Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

LE 16-6 Franklin’s X-ray diffraction photograph of DNA Rosalind Franklin

LE end 3 end 5 end 3 end Space-filling modelPartial chemical structure Hydrogen bond Key features of DNA structure 0.34 nm 3.4 nm 1 nm

LE 16-UN298 Purine + purine: too wide Pyrimidine + pyrimidine: too narrow Purine + pyrimidine: width consistent with X-ray data

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Watson and Crick reasoned that the pairing was more specific, dictated by the base structures They determined that adenine paired only with thymine, and guanine paired only with cytosine

LE 16-8 Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Sugar

LE 16-9_2 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands.

LE 16-9_3 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands. Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.

LE 16-9_4 The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C. The first step in replication is separation of the two DNA strands. Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand. The nucleotides are connected to form the sugar-phosphate back- bones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.

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

LE 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).

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animation: Origins of Replication Animation: Origins of Replication

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

LE New strand 5 end Phosphate Base Sugar Template strand 3 end 5 end 3 end 5 end 3 end 5 end 3 end Nucleoside triphosphate DNA polymerase Pyrophosphate

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

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

LE Parental DNA 5 3 Leading strand Okazaki fragments Lagging strand DNA pol III Template strand Leading strand Lagging strand DNA ligase Template strand Overall direction of replication

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animation: Leading Strand Animation: Leading Strand

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

LE 16-15_1 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication

LE 16-15_2 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication RNA primer DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment.

LE 16-15_3 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication RNA primer DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment. Okazaki fragment After reaching the next RNA primer (not shown), DNA pol III falls off.

LE 16-15_4 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication RNA primer DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment. Okazaki fragment After reaching the next RNA primer (not shown), DNA pol III falls off After the second fragment is primed, DNA pol III adds DNA nucleotides until it reaches the first primer and falls off.

LE 16-15_5 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication RNA primer DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment. Okazaki fragment After reaching the next RNA primer (not shown), DNA pol III falls off After the second fragment is primed, DNA pol III adds DNA nucleotides until it reaches the first primer and falls off DNA pol I replaces the RNA with DNA, adding to the 3 end of fragment 2.

LE 16-15_6 5 3 Primase joins RNA nucleotides into a primer. Template strand 5 3  Overall direction of replication RNA primer DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment. Okazaki fragment After reaching the next RNA primer (not shown), DNA pol III falls off After the second fragment is primed, DNA pol III adds DNA nucleotides until it reaches the first primer and falls off DNA pol I replaces the RNA with DNA, adding to the 3 end of fragment DNA ligase forms a bond between the newest DNA and the adjacent DNA of fragment 1. The lagging strand in the region is now complete.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animation: Lagging Strand Animation: Lagging Strand

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

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

LE Parental DNA 3 5 Overall direction of replication DNA pol III Replication fork Leading strand DNA ligase Primase OVERVIEW Primer DNA pol III DNA pol I Lagging strand Lagging strand Leading strand Leading strand Lagging strand Origin of replication

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animation: DNA Replication Review Animation: DNA Replication Review

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

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

LE 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.

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

LE 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 Further rounds of replication New leading strand Shorter and shorter daughter molecules

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

LE µm

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