Sept 16 Flashcards
What amino acids are in helix 3 of C1 and Cro that are conserved and both help with binding to operator sites from the major groove?
Gln and Ser, they are both polar but not charged, they have H-bonds with the nucleotide bases.
What would a non polar and non charged AA and a charged AA have for interactions with DNA bases?
A non polar AA like Ala displaces water like the H-phobic effect, allows the other interactions to happen. Charged AA has stronger interactions with DNA bases.
How does Helix 2 stabilize helix 3 for lambda repressor and Cro?
On helix 2 they have an ala that interacts with another H-phobic AA like Val or Ile. This is H-phobic effect bringing them together. There is also Gln on edge of helix 2 that interacts with the DNA PO4 backbone. Helix 2 stabilizes via backbone, so it can then interact with helix 3 and push it into the major groove.
What 2 binding sites important in RNA polymerase binding site?
The -35 and -10 region.
What are 2 other names for the -10 region of promotor for RNA polymearse?
It is TATA box (Eukaryotes) and Pribnow box in prokaryotes
In prokaryotes, what is recruits RNA poly to the promotor?
The sigma factor, it recognizes the -10 and -35 sites, leaves once transcription starts
Why is RNA polymerase exclusively bound to either PRM or PR? How does the lambda repressor play into this?
The C1 repressor is first bound to OR1, which enhances binding for OR2 (cooperative binding).
When C1 is bound to OR1, it stops sigma factor from binding to the -35 and -10 on Promotor R = No Cro.
When C1 is bound to OR2 it blocks 2 nucleotides of the -35 for PRM and 3 nucleoties of the -35 for PR. As is now bound to part of the PRM, some AAs in helix 2 and some in the link between helix 2 and 3 interact with RNA poly and increase it’s binding affinity, increasing the expression of itself (C1)
Which carbon on the pentose sugar on DNA/RNA has the H or OH?
Carbon 2’
Which Nitrogen atoms of purines and pyrimidines are linked to the 1’ carbon of the pentose sugar in DNA/RNA?
N1 for purines and N9 for pyrimidines
Why are Cytosine-Guanine interactions stronger than AT ?
Yes, GC does have 3 H-bonds not 2, however it is the pi bond stacking that is stronger for GC with the base pairs above and below it that make it a more durable base pair
What is the main reason that DNA bases face inwards and not outwards of DNA helix?
It is so they can pi bond stack, like the H-phobic effect as the DNA is in an aqueous environment
What is the 2 factors that enables 10nm chromatin fiber to become 30 nm?
It is Histone subunit H1, and the N terminal Histone tails that interact with neighbouring nuclosomes, charge neutralization
What enables 30nm fibers to condense even further?
They form loops attaching to a scaffold. Topoisomerase 2 holds base of the loops, keeps them isolated so they don’t tangle up, allows the loops to still be close together = more compaction
What links loop regions of chromatid together following duplication?
It is cohesin
How do condensin, cohesin, and topoisomerase 2 condense DNA during interphase (after duplication)
Cohesin binds to DNA and forms loop regions. Topoisomerase 2 cuts dsDNA and the loose strands form knots with the same molecule and other DNA molecules (intra and inter). Condensin then corrects for knots, extrudes loops.
