1. 1 DNA Replication 複製

2. Ex Biochem c18-DNA replication 2 18.2 DNA Polymerases Are the Enzymes That Make DNA DNA is synthesized in both semiconservative replication and repair reactions. A bacterium or eukaryotic cell has several different DNA polymerase 聚合酶 enzymes. One bacterial DNA polymerase undertakes semiconservative replication. The others are involved in repair reactions. Eukaryotic nuclei 細胞核, mitochondria, and chloroplasts 葉綠體 each have: a single unique DNA polymerase required for replication other DNA polymerases involved in ancillary or repair activities

3. Ex Biochem c18-DNA replication 3 Figure 18.2 Figure 18.1

4. Ex Biochem c18-DNA replication 4 18.3 DNA Polymerases Have Various Nuclease Activities DNA polymerase I has a unique 5′ – 3′ exonuclease activity. It can be combined with DNA synthesis to perform nick translation. Figure 18.5

5. Ex Biochem c18-DNA replication 5 18.4 DNA Polymerases Control the Fidelity of Replication 偵錯 : DNA polymerases often have a 3′ – 5′ exonuclease 外核 酸脢 activity. It is used to excise incorrectly paired bases. The fidelity 忠實度 of replication is improved by proofreading 檢查 by a factor of ∼ 100. Figure 18.6

6. Ex Biochem c18-DNA replication 6 18.5 DNA Polymerases Have a Common Structure Many DNA polymerases have a large cleft composed of three domains that resemble a hand. DNA lies across the “ palm ” in a groove created by the “ fingers ” and “ thumb. ” Figure 18.7

7. Ex Biochem c18-DNA replication 7 18.6 DNA Synthesis Is Semidiscontinuous (semicontinuous) The DNA replicase advances continuously when it synthesizes the leading strand (5′ – 3′) 領先股. It synthesizes the lagging strand 落後股 by making short fragments that are subsequently joined together. Figure 18.9

8. Ex Biochem c18-DNA replication 8 18.7 The ϕ X Model System: Single-Stranded DNA Is Generated for Replication Replication requires a helicase to separate the strands of DNA using energy provided by hydrolysis of ATP. Figure 18.10

9. Ex Biochem c18-DNA replication 9 A single-strand binding protein is required to maintain the separated strands. The combination of helicase, SSB, and A protein separates a ϕ X174 duplex into: a single-stranded circle and a single-stranded linear strand Figure 18.11 18.7 The ϕ X Model System: Single-Stranded DNA Is Generated for Replication

10. Ex Biochem c18-DNA replication 10 18.8 Priming Is Required to Start DNA Synthesis All DNA polymerases require a 3′ – OH priming 啟 始 end to initiate DNA synthesis. Primer 起始子, 起始段, Figure 18.12

11. Ex Biochem c18-DNA replication 11 The priming end can be provided by: an RNA primer a nick in DNA a priming protein Figure 18.13 18.8 Priming Is Required to Start DNA Synthesis

12. Ex Biochem c18-DNA replication 12 For DNA replication, a special RNA polymerase called a primase synthesizes an RNA chain that provides the priming end. E. coli has two types of priming reaction, which occur at: the bacterial origin (oriC) the ϕ X174 origin 18.8 Priming Is Required to Start DNA Synthesis

13. Ex Biochem c18-DNA replication 13 Priming of replication on double-stranded DNA always requires: a replicase SSB primase DnaB is the helicase that unwinds DNA for replication in E. coli. Figure 18.14

14. Ex Biochem c18-DNA replication 14 18.9 DNA Polymerase Holoenzyme Has Three Subcomplexes The E. coli replicase DNA polymerase III is a 900-kD complex with a dimeric structure. Each monomeric unit has: a catalytic core a dimerization subunit a processivity component

15. Ex Biochem c18-DNA replication 15 A clamp loader places the processivity subunits on DNA. They form a circular clamp around the nucleic acid. One catalytic core is associated with each template strand. Figure 18.15 18.9 DNA Polymerase Holoenzyme Has Three Subcomplexes

16. Ex Biochem c18-DNA replication 16 18.10 The Clamp Controls Association of Core Enzyme with DNA The core on the leading strand is processive because its clamp keeps it on the DNA. Figure 18.17

17. Ex Biochem c18-DNA replication 17 The clamp associated with core on the lagging strand: dissociates at the end of each Okazaki fragment reassembles for the next fragment The helicase DnaB is responsible for interacting with the primase DnaG to initiate each Okazaki fragment. Figure 18.19 18.10 The Clamp Controls Association of Core Enzyme with DNA

18. Ex Biochem c18-DNA replication 18 Different enzyme units are required to synthesize the leading and lagging strands. 18.11 Coordinating Synthesis of the Lagging and Leading Strands Figure 18.20

19. Ex Biochem c18-DNA replication 19 In E. coli both these units contain the same catalytic subunit (DnaE). In other organisms, different catalytic subunits may be required for each strand. Figure 18.21 18.11 Coordinating Synthesis of the Lagging and Leading Strands

20. Ex Biochem c18-DNA replication 20 18.12 Okazaki Fragments Are Linked by Ligase 連結脢 Each Okazaki fragment 岡 崎片段 starts with a primer and stops before the next fragment. DNA polymerase I removes the primer and replaces it with DNA in an action that resembles nick translation. Figure 18.22

21. Ex Biochem c18-DNA replication 21 DNA ligase 連結酶 makes the bond that connects the 3′ end of one Okazaki fragment to the 5′ beginning of the next fragment. Figure 18.24 18.12 Okazaki Fragments Are Linked by Ligase

22. Ex Biochem c18-DNA replication 22 18.13 Separate Eukaryotic DNA Polymerase undertake Initiation and Elongation A replication fork has: one complex of DNA polymerase α/primase two complexes of DNA polymerase δ and/or ε The DNA polymerase α/primase complex initiates the synthesis of both DNA strands. DNA polymerase δ elongates the leading strand A second DNA polymerase δ or DNA polymerase ε elongates the lagging strand.

23. Ex Biochem c18-DNA replication 23 18.15 Creating the Replication Forks at an Origin Initiation at oriC requires the sequential assembly of a large protein complex. DnaA: binds to short repeated sequences forms an oligomeric complex that melts DNA Six DnaC monomers bind each hexamer of DnaB This complex binds to the origin. A hexamer of DnaB forms the replication fork. Gyrase and SSB are also required. Figure 18.28

24. Ex Biochem c18-DNA replication 24 18.16 Common Events in Priming Replication at the Origin The general principle of bacterial initiation is: The origin is initially recognized by a protein that forms a large complex with DNA. A short region of A-T-rich DNA is melted. DnaB is bound to the complex and creates the replication fork. Figure 18.31

25. Ex Biochem c18-DNA replication 25 Initiation of ϕ X replication requires the primosome complex to displace SSB from the origin. A replication fork stalls when it arrives at damaged DNA. After the damage has been repaired, the primosome is required to reinitiate replication. Figure 18.34 18.17 Primosome Needed to Restart Replication

26. Ex Biochem c18-DNA replication 26 The Tus protein binds to ter sites and stops DnaB from unwinding DNA, which causes replication to terminate. Figure 18.36 18.17 Primosome Needed to Restart Replication

27. Ex Biochem c18-DNA replication 27 Related videos https://www.youtube.com/watch?v=dKubyIR iN84 https://www.youtube.com/watch?v=dKubyIR iN84 http://www.youtube.com/watch?v=4jtmOZaI vS0 http://www.youtube.com/watch?v=4jtmOZaI vS0 http://www.youtube.com/watch?v=hfZ8o9D 1tus http://www.youtube.com/watch?v=hfZ8o9D 1tus

28. Polymerase chain reaction (PCR) 聚合酶連鎖反應 放大 DNA 數量 非常高的忠實度 人工 DNA 複製 加熱  Denaturation 變性  單股 DNA 65-95 C https://www.youtube.com/watch?v=iQsu3Kz 9NYo Ex Biochem c18-DNA replication 28