DNA

1. DNA The Molecule of Life: Replication

2. Replication: • Why? • When cells replicate, each new cell needs it’s own copy of DNA. • Where? • Nucleus in Eukaryotes. • Cytosol in Prokaryotes

3. Replication: • When? • S phase of cell cycle (S for synthesis, during interphase) • What? • Many proteins involved as enzymes: major one is DNA Polymerase • How?

4. Replication (def’ns) • Using one side of the DNA strand as a TEMPLATE to make a complementary side.

5. Replication - (def’ns-cont’d) • Template – parental strand • Complementary copy – daughter strand • Both sides of the DNA double strand do this. • End result – two identical double helixes (helices).

6. DNA Replication is Semiconservative • Each double helix has one parent strand that is conserved and one daughter strand that is new • The new strand forms by base-pairing that is complementary to the parent strand. (A-T and C-G) • Meselson and Stahl Experiment http://preuniversity.grkraj.org/html/10_MOLECULAR_BIOLOGY.htm

7. http://www.cpsd.us/CRLS/LC_R/classrooms/AUGUSTINE/DNA_structure_function/index_files/frame.htmlhttp://www.cpsd.us/CRLS/LC_R/classrooms/AUGUSTINE/DNA_structure_function/index_files/frame.html Semiconservative:

8. Replication: Here’s How • How? • Enzymes! • 5’3’ directionality • Starts with RNA primer • Leading Strand • Lagging Strand • Okasaki Fragments • Sequence determined by base pairing • DNA Replication Animation

9. Replication: Prerequisites • Parent DNA needs to unwind and “unzip” • The hydrogen bonds between the paired bases break. • RECALL hydrogen bonds are not really bonds, they are forces between atoms of H and either N or O (for DNA and RNA). • Weaker than covalent bonds in rungs • Phosphate/sugar bond • Nucleotide bases are always present in the nucleus

10. Replication Enzymes • Helicase: the enzyme required to unwind and split the H-bonds in the DNA double helix – exposing the bases. • Primase is the enzyme that lays down the RNA primer (establishes starting point) • Needs a “primer” or a place to start from—they cannot pick up the first two required nucleotides unless they have the RNA primer (primase).

11. DNA Polymerase: • DNA Polymerase III recognizes the exposed bases and matches them up with free, complementary nucleotides (H bonds). • Theenzyme then bonds the sugars and phosphates together to form the backbone of the new strand

12. Proofreading 5. Makes only one mistake every 10^8 or 10^11 bases it adds. Has proof-reading abilities! • A single strand of DNA has about 10^7 – 10^11 base pairs • DNA replication occurs fairly quickly; as many as 4000 nucleotides per second are replicated. • This helps explain why bacterial cells, under ideal conditions, can reproduce in 20 minutes.

13. Proofreading (cont’d) 6. DNA polymerase I removes the RNA primers when done and fills in the RNA gaps with DNA. • DNA ligase seals any nicks in the DNA by linking up the deoxyribose to the phosphate to seal the new DNA strand together. • There are a few others, but this is enough for now.

14. Enzyme Summary http://www.nature.com/nature/journal/v421/n6921/box/nature01407_bx1.html

15. Deoxy vs ribose sugar http://www.mun.ca/biology/scarr/iGen3_02-07.html

16. 5’ to 3’ Direction http://www.sciencegeek.net/Biology/review/U5Storyboard.htm

17. 5’ to 3’ http://click4biology.info/c4b/7/pro7.2.htm#one Animation

18. Replication is 5’-3’ • Replication is always 5’ to 3’. But this means one strand is made in one long segment but the other ends up in fragments… http://www.britannica.com/EBchecked/media/110068/In-semiconservative-DNA-replication-an-existing-DNA-molecule-is-separated

19. One strand: Continuous • One strand of DNA is synthesized continuously from 5’ to 3’ end. • This strand is called the leading strand • It is called this because it requires only one primer • Replication proceeds in the same direction/towards as the replication fork in the DNA strand • At the end of the strand, a TELOMERE is added by another enzyme. • Telomere: none-coding redundant sequences.

20. Other: Discontinuous • The other strand of DNA is synthesized discontinuously – in pieces – because it also needs to be made 5’ to 3. • This strand is called the lagging strand. • The many small fragments are called Okazaki fragments

21. Other: Discontinuous It requires multiple primers because it replications AWAY from the replication fork As a fork opens up, a RNA primer attaches, DNA polymerase adds bases 5’ to 3’ until it reaches the “other” RNA primer. This process continues as the fork opens up until the end of the DNA. At the end, another enzyme adds a telomere.

22. http://www.esb.utexas.edu/mabrybio211/chapter05/ch5.htm)

23. DNA polymerase assembles new complementary strands http://dnainfo.wikispaces.com/DNA+Replication

24. SUMMARY and demo • How? • Enzymes make it happen correctly. There are many • 5’3’ directionality for both strands • Starts with RNA primer for DNA polymerase to attach • Leading Strand is continuous • Lagging Strand is discontinuous • Okasaki Fragments are connected by polymerase I • Sequence determined by complementary basepairing • enzyme roles • Replication animation-slow • Animation-johnkyrk • Animation-fast

25. Sources of info, Assignments • Good sources of info: • Your textbook! Chapter 11 pg. 280-287 • Especially pg 286-287 Copying DNA Fig 11.5 • Assignment • Worksheets • Text pg. 287 Q 1-5 ? • The internet has a LOT of good animations you could view. Google DNA replication animations.