Harpers

DNA ORGANIZATION, REPLICATION, & REPAIR / 3313′DNA template5′5′ 3′Newly synthesizedRNA10 bp10 bpDNA strandprimer100 bpOkazaki fragmentsFigure 36–16. The discontinuous polymerization of deoxyribonucleotides on the laggingstrand; formation of Okazaki fragments during lagging strand DNA synthesis is illustrated.Okazaki fragments are 100–250 nt long in eukaryotes, 1000–2000 bp in prokaryotes.nucleotides in short spurts of 150–250 nucleotides,again in the 5′ to 3′ direction, but at the same time itfaces toward the back end of the preceding RNAprimer rather than toward the unreplicated portion.This process of semidiscontinuous DNA synthesis isshown diagrammatically in Figures 36–13 and 36–16.In the mammalian nuclear genome, most of theRNA primers are eventually removed as part of thereplication process, whereas after replication of the mitochondrialgenome the small piece of RNA remains asan integral part of the closed circular DNA structure.Formation of Replication BubblesReplication proceeds from a single ori in the circularbacterial chromosome, composed of roughly 6 × 10 6 bpof DNA. This process is completed in about 30 minutes,a replication rate of 3 × 10 5 bp/min. The entiremammalian genome replicates in approximately 9hours, the average period required for formation of atetraploid genome from a diploid genome in a replicatingcell. If a mammalian genome (3 × 10 9 bp) replicatedat the same rate as bacteria (ie, 3 × 10 5 bp/min)from but a single ori, replication would take over 150hours! Metazoan organisms get around this problemusing two strategies. First, replication is bidirectional.Second, replication proceeds from multiple origins ineach chromosome (a total of as many as 100 in humans).Thus, replication occurs in both directionsalong all of the chromosomes, and both strands arereplicated simultaneously. This replication process generates“replication bubbles” (Figure 36–17).The multiple sites that serve as origins for DNAreplication in eukaryotes are poorly defined except in afew animal viruses and in yeast. However, it is clear thatinitiation is regulated both spatially and temporally,since clusters of adjacent sites initiate replication synchronously.There are suggestions that functional domainsof chromatin replicate as intact units, implyingthat the origins of replication are specifically locatedwith respect to transcription units.During the replication of DNA, there must be a separationof the two strands to allow each to serve as atemplate by hydrogen bonding its nucleotide bases tothe incoming deoxynucleoside triphosphate. The separationof the DNA double helix is promoted by SSBs, specificprotein molecules that stabilize the single-strandedstructure as the replication fork progresses. These stabi-Origin of replication“Replication bubble”3′5′5′3′Unwinding proteinsat replication forksDirectionsof replicationFigure 36–17. The generation of “replication bubbles” during the process of DNA synthesis. The bidirectionalreplication and the proposed positions of unwinding proteins at the replication forks are depicted.