Chapter 4 GENES ARE DNA.doc

第四章 基因是DNAThe genome is the complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles. Nucleic acids are molecules that encode genetic information. They consist of a series of nitrogenous bases connected to ribose molecules that are linked by phosphodiester bonds. DNA is deoxyribonucleic acid, and RNA is ribonucleic acid. A gene(cistron) is the segment of DNA specifying production of a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). An allele is one of several alternative forms of a gene occupying a given locus on a chromosome. A locus is the position on a chromosome at which the gene for a particular trait resides; a locus may be occupied by any one of the alleles for the gene. Linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome; measured by percent recombination between loci基因组是一个生物遗传物质的全套序列，它包括每条染色体和细胞器DNA中得原则。核酸是编码遗传信息的分子，他们由一系列以磷酸二酯键与核糖分子连接的含N碱基构成。DNA是脱氧核糖核酸。RNA是核糖核酸。一个基因（顺反子）是特异产生一条多肽链的DNA片段，它包括编码之前和之后的区域（头和尾），以及在每个编码片段（外元）之间的序列（内元）。等位基因是占据染色体特定位点的一个基因多种形式之一。位点是染色体上的一个位置，在此位置上存在着某种特定性状的基因，一个位点可以被一个基因的任何一种等位基因占据。连锁指的是不同基因被一起遗传的趋势。这是由它们定位在同一染色体上导致的，并通过位点之间的重组百分率等衡量。The hereditary nature of every living organism is defined by its genome, which consists of a long sequence of nucleic acid that provides the information need to construct the organism. We use the term information because the genome does not itself perform any active role in building the organism; rather it is the sequence of the individual subunits (bases) of the nucleic acid that determines hereditary features. By a complex series of interactions, this sequence is used to produce all the proteins of the organism in the appropriate time and place. The proteins either form part of the structure of the organism, or have the capacity to build the structures or to perform the metabolic reactions necessary for life.任何生物的遗传本质是由基因组来定义的，它由提供构建生物体所需信息的核苷酸长序列组成，我们用术语“信息”，因为基因组本身并不在生物体构建中祈祷任何主动作用。而是多个核苷酸亚基（碱基）的序列决定着遗传特征。通过一系列复杂的相互作用，这序列被用来在合适的时间和空间里生产机体所有的蛋白，这些蛋白或构件机体的部分结构，或有构建结构的功能，或进行生命必须的代谢反应。The genome contains the complete set of hereditary information for any organism. Physically the genome may be divided into a number of different nucleic acid molecules. Functionally it may be divided into genes. Each gene is a sequence within the nucleic acid that represents a single protein. Each of the discrete nucleic acid molecules comprising the genome may contain a large number of genes. Genomes for living organisms may contain as few as 40,000 for Man.对于任何物种来说，基因组包含全套的遗传信息。从结构上来说，基因组可被划分为许多不同的核苷酸分子。从功能上来说，它可被分为很多基因。每个基因都是一个由核苷酸构成的序列，此序列表达单一蛋白，构成基因组的每个分离的核苷酸分子都包含很多基因。生命有机体的基因组可能包含少则500个（支原体，一种细菌）。多则4000个（人类）基因。In this Chapter, we analyze the properties of the gene in terms of its basic molecular construction. Figure 1.1 summarizes the stages in the transition from the historical concept of the gene to the modern definition of the genome.在这一章，我们将根据基因的分子结构分析其特性，图11总结了从过去对基因的认识到现代基因组的定义的各个转变阶段，The basic behavior of the gene was defined by Mendel more than a century ago. Summarized in his two laws, the gene was recognized as a particulate factor that passes unchanged from parent to progeny. A gene may exist in alternative forms. These forms are called alleles.早在一世纪之前，孟德尔就定义了基因的基本行为，在她得两大定律总结中，基因被认为是从亲代到子代稳定传递的“特异性因子”。一个基因可以成双的形式存在，这些形式成为等位基因。In diploid organisms, which have two sets of chromosomes, one copy of each chromosome is inherited from each parent. This is the same behavior that is displayed by genes. One of the two copies of each gene is the paternal allele (inherited from the father), the other is the maternal allele (inherited from the mother). The equivalence led to the discovery that chromosomes in fact carry the genes.在有两套染色体的二倍体生物中，每一个染色体的拷贝都继承于一个亲本。这也是记忆所表现得行为。每个基因的两个拷贝中得一个是父本等位基因（继承与父方），另一条为母本等位基因（继承母本），这样的对等性引出这样的发现：实际上染色体携带基因。Each chromosome consists of a linear array of genes. Each gene resides at a particular location on the chromosome. This is more formally called a genetic locus. We can then define the alleles of this gene as the different forms that are found at this locus.每个染色体包含线性平排列的很多基因，每个基因位于染色体特定位置上。这位点被正式定义为基因座。由此我们可将此基因的等位基因定义为在此位点的不同形式。The key to understanding the organization of genes into chromosomes was the discovery of genetic linkage. This describes the observation that alleles on the same chromosome tend to remain together in the progeny instead of assorting independently as predicted by Mendels laws (see 32.3Linkage and mapping). Once the unit of recombination (reassortment) was introduced as the measure of linkage, the construction of genetic maps became possible.理解基因组成染色体的关键是基因连锁的发现。它描述了这样的发现：在同一染色体的上的基因趋向于在后代中保持在一起，而不是像孟德尔法则中预言的独立分配（见32.3连锁与构图）。当重组率（ ）被当做连锁的量度，遗传图谱的构建也就成为可能。On the genetic maps of higher organisms established during the first half of this century, the genes are arranged like beads on a string. They occur in a fixed order, and genetic recombination involves transfer of corresponding portions of the string between homologous chromosomes. The gene is to all intents and purposes a mysterious object (the bead), whose relationship to its surroundings (the string) is unclear.在本世纪上半页推测高等生物遗传图谱时，基因被排列成一条线上的珠子。它们以固定的顺序出现，基因重组包括同源染色体相应部分之间的转移。实际上，基因（珠子）是一个神秘的物体，也与其环境（念珠线）的关系还不清楚。The resolution of the recombination map of a higher eukaryote is restricted by the small number of progeny that can be obtained from each mating. Recombination occurs so infrequently between nearby points that it is rarely observed between different mutations in the same gene. By moving to a microbial system in which a very large number of progeny can be obtained from each genetic cross, it became possible to demonstrate that recombination occurs within genes. It follows the same rules that were previously deduced for recombination between genes.对高等真核生物基因图谱的破译度限于每次交配中，只能获得少数后代。在相邻位点之间的重组发生的如此不频繁，以至于在同一个基因不同个体之间的重组很少被观察到。通过将用于多次杂交都能获得大量后代的微生物界，证明基因内重组的发生成为可能，它与之前推断的及印鉴重组规律相同。Mutations within a gene can be arranged into a linear order, showing that the gene itself has the same linear construction as the array of genes on a chromosome. So the genetic map is linear within as well as between loci: it consists of an unbroken sequence within which the genes reside. This conclusion leads naturally into the modern view that the genetic material of a chromosome consists of an uninterrupted length of DNA representing many genes.基因内的突变也可被排列成一个线性顺序，标明基因自身也有同样的线性机构，就像基因在染色体上的排列。因此基因座之内和之间的遗传图谱是线性的，它包括基因存在于其中的连续序列。这样的结论很自然的引出了这样的现代观点。染色体的遗传物质由很多基因的不间断的DNA片段构成。A genome consists of the entire set of chromosomes for any particular organism. It therefore comprises a series of DNA molecules (one for each chromosome), each of which contains many genes. The ultimate definition of a genome is to determine the sequence of the DNA of each chromosome.基因组包括任何特定生物的圈套染色体，一次，他包含一系列DNA分子，（每个染色体是一个DNA），其中每一个包含很多基因。基因组的最终定义是测定的每条贪色提的DNA序列。The first definition of the gene as a functional unit followed from the discovery that individual genes are responsible for the production of specific proteins. The difference in chemical nature between the DNA of the gene and its protein product led to the concept that a gene codes for a protein. This in turn led to the discovery of the complex apparatus that allows the DNA sequence of gene to generate the amino acid sequence of a protein.基因作为一个功能单位，最初的定义源于这样的发展，每个基因都负责特定蛋白的产生。基因的DNA与其蛋白产物化学特性的而不同引出这样的认识，一个基因编码一个蛋白。这又导致了基因的DNA序列产生蛋白的氨基酸序列的复杂机制的发现。A gene codes for an RNA, which may code for protein.Understanding the process by which a gene is expressed allows us to make a more rigorous definition of its nature. Figure 1.2 shows the basic theme of this chapter. A gene is a sequence of DNA that produces another nucleic acid, RNA. The DNA has two strands of nucleic acid, and the RNA has only one strand. The sequence of the RNA is determined by the sequence of the DNA (in fact, it is identical to one of the DNA strands). In many, but not in all cases, the RNA is in turn used to direct production of a protein. Thus a gene is a sequence of DNA that codes for an RNA; in protein-coding genes, the RNA in turn codes for a protein. 一个基因编码一种RNA，一种RNA编码一种蛋白。对基因表达过程的理解，使我们可以对其本质做一个更精确的定义。图4.1解释了本节的基本主题，一个基因是一个编码另一个核苷酸RNA的DNA序列。DNA有两条核苷酸链，而RNA只有一条。RNA的序列由DNA序列决定（实际上，它与一条DNA链相同），在很多而非全部情况下，RNA反而是直接用来产生蛋白的。因此一个基因是一个编码RNA的DNA序列，在编码蛋白的基因中，RNA反而编码蛋白。From the demonstration that a gene consists of DNA, and that a chromosome consists of a long stretch of DNA representing many genes, we move to the overall organization of the genome in terms of its DNA sequence.通过这样的结论，基因包含DNA序列，而且一条染色体由代表基因的DNA长链组成，我们根据DNA序列得出全面的基因组成，在2 断裂基因中，我们详细的了解了基因的组成和它对蛋白的表达，在3 基因组概念中，我们考虑了基因的总数，在4序列重复与循环中，我们讨论基因组的其他成分以及其结构和维持。DNA is the genetic material of bacteria DNA是细菌的遗传物质Transformation of bacteria is the acquisition of new genetic material by incorporation of added DNA. Avirulent mutants of a bacterium or virus have lost the capacity to infect a host productively, that is, to make more bacterium or virus. The transforming principle is DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell. Deoxyribonucleic acid(DNA) is a nucleic acid molecule consisting of long chains of polymerized (deoxyribo)nucleotides. In double-stranded DNA the two strands are held together by hydrogen bonds between complementary nucleotide base pairsThe idea that genetic material is nucleic acid had its roots in the discovery of transformation in 1928. The bacterium Pneumococcus kills mice by causing pneumonia. The virulence of the bacterium is determined by its capsular polysaccharide. This is a component of the surface that allows the bacterium to escape destruction by the host. Several types (I, II, III) of Pneumococcus have different capsular polysaccharides. They have a smooth (S) appearance.Each of the smooth Pneumococcal types can give rise to variants that fail to produce the capsular polysaccharide. These bacteria have a rough (R) surface (consisting of the material that was beneath the capsular polysaccharide). They are avirulent. They do not kill the mice, because the absence of the polysaccharide allows the animal to destroy the bacteria.When smooth bacteria are killed by heat treatment, they lose their ability to harm the animal. But inactive heat-killed S bacteria and the ineffectual variant R bacteria together have a quite different effect from either bacterium by itself. Figure 1.3 shows that when they are jointly injected into an animal, the mouse dies as the result of a Pneumococcal infection. Virulent S bacteria can be recovered from the mouse postmortem.In this experiment, the dead S bacteria were of type III. The live R bacteria had been derived from type II. The virulent bacteria recovered from the mixed infection had the smooth coat of type III. So some property of the dead type III S bacteria can transform the live R bacteria so that they make the type III capsular polysaccharide, and as a result become virulent (Griffith, 1928).细菌的转化作用是通过对加入DNA的整合作用获得新的遗传物质。细菌或病毒知名的突变体已丧失有效侵染宿主的能力，也就是产生更多细菌或病毒的能力。转化因子是被细菌占用的DNA，其表达会改变受体细胞的特性。脱氧核糖核酸（DNA）是一个由长链多聚（脱氧）核苷酸构成的核酸分子，在双链DNA中，两条链是通过互补的核苷酸碱基对间的氢键连接在一起的。核酸是遗传物质的观点是根据1928年转化现象的发现，肺炎双球菌通过导致肺炎致死小鼠，此细菌的毒性是由其荚膜多糖决定的。这是一种能事细菌躲过宿主的破坏其表面成分，几种类型（，）的肺炎双球菌有不同的荚膜多糖，他们表面光滑（S）每种光滑型肺炎双球菌类型，都可以产生无法产生荚膜多糖的突变体，这些细菌的粗糙（R）的表面（由荚膜下得物质构成），他们是无毒的，不会杀死小鼠，因为缺乏荚膜多糖会使动物破坏细菌。当光滑型细菌别热处理杀死后，他们将失去伤害动物的能力，但是失活的热致死的S型菌和无毒性R型菌共同作用与他们各自的大不相同。图1.3展示，当他们被共同注射到动物体内时，小鼠死于肺炎双球菌感染，从小鼠尸体中可以分离提取到S细菌。在此实验中，死亡的S型菌是型，或者的R型菌来自型。从混合注射物中分离出的毒性细菌有型光滑外壳。一次一些死亡的型S菌的后代可以转化活的R型菌，以至于他们能产生型荚膜多糖，并因此产生毒性。DNA is the genetic material of viruses Having shown that DNA is the genetic material of bacteria, the next step was to demonstrate that DNA provides the genetic material in a quite different system. Phage T2 is a virus that infects the bacterium E. coli. When phage particles are added to bacteria, they adsorb to the outside surface, some material enters the bacterium, and then 20 minutes later each bacterium bursts open (lyses) to release a large number of progeny phage.Figure 1.5 illustrates the results of an experiment in 1952 in which bacteria were infected with T2 phages that had been radioactively labeled either in their DNA component (with 32P) or in their protein component (with 35S). The infected bacteria were agitated in a blender, and two fractions were separated by centrifugation. One contained the empty phage coats that were released from the surface of the bacteria. The other fraction consisted of the infected bacteria themselves.Most of the 32P label was present in the infected bacteria. The progeny phage particles produced by the infection contained 30% of the original 32P label. The progeny received very littleless than 1%of the protein contained in the original phage population. The phage coats consist of protein and therefore carried the 35S radioactive label. This experiment therefore showed directly that only the DNA of the parent phages enters the bacteria and then becomes part of the progeny phages, exactly the pattern of inheritance expected of genetic material (Hershey and Chase, 1952).A phage (virus) reproduces by commandeering the machinery of an infected host cell to manufacture more copies of itself. The phage possesses genetic material whose behavior is analogous to that of cellular genomes: its traits are faithfully reproduced, and they are subject to the same rules that govern inheritance. The case of T2 reinforces the general conclusion that the genetic material is DNA, whether part of the genome of a cell or virus.DNA是病毒的遗传物质。已经揭示了DNA是细菌的遗传物质，下一步是证明DNA以十分不同的机制提供遗传物质。T2噬菌体是一种侵染大肠杆菌的病毒，当噬菌体颗粒被加入细菌，他们吸附在外表面，一些物质进入细菌，在20分钟后每个细菌破裂开（裂解）释放出大量的噬菌体颗粒。图4.2说明了1952年的一个实验结果，其中细菌被放射性标记了DNA成分（用32p）或蛋白质（用35S）的T2噬菌体侵染，被侵染的细菌在搅拌机中被搅拌，并被离心机分为两个组分，一个包含从细菌释放的空的噬菌体空壳，另一个组分包含被侵染的细菌本身。大多32P标记出现在被侵染的细菌中，由侵染所产生的子代噬菌体颗粒包含30%。最初的32P标记。子代获得极少原噬菌体种群中得蛋白不到1%。噬菌体外壳由蛋白构成，因此含有35S放射性标记。因此这个实验直接揭示只有亲代噬菌体的DNA会进入细菌，并成为子代噬菌体的一部分，正好符合对遗传物质方式的预想。噬菌体（病毒）靠指导宿主细胞的组阵来合成自身的拷贝来繁殖，噬菌体拥有与细胞基因组行为相似的遗传物质。其形状被精确的复制，且遵守相同的控制遗传的规律。T2噬菌体的实验进一步证实了这样一个普遍的结论，不论对于细胞还是病毒的基因组，DNA是遗传物质。Mutations change the sequence of DNA All mutations consist of changes in the sequence of DNA. Mutations may occur spontaneously or may be induced by mutagens. Mutations provide decisive evidence that DNA is the genetic material. When a change in the sequence of DNA causes an alteration in the sequence of a protein, we may conclude that the DNA codes for that protein. Furthermore, a change in the phenotype of the organism may allow us to identify the function of the protein. The existence of many mutations in a gene may allow many variant forms of a protein to be compared, and a detailed analysis can be used to identify regions of the protein responsible for individual enzymatic or other functions.All organisms suffer a certain number of mutations as the result of normal cellular operations or random interactions with the environment. These are called spontaneous mutations; the rate at which they occur is characteristic for any particular organism and is sometimes called the background level. Mutations are rare events, and of course those that damage a gene are selected against during evolution. It is therefore difficult to obtain large numbers of spontaneous mutants to study from natural populations.The occurrence of mutations can be increased by treatment with certain compounds. These are called mutagens, and the changes they cause are referred to as induced mutations. Most mutagens act directly by virtue of an ability either to modify a particular base of DNA or to become incorporated into the nucleic acid. The effectiveness of a mutagen is judged by how much it increases the rate of mutation above background. By using mutagens, it becomes possible to induce many changes in any gene (for review see Drake and Balz, 1976).Spontaneous mutations that inactivate gene function occur in bacteriophages and bacteria at a relatively constant rate of 3-4 103 per genome per generation (Drake, 1991). Given the large variation in genome sizes between bacteriophages and bacteria, this corresponds to wide differe