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16.2 DNA Replication
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Layout of the Eukaryote DNA
Two DNA strands are antiparallel Run in opposite directions 3’ (three prime) – 5’ (five prime) 5’ (five prime) – 3’ (three prime)
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DNA Replication Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material
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DNA Replication Since the two strands of DNA are complementary, each strand 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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Fig. 16-9-1 A T C G T A A T G C (a) Parent molecule
Figure 16.9 A model for DNA replication: the basic concept
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(b) Separation of strands
Fig A T A T C G C G T A T A A T A T G C G C (a) Parent molecule (b) Separation of strands Figure 16.9 A model for DNA replication: the basic concept
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(b) Separation of strands
Fig A T A T A T A T C G C G C G C G T A T A T A T A A T A T A T A T G C G C G C G C (a) Parent molecule (b) Separation of strands (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand Figure 16.9 A model for DNA replication: the basic concept
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Semiconservative Model
Each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand
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(a) Conservative model
Fig First replication Second replication Parent cell (a) Conservative model (b) Semiconserva- tive model Figure Three alternative models of DNA replication (c) Dispersive model
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Matthew Meselson and Franklin Stahl
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DNA in Prokaryotes and Eukaryotes
ring of chromosome holds nearly all of the cell’s genetic material
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Prokaryote DNA Replication
DNA replication begins at a single point and continues to replicate whole circular strand Replication goes in both directions around the DNA (begins with replication fork)
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Fig. 16-12 Origin of replication Parental (template) strand
Daughter (new) strand Replication fork Double- stranded DNA molecule Replication bubble 0.5 µm Two daughter DNA molecules (a) Origins of replication in E. coli Origin of replication Double-stranded DNA molecule Parental (template) strand Figure Origins of replication in E. coli and eukaryotes Daughter (new) strand 0.25 µm Bubble Replication fork Two daughter DNA molecules (b) Origins of replication in eukaryotes
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DNA Replication Overview
DNA splits into two strands Complementary base pairs fill in (A with T, C with G) Left with two DNA molecules Semiconservative model Identical
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Eukaryote DNA Replication
Begins in hundreds of locations along the chromosome Origins of replication
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Initiation of DNA Replication
Begins when the DNA molecule “unzips” Replication fork Replication “bubble” Hydrogen bonds between base pairs breaks Helicase Single-strand binding proteins Topoisomerase – relieves pressure of DNA ahead of replication fork
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Single-strand binding proteins
Fig Primase Single-strand binding proteins 3 Topoisomerase 5 3 RNA primer Figure Some of the proteins involved in the initiation of DNA replication 5 5 3 Helicase
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Synthesis of a New DNA Strand
Each strand serves as a template for a new strand to form Primer of RNA The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand Complimentary bases will attach DNA polymerase E. coli – DNA polymerase III and DNA polymerase I Humans – 11 different DNA polymerase molecules
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Synthesis of a New DNA Strand
RNA primer Nucleoside triphosphate As each nucleotide is added to the new strand, 2 phosphates are lost Hydrolysis releases energy to drive reaction
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Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate
dATP supplies adenine to DNA and is similar to the ATP of energy metabolism The difference is in their sugars: dATP has deoxyribose while ATP has ribose As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
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Synthesis of a New DNA Strand
Antiparallel Elongation Remember 3’ – 5’ and 5’ – 3’ Replication in the 3’ to 5’ direction ONLY MEANING the NEW strand of DNA will form starting with the 5’ end Leading strand (only 1 primer needed – moves toward the replication fork) Lagging strand (many primers needed – moves away from replication fork)
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Fig. 16-16b1 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand Figure 16.6 Synthesis of the lagging strand
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Fig. 16-16b2 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5 RNA primer 3 1 5 Figure 16.6 Synthesis of the lagging strand
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Fig. 16-16b3 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5 RNA primer 3 1 5 3 Okazaki fragment 5 3 1 5 Figure 16.6 Synthesis of the lagging strand
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Fig. 16-16b4 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5 RNA primer 3 1 5 3 Okazaki fragment 5 3 5 1 3 5 3 2 1 5 Figure 16.6 Synthesis of the lagging strand
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Fig. 16-16b5 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5 RNA primer 3 1 5 3 Okazaki fragment 5 3 5 1 3 5 3 2 1 5 5 3 Figure 16.6 Synthesis of the lagging strand 3 5 2 1
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Fig. 16-16b6 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5 RNA primer 3 1 5 3 Okazaki fragment 5 3 5 1 3 5 3 2 1 5 5 3 Figure 16.6 Synthesis of the lagging strand 3 5 2 1 5 3 3 1 5 2 Overall direction of replication
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Important Enzymes Helicase, single-strand binding protein, topoisomerase Primase Synthesis of RNA primer DNA polymerase III (DNA pol III) Add new bases to DNA strand DNA polymerase I (DNA pol I) Removes and replaces RNA primer from 5’ end DNA ligase Links Okazaki fragments and replaces RNA primer from 3’ end
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Topoisomerase Video
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The Finished Product Each DNA molecule has one original strand and one new strand Molecules are identical
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DNA Replication Video
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Fig. 16-UN5
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Repair of DNA DNA polymerase Nuclease
Proofreads and repairs damaged/mismatched DNA Nuclease Removes section of DNA that is damaged DNA polymerase and DNA ligase replace missing portion
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Telomeres Found at the ends of each chromosome Contain no genes
Sequence that can be cut short and will not affect normal functioning TTAGGG Telomerase lengthens telomeres in gametes Aging? Cancer? As telomeres get shorter, aging may be triggered. Telomeres shorten and may start affecting replication (cancer cells) – trigger cell death - apoptosis
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Telomeres The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist
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16.3 A chromosome consists of a DNA molecule packed together with proteins
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Chromosomes
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Chromosome Structure Bacterial chromosome Eukaryotic chromosomes
double-stranded circular small amount of protein Eukaryotic chromosomes Linear DNA molecules large amount of protein DNA in bacteria is “supercoiled” and found in a region of the cell called the nucleoid
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Chromatin and Histones
Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells Histones are proteins that are responsible for the first level of DNA packing in chromatin Form a tight bond because DNA is negatively charged and the histones have a positive charge
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Nucleosomes, or “beads on a string” (10-nm fiber)
Fig a Nucleosome (10 nm in diameter) DNA double helix (2 nm in diameter) H1 Histone tail Histones Figure 16.21a Chromatin packing in a eukaryotic chromosome DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)
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Looped domains (300-nm fiber) Metaphase chromosome
Fig b Chromatid (700 nm) 30-nm fiber Loops Scaffold 300-nm fiber Figure 16.21b Chromatin packing in a eukaryotic chromosome Replicated chromosome (1,400 nm) 30-nm fiber Looped domains (300-nm fiber) Metaphase chromosome
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Chromosome Organization
Chromatin is organized into fibers 10-nm fiber DNA winds around histones to form nucleosome “beads” Nucleosomes are strung together 30-nm fiber Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber
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Chromosome Organization
300-nm fiber The 30-nm fiber forms looped domains that attach to proteins Metaphase chromosome The looped domains coil further The width of a chromatid is 700 nm
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Euchromatin Most chromatin is loosely packed in the nucleus during interphase Condenses prior to mitosis Euchromatin
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Heterochromatin During interphase, a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions
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