2. 1 Chapter 1 Molecular Biology and Biological Chemistry 暨南大學資訊工程學系 黃光璿 (HUANG, Guan-Shieng) 2004/02/23

3. 2 常見的化學元素

4. 3

5. 4 週期表 Link 1 ( 注音 ) Link 1 Link 2 ( 台灣師大 ) Link 2

6. 5 水： H 2 O 氧氣： O 2 氮氣： N 2 乙醇（酒精）： C 2 H 5 OH

7. 6 1.1 Genetic Material DNA: （ deoxyribonucleic acid, 去氧核醣核酸）  phosphate group ( 磷酸鹽 )  deoxyribose sugar  nitrogenous base A: Adenine G: Guanine C: Cytosine T: Thymine  RNA

8. 7 1.1.1 DNA --- A, G, C, T

9. 8 1.1.2 DNA is oriented 5’ – GTATCC – 3’ 3’ – GTATCC – 5’not equal

10. 9

11. 10 gene (Mendel, 1860s) genome: all of an organism’s genetic instructions

12. 11 1.1.3 Base paring of DNA G pairs with C and A pairs with T. reverse complement  5’- GTATCC – 3’  3’- CATAGG – 5’ upstream: 5’ downstream: 3’

13. 12

14. 13 DNA 雙螺旋體（ DNA double helix ）

15. 14 1.1.4 Central Dogma of Molecular Biology

16. 15 1.1.5 RNA RNA: （ ribonucleic acid, 核醣核酸）  phosphate group  ribose sugar  nitrogenous base (A, G, C, U: Uracil)  DNA

17. 16 1.2 Gene Structure and Information Content promoter sequence

18. 17 1.2.1 Regulatory Proteins positive regulation negative regulation

19. 18 1.2.2 Amino Acids ( 胺基酸 ) amino carboxyl alpha

20. 19

21. 20

22. 21 1.2.3 Genetic Code

23. 22 4 nucleotides 20 amino acid 4x4x4=64 > 20  triplet code (codon) This genetic code is universally used by all living things today with only a few exceptions.

24. 23 1.2.4 Open Reading Frames A substring in DNA that contains no stop codons (UAA, UAG, UGA) while reading in a single reading frame. How can one detect ORFs?  Long ORFs are easy, since the probability that a stop codon appears randomly is 3/64.

25. 24 1.2.5 Introns and Exons eukaryotes ˇ prokaryotes × Extreme example  cystic fibrosis: 24 introns, 1K/1M nts splicing & alternative splicing

26. 25 1.3 Protein Structure and Function Proteins  structure proteins: collagen ( 膠原 )  enzymes: pepsin ( 胃液素 )  transportation: hemoglobin ( 血紅素 )  signaling & intercellular communication: insulin ( 胰島素 )  absorbing photons: rhodopsin ( 視網膜色素 )

27. 26 1.3.1 Primary Structure amino acid, polypeptide chain amino terminus: H 2 N- ( 胺基 ) carboxyl terminus: -COOH ( 羧基 )

28. 27

29. 28

30. 29 蛋白質是由 20 種胺基酸所組成

31. 30

32. 31

33. 32 1.3.2 Secondary Structure α-helix and β-sheet

34. 33

35. 34 1.3.3 Tertiary and Quaternary Structure

36. 35 1.4 The Nature of Chemical Bonds anatomy of an atom  neutron ( 中子 )  proton ( 質子 ) +  electron ( 電子 ) – potential energy valence ( 原子價 )  covalent bond ( 共價鍵 )

37. 36 electronegativity  polar bond, hydrogen bond hydrophilicity ( 親水性 ) and hydrophobicity ( 疏水性 )

38. 37 1.5 Molecular Biology Tools

39. 38 1.5.1 Restriction Enzyme Digests CUT H. Smith restriction enzyme  like a scissor that cuts the restriction sites

40. 39 Restriction Mapping SEPARATE

41. 40 1.5.2 Gel Electrophoresis Fig. 1.11

42. 41 1.5.3 Blotting and Hybridization SEARCH steps:  blotting( 漬墨法 ): gel separation ( 先分離 ) transfering ( 再固定 )  hybridization( 雜交 ): probe: chemically synthesized radioactivity, fluorescent dyes, enzyme, antibody  washing

43. 42

44. 43 Southern blotting (DNA), named after Edwin Southern Northern blotting (RNA) Western blotting (proteins) DNA chip, microarray

45. 44 1.5.4 Cloning ( 選殖 ) PURIFY & ENLARGE DNA fragment   inserted into vectors (phage, plasmid)   replicate   purify library  genetic library (for DNA)  cDNA library (for RNA)

46. 45 1.5.5 Polymerase Chain Reaction AMPLIFY K. Mullis, 1985 Required  DNA polymerase: 5’ extends to 3’  primer Repeat 20 times  1 M copies in a couple of hours

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48. 47

49. 48 1.5.6 DNA Sequencing Determine the order of nucleotides in a DNA fragment Maxam-Gilbert method, 1970 Sanger’s Chain-termination method

50. 49

51. 50 1.6 Genomic Information Content (Before sequencing is available…) C-Value Paradox  The amount of DNA in every cell of a given organism is the same.  C-Value paradox: complexity & genome size are not correlated.

52. 51

53. 52 Reassociation Kinetics  R. Britten et al, 1960s  cot equation: c 0 t 1/2 measures the weight (or amount) non-repeated sequences.  t 1/2 : time for renaturing (i.e. c/c 0 =0.5)

54. 53 參考資料及圖片出處 1. Biochemistry, by J. M. Berg, J. L. Tymoczko, and L. Stryer, Fith Edition, 2001. Biochemistry 2. DNA 的 14 堂課, by Karl Drlica, 1996, 周業仁 翻譯, 天下文化, 2002 翻譯. DNA 的 14 堂課 3. 多數圖片來自課本 Fundamental Concepts of Bioinformatics Fundamental Concepts of Bioinformatics Dan E. Krane and Michael L. Raymer, Benjamin/Cummings, 2003.

55. 54 語音出處 http://www.merriam-webster.com/