Chapter 1 Molecular Biology and Biological Chemistry

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

2. 常見的化學元素

4. 週期表 • Link 1 (注音) • Link 2 (台灣師大)

5. 水：H2O • 氧氣：O2 • 氮氣：N2 • 乙醇（酒精）：C2 H5 OH

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

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

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

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

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. DNA 雙螺旋體（DNA double helix）

14. 1.1.4 Central Dogma of Molecular Biology

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

16. 1.2 Gene Structure and Information Content • promoter sequence

17. 1.2.1 Regulatory Proteins • positive regulation • negative regulation

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

21. 1.2.3 Genetic Code

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.

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.

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

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)

26. 1.3.1 Primary Structure • amino acid, polypeptide chain • amino terminus: H2N- (胺基) • carboxyl terminus: -COOH (羧基)

29. 蛋白質是由20種胺基酸所組成

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

34. 1.3.3 Tertiary and Quaternary Structure

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)

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

37. 1.5 Molecular Biology Tools

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

39. Restriction Mapping • SEPARATE

40. 1.5.2 Gel Electrophoresis • Fig. 1.11

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

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)

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

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. 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.