1. Engineering magnetosomes to express novel proteins Which ones? Must be suitable for expressing in Magnetospyrillum! Can’t rely on glycosylation, disulphide bonds, lipidation, selective proteolysis, etc for function! Best bets are bacterial proteins Alternatives are eukaryotic proteins that don’t need any of the above Short peptides Tweaking p18 Linker Deleting or replacing GFP TRZN Oxalate decarboxylases Lactate dehydrogenase or other oxalate metab enzyme

2. Plasmid numbers vary depending upon origin i.e. factors that bind to them Plasmids in same “incompatibility group” use same factors, so should not be cotransformed

3. Plasmid numbers vary depending upon origin Plasmids in same “incompatibility group” use same factors, so should not be cotransformed Some, eg colE1 are controlled by antisense RNA DNA pol III needs primer RNA & DnaA to replicate

4. Some, eg colE1 are controlled by antisense RNA Others (eg R6K) are controlled by iterons: binding sites for regulatory proteins (eg Pi or RepA) DNA pol III needs primer RNA & DnaA to replicate

5. Many plasmids (pBS, pR6K) replicate by” theta mode”

6. SS-phage and some plasmids replicate by “rolling circle”

7. Other replicate by ”strand displacement”

8. Initiating DNA replication Prokaryotes have one origin/DNA molecule Pulse-chase experiments show eukaryotes have multiple origins/chromosome

9. Initiating DNA replication In Euk ORC (Origin Recognition Complex) binds ARS A is invariant, but B1, B2 and B3 vary A B1B2B3

10. Initiating DNA replication In Euk ORC binds ARS licensing factors ensure each ARS is only replicated once/S

11. Initiating DNA replication In Euk ORC binds ARS licensing factors ensure each ARS is only replicated once/S Activation factors initiate DNA replication

12. Initiating DNA replication licensing factors ensure each ARS is only replicated once/S Activation factors initiate DNA replication Licensing & activation factors fall off once replication starts, don't reattach until after mitosis

13. DNA replication must melt DNA @ physiological T Helicase melts DNA

14. DNA replication must melt DNA @ physiological T Helicase melts DNA Forms “replication bubble”

15. DNA replication Helicase melts DNA SSB proteins separate strands until they are copied

16. DNA replication helicase melts DNA unwinding DNA increases supercoiling elsewhere

17. DNA replication helicase melts DNA unwinding DNA increases supercoiling elsewhere DNA gyrase relieves supercoiling

18. Topoisomerases : enzymes that untie knots in DNA Type I nick backbone & unwind once as strand rotates Type II cut both strands: relieve two supercoils/rxn

19. DNA replication 1) where to begin? 2) “melting” 3) “priming” DNA polymerase can only add

20. DNA replication “priming” DNA polymerase can only add primase makes short RNA primers

21. DNA replication DNA polymerase can only add primase makes short RNA primers DNA polymerase adds to primer

22. DNA replication DNA polymerase can only add primase makes short RNA primers DNA polymerase adds to primer later replace primers with DNA

23. DNA replication 1) where to begin? 2) “melting” 3) “priming” 4) DNA replication

24. DNA replication add bases bonding 5’ P to 3’ OH @ growing end

25. DNA replication add bases bonding 5’ P to 3’ OH @ growing end Template holds next base until make bond

26. DNA replication add bases bonding 5’ P to 3’ OH @ growing end Template holds next base until make bond - only correct base fits

27. DNA replication add bases bonding 5’ P to 3’ OH @ growing end Template holds next base until make bond - only correct base fits - energy comes from 2 PO 4

28. DNA replication energy comes from 2 PO 4 "Sliding clamp" keeps polymerase from falling off

29. DNA replication energy comes from 2 PO 4 "Sliding clamp" keeps polymerase from falling off Proof-reading: only correct DNA can exit

30. DNA replication Proof-reading: only correct DNA can exit Remove bad bases & try again

31. DNA replication Only make DNA 5’ -> 3’

32. Leading and Lagging Strands Only make DNA 5’ -> 3’ strands go both ways!

33. Leading and Lagging Strands Only make DNA 5’ -> 3’ strands go both ways! Make leading strand continuously

34. Leading and Lagging Strands Make leading strand continuously Make lagging strand opposite way

35. Leading and Lagging Strands Make leading strand continuously Make lagging strand opposite way wait for DNA to melt, then make Okazaki fragments

36. Leading and Lagging Strands Make lagging strand opposite way wait for DNA to melt, then make Okazaki fragments each Okazaki fragment has its own primer: made discontinuously

37. Leading and Lagging Strands each Okazaki fragment has its own primer made discontinuously DNA replication is semidiscontinuous

38. Leading and Lagging Strands each Okazaki fragment has its own primer made discontinuously DNA replication is semidiscontinuous Okazaki fragments grow until hit one in front

39. RNAse H removes primer & gap is filled

40. Okazaki fragments grow until hit one in front RNAse H removes primer & gap is filled DNA ligase joins fragments

41. Okazaki fragments grow until hit one in front RNAse H removes primer & gap is filled DNA ligase joins fragments Energy comes from ATP-> AMP

42. DNA replication Real process is far more complicated! Proteins replicating both strands are in replisome

43. DNA replication Real process is far more complicated! Proteins replicating both strands are in replisome Attached to membrane & feed DNA through it

44. DNA replication Proteins replicating both strands are in replisome Attached to membrane & feed DNA through it lagging strand loops out so make both strands in same direction

45. DNA pol detaches when hits previous primer, reattaches at next primer