Control of Gene Expression 1: Transcriptional Controls Flashcards
What does gene regulation require?
- short stretches of DNA of defined sequence- recognition sites for DNA binding proteins
- Gene regulatory proteins- transcription factors that will bind and activate gene
What are the steps to DNA motif recognition?
- association of regulatory proteins with major groove
- proteins recognize and bind to bases in major groove
- major groove presents a specific face for each of the specific base pairs
- gene regulatory protein recognizes a specific DNA sequence
- surface of the protein is extensively complementary to the surface of the DNA region to which it binds
- series of contacts is made with the DNA involving 4 possible configurations
Typical gene regulatory protein-DNA interaction involves _____ interactions
10-20
Describe the helix turn helix DNA binding motif
simplest, most common
two alpha helices connected by short chain of amino acids that make long turn at fixed angle
longer helix= recognition module- DNA binding module - fits into major groove
Explain the zinc finger domain
DNA binding motif includes Zn atom binds to major groove of DNA found in tandem clusters stabilizes interaction with DNA multiple contact points
Explain the leucine zipper motif
-two alpha helical DNA binding domain
-grabs DNA like clothespin
-activation domain overlaps dimer domain
-interactions between hydrophobic amino acid side chain
-
Explain the helix loop helix domain
consists of short alpha chain connected by a loop to a second longer alpha chain
can occur as homo or heterodimers
three domains or modules of protein: DNA binding domain, dimerization domain, activation domain
What is hereditary spherocytosis?
hemolytic anemia characterized by spherical and fragile red blood cells that lyse and release hemoglobin
HS is ____ inherited
dominantly
What does the erythrocyte membrane Skelton (EMS) do?
confers property of durability and stability to RBCs
HS can be mutation in zinc finger protein gene _____
Klf1
KLF1 zinc finger protein binds to ______ of all genes in EMS, which _____
promoters; turns them on
What is the mutation in KLF1 that leads to HS?
mutation of non functioning KLF1 Zn finger protein which leads to no EMS made, leading to HS
What is the HS mutation sequence?
RER to RDR
which is GAA to GAT or Glu to Asp
HS KLF1 finger domain 2 binds to the ______ strand and leads to no ______
opposite; transcription
What is EMSA?
electrophoretic mobility shift assay
Describe EMSA
mix radioactive DNA fragment with protein extract from cell
run electrophoretic gel
proteins with DNA attached migrate according to size
shift of radioactive band when protein is bound to DNA
isolate protein to identify
What does affinity chromatography do?
isolate DNA binding protein
purification of sequence specific binding proteins
What is CHIP?
chromatin immuno- precipitation
What does CHIP do?
allows identification of the sites in the genome that a known regulatory protein binds to
What is the gene control region?
DNA region involved in regulating and initiating transcription of a gene, includes the promoter
_____ and _____ assemble at the promoter
RNA polymerases and general transcription factors
What is a mediator?
serves as an intermediary between gene regulatory proteins and RNA polymerase II
DNA _____ and a _____ complex allow the gene regulatory proteins to interact with the proteins that assemble at the promoter
looping; mediator
How does nucleosome remodeling and histone removal favor transcription?
increasing accessibility of DNA to proteins
