Biochemistry II lecture 9 Flashcards
What happens in the topoisomerase II mechanism?
-ATP dependent
-in prokaryotes: creates supercoils
-in eukaryotes: only relaxes supercoiled DNA (ligation and religation)
-passes double-stranded DNA through gap then reseals gap
Where can you find G-quadruplexes?
-anywhere there is single strand DNA
-during replication,transcription,telomeres
What is the biological role of G-quadruplexes that are of interest to drug developers?
-regulation of expression or replication or translation
-potential for anticancer drug target
When DNA wraps around a histone core what type of supercoiling occurs?
-negative supercoil is wrapped around histone cone and a positive supercoil is formed outside the supercoil
-Lk is constant!!
How does the Helix-Turn-Helix motif form?
-2 helices connected by a short turn
1st helix is stabilizing; 2nd helix is sequence-specific binding (major groove)
ex. antennapedia
How does the Zinc Fingers binding motif form?
-a-helix is sequence specific (major groove) and antiparallel B-sheet
-histidine & cysteine (4 cys or 2 and 2)
How does basic region-leucine zippers form?
-a-helix (leucine residues every 7th position) to stabilize
-basic amino acids interact with phosphate backbone of DNA
ex: fos and jun; cAMP response element-binding protein (CREB)
How does the Helix-loop-Helix motif form?
-two amphipathic a-helices connected by a loop
-4-helix bundle structure
ex: myoD, myc, max
What is the function of Transcription factors?
-DNA binding factor (sequence specific)
-controls rate of transcription by activating/repressing the recruitment of RNA polymerase
How are Transcription factors regulated to turn on or repress transcription?
-activated/deactivated by ligand binding
-chemical modification
-interaction coregulatory proteins or other transcription factors (homo/hetero dimerization)
how does CREB display modular structure?
has a DNA binding domain (bZIP)
has an activation domain (Q1 and Q2)
has a protein interaction domain (KID)
How are Nuclear Receptors unique transcription factors?
-have direct interaction with DNA and control of gene expression
-multiple domains bind DNA (DBD-hinge-LBD) region
What are HREs?
Hormone response elements
a nucleosome
1. comprises both RNA and several types of proteins
2. is a disk shaped complex with histones packed around a core of DNA
3. stabilizes a bent form of DNA that does not occur when DNA is present on its own
4. is stabilized by electrostatic interactions between the polyphosphate backbone and Asp sidechains
5. comprises multiple histone proteins, which are highly variable in sequence among eukaryotes
- stabilized a bent form of DNA that does not occur when DNA is present on its own
- is stabilized by electrostatic interactions between the polyphosphate backbone and Asp sidechains
