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Molecular Biology Test 1 > Chapter 28, 29 > Flashcards

Chapter 28, 29 Flashcards

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1
Q

What is required for gene transcription in eukaryotic cells?

A

Chromatin must be in an open structure (non-condensed)`
Promoter must be nucleosome-free
Gene must include a core promoter and start point
RNA Polymerase binds
Basal transcription machinery binds

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2
Q

Epigenetics

A

Inheritable changes in a cell’s phenotype that is independent of changes to the primary DNA sequence or genotype.

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3
Q

Epigenetics

A

Inheritable changes in a cell’s phenotype that is independent of changes to the primary DNA sequence or genotype.

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4
Q

Mechanism associated with Epigenetics:

A
  1. Histone Post-translational Modifications
  2. DNA Methylation
  3. Regulatory RNA (non-coding RNA)
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5
Q

Transcription factors turn on genes by:

A 
• Compete with histones as observed
during Replication
• Bind DNA targets even in closed
chromatin states
• Recruit RNA Polymerase and Basal
Transcription Apparatus directly
• Form a Complex with Other
Transcription Factors called Coregulatory
proteins (specifically:
coactivators or corepressors)
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6
Q

Transcription factors turn on genes by:

A
  • Compete with histones as observed during Replication
  • Bind DNA targets even in closed chromatin states
  • Recruit RNA Polymerase and Basal Transcription Apparatus directly
  • Form a Complex with Other Transcription Factors called Coregulatory proteins (coactivators or corepressors)
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7
Q

Activator (definition)

A

Transcription Factors proteins that stimulate gene transcription.

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8
Q

Activators can be divided into 3 functional classes:

A
  1. True Activators
  2. Anti-Repressors
  3. Architectural Proteins
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9
Q

Activators can be divided into 3 functional classes:

A
  1. True Activators
  2. Anti-Repressors
  3. Architectural Proteins
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10
Q

True Activators:

A

Making contact, direct or indirect, with the basal apparatus to activate transcription.

Regulated by:

  1. Tissue Specific Expression
  2. Post-translational Modification
  3. Ligand Binding
  4. Subcellular Localization
  5. Association with Binding Partner
  6. Cleavage from Inactive Precursor
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11
Q

True Activators:

A

Making contact, direct or indirect, with the basal apparatus to activate transcription.

Regulated by:

  1. Tissue Specific Expression
  2. Post-translational Modification
  3. Ligand Binding
  4. Subcellular Localization
  5. Association with Binding Partner
  6. Cleavage from Inactive Precursor
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12
Q

Anti-Repressor Activators:

A

Causes the opening chromatin

  • Recruit histone modifying and/or chromatin remodeling proteins.
  • No function on the DNA.
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13
Q

Architectural Activators:

A

Bind DNA and promote a structural change, commonly a bend

  • Functions to promote a physical change in the DNA structure but no additional function.
  • Enhances interaction between the complex of proteins required for gene transcription
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14
Q

Repressor (definition)

A

Proteins that inhibit gene transcription.

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15
Q

“True” Repressors

A

a. Sequester Activator
b. Mask Activation Domain of an Activator
c. Enhanced Subcellular Localization
d. Competition for an Enhancer

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16
Q

Anti-Repressor Repressor

A

Causes the closed chromatin

Recruits histone modifying and/or chromatin remodeling proteins

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17
Q

Architectural Repressors

A

Bind DNA and promote a structural change, commonly a bend

- enhances interaction between the complex of proteins that inhibit gene transcription

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18
Q

Activator (definition)

A

Transcription Factors proteins that stimulate gene transcription.
Includes independent domains for:
(1) DNA-binding
(2) transcription-activation activities.

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19
Q

Anti-Repressor Activators:

A

Causes the opening chromatin
Recruit histone modifying and/or chromatin remodeling proteins.
No function on the DNA.

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20
Q

Architectural Activators:

A

Bind DNA and promote a structural change, commonly a bend
Functions to promote a physical change in the DNA structure but no additional function.
Enhances interaction between the complex of proteins required for gene transcription

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21
Q

Architectural Repressors

A

Bind DNA and promote a structural change, commonly a bend

Enhances interaction between the complex of proteins that inhibit gene transcription

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22
Q

The role of the DNA-binding domain of an Activator

A

Bring the transcription-activation domain in the vicinity of the basal apparatus (promote RNAP binding).

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23
Q

Activators interact with:

A
  • TAFs in TFIID complex

- TFIIB

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24
Q

Activator/Basal Apparatus interaction:

A
  • stabilizes basal apparatus
  • increase RNAP binding to promoter
  • increase transcription efficiency
    ex. CTD phosphorylation
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25
Q

Coactivator protein

A

Activator that lacks an effective transcription-activating domain works concurrently with a coactivator protein.
Does NOT bind DNA directly.

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26
Q

Zinc finger

A 
DNA-binding motif 
Typifies a class of transcription factor that contain one or more zinc ions to help stabilize the protein and insert
into the major groove of DNA
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27
Q

Steroid receptor

A

Different type of zinc finger transcription factor that

is activated by binding of a steroid ligand.

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28
Q

Helix-turn-helix

A

DNA-binding motif
Arrangement of two α-helices that form a site that binds to
DNA, one fitting into the major groove of DNA and other lying across it.

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29
Q

Helix-loop-helix

A

DNA-binding motif
Responsible for dimerization of a class of transcription factors called HLH proteins.
- two basic HLH can dimerize and bind DNA
- a nonbasic HLH can dimerize but the dimer cannot bind DNA

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30
Q

Leucine zipper

A

Class of transcription factors that includes:
- a hydrophobic face with leucine resides that serves as the
dimerization motif
- a basic zipper (bZIP) that is responsible for binding DNA.

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31
Q

Leucine zipper

A

Class of transcription factors that includes:
- a hydrophobic face with leucine resides that serves as the
dimerization motif
- a basic zipper (bZIP) that is responsible for binding DNA.

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32
Q

Chromatin Remodeling

A 
Reorganization or displacement of nucleosomes to facilitate access to the DNA. 
Governed by two processes:
1. chromatin-remodeling complexes
= nucleosome displacement
2. histone-modifying complexes =
nucleosome reorganization
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33
Q

Chromatin-remodeling complexes

A

Nucleosome displacement

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34
Q

Histone-modifying complexes

A

Nucleosome reorganization

35
Q

Chromatin Remodeling

A

Reorganization or displacement of nucleosomes to facilitate access to the DNA.

Governed by two processes:

  1. chromatin-remodeling complexes
  2. histone-modifying complexes

Remodeling complexes can alter, slide, or displace nucleosomes by ATP hydrolysis

36
Q

Histone-modifying complexes

A

Nucleosome reorganization

37
Q

SWI/SNF

A

“Twist” releases a small DNA region from the nucleosome surface that can be repositioned.

38
Q

INO80/SWR1

A

Can cause the exchange of histone H2A/H2B dimers with a histone variant.

39
Q

INO80/SWR1

A

Can cause the exchange of histone H2A/H2B dimers with a histone variant.

40
Q

How remodeling complex is targeted to specific chromatin sites?

A

Remodeling complexes are recruited to promoters by sequence-specific activators or repressors.
The factor may be released once the remodeling complex has bound.

41
Q

How remodeling complex is targeted to specific chromatin sites?

A

Remodeling complexes are recruited to promoters by sequence-specific activators or repressors.
The factor may be released once the remodeling complex has bound.

42
Q

Transcription of PHO 5 gene

A

Change in nucleosome organization required for gene transcription with yeast PHO5 gene.
Phosphate starvation activates the activators Pho4 and Pho2 to initiate transcription of the PHO5.
Two binding sites for each activator.
Requires chromatin remodelers to assess 2nd binding site and clear PHO5 promoter.

43
Q

Nucleosome free regions

A

Promoters contain nucleosome free regions (NFR) flanked by nucleosomes containing the H2A variant H2AZ (Htz1 in yeast).

44
Q

Nucleosome free regions (NFR)

A

Promoters contain nucleosome free regions (NFR) flanked by nucleosomes containing the H2A variant H2AZ.

45
Q

The nucleosome can potentiate interaction between an activator and its DNA binding site by:

A
  • Changing the rotational position of the nucleosomal DNA.

- Enhancing contact between the activator and the histones, co-activators, and/or remodeling proteins.

46
Q

Histone acetylation is

A

Associated with activation of gene expression.

47
Q

Histone acetyltransferase (HAT)

A

An enzyme that acetylates lysine residues in histones (or other proteins).
Many transcription activators have HAT activity or associate with HATs in large multi-protein
complexes.

48
Q

Histone deacetylase (HDAC)

A

Enzyme that removes acetyl groups from histones
Repressors often associate with HDACs in large multi-protein complexes to prevent transcription.
• Example of Repressor Complex in yeast.
• Equivalent in mammalian cells:
- DNA-binding: Mad/Max
- Co-repressor: Sin3
- Deacetylase: HDAC1 or HDAC2

49
Q

Histone deacetylase (HDAC)

A

Enzyme that removes acetyl groups from histones

Repressors often associate with HDACs in large multi-protein complexes to prevent transcription.

50
Q

Example of Repressor Complex in yeast

A
  • DNA-binding: Mad/Max
  • Co-repressor: Sin3
  • Deacetylase: HDAC1 or HDAC2
51
Q

Protein that contain a BROMOdomain

A

Recognize acetylated sites on histones to interact with chromatin.
Example: SWI/SNF chromatin remodeling protein

52
Q

Histone methylation associated with

A

Either activation or repression of transcription.
• Ex. H3K4me3 = activation
• Ex. H3K9me = repression

53
Q

H3K4me3

A

Activation

54
Q

H3K9me

A

Repression

55
Q

H3K9me

A

Repression

56
Q

Histone methyltransferase (HMT)

A

An enzyme that methylates a histone tail.

57
Q

Histone methyltransferase (HMT)

A

An enzyme that methylates a histone tail.

58
Q

HIstone demethylase (HDM)

A

An enzyme that removes the methyl group from the histone tail.

59
Q

Protein that contain a BROMOdomain recognize

A

Acetylated sites on histones to interact with chromatin.

Example: SWI/SNF chromatin remodeling protein

60
Q

HIstone demethylase (HDM)

A

An enzyme that removes the methyl group from the histone tail.

61
Q

Protein that contain a CHROMOdomain recognize

A

Methylated sites (lysine or arginine) on histones to interact with chromatin.

62
Q

Protein that contain a CHROMOdomain recognize

A

Methylated sites (lysine or arginine) on histones to interact with chromatin.

63
Q

Formation of Heterochromatin occurs in two steps:

A
  1. Nucleation at a specific site.

2. Propagation of the inactive structure.

64
Q

Position effect variegation (PEV)

A

Silencing of a gene due to its close proximity to

heterochromatin.

65
Q

Position effect variegation (PEV)

A

Silencing of a gene due to its close proximity to

heterochromatin.

66
Q

Propagation of the inactive heterochromatin structure is

dictated by:

A
  1. Availability of silencing proteins.
  2. Activation of promoters in the region.
  3. Presence of insulator/boundary sequence.
    • Example: Drosophila eye color
67
Q

Polycomb group proteins (Pc-G)

A

Do NOT initiate repression but are responsible for maintaining it through cell divisions.
Broken into functional complexes:

68
Q

Polycomb Response Element

A

In Drosophila, Pc-G binds a Polycomb Response Element
(PRE) DNA sequence.
The PRE = nucleation center from which Pc-G proteins propagate inactive structure.

69
Q

Dosage compensation

A

Mechanisms that compensates for the discrepancy between the presence of two X chromosomes in one sex but only one X chromosome in the other sex.

70
Q

Mammalian X chromosomes in females

A

Example of facultative heterochromatin as 1 X-chromosome is euchromatic and 1 X-chromosome is heterochromatic.

71
Q

Mammalian X-chromosomes in females

A

Example of facultative heterochromatin as 1 X-chromosome is euchromatic and 1 X-chromosome is heterochromatic.

72
Q

Xic

A

The Xic (X-inactivation center) is a cis-acting region on the X-chromosome that is necessary to ensure:
- Only one X-chromosome remains active
- Includes the Xist gene, which codes regulatory RNA (non-coding RNA).
Xist ncRNA is regulated in a negative manner by Tsix, its anti-sense partner.

73
Q

Xist

A 
Coats the X-chromosome
Excludes the transcription machinery
Recruits the Polycomb complex
Triggers histone modifications
Incorporates X-specific histone variant, macroH2A
Promoter DNA is methylated
74
Q

Xic

A

The Xic (X-inactivation center) is a cis-acting region on the X-chromosome that is necessary to ensure:

  • Only one X-chromosome remains active
  • Includes the Xist gene, which codes regulatory RNA (non-coding RNA).
75
Q

Xist

A
  1. Coats the X-chromosome
  2. Excludes the transcription machinery
  3. Recruits the Polycomb complex
  4. Triggers histone modifications
  5. Incorporates X-specific histone variant, macroH2A
  6. Promoter DNA is methylated
76
Q

Histone Methylation connected to DNA Methylation in a

positive feedback loop.

A
  1. HP1 binds H3K9me sites.
  2. HP1 recruits DNMT1
  3. DNMT1 methylates DNA.
  4. DNMT1 interacts with HMT.
  5. HMT propagates H3K9me.
77
Q

Histone Methylation connected to DNA Methylation in a

positive feedback loop.

A
  1. HP1 binds H3K9me sites.
  2. HP1 recruits DNMT1
  3. DNMT1 methylates DNA.
  4. DNMT1 interacts with HMT.
  5. HMT propagates H3K9me.
78
Q

CpG islands

A

1-2 kbp stretches of CG dinucleotides
Frequently located in gene promoter regions.
All housekeeping genes that are constitutively expressed have CpG islands

79
Q

Methylation of a CpG island

A

Prevents activation of a promoter within it

Proteins bind to methylated CpG doublets.

80
Q

Methylation of a CpG island

A

Prevents activation of a promoter within it

Proteins bind to methylated CpG doublets.

81
Q

Maintenance methyltransferase:

A

Converts hemimethylated sites to fully methylated site.

82
Q

De novo methyltransferase:

A

Adds methyl group to unmethylated site.

83
Q

Imprinting:

A

Specific DNA methylation pattern in the germ cells, produces different properties in the embryo depending on whether the maternal or paternal allele was acquired.

84
Q

Imprinted allele

A

Allele that is silenced due DNA methylation.

Molecular Biology Test 1 (4 decks)

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