1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Basic Principle: Base Pairing to a Template Strand 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 Animation: DNA Replication Overview Animation: DNA Replication Overview

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand Competing models were the conservative model and the dispersive model

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings DNA Replication: A Closer Look The copying of DNA is remarkable in its speed and accuracy More than a dozen enzymes and other proteins participate in DNA replication

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Getting Started: Origins of Replication Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” A eukaryotic chromosome may have hundreds or even thousands of origins of replication Replication proceeds in both directions from each origin, until the entire molecule is copied At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating

5. LE 16-12 In eukaryotes, DNA replication begins at may sites along the giant DNA molecule of each chromosome. Two daughter DNA molecules Parental (template) strand Daughter (new) strand 0.25 µm Replication fork Origin of replication Bubble In this micrograph, three replication bubbles are visible along the DNA of a cultured Chinese hamster cell (TEM).

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Elongating a New DNA Strand Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Antiparallel Elongation The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication DNA polymerases add nucleotides only to the free 3  end of a growing strand; therefore, a new DNA strand can elongate only in the 5  to  3  direction

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Along one template strand of DNA, called the leading strand, DNA polymerase can synthesize a complementary strand continuously, moving toward the replication fork To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Priming DNA Synthesis DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end The initial nucleotide strand is a short one called an RNA or DNA primer An enzyme called primase can start an RNA chain from scratch Only one primer is needed to synthesize the leading strand, but for the lagging strand each Okazaki fragment must be primed separately

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Other Proteins That Assist DNA Replication Helicase untwists the double helix and separates the template DNA strands at the replication fork Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Primase synthesizes an RNA primer at the 5 ends of the leading strand and the Okazaki fragments DNA pol III continuously synthesizes the leading strand and elongates Okazaki fragments DNA pol I removes primer from the 5 ends of the leading strand and Okazaki fragments, replacing primer with DNA and adding to adjacent 3 ends DNA ligase joins the 3 end of the DNA that replaces the primer to the rest of the leading strand and also joins the lagging strand fragments

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The DNA Replication Machine as a Stationary Complex The proteins that participate in DNA replication form a large complex, a DNA replication “machine” The DNA replication machine is probably stationary during the replication process Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides In mismatch repair of DNA, repair enzymes correct errors in base pairing In nucleotide excision repair, enzymes cut out and replace damaged stretches of DNA

14. LE 16-17 DNA ligase DNA polymerase DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete. Repair synthesis by a DNA polymerase fills in the missing nucleotides. A nuclease enzyme cuts the damaged DNA strand at two points and the damaged section is removed. Nuclease A thymine dimer distorts the DNA molecule.

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Replicating the Ends of DNA Molecules Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes The usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules

16. LE 16-18 End of parental DNA strands 5 3 Lagging strand 5 3 Last fragment RNA primer Leading strand Lagging strand Previous fragment Primer removed but cannot be replaced with DNA because no 3 end available for DNA polymerase 5 3 Removal of primers and replacement with DNA where a 3 end is available Second round of replication 5 3 5 3 Further rounds of replication New leading strand Shorter and shorter daughter molecules

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences called telomeres Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells