1. DNA Structure and Replication Review

2.  Click here if you’d like to review part 1: DNA Discovery and Structure Click here if you’d like to review part 1: DNA Discovery and Structure  Click here if you’d like to jump to part 2: DNA Replication Click here if you’d like to jump to part 2: DNA Replication  Or just click to forward the presentation normally to go through the whole thing!

3. Part 1: DNA Discovery and Structure

4. What did Erwin Chargaff do?  Observed that in DNA molecules:  % A = % T  % C = % G

5. What was Rosalind Franklin’s contribution to the discovery of DNA’s structure?  1 st to recognize helix shape of DNA using x-ray diffraction (aka x-ray crystallography)

6. What was Maurice Wilkins’s role in the race for the double helix?  Worked with Franklin  Shared her photo with Watson and Crick

7. What did Watson and Crick do?  Put it all together!  Came up with a model of DNA’s structure (the double helix) and proposed how DNA replicated

8. DNA is a polymer made of repeating monomers. What are the monomers of DNA?  nucleotides

9. What are the three parts of a nucleotide (n.t.)?  Sugar (deoxyribose)  Phosphate  Nitrogen base

10. In every DNA nucleotide, which two parts are the same? Which part may differ?  Same – deoxyribose and phosphate  Different - base

11. What are the four DNA bases?  adenine (A)  thymine (T)  cytosine (C)  guanine (G)

12. In a nucleotide, how are the carbon atoms in the deoxyribose numbered?  Find the oxygen in the ring of the deoxyribose.  Move clockwise to the first C atom. This is the 1’ (one prime) carbon  Continue moving clockwise numbering the carbons: 2’, 3’, and 4’  The 5’ C is the carbon outside of the ring

13. The four DNA bases are divided into two groups. What are the groups and what’s the difference between the two? PurinesPyrimidines Two ring structure1 ring strucure

14. Which two bases are purines? Which two are pyrimidines?  Purines = A and G  Pyrimidines = T and C

15. What is the shape of DNA?  Double helix

16. In a DNA molecule, which parts of the nucleotides are on the outside and which part faces the center?  Sugars and phosphates alternate on the outside making up the “backbone”  Bases face the inside

17. What type of bond connects one nucleotide to its neighbors in one strand of the DNA  Covalent new covalent bond The 5’ phosphate group of one nucleotide bonds to the 3’ end of its neighbor by a covalent bond

18. A DNA molecule is double stranded. It’s made of two polynucleotide strands held together by what type of bonds?  Hydrogen bonds!  Remember, covalent bonds are shown with solid lines but H bonds are shown with dashed lines H bonds down the center of the molecule Covalent bonds in backbone holding one n.t. to the next

19. What ensures that the backbone of the DNA stays parallel?  Purines always pair with pyrimidines  The chart above shows the base-pairing rules in DNA! Purine - always pairs withPyrimidine AT GC

20. What are those base pairing rules again?  A always pairs with T  C always pairs with G

21. How many H bonds occur between each base pair?  3 between C and G  2 between A and T

22. If a molecule of DNA is 34% cytosine, determine the percentages of the remaining bases.  34% G (because % C = % G)  16% A and 16% T  Bases must add up to 100%  34% G + 34% C + X = 100%  X = 32% BUT that must be divided evenly between the remaining two bases (A and T)  32/2 = 16; so 16% A and 16% T

23. Part 2: DNA Replication

24. What are the 3 enzymes involved in DNA replication? Give their names and functions.  DNA helicase – unwinds and “unzips” the double helix  DNA polymerase – builds the new DNA polymer  DNA ligase – seals gaps left behind in DNA after RNA primers are removed

25. What are the 3 basic steps of replication? 1. Helicase separates the strands by breaking H bonds between bases 2. RNA primers anneal (attach) 3. DNA polymerase adds new complementary bases to build new strands

26. What do we call the region the is opened by the DNA helicase?  Replication bubble

27. The replication bubble is made of 2 __________________ that move in opposite directions.  replication forks

28. What is an RNA primer?  a short segment of RNA complementary to the DNA  starting point for DNA polymerase

29. Where are the nucleotides being added to build new DNA found?  floating in the nucleus

30. We call each original DNA strand a “template” strand. Why?  Each original strand must serve as a pattern for DNA polymerase to build new complementary strands. Original strands are in blue Each original strand serves as a template to build new complementary strands shown in red The resulting two DNA molecules are identical to the original one

31. What’s the result of replication again?  Two double stranded DNA molecules identical to the orignal

32. DNA replication is semi-conservative. What does that mean?  Each new double stranded DNA is 1 original strand + 1 new complementary strand

33. What does antiparallel mean?  The strands are parallel BUT they run in opposite directions  One strands runs 5’ → 3’  The complementary strand runs 3’ → 5’

34. How are the two ends of the polynucleotide chains different?  One end has a phosphate group – it’s the 5’ end  One end has a hydroxyl group on the deoxyribose – it’s the 3’ end  See the next slide!

35. 5’ end has the phosphate group of the nt hanging off 3’ end has a deoxyribose sugar with a hydroxyl group on the 3’ carbon Notice how in this complementary strand, the nucleotides are upside down so that the 5’ and 3’ ends are opposite of the other strand

36. In which direction does DNA polymerase read? In which direction does it work?  DNA pol reads 3’ → 5’ meaning that it looks at the strand running 3’ → 5’ in the same direction as the replication fork so it knows which bases to add  DNA pol works 5’ → 3’ meaning that it builds a new strand that is 5’ → 3’ complementary to the strand that it’s reading  Since the two DNA strands are antiparallel and DNA pol can only work 5’ → 3’ replication happens differently on the two DNA strands

37. Replication on the leading strand is pretty basic. What are the steps?  Helicase unwinds/unzips DNA  RNA primers anneal  DNA pol reads the 3’ → 5’ template following the replication fork  DNA pol builds a new complementary strand 5’ → 3’

38. Because DNA pol can work nonstop on the leading strand, we say replication on that strand is ________________.  Continuous or contiguous

39. Just a reminder… on the lagging strand,  After helicase unwinds/unzips the DNA, RNA primers still anneal  DNA pol still reads 3’ → 5’ and builds a new strand 5’ → 3’

40. What is the difference in replication on the lagging strand?  DNA pol moves away from the replication fork so that it’s reading 3’ → 5’ and working 5’ → 3’  Bases are added in short stretches called Okazaki fragments There is one RNA primer needed on the leading strand, but it isn’t shown above in green See how the leading strand runs 3’ to 5’ toward the replication fork and a new 5’ to 3’ strand is made continuously? On the lagging strand, DNA is built away from the fork in the 5’ to 3’ direction. Several RNA primers are needed and they’re shown in green.

41. Because replication happens in fragments on the lagging strand, we refer to replication on that strand as being __________.  Discontinuous or discontigous

42. What are the DNA fragments on the lagging strand called?  Okazaki fragments

43. What happens to RNA primers once replication is complete?  Primers must be removed and replaced with DNA nt

44. What does DNA ligase do then?  After RNA primers are removed and replaced with DNA nt, ligase seals the “nicks” or gaps left behind in the DNA backbone

45. How is DNA replication different in prokaryotes and eukaryotes?  Prokaryotic replication has only one origin of replication (one replication bubble)  Eukaryotic replication has multiple origins and multiple replication bubbles  See the next two slides for diagrams!

46. Prokaryotic: 1 bubble with 2 forks that move in opposite directions around the circular chromosome until that meet at the other side and replication is complete

47. Eukaryotic: 1 DNA strand has multiple replication bubbles each with two forks that move away from each other; replication bubbles eventually merge as they grow; this speeds up replication! Without multiple bubbles, it would take about 1 month for our DNA to replicate instead of 1 hour!

48. How accurate is DNA replication before repair?  About 1/10000 bases are paired incorrectly

49. What do we call the repair that happens after replication?  Mismatch and excision repair

50. After repair, the error rate goes down to _______?  1/1000000000 bases (the human genome is 3.2 billion bp, so there may be only 3 mistakes after repair!!!)

51. What causes errors in DNA replication?  Can be random/spontaneous  Chemicals  UV radiation

52. What do we call changes in the nt sequence?  mutations

53. Are all mutations harmful?  No – most are. Some are silent – no effect. Some may actually be beneficial.  That’s the end of the review! Click here if you’d like to go back to the beginning. That’s the end of the review! Click here if you’d like to go back to the beginning.