Long Polymer; backbone consists of alternating sugar (2-deoxyribose) and phosphate groups
Bases (A, G, C, T) attach to each sugar via glycosidic linkage
5'
Þ 3' polarity; double helix; bases on inside and pair with bases on opposite side
A – T (2 H-bonds) and C – G (3 H-bonds)
No covalent linkages
cations (ie Mg2+) neutralize much of the mutual repulsion of the (-) backbones
stacking of the bases
exclusion of water from the hydrophobic bases
high G – C content
Þ higher stability
Strand separation: helicases (ATP hydrolyzing enzymes); DNA supercoiling (topoisomerases)
Denatured DNA can renature (hybridize or reanneal)
Proteins can interact with DNA without disrupting base pairing
DNA Replication
Due to base pairing rules (A-T, C-G), a single strand of DNA carries the full genetic info of the double stranded DNA
Template strand directs assembly of a complimentary strand
Energy is required: derived from each dNTP used (pyrophosphate); derived from ATP (helicases)
Replication Fork
– semi-discontinuous
DNA polymerase
: synthesizes from 5' Þ 3' only
Adds to 3'OH end (needs primer to begin)
DNA ligase
: links the Okazaki fragments
How do you begin an Okazaki fragment or primer? (strand initiation problem)
Begins with RNA primase
Þ chain is begun as RNA and the short RNA primers are extended as DNA using DNA polymerase Þ each Okazaki fragment has an RNA primer Þ the RNA primer is degraded and replaced with DNA before ligase links the Okazaki fragments
: control level of supercoiling; works in unreplicated region; when DNA opens (+ supercoiling), topoisomerases counteract (- supercoiling); it cuts the DNA, rearranges it, then reconnects the DNA
Fidelity
: errors occur every 10-4 to 10-5 bp due to tautomerization
Cytosine – can have "amino" or "imino" form – amino pairs with guanine (correct), imino with adenine (mutation)
Other errors: dUTP in DNA, not replaced
Most misincorporated bases are fixed with DNA polymerase: frequency of misincorporations not fixed ~10-7
Post replication checking improves fidelity ratio to ~10-9
Additional worries for eukaryotes
replicating telomeres: special structure Þ (GGGTTA)n
telomerase
replicates this end: protein containing RNA whose sequence compliments the GGGTTA
terminally differentiated cells have no telomerase
telomerase shorten with division Þ death
if cancerous, telomerase is found Þ divide indefinitely
Orderly activation of multiple origins
(and once per round)
due to organization of heterochromatin and euchromatin
euchromatin fires early; heterochromatin fires late
chromatin bound factor ensures only one firing per round
