to severe anemia and can be fatal

27
Q

What is HS caused by?

A

mutations in genes for the erythrocyte membrane skeleton of RBCs

28
Q

Is HS dominantly or recessively inherited?

A

dominantly

29
Q

The erythrocyte membrane skeleton (EMS) confers what to RBCs?

A

durability and stability

30
Q

How many EMS passages are in the circulation?

A

1/2 million

31
Q

What is the incidence rate of HS?

A

1/2000

note: HS is the most common hereditary anemia in people of Northern European Descent

32
Q

True or false?

HS can be caused by a mutation in zinc finger protein gene Klf1

A

true

note: the Klf1 zinc finger protein binds to promoters of all genes in EMS - turns them on

33
Q

Where is the HS mutation found in the Klf1 gene?

A

GAA to GAT or Glutamic acid (Glu) to Aspartic acid (Asp) in exon 3 (zinc finger domain 2)

note: the mutation causes there to be less RNA made from target promoter

34
Q

What is the chain of amino acids in the mutated form of Klf1 DNA binding motif?

A

Arg-Asp-Arg

35
Q

In normal Klf1, the R (Arg) interacts with E (Glu Acid) in RER to stabilize interaction with C in the major groove of what?

A

CACCC recognition sequence

36
Q

What is the result of the HS Klf1 mutation?

A

DNA cannot be unwound - no transcription

37
Q

In regards to detection of sequence-specific DNA proteins, how does affinity chromatography work?

A

DNA binding protein is isolated, then the purification of sequence specific binding proteins

38
Q

What does CHIP: chromatin immune precipitation allow one to identify?

A

allows identification of the sites in the genome that a regulatory protein binds; the pcr product at the end can be used to screen a microarray gene chip

39
Q

What is the gene control region of a typical eukaryotic gene?

A

DNA region involved in regulating and initiating transcription of a gene

40
Q

Does the gene control region of a typical eukaryotic gene include the promoter?

A

yes; where transcription factors and RNA polymerase II assembles

41
Q

Of the 25,000 human genes, __% encode gene regulatory proteins

A

8

42
Q

In regards to the gene control region of a typical eukaryotic gene, RNA polymerase and general transcription factors assemble at the promoter. Other gene regulatory proteins bind to regulatory sequences located where?

A

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

43
Q

What is the model for Transcriptional activation?

A

DNA looping and a mediator complex allowing regulatory proteins to interact with the proteins that assemble at the promoter

44
Q

In regards to transcriptional activation, the mediator serves as an intermediary between what?

A

gene regulatory proteins and RNA polymerase II

45
Q

Gene activator proteins modify local chromatin structure. Histone acetylation does what?

A

makes it easier to remove histones - favors transcription

46
Q

What is the sequence of events starting from gene activation to transcription initiation?

A

gene activator protein binds to chromatin; chromatin remodeling; covalent histone modification; additional activator proteins bound to gene regulatory region; assembly of pre-initiation complex at the promoter; transcription initiation

47
Q

Gene repressors inhibit transcription in different ways. The first being that gene activators and repressers compete for the same what?

A

binding site

48
Q

Another way gene repressors inhibit transcription when both activator and repressor bind to DNA but the repressor also binds to what?

A

the activation domain of the activator protein - masks the activation surface

49
Q

Another way gene repressors inhibit transcription is by binding DNA and directly interacting (blocking) with what?

A

general transcription factors

50
Q

Another way gene repressors inhibit transcription is by recruiting a ___ ___ __ which returns the promoter to the pre-transcriptional nucleosome state

A

chromatin remodeling complex

51
Q

Another way gene repressors inhibit transcription is by recruiting a ___ ___ to the promoter which makes it harder to remove deacetylated histones

A

histone deacetylase

52
Q

Another way gene repressors inhibit transcription is by recruiting a ___ ___ ___ which methylates histones. These methylated histones are bound to proteins which act to maintain chromatin in a transcriptionally silent form..

A

histone methyl transferase

53
Q

True or false?
depending on their composition, the complexes can be either activating or repressing. The same protein can be part of an activating or repressing complex

A

true

54
Q

What are the seven ways gene regulatory proteins are controlled?

A
  1. synthesis
  2. ligand binding
  3. covalent modificaiton-phosphorylation
  4. addition of subunit
  5. unmasking
  6. nuclear entry
  7. proteolysis
55
Q

In regards to the globin genes, what are alpha like chains? and beta like chains?

A

alpha like: zeta and alpha

beta like: epsilon, gamma, delta, and beta

56
Q

In regards to beta globin gene regulation, what do regulatory proteins bind to?

A

LCR

Molecular Biology (17 decks)

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