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2 1. ( prokaryotic cell ) ( nucleus ) ( bacteria ) ( Escherichia coli ) 2. (eukaryotic cell ) ( nucleus ) ( fungi ) ( yeast )

4 (nucleotide) S (pentose) B (nitrogenous base) P (phosphate group)

5 (pentose) 1 ' ' 1 5 ' 5 '

6 (Nitrogenous Base) Two types of nitrogenous bases: purine (fused five and six member rings) pyrimidine (six member ring)

7 (Nitrogenous Base) nucleotide nucleotide Nucleic acid bases, including the atom types and partial atomic charges.

8 (base pairing) C G Hydrogen bond A=T Hydrogen bond G T C T

9 (polynucleotide chain)

10 DNA DNA ( Double Strands DNA) 3D DNA DNA 3D DNA

11 An α helix can be either right-handed handed or left- handed, as defined in the following figure. (a) (b) (a) The right-handed handed a helix without showing atoms. (b) the left-handed a helix.

12 Translation of mrna to protein

13 RNA structure The major role of RNA is to participate in protein synthesis RNA may be double stranded, but most cellular RNA molecules are single stranded. This requires three classes of RNA: 1. ribosomal RNA (rrna ) 2. messenger RNA (mrna) 3. transfer RNA ( trna )

14 Messenger RNA mrna is transcribed from DNA, carrying information for protein synthesis. The consecutive trinucleotides is know as a codon Three consecutive nucleotides in mrna encode an amino acid or a stop signal for protein synthesis.

15 Transfer RNA The major role of trna is to translate mrna sequence into amino acid sequence Some nucleotides in trna have been modified, such as: dihydrouridine (D) pseudouridine (Y) inosine (I) A trna molecule consists of nucleotides

18 The overlapping range of amino acid properties 脂肪族 ( aliphatic ) 芳香族 ( aromatic ) M I L V F Tiny Y W A T P H C K G R S Small D E N Q 帶負電 ( negative ) 帶正電 ( positive ) 疏水性 ( hydrophobic ) 帶電性 ( charged ) 親水性 ( hydrophilic )

19 20 Amino Acid /Formula/Number of atoms/

20 酸性 (acidic) R 基在性溶液失去氫離子而帶負電冬氨酸 Aspartate;Asp;D 麩氨酸 Glutamate;Glu;E

21 鹼性 (basic) R 基在性溶液獲得氫離子而帶正電賴氨酸 Lysine;Lys;K 精氨酸 Arginine;Arg;R 組氨酸 Histidine;His;H

22 芳香族 (aromatic) R 基含碳環酪氨酸 Tyrosine;Tyr;Y 色氨酸 Tryptophan;Trp;W 苯氨酸 Phenylalanine;Phe;F

23 硫族 (sulfur) R 基含有硫原子胱氨酸 Cysteine;Cys;C 硫氨酸 Methionine;Met;M

24 親水性 (hydrophilic) R 基為極性基 (polar group) 絲氨酸 Serine;Ser;S 蘇氨酸 Threonine;Thr;T 冬醯胺 Asparagine;Asn;N 麩氨醯胺 Glutamine;Glu;Q

25 疏水性 (hydrophobic) R 基為非極性基 (non-polar group) 甘氨酸 Glycine;Gly;G 氨酸 Alanine;Ala;A 纈氨酸 Valine;Val;V Aliphatic 白氨酸 Leucine;Leu;L Aliphatic

26 疏水性 (hydrophobic) R 基為非極性基 (non-polar group) 異白氨酸 Isoleucine;Ile;I

27 特殊結構氨基 (amino group) 與 R 基形成環狀結構脯氨酸 Proline;Pro;P 在蛋白質立體結構, 脯氨酸經常位於 peptide chain 轉彎之處

28 維持蛋白質結構之力量 Peptide Bond: 連接氨基酸鏈之骨架 (backbone) 鹽鍵 (salt bridge) : 帶正電之 R 基與帶負電之 R 基所形成雙硫鍵 (disulfide bond) : 由兩個胱氨酸所形成氫鍵 (hydrogen bond) Alanine & Leucine 利於形成 α 質結構之穩定性 helix 能增加蛋白

29 親水性 (hydrophilic) 疏水性 (hydrophobic) 親疏水性在蛋白質構形為最重要之交互作用力由實驗數據得知當疏水性氨基酸互相靠近時能量降低最多, 疏水 - 疏水氨基酸的鄰接數目愈多蛋白質的結構就越穩定疏水性氨基酸通常聚集在蛋白質的內部形成疏水核心 ; 親水性的蛋白質覆蓋在表面以增加與水接觸的面積

30 N-C-C-N-C-C-N-C-C-N-C-C-N-C-C α α α α N-C-C-N-C-C-N-C-C-N-C-C-N-C-C α α N-C-C-N-C-C-N-C-C-N-C-C-N-C-C Peptide Bond N-C-C-N-C-C-N-C-C-N-C-C-N-C-C

32 + H 3 N H C α R 1 C O O H 2 O H C O + + H 3 N α C + O R 2 H 2 O + H 3 N H C α R 3 C O O Form peptide bond Form peptide bond + H 3 N H C α R 1 O C N H H H C α R 2 C O O H N H C α R 3 C O O O C α C N φ H C α R 1 ψ C N H C α

35 1 3 MD method MC method molecular Mechanics

36 PDB Holdings List:27 27-Feb-2001 PDB Holdings List:05 05-Mar-2002

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