Chapter_28

Chapter_28 - Chapter28DNAReplication,Recombinationand...

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1. Proteins aid unwinding 2. Topoisomerases reduce strain  from overwinding 3. Proofreading increases  accuracy from 10-4 to 10-10 4. 4.8 million bps in <40 minutes 5. Synthesis in same direction on  both strands 6. Telomeres at chromosome ends 7. Recombinases facilitate rapid  sequence changes 8. Repair enzymes Chapter 28 DNA Replication, Recombination and  Repair
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The Structural Forms of DNA The “Canonical” Forms of DNA: A DNA and B DNA A Form is observed in 1) dehydrated crystals/fibers 2) RNA 3) RNA/DNA hybrids 2’-OH in RNA would produce steric clashes in a B- form helix
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The Major and Minor Grooves have Sequence Dependent  Patterns of Hydrogen Bond Donors and Acceptors The major groove is more accessible to proteins than the minor groove and has more distinctive features 12 Å wide, 8.5  deep 6.5,  7.5
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Sequence Dependence of DNA Structure Dickerson Dodecamer: Rotation between residues ranges from 28 degrees to 42 degrees Propeller twisting 355D (pdb) DNA binding proteins may identify target DNA by structure as well as sequence dCGCGAATTGCGC
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Left-Handed Z-DNA Z DNA is favored for alternating purine/pyrimidine  sequences in vitro, depending on salt, methylation,  and other conditions Alternating syn and anti  glycosidic bond/ C2’, C3’ endo  sugars are linked to zizgzag  phosphorus configuration N N N N H H O N H H O O O O H H H H H H N N N N H O H N H H O O O O H H H H H H Syn   conformatio n: most  common in  G Anti  conformation dCGCGCG Pdb: 1dcg
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DNA Polymerases Catalyze the formation of the polynucleotide chain Nucleotides are added to the 3’OH of the growing chain Primer and template are required
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DNA Polymerases Fall into 5 Classes, all Homologous Klenow fragment: 2 subunits: polymerase and 3’ to 5’ exonuclease 2 metal ions held in place by 2 Asps Negative charges are neutralized OH- nucleophilic attack on phosphate
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Fidelity of Replication is reinforced by Several  Factors Hydrogen Bonds in the bp Positions of groups in minor groove Proofreading activities Conformational  in  polymerase upon  nucleotide binding  confers shape to fit W-C  H bonding Tyr mutation  increases errors by  40fold Distorted B DNA
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Chapter_28 - Chapter28DNAReplication,Recombinationand...

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