Chapter 2 & 3: DNA Structure and Replication

1. Chapter 2 & 3: DNA Structure and Replication Ms. Gaynor Honors Genetics

2. DNA and Its Structure (Part 2) • From 1953

3. DNA and RNA are nucleic acids • An important macromolecule in organisms that stores and carries genetic information Recall…

4. What is the Double Helix? • Shape of DNA • Looks like a twisted ladder • 2coils are twisted around each other • Double means 2 • Helix means coil

5. The Structure of DNA • Made out of nucleotides • Includes a phosphate group, nitrogenous base and 5-carbon pentose sugar Nucleotide Structure 1 “link” in a DNA chain

6. A Polynucleotide • MANY nucleotides (“links”) bonded together DNA has a overall negative charge b/c of the PO4-3 (phosphate group)

7. The Structure of DNA • Backbone = alternating P’s and sugar • Held together by COVALENT bonds (strong) • Inside of DNA molecule = nitrogen base pairs • Held together by HYDROGEN bonds (weaker) Backbone

8. Phosphodiester Bond • The covalent that holds together the backbone • Found between P & deoxyribose sugar • STRONG!!!

9. Minor Groove Major Groove

10. DNA is antiparallel • Antiparallel means that the 1st strand runs in a 5’ 3’ direction and the 2nd 3’ 5’ direction • THEY RUN IN OPPOSITE or ANTIPARALLEL DIRECTIONS • P end is 5’ end (think: “fa” sound) • -OH on deoxyribose sugar is 3’ end • 5’ and 3’ refers to the carbon # on the pentose sugar that P or OH is attached to

11. DNA in Cells • 2 broad categories of cells 1. Eukaryotic cells: have nucleus with DNA • DNA is contained in structure called a chromosome • Chromosomes are a LINEAR (line) shape with ENDS called telomeres (protective “caps”) 2. Prokaryotic cells: no nucleus (nucleoid region instead) which contains DNA • DNA is a CIRCULAR shaped chromosome without ENDS (no telomeres)

12. DNA Bonding • Purines (small word, big base) • Adenine • Guanine • Pyrimidines • (big word, small base) • Cytosine • Thymine • Chargaff’s rules • A=T, C=G • Hydrogen Bondsattractions between the stacked pairs; WEAK bonds

13. Why Does a Purine Always Bind with A Pyrimidine?

14. DNA Double Helix • http://www.sumanasinc.com/webcontent/animations/content/DNA_structure.html • Watson & Crick said that… • strands are complementary; nucleotides line up on template according to base pair rules (Chargaff’s rules) • A to T and C to G • LET’S PRACTICE… • Template: 5’AATCGCTATAC3’ • Complementary strand: 3’ TTAGCGATATG5’

15. DNA Replication(Part 3A-initiation)

16. DNA Replication • DNA Replication = DNA  DNA • Parent DNA makes 2 exact copies of DNA • Why?? • Occurs in Cell Cycle before MITOSIS so each new cell can have its own FULL copy of DNA

17. Models of DNA Replication http://www.sumanasinc.com/webcontent/animations/content/meselson.html

18. DNA Replication • How does it occur? • Matthew Meselson & Frank Stahl • Discovered replication is semiconservative • PROCEDURE varying densities of radioactive nitrogen (Nitrogen is in DNA)

19. Meselson & Stahl Experiment**DNA is semiconservative http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html

20. DNA Replication: a closer look http://henge.bio.miami.edu/mallery/movies/replication.mov

21. DNA Replication Steps: • Initiation • involves assembly of replication fork (bubble) at origin of replication • sequence of DNA found at a specific site • Elongation • Parental strands unwind and daughter strands are synthesized. • the addition of bases by proteins • Termination: • the duplicated chromosomes separate from each other. Now, there are 2 IDENTICAL copies of DNA.

22. Segments of single-stranded DNA are called template strands. Copied strand is called the complement strand (think “c” for copy) BEGINNING OF DNA REPLICATION (INITIATION) • Gyrase (type of topoisomerase) • relaxes the supercoiled DNA. • DNA helicase (think “helix”) • binds to the DNA at the replication fork • untwist (“unzips”) DNA using energy from ATP • Breaks hydrogen bonds between base pairs • Single-stranded DNA-binding proteins (SSBP) • stabilize the single-stranded template DNA during the process so they don’t bond back together.

23. Supercoiled DNA relaxed by gyrase & unwound by helicase SSB Proteins 5’ SSB Proteins ATP Helicase Gyrase 3’ base pairs 5’ 3’ http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

24. DNA Replication (Elongation) After SSBP’s bind to each template… • RNA Primase binds to helicase • primase is required for DNA synthesis • Like a “key” for a car ignition • makes a short RNA primers • Short pieces of RNA needed for DNA synthesis • DNA polymerase • adds nucleotides to RNA primer  makes POLYNUCLEOTIDES (1st function) • After all nucleotides are added to compliment strand… • RNA primeris removed and replaced with DNA by DNApolymerase (2nd function) • DNA ligase • “seals” the gaps in DNA • Connects DNA pieces by making phosphodiester bonds

25. Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins: 5’ SSB Proteins ATP 1 DNA Polymerase 2 Helicase Gyrase 3’ primase base pairs 5’ DNA Polymerase RNA primer replaced by DNA Polymerase & gap is sealed by ligase Leading strand RNA Primer 3’ http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

26. Elongation Antiparallel nature: • Sugar (3’end)/phosphate (5’ end) backbone runs in opposite directions • one strand runs 5’  3’, • other runs 3’  5’ • DNA polymerase only adds nucleotides at the free 3’ end of NEW STRANDforming new DNA strands in the 5’  3’ direction only!!!

28. Elongation (con’t) • Leading (daughter) strand • NEW strand made toward the replication fork (only in 5’  3’ direction from the 3’  5’ master strand • NeedsONE (1)RNA primer made by Primase • This new leading strand is made CONTINOUSLY

29. Elongation (con’t) Lagging (daughter) strand • NEW strand synthesis away from replication fork • Replicate DISCONTINUOUSLY • Creates Okazaki fragments • Short pieces of DNA • Okazaki fragments joined by DNA ligase • “Stitches” fragments together • Needs MANYRNA primer made by Primase

30. Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins: 5’ SSB Proteins Okazaki Fragments 1 DNA Polymerase ATP 2 3 Gyrase Lagging strand Helicase 3’ primase base pairs 5’ DNA Polymerase RNA primer replaced by DNA Polymerase & gap is sealed by DNA ligase 5’  3’ RNA Primer Leading strand 3’ http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

32. DNA Replication:Elongation http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html

33. DNA Replication(Part 3C-termination)

34. Termination (Telomeres) • Telomeres • Short repeats of “G” base found at END of LINEAR chromosomes in eukaryotes • protect ends of linear chromosomes • The repeated sequence of GGGTTA make up the human telomeres. • Telomerase is the enzyme that makes telomeres.

35. Telomeres, Aging & Cancer • Telomeres get shorter as cell divides leads to aging??? • Most cancers come from body cells. • Cancers cell have ability to divide indefinitely. • Normal cells limited to ~50-75 divisions  stop making telomerase. • 85–90% cancer cells continue to make high levels of telomerase & are able to prevent further shortening of their telomeres. • Leads to “immortality”

36. Mistakes Made during DNA Replication • Mutation • Change in DNA (genetic material) • Frameshift(s) • extra or missing base(s). • Substitutions • when the wrong nucleotide is incorporated (mismatch mutation). • Deletions • Nucleotides are deleted shortening the DNA

37. DNA Repair Errors occur 1/10 billion nucleotides (Humans have 3 billion base pairs in their DNA) • Mismatch repair • DNA polymerase (yes…it’s 3rd function) • “Proofread” new DNA • Like the “delete” key on computer • Excision (“cut out”) repair • Nuclease

39. DNA Repair