Eukaryotic Gene - Venk Flashcards
What are the upstream DNA promoter elements that control basal level (house keeping) gene expressions?
- TATA Box (-25)
- CCAAT Box (-75)
- GC region (in between TATA and CCAAT box)
Name the respective protein factor’s that binds to TATA, GC and CCAAT boxes (promoter elements).
TATA box: TBP binds to TATA box, and TFIID binds to TBP
GC: SP1 (Specific Protein 1) binds to GC
CCAAT box: NF1 (nuclear factor 1) binds to CCAAT box
What are Enhancer elements?
ERE, CRE, GRE (going up stream)
ERE =Estrogen Response Element
CRE = Cyclic AMP Response Element
GRE = Glucocorticoid Response Element (controls glucose metabolism - ex. cortisol)
What are the different possible locations of enhancers in relations to transcription start site of a particular gene?
1000s of bp away upstream (5’) or downstream (3’) from transcription start site. Can also be located in the introns.
True or False: Basal promoters such as TATA, GC and CCAAT box DNA sequences are located within -100 bp regions, upstream to that of transcription start site
True.
- TATA Box (25 bp upstream)
- CCAAT Box (75 bp upstream)
- GC region (in between TATA and CCAAT box)
Name few transcription factors.
TBP and TFIID, SP1 (Specific Protein 1), NF1 (nuclear factor 1)
What are CRE, GRE and ERE’s?
Enhancers
Name the respective proteins that binds to CRE and GRE
- CRE: CRE Binding protein (CREB) binds to CRE (this will bind later to the NF-1, which is bound to the CCAAT box part of the promoter region)
- GRE: Cortisol Receptor (w/ Cortisol) binds to GRE (this will later bind to the GC portion of the promotor region)
All of these enhance RNA Polymerase II binding to TBP/TFIID/TATA.
Describe how Phosphoenolpyruvate carboxykinase (PEPCK) gene expression can be controlled?
PEPCK gene expression can be controlled via the hormones cortisol and glucagon levels binding to GRE and CRE, respectively.
Cortisol induces some amount of PEPCK expression and glucagon induces some amount of PEPCK expression. Therefore, their availability influences PEPCK gene expression.
What are silencers? and repressors?
…
What are euchromatin and heterochromatins?
Euchromatin have open regions for transcription with no-charge Lysine part of the histone not binding to DNA.
Heterochromatin - condensed regions of DNA. Lysine of Histone have a very tight interaction with the DNA.
Describe the role of histone acetylase (HAT) and deacetylase (HDAC) in Euchromatin/Heterochromatin transitions.
Histone Acetylase (HAT) removes the positive charge on the amine group attached to Lysine. This results in the freeing up of DNA, allowing binding proteins to bind.
Histone Deacetaylase (HDAC) removes the acetone, making Lys (+), which causes the histone to bind to the DNA again.
What are zinc fingers? and briefly describe the two types of zinc fingers that can be present in some of the transcription factor proteins.
Zinc fingers are the element Zinc bound to 2 Cys and 2 His OR 4 Cys.
SP-1, which binds to the GC region has the zync finger moteif of 2Cys/2His
True or False: Homeobox (HOX), paired box (PAX), sonic hedgehog (SHH) genes control
cell differentiation during development. This means the mutated gene products of these genes (HOX, PAX, SHH) can cause developmental
disorder.
True
True or False: Klein-Waardenburg syndrome is a single gene developmental disorder. This condition is perhaps due to a defect in homeotic genes.
True
