2. DNA Replication

3. Functions of DNA 1. Replication – Occurs before Mitosis and meiosis only Produces an exact copy of DNA 2. Transcription – DNA makes mRNA in order to make protein (DNA---RNA----Protein) This is the function of individual genes

4. proteinRNA The “Central Dogma” DNA Flow of genetic information in a cell Replication transcriptiontranslation

5. Double helix structure of DNA “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”Watson & Crick

6. Models of DNA Replication Alternative models –become experimental predictions Can you design a nifty experiment to verify? 1 2 P ConservativeSemi conservativeDispersive

7. Semiconservative replication Meselson & Stahl –label “parent” nucleotides in DNA strands with heavy nitrogen = 15 N –label new nucleotides with lighter isotope = 14 N “The Most Beautiful Experiment in Biology” 1958 parentreplication Make predictions … 15 N parent strands 15 N/ 15 N

8. Predictions 1st round of replication conservative N-14 semi- conservative dispersive conservative semi- conservative dispersive 2nd round of replication 15 N parent strands 15 N/ 15 N 1 2 P N-15 N-14/N-15 N-14______ N-15 N-14 N-14/N-15

9. http://highered.mcgraw- hill.com/olc/dl/120076/bio22.swf http://highered.mcgraw- hill.com/olc/dl/120076/bio23.swf

10. DNA Replication Semi- Conservative replication Each half of the old DNA makes a new half Thus, The two new DNA’s are half “old” and half “new”

11. Directionality of DNA You need to number the carbons! –it matters! OH CH 2 O 4 5 3 2 1 PO 4 N base ribose nucleotide This will be IMPORTANT!!

12. The DNA backbone Putting the DNA backbone together –refer to the 3 and 5 ends of the DNA the last trailing carbon OH O 3 PO 4 base CH 2 O base O P O C O –O–O CH 2 1 2 4 5 1 2 3 3 4 5 5 Sounds trivial, but … this will be IMPORTANT!!

13. Anti-parallel strands Nucleotides in DNA backbone are bonded from phosphate to sugar between 3 & 5 carbons –DNA molecule has “direction” –complementary strand runs in opposite direction –This is called “anti-parallel” 3 5 5 3

14. Bonding in DNA ….strong or weak bonds? How do the bonds fit the mechanism for copying DNA? 3 5 3 5 covalent phosphodiester bonds hydrogen bonds

15. Base pairing in DNA Purines –adenine (A) –guanine (G) Pyrimidines –thymine (T) –cytosine (C) Pairing –A : T 2 bonds –C : G 3 bonds

16. Copying DNA Replication of DNA –base pairing allows each strand to serve as a template for a new strand –new strand is 1/2 parent template & 1/2 new DNA semi-conservative copy process

17. Names you need to know Origin of replication Replication fork Helicase Primer and primase DNA polymerase Leading and laggin strands Okasaki fragments ligase

18. animation Replication replication2

19. DNA Replication Large team of enzymes coordinates replication

20. DNA Polymerase III Replication: 2nd step But … We ’ re missing something! What? Where ’ s the ENERGY for the bonding! Build daughter DNA strand –add new complementary bases –DNA polymerase III

21. energy ATP Energy of Replication Where does energy for bonding usually come from? ADPAMP modified nucleotide energy We come with our own energy! And we leave behind a nucleotide!

22. Adding bases –can only add nucleotides to 3 end of a growing DNA strand need a “starter” nucleotide to bond to –strand only grows 5  3 DNA Polymerase III DNA Polymerase III DNA Polymerase III DNA Polymerase III energy Replication energy 3 3 5 B.Y.O. ENERGY! The energy rules the process 5

23. energy 35 5 5 3 need “primer” bases to add on to energy 3 no energy to bond energy ligase 35 

24. Limits of DNA polymerase III –can only build onto 3 end of an existing DNA strand Leading & Lagging strands 5 5 5 5 3 3 3 5 3 5 3 3 Leading strand Lagging strand Okazaki fragments ligase Okazaki Leading strand –continuous synthesis Lagging strand –Okazaki fragments –joined by ligase “spot welder” enzyme DNA polymerase III  3 5 growing replication fork

25. DNA polymerase III Replication fork / Replication bubble 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

26. DNA polymerase III RNA primer –built by primase –serves as starter sequence for DNA polymerase III Limits of DNA polymerase III –can only build onto 3 end of an existing DNA strand Starting DNA synthesis: RNA primers 5 5 5 3 3 3 5 3 5 3 5 3 growing replication fork primase RNA

27. DNA polymerase I –removes sections of RNA primer and replaces with DNA nucleotides But DNA polymerase I still can only build onto 3 end of an existing DNA strand Replacing RNA primers with DNA 5 5 5 5 3 3 3 3 growing replication fork DNA polymerase I RNA ligase

28. DNA replication film http://www.hhmi.org/biointeractive/dna- replication-basic-detailhttp://www.hhmi.org/biointeractive/dna- replication-basic-detail

29. Loss of bases at 5 ends in every replication –chromosomes get shorter with each replication –limit to number of cell divisions? DNA polymerase III All 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 RNA Houston, we have a problem!

30. Repeating, non-coding sequences at the end of chromosomes = protective cap –limit to ~50 cell divisions Telomerase –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

31. DNA polymerases DNA polymerase III –1000 bases/second! –main DNA builder DNA polymerase I –20 bases/second –editing, repair & primer removal DNA polymerase III enzyme Arthur Kornberg 1959 Roger Kornberg 2006

32. Editing & proofreading DNA 1000 bases/second = lots of typos! DNA polymerase I –proofreads & corrects typos –repairs mismatched bases –removes abnormal bases repairs damage throughout life –reduces error rate from 1 in 10,000 to 1 in 100 million bases

33. Fast & accurate! It takes E. coli <1 hour to copy 5 million base pairs in its single chromosome –divide to form 2 identical daughter cells Human cell copies its 6 billion bases & divide into daughter cells in only few hours –remarkably accurate –only ~1 error per 100 million bases –~30 errors per cell cycle