Chapter 1 Molecular Biology and Biological Chemistry

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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

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常見的化學元素

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週期表

Link 1 ( 注音 ) Link 2 ( 台灣師大 )

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水： H2O 氧氣： O2

氮氣： N2

乙醇（酒精）： C2 H5 OH

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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: GuanineC: Cytosine T: Thymine

RNA

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

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1.1.2 DNA is oriented

5’ – GTATCC – 3’3’ – GTATCC – 5’ not equal

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

instructions

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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’

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DNA 雙螺旋體（ DNA double helix ）

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1.1.4 Central Dogma of Molecular Biology

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1.1.5 RNA

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

NAD

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1.2 Gene Structure and Information Content promoter sequence

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1.2.1 Regulatory Proteins

positive regulation negative regulation

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1.2.2 Amino Acids ( 胺基酸 )

amino

carboxyl

alpha

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1.2.3 Genetic Code

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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.

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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.

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1.2.5 Introns and Exons

eukaryotes ˇ prokaryotes × Extreme example

cystic fibrosis: 24 introns, 1K/1M nts splicing & alternative splicing

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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: insuli

n ( 胰島素 ) absorbing photons: rhodopsin ( 視網膜色素 )

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1.3.1 Primary Structure

amino acid, polypeptide chain amino terminus: H2N- ( 胺基 ) carboxyl terminus: -COOH ( 羧基 )

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蛋白質是由 20 種胺基酸所組成

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1.3.2 Secondary Structure

α-helix and β-sheet

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1.3.3 Tertiary and Quaternary Structure

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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 )

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electronegativity polar bond, hydrogen bond

hydrophilicity ( 親水性 ) and hydrophobicity ( 疏水性 )

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1.5 Molecular Biology Tools

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1.5.1 Restriction Enzyme Digests CUT H. Smith restriction enzyme

like a scissor that cuts the restriction sites

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Restriction Mapping

SEPARATE

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1.5.2 Gel Electrophoresis

Fig. 1.11

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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

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Southern blotting (DNA), named after Edwin Southern

Northern blotting (RNA) Western blotting (proteins)

DNA chip, microarray

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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)

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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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1.5.6 DNA Sequencing

Determine the order of nucleotides in a DNA fragment

Maxam-Gilbert method, 1970 Sanger’s Chain-termination method

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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.

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Reassociation Kinetics R. Britten et al, 1960s cot equation: c0t1/2 measures the weight (or amo

unt) non-repeated sequences. t1/2: time for renaturing (i.e. c/c0=0.5)

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參考資料及圖片出處

1. Biochemistry, by J. M. Berg, J. L. Tymoczko, and L. Stryer, Fith Edition, 2001.

2. DNA的14堂課, by Karl Drlica, 1996, 周業仁翻譯 , 天下文化 , 2002 翻譯 .

3. 多數圖片來自課本Fundamental Concepts of BioinformaticsDan E. Krane and Michael L. Raymer, Benjamin/Cummings, 2003.

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語音出處

http://www.merriam-webster.com/