2. AP Biology A A A A T C G C G T G C T

3. Macromolecules: Nucleic Acids  Examples:  RNA (ribonucleic acid)  single helix  DNA (deoxyribonucleic acid)  double helix  Structure:  monomers = nucleotides RNADNA

4. AP Biology Nucleotides  3 parts  nitrogen base (C-N ring)  pentose sugar (5C)  ribose in RNA  deoxyribose in DNA  phosphate (PO 4 ) group Are nucleic acids charged molecules? Nitrogen base I’m the A,T,C,G or U part!

5. AP Biology Types of nucleotides  2 types of nucleotides  different nitrogen bases  purines  double ring N base  adenine (A)  guanine (G)  pyrimidines  single ring N base  cytosine (C)  thymine (T)  uracil (U) Purine = AG Pure silver!

6. AP Biology Nucleic polymer  Backbone  sugar to PO 4 bond  phosphodiester bond  new base added to sugar of previous base  polymer grows in one direction  N bases hang off the sugar-phosphate backbone Dangling bases? Why is this important?

7. AP Biology Pairing of nucleotides  Nucleotides bond between DNA strands  H bonds  purine :: pyrimidine  A :: T  2 H bonds  G :: C  3 H bonds Matching bases? Why is this important?

8. AP Biology DNA molecule  Double helix  H bonds between bases join the 2 strands  A :: T  C :: G H bonds? Why is this important?

9. AP Biology Copying DNA  Replication  2 strands of DNA helix are complementary  have one, can build other  have one, can rebuild the whole Matching halves? Why is this a good system?

10. AP Biology When does a cell copy DNA?  When in the life of a cell does DNA have to be copied?  cell reproduction  mitosis  gamete production  meiosis

11. AP Biology Learning Check  Use the candy and instructions to build a DNA model that follows Chargaff’s rules of base pairing

12. AP Biology But how is DNA copied?  Replication of DNA  base pairing suggests that it will allow each side to serve as a template for a new strand

13. AP Biology Models of DNA Replication  Alternative models  become experimental predictions conservativesemiconservative Can you design a nifty experiment to verify? dispersive 1 2 P

14. AP Biology Semiconservative replication  Meselson & Stahl  label “parent” nucleotides in DNA strands with heavy nitrogen = 15 N  label new nucleotides with lighter isotope = 14 N 1958 parentreplication Make predictions … 15 N parent strands 15 N/ 15 N

15. AP Biology Semiconservative replication  Make predictions…  15 N strands replicated in 14 N medium  1st round of replication?  2nd round? 1958 where should the bands be?

16. AP Biology Franklin Stahl Matthew Meselson Franklin Stahl Meselson & Stahl

17. AP Biology DNA Replication  Origin(s) of replication  specific sequence of nucleotides recognized by replication enzymes  Prokaryotes –  Single sequence  Bidirectional Synthesis  Replication proceeds in both directions  Eukaryotes –  hundreds/thousands of origin sites per chromosome  Replication forks  Bubbles elongate as DNA is replicated and eventually fuse

18. AP Biology Bidirectional Synthesis  In prokaryotes, the circular DNA is opened up, and synthesis occurs in both directions

19. AP Biology  In eukaryotes, the linear DNA has many replication forks Replication forks

20. AP Biology

21. Learning Check  Break the toothpicks at the center of your models and replicate your DNA strand  You should end up with 2 complete strands of DNA  Keep in mind Chargaff’s rules and Meselson & Stahl’s semi-conservative model  Animation Animation

22. AP Biology Replication- Create a diagram that shows how the following components interact with each other (15 min)  Lagging strand  Helicase  DNA polymerase  Single stranded binding protein  Topoisomerase  Replication fork  RNA primer  Leading strand  DNA ligase  RNA primase  Okazaki fragments

23. AP Biology DNA Replication Issues 1. DNA strands must be unwound during replication  DNA helicase  unwinds the strands  Single stranded binding proteins (SSB)  prevent immediate reformation of the double helix  Topoisomerases  “untying” the knots that form

24. AP Biology Replication Issues 2. A new DNA strand can only elongate in the 5’  3’ direction  DNA polymerase can add only at the 3’ end  Replication is continuous on one strand  Leading Strand  discontinuous on the other  Lagging strand  Okazaki fragments

25. AP Biology Okazaki fragments  Synthesis of the leading strand is continuous  The lagging strand (discontinuous) is synthesized in pieces called Okazaki fragments

26. AP Biology

27. Replication Issues 3. DNA polymerase cannot initiate synthesis because it can only add nucleotides to end of an existing chain  Requires a “primer” to get the chain started  RNA Primase  can start an RNA chain from a single template strand  DNA polymerase can begin its chain after a few RNA nucleotides have been added

28. AP Biology

29. Summary  At the replication fork, the leading strand is copied continuously into the fork from a single primer  Lagging strand is copied away from the fork in short okazaki fragments, each requiring a new primer

30. AP Biology

31. Learning Check 1. What is the purpose of DNA replication? 2. How is the new strand ensured to be identical to the original strand? 3. How is replication on one side of the strand different from the other side?

32. AP Biology Replication Issues 4. Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA  Repeated rounds of replication produce shorter and shorter DNA molecules  Telomeres  protect genes from being eroded through multiple rounds of DNA replication

33. AP Biology Telomeres  Ends of eukaryotic chromosomes, the telomeres, have special nucleotide sequences  Humans - this sequence is typically TTAGGG, repeated 100 - 1,000 times  Telomerase adds a short molecule of RNA as a template to extend the 3’ end  Room for primase & DNA pol to extend 5’ end

34. AP Biology Summary  Explain how the cell overcomes each of the following issues in DNA replication 1. DNA strands must be unwound during replication 2. A new DNA strand can only elongate in the 5’  3’ direction 3. DNA polymerase cannot initiate synthesis and can only add nucleotides to end of an existing chain 4. Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA