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Advanced Molecular Biology Eukaryotes > Regulatory Sequences In Eukaryotes > Flashcards

Regulatory Sequences In Eukaryotes Flashcards

1
Q

Enhancers are?

A

Groups of regulatory sequences that control gene expression

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2
Q

Action at distance

A

When DNA Loops out to accommodate the interaction between proteins. This happens because some regulators bind far from the gene they control

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3
Q

Function of insulators

A

Block activation of promoter by activators bound at enhancers.
found between enhancers and promoters

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4
Q

What are activators?

A

They activate transcription by recruiting proteins to specific genes. They have DBD and AD

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5
Q

Example of activator in S cervisiae?

A

Gal4 activates transcription of galactose gene

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6
Q

Gal4 binds to?

A

4 sites located 275bp upstream of Gal1

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7
Q

Gal 4 activates the transcription of Gal1 in presence of?

A

Galactose

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8
Q

Domain swap experiment

A

Attaching AD of Gal4 to the DBD of LexA creates hybrid protein that activates transcription

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9
Q

What is a promoter?

A

Region at the gene where the transcriptional machinery binds

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10
Q

Helix- turn- helix motif consist of?

A

2 alpha helices separated by short turn.

The recognition helix fits in major groove. Other helix makes contact with DNA backbone

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11
Q

DBD motif that incorporate zinc?

A

Zinc fingers and zinc clusters.

In both cases zinc interact with cystine and histidine residues

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12
Q

Homeodomains are?

A

A type of helix-turn-helix motif.
consists of 3 alpha helices.
Helix 3 is the recognition helix.
Other 2 resemble HTH motif

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13
Q

Leucine zipper motifs are?

A

Made of 2 alpha helices that form a pincer like structure that grips DNA
each alpha helix is inserted into major groove half a turn apart

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14
Q

In leucine zipper motif dimerisation is mediated by?

A

Coiled- coil

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15
Q

Helix-loop-helix motifs:

A

An extended alpha helical region from each of the two monomers inserts into the major groove.
Similar how to leucine zipper works

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16
Q

Dimerisation in HLH motif caused by?

A

Interactions of recognition helix and shorter helix.

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17
Q

Dimerisation surface of HLH motif formed of?

A

Two helical regions. The first is part of the helix involved in recognition, the other is a shorter helix.
These two helices are separated by a flexible loop

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18
Q

In eukaryotes activators rarely interact with?

A

Polymerase

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19
Q

Eukaryotic activators recruit ………….. Indirectly and other ……………. Needed after polymerase has bound

A

Polymerase, factors

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20
Q

Functions of activators are?

A 
Interact with:
1.transcription factors
2. chromatin modifying proteins
3. factors involved in elongation and initiation 
May recruit:
1. individual element TFIID or mediator
2. pre initiation holoenzyme
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21
Q

Activators recuit all ……………. To the …………..

A

Elements, promoter

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22
Q

Activators interact with parts of ……………. …………….. Other than………….

A

Transcriptional machinery , polymerase

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23
Q

TFIID is?

A

Transcription factor for polymerase II

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24
Q

TATA is recognised by

A

TFIID

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25
Q

Activator bypass experiment?

A

Gal1 gene activated in absence of Gal4

by fusion of DBD of LexA to a component of the mediator complex Gal11

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26
Q

In chromatin modification activators recruit…………… …………….. To help activate a gene packed within………………..

A

Nucleosome modifiers

Chromatin

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27
Q

Types of nucleosome modifiers?

A
  1. Histone acetyltranferases add acetyl group to tails of histones
  2. SWI/SNF displace nucleosome to remodel chromatin
28
Q

Chromatin modification results in?

A
  1. Uncovering of DNA sequence
  2. Mobility of nucleosome to free up binding sites
  3. Addition of acetyl groups to histones tails alters interaction between tails and adjacent nucleosomes
29
Q

Adding acetyl groups also help transcriptional machinery because?

A

It creates binding sites on nucleosomes for proteins bearing called Bromodomains

30
Q

A components of TFIID complex bears………………. And also binds ………………… …………………. Better

A

Bromodomains

Acetylated nucleosomes

31
Q

hps70 activated by ……….. ……………

A

Heat shock

32
Q

GAGA factor believed to recruit enough of the ……………… ……….. To the gene for ………….

A

Transcriptional machinery

Initiation

33
Q

Non heat shock conditions

A
  1. GAGA factor causes chromatin remodelling and initiate transcription
  2. RNA polymerase II stalls afters 20-50 nucleotides
34
Q

Under heat shock conditions

A
  1. HSF binds at promoter and interacts with mediator

2. HSF recruits P-TEF which phosphorylates RNA polymerase II allowing transcription to continue

35
Q

HSF is……………….. ………… ………….

P-TEF is……………. ………. ………… ………

A

Heat shock factor

Positive transcription elongation factor

36
Q

HIV TAT recognises a specific sequence near the start of ……. ……… And present in the transcript made by stalled…………….

A

HIV RNA

Polymerase

37
Q

On domain of ……… interacts with ………… And recruits it to the stalled………..

A

TAT
PTEF
polymerase

38
Q

Activator SP1 initiates ……………. From ………… …………

A

Transcription

HIV promoter

39
Q

Polymerase………… Having only produced a small amount of………… (……… ……….)

A

Stalls

RNA (TAR RNA)

40
Q

………… Bind to …….. ………And recruits …………… Results in ………… Of RNA polymerase allowing transcription of ………. …….. To continue

A 
TAT
TAR RNA
PTEF 
Phosphotylation
HIV RNA
41
Q

Models of action at distance?

A

Activator bind to enhancer and:

  1. may change DNA topology
  2. move along DNA to promoter
  3. Loop DNA to be closer to promoter
  4. loop DNA And increase size of loop until promoter reached
42
Q

Insulators functions are?

A
  1. ENHANCER BLOCKING
    Inhibit activation of gene by enhancer
  2. BARRIER
    Inhibit spread of chromatin modification
43
Q

Insulators are placed ?

A

Between enhancer and promoter

44
Q

Silencing is ?

A

A form of repression that can spread along chromatin switching off multiple genes

45
Q

Drosophila insulator su(Hw)

A
  1. Two copies near each other.
    NO INSULATION ACTIVITY
  2. Place between enhancer and promoter.
    SOME INSULATION ACTIVITY
  3. A copy placed on either side of enhancer. HIGHEST INSULATOR ACTIVITY
46
Q

S. Cervisiae maturing type switching

A
  • mother becomes a before dividing

- switching controlled by the presence of HO gene

47
Q

HO protein is a ………….. ………….. Which triggers………….. ……….. By creating a …………. …………. Break

A

Specific endonuclease
Gene conversion
Double strand

48
Q

HO is ……… In the mother cell and kept………… In the …………. …….. Because of selective repressor ……..

A

Activated
Silenced
Daughter cell
Ash1

49
Q

SW15 protein responsible for activating expression of ……. ……. It’s present in the ………. …….. And …….. …….. During budding.
But it’s ability to turn on HO is restricted because of presence of ……… In daughter cell

A

HO gene
Mother cell
Daughter cell
Ash1

50
Q

SBF induces expression of …….. Binds near ….. ……….. It’s only ………… At the correct ……….. Of ……… ………..

A 
HO 
HO Promoter
Active
Stage
Cell cycle
51
Q

In Mother cell ?

A
  1. SW15 binding recruits a chromatin remodelling complex SWI/SNF and histone acetyltranferase SAGA
  2. Results in SBF binding site becoming accessible
  3. SBF recruits transcriptional machinery and HO gene is expressed
52
Q

In daughter cell?

A
  1. SW15 binding results in the transcription of Ash1
  2. Ash1 binds to HO promoter preventing SBF from binding
  3. HO gene is not expressed
53
Q

Combinatorial control S. Cervisiae mat locus

In a cells

A
  1. Mat-a encodes the transcription factor a1
  2. MCM1 binds to promoters of a-specific genes
  3. Alpha-specific genes are silent without alpha1 protein
54
Q

Combinatorial control S. Cervisiae mat locus

In alpha cells

A
  1. Mat-alpha encodes for factors alpha1 and alpha2
  2. MCM1 binds alpha1 to promoter of alpha-specific genes and represses their transcription
  3. MCM1 binds to promoters of haploid-specific genes and activates transcription
55
Q

Combinatorial control S. Cervisiae mat locus

In diploid cells a/alpha

A
  1. Mat-a expresses the a1 protein
  2. Mat-alpha expresses alpha2 protein
  3. A hetorodimer of a1/alpha2 represses transcription of alpha1 and all haploid specific genes
  4. MCM1/alpha2 complex represses a-specific genes
  5. Alpha specific genes are silent without alpha1 protein
56
Q

MCM1 is a

A

Transcription factor; involved in cell-type-specific transcription

57
Q

Transcriptional repressors. Ways of working:

A. competition for activator binding site

A

Repressor can inhibit binding of the activator to a gene, thus block activation of that gene

58
Q

Transcriptional repressors. Ways of working:

B. Inhibition of the activator

A

Repressor binds to a site on DNA beside activator and interacts with that activator.

59
Q

Transcriptional repressors. Ways of working:

C. Interaction with components of transcriptional machinery at promoter

A

Repressor interacts with transcriptional machinery at promoter

60
Q

Transcriptional repressors. Ways of working:

D. Recruitment of nucleosome modifiers

A
  • histone deacetylases: remove acetyl groups from histones

- histones methylases: add methyl groups to histones

61
Q

Repressor is:

A

A regulatory protein that bind to an operator and blocks transcription of genes

62
Q

Gal genes. Mig1 Repressor

A
  1. Mig1 binding site between UAs and promoter
  2. Mig1 binds to this site in presence of glucose
  3. Mig1 recruits repressor complex containing Tup1
  4. Tup1 interacts with transcriptional machinery to repress initiation and recruits histone deacetylases
  5. Alpha2 recruits this repressor complex to prevent expression of a-specific genes in alpha cells
63
Q

Signal transduction
How does the signal induce regulator activation?
1. Unmaking of activator domain

A
  • Gal4 bound to the UAs in absence of galactose
  • Gal80 masks the Gal4 AD
  • Gal80 also recruits histone deacetylases
  • Galctose cause Gal 80 to release from Gal4 AD
64
Q

Signal transduction
How does the signal induce regulator activation?
2. Movement of regulator from cytoplasm by inhibitor cactus

A
  • Drosophila dorsal protein held in the cytoplasm by the inhibitor cactus
  • Ligand binding and signal cascade results in phosphorylation and destruction of cactus
  • Released dorsal enters nucleus and activates genes.
65
Q

Signal transduction
How does the signal induce regulator activation?
3. Controlled destruction of regulator

A
  • in absence of signal, regulator B-catenin is phosphorylated by GSK-3B, regulating ubiquitylation and destruction
  • ligand binding to Wnt receptor inhibits GSK-3B activity. B-catenin not destroyed
  • enters nucleus and activates gene
66
Q

What is Coiled- coil?

A

where the two helices are held together by hydrophobic interactions between leucine residues

Advanced Molecular Biology Eukaryotes (2 decks)

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