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Molecular Biology > Control of Gene Expression 1: Transcriptional Controls (lecture 9) > Flashcards

Control of Gene Expression 1: Transcriptional Controls (lecture 9) Flashcards

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1
Q

if skin cells are isolated from adult frogs and the nucleus implanted into a de-nucleated cell then a _____ embryo is formed

A

normal

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2
Q

Different cells contain the same genes about _____ in humans but they express different sets of ___

A

25,000 in humans, proteins

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3
Q

Each cell has the same genome, but differentiation in cells depends on

A

changes in gene expression

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4
Q

Common proteins are called _______ what is an example

A

housekeeping proteins, glucose metabolism

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5
Q

what is an example of a specifically limited protein

A

hemoglobin

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6
Q

The typical human cell expresses _____ of its 25,000 genes but level of gene expression varies. What is an example

A

30-50%, ex. fingerprint expression profiles, microarrays or RNA sequence

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7
Q

What are some of the ways to control gene expression

A
  • transcriptional control
  • RNA processing control
  • RNA transport and localization control
  • Translation control
  • mRNA degradation control
  • translation control
  • protein activity control
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8
Q

Gene regulation requires

A
  • short stretch of DNA of defined sequence- recognition sites for DNA binding proteins
  • Gene regulatory proteins- transcription factors that will bind and activate gene
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9
Q

Recognition sequences for regulatory proteins ex.

A

GATA1: TGATAG

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10
Q

Heterodimers are often formed from tow different transcription regulators. Transcription regulators may form heterodimers with more than one patterned proteins, the same transcription regulator can be “reused” to breast several

A

distinct DNA-binding specificities

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11
Q

What does the “logo” shows that the protein can

A

recognize a collectin of closely related DNA sequences and gives the preferred nucleotide pair at each position.

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12
Q

Recognition sequences can be ___ or ___ to the first exon

A

Proximal or distal

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13
Q

Regulatory proteins recognize and bind to bases in the ____ groove

A

major

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14
Q

The ____ groove presents a specific face for each of the specific base pairs

A

Major

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15
Q

A gene regulatory protein recognizes a

A

specific DNA sequence

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16
Q

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

A

complimentary

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17
Q

The gene regulatory protein makes a series of contacts with the DNA involving ____ possible configurations

A

4

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18
Q

What are the 4 possible configurations of base pairs for recognition of gene protein regulator

A
  • possible hydrogen bond donor
  • Possible hydrogen bond acceptor
  • methyl groups
  • Hydrogen atom
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19
Q

a typeical gene regulatory protein-DNA interaction involves _____ interactions

A

10-20

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20
Q

The parts of a DNA transcription factor: sequence specific transcription factors are _____

A

modular

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21
Q

What is the sequence of specific transcription factors Modules

A

N-terminus—DNA binding module— Dimerization module—Activation module– Regulatory module– C-terminus

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22
Q

Does every transcription factor have all the modules

A

no

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23
Q

What modules must a transcription factor have

A

DNA-binding module and Activation module

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24
Q

What is the function of the dimerization module

A

forms dimer with other protein subunits

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25
Q

What 2 modules can transcription factors have but don’t have to have

A

Dimerization module and Regulatory module

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26
Q

What is the function of the regulatory module

A

regulate transcription factor

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27
Q

DNA-binding domain structural motifs

A
  • Helix-turn-helix
  • Zinc finger motif
  • Leucine zipper
  • Helix-loop-helix
    (also homeodomain and beta-sheet)
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28
Q

What is the simplest, most common DNA-binding motif

A

Helix-turn-helix

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29
Q

Explain helix-turn-helix

A

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

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30
Q

The longer helix in a helix turn helix equals the

A

recognition module- DNA binding module-fits into major groove

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31
Q

Side changes of ____ in the helix turn helix recognize ____

A

Amino acids in the helix turn helix DNA motif

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32
Q

The helix turn helix proteins bind DNA as ____ in which the two copies of the recognition helix are separated by exactly one turn of the DNA helix

A

Dimers

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33
Q

The since finger proteins contain one or more ___ atoms as structural components

A

zinc

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34
Q

zinc finger proteins bind DNA in the ____ groove

A

major

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35
Q

Zinc finger domains found in tandem ____

A

clusters

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36
Q

What is the function of the zinc in zinc finger

A

stabilizes interactions with DNA

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37
Q

Leucine zipper motif has ____ DNA binding domains

A

-Two alpha helical DNA binding domains

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38
Q

Leucine zipper motif Dimerizes through ____ zipper region

A

leucine zipper region

39
Q

the leucine zipper motif is named because of the way the

A

two alpha helices, one from each monomer, are joined together to form a short coiled-coil.

40
Q

The leucine zipper proteins bind DNA as dimers where the two long alpha helices are held together by interactions between _______ amino acid chains

A

hydrophobic

41
Q

The leucine zipper has a leucine residue every ___ amino acids down one side of the alpha helix in dimerization form: forms zipper structure

A

7

42
Q

The dimerization of the leucine zipper grapes _____ like a clothespin

A

DNA

43
Q

The activation domain overlaps _____ domain in a leucine zipper

A

dimer

44
Q

The helix-loop-helix motif consists of a

A

short alpha helix connected by a loop to a second, longer alpha helix.

45
Q

The helix-loop-helix motif can occur as ____ or _____

A

homodimers or heterodimers

46
Q

what are the three domains or modules to the helix-loop-helix motif

A

DNA binding domain, dimerization domain, activation domain

47
Q

Hereditary spherocytosis (HS) is an example of a ______ transcription factor mutation leading to disease

A

Zinc finger

48
Q

__________ is a hemolytic anemia characterized by spherical and fragile red blood cells that lyse and release hemoglobin

A

Hereditary spherocytosis (HS)

49
Q

What is the clinical presentation of Hereditary spherocytosis (HS)

A

hemolysis, anemia, splenomegaly

50
Q

The HS clinical presentation ranges from ____ to ___ anemia and can be fatal

A

mild to severe

51
Q

Hereditary spherocytosis (HS) is caused by mutations in genes for the erythrocyte membrane skeleton of _______

A

red blood cells- not making enough protein

52
Q

_________ is the most common hereditary anemia in people of northern european descent (incidence 1/2,000)

A

Hereditary Spherocytosis (HS)

53
Q

Hereditary Spherocytosis is _____ inherited

A

Dominantly

54
Q

Hereditary Spherocytosis can be mutation in zinc finger protein gene _____

A

Klf1 (Kruppel-like factor 1)

55
Q

______ zinc finger protein binds to promoters of all genes in EMS-and turns them on

A

KLF1

56
Q

how many zing finger domains are there for KLF1

A

3

57
Q

Klf1 has ___ exons

A

3, which encodes 3 zinc finger domains

58
Q

A non-functioning KLF1 Zn finger protein leads to no ___

A

no EMS protein made and thus leads to HS (hereditary spherocytosis)

59
Q

____ are critical amino acids for DNA binding in EMC proteins

A

RER

60
Q

HS mutation: GAA to ____ or Glu to ___ in exon 3 (zinc finger domain 2)

A

GAT, Asp

61
Q

_____ is the wild type DNA binding motif in exon 3 (zinc finger domain2) and the mutant form _____ leads to HS

A
  • RER (Arg-Glu-Arg)

- RDR (Arg-Asp-Arg)

62
Q

Normal KLF1 binds to DNA and

A

unwinds DNA causing transcription

63
Q

HS KLF1 zinc finger binds to

A

opposite strand of DNA than the normal KLF1 so DNA cannot unwind and thus no transcription

64
Q

Ways to identify Transcription factors

A
  • Detection of sequence- specific DNA binding proteins
  • Gel mobility shift assay
  • EMSA: electrophoretic mobility shift assay
  • use radioactive DNA from known promoter
  • mix radioactive DNA fragment (regulatory DNA sequence) with protein extract from cell
  • Run electrophoretic gel
  • Proteins with DNA attached migrate according to size
  • see shift of radioactive bad when protein is bound to DNA
  • Isolate protein to identify
  • affinity chromatography
  • isolate DNA binding protein
  • purification of sequence specific binding proteins
65
Q

Technique that allows identification of the sites in the genome that a known regulatory protein binds to

A

CHIP: chromatin Immuno-precipitation

66
Q

is Chromatin immunoprecipitation done on living cells

A

yes

67
Q

DNA region involved in regulating and initiating transcription of a gene

A

Gene control region

68
Q

Where transcription factors and RNA polymerase II assembles

A

Promoter

69
Q

of the 25,000 human genes ___% (or _____ genes) encode gene regulatory proteins

A

8% or 2,000 genes

70
Q

The gene control region contains the promoter and regulatory sequences to which

A

regulatory proteins bind to control rate of assembly process at the promoter

71
Q

____ and ____ assemble at the promoter

A

RNA polymerase and general transcription factors

72
Q

Gene regulatory proteins (activators or repressors) bind to regulatory sequences which can be

A

adjacent, far upstream or in introns downstream of the promoter

73
Q

DNA looping and a mediator complex allow the gene regulatory proteins to interact with the proteins that assemble at the

A

promoter

74
Q

The ____ serves as an intermediary between gene and regulatory proteins and RNA polymerase II

A

Mediator

75
Q

Nucleosome remodeling and histone removal favors ____ by

A

transcription by increasing the accessibility of DNA to proteins

76
Q

Histone acetylation makes it easier to ____ histones

A

remove

77
Q

what are some of the different ways gene repressors inhibit transcription

A
  • competitive DNA binding
  • Masking activation surface (both proteins bind to DNA but the repressor binds to the activation domain of the activator protein)
  • Direct interaction with the general transcription factors (the repressor binds to DNA and blocks assembly of general transcription factors)
  • Recruitment of chromatin remodeling complexes (the repressor recruits a chromatin remodeling complex which returns the promoter to the pre transcriptional nucleosome state
  • Recruitment of histone deacetylases (repressor attracts a histone deacetylase to the promoter-harder to remove deacetylated histones and open up DNA)
  • Recruitment of histone methyl transferase (repressor attracts a histone methyl transferase which methylates histones.)(these methylated histones are bound to proteins which act to maintain chromatin in a transcriptionally silent form)
78
Q

Gene regulatory proteins assemble into _____ on DNA

A

Complexes

79
Q

Depending on the composition of complexes, proteins can be either ____ or ____

A

activating or repressing

80
Q

The same protein can be part of an ____ or ___ complex

A

activating or repressing complex

81
Q

What is meant by regulation by committee

A

Depending on the composition of complexes, proteins can be either activating or repressing and the same protein can be part of an activating or repressing complex

82
Q

How are gene regulatory proteins controlled

A
  • Synthesis
  • Ligan binding
  • Covalent modification phosphorylation
  • Addition of subunit
  • Unmasking
  • Nuclear entry
  • Proteolysis
83
Q

What are the alpha like chains

A

zeta and alpha

84
Q

what are the beta like chains

A

epsilon, gamma, delta, beta

85
Q

Embryonic Hb=

A

zeta and epsilon

86
Q

fetal Hb=

A

Alpha and gamma

87
Q

Adult Hb=

A

Alpha and beta

88
Q

Globin genes are arranged in ____ fashion

A

linear

89
Q

Globin genes are ordered in the ___ to ___ direction in the same sequence of activation and expression during embryonic, fetal, and adult development

A

5’ to 3’

90
Q

Globin genes are on chromosomes

A

16 (zeta, alpha) and #11 (epsilon, gamma, delta, beta)

91
Q

The beta globin gene regulation is a ____kb region containing ____ beta globin genes and locus control region (LCR

A

100 kb, five

92
Q

Regulatory proteins for globin genes bind to the ____

A

LCR (locus control region)

93
Q

Understanding of globin gene regulation may allow the induction of ______ in sickle cell anemia

A

fetal hemoglobin

94
Q

What is the beta globin gene regulation order

A

LCR, Epsilon, gamma(G), Gamma(A), delta, beta

Molecular Biology (14 decks)

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