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

2 常見的化學元素

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

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

DNA --- A, G, C, T

DNA is oriented 5’ – GTATCC – 3’ 3’ – GTATCC – 5’not equal

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

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’

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13 DNA 雙螺旋體（ DNA double helix ）

Central Dogma of Molecular Biology

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

Gene Structure and Information Content promoter sequence

Regulatory Proteins positive regulation negative regulation

Amino Acids ( 胺基酸 ) amino carboxyl alpha

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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.

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.

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

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 )

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

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29 蛋白質是由 20 種胺基酸所組成

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Secondary Structure α-helix and β-sheet

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Tertiary and Quaternary Structure

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 )

Molecular Biology Tools

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

39 Restriction Mapping SEPARATE

Gel Electrophoresis Fig. 1.11

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

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

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

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

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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.

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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)

53 參考資料及圖片出處 1. Biochemistry, by J. M. Berg, J. L. Tymoczko, and L. Stryer, Fith Edition, 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.

54 語音出處