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 Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Animation: Origins of Replication Getting Started Replication begins at special sites called _____________________, where the two DNA strands are separated, opening up a ______________________ Animation: Origins of Replication Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Parental (template) strand Fig. 16-12a Origin of replication Parental (template) strand Daughter (new) strand Replication fork Double-stranded DNA molecule Replication bubble 0.5 µm Two daughter DNA molecules Figure 16.12 Origins of replication in E. coli and eukaryotes (a) Origins of replication in E. coli

Double-stranded DNA molecule Fig. 16-12b Origin of replication Double-stranded DNA molecule Parental (template) strand Daughter (new) strand 0.25 µm Bubble Replication fork Figure 16.12 Origins of replication in E. coli and eukaryotes Two daughter DNA molecules (b) Origins of replication in eukaryotes

Single-strand binding protein Topoisomerase Primer Primase Replication fork Helicases Single-strand binding protein Topoisomerase Primer Primase Have students look at Fig16.13 and specify functions of each term. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Single-strand binding proteins Fig. 16-13 Primase Single-strand binding proteins 3 Topoisomerase 5 3 RNA primer Figure 16.13 Some of the proteins involved in the initiation of DNA replication 5 5 3 Helicase

STOPPED HERE!

Synthesizing a New DNA Strand Enzymes called ___________________ catalyze the elongation of new DNA at a replication fork Most DNA polymerases require a _________ and a ________________ Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Nucleoside triphosphate Fig. 16-14 New strand 5 end Template strand 3 end 5 end 3 end Sugar A T A T Base Phosphate C G C G G C G C DNA polymerase 3 end A T A Figure 16.14 Incorporation of a nucleotide into a DNA strand T 3 end C Pyrophosphate C Nucleoside triphosphate 5 end 5 end

Antiparallel Elongation DNA has an antiparallel structure 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 © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Overall directions of replication Fig. 16-15 Overview Origin of replication Leading strand Lagging strand Primer Lagging strand Leading strand Overall directions of replication Origin of replication 3 5 RNA primer 5 “Sliding clamp” 3 5 DNA poll III Parental DNA Figure 16.15 Synthesis of the leading strand during DNA replication 3 5 5 3 5

Overall directions of replication Fig. 16-16 Overview Origin of replication Leading strand Lagging strand Lagging strand 2 1 Leading strand Overall directions of replication 3 5 5 3 Template strand 3 RNA primer 3 5 1 5 Okazaki fragment 3 5 3 1 5 5 3 3 Figure 16.6 Synthesis of the lagging strand 2 1 5 3 5 3 5 2 1 5 3 3 1 5 2 Overall direction of replication

Overall directions of replication Fig. 16-16a Overview Origin of replication Leading strand Lagging strand Lagging strand 2 1 Leading strand Figure 16.6 Synthesis of the lagging strand Overall directions of replication

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b1 3 5 5 3 Template strand Figure 16.6 Synthesis of the lagging strand

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b2 3 5 5 3 Template strand 3 5 RNA primer 3 1 5 Figure 16.6 Synthesis of the lagging strand

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b3 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

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b4 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

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b5 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

Figure 16.6 Synthesis of the lagging strand Fig. 16-16b6 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

Table 16-1

Single-strand binding protein Overall directions of replication Fig. 16-17 Overview Origin of replication Leading strand Lagging strand Leading strand Lagging strand Single-strand binding protein Overall directions of replication Helicase Leading strand 5 DNA pol III 3 3 Primer Primase 5 Parental DNA 3 Figure 16.17 A summary of bacterial DNA replication DNA pol III Lagging strand 5 DNA pol I DNA ligase 4 3 5 3 2 1 3 5 http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides Mismatch repair: ______________________________________________________________________________ Nucleotide excision repair: ______________________________________________________________________________ Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Nuclease DNA polymerase DNA ligase Fig. 16-18 Figure 16.18 Nucleotide excision repair of DNA damage DNA ligase

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 Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Figure 16.19 Shortening of the ends of linear DNA molecules 5 Ends of parental DNA strands Leading strand Lagging strand 3 Last fragment Previous fragment RNA primer Lagging strand 5 3 Parental strand Removal of primers and replacement with DNA where a 3 end is available 5 3 Second round of replication Figure 16.19 Shortening of the ends of linear DNA molecules 5 New leading strand 3 New lagging strand 5 3 Further rounds of replication Shorter and shorter daughter molecules

Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences called _______________________ Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules It has been proposed that the shortening of telomeres is connected to aging Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig. 16-20 Figure 16.20 Telomeres 1 µm

________________– cells that make gametes in the ovaries and testes What would happen if chromosomes of germ cells became shorter with every cell cycle? An enzyme called ________________ catalyzes the lengthening of telomeres in germ cells Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

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 Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

How DNA is packaged http://www.dnalc.org/resources/3d/08-how-dna-is-packaged-advanced.html http://www.dnalc.org/resources/3d/08-how-dna-is-packaged-advanced.html

You should now be able to: Describe the contributions of the following people: Griffith; Avery, McCary, and MacLeod; Hershey and Chase; Chargaff; Watson and Crick; Franklin; Meselson and Stahl Describe the structure of DNA Describe the process of DNA replication; include the following terms: antiparallel structure, DNA polymerase, leading strand, lagging strand, Okazaki fragments, DNA ligase, primer, primase, helicase, topoisomerase, single-strand binding proteins Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Describe the function of telomeres Compare a bacterial chromosome and a eukaryotic chromosome Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings