DNA stucture and replication

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Rosalind Franklin Franklin’s X-ray diffraction photograph of DNA DNA accepted as the genetic material, but not understood how its structure accounts for its role in heredity Franklin produced a picture of DNA molecule using X-ray crystallography

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Figure 16.5 Nitrogenous base Phosphate DNA nucleotide Sugar Sugar–phosphate backbone Franklin had also determined ------ two outer sugar-phosphate backbones, with nitrogenous bases paired in the interior Nitrogenous base

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Chargaff’s rules………… 1- The base composition of DNA varies between species 2 - In any species the number of A and T bases are equal and the number of G and C bases are equal The basis of this was not understood until the discovery of the double helix

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Figure 16.1 In 1953 Watson and Crick introduced the double-helical model as structure of deoxyribonucleic acid (DNA) The images enabled Watson and Crick to deduce the width of the helix and the spacing of the nitrogenous bases

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Figure 16.8 Adenine (A) Thymine (T) Guanine (G) Cytosine (C) PURINES PYRIMIDINES

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Purine  purine = too wide (A + G) Pyrimidine  pyrimidine = too narrow (C + T) Purine  pyrimidine: uniform width consistent with X-ray data Complementary Base Pairing Rule: A only pairs with T G only pairs with C This also explains Chargaff’s rules: quantity of A = T, and G = C in any species DNA

Figure 16.5:

3.4 nm 1 nm 0.34 nm Hydrogen bond 3  end 5  end 3  end 5  end T T A A G G C C C C C C C C C C C G G G G G G G G G T T T T T T A A A A A A Hydrophobic bases on interior and Hydrophilic negatively charged Phosphate on exterior Watson and Crick determined the backbones run is opposite directions = antiparallel

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Figure 16.10 (a) Conservative model (b) Semiconservative model (c) Dispersive model Parent cell First replication Second replication

Figure 16.1:

Figure 16.9-1 (a) Parent molecule A A A T T T C C G G

Figure 16.8:

Figure 16.9-2 (a) Parent molecule (b) Separation of strands A A A A A A T T T T T T C C C C G G G G the two strands of DNA are complementary…… and each acts as a template for building a new strand in replication In DNA replication , the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

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Figure 16.9-3 (a) Parent molecule (b) Separation of strands (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand A A A A A A A A A A A A T T T T T T T T T T T T C C C C C C C C G G G G G G G G Watson and Crick’s semiconservative model of replication… each daughter DNA molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

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Figure 16.12b Origin of replication Double-stranded DNA molecule Parental (template) strand Daughter (new) strand Bubble Replication fork Two daughter DNA molecules Replication begins at many origins of replication - “bubbles” remarkable in its speed and accuracy Many enzymes and proteins involved DNA Replication:

Figure 16.10:

Topoisomerase Primase RNA primer Helicase Single-strand binding proteins 5  3  5  5  3  3  Replication Fork Topoisomerase - relieves strain ……. corrects “overwinding” ahead of replication fork Primase – makes RNA primer Helicases - untwist the double helix, and separating the strands Single-strand binding proteins bind to and stabilize single-stranded DNA, keeping them apart The initial nucleotide strand is a short RNA primer

Figure 16.9-1:

Figure 16.14 New strand Template strand Sugar Phosphate Base Nucleoside triphosphate DNA polymerase Pyrophosphate 5  5  5  5  3  3  3  3  OH OH OH P P i 2 P i P P P A A A A T T T T C C C C C C G G G G Antiparallel Elongation DNA polymerases can only add nucleotides to the free 3  end Thus, a new DNA strand can elongate only in the 5  to  3  direction

Figure 16.9-2:

Leading strand Lagging strand Overview Origin of replication Lagging strand Leading strand Primer Overall directions of replication Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork The lagging strand is synthesized as a series of segments called Okazaki fragments , which are joined together by DNA ligase

Figure 16.9-3:

Origin of replication RNA primer Sliding clamp DNA pol III Parental DNA 3  5  5  3  3  5  3  5  3  5  3  5  Synthesis of Leading strand by DNA polymerase III

Figure 16.12b:

Figure 16.16b-1 Template strand 3  3  5  5  Synthesis of Lagging strand Primase joins RNA nucleotides into a primer

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Figure 16.16b-2 Template strand RNA primer for fragment 1 3  3  3  3  5  5  5  5  1 DNA polymerase adds DNA nucleotides to the primer – forming the first Okazaki Fragment Synthesis of Lagging strand

Figure 16.14:

Figure 16.16b-3 Template strand RNA primer for fragment 1 Okazaki fragment 1 3  3  3  3  3  3  5  5  5  5  5  5  1 1 Upon reaching the next RNA primer…… DNA polymerase detaches Synthesis of Lagging strand

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Figure 16.16b-4 Template strand RNA primer for fragment 1 Okazaki fragment 1 RNA primer for fragment 2 Okazaki fragment 2 3  3  3  3  3  3  3  3  5  5  5  5  5  5  5  5  2 1 1 1 Each okazaki fragment requires a separate RNA primer Synthesis of Lagging strand Fragment 2 is primed…..DNA polymerase III adds DNA nucleotides……detaches when it reaches fragment 1

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Figure 16.16b-5 Template strand RNA primer for fragment 1 Okazaki fragment 1 RNA primer for fragment 2 Okazaki fragment 2 3  3  3  3  3  3  3  3  3  3  3  5  5  5  5  5  5  5  5  5  5  5  2 2 1 1 1 1 Synthesis of Lagging strand (A different) DNA polymerase I replaces RNA with DNA where fragments meet

Figure 16.16b-1:

Template strand RNA primer for fragment 1 Okazaki fragment 1 RNA primer for fragment 2 Okazaki fragment 2 Overall direction of replication 3  3  3  3  3  3  3  3  3  3  3  3  5  5  5  5  5  5  5  5  5  5  5  5  2 2 2 1 1 1 1 1 Synthesis of Lagging strand DNA ligase forms sugar-phosphate bond between the fragments ….. Forming backbone

Figure 16.16b-2:

Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides……….. © 2011 Pearson Education, Inc. DNA can also be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes…… thus, there are MANY DNA repair enzymes working all the time

Figure 16.16b-3:

Figure 16.19 Nuclease DNA polymerase DNA ligase 5  5  5  5  5  5  5  5  3  3  3  3  3  3  3  3  nucleotide excision repair nuclease cuts out damaged stretches of DNA DNA polymerase fills in the missing (correct) nucleotides DNA ligase bonds the new fragment to the strand

Figure 16.16b-4:

Evolutionary Significance of Altered DNA Nucleotides Error rate after proofreading repair is low …… but not zero Sequence changes may become permanent and can be passed on to the next generation These changes (mutations) are the source of the genetic variation upon which natural selection operates © 2011 Pearson Education, Inc.

Figure 16.16b-5:

Figure 16.20 Ends of parental DNA strands Leading strand Lagging strand Last fragment Next-to-last fragment Lagging strand RNA primer Parental strand Removal of primers and replacement with DNA where a 3  end is available Second round of replication Further rounds of replication New leading strand New lagging strand Shorter and shorter daughter molecules 3  3  3  3  3  5  5  5  5  5  DNA polymerase can only add nucleotides to the 3’ end There is no way to complete the 5  ends, so repeated rounds of replication produce shorter DNA molecules with uneven ends

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Eukaryotic DNA has special (“non-gene”) nucleotide sequences at their ends called telomeres Telomeres act as “buffers” – postpone the erosion of genes near the ends of DNA molecules ……. the telomeres shorten with each round of replication, rather than important gene sequences Telomerase lengthens telomeres in germ cells to restore their length compensate for shortening during multiple replications in germ cells There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist

Proofreading and Repairing DNA:

replication in an E. coli cell Origin of replication Parental (template) strand Double- stranded DNA molecule Daughter (new) strand Replication fork Replication bubble Two daughter DNA molecules 0.5  m The bacterial chromosome a circular DNA molecule “ supercoiled ” and found in a region of the cell called the nucleoid

Figure 16.19:

DNA double helix (2 nm in diameter) DNA, the double helix Nucleosome Histones Nucleosomes, or “beads ona string” Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein ……… Chromatin - complex of DNA and proteins

Evolutionary Significance of Altered DNA Nucleotides:

Figure 16.22b Loops Scaffold Chromatid Replicated chromosome Looped domains Metaphase chromosome Chromosomes fit into the nucleus through an elaborate, multilevel system of packing

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