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BIO311: Molecular Biology

Unit 4: DNA Replication   High fidelity characteristics of DNA replication ensure that cell proliferation results in genetically identical daughter cells.  DNA polymerases synthesize a complement strand on the template strand, but the cooperation of many other proteins is needed as well.  First the strands of the dsDNA must be separated, and then a primer should be provided before the DNA polymerase can start to work. DNA polymerase continuously copies one strand of the dsDNA, but the complement is copied in pieces and must be ligated.  Circular dsDNA replicates to two identical dsDNA.  Linear dsDNA becomes shorter with each round of replication, because DNA polymerases have only 5'–>3' activity and cannot replace RNA primers.  This is why telomere regions become shorter and shorter during aging.

Unit 4 Time Advisory
This unit should take you approximately 13 hours to complete.

☐    Subunit 4.1: 3.5 hour

☐    Subunit 4.2: 3.0 hours

☐    Subunit 4.3: 3.0 hours

☐    Subunit 4.4: 1.5 hours

☐    Subunit 4.5: 1.0 hour

☐    Subunit 4.6: 1.0 hour

Unit4 Learning Outcomes
Upon successful completion of this unit, students will be able to: - Compare DNA replication in prokaryotes and eukaryotes. - Discuss how enzymes unwind dsDNA. - Discuss the role of primase in DNA proliferation. - Compare and contrast DNA synthesis on the leading and on the lagging strand. - Discuss the role of sliding clamps in DNA proliferation. - Describe the proofreading activity of DNA polymerase. - Compare and contrast replication of circular and linear DNAs. - Discuss telomere shortening and its link to aging.

4.1 General Mechanism of DNA Synthesis   - Reading: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" Link: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" (HTML)
 
Instructions: Please study the following sections: "An RNA Primer Synthesized by Primase Enables DNA Synthesis to Begin;" "One Strand of DNA Is Made Continuously, Whereas the Other Strand Is Synthesized in Fragments;" "DNA Ligase Joins Ends of DNA in Duplex Regions;" "DNA Replication Requires Highly Processive Polymerases;" "The Leading and Lagging Strands Are Synthesized in a Coordinated Fashion;" and "DNA Synthesis Is More Complex in Eukaryotes than in Prokaryotes."  In prokaryotes, DNA synthesis takes place in the cytoplasm; in eukaryotes, DNA synthesis takes place in the nucleus.
 
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  • Web Media: YouTube: Mrjonthetube's "DNA Replication Animation" Link:  YouTube: Mrjonthetube's "DNA Replication Animation" (YouTube)
     
    Instruction: Please watch this video (1 min).
     
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  • Web Media: YouTube: Oregon State University: Kevin Ahern's "DNA Replication, Recombination, Repair II" Link: YouTube: Oregon State University: Kevin Ahern's "DNA Replication, Recombination, Repair II" (YouTube)
     
    Instruction: Please watch this video (50 min).
     
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  • Web Media: YouTube: Oregon State University: Kevin Ahern's " DNA Replication, Recombination, Repair III" Link: YouTube: Oregon State University: Kevin Ahern's "DNA Replication, Recombination, Repair III" (YouTube)
     
    Instruction: Please watch this video (50 min).
     
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  • Assessment: University of Arizona: The Biology Project: "Problem 3: The Replication Fork," "Problem 4: The Replication Fork," and "Problem 5: More on the Replication Fork" Link:  University of Arizona: The Biology Project: "Problem 3: The Replication Fork," (HTML) "Problem 4: The Replication Fork," (HTML) and "Problem 5: More on the Replication Fork" (HTML)
     
    Instruction: Please complete these problems. After answering a question, please click on and study each tutorial page as well.
     
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4.2 Mechanisms of DNA Replication   4.2.1 Topoisomerase   - Reading: NCBI Bookshelf: Lodish et al's "The Role of Topoisomerases in DNA Replication" Link:  NCBI Bookshelf: Lodish et al's "The Role of Topoisomerases in DNA Replication" (HTML)
 
Instruction: Please read this page.

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  • Web Media: YouTube: rdb07959's "Topoisomerase 1 and 2" Link:  YouTube: rdb07959's "Topoisomerase 1 and 2"(YouTube)
     
    Instruction: Please watch this video (2 min).
     
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4.2.2 Helicase   - Reading: NCBI Bookshelf: Berg et al's "DNA Polymerases Require a Template and a Primer" Link:  NCBI Bookshelf: Berg et al's "DNA Polymerases Require a Template and a Primer" (HTML)
 
Instruction: Please read "The Separation of DNA Strands Requires Specific Helicases and ATP Hydrolysis" section on this page.
 
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  • Web Media: YouTube: GarlandScience's "DNA Helicase" Link: YouTube: GarlandScience's "DNA Helicase"(YouTube)
     
    Instruction: Please watch this video (2 min).
     
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4.2.3 Origin of Replication   - Reading: NCBI Bookshelf: Lodish et al's "General Features of Chromosomal Replication" Link:  NCBI Bookshelf: Lodish et al's "General Features of Chromosomal Replication" (HTML)
 
Instructions:  Please read the "DNA Replication Begins at Specific Chromosomal Sites" section on this page.
 
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4.3 The Replication Fork   4.3.1 Template Dependent DNA Polymerases   - Reading: NCBI Bookshelf: Berg et al.’s "DNA Polymerases Require a Template and a Primer" Links: NCBI Bookshelf: Berg et al.’s "DNA Polymerases Require a Template and a Primer" (HTML)
 
Instructions: Please study this page.  Please note that DNA polymerases cannot start the synthesis of a complement DNA strand, but they can add nucleotides to the 3' end of a polynucleic acid.
 
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4.3.2 Primase   - Reading: City of Hope National Medical Center: Li Zheng and Binghui Shen’s "Okazaki Fragment Maturation: Nucleases Take Centre Stage" Links: City of Hope National Medical Center: Li Zheng and Binghui Shen’s "Okazaki Fragment Maturation: Nucleases Take Centre Stage" (HTML)
 
Instructions: Please read the "Introduction" section on this page.  Please note that primase is priming both the leading and the lagging strands.
 
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4.3.3 Leading and Lagging Strands   - Reading: NCBI Bookshelf: Cooper’s "DNA Replication" Links: NCBI Bookshelf: Cooper’s "DNA Replication" (HTML)
 
Instructions: Please study the "The Replication Fork" section on this page.  Please note that the DNA synthesis on the lagging strand results in short DNA segments with RNA at their 5' end: These are the Okazaki fragments.  These fragments are linked to each other by the DNA ligase enzyme after the RNA is replaced by DNA. 
 
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  • Web Media: YouTube: FreeScienceLectures' "DNA Replication Process" Link:  YouTube: FreeScienceLectures' "DNA Replication Process" (YouTube)
     
    Instruction: Please watch this video (2 min).
     
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4.4 Sliding DNA Clamps   - Reading: St. Edward's University’s "Sliding DNA Clamp—Clamp Loader Complex" Links: St Edward's University’s "Sliding DNA Clamp—Clamp Loader Complex" (HTML)
 
Instructions:  Please read this page.
 
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4.5 Proofreading Mechanisms   - Reading: NCBI Bookshelf: Alberts et al.'s "DNA Replication Mechanisms" Link: NCBI Bookshelf: Alberts et al.'s "DNA Replication Mechanisms" (HTML)
 
Instructions:  Please study "The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms" and "Only DNA Replication in the 5'-to-3' Direction Allows Efficient Error Correction" sections on this page. 
 
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4.6 Telomeres and the End-Replication Problem   - Reading: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" Link: NCBI Bookshelf: Berg et al.'s "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites" (HTML)
 
Instructions:  Please study the "Telomeres Are Unique Structures at the Ends of Linear Chromosomes" and "Telomeres Are Replicated by Telomerase, a Specialized Polymerase That Carries Its Own RNA Template" sections on this page.  Please notice that only linear chromosomes have telomere regions.  Also, telomere regions become shorter as the cell grows older. 
 
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  • Reading: University of Liverpool: Dr. João Pedro de Magalhães's "Cellular Senescence" Link: University of Liverpool: Dr. João Pedro de Magalhães's "Cellular Senescence" (HTML)
     
    Instructions:  Please study this page. 
     
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