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DNA Structure: Nucleotides and Replication Mechanism

Understand the composition and function of DNA nucleotides, the process of replication, and repairs. Learn about telomeres, telomerase, and DNA polymerase. Figure out how DNA encodes protein sequences and the importance of precise DNA replication.

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DNA Structure: Nucleotides and Replication Mechanism

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  1. DNA Structure Chapter 16B AP Biology

  2. NUCLEOTIDES • Monomer of nucleic acids • Composed of • Base – A, T, C, G • Sugar – Deoxyribose • Phosphate – PO43- • Which elements are found in nucleic acids?

  3. Nucleosides vs. Nucleotides

  4. What energy is needed for polymerization? • Energy from coupled reactions drives polymerization • Nucleoside triphosphate • i.e. deoxyadenosine triphosphate • Not ATP!!! • Ribose vs. Deoxyribose • Triphosphate tail is unstable cluster of negative charge • Hydrolysis of the two phosphates(the ones taken off) drives polymerization • See pic on next slide

  5. BASES vs. SUGAR/PHOSPHATE • Outside (backbone) • Sugar – Phosphate – Sugar – Phosphate… • Covalently bonded • Inside (“rungs” of DNA ladder) • Bases • DNA: A = T; C = G • Hydrogen attracted

  6. ANTI-PARALLEL • 3’ – 5’ • 5’ – 3’ • Distinguishes DNA strand for identification, replication, transcription • Complementary strands

  7. Just some figures: • Each E. coli cell has 1 chromosome with 5 million base pairs • Cell replicates DNA and divides in < 1 hour • Each normal, human cell has 46 DNA molecules totaling 68 billion base pairs • Cell replicates DNA and divides in just a few hours So how does DNA replication work?

  8. Development of Semi-Conservative Model of DNA Replication

  9. Meselson and Stahl proved semi-conservative replication

  10. DNA Replication:Steps “in order” Chapter 16B

  11. Figure 16.10 Origins of replication in eukaryotes

  12. HELICASE • Enzyme that unwinds double helix, exposing replication fork • Breaks hydrogen attractions between base-pairs

  13. SINGLE-STRAND BINDING PROTEINS • Bind to open DNA single-strands to prevent DNA from sticking back together

  14. RNA PRIMASE • Binds a short piece of RNA nucleotides along the open DNA at origin of replication • Only 1 primer on leading strand • Each fragment needs primer on lagging strand • Jumpstarts DNA polymerase • Primers converted to DNA before fragments are joined by ligase

  15. Priming DNA synthesis

  16. DNA POLYMERASE • Comes in to join nucleotides together • About 50 bases/sec • Reads template strand from 3’-5’ only • Creates polynucleotide chains from 3’ end • Creates leading and lagging strands • Very specific enzyme • Adenosine triphosphate vs. Deoxyadenosine triphosphate • Sugars!!!!

  17. LEADING and LAGGING STRANDS • Leading Strand • Free nucleotides added easily and very quickly, one after another • In direction that polymerase can work (3’-5’) • Lagging Strand • Free nucleotides added in chunks • Okazaki Fragments • “Backwards” for polymerase

  18. Figure 16.13 Synthesis of leading and lagging strands during DNA replication

  19. LIGASE • Covalently bonds Okazaki fragments together (sugar/phosphate backbone)

  20. TOPOISOMERASES • Cuts and rejoins helix together as replication occurs • Decreases tangling of DNA strands

  21. TERMINATION • When DNA polymerase is at end • Primers are removed • Holes where primers were are now filled in and ligased • What about 5’ end? • Telomeres shortened • What’s a telomere?

  22. What are telomeres? • Noncoding, repetitive segments of DNA • TTAGGG • Prevent genes from being eroded through successive rounds of replication • Associated proteins prevent ends from activating “DNA damage control” • How can we restore telomere lengths? • Telomerase • Catalyzes lengthening of telomeres to original length in gamete formation • But how can it create new DNA segments without a template????

  23. Telomeres cont’d • Prokaryotes have circular DNA, so no problem • Eukaryotes have telomeres 100-1000 repetitions • Want this b/c 5’ end keeps shortening through generations of cells • 5’ → 3’ creation of new strand = no way to complete the 5’ ends….get shorter and shorter

  24. Figure 16.19a Telomeres and telomerase: Telomeres of mouse chromosomes

  25. REPARING and FIXING DNA • What if DNA is incorrect and needs to be fixed? • DNA polymerase is not 100% correct! • Errors every 10,000 bases (on average) • At completion, errors every 1 billion bases (on average) • Also, there are errors caused by • reactive chemicals, x ray, UV light, spontaneous changes • Constant repair is done by 130+ human enzymes • Exonuclease comes in and removes incorrect DNA sequence • DNA polymerase then fills nucleotide gaps • Ligase binds together

  26. Figure 16.17 Nucleotide excision repair of DNA damage

  27. Thymine Dimer Picture

  28. Figure 16.15 The main proteins of DNA replication and their functions

  29. Figure 16.16 A summary of DNA replication

  30. Xeroderma pigmentosa faulty repair mechanism

  31. In DNA, all the information there twice! • Correct order and complementary order • What initiates the replication process? • Why does it sometimes go out of control? • Why is DNA so important that we guard it inside nucleus, copy it meticulously, repair it constantly? • DNA SPECIFIES AMINO ACID SEQUENCE IN PROTEINS!!!

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