DNA , RNA basic structure and components

DNA , RNA basic structure and components

1. DNA replication Fork

2. DNA replication Fork

3. Denaturation & Renaturation

4. Denaturation & Renaturation

5. Denaturation & Renaturation

6. Different topological forms of DNA Genes VI : Figure 5-9

7. Negative and positive supercoils Negative supercoils twist the DNA about its axis in the opposite direction from the clockwise turns of the right-handed (R-H) double helix. U nderwound (favors unwinding of duplex). Has right-handed supercoil turns. Positive supercoils twist the DNA in the same direction as the turns of the R-H double helix. Overwound (helix is wound more tightly). Has left-handed supercoil turns.

8. L= W + T Relationship of writhing number and twist numbers DNA structure: Tertiary Structure: topology of plasmids

9. Components of DNA Topology : Twist Number of times one strand completely wrap around the other strand. The clockwise turns of R-H double helix generate a positive Twist (T). The counterclockwise turns of L-H helix (Z form) generate a negative T. T = Twisting Number B form DNA: + (# bp /10 bp per twist) A form NA: + (# bp /11 bp per twist) Z DNA: - (# bp /12 bp per twist)

10. Components of DNA Topology : Writhe W = Writhing Number writhe  is the number of times the double helix crosses over on itself   Refers to the turning of the axis of the DNA duplex in space Number of times the duplex DNA crosses over itself Relaxed molecule W=0 Negative supercoils , W is negative Positive supercoils , W is positive

11. Relationship between supercoiling and twisting Figure from M. Gellert; Kornberg and Baker

12. Two forms of supercoils: a toroidal helix DNA structure: Tertiary Structure: topology of plasmids

13. Components of DNA Topology : Linking number L = Linking Number = total number of times one strand of the double helix (of a closed molecule) encircles (or links) the other. L = Wr (Writhe)+ Tw (twist)

14. L cannot change unless one or both strands are broken and reformed A change in the linking number, D L, is partitioned between T and W, i.e. D L= D W+ D T if D L = 0, then D W= - D T

15. DNA in most cells is negatively supercoiled The superhelical density is simply the number of superhelical (S.H.) turns per turn (or twist) of double helix. Superhelical density = s = W/T = -0.05 for natural bacterial DNA i.e., in bacterial DNA, there is 1 negative S.H. turn per 200 bp (calculated from 1 negative S.H. turn per 20 twists = 1 negative S.H. turn per 200 bp)

16. Negatively supercoiled DNA favors unwinding Negative supercoiled DNA has energy stored that favors unwinding, or a transition from B-form to Z DNA. For s = -0.05, D G=-9 Kcal/mole favoring unwinding Thus negative supercoiling could favor initiation of transcription and initiation of replication.

17. Introducing one supercoil into a DNA with 10 duplex turns DNA structure: Tertiary Structure: topology of plasmids

18. What can Topoisomerase I do to the DNA? DNA structure: Tertiary Structure: topology of plasmids

19. Topoisomerase II (DNA gyrase) DNA structure: Tertiary Structure: topology of plasmids

20. DNA structure: Tertiary Structure: topology of plasmids

21. Topoisomerase I Topoisomerases: catalyze a change in the Linking Number of DNA Topo I = nicking-closing enzyme, can relax positive or negative supercoiled DNA Makes a transient break in 1 strand E. coli Topo I specifically relaxes negatively supercoiled DNA. Calf thymus Topo I works on both negatively and positively supercoiled DNA.

22. Topoisomerase I: nicking & closing Genes VI : Figure 17-15 One strand passes through a nick in the other strand.

23. Topoisomerase II Topo II = gyrase Uses the energy of ATP hydrolysis to introduce negative supercoils Its mechanism of action is to make a transient double strand break, pass a duplex DNA through the break, and then re-seal the break.

24. TopoII: double strand break and passage

25. RNA vs. DNA nucleoside nucleotide glycosidic bond

26. RNA vs. DNA: who cares? Base-catalyzed RNA cleavage! - OH Stable backbone Unstable backbone

27. RNA transesterification mechanism Base-catalyzed RNA cleavage! transition state + + - OH

28. Different bases in RNA and DNA RNA only DNA only DNA and RNA

29. RNA chain is made single stranded! Chain is directional. Convention: 5’ 3’. Chemical schematic One-letter code ssDNA can signal DNA damage and promote cell death dsRNA can block protein synthesis and signal viral infections

30. Six backbone dihedral angles () per nucleotide in RNA and DNA Is ssDNA floppy or rigid? Is RNA more or less flexible than ssDNA?

31. Two orientations of the bases: Anti and syn DNA and RNA Absent from undamaged dsDNA

32. -OH, what a difference an O makes! Different functions of DNA and RNA Stores genetic info Stores genetic info ssDNA signals cell death ssRNA OK E.g. mRNA = gene copy dsDNA OK dsRNA (“A” form) signals infection, mediates editing, RNA interference, . . . Double helical (B form) Forms complex structures Supercoiled Enzymes (e.g. ribosome), Binding sites & scaffolds Signals Templates (e.g. telomeres) gene1gene2 gene3 . . .