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Molecular Biology > Chapter 12: Transcriptional Activators in Eukaryotes > Flashcards

Chapter 12: Transcriptional Activators in Eukaryotes Flashcards

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1
Q

Jun & Fos (x4)

-AP1, specifically binds TGACTCA sequence (called?)

A

proto-oncogene proteins and cell signaling targets in bZIP family of activators; they dimerize

  • dimerized form?
  • tissue plasminogen activator (TPA) response element (TRE)
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2
Q

human metallothionine gene (x2)

A

example of multiple enhancers upstream of gene functioning cooperatively to regulate same gene

-uses glucocorticoid response element (GRE), basal level enhancer (BLE; AP1), and metal response element (MRE)

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3
Q

example of multiple enhancers upstream of gene functioning cooperatively to regulate same gene

-uses glucocorticoid response element (GRE), basal level enhancer (BLE; AP1), and metal response element (MRE)

A

human metallothionine gene (x2)

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4
Q

3 models of recruitment/activation

A
  1. sequential complex formation (binding by large pre-formed complex)
  2. RNA polymerase II holoenzyme
  3. combo of first 2
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4
Q

Endo 16 gene

  1. A activated
  2. G & B
  3. F & E
  4. DC
  5. F, E, & DC
A

basal promoter is activated in early development to form mesoderm tissues (muscle & skeleton)

  • later, transcription is repressed to allow for development of ectoderm (CNS and skin)
    1. early development (vegetal plate)
    2. later development (mesoderm)
    3. repression (ectoderm)
    4. repression (skeletogenic mesenchyme)
    5. LiCi treatment (ectoderm and skeletogenic mesenchyme)
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4
Q

Proteasome

  • reduces concentration of (co)activators, providing additional transcriptional control
  • e.g.?
A

large protein complex which breaks down/digests proteins to stop their function

  • effect?
  • e.g. LIM family of transcription factors can be tagged with ubiquitin and broken down inside cell
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4
Q

activator, directly phosphorylated by protein kinase A (PKA) from hormonal signals that act through receptors increasing cAMP levels

-dimerizes after phosphorylated b/c of shape change; stimulates transcription with CBP

A

CREB (cAMP response element [CRE]-binding protein)

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5
Q

2 categories of transcriptional activators

  1. e.g. zince finger (Sp1 & TFIIIA), homeodomain (HD) w/ helix-turn-helix (Lambda phage repressor), & bZIP and bHLH (Myo D)
  2. acidic, glutamine-rich, and proline-rich domains help drive RNA polymerase activation (e.g. CREB & Elk-1)
A
  1. DNA-binding
    - structures? e.g?
  2. transcription-activating domains
    - structures? e.g.?
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5
Q

provided evidence for holoenzyme complexbeing recruited to promoter in yeast

  • how?
  • TFIID was not part of holoenzyme but recruited simultaneously with holoenzyme to promoter
A

Ptashne et al 1995

  • GAL11-P (part of holoenzyme) could directly bind GAL4
  • unique?
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6
Q

insulators (GAGA boxes)

type 1=enhancer-blocking: prevent enhancer or protein triggering transcription

  • 2 methods?
  • e.g. Tr1

type 2=blocking “gene silencing”: block chromatin from covering/interfering w/ gene expression

A

sequences of DNA that function to help control the specificity of gene expression (sequence?)

-2 types activity?

method 1=stop activator or other associated proteins from contacting promoter (blocks DABPolFEH) (e.g.?)

method 2=DNA looping by protein dimerization, preventing activator and enhancer from stimulating transcription

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7
Q

basal promoter is activated in early development to form mesoderm tissues (muscle & skeleton)

  • later, transcription is repressed to allow for development of ectoderm (CNS and skin)
    1. early development (vegetal plate)
    2. later development (mesoderm)
    3. repression (ectoderm)
    4. repression (skeletogenic mesenchyme)
    5. LiCi treatment (ectoderm and skeletogenic mesenchyme)
A

Endo 16 gene

  1. A activated
  2. G & B
  3. F & E
  4. DC
  5. F, E, & DC
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7
Q

bend DNA to enhance transcription by forming an enhanceosome

A

NF-kB, ATF

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8
Q

bind zinc and steroid hormones (i.e. ?) after which receptor complex (HR) moves into nucleus and activates transcription by binding hormone response elements (HREs) in the DNA

-3 types: types 1 & 2?

A

nuclear receptors

  • i.e. testosterone, estrogen, & glucocorticoids
  • 1=glucocorticoid; 2=thyroid hormone
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8
Q

coactivator with CREB, binds downstream of signaling events to regulate nerve cell development (synaptic plasticity)

  • also coactivator for?
  • with receptor and steroid receptor coactivators (SCR) to assemble transcription machinery and activate transcription
  • additional function?
A

CBP

  • hormone receptors and MAPK-response activators (ERK)
  • interacts with?
  • acetylate histone proteins to enhance gene transcription
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9
Q

NF-kB, ATF

A

bend DNA to enhance transcription by forming an enhanceosome

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10
Q

determined concentration of transcription factor proteins of yeast cell; found that weren’t in equal amounts

  • suggests?
  • discovered protein coactivators (mediators) in 1991 that further stimulate transcription that’s been activated by an activator (GAL4)
  • how?
A

Kornberg et al (x2)

  • preinitiation complex may assemble either as holoenzyme or in a sequence depending on promoter/gene
  • used strand of DNA containing a promoter and GAL4-binding site and measured the synthesis of RNA in vitro
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11
Q

function to recruit & trigger transcription factor and polymerase binding to promoter: DNA-binding, transcription-activating, & dimerization

-essential preinitiation targets?

A

activators: 3 activator domains
- TFIID & TFIIB

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12
Q
  1. DNA-binding
    - structures? e.g?
  2. transcription-activating domains
    - structures? e.g.?
A

2 categories of transcriptional activators

  1. e.g. zince finger (Sp1 & TFIIIA), homeodomain (HD) w/ helix-turn-helix (Lambda phage repressor), & bZIP and bHLH (Myo D)
  2. acidic, glutamine-rich, and proline-rich domains help drive RNA polymerase activation (e.g. CREB & Elk-1)
How well did you know this?
1
Not at all
2
3
4
5
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14
Q

Kornberg et al (x2)

  • preinitiation complex may assemble either as holoenzyme or in a sequence depending on promoter/gene
  • used strand of DNA containing a promoter and GAL4-binding site and measured the synthesis of RNA in vitro
A

determined concentration of transcription factor proteins of yeast cell; found that weren’t in equal amounts

  • suggests?
  • discovered protein coactivators (mediators) in 1991 that further stimulate transcription that’s been activated by an activator (GAL4)
  • how?
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15
Q
  1. increases affinity for DNA
  2. provides sustained DNA binding/transcription
  3. enhances their function at low concentrations
A

activator dimerization (x3)

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17
Q

glucocorticoid receptor (x3)

-Hsp90 released and receptor complex binds to glucocorticoid response elements (GREs)

A

type I receptor retained in cytoplasm by Hsp90 protein until it binds to glucocorticoid

  • receptor complex associates with DNA via helical region and can dimerize w/ second receptor complex to activate transcription of hormonally-responsive genes
  • hormone binding effect?
How well did you know this?
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18
Q

sequences of DNA that function to help control the specificity of gene expression (sequence?)

-2 types activity?

method 1=stop activator or other associated proteins from contacting promoter (blocks DABPolFEH) (e.g.?)

method 2=DNA looping by protein dimerization, preventing activator and enhancer from stimulating transcription

A

insulators (GAGA boxes)

type 1=enhancer-blocking: prevent enhancer or protein triggering transcription

  • 2 methods?
  • e.g. Tr1

type 2=blocking “gene silencing”: block chromatin from covering/interfering w/ gene expression

18
Q

regulate transcription/gene expression to control growth, division, and metabolism

-e.g.?

A

signal transduction pathways

-e.g. extracellular growth factor (EGF) activating MAPK (ERK) pathway & gene transcription, causing cell growth and division

19
Q

nuclear receptors

  • i.e. testosterone, estrogen, & glucocorticoids
  • 1=glucocorticoid; 2=thyroid hormone
A

bind zinc and steroid hormones (i.e. ?) after which receptor complex (HR) moves into nucleus and activates transcription by binding hormone response elements (HREs) in the DNA

-3 types: types 1 & 2?

20
Q

enhance transcription from close promixity to promoter: bind minor groove of DNA, bending DNA

-e.g.?

A

architectural transcriptional activators

-e.g. LEF-1, Ets family (Ets-1 & Elk-1), & CREB

21
Q

proto-oncogene proteins and cell signaling targets in bZIP family of activators; they dimerize

  • dimerized form?
  • tissue plasminogen activator (TPA) response element (TRE)
A

Jun & Fos

-AP1, specifically binds TGACTCA sequence (called?)

22
Q

CREB (cAMP response element [CRE]-binding protein) (x3)

A

activator, directly phosphorylated by protein kinase A (PKA) from hormonal signals that act through receptors increasing cAMP levels

-dimerizes after phosphorylated b/c of shape change; stimulates transcription with CBP

23
Q

Myo D (bHLH protein) (x2)

A

Helix 2 functions as dimerization domain, helix 1 grasps DNA in its major groove w/ basic region (bends DNA)

-transcriptional activator w/ essential role in muscle cell development

23
Q

Ptashne et al 1995

  • GAL11-P (part of holoenzyme) could directly bind GAL4
  • unique?
A

provided evidence for holoenzyme complexbeing recruited to promoter in yeast

  • how?
  • TFIID was not part of holoenzyme but recruited simultaneously with holoenzyme to promoter
24
Q

H. Weintraub et al

A

determined the structure of the bHLH protein Myo D (looks similar to bZIP proteins)

25
Q
  1. sequential complex formation (binding by large pre-formed complex)
  2. RNA polymerase II holoenzyme
  3. combo of first 2
A

3 models of recruitment/activation

26
Q

zinc finger protein and yeast activator that controls galactose metabolism

  • binds to specific upstream activating sequences (UASGs) in major groove of DNA w/ hydrogen bonds
  • key amino acids? (bind cysteine and guanine)
  • dimerizes (where?) & complexes w/ 2 zinc ions and short alpha-helix that binds to DNA major groove
  • dimerized regions form…?
A

GAL 4

  • K18/20/23, R15, & Q9
  • residues 50-94
  • form parallel coiled-coil in minor groove of DNA
27
Q

Ras activation (G-protein)

-active ERK can then enter nucleus and specifically phosphorylate the transcription factor Elk-1 to enhance transcription and cell division

A

triggers signaling cascade through kinases Raf-1 and MEK that directly phosphorylate/activate ERK

-then what?

28
Q

TRAP (thyroid-hormone-receptor-associated protein), CRSP (cofactor required for Sp1 activation) and CBP (ID’d by?)

A

coactivators

-ID’d by Ryan Goodman et al

31
Q

bind DNA using zinc ions to alter its helical conformation in order for it to fit within the major groove of DNA

  • e.g.?
  • contains 2 cysteine & 2 histidine residues + basic residues w/ alpha-helix that contacts DNA by direct amino acid-base bonding
  • mouse e.g.?
A

zinc finger domains

  • e.g. TFIIIA
  • structure?
  • mouse e.g. Zif268 w/ 3 zinc fingers
32
Q

triggers signaling cascade through kinases Raf-1 and MEK that directly phosphorylate/activate ERK

-then what?

A

Ras activation (G-protein)

-active ERK can then enter nucleus and specifically phosphorylate the transcription factor Elk-1 to enhance transcription and cell division

34
Q

bZIP (leucine zipper) & bHLH (basic helix-loop-helix)

  • basic region of the protein that directly binds the DNA (with positive charge)
  • contains 2 parallel helices that function like a zipper that grasps the DNA by fitting in the major groove
A

can bind both DNA and dimerize; may regulate amio acid metabolism in yeast

  • b=?
  • bZIP motif?
35
Q

signal transduction pathways

-e.g. extracellular growth factor (EGF) activating MAPK (ERK) pathway & gene transcription, causing cell growth and division

A

regulate transcription/gene expression to control growth, division, and metabolism

-e.g.?

36
Q

large protein complex which breaks down/digests proteins to stop their function

  • effect?
  • e.g. LIM family of transcription factors can be tagged with ubiquitin and broken down inside cell
A

Proteasome

  • reduces concentration of (co)activators, providing additional transcriptional control
  • e.g.?
37
Q

combination of activators dictating how a gene is expressed

  • relies on precise actions of multiple enhancers to precisely activate a specific gene at a specific time
  • e.g.?
A

combinatorial code

-e.g. Endo16 gene in sea urchins w/ multiple enhancers regulated by multiple activators; enables proper development of muscle, gut, and connective tissues

38
Q

activator dimerization (x3)

A
  1. increases affinity for DNA
  2. provides sustained DNA binding/transcription
  3. enhances their function at low concentrations
39
Q

type I receptor retained in cytoplasm by Hsp90 protein until it binds to glucocorticoid

  • receptor complex associates with DNA via helical region and can dimerize w/ second receptor complex to activate transcription of hormonally-responsive genes
  • hormone binding effect?
A

glucocorticoid receptor (x2)

-Hsp90 released and receptor complex binds to glucocorticoid response elements (GREs)

40
Q

combinatorial code (x2)

-e.g. Endo16 gene in sea urchins w/ multiple enhancers regulated by multiple activators; enables proper development of muscle, gut, and connective tissues

A

combination of activators dictating how a gene is expressed

  • relies on precise actions of multiple enhancers to precisely activate a specific gene at a specific time
  • e.g.?
42
Q

activators: 3 activator domains
- TFIID & TFIIB

A

function to recruit & trigger transcription factor and polymerase binding to promoter: DNA-binding, transcription-activating, & dimerization

-essential preinitiation targets?

44
Q

GAL 4

  • K18/20/23, R15, & Q9
  • residues 50-94
  • form parallel coiled-coil in minor groove of DNA
A

zinc finger protein and yeast activator that controls galactose metabolism

  • binds to specific upstream activating sequences (UASGs) in major groove of DNA w/ hydrogen bonds
  • key amino acids? (bind cysteine and guanine)
  • dimerizes (where?) & complexes w/ 2 zinc ions and short alpha-helix that binds to DNA major groove
  • dimerized regions form…?
46
Q

architectural transcriptional activators

-e.g. LEF-1, Ets family (Ets-1 & Elk-1), & CREB

A

enhance transcription from close promixity to promoter: bind minor groove of DNA, bending DNA

-e.g.?

47
Q

determined the structure of the bHLH protein Myo D (looks similar to bZIP proteins)

A

H. Weintraub et al

48
Q

utilized GAL4 to trigger formation of preinitiation complex and transcription in presence of TFIIB through recruitment of TFIIE & TFIIF/RNA Polymerase to preinitiation complex

A

Green et al

49
Q

Green et al

A

utilized GAL4 to trigger formation of preinitiation complex and transcription in presence of TFIIB through recruitment of TFIIE & TFIIF/RNA Polymerase to preinitiation complex

50
Q

CBP

  • hormone receptors and MAPK-response activators (ERK)
  • interacts with?
  • acetylate histone proteins to enhance gene transcription
A

coactivator with CREB, binds downstream of signaling events to regulate nerve cell development (synaptic plasticity)

  • also coactivator for?
  • with receptor and steroid receptor coactivators (SCR) to assemble transcription machinery and activate transcription
  • additional function?
51
Q

zinc finger domains

  • e.g. TFIIIA
  • structure?
  • mouse e.g. Zif268 w/ 3 zinc fingers
A

bind DNA using zinc ions to alter its helical conformation in order for it to fit within the major groove of DNA

  • e.g.?
  • contains 2 cysteine & 2 histidine residues + basic residues w/ alpha-helix that contacts DNA by direct amino acid-base bonding
  • mouse e.g.?
52
Q

can bind both DNA and dimerize; may regulate amio acid metabolism in yeast

  • b=?
  • bZIP motif?
A

bZIP (leucine zipper) & bHLH (basic helix-loop-helix)

  • basic region of the protein that directly binds the DNA (with positive charge)
  • contains 2 parallel helices that function like a zipper that grasps the DNA by fitting in the major groove
53
Q

coactivators

-ID’d by Ryan Goodman et al

A

TRAP (thyroid-hormone-receptor-associated protein), CRSP (cofactor required for Sp1 activation) and CBP (ID’d by?)

54
Q

Helix 2 functions as dimerization domain, helix 1 grasps DNA in its major groove w/ basic region (bends DNA)

-transcriptional activator w/ essential role in muscle cell development

A

Myo D (bHLH protein) (x2)

Molecular Biology (13 decks)

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