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  • 生命编码

    Scientists, Structures, and Secrets - DNA
    ::科学家、结构和秘密 -- -- DNA

    The  nucleotide bases serve as letters  for our  genetic code and provide the functionality of DNA and RNA. When DNA was  decomposed  into nucleotides, it was discovered that certain bases always appeared in the same proportions. The  number of adenine and thymine nucleotides  was  always   equal, and  the  number of cytosine nucleotides  was the same as  guanine. In 1949, Erwin Cargoff proposed that  b ase pairing would explain why  nucleotides A-T and C-G always appeared in equal numbers.
    ::核糖核酸基数作为我们基因代码的字母,提供DNA和RNA的功能。当DNA分解成核酸时,发现某些基数总是以同样的比例出现。 腺和胸核酸基数总是相等,而细胞核酸基数与guanine相同。 1949年,Erwin Carff提议基数配对可以解释核酸A-T和C-G总和为何核酸基数相同。

    Observations of DNA using   x-ray crystallography further revealed the structure of the molecule. This method is akin to shining a flashlight into a hall of mirrors and determining where the mirrors are placed based on  the way that the light bounces around.  had a background in physical chemistry,  and she had  improved on x-ray crystallography techniques at the time. She produced unprecedentedly precise x-ray crystallography images while working in the lab of Maurice Wilkins. Her most  held the key to DNA's structure and was known as "Photo 51." It was heralded by J.D. Bernal, the father of x-ray crystallography in biochemistry, as "among the most beautiful x-ray photographs of any substance ever taken."
    ::使用X射线晶体学对DNA的观察进一步揭示了分子的结构。 这个方法类似于将手电筒光照到镜子大厅中,并根据光在周围反射的方式确定镜子的位置。 她具有物理化学背景,当时在X射线晶体学技术方面有了改进。 她在Maurice Wilkins实验室工作时制作了史无前例的精确X射线晶体学图像。 她最擅长DNA结构的钥匙,并被称为“Photo 51 ”。 它被生物化学中X射线晶学之父J.D. Bernal所预示,“是任何物质中最美丽的X射线照片之一 ” 。

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    (left) the x-ray crystallography image of DNA taken by Rosalind Franklin (right) confirmed the double helix model.
    ::Rosalind Franklin(右)拍摄的DNAX射线晶体学图像证实了双螺旋模型。

     

    Watson and Crick were theoretical biochemists. Watson discovered that the adenine-thymine bond was exactly the same length as the cytosine-guanine bond, which helped him form the picture of each base pair as rungs of a helical ladder.  Francis Crick  helped to develop   a mathematical model for the  diffraction pattern of a helical structure. In 1951, Crick and Watson began to work together, and when Maurice Wilkins showed them Rosalind Franklin's Photo 51, they were able to piece together the . 
    ::Watson和Crick是理论生物化学家。 Watson发现,亚丁-硫金债券的长度与cytosine-guayine债券的长度完全相同,后者帮助他将每对基配成一个螺旋梯子。Francis Crick帮助开发了一个用于直升机结构分解模式的数学模型。 1951年,Crick和Watson开始合作,而当Maurice Wilkins向他们展示了Rosalind Franklin的51号照片时,他们能够拼凑在一起。

     

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    The double helix of DNA contains nucleotides with bases A-T and C-G connected by weak hydrogen bonds.
    ::脱氧核糖核酸的双螺旋含有核核素,其基础为A-T和C-G,由微弱的氢联结连接。

     

    The double-helix of DNA is composed of the sugar and phosphate components of nucleotides. The bases stick out from this backbone and bind to their appropriate counterpart through  relatively weak  hydrogen bonds. In the most common form, the bases appear parallel to each other, like a well-designed stairwell.  A slight electrostatic repulsion  helps to support this structure. This structure is stable in aqueous environments because the hydrophobic base pairs are  protected by the sugar and phosphate backbone.  The double-stranded nature of DNA affords a rigid, stable, and long-lived structure. During DNA replication, each strand is  checked against the other to reduce  copying errors or accidental mutations. 
    ::DNA的双螺旋双螺旋由核糖和磷酸盐成分组成。 基底从这个骨干伸出来,通过相对疲软的氢结壳与适当的对应方捆绑在一起。 最常见的形式是, 基底彼此平行, 像一个设计良好的楼梯。 轻微的静电反射有助于支持这一结构。 这种结构在水环境中是稳定的, 因为对口的防水基底对口受到糖和磷酸基脊的保护。 双柱式的DNA具有僵硬、稳定和长寿的结构。 在DNA复制过程中, 每条底部都要相互检查, 以减少复制错误或意外突变。

    The Genetic Code
    ::《遗传法》

    DNA encodes and stores   genes, which provide a  very lengthy instruction manual  for all living creatures on Earth. If you took the DNA in one human cell and completely stretched it out, it would measure roughly 2 meters, the average height of an NBA player. If you took all of the DNA  from  all of the cells  in a human body and joined them end-to-end, they would cross the diameter of the Solar System   twice .
    ::DNA编码和储存基因,这些基因为地球上所有生物提供了非常长的指令手册。如果将DNA在一个人类细胞中提取出来,并完全拉开,它将测量出大约2米,即NBA玩家的平均高度。如果你从人体中所有细胞中提取所有DNA,并把它们连接起来,它们就会两次跨越太阳系直径。

    Different segments of DNA are known as chromosomes. An organism's genome is the complete collection of chromosomes.  Humans have 23 pairs of chromosomes, encoding roughly 25,000 genes using about 3 billion base pairs. A mosaic of the entire human genome was sequenced between 1990 and 2008 in twenty different institutions in six different countries. This remains one of the most impressive collaborative projects in science. 
    ::DNA的不同部分被称为染色体。有机体的基因组是染色体的完整收集。人类有23对染色体,用大约30亿对基对编码了大约25 000个基因。1990年至2008年间,在六个不同国家的20个不同的机构里,对整个人类基因组进行了组合。这仍然是科学领域最令人印象深刻的合作项目之一。

     

    Species Base Pairs Genes
    Virus 170,000 ?
    E. Coli 4,600,000 3,200
    Fruit Fly 180,000,000 13,600
    Chicken 1,000,000,000 23,000
    Corn 2,500,000,000 59,000
    Human 3,000,000,000 25,000
    Lily 100,000,000,000 ?
    Grasshopper 180,000,000,000 ?
    Amoeba 670,000,000,000 ?

        My, What Big Genomes You Have
    ::我的,你有什么大基因组

    All the better to encode with... or is it?  It  seems  intuitive that  a larger genome should corresponds to more complex organisms, but that would be wrong.  An example of different genome sizes is given by the table above; humans have longer genomes than chickens, but we  lose out to   corn.
    ::与... 或者它编码更好吗? 更大的基因组似乎直观地应该与更复杂的生物相对应,但这是错误的。 上面的表格给出了不同基因组大小的例子;人类的基因组比鸡长,但我们输给了玉米。

    Most DNA is known as   noncoding DNA and does not translate directly to genes. It  is used instead to signal the start of a gene, to help with DNA coiling, and potentially to carry out several other functions that we have yet to discover. Remarkably, more than 98% of the human genome is non-coding.  In contrast, only 20% of the DNA in bacteria  is noncoding DNA.  The bladderwort plant currently holds the record for most efficient genome with only 3% noncoding DNA.
    ::大部分DNA被称为非编码DNA,并不直接转换为基因。 相反,它被用于信号基因的开始,帮助DNA编码,并有可能完成我们尚未发现的其他一些功能。 值得注意的是,98%以上的人类基因组是非编码的。 相反,细菌中只有20%的DNA是非编码的DNA。 膀胱织植物目前拥有最有效的基因组的记录,只有3%的非编码DNA。

    DNA  encodes important instructions for life, but it can become damaged when base pairs or w hole segments of DNA  are  deleted, inverted, duplicated, or moved around. Mutations can be damaging, for example, causing cells to become cancerous. Damage sustained to the phosphate-sugar backbone of DNA is one of the primary causes of mutations and can be a result of exposure to UV radiation. For this reason, sunscreen remains a multi-million dollar industry. 
    ::DNA编码了生命的重要指令,但当基对或整个DNA部分被删除、倒置、复制或移动时,DNA可能会受损。 变异可能会造成损害,例如,导致细胞癌。 DNA磷酸盐糖脊椎的损伤是突变的主要原因之一,也可能是紫外线辐射照射的结果。 因此,防晒霜仍然是一个数百万美元的行业。

    However,   mutations   can  also occur naturally, resulting in expressed altered genes that give rise to new  characteristics .  This is the mechanism for   Darwinian evolution:  beneficial traits arising from mutation will be preferentially selected when mating and propagated through succeeding generations.  Natural mutations arise at measurable rates for different species. This   mutation rate   allows us to measure the   genetic distance   between species. This value is obtained  by   determining the statistical number of mutations required to change one species' genome into another's. For example, deer and giraffes are close in genetic difference. But, both deer and giraffes are genetically  quite far from sunflowers. A genome of a species helps to reveal its   evolutionary path .
    ::然而,突变也可能自然发生,导致出现出现新特征的变异基因。这是达尔文进化机制:在交配和通过后代传播时,会优先选择突变产生的有利特征。自然突变以可测量的速度在不同物种中产生。这种突变速度使我们能够测量物种之间的遗传距离。通过确定将一个物种基因组改变为另一个物种基因组所需的变异的统计数量,可以得出这一数值。例如,鹿和长颈鹿在遗传上存在密切差异。但是,鹿和长颈鹿的基因都远离日葵。一种物种的基因组有助于揭示其进化路径。

       Question for Thought
    ::思考问题

    If the history of organisms can be traced through their genetic code, is it possible to trace this history all the way back to the beginning of life?

    Translating the Genetic Code
    ::翻译《遗传法》

    The genetic code in DNA is  used to manufacture proteins with the help of RNA.   Messenger RNA (mRNA) transcribes the code from the DNA and  carries this information to the ribosome (the protein factories of the cell). A ribosome will read the nucleotide code from mRNA and translate it to build amino acids. Each amino acid  is specified by different   codons, a sequence of three base pairs. Transfer RNA (tRNA)  matches up each codon with the appropriate amino acid.  The resulting polypeptide chain can then be folded into the needed proteins. 
    ::DNA中的遗传代码用于在RNA的帮助下制造蛋白质。 送信者RNA(mRNA)将代码从DNA中加密,并将这些信息传送给血清(细胞的蛋白工厂 ) 。 血清将阅读来自 mRNA的核糖酸代码并将其翻译为制造氨基酸。 每种氨基酸都由不同的codon(三对基底)排列。 传输RNA(tRNA)将每个codon(tRNA)与适当的氨基酸匹配。 由此产生的聚苯二酸链随后可以折叠到所需的蛋白中 。

     

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    The process of translating the genetic code to proteins. mRNA, pictured in blue, carries the genetic information from DNA. This information is interpreted via codons (three base pairs) into amino acids with the help of tRNA carrying the specified amino acid. The RNA in the ribosome then helps to link together the amino acids into a polypeptide chain ready to be folded into a protein. What about the tRNA pictured here allows it to correspond a specific codon to a specific amino acid?
    ::将基因代码转换为蛋白质的过程。 以蓝色绘制的 mRNA, 携带DNA的遗传信息。 这些信息通过codons (三对基对) 被解释成氨基酸, 借助tRNA 携带指定的氨基酸 。 排卵体中的 RNA 有助于将氨基酸连接到一个可被折叠成蛋白质的聚苯二酸链中。 这里所绘制的 tRNA 允许它将特定codon 与特定氨基酸相对应吗 ?

     

    RNA World
    ::RNA 世界

    How did this amazing biochemical system begin and how did it evolve? Proteins are needed to  catalyze chemical reactions critical to the survival of  cells. But, it is difficult to  imagine how proteins could have been the precursor to living cells because DNA is required to manufacture proteins, presenting a "chicken-and-egg" problem. A breakthrough came when Sidney Altman and Thomas Czech discovered a class of RNA molecules called ribozymes that could catalyze their own replication . Ribozymes show that RNA, which can encode genetic information, can also act as an enzyme.  This discovery was awarded the Nobel prize in 1989 and supported a  hypothesis called the Early RNA world, where ancient life used RNA for storing genetic information and catalyzing chemical reactions. This hypothesis had been suggested in the 1960's by Carl Woese, Frances Crick and Leslie Orgel. According to this hypothesis, the instability of RNA promoted mutations and natural selection eventually evolved a more stable, double-stranded DNA molecule as ribozymes were phased out.  A fascinating "smoking gun" for this hypothesis is the fact that the ribosome, which assembles proteins in cells today, is a ribozyme.   While the current day ribosome incorporates some proteins, none of the proteins  are anywhere near  the active site where the reactions take place. They appear to  exist largely for structural support.  
    ::这个惊人的生化系统是如何开始的,是如何演变的?需要蛋白质来催化对细胞生存至关重要的化学反应。但是,很难想象蛋白质是如何成为活细胞的前身的,因为DNA是制造蛋白质所需要的,提出了“芯和卵”问题。一个突破是Sidney Altman和Thomas Cutman和Thomas Cretain发现了一类RNA分子,它们叫做核糖核酸,可以催化它们自己的复制。Ribozymes显示,可以将基因信息加密的RNA可以起到酶的作用。这个发现在1989年被授予诺贝尔奖,并且支持一个称为早期RNA世界的假设,在这个假设中,古代生命利用RNA储存基因信息和催化化学反应。1960年代,Carl Woese,Frances Crick和Leslie Orgel就提出了这一假设。根据这个假设,RNA的不稳定性促进了突变和自然选择,最终演变出一个更稳定、双弦和DNA分子,可以起到酶的作用。1989年获得诺奖项奖项奖项的。一个称为“早期”的分解。一个称为“古体,今天的蛋白蛋白的蛋白质在任何地方在任何地方里,今天的蛋白质的蛋白质在任何地方中出现。

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    Ribosome is shown in brown with proteins depicted in blue. The proteins are not near active sites and appear to provide structural support.
    ::Ribosome以棕色显示,蛋白质以蓝色显示,蛋白质不靠近活动地点,似乎提供结构支持。

    While the capabilities of RNA seem to make it the perfect candidate to explain the origin of life, RNA is a far more complicated structure and not as easy to make as amino acids. Miller-Urey experiments have been capable of synthesizing a series of smaller, very reactive molecules. When enough of these molecules are made, detectable amounts of purine and pyrimidine bases can be detected. Components of nucleotides have also been discovered on meteorites like the Murchison Meteorite. However, no complete extraterrestrial nucleotides or nucleic acid chains have been discovered yet.
    ::虽然RNA的能力似乎使它成为解释生命起源的完美人选,但RNA的结构复杂得多,不像氨基酸那样容易制造。Miller-Urey实验能够合成一系列较小的、非常活性分子。当这些分子制造出足够的分子时,可以检测到纯和基。在Murchison Meteorite等陨石上也发现了核糖化物的成分。然而,尚未发现完整的外星核糖核酸或核糖酸链。

    A breakthrough came in 2009 from British chemist John Sutherland along with Matthew Powner and Beatrice Gerland. Sutherland's group determined a chemically efficient pathway for nucleotides to form that is plausible in a prebiotic environment. Rather than form each component of the nucleotide individually, they proposed a method that formed and attached a purine and a ribose sugar in the same reaction. Phosphate is used to help catalyze the reaction and incorporated into the nucleotide later. 
    ::2009年,英国化学家约翰·苏瑟兰(John Sutherland)与马修·普克拥有者和比阿特丽斯·格尔兰(Beatrice Gerland)一道,在2009年取得了突破。 萨瑟兰的团体决定了一种化学效率高的核糖酸在化学前环境中形成的一种途径,在生物前环境中是有道理的。 他们提出的方法不是单独构成核酸的每一个组成部分,而是形成并附着一种纯和根糖的同一反应。 磷酸盐被用于帮助催化反应,后来又被纳入核酸。

    Once nucleotides are assembled, perhaps they themselves could assemble to form RNA. RNA is capable of assembling proteins, and proteins run the reactions that organize life. Is that all there is to life then? At what point does a collection of molecules and equilibrium reactions become a living organism ?
    ::核糖核化物一旦组装,也许他们自己可以组成RNA。 RNA有能力组装蛋白质,蛋白质会引发生命组织的反应。 那么生命就只有这些吗?分子和平衡反应的集合在什么时候会变成活体?

    Biochemistry to Biology
    ::生物生物生物生物化学

    What is life? This is a hard enough question for philosophers to answer, but perhaps even harder to answer scientifically. Biologists can distinguish smaller and smaller structures and biochemists are reaching a greater understanding of the chemistry  of life, but there is still a wide gap in our understanding. How do we bridge our understanding of chemistry with our understanding of living cells?  
    ::生命是什么?这是哲学家必须回答的足够困难的问题,但也许更难从科学角度回答。 生物学家可以区分较小和较小结构,生物化学家对生命化学有了更深刻的理解,但在理解上仍然存在巨大的差距。 我们如何用对生物细胞的理解来弥合我们对化学的理解呢?

    A n over-arching, all-encompassing,     currently eludes us. The working definition used within  NASA  is that life is "a self-sustaining chemical system capable of Darwinian evolution." Life is a chemical system: CHON, amino acids, nucleotides. Life is self-sustaining: life generates its own energy for reactions and so must also maintain reactions that generate energy. Life is capable of Darwinian evolution: an imperfect genetic system stores the information that defines an organism  and also suffers from errors that give rise to mutations and new characteristics. Living organisms reproduce  and are capable of adapting and changing to become better suited for different environments. 
    ::目前,我们无法了解一个包罗万象、包罗万象、包罗万象的包罗万象。美国航天局内部使用的工作定义是生命是“一个能够促进达尔文进化的自我维持的化学系统 ” 。生命是一个化学系统:中国、氨基酸、核酸。生命是自我维持的:生命产生自己的反应能量,因此也必须保持产生能量的反应。生命是达尔文进化的能力:一个不完善的基因系统储存着一个有机体的定义信息,也存在引起突变和新特征的错误。活生物体繁殖并能够适应和改变以适应不同的环境。

    Membranes
    ::膜膜

    Cells are bound and regulated by membranes. Membranes are composed of of p hospholipids   with  a hydrophilic "head" that  are water soluble and two hydrophobic "tails," which try to avoid interacting with water . It is not clear how the first phospholipids formed, but it is possible that the earliest membranes were first composed of a less complicated lipid connected to hydrocarbon chains .
    ::细胞是由膜膜捆绑和调节的。 膜膜由含有水溶解的具有水利病“头”和两个疏水性“尾巴”的磷素组成,它们试图避免与水的相互作用。 不清楚第一种磷素是如何形成的,但最早的膜可能首先由与碳氢化合物链相连的不那么复杂的脂质组成。

    Phospholipids assembled into bilayer sheets allow cell membranes to be both fluid and semi-permeable. Cell membranes are fluid in the sense that the different phospholipids can move around past each other, which allow proteins that are incorporated into the membrane to be inserted and similarly move around. Cell membranes  are also  semi-permeable, allowing only certain substances through. Most molecules cannot spontaneously diffuse though both a polar and nonpolar region. Substances can therefore only cross the phospholipid bilayer if there is significant pressure (either physical or chemical) driving diffusion or they  have  some help. To this end, cell membranes incorporate several proteins specially designed to  control the traffic of molecules in and out of the cell. Membranes provide a self-contained environment  to safeguard  the reactions that drive life.
    ::聚光膜组装成双层薄膜的磷光滑物使细胞膜既能流体,也能半透膜。细胞膜是液体,因为不同的磷蛋白质可以相互移动,这样可以插入嵌入膜内的蛋白质,并同样移动。细胞膜也是半透膜,只允许某些物质通过。大多数分子不能自发扩散,尽管是极地和非极地。因此,只有存在(物理或化学)强力驱散或有某些帮助,物质才能穿过磷素双层。为此,细胞膜中含有若干专门设计用于控制细胞内和外分子流量的蛋白质。膜提供了一种自成一体的环境,以保障驱动生命的反应。

     

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    A phospholipid membrane. Green channels are embedded into the membrane that may allow certain compounds to pass from one side to the other. Note how the right channel needs an input of energy, represented by the glowing red ball, in order to operate.
    ::磷素膜:绿色通道嵌入膜内,可能允许某些化合物从一边传到另一边。请注意,正确的通道需要以发光的红球为代表的能量投入才能运作。

     

     The Last Universal Common Ancestor
    ::最后一个世界共同祖先

    The   Last Universal Common Ancestor (LUCA) on Earth is a concept, rather than an actual  organism. Any universal characteristics of life on Earth are universal either because they are inherited or because they are truly fundamental to life in general. Without a second example of life we are unable to understand how common these features will be on other worlds. 
    ::地球上的最后一个世界共同祖先(LUCA)是一个概念,而不是一个实际的有机体。 地球上生命的任何普遍性特征都是普遍的,要么因为它们是继承的,要么因为它们真正是整个生命的根本。 没有第二个生命例子,我们就无法理解这些特征在其他世界中是如何共同的。

    LUCA represents the earliest shared qualities of ancestral life and likely appeared on Earth between 3.5 to 4 Gya and seeded our planet with life. All of the features of life today would have been inherited from LUCA. From what we know about terrestrial biology, this means that LUCA  would have been carbon-based, dependent on water, incorporated left-handed amino acids, and used ATP for energy transport. LUCA  would have used DNA  or RNA to encode genes and translate them into proteins.  Significantly, t he codons that translate  for   specific amino acids  are the same  in every known organism. This code must have been passed down from a common ancestor from which every other species has since evolved. LUCA might not have even been as sophisticated as a single celled organism.
    ::LUCA代表了祖先生命的最早共同特性,可能出现在地球上3.5至4Gya之间,并给我们的星球带来了生命。今天,生命的所有特征本来都是从LUCA继承的。根据我们对陆地生物学的了解,这意味着LUCA会以碳为基础,依靠水,结合左手氨基酸,并使用ATP进行能源运输。LUCA本来会利用DNA或RNA来编码基因并将其转换成蛋白质。重要的是,在每一个已知生物体中,转化成特定氨基酸的codon都是相同的。这个代码一定是从一个共同的祖先那里传下来的,所有其他物种都从那里演化出来。LUCA可能甚至没有像一个单一的细胞生物体那样精密。

    One can only imagine how the  field  of biology will change the moment extraterrestrial life is  discovered for the first time. Will we see shocking similarities? Or will life elsewhere  be so different that it is barely recognizable to us?
    ::人们只能想象生物学领域将如何改变首次发现地球外生命的时刻。 我们能看到令人震惊的相似之处吗? 还是其他地方的生活会如此不同,以至于我们几乎无法辨认?