DNA Backbonealternating sugar-phosphate backbonesugar and phosphate backbone attached by a phosphodiester bond

DNA is said to be read from 5 to 3

opposing backbones are antiparallel

Complementary Base PairingChargaffs Ruleadenine : thymine (1:1)guanine : cytosine (1:1)

the diameter of a base pair is 2 nm

3 H-bonds between G&C2 H-bonds between A&T

Overall DNA Structureright handed helix

0.34 nm between adjacent base pairs

one turn of the helix is 10 base pairs (3.4 nm)A nm = one thousand-millionth of a m. It can be written as 1 m / 1,000,000,000.

Overall DNA Structuremajor grooveminor groove

A-DNAB-DNAZ-DNA

A-DNAB-DNAZ-DNAhelical rotationright-handedright-handedleft-handed# base pairs per 36010.71012helical diameter25.5 23.7 18.4

major/minor groovesyesyesno all grooves very similar in height

DNA Structure - Review

DNA ReplicationAll cells are capable of giving rise to a new generation of cells through DNA replication (copying) and cell division.

Mitosis: replicated DNA in nucleus is divided equally between two daughter cells

1958 Meselson & Stahlhttp://www.youtube.com/watch?v=JcUQ_TZCG0wgrew E. coli in 15N media

14N is the usual isotope; 15N is heavier

ensured that the bacterial DNA only contained 15N

CONSERVATIVE MODELSEMI-CONSERVATIVE MODELDISPERSIVE MODELDark Blue = parental strand (original DNA)

Light Blue = new strand

Meselson & Stahl ExperimentDNA was isolated and its weight determined through centrifugation

DNA ReplicationDNA replicates in a semi-conservative mannerone strand of DNA is used as a template for the other strand5 A T G T C A G 33 T A C A G T C 5

553355335533553353553533

DNA Replication

DNA replication starts at a number of sites along a chromosome origins of replication

dozens of proteins are involved in the process of DNA replication

DNA Replication InitiationDNA helicase unwinds DNA to break its bonds

single-stranded binding proteins (SSBPs) bind to each of the single stranded pieces of DNA and keeps them seperatedif there were nothing to keep the strands apart, they would reanneal (stick back together)DNA Replication Animationhttp://www.youtube.com/watch?v=I9ArIJWYZHI

Proteins / Enzymes of DNA Replication

as DNA is being unwound by helicase, DNA in front of the helicase gets bunched up

DNA gyrase enzyme that loosens the tension in front of the replication fork

Replication Structuresreplication occurs in both directions from the origin of replication

replication fork structure generated by DNA helicase and SSBPs

replication bubble two replication forks which are close in proximity

DNA PolymeraseDNA polymerase enzyme which synthesizes nucleotide chainsin prokaryotes: DNA polymerase I, II, III, IV & Vin eukaryotes: over 15 different types

nucleotide chains only form in the 5 3 directionn (can only add to the 3 end of the new strand)

DNA polymerase III is primarily responsible for DNA replication in prokaryotes

DNA Polymerase III SubstratesDNA templatedeoxyribonucleoside triphosphates (dNTPs)

RNA primer535353

ATP (Adenosine Triphosphate)ADENINERIBOSE3 PHOSPHATES

DNA Polymerasedeoxyribonucleoside triphosphates (dNTPs)3

Step 1Primase makes a short RNA primer on the exposed single-stranded DNA (ssDNA).53

ASteps 2, 3, and 4DNA polymerase III binds to the end of the RNA primer.The appropriate nucleoside triphosphate binds to the polymerase.A pyrophosphate group (PPi, a diphosphate group originally isolated by heating phosphates) is cleaved, while the nucleotide is added to the end of the nucleotide chain.ATTTPPP

DNA Polymerasedeoxyribonucleoside triphosphates (dNTPs)3

5533helicaseSSBPsgyraseprimaseDNA polymerase IIIThe leading strand is synthesized continuously during DNA replication

Okazaki fragment533553

Connecting Lagging StrandsDNA polymerase I removes the RNA primeroccurs in the 5 3 direction

DNA ligase connects the sugar-phosphate backbone (by creating phosphodiester bonds) of Okazaki fragments Okazaki fragments are typically 1000 to 2000 nucleotides (NTs) in length

ReplicationDNA replication occurs:continuously on the leading stranddiscontinuously on the lagging strand

Replication Animation

Replication Overview - 1helicase unwinds the double stranded DNA structure creating a replication fork

the single stranded region of the replication fork are maintained by SSBPs

gyrase relieves the tension ahead of the replication fork

Replication Overview - 2two original parent strands serve as templates for the new daughter strands

daughter strands are produced in one of two methodsleading strand (continuous polymerization)lagging strand (discrete polymerization)1000 2000 NTs Okazaki fragments joined together

Replication Overview - 3primase begins each new daughter strand with a short RNA primer

DNA polymerase III extends a DNA strand from the RNA primer

DNA polymerase I removes the RNA primer AND fills it in with DNA

DNA ligase joins the sugar-phosphate backbones of all adjacent DNA segments

Mistakes in DNA Replicationless than 1 error in 107 (10 million) NTs

exonuclease enzymes which can cut out sections of nucleic acids

DNA polymerase I and III have polymerase and exonuclease activity to fix mistakes

DNA RepairFigure 16.17NucleaseDNApolymeraseDNAligase A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved. Repair synthesis bya DNA polymerasefills in the missingnucleotides.3 DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.

Homework helps prepare you for tests!!!!Homework will be checked each class:Pg. pg. 209 #1-4pg. 216 #1-9Pg. 223 #1-5, 7-8

Antiparallel = upside down5 3 labeled similarly to proteins with numbered carbons (1-4), except we use prime for DNA. *2 nm = 2 nanometers *Major and Mionor groove because DNA molecule is not a perfect helix. Consider a spiral stair case What makes it uniform in diameter? The support beam down the centre. There is no support beam down the centre of a DNA molecule. *Dont need to memorize.A and B DNA are found naturally in our bodies.Z DNA reverse direction, or left handed. Much less common. *DNA gyrase shoe lace demo (prevents coil from unwinding too much or getting too tight)DNA polymerase III main enzyme of DNA replication, called III simply because it was discovered after DNA polymerase I.RNA primer needed to start relipcation*