Download DNA 簡介

Biopolymer － DNA
計算科學總論
Dept. Phys. Tunghai Univ.
C. T. Shih
“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
“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)
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
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）。
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。
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。
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。
1928: Griffith
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。
為什麼細胞會發生
轉化？
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。
Beadle & Tatum’s Experiment



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）
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 B1
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
一基因 – 一酵素理論
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。
The Discovery of Double Helix
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
A structure for Deoxyribose Nucleic Acid
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).
1966: Genetic Code
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
Structure of DNA
Component



Deoxyribose (a
pentose = sugar with 5
carbons)
Phosphoric Acid
Organic (nitrogenous)
bases


Purines - Adenine and
Guanine
Pyrimidines -Cytosine
and Thymine)
Base
+
Sugar
=
Nucleoside
Nucleoside
+
phosphate
=
Nucleotide
Nucleotide – OH = Deoxy Nucleotide
DNA Backbone (Single Strand)
Polarity
Features of the 5’- Structure
Alternating backbone of deoxyribose and
phosphodiester groups
 Chain has a direction (known as polarity),
5'- to 3'- from top to bottom
 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
 Bases are hydrophobic

DNA Double Helix
Features of the DNA Double Helix




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 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
Base Pairs

Chargaff’s Law: A—T, C—G by H-bonds
Spatial Geometry and Secondary Structure
Two polynucleotide chains are
wound around a common axis to
produce a double helix
 Diameter = 20Å
 Distance of adjacent bases = 3.4Å
 Rotation of adjacent bases = 36°

Forces Stabilizing DNA Secondary
Structure: H-Bonds

H-Bond strength of the base pairs:
A—T ~ 7 kcal/mole
 C—G ~ 17 kcal/mole
 Comparison: Covalent bond EC—C =83.1
kcal/mole


Rigidity of bonds: to lengthen the bonds by
0.1Å, we need the energy
0.1 kcal/mole for H-bonds
 3.25 kcal/mole for C—C covalent bond

Forces Stabilizing DNA Secondary Structure:
Stacking Interactions
Polymorphism of DNA



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
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
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.
Biological Functions of DNA
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
Growth of GenBank
年份
Seq.
Bp.
1982
606
680338
1985
5700
5204420
1990
39533
49179285
1995
555694
3.8×108
2000
10106023
1.1×1010
2001
14976310
1.6×1010
2002
22318883
2.9×1010
2003
30968418
3.7×1010
2004
40604319
4.5×1010
Duplication of DNA
Central Dogma: The Path of the
Information
Protein
DNA
RNA
RNA: Ribonucleic Acid





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
A-T pair 變成 A-U pair
C-G pair 仍然不變
DNA 是雙股結構，RNA 是單股結構
The Path of the Information
Transcription
轉錄
Copies
and splices a gene (single strand of
DNA sequence) into an mRNA sequence
Translation
Converts
翻譯
mRNA into a protein (string of
amino acids)
Promoter
Transcription
Start
signal (e.g.
TATAAT) and stop
signal (e.g. AAAAA)
Splicing:
keep
exons（外碼子）,
throw out intron
（內碼子）
mRNA:
Transcription: Copying
Transcription: Splicing
Translation: Genetic Code

Genetic
code:

3-nucleotides
= a CODON

64 codons

3 stop codons

Rest (61)
codes to 20
amino acids
DNA
Ribosome
tRNA
mRNA
GCA → ALA
Mutation of
Chromosome
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。