DNA structure+replication (lect 14-16)

A,T

nt pair has two H bonds

C,G

nt pair has 3 H bonds

B form

Most stable form of the DNA helix

C’2 endo sugar pucker

Component of DNA that makes the B form more stable as the “pucker” sits higher on the plane reducing steric clash

Soluble, can’t cross membranes, stable, abundant

Why is phosphorus a component of the sugar backbone? (Give four reasons)

Anhydride bonds

Types of bonds between the phosphate heads

Phosphodiester bonds

Types of bonds between two sugar backbones linked by phosphate head

Major groove

Component of DNA double helix structure creates a “gap” proteins can interact in

Histone

Small positively charged proteins wind dna, act like beads on a string

Nucleosome, coil, supercoil

List the three forms of compact dna wrapped around histones from smallest to largest

H1

Linker histone, less abundant (one per octamer), further compacts DNA

Chromatin

Molds the genome into active or repressed transcriptional domains critical for cellular identity

Topological domain

A DNA segment that

is constrained so that free rotation is impossible

Topoisomerase I

Relieves supercoiling by breaking a single strand of DNA reducing the twist by one without needing ATP

Topoisomerase II

Relieves supercoils in DNA by breaking both strands of DNA reducing the writhe by 2 using 2 ATP

Tyr

topo I doesn’t use ATP to create ss break, what does it use as an e- donor instead?

camptothecin

type I chemotherapy, topoisomerase poison locks topo into a cleavage complex preventing DNA religation

anthracyclines

type II chemotherapy, topoisomerase poison locks topo into a cleavage complex preventing DNA religation

dexrazoxane

type II therapeutic, ATP hydrolysis inhibition prevents DNA release locking Topo into a closed clamp complex

S phase

phase in cell cycle DNA replication occurs in eukaryotes

topoisomerase

releases helical tension due to helicase activity at the replication fork

helicase

breaks DNA hydrogen bonds hybridizing DNA strands and disrupting nucleosomes “zipper”

pol epsilon

primary leading strand DNA polymerase

pol a

polymerase synthesizes the first stretch of DNA after primer, also acts as primase polymerizing enzyme and primase activity synthesizing RNA primers 5→3 extending first lagging strand synthesis

primase/pol a

polymerizing enzyme synthesizing RNA primers 5→3 extending first lagging strand synthesis

pol delta

DNA polymerase used to synthesize lagging strand

6’C

which carbon sugar is attached to phosphate head?

3’C OH

where does phosphate bind in DNA replication to form an ester bond

GINS, CD45

engagement of these two proteins is required for initiation of CMG helicase activity

CMG helicase

helicase requires GINS and CD45 for initiation, uses ATP hydrolysis to move the helicase down 2 nts

pyrophosphatase

enzyme catalyzes the breaking down of 2Pi from DNA backbone to form ester bond between two sugar backbones, very favorable and irreversible reaction

SSBs

binds ssDNA during replication stabilizing it

Mg2+

one of these metal ions coordinated by Asp in DNAP facilitates nucleophilic attack of OH of growing DNA strand, the second stablizes interaction with incoming dNTP

Asp

coordinate Mg2+ in DNAP for the formation of phosphodiester bonds in the active site

conformational change

DNA change that occurs when wrong base is inserted during replication activates exonuclease to excise this base, a line of defense preventing replication errors

sliding clamp PCNA

maintains affiliation of replisome with the DNA

RNase H

removes RNA primers from lagging strands

DNA ligase

catalyzes formation of phosphodiester bonds, lysine in active site steals an AMP from ATP which is transferred to 5’ phosphate of the nick

lysine

residue in DNA ligase active site that “steals” AMP from ATP to help form phosphodiester bond

telomerase

has an RNA loop within enzyme helping synthesize and extend 3’ DNA end during replication, uses RNA as a primer to add to the same template of repeats at the end of DNA synthesis to protect coding regions

histone chaperones

leading and laging strand assemble old and new histones behind replication fork using this as help

CAF1

transfers new histones to replicating DNA, however, these new histones do not have the same modifictions as the old ones