1. Welcome to My Molecular Biology Lecture

2. Molecular Biology of the Gene, 5/E --- Watson et al. (2004) Part I: Chemistry and Genetics Part II: Maintenance of the Genome Part III: Expression of the Genome Part IV: Regulation Part V: Methods

3. Part II: Maintenance of the Genome DNA Dedicated to the structure of DNA and the processes that propagate ( 传递 ), maintain ( 保持 ) and alter ( 改变 ) it from one cell generation to the next

4. Maintenance of the Genome Ch 6: The structures of DNA and RNA Ch 7: Chromosomes, chromatins and the nucleosome Ch 8: The replication of DNA Ch 9: The mutability and repair of DNA Ch 10: Homologous recombination at the molecular level Ch 11: Site-specific recombination and transposition of DNA PROPAGATE & MAINTAIN ALTER

5. CHAPTER 6 The Structures of DNA and RNA How do the structures of DNA and RNA account for their functions?

6. OUTLINE 1.DNA StructureDNA Structure 2.DNA TopologyDNA Topology 3.RNA StructureRNA Structure

7. DNA STRUCTURE 1.The building blocks and base pairing. 2.The structure: two polynucleotide chains are twisting around each other in the form of a double helix.

8. DNA STRUCTURE (1) DNA building blocks Base ( 碱基 ) Nucleoside ( 核苷 ) Nucleotide ( 核苷酸 ) is the fundamental building block of DNA.

9. Purines pyrimidines Adenine (A) Guanine (G) Cytosine (C) Thymine (T) N9 N1 Bases in DNA

10. Each bases has its preferred tautomeric form (Related to Ch 9)

11. The strictness of the rules for “Waston-Crick” pairing derives from the complementarity both of shape and of hydrogen bonding properties between adenine and thymine and between guanine and cytosine. “Waston-Crick” pairing Maximal hydrogen bonding

12. A:C incompatibility

13. glycosidic bond phosphoester bond Nucleoside Nucleosides & Nucleotides

14. 3’ 5’ Asymmetric

15. A DNA molecule is composed of two antiparallel polynucleotide chains

16. DNA polarity: DNA polarity: is defined by the asymmetry of the nucleotides and the way they are joined. Phosphodiester linkages Phosphodiester linkages: repeating, sugar- phosphate backbone of the polynucleotide chain

17. antiparallel The two strands are held together by base pairing in an antiparallel orientation: a stereochemical ( 立体化学的 ) consequence of the way that A-T and G-C pair with each other. (Related to replication and transcription)

18. DNA STRUCTURE (2) DNA structure two antiparallel polynucleotide chains are twisting around each other in the form of a double helix.

20. 1. The Two Chains of the Double Helix Have Complementary Sequences Example: If sequence 5’-ATGTC-3’ on one chain, the opposite chain MUST have the complementary sequence 3’- TACAG-5’ Watson-Crick Base Pairing (Related to replication and transcription)

21. 2. Hydrogen Bonding determines the Specificity of Base Pairing, while stacking interaction determines the stability a helix.

22.  Hydrogen bonding also contribute to the thermodynamic stability of the helix (?)  Stacking interactions (  ) between bases significantly contribute to the stability of DNA double helix H 2 O molecules lined up on the bases are displaced by base-base interactions, which creates disorder/hydrophobicity.

23. 3. Two different models illustrate structure a DNA double helix. Schematic model Space-filling model

24. 4. DNA is usually a right-handed double helix.

25. (See the Structural Tutorial of this chapter for details) It is a simple consequence of the geometry of the base pair. 5. The double helix has Minor and Major grooves (What & Why)

26. The Major groove is rich in chemical information (What are the biological relevance?) The edges of each base pair are exposed in the major and minor grooves, creating a pattern of hydrogen bond donors and acceptors and of van der Waals surfaces that identifies the base pair.

27. A: H-bond acceptorsD: H-bond donors H: non-polar hydrogens M: methyl groups

28.  The B form (10 bp/turn), which is observed at high humidity, most closely corresponds to the average structure of DNA under physiological conditions  A form (11 bp/turn), which is observed under the condition of low humidity, presents in certain DNA/protein complexes. RNA double helix adopts a similar conformation. 6. The double helix exists in multiple conformations.

31. DNA strands can separate and reassociate DNA STRUCTURE (3) Key terms to understand 1.Denaturation ( 变性 ) 2.Hybridization ( 杂交 ) 3.Annealing/renature ( 复性 ) 4.Absorbance ( 吸收度 ) 5.Hyperchromicity ( 增色性 ) 6.Tm (melting point) ( 熔点 )

32. DNA TOPOLOGY

33. DNA TOPOLOGY (1) Structure (1): Linking number is an invariant topological property of covalently closed, circular DNA (cccDNA) Linking number is the number of times one strand have to be passed through the other strand in order for the two strands to be entirely separated from each other.

34. Species of cccDNA 1.Plasmid and circular bacterial chromosomes 2.Linear DNA molecules of eukaryotic chromosomes due to their extreme length, entrainment ( 缠卷 ) in chromatin and interaction with other cellular components (Ch 7)

35. Structure (2): Linking number is composed of Twist and Writhe The linking number is the sum of the twist and the writhe. Twist is the number of times one strand completely wraps around the other strand. Writhe is the number of times that the long axis of the double helical DNA crosses over itself in 3-D space. DNA TOPOLOGY (2)

36. Local disruption of base pairs

37. Function (1): DNA in cells is negatively supercoiled; nucleosomes introduces negative supercoiling in eukaryotes Negative supercoils serve as a store of free energy that aids in processes requiring strand separation, such as DNA replication and transcription. Strand separation can be accomplished more easily in negatively supercoiled DNA than in relaxed DNA. DNA TOPOLOGY (3)

38. Function (2): Topoisomerases (P115-119) 1.The biological importance of topoisomerase? 2.The functional difference of the two types of topoisomerases? 3.The working mechanism of topoisomerase (See the animation for detail) DNA TOPOLOGY (4)

40. RNA STRUCTURE

41. Biological roles of RNA

42. 1.RNA is the genetic material of some viruses 2.RNA functions as the intermediate (mRNA) between the gene and the protein-synthesizing machinery. 3.RNA functions as an adaptor (tRNA) between the codons in the mRNA and amino acids. 4.Through sequence complementarity, RNA serves as a regulatory molecule to bind to and interfere with the translation of certain mRNAs; or as a recognition molecule to guide many post-transcriptional processing steps. 5.Through the tertiary structures, some RNAs function as enzymes to catalyze essential reactions in the cell (RNase P ribozyme, large rRNA in ribosomes, self-splicing introns, etc).

43. Structures of RNA 1.Primary structure 2.Sequence complementarity: base pairing as DNA 3.Secondary structure 4. Tertiary structure 1.Primary structure 2.Sequence complementarity: base pairing as DNA 3.Secondary structure 4. Tertiary structure

44. RNA STRUCTURE RNA contains ribose and uracil and is usually single-stranded 1.Primary structure

45. RNA STRUCTURE (1) Watson-Crick base pairing U A-U G-C 2.Sequence complementarity: inter- and intra-molecular base pairing

46. 3.Secondary structures and interactions

47. RNA chains fold back on themselves to form local regions of double helix similar to A-form DNA RNA STRUCTURE (2) hairpin bulge loop RNA helix are the base- paired segments between short stretches of complementary sequences, which adopt one of the various stem-loop structures 2 nd structure elements

48. Some tetraloop sequence can enhance the stability of the RNA helical structures For example, UUCG loop is unexpectedly stable due to the special base-stacking in the loop 1 2 3 4 Special interactions

49. Pseudoknots are complex secondary structure resulted from base pairing of discontiguous RNA segments Figure 6-32 Pseudoknot. Structurally special base-pairing

50. Non-Watson-Crick G:U base pairs represent additional regular base pairing in RNA, which enriched the capacity for self-complementarity. Figure 6-33 G:U base pair Chemically special base-pairing

51. The double helical structure of RNA resembles the A-form structure of DNA. The minor groove is wide and shallow, but offers little sequence-specific information. The major groove is so narrow and deep that it is not very accessible to amino acid side chains from interacting proteins. Thus RNA structure is less well suited for sequence-specific interactions with proteins.

52. RNA STRUCTURE  RNA has enormous rotational freedom in the backbone of its non-base-paired regions. Why? 4. RNA can fold up into complex tertiary structures

53. The structure of the hammerhead ribozyme

54. Interactions in the tertiary structure  Unconventional base pairing, such as base triples, base-backbone interactions  Proteins can assist the formation of tertiary structures by large RNA molecule

55. The crystal structure of a 23S ribosme

56. Some RNAs with tertiary structures can catalyze RNA STRUCTURE (4) Ribozymes are RNA molecules that adopt complex tertiary structure and serve as biological catalysts. RNase P and self-splicing introns are ribozymes

57. Structure & Function: The hammerhead ribozyme cleaves RNA by formation of a 2’,3’ cyclic phosphate RNA STRUCTURE (5) See animation for detail C 17

58. Key points for Chapter 6 1.DNA structure Building blocks and base pairing Double helical structure Application of the property of strand separation and association in DNA techniques Critical thinking: how DNA structure influence the processes of genome maintenance and expression? [You are encouraged to take this question and find out the answers when we discuss the related contents]

59. 2. DNA topology The biological relevance of cccDNA Linking number, twist and writhe: how these topological features are changed during DNA replication [answer the question after the related lecture]. Topoisomerases 3. RNA structure Composition, structure (2 nd and tertiary) and functions (differences from DNA)