1. Biopolymer － DNA 計算科學總論 Dept. Phys. Tunghai Univ. C. T. Shih

2. “Quantum” in Evolution 達爾文學說所遇到的挑戰：當時 流行的遺傳學觀點是，遺傳因子 由血液所攜帶，兒女的性狀是由 雙親的性狀（血液）混合而成。 然而由前述「熵」的統計意義可 知，經過許多世代的繁殖後，最 後的性狀特徵會「均一化」：融 合成一種中間態，就好像把不同 溫度的水逐漸混合，最後會變成 全部均一溫度。這樣一來，物種 只會被消滅而不會有演化。 Charles Darwin 1809~1886

3. “Quantum” in Evolution 孟德爾的豌豆實驗（ 1857~1865 ）： 選取了「莖的高矮」、「豆莢綠黃」、 「種子圓皺」等幾組相對的性狀的豌 豆作雜交研究。統計的結果顯示， 「高：矮」、「綠：黃」、「圓：皺」 的比例大致都 3:1 。這個簡單整數比 的」結果類似化學中的定比定律及倍 比定律（ Dalton 因此得到了「不可分 割的原子」的概念），而孟德爾則因 此領悟了「遺傳因子為不可分割的單 位」的概念。 Gregor Mendel (1823~1884)

4. The Structure of a Gene “We shall assume the structure of a gene to be that of a huge molecule, capable of only discontinuous change, which consists in the rearrangement of the atoms and leads to an isomeric molecule. The rearrangement may affect only a small region of the gene, and a vast number of different rearrangements may be possible.” － What is Life? E. Schrödinger － What is Life? E. Schrödinger

5. 1869: Miescher 1869 年，瑞士生物學家 Johann Miescher (1844~ 1895) 在病患繃帶的膿汁 中發現一種新物質，由於 是在細胞核中，他將之取 名為「核素」 (nuclein) ， 此即為 DNA （去氧核糖 核酸）。 1869 年，瑞士生物學家 Johann Miescher (1844~ 1895) 在病患繃帶的膿汁 中發現一種新物質，由於 是在細胞核中，他將之取 名為「核素」 (nuclein) ， 此即為 DNA （去氧核糖 核酸）。

6. 1908: Morgan Thomas Morgan (1866 ~1945) 首先利 用果蠅來研究遺傳學， 他發現有許多基因是一 起遺傳的，因此推測有 些基因在染色體上的位 置是相連的，並且訂出 了果蠅的基因圖譜。 Morgan 於 1933 年獲得 諾貝爾生理及醫學獎。 Thomas Morgan (1866 ~1945) 首先利 用果蠅來研究遺傳學， 他發現有許多基因是一 起遺傳的，因此推測有 些基因在染色體上的位 置是相連的，並且訂出 了果蠅的基因圖譜。 Morgan 於 1933 年獲得 諾貝爾生理及醫學獎。

7. Drosophila Melanogaster 果蠅是遺傳學研究中極為重要的研究對象， 牠的優點是：生命史短（每十二天繁殖一 代）、多產（平均一隻雌果蠅產一千個卵）、 飼養容易、成本低廉。 果蠅是遺傳學研究中極為重要的研究對象， 牠的優點是：生命史短（每十二天繁殖一 代）、多產（平均一隻雌果蠅產一千個卵）、 飼養容易、成本低廉。

8. 1909: Garrod 英國遺傳學家 Archibald Garrod (1857~1936) 指出，當 一些特殊的蛋白質無法 執行正常功能時，會引 起某些遺傳疾病。這個 假說可說是日後「一基 因、一蛋白」之前身。 英國遺傳學家 Archibald Garrod (1857~1936) 指出，當 一些特殊的蛋白質無法 執行正常功能時，會引 起某些遺傳疾病。這個 假說可說是日後「一基 因、一蛋白」之前身。

9. 1928: Griffith 1928 年，英國軍醫 Frederick Griffith (1881~1941) 1928 年，英國軍醫 Frederick Griffith (1881~1941) 以老鼠實驗發現， 將活的良性肺炎雙球 菌與死的惡性肺炎雙 球菌混合，可以引起 轉型，得到活的惡性 菌，使老鼠死亡。 以老鼠實驗發現， 將活的良性肺炎雙球 菌與死的惡性肺炎雙 球菌混合，可以引起 轉型，得到活的惡性 菌，使老鼠死亡。 為什麼細胞會發生 轉化？ 為什麼細胞會發生 轉化？

10. 1942: Beadle & Tatum 1942 年， George Beadle (1903~1989) 與 Edward Tatum (1909~1975) 以麵包上 的紅黴菌（ Neurospora ） 實驗證實， DNA 上所帶 的遺傳訊息，其功能是 製造特定的酵素。他們 獲得了 1958 年的諾貝爾 生理與醫學獎。 1942 年， George Beadle (1903~1989) 與 Edward Tatum (1909~1975) 以麵包上 的紅黴菌（ Neurospora ） 實驗證實， DNA 上所帶 的遺傳訊息，其功能是 製造特定的酵素。他們 獲得了 1958 年的諾貝爾 生理與醫學獎。

11. Beadle & Tatum’s Experiment 以 X 光照射黴菌 以 X 光照射黴菌 將黴菌分類：有突變（在最低條件的培養皿中仍 可繁殖）以及沒有突變（不會繁殖） 將黴菌分類：有突變（在最低條件的培養皿中仍 可繁殖）以及沒有突變（不會繁殖） 在有突變的族群中加入不同的酵素後，又會開始 繁殖，由觀察知，有三種突變種： 在有突變的族群中加入不同的酵素後，又會開始 繁殖，由觀察知，有三種突變種： 無法合成維生素 B6 無法合成維生素 B6 無法合成維生素 B1 無法合成維生素 B1 無法合成 para-aminobenzoic acid 無法合成 para-aminobenzoic acid 每個突變都是一個基因遭破壞，而缺少對應的酵 素來合成繁殖所需之營養素 每個突變都是一個基因遭破壞，而缺少對應的酵 素來合成繁殖所需之營養素 一基因 – 一酵素理論 一基因 – 一酵素理論

12. 1949: Chargaff 1949 年， Irwin Chargaff (1905~) 提出 了所謂的 Chargaff 法 則： DNA 中的四種核 甘酸： A 與 T 的含量相 同， C 與 G 的含量相同， 推翻了過去 ATCG 含量 均勻的假說。 1949 年， Irwin Chargaff (1905~) 提出 了所謂的 Chargaff 法 則： DNA 中的四種核 甘酸： A 與 T 的含量相 同， C 與 G 的含量相同， 推翻了過去 ATCG 含量 均勻的假說。

13. The Discovery of Double Helix 1951 年， Rosalind Franklin 得到 DNA 分子 的 X-ray 繞射照片， 1953 年， Watson 與 Crick 解出了 DNA 的雙螺旋結構，此為分子生物學 的大躍進。 1951 年， Rosalind Franklin 得到 DNA 分子 的 X-ray 繞射照片， 1953 年， Watson 與 Crick 解出了 DNA 的雙螺旋結構，此為分子生物學 的大躍進。

14. We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest. A structure for nucleic acid has already been proposed by Pauling and Corey (1). They kindly made their manuscript available to us in advance of publication. Their model consists of three intertwined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory for two reasons: (1) We believe that the material which gives the X-ray diagrams is the salt, not the free acid. Without the acidic hydrogen atoms it is not clear what forces would hold the structure together, especially as the negatively charged phosphates near the axis will repel each other. (2) Some of the van der Waals distances appear to be too small. Another three-chain structure has also been suggested by Fraser (in the press). In his model the phosphates are on the outside and the bases on the inside, linked together by hydrogen bonds. This structure as described is rather ill-defined, and for this reason we shall not comment on it. We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid. This structure has two helical chains each coiled round the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining ß-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right- handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions. Each chain loosely resembles Furberg's2 model No. 1; that is, the bases are on the inside of the helix and the phosphates on the outside. The configuration of the sugar and the atoms near it is close to Furberg's 'standard configuration', the sugar being roughly perpendicular to the attached base. There is a residue on each every 3.4 A. in the z-direction. We have assumed an angle of 36° between adjacent residues in the same chain, so that the structure repeats after 10 residues on each chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10 A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more compact. The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases. The planes of the bases are perpendicular to the fibre axis. The are joined together in pairs, a single base from the other chain, so that the two lie side by side with identical z-co-ordinates. One of the pair must be a purine and the other a pyrimidine for bonding to occur. The hydrogen bonds are made as follows : purine position 1 to pyrimidine position 1 ; purine position 6 to pyrimidine position 6. If it is assumed that the bases only occur in the structure in the most plausible tautomeric forms (that is, with the keto rather than the enol configurations) it is found that only specific pairs of bases can bond together. These pairs are : adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine). In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine ; similarly for guanine and cytosine. The sequence of bases on a single chain does not appear to be restricted in any way. However, if only specific pairs of bases can be formed, it follows that if the sequence of bases on one chain is given, then the sequence on the other chain is automatically determined. It has been found experimentally (3,4) that the ratio of the amounts of adenine to thymine, and the ration of guanine to cytosine, are always bery close to unity for deoxyribose nucleic acid. It is probably impossible to build this structure with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would make too close a van der Waals contact. The previously published X-ray data (5,6) on deoxyribose nucleic acid are insufficient for a rigorous test of our structure. So far as we can tell, it is roughly compatible with the experimental data, but it must be regarded as unproved until it has been checked against more exact results. Some of these are given in the following communications. We were not aware of the details of the results presented there when we devised our structure, which rests mainly though not entirely on published experimental data and stereochemical arguments. It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. Full details of the structure, including the conditions assumed in building it, together with a set of co-ordinates for the atoms, will be published elsewhere. We are much indebted to Dr. Jerry Donohue for constant advice and criticism, especially on interatomic distances. We have also been stimulated by a knowledge of the general nature of the unpublished experimental results and ideas of Dr. M. H. F. Wilkins, Dr. R. E. Franklin and their co-workers at King's College, London. One of us (J. D. W.) has been aided by a fellowship from the National Foundation for Infantile Paralysis. J. D. WATSON F. H. C. CRICK Medical Research Council Unit for the Study of Molecular Structure of Biological Systems, Cavendish Laboratory, Cambridge. April 2. 1. Pauling, L., and Corey, R. B., Nature, 171, 346 (1953); Proc. U.S. Nat. Acad. Sci., 39, 84 (1953). 2. Furberg, S., Acta Chem. Scand., 6, 634 (1952). 3. Chargaff, E., for references see Zamenhof, S., Brawerman, G., and Chargaff, E., Biochim. et Biophys. Acta, 9, 402 (1952). 4. Wyatt, G. R., J. Gen. Physiol., 36, 201 (1952). 5. Astbury, W. T., Symp. Soc. Exp. Biol. 1, Nucleic Acid, 66 (Camb. Univ. Press, 1947). 6. Wilkins, M. H. F., and Randall, J. T., Biochim. et Biophys. Acta, 10, 192 (1953). A structure for Deoxyribose Nucleic Acid

15. 1966: Genetic Code Marshall Nirenberg 與 H. Gobind Khorana 研究 小組找到了遺傳碼 （ genetic code ）。在 DNA 序列中每三個核甘酸 鹼基代表一個氨基酸，稱 為一個「編碼子」 （ codon ）。他們因此獲 得了 1968 年諾貝爾獎。 Marshall Nirenberg 與 H. Gobind Khorana 研究 小組找到了遺傳碼 （ genetic code ）。在 DNA 序列中每三個核甘酸 鹼基代表一個氨基酸，稱 為一個「編碼子」 （ codon ）。他們因此獲 得了 1968 年諾貝爾獎。

16. Structure of DNA

17. Component Deoxyribose (a pentose = sugar with 5 carbons) Deoxyribose (a pentose = sugar with 5 carbons) Phosphoric Acid Phosphoric Acid Organic (nitrogenous) bases Organic (nitrogenous) bases Purines - Adenine and Guanine Purines - Adenine and Guanine Pyrimidines -Cytosine and Thymine) Pyrimidines -Cytosine and Thymine)

20. Base + Sugar = Nucleoside + phosphate = Nucleotide

21. Nucleotide – OH = Deoxy Nucleotide

22. DNA Backbone (Single Strand) Polarity

23. Features of the 5’- Structure Alternating backbone of deoxyribose and phosphodiester groups Alternating backbone of deoxyribose and phosphodiester groups Chain has a direction (known as polarity), 5'- to 3'- from top to bottom Chain has a direction (known as polarity), 5'- to 3'- from top to bottom Oxygens (red atoms) of phosphates are polar and negatively charged Oxygens (red atoms) of phosphates are polar and negatively charged A, G, C, and T bases can extend away from chain, and stack atop each other A, G, C, and T bases can extend away from chain, and stack atop each other Bases are hydrophobic Bases are hydrophobic

24. DNA Double Helix

26. Features of the DNA Double Helix Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral The two polynucleotide chains run in opposite directions The two polynucleotide chains run in opposite directions The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a spiral staircase The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a spiral staircase The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase

27. Base Pairs Chargaff’s Law: A—T, C—G by H-bonds Chargaff’s Law: A—T, C—G by H-bonds

29. Spatial Geometry and Secondary Structure Two polynucleotide chains are wound around a common axis to produce a double helix Two polynucleotide chains are wound around a common axis to produce a double helix Diameter = 20Å Diameter = 20Å Distance of adjacent bases = 3.4Å Distance of adjacent bases = 3.4Å Rotation of adjacent bases = 36° Rotation of adjacent bases = 36°

31. Forces Stabilizing DNA Secondary Structure: H-Bonds H-Bond strength of the base pairs: H-Bond strength of the base pairs: A—T ~ 7 kcal/mole A—T ~ 7 kcal/mole C—G ~ 17 kcal/mole C—G ~ 17 kcal/mole Comparison: Covalent bond E C—C =83.1 kcal/mole Comparison: Covalent bond E C—C =83.1 kcal/mole Rigidity of bonds: to lengthen the bonds by 0.1Å, we need the energy Rigidity of bonds: to lengthen the bonds by 0.1Å, we need the energy 0.1 kcal/mole for H-bonds 0.1 kcal/mole for H-bonds 3.25 kcal/mole for C—C covalent bond 3.25 kcal/mole for C—C covalent bond

32. Forces Stabilizing DNA Secondary Structure: Stacking Interactions

34. Polymorphism of DNA

35. B-DNA: 正常條件下的結構 B-DNA: 正常條件下的結構 A-DNA: 低濕度下可能由 B-DNA 變為 A-DNA A-DNA: 低濕度下可能由 B-DNA 變為 A-DNA Z-DNA: 某些特殊序列在特殊條件下，如 GCGCGC 在高濃 度的食鹽水中可能變成這種結構 Z-DNA: 某些特殊序列在特殊條件下，如 GCGCGC 在高濃 度的食鹽水中可能變成這種結構

36. Tertiary Structure: Supercoil This is a famous electron micrograph of an E. coli cell that has been carefully lysed, then all the proteins were removed, and it was spread on an EM grid to reveal all of its DNA.

40. Biological Functions of DNA

41. The Book of Life 大英百科全書 Human Genome 26 英文字母四種核甘酸 23 卷 23 對染色體 200,000 篇文章 35,000 基因 兩億個字元 30 億鹼基對 8.5”×12×20,000 頁長 1m× 直徑 100Å

42. Growth of GenBank 年份 Seq.Bp. 1982606680338 198557005204420 19903953349179285 19955556943.8×10 8 2000101060231.1×10 10 2001149763101.6×10 10 2002223188832.9×10 10 2003309684183.7×10 10 2004406043194.5×10 10

43. Duplication of DNA

44. Central Dogma: The Path of the Information DNA RNA Protein

45. RNA: Ribonucleic Acid 五碳糖的第二個碳上面多了一個氧 五碳糖的第二個碳上面多了一個氧 胸腺嘧啶（ T ）由尿嘧啶（ U ）取代 胸腺嘧啶（ T ）由尿嘧啶（ U ）取代 A-T pair 變成 A-U pair A-T pair 變成 A-U pair C-G pair 仍然不變 C-G pair 仍然不變 DNA 是雙股結構， RNA 是單股結構 DNA 是雙股結構， RNA 是單股結構

46. The Path of the Information Transcription 轉錄 Transcription 轉錄 Copies and splices a gene (single strand of DNA sequence) into an mRNA sequence Copies and splices a gene (single strand of DNA sequence) into an mRNA sequence Translation 翻譯 Translation 翻譯 Converts mRNA into a protein (string of amino acids) Converts mRNA into a protein (string of amino acids) Promoter Promoter tells the cell when to turn on the gene and how much transcription will occur tells the cell when to turn on the gene and how much transcription will occur

47. Transcription Start signal (e.g. TATAAT) and stop signal (e.g. AAAAA) Start signal (e.g. TATAAT) and stop signal (e.g. AAAAA) Splicing: keep exons （外碼子）, throw out intron （內碼子） Splicing: keep exons （外碼子）, throw out intron （內碼子） mRNA: concatenation of exons mRNA: concatenation of exons

48. Transcription: Copying

49. Transcription: Splicing

50. Translation: Genetic Code Genetic code: Genetic code: 3-nucleotides = a CODON 3-nucleotides = a CODON 64 codons 64 codons 3 stop codons 3 stop codons Rest (61) codes to 20 amino acids Rest (61) codes to 20 amino acids

52. GCA → ALA Ribosome mRNA tRNA DNA

54. 染色體異常是許 多遺傳疾病的起因， 可能在細胞分裂時 自然發生，也可能 由外在的物理或化 學因子誘發，通常 的形式有：缺失、 重複、倒轉、異位。 染色體異常是許 多遺傳疾病的起因， 可能在細胞分裂時 自然發生，也可能 由外在的物理或化 學因子誘發，通常 的形式有：缺失、 重複、倒轉、異位。 Mutation of Chromosome