Lecture 7: DNA Structure + Replication

DNA 5’ carbon

phosphoryl group

DNA 3’ carbon

free hydroxyl

how many hydrogen bonds in A + T pair?

2

how many hydrogen bonds in G + C pair?

3

intercalating agents

flat, hydrophobic molecules that slip between base pairs to cause unwinding and lengthening

what groove are intercalating agenst mainly found in?

minor groove

common intercalating agents

ethidium bromide, acridine orange, actinomycin D

helicase

unwinds double helix

primase

synthesizes short RNA primers on lagging strand

what does primase provide?

3’-OH

DNA polymerase III

elongates new DNA strand

DNA polymerase I

removes RNA primers and replaces them with DNA

prokaryotic DNA synthesis is…

bidirectional, semi-conservative

what direction is DNA synthesized from?

5’ → 3’

SSB (single-strand DNA-binding protein)

binds to single strands for separation and protection

how many origins of replication in eukaryotes vs prokaryotes?

eukaryotes - multiple origins

prokaryotes - single origin

DNA polymerase III 5’ → 3’

polymerase activity - adds correct nucleotides

DNA polymerase III 3’ → 5’

exonuclease activity - removes incorrect nucleotides

topoisomerases

introduce breaks to relieve tension

type 1 topoisomerase

cuts one strand

type 2 topoisomerase

cuts both strands (DNA gyrase)

ciprofloxacin

inhibits gyrase → prevents resealing

quinolones

inhibits type 2 topoisomerase → cell death

eukaryotic pol S

lagging strand

eukaryotic pol E

leading strand

RNase H

removes RNA primase

telomerase

extends telomeres (chromosome ends) to prevent shortening; adds repeats to lagging 3’ end

nucleoside analogs

modify 3’-OH

dideoxynucleosides

no 3’-OH

arabinonucleosides

2’-OH or 3’-H; vidarabine

cytarabine

inhibits polymerase

cisplatin

cross-linking agent that replaces chloride ligands with N atoms of adjacent purines

methotrexate

inhibits DHFR

5-fluorouracil

inhibits thymidylate synthase