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

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

normal

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

25,000 in humans, proteins

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

changes in gene expression

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Common proteins are called _______ what is an example

housekeeping proteins, glucose metabolism

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what is an example of a specifically limited protein

hemoglobin

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

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

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What are some of the ways to control gene expression

transcriptional control
RNA processing control
RNA transport and localization control
Translation control
mRNA degradation control
translation control
protein activity control

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Gene regulation requires

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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Recognition sequences for regulatory proteins ex.

GATA1: TGATAG

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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

distinct DNA-binding specificities

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What does the “logo” shows that the protein can

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

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Recognition sequences can be ___ or ___ to the first exon

Proximal or distal

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Regulatory proteins recognize and bind to bases in the ____ groove

major

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

Major

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A gene regulatory protein recognizes a

specific DNA sequence

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

complimentary

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

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

possible hydrogen bond donor
Possible hydrogen bond acceptor
methyl groups
Hydrogen atom

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a typeical gene regulatory protein-DNA interaction involves _____ interactions

10-20

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

modular

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What is the sequence of specific transcription factors Modules

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

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Does every transcription factor have all the modules

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What modules must a transcription factor have

DNA-binding module and Activation module

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What is the function of the dimerization module

forms dimer with other protein subunits

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

Dimerization module and Regulatory module

What is the function of the regulatory module

regulate transcription factor

DNA-binding domain structural motifs

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

What is the simplest, most common DNA-binding motif

Helix-turn-helix

Explain helix-turn-helix

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

The longer helix in a helix turn helix equals the

recognition module- DNA binding module-fits into major groove

Side changes of ____ in the helix turn helix recognize ____

Amino acids in the helix turn helix DNA motif

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

Dimers

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

zinc

zinc finger proteins bind DNA in the ____ groove

major

Zinc finger domains found in tandem ____

clusters

What is the function of the zinc in zinc finger

stabilizes interactions with DNA

Leucine zipper motif has ____ DNA binding domains

-Two alpha helical DNA binding domains

Leucine zipper motif Dimerizes through ____ zipper region

leucine zipper region

the leucine zipper motif is named because of the way the

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

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

hydrophobic

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

The dimerization of the leucine zipper grapes _____ like a clothespin

DNA

The activation domain overlaps _____ domain in a leucine zipper

dimer

The helix-loop-helix motif consists of a

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

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

homodimers or heterodimers

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

DNA binding domain, dimerization domain, activation domain

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

Zinc finger

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

Hereditary spherocytosis (HS)

What is the clinical presentation of Hereditary spherocytosis (HS)

hemolysis, anemia, splenomegaly

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

mild to severe

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

red blood cells- not making enough protein

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

Hereditary Spherocytosis (HS)

Hereditary Spherocytosis is _____ inherited

Dominantly

Hereditary Spherocytosis can be mutation in zinc finger protein gene _____

Klf1 (Kruppel-like factor 1)

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

KLF1

how many zing finger domains are there for KLF1

Klf1 has ___ exons

3, which encodes 3 zinc finger domains

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

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

____ are critical amino acids for DNA binding in EMC proteins

RER

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

GAT, Asp

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

- RER (Arg-Glu-Arg) | - RDR (Arg-Asp-Arg)

Normal KLF1 binds to DNA and

unwinds DNA causing transcription

HS KLF1 zinc finger binds to

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

Ways to identify Transcription factors

- 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

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

CHIP: chromatin Immuno-precipitation

is Chromatin immunoprecipitation done on living cells

yes

DNA region involved in regulating and initiating transcription of a gene

Gene control region

Where transcription factors and RNA polymerase II assembles

Promoter

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

8% or 2,000 genes

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

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

____ and ____ assemble at the promoter

RNA polymerase and general transcription factors

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

adjacent, far upstream or in introns downstream of the promoter

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

promoter

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

Mediator

Nucleosome remodeling and histone removal favors ____ by

transcription by increasing the accessibility of DNA to proteins

Histone acetylation makes it easier to ____ histones

remove

what are some of the different ways gene repressors inhibit transcription

- 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)

Gene regulatory proteins assemble into _____ on DNA

Complexes

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

activating or repressing

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

activating or repressing complex

What is meant by regulation by committee

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

How are gene regulatory proteins controlled

- Synthesis - Ligan binding - Covalent modification phosphorylation - Addition of subunit - Unmasking - Nuclear entry - Proteolysis

What are the alpha like chains

zeta and alpha

what are the beta like chains

epsilon, gamma, delta, beta

Embryonic Hb=

zeta and epsilon

fetal Hb=

Alpha and gamma

Adult Hb=

Alpha and beta

Globin genes are arranged in ____ fashion

linear

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

5' to 3'

Globin genes are on chromosomes

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

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

100 kb, five

Regulatory proteins for globin genes bind to the ____

LCR (locus control region)

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

fetal hemoglobin

What is the beta globin gene regulation order

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