Welcome to My Molecular Biology Lecture

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 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. The Structures of DNA and RNA CHAPTER 6

6. The structure of the genetic materials sustaining the beautiful living creatures

7. Appreciate the simple and stable beauties of the DNA structure. Appreciate the flexible beauty of RNA structure Appreciate the beautiful link between the structures of DNA and RNA and their biological functions?

8. OUTLINE 1.DNA Structure*** 2.DNA Topology 3.RNA Structure**

9. DNA STRUCTURE The building blocks and base pairing. The structure: two polynucleotide chains are twisting around each other in the form ofa double helix.

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

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

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

13. “Waston-Crick” pairing 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. Maximal hydrogen bonding and the same sugar-sugar distance

14. A:C incompatibility

15. phosphoester bond glycosidic bond Nucleosides & Nucleotides Nucleoside

16. Asymmetric 5’ 3’

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

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

19. 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)

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

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

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

24. Hydrogen bonding also contribute to the thermodynamic stability of the helix • Stacking interactions (p-p) between bases significantly contribute to the stability of DNA double helix H2O molecules lined up on the bases are displaced by base-base interactions, which creates disorder/hydrophobicity.

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

26. Considering the extraordinary length/width ratio of your genomic DNA, take some time to appreciate its amazingly ordered packing in your cells, to give thanks to the creator, and to think of the possible ways to ensure DNA function.

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

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

29. 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.

30. A: H-bond acceptors D: H-bond donors H: non-polar hydrogens M: methyl groups

31. 6. The double helix exists in multiple conformations. • 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.

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

35. DNA TOPOLOGY

36. Structure (1): Linking number is an invariant topological property of covalently closed, circular DNA (cccDNA) DNA TOPOLOGY (1) 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.

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

38. Structure (2): Linking number is composed of Twist and Writhe DNA TOPOLOGY (2) 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.

39. Local disruption of base pairs

40. Biological (1): DNA in cells is negatively supercoiled; nucleosomes introduces negative supercoiling in eukaryotes DNA TOPOLOGY (3) 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.

41. Function (2): Topoisomerases DNA TOPOLOGY (4) • Two different types of topoisomerases: • --Type I makes transient single-stranded breaks in DNA, changes the linking number of DNA in steps of one, do not require ATP • --Type II makes transient double-strand breaks in DNA, changes the linking number of DNA in steps of two, requires ATP

43. Function (2): Topoisomerases DNA TOPOLOGY (4) 2. Biological functions: --Relax supercoiled DNA. --introduce supercoils into DNA --unknot and disentangle DNA

44. RNA STRUCTURE

45. Biological roles of RNA

46. RNA is the genetic material of some viruses • RNA functions as the intermediate (mRNA) between the gene and the protein-synthesizing machinery. • RNA functions as an adaptor (tRNA) between the codons in the mRNA and amino acids. • 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. • 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).

47. Structures of RNA • Primary structure • 2.Sequence complementarity: base pairing as DNA • 3.Secondary structure • 4. Tertiary structure • 5. Ribozymes are catalytic RNAs

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

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

50. 3.Secondary structures and interactions