2. Chapter 6

3. DNA  Consists of Deoxyribose sugar Phosphate group A, T, C, G  Double stranded molecule (Double Helix) Two strands of DNA run antiparallel to each other (opposite direction) 5’ to 3’ 5’ is the end with the phosphate group 3’ is where deoxyribose sugar is located  Nitrogenous bases Held together by hydrogen bonds A pairs with T ( forms double bond) C pairs with G (forms a triple bond)

4. Four Requirements for DNA to be Genetic Material Must carry information Cracking the genetic code Must replicate DNA replication Must allow for information to change Mutation Must govern the expression of the phenotype Gene function

5. DNA Replication Process of duplication of the entire genome prior to cell division Biological significance  extreme accuracy of DNA replication is necessary in order to preserve the integrity of the genome in successive generations  In eukaryotes, replication only occurs during the S phase of the cell cycle. Mitosis -prophase -metaphase -anaphase -telophase G1G1 G2G2 S phase interphase

6. Basic rules of replication A.Semi-conservative B.Starts at the ‘origin’ C.Synthesis always in the 5-3’ direction D.Semi-discontinuous E.RNA primers required

7. Mechanism of DNA Replication  Step 1: Strand Separation Proteins bind to DNA and open up double helix Prepare DNA for complementary base pairing  Step 2: Building Complementary Strands Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA  Step 3: Dealing With Errors during DNA Replication Proteins release the replication complex

8. DNA Replication is Semi-Conservative  Separating the two parent strands and building new complementary strand for each  New DNA has one new strand and one old strand

9. Strand Separation  Double Helix Unwound at replication origins (many origins on DNA) Enzyme called helicase binds to origins and unwinds the two strands creating replication bubbles Two strands separating creates a replication fork

10. Strand Separation  Unwinding DNA creates tension Enzymes called topoisomerases relieves tension by cutting strands near the replication fork (supercoil)  Single strands want to join back together Prevented by single-strand binding proteins (SSBs) by attaching to the DNA strands stabilizing them

11. Topoisomerase Enzyme DNA Enzyme

12. Strand Separation Multiple replication origins decrease the overall time of DNA replication to about 1 hour

13. Building Complementary Strands  DNA polymerase III Adds nucleotides to the 3’ end of a strand New strands are always assembled 5’ to 3’ Builds new strand using nucleoside triphosphates

14. Building Complementary Strands  RNA primase begins the replication process Builds small complementary RNA segments on strand at beginning of replication fork RNA primers DNA polymerase III can start to add nucleotides

15. Building Complementary Strands  Leading Strand DNA that is copied in the direction toward the replication fork  Lagging Strand DNA that is copied in the direction away from the replication fork

16. Leading and Lagging Strands DNA polymerase III 5 3 5 3 leading strand lagging strand leading strand lagging strand leading strand 5 3 3 5 5 3 5 3 5 3 5 3 growing replication fork growing replication fork 5 5 5 5 5 3 3 5 5 lagging strand 5 3

17. Building Complementary Strands Anti parallel strands replicated simultaneously  Leading strand synthesis continuously in 5’– 3’  Lagging strand synthesis in fragments in 5’-3’

18. Leading Strand  Single primer is used to start strand  DNA polymerase III moves towards replication fork 5’ to 3’ direction  Continuous

19. Lagging Strand  DNA polymerase III moves away from replication fork  Discontinuous  Okazaki fragments are used to solve problem 1000 – 2000 base pairs long  Multiple primers are used

20. Lagging Strand  DNA polymerase I removes RNA primers and replaces with DNA nucleotide  Fills the gaps

21. Building Complementary Strands  DNA ligase Links last nucleotide to Okazaki fragment Formation of phosphodiester bond

22. Dealing With Errors  DNA polymerase Proofread and correct errors Errors are usually base pair mismatches  After replication Average of 1 error per million base pairs  DNA polymerase II Repairs damage after strands have been synthesized

23. Loss of bases at 5 ends in every replication DNA polymerase I cannot replace final RNA primer DNA polymerase III DNA polymerases can only add to 3 end of an existing DNA strand Chromosome Erosion 5 5 5 5 3 3 3 3 growing replication fork DNA polymerase I

24. Does it Create a Problem?

25. Repeating, non-coding sequences at the end of chromosomes = protective cap  limit to ~50 cell divisions  enzyme extends telomeres  can add DNA bases at 5 end  different level of activity in different cells  high in stem cells & cancers -- Why? telomerase Telomeres 5 5 5 5 3 3 3 3 growing replication fork TTAAGGG

26. Cells Aging Process  Cell senescence Cells loses ability to function properly as a person ages  Decrease in telomeres with age No longer provide protection for the chromosome  Known as the Hayflick limit  Possibly links to age- related diseases Dementia, atherosclerosis, macular degeneration

27. Packing of Eukaryotic DNA  Organization Negative DNA wraps around positive histones Nucleosome – cluster of 8 histones Solenoids – coiled strings of nucleosomes (chromatin fibres)

28. Prokaryotic DNA Organization  Eubacteria/Archaea DNA One chromosome – circular in shape Unbound by a nuclear membrane

29. Genetic Variation Among Bacteria  Plasmids Smaller circular pieces of DNA that float throughout cell  Conjugation Plasmids are able to exit one cell and enter another (when two bacteria are close)  Useful in genetic engineering