Download DNA Structure and Analysis and more Lecture notes Biology in PDF only on Docsity!
231
many complex processes that lead to an organism’s adult form. Until 1944, it was not clear what chemical compo- nent of the chromosome makes up genes and constitutes the genetic material. Because chromosomes were known to have both a nucleic acid and a protein component, both were candidates. In 1944, however, direct experimental evi- dence emerged showing that the nucleic acid DNA serves as the informational basis for the process of heredity. Once the importance of DNA to genetic processes was realized, work was intensified with the hope of discerning not only the structure of this molecule but also the relation- ship of its structure to its function. Between 1944 and 1953, many scientists sought information that might answer the most significant and intriguing question in the history of biology: How does DNA serve as the genetic basis for living processes? Researchers believed the answer must depend strongly on the chemical structure of the DNA molecule, given the complex but orderly functions ascribed to it. These efforts were rewarded in 1953, when James Watson and Francis Crick put forth their hypothesis for the double-helical nature of DNA. The assumption that the molecule’s functions would be easier to clarify once its general structure was determined proved to be correct. In this chapter, we first review the evidence that DNA is the genetic material and then discuss the elucidation of its structure. We conclude the chapter with a discussion of
DNA Structure and Analysis
C h a p t e r C o n C e p t s
■ (^) Except in some viruses, DNA serves as the genetic material in all living organisms on Earth. ■ (^) According to the Watson–Crick model, DNA exists in the form of a right-handed double helix. ■ (^) The strands of the double helix are antiparallel and are held together by hydrogen bonding between complementary nitrogenous bases. ■ (^) The structure of DNA provides the means of storing and expressing genetic information. ■ (^) RNA has many similarities to DNA but exists mostly as a single-stranded molecule. ■ (^) In some viruses, RNA serves as the genetic material. ■ (^) Many techniques have been developed that facilitate the analysis of nucleic acids, most based on detection of the complementarity of nitrogenous bases.
U
p to this point in the text, we have described chro- mosomes as containing genes that control pheno- typic traits transmitted through gametes to future offspring. Logically, genes must contain some sort of infor- mation that, when passed to a new generation, influences the form and characteristics of each individual. We refer to that information as the genetic material. Logic also sug- gests that this same information in some way directs the
Bronze sculpture of the Watson–Crick model for double-helical DNA.
FOR REVIEW ONLY
232 10 DNA S tructure AND ANAlySiS
translation , the chemical information in mRNA directs the construction of a chain of amino acids, called a polypeptide, which then folds into a protein. Collectively, these processes serve as the foundation for the central dogma of molecular genetics : “DNA makes RNA, which makes proteins.” The genetic material is also the source of variabil- ity among organisms, through the process of mutation. If a mutation—a change in the chemical composition of DNA—occurs, the alteration is reflected during transcrip- tion and translation, affecting the specific protein. If a mutation is present in a gamete, it may be passed to future generations and, with time, become distributed in the pop- ulation. Genetic variation, which also includes alterations of chromosome number and rearrangements within and between chromosomes (as discussed in Chapter 8), pro- vides the raw material for the process of evolution.
10.2 until 1944, Observations Favored Protein as the Genetic Material
The idea that genetic material is physically transmitted from parent to offspring has been accepted for as long as the concept of inheritance has existed. Beginning in the late nineteenth century, research into the structure of biomolecules progressed considerably, setting the stage for describing the genetic mate- rial in chemical terms. Although proteins and nucleic acid were both considered major candidates for the role of genetic material, until the 1940s many geneticists favored proteins.
various analytical techniques useful during the investiga- tion of the nucleic acids, DNA and RNA. Please note that some of the topics discussed in this chapter are explored in greater depth later in the text (see Special Topic Chapter 2—Emerging Roles of RNA).
10.1 the Genetic Material Must
exhibit Four characteristics
For a molecule to serve as the genetic material, it must exhibit four crucial characteristics: replication, storage of information, expression of information , and variation by mutation. Replication of the genetic material is one facet of the cell cycle and as such is a fundamental property of all living organisms. Once the genetic material of cells repli- cates and is doubled in amount, it must then be partitioned equally—through mitosis—into daughter cells. The genetic material is also replicated during the formation of gametes, but is partitioned so that each cell gets only one-half of the original amount of genetic material—the process of meiosis (discussed in Chapter 2). Although the products of mitosis and meiosis are different, these processes are both part of the more general phenomenon of cellular reproduction. Storage of information requires the molecule to act as a repository of genetic information that may or may not be expressed by the cell in which it resides. It is clear that while most cells contain a complete copy of the organism’s genome, at any point in time they express only a part of this genetic potential. For example, in bacteria many genes “turn on” in response to specific environmental cues and “turn off ” when conditions change. In vertebrates, skin cells may display active melanin genes but never activate their hemoglobin genes; in contrast, digestive cells activate many genes specific to their function but do not activate their melanin genes. Inherent in the concept of storage is the need for the genetic material to be able to encode the vast variety of gene products found among the countless forms of life on our planet. The chemical language of the genetic material must have the capability of storing such diverse informa- tion and transmitting it to progeny cells and organisms. Expression of the stored genetic information is a com- plex process that is the underlying basis for the concept of information flow within the cell ( Figure 10–1 ). The initial event in this flow of information is the transcription of DNA, in which three main types of RNA molecules are syn- thesized: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Of these, mRNAs are trans- lated into proteins, by means of a process mediated by the tRNA and rRNA. Each mRNA is the product of a specific gene and leads to the synthesis of a different protein. In
Figure 10–1 Simplified diagram of information flow (the cen- tral dogma) from DNA to rNA to produce the proteins within cells.
Transcription
mRNA rRNA tRNA
Ribosome
Protein
DNA
Translation
FOR REVIEW ONLY
234 10 DNA S tructure AND ANAlySiS
Griffith’s work led other physi- cians and bacteriologists to research the phenomenon of transforma- tion. By 1931, M. Henry Dawson at the Rockefeller Institute had con- firmed Griffith’s observations and extended his work one step further. Dawson and his coworkers showed that transformation could occur in vitro (in a test tube). When heat- killed IIIS cells were incubated with living IIR cells, living IIIS cells were recovered. Therefore, injec- tion into mice was not necessary for transformation to occur. By 1933, J. Lionel Alloway had refined the in vitro experiments by using crude extracts of IIIS cells and living IIR cells. The soluble filtrate from the heat-killed IIIS cells was as effective in inducing transformation as were the intact cells. Alloway and others did not view transformation as a genetic event, but rather as a physi- ological modification of some sort. Nevertheless, the experimental evi- dence that a chemical substance was responsible for transformation was quite convincing.
Transformation: The Avery, MacLeod, and McCarty Experiment The critical question, of course, was what molecule serves as the trans- forming principle? In 1944, after 10 years of work, Avery, MacLeod, and McCarty published their results in what is now regarded as a classic paper in the field of molecular genetics. They reported that they had obtained the trans- forming principle in a purified state and that beyond rea- sonable doubt it was DNA. The details of their work, sometimes called the Avery, MacLeod, and McCarty experiment, are outlined in Figure 10–3. These researchers began their isolation proce- dure with large quantities (50–75 liters) of liquid cultures of type IIIS virulent cells. The cells were centrifuged, collected, and heat killed. Following homogenization and several extrac- tions with the detergent deoxycholate (DOC), the research- ers obtained a soluble filtrate that retained the ability to induce transformation of type IIR avirulent cells. Protein was removed from the active filtrate by several chloroform extrac- tions, and polysaccharides were enzymatically digested and
only with living avirulent IIR bacteria for this set of experi- ments, did not develop pneumonia and remained healthy. This ruled out the possibility that the avirulent IIR cells simply changed (or mutated) to virulent IIIS cells in the absence of the heat-killed IIIS bacteria. Instead, some type of interaction had taken place between living IIR and heat- killed IIIS cells. Griffith concluded that the heat-killed IIIS bacteria somehow converted live avirulent IIR cells into virulent IIIS cells. Calling the phenomenon transformation , he suggested that the transforming principle might be some part of the polysaccharide capsule or a compound required for capsule synthesis, although the capsule alone did not cause pneumonia. To use Griffith’s term, the transforming principle from the dead IIIS cells served as a “pabulum”— that is, a nutrient source—for the IIR cells.
Living III S (virulent)
Inject
Living III S heat-killed IIILiving II R^ and S^ recovered
Mouse dies
Tissue analyzed
Heat-killed III S
Griffith’s critical experiment
Controls
Living II R (avirulent)
Inject
Mouse lives
Inject
Mouse lives
Inject
Mouse dies
Figure 10–2 Griffith’s transformation experiment.
FOR REVIEW ONLY
10.3 eviDeNce FAvOriNG DNA AS the GeNetic MAteriAl WAS FirSt ObtAiNeD DuriNG the StuDy OF bActeriA AND bActeriOPhAGeS 235
removed. Finally, precipitation with ethanol yielded a fibrous mass that still retained the ability to induce transformation of type IIR avirulent cells. From the original 75-liter sample, the procedure yielded 10 to 25 mg of this “active factor.” Further testing clearly established that the transform- ing principle was DNA. The fibrous mass was first ana- lyzed for its nitrogen: phosphorus ratio, which was shown to coincide with the ratio of “sodium desoxyribonucle- ate,” the chemical name then used to describe DNA. To solidify their findings, Avery, MacLeod, and McCarty sought to eliminate, to the greatest extent possible, all probable contaminants from their final product. Thus, it was treated with the proteolytic enzymes trypsin and chymotrypsin and then with an RNA-digesting enzyme, called ribonuclease ( RNase ). Such treatments destroyed any remaining activity of proteins and RNA. Neverthe- less, transforming activity still remained. Chemical testing of the final product gave strong positive reactions for DNA.
Centrifuge Heat-kill
lll S cells in liquid culture medium
lll S cells spun to bottom of tube
Treat with ribonuclease
Treat with deoxyribonuclease
ll R cells
DNase-treated lll S filtrate
Recover lll S filtrate
ll R cells
RNase-treated lll S filtrate
ll R cells
Protease-treated lll S filtrate
ll R cells
lll S filtrate
Homogenize cells
ll R cells
lll S cells
ll R cells
lll S cells
ll R cells
lll S cells
Only ll R cells
Conclusion: Active factor is DNA
Conclusion: Active factor is not RNA
Conclusion: Active factor is not protein
ll R cells
lll S cells
Control: lll S contains active factor
Treat with protease
Extract carbohydrates, lipids, and proteins
No transformation occurs
Transformation occurs
Transformation occurs
Transformation occurs
Test for Transformation
Figure 10–3 Summary of Avery, Macleod, and Mccarty’s experiment demonstrating that DNA is the transforming principle.
The final confirmation came with experiments using crude samples of the DNA-digesting enzyme deoxyribonuclease (DNase ), which was isolated from dog and rabbit sera. Digestion with this enzyme destroyed the transform- ing activity of the filtrate—thus Avery and his coworkers were certain that the active transforming principle in these experiments was DNA. The great amount of work involved in this research, the confirmation and reconfirmation of the conclusions drawn, and the unambiguous logic of the experimental design are truly impressive. Avery, MacLeod, and McCarty’s conclusion in the 1944 publication was, however, very simply stated: “The evidence presented supports the belief that a nucleic acid of the desoxyribose* type is the fundamental unit of the transforming principle of Pneumococcus Type III.”
*Desoxyribose is now spelled deoxyribose.
FOR REVIEW ONLY
10.3 eviDeNce FAvOriNG DNA AS the GeNetic MAteriAl WAS FirSt ObtAiNeD DuriNG the StuDy OF bActeriA AND bActeriOPhAGeS 237
Following this separation, the bacterial cells, which now contained viral DNA, were eventually lysed as new phages were produced. These progeny phages contained (^32) P, but not 35 S. Hershey and Chase interpreted these results as indicat- ing that the protein of the phage coat remains outside the host cell and is not involved in directing the production of new phages. On the other hand, and most important, phage DNA enters the host cell and directs phage reproduction. Hershey and Chase had demonstrated that the genetic material in phage T2 is DNA, not protein. These experiments, along with those of Avery and his colleagues, provided convincing evidence that DNA was the molecule responsible for heredity. This conclusion has since served as the cornerstone of the field of molecular genetics.
Transfection Experiments During the eight years following publication of the Her- shey–Chase experiment, additional research using bacte- rial viruses provided even more solid proof that DNA is the genetic material. In 1957, several reports demonstrated that if E. coli is treated with the enzyme lysozyme, the outer wall of the cell can be removed without destroying the bacterium. Enzymatically treated cells are naked, so to speak, and contain only the cell membrane as their outer boundary. Such structures are called protoplasts (or sphe- roplasts ). John Spizizen and Dean Fraser independently reported that by using protoplasts, they were able to initi- ate phage reproduction with disrupted T2 particles. That is, provided protoplasts were used, a virus did not have to be intact for infection to occur. Thus, the outer protein coat structure may be essential to the movement of DNA through the intact cell wall, but it is not essential for infec- tion when protoplasts are used. Similar, but more refined, experiments were reported in 1960 by George Guthrie and Robert Sinsheimer. DNA was purified from bacteriophage ϕX174, a small phage
in 1952 for a T-even bacteriophage such as T2. Briefly, the phage adsorbs to the bacterial cell, and some genetic com- ponent of the phage enters the bacterial cell. Following infection, the viral component “commandeers” the cellular machinery of the host and causes viral reproduction. In a reasonably short time, many new phages are constructed and the bacterial cell is lysed, releasing the progeny viruses. This process is referred to as the lytic cycle. In 1952, Alfred Hershey and Martha Chase published the results of experiments designed to clarify the events leading to phage reproduction. Several of the experiments clearly established the independent functions of phage pro- tein and nucleic acid in the reproduction process associated with the bacterial cell. Hershey and Chase knew from exist- ing data that:
1. T2 phages consist of approximately 50 percent protein and 50 percent DNA. 2. Infection is initiated by adsorption of the phage by its tail fibers to the bacterial cell. 3. The production of new viruses occurs within the bacte- rial cell.
It appeared that some molecular component of the phage— DNA or protein (or both)—entered the bacterial cell and directed viral reproduction. Which was it? Hershey and Chase used the radioisotopes 32 P and (^35) S to follow the molecular components of phages during
infection. Because DNA contains phosphorus (P) but not sulfur, 32 P effectively labels DNA; because proteins contain sulfur (S) but not phosphorus, 35 S labels pro- tein. This is a key feature of the experiment. If E. coli cells are first grown in the presence of 32 P or 35 S and then infected with T2 viruses, the progeny phages will have either a radioactively labeled DNA core or a radioactively labeled protein coat, respectively. These labeled phages can be isolated and used to infect unlabeled bacteria ( Figure 10–5 ). When labeled phages and unlabeled bacteria were mixed, an adsorption complex was formed as the phages attached their tail fibers to the bacterial wall. These com- plexes were isolated and subjected to a high shear force in a blender. The force stripped off the attached phages so that the phages and bacteria could be analyzed separately. Centrifugation separated the lighter phage particles from the heavier bacterial cells (Figure 10–5). By tracing the radioisotopes, Hershey and Chase were able to demon- strate that most of the 32 P-labeled DNA had been trans- ferred into the bacterial cell following adsorption; on the other hand, almost all of the 35 S-labeled protein remained outside the bacterial cell and was recovered in the phage “ghosts” (empty phage coats) after the blender treatment.
10–1 Would an experiment similar to that performed by Hershey and Chase work if the basic design were applied to the phenomenon of transformation? Explain why or why not. hint: This problem involves an understanding of the protocol of the Hershey–Chase experiment as applied to the investiga- tion of transformation. The key to its solution is to remember that in transformation, exogenous DNA enters the soon-to-be transformed cell and that no cell-to-cell contact is involved in the process.
FOR REVIEW ONLY
238 10 DNA S tructure AND ANAlySiS
that ϕX174 DNA alone contains all the necessary infor- mation for production of mature viruses. Thus, the evi- dence that DNA serves as the genetic material was further strengthened, even though all direct evidence to that point had been obtained from bacterial and viral studies.
that contains a single-stranded circular DNA molecule of some 5386 nucleotides. When added to E. coli protoplasts, the purified DNA resulted in the production of complete ϕX174 bacteriophages. This process of infection by only the viral nucleic acid, called transfection , proves conclusively
Phage T2 (unlabeled)
Phage added to E. coli in radioactive medium
Progeny phages become labeled
Separation of phage “ghosts” from bacterial cells
Labeled phages infect unlabeled bacteria
Phage “ghosts” are Infected bacteria are unlabeled labeled with 35 S
Phage “ghosts” Infected bacteria are labeled with 32 P are unlabeled
Viable 32 P-labeled phages are produced Viable unlabeled phages produced
(^32) P (^35) S
(^32) P 35 S
or
( )
Figure 10–5 Summary of the hershey–chase experiment demonstrating that DNA, and not protein, is responsible for directing the reproduction of phage t2 during the infection of E. coli.
FOR REVIEW ONLY
240 10 DNA S tructure AND ANAlySiS
In 1965 and 1966, Norman Pace and Sol Spiegelman demonstrated that RNA from the phage Qb can be isolated and replicated in vitro. Replication depends on an enzyme, RNA replicase , which is isolated from host E. coli cells fol- lowing normal infection. When the RNA replicated in vitro is added to E. coli protoplasts, infection and viral multipli- cation (transfection) occur. Thus, RNA synthesized in a test tube serves as the genetic material in these phages by direct- ing the production of all the components necessary for viral reproduction. While many viruses, such the T2 virus used by Hershey and Chase, use DNA as their hereditary material, another group of RNA-containing viruses bears mention. These are the retroviruses , which replicate in an unusual way. Their RNA serves as a template for the syn- thesis of the complementary DNA molecule. The process, reverse transcription , occurs under the direction of an RNA-dependent DNA polymerase enzyme called reverse transcriptase. This DNA intermediate can be incorporated into the genome of the host cell, and when the host DNA is transcribed, copies of the original retroviral RNA chro- mosomes are produced. Retroviruses include the human immunodeficiency virus (HIV), which causes AIDS, as well as several RNA tumor viruses.
10.6 knowledge of Nucleic Acid chemistry is essential to the understanding of DNA Structure
Having established the critical importance of DNA and RNA in genetic processes, we will now take a brief look at the chemical structures of these molecules. As we shall see, the structural components of DNA and RNA are very simi- lar. This chemical similarity is important in the coordinated functions played by these molecules during gene expres- sion. Like the other major groups of organic biomolecules (proteins, carbohydrates, and lipids), nucleic acid chemis- try is based on a variety of similar building blocks that are polymerized into chains of varying lengths.
Nucleotides: Building Blocks of Nucleic Acids DNA is a nucleic acid, and nucleotides are the build- ing blocks of all nucleic acid molecules. Sometimes called mononucleotides, these structural units consist of three essential components: a nitrogenous base , a pentose sugar (a 5-carbon sugar), and a phosphate group. There are two kinds of nitrogenous bases: the nine-member double-ring purines and the six-member single-ring pyrimidines. Two types of purines and three types of pyrimidines are commonly found in nucleic acids. The two purines are adenine and guanine , abbreviated A and G. The three
in eukaryotes, those observations spurred researchers to forge ahead using this supposition as the underlying hypoth- esis. Today, there is no doubt of its validity; DNA is the genetic material in all eukaryotes. The strongest evidence is provided by molecular analysis utilizing recombinant DNA technology. In this procedure, segments of eukaryotic DNA corresponding to specific genes are isolated and spliced into bacterial DNA. The resulting complex can be inserted into a bacterial cell, and then its genetic expression is monitored. If a eukaryotic gene is introduced, the subsequent produc- tion of the corresponding eukaryotic protein product dem- onstrates directly that the eukaryotic DNA is now present and functional in the bacterial cell. This has been shown to be the case in countless instances. For example, the prod- ucts of the human genes specifying insulin and interferon are produced by bacteria after the human genes that encode these proteins are inserted. As the bacterium divides, the eukaryotic DNA replicates along with the bacterial DNA and is distributed to the daughter cells, which also express the human genes by creating the corresponding proteins. The availability of vast amounts of DNA coding for specific genes, derived from recombinant DNA research, has led to other direct evidence that DNA serves as the genetic material. Work in the laboratory of Beatrice Mintz has demonstrated that DNA encoding the human β-globin gene, when microinjected into a fertilized mouse egg, is later found to be present and expressed in adult mouse tis- sue and transmitted to and expressed in that mouse’s prog- eny. These mice are examples of what are called transgenic animals. Other work has introduced rat DNA encoding a growth hormone into fertilized mouse eggs. About one- third of the resultant mice grew to twice their normal size, indicating that foreign DNA was present and functional. Subsequent generations of mice inherited this genetic information and also grew to a large size. This clearly dem- onstrates that DNA meets the requirement of expression of genetic information in eukaryotes. Later, we will see exactly how DNA is stored, replicated, expressed, and mutated.
10.5 rNA Serves as the Genetic
Material in Some viruses
Some viruses contain an RNA core rather than a DNA core. In these viruses, it appears that RNA serves as the genetic material—an exception to the general rule that DNA per- forms this function. In 1956, it was demonstrated that when purified RNA from tobacco mosaic virus ( TMV ) was spread on tobacco leaves, the characteristic lesions caused by viral infection subsequently appeared. Thus, it was con- cluded that RNA is the genetic material of this virus.
FOR REVIEW ONLY
10.6 kNOWleDGe OF Nucleic AciD cheMiS try iS eSSeNtiAl tO the uNDerS tANDiNG OF DNA S tructure 241
the absence of the C-2ʹ hydroxyl group, the sugar is more specifically named 2-deoxyribose. If a molecule is composed of a purine or pyrimidine base and a ribose or deoxyribose sugar, the chemical unit is called a nucleoside. If a phosphate group is added to the nucleoside, the molecule is now called a nucleotide. Nucle- osides and nucleotides are named according to the specific nitrogenous base (A, T, G, C, or U) that is part of the mol- ecule. The structures of a nucleoside and a nucleotide and the nomenclature used in naming nucleosides and nucleo- tides are given in Figure 10–. The bonding between components of a nucleotide is highly specific. The C-1ʹ atom of the sugar is involved in the chemical linkage to the nitrogenous base. If the base is a purine, the N-9 atom is covalently bonded to the sugar; if the base is a pyrimidine, the N-1 atom bonds to the sugar. In deoxyribonucleotides, the phosphate group may be bonded to the C-2ʹ, C-3ʹ, or C-5ʹ atom of the sugar. The
pyrimidines are cytosine , thymine , and uracil , abbreviated C, T , and U , respectively. The chemical structures of A, G, C, T, and U are shown in Figure 10–7(a). Both DNA and RNA contain A, C, and G, but only DNA contains the base T and only RNA contains the base U. Each nitrogen or car- bon atom of the ring structures of purines and pyrimidines is designated by an unprimed number. Note that corre- sponding atoms in the two rings are numbered differently in most cases. The pentose sugars found in nucleic acids give them their names. Ribonucleic acids (RNA) contain ribose , while deoxyribonucleic acids (DNA) contain deoxyribose. Figure 10–7(b) shows the ring structures for these two pen- tose sugars. Each carbon atom is distinguished by a number with a prime sign (e.g., C-1ʹ, C-2ʹ). Compared with ribose, deoxyribose has a hydrogen atom rather than a hydroxyl group at the C-2ʹ position. The absence of a hydroxyl group at the C-2ʹ position thus distinguishes DNA from RNA. In
H
H
H
1
2
3
4 5
N
C
C
C N
(^6) C H Pyrimidine ring
Guanine Adenine
(a) NH (^2)
Cytosine
O
Uracil
O
Thymine NH (^2)
Purine ring
H
H
(b) (^) HOCH 2 OH
C
O C
C C
OH OH
H H
1’
3’ 2’
4’
5’
Ribose
HOCH 2 OH
C
O C
C C
OH H
H H
1’
3’ 2’
4’
5’
2-Deoxyribose
H H H H
8 9
H
H
O
H
N
C
C
C N
C H
H
O
H
N
C
C
C N
C
H
H
H 3 C
O
H
N
C
C
C N
C
H
H
3
2
1
6 5
N
C
C
C N
(^4) C H
C
N
N
7
H
H
O
N (^) N
C
C
C N
C NH 2
C
N
H
H
H
N (^) N
C
C
C N
C H
C
N
Figure 10–7 (a) chemical structures of the pyrimidines and purines that serve as the nitrogenous bases in rNA and DNA. the convention for numbering carbon and nitrogen atoms making up the two categories of bases is shown within the structures that appear on the left. (b) chemical ring structures of ribose and 2-deoxyribose, which serve as the pentose sugars in rNA and DNA, respectively.
FOR REVIEW ONLY
10.7 the S tructure OF DNA hOlDS the key tO uNDerS tANDiNG it S FuNctiON 243
of 10^6 to 10^9 daltons, far in excess of that of a tetranucleotide. The current view of DNA is that it consists of exceedingly long polynucleotide chains. Long polynucleotide chains account for the large molecular weight of DNA and explain its most important property—storage of vast quantities of genetic information. If each nucleotide position in this long chain can be occu- pied by any one of four nucleotides, extraordinary variation is possible. For example, a polynucleotide only 1000 nucle- otides in length can be arranged 4 1000 different ways, each one different from all other possible sequences. This poten- tial variation in molecular structure is essential if DNA is to store the vast amounts of chemical information necessary to direct cellular activities.
10.7 the Structure of DNA holds the key to understanding its Function
The previous sections in this chapter have established that DNA is the genetic material in all organisms (with certain viruses being the exception) and have provided details as to the basic chemical components making up nucleic acids. What remained to be deciphered was the precise structure of DNA. That is, how are polynucleotide chains organized into DNA, which serves as the genetic material? Is DNA composed of a single chain or more than one? If the lat- ter is the case, how do the chains relate chemically to one another? Do the chains branch? And more important, how does the structure of this molecule relate to the various genetic functions served by DNA (i.e., storage, expression, replication, and mutation)?
Figure 10–9 Structures of nucleoside diphosphates and triphosphates. Deoxythymidine diphosphate and adenosine triphosphate are diagrammed here.
Deoxynucleoside diphosphate (dNDP)
(5’)
Deoxythymidine diphosphate (dTDP)
(3’)
CH 2
C
O C
C C
OH H
H H
H H
H
H 3 C H
O
N
C
C
C N
C O
(1)
Nucleoside triphosphate (NTP)
(5’)
Adenosine triphosphate (ATP)
(3’)
CH 2
C
O C
C C
OH OH
H H
H H
H
NH 2
N (^) N
C
C
C N
C H
C
N
(9)
(1’) (1’)
P O O-
O-
O P O O-
O P O O-
O
O P O-
O-
O P O O-
O
Figure 10–10 (a) linkage of two nucleotides by the forma- tion of a c-3´-c-5´ (3´-5´) phosphodiester bond, producing a dinucleotide. (b) Shorthand notation for a polynucleotide chain.
OH
A T G C A 1’ 1’ 3’
5’
3’
5’
CH 2
CH 2
C
O C
C C
OH H
H H
(1’)
(5’)
C
O C
C C
H
H H
(1’)
(3’)
(a)
(b)
T
G
5’ end
3’ to 5’ phosphodiester bond
3’ end
P O
O O O–
P O
O O^ –
O–
P P P P P
Although Levene’s tetranucleotide hypothesis (described earlier in this chapter) was generally accepted before 1940, research in subsequent decades revealed it to be incorrect. It was shown that DNA does not necessarily contain equi- molar quantities of the four bases. In addition, the molecular weight of DNA molecules was determined to be in the range
FOR REVIEW ONLY
244 10 DNA S tructure AND ANAlySiS
Before learning the details of this far-reaching discov- ery, you may find some of the background on James Watson and Francis Crick to be of interest. Watson began his under- graduate studies at the University of Chicago at age 15, and was originally interested in ornithology. He then pursued his Ph.D. at Indiana University, where he studied viruses. He was only 24 years old in 1953, when he and Crick proposed the double-helix theory. Crick, now considered one of the great theoretical biologists of our time, had studied under- graduate physics at University College, London, and went on to perform military research during World War II. At the time of his collaboration with Watson, he was 35 years old and was performing X-ray diffraction studies of polypeptides and proteins as a graduate student. Immediately after they made their major discovery, Crick is reputed to have walked into the Eagle Pub in Cambridge, where the two frequently lunched, and announced for all to hear, “We have discovered the secret of life.” It turns out that more than 50 years later, many scientists would quite agree!
Base-Composition Studies Between 1949 and 1953, Erwin Chargaff and his colleagues used chromatographic methods to separate the four bases in DNA samples from various organisms. Quantitative methods were then used to determine the amounts of the four bases from each source. Table 10.3(a) lists some of Chargaff ’s original data. Parts (b) and (c) of the table show
From 1940 to 1953, many scientists were interested in solving the structure of DNA. Among others, Erwin Char- gaff, Maurice Wilkins, Rosalind Franklin, Linus Pauling, Francis Crick, and James Watson sought information that might answer what many consider to be the most signifi- cant and intriguing question in the history of biology: How does DNA serve as the genetic basis for life? The answer was believed to depend strongly on the chemical structure and organization of the DNA molecule, given the complex but orderly functions ascribed to it. In 1953, James Watson and Francis Crick proposed that the structure of DNA is in the form of a double helix. Their model was described in a short paper published in the journal Nature. (The article is reprinted in its entirety on page 248.) In a sense, this publication was the finish of a highly competitive scientific race. Watson’s book The Double Helix recounts the human side of the scientific drama that eventually led to the elucidation of DNA structure. The data available to Watson and Crick, crucial to the development of their proposal, came primarily from two sources: (1) base composition analysis of hydrolyzed samples of DNA and (2) X-ray diffraction studies of DNA. Watson and Crick’s analytical success can be attributed to their focus on building a model that conformed to the exist- ing data. If the correct solution to the structure of DNA is viewed as a puzzle, Watson and Crick, working at the Cav- endish Laboratory in Cambridge, England, were the first to fit the pieces together successfully.
table 10.3 DNA Base-Composition Data
(a) Chargaff’s Data* (^) Molar Proportions a 1 2 3 4 Organism/Source A T G C Ox thymus 26 25 21 16 Ox spleen 25 24 20 15 Yeast 24 25 14 13 Avian tubercle bacilli 12 11 28 26 Human sperm 29 31 18 18
- Source: Data from Chargaff, 1950. aMoles of nitrogenous constituent per mole of P. (Often, the recovery was less than 100 percent.)
(b) Base Compositions of DNAs from Various Sources Base Composition Base Ratio Combined Base Ratios 1 2 3 4 5 6 7 8 Organism A T G C A/T G/C (A + G)/(C + T) (A + T)/(C + G) Human 30.9 29.4 19.9 19.8 1.05 1.00 1.04 1. Sea urchin 32.8 32.1 17.7 17.3 1.02 1.02 1.02 1. E. coli 24.7 23.6 26.0 25.7 1.04 1.01 1.03 0. Sarcina lutea 13.4 12.4 37.1 37.1 1.08 1.00 1.04 0. T7 bacteriophage 26.0 26.0 24.0 24.0 1.00 1.00 1.00 1.
G + C Content in Several Organisms
Organism %G + C Phage T2 36. Drosophila 45. Maize 49. Euglena 53. Neurospora 53.
(c)
FOR REVIEW ONLY
246 10 DNA S tructure AND ANAlySiS
its genetic functions. Before we discuss it, however, sev- eral other important features warrant emphasis. First, the antiparallel arrangement of the two chains is a key part of the double-helix model. While one chain runs in the 5′-to-3′ orientation (what seems right side up to us), the other chain goes in the 3′-to-5′ orientation (and thus appears upside down). This is indicated in Figure 10–12(b) and (c). Given the bond angles in the structures of the various nucleotide components, the double helix could not be constructed easily if both chains ran parallel to one another. Second, the right-handed nature of the helix modeled by Watson and Crick is best appreciated by comparison with its left-handed counterpart, which is a mirror image,
as shown in Figure 10–13. The conforma- tion in space of the right-handed helix is most consistent with the data that were available to Watson and Crick, although an alternative form of DNA (Z-DNA) does exist as a left-handed helix, as we discuss below. The key to the model proposed by Watson and Crick is the specificity of base pairing. Chargaff’s data suggested that A was equal in amount to T and that G was equal in amount to C. Watson and Crick realized that pairing A with T and C with G would account for these proportions, and that such pairing could occur as a result of hydrogen bonds between base pairs [Figure 10–12(b)], which would also provide the chemical stability necessary to hold the two chains together. Arrangement of the components in this way produces the major and minor grooves along the molecule’s length. Furthermore, a purine (A or G) opposite a pyrimidine (T or C) on each “rung of the spiral staircase” in the proposed helix accounts for the 20-Å (2-nm) diameter suggested by X-ray dif- fraction studies. The specific A “ T and G ‚ C base pairing is described as complementarity and results from the chemical affinity that produces the hydrogen bonds in each pair of bases. As we will see, complementarity is very important in the processes of DNA rep- lication and gene expression.
Diameter 20 Å 5 '
A
A A
G C
G C C G
T
T
T A
P P
P
P
P
P P
P P P P P P
P
P
P
P
P
P
P
S S
S
S
S
S
S
S
S
S S
S S S S S S
S S S
3 '
3 ' 5 '
(b)
(c)
5 '
G C
A T 5 ' 3 '
3 '
P
P
(a)
One complete turn 34 Å
Sugar–phosphate backbone
Minor groove (12 Å)
Nitrogenous base pair
Major groove (22 Å)
3.4 Å
Central axis Figure 10–12 (a) the DNA double helix as proposed by Watson and crick. the ribbon-like strands represent the sugar-phosphate backbones, and the horizontal rungs depict the nitrogenous base pairs, of which there are 10 per complete turn. the major and minor grooves are apparent. A solid vertical line shows the central axis. (b) A detailed view depicting the bases, sugars, phosphates, and hydrogen bonds of the helix. (c) A demonstration of the antiparallel arrange- ment of the chains and the horizontal stacking of the bases.
Figure 10–13 the right- and left-handed helical forms of DNA. Note that they are mirror images of one another.
Right-handed double helix Left-handed double helix
FOR REVIEW ONLY
10.7 the S tructure OF DNA hOlDS the key tO uNDerS tANDiNG it S FuNctiON 247
were also discounted, even though those pairs would each consist of one purine and one pyrimidine. The second question concerns the properties of hydrogen bonds. Just what is the nature of such a bond, and is it strong enough to stabilize the helix? A hydrogen bond is a very weak electrostatic attraction between a covalently bonded hydrogen atom and an atom with an unshared elec- tron pair. The hydrogen atom assumes a partial positive charge, while the unshared electron pair—characteristic of covalently bonded oxygen and nitrogen atoms— assumes a partial negative charge. These opposite charges are responsible for the weak chemical attraction that is the basis of the hydrogen bond. As oriented in the double helix, adenine forms two hydro- gen bonds with thymine, and guanine forms three hydrogen bonds with cytosine ( Figure 10–14 ). Although two or three hydrogen bonds taken alone are ener- getically very weak, thousands of bonds in tandem (as found in long polynucleotide chains) provide great stability to the helix. Another stabilizing factor is the arrangement of sugars and bases along the axis. In the Watson–Crick model, the hydrophobic (“water-fearing”) nitrog- enous bases are stacked almost horizon- tally on the interior of the axis and are thus shielded from the watery environ- ment that surrounds the molecule within the cell. The hydrophilic (“water-loving”) sugar-phosphate backbones are on the out- side of the axis, where both components may interact with water. These molecular arrangements provide significant chemical stabilization to the helix. A more recent and accurate analysis of the form of DNA that served as the basis for the Watson–Crick model has revealed a minor structural difference between the sub- stance and the model. A precise measurement of the num- ber of base pairs per turn has demonstrated a value of 10.4, rather than the 10.0 predicted by Watson and Crick. In the classic model, each base pair is rotated 36° around the helical axis relative to the adjacent base pair, but the new finding requires a rotation of 34.6°. This results in slightly more than 10 base pairs per 360° turn. The Watson–Crick model had an instant effect on the emerging discipline of molecular biology. Even in
Two questions are particularly worthy of discus- sion. First, why aren’t other base pairs possible? Wat- son and Crick discounted the pairing of A with G or of C with T because these would represent purine–purine and pyrimidine–pyrimidine pairings, respectively. Such pairings would lead to aberrant diameters of, in one case, more than and, in the other case, less than 20 Å because of the respective sizes of the purine and pyrimidine rings. In addition, the three-dimensional configurations that would be formed by such pairings would not produce an alignment that allows sufficient hydrogen-bond forma- tion. It is for this reason that A “ C and G ‚ T pairings
d+^ d-
d-^ d+
Adenine-thymine base pair
Adenine (^) Thymine
C-1’ of deoxyribose
d+
d-
d+ d-
Guanine-cytosine base pair
Guanine Cytosine
C-1’ of deoxyribose
C-1’ of deoxyribose
d-
d+
C1’
C1’
C1’
C1’
Hydrogen bond
H N
H
N (^) H
C
C
N
C
C
N
N
C
H
O
C
H H C (^) H
C
C H
N
H N
C
O
H
H N^ H
C
C H
N
O
C
C
N
O
C
N H
C
N H
H
C
N C
H
N C
N
C-1’ of deoxyribose
Figure 10–14 ball-and-stick models of A “ t and G ‚ c base pairs. the dashes (- - -) represent the hydrogen bonds that form between bases.
FOR REVIEW ONLY
10.8 AlterNAtive FOrMS OF DNA eXiS t 249
scrutinized. In comparison to B-DNA, A-DNA is slightly more compact, with 9 base pairs in each complete turn of the helix, which is 23 Å (2.3 nm) in diameter ( Figure 10–15 ). While it is also a right-handed helix, the orientation of the bases is somewhat different—they are tilted and displaced laterally in relation to the axis of the helix. As a result, the appearance of the major and minor grooves is modified. It seems doubtful that A-DNA occurs in vivo (under physiolog- ical conditions). Still other forms of DNA right-handed helices have been discovered when investigated under various labora- tory conditions. These have been designated C-, D-, E-, and most recently P-DNA. C-DNA is found under even greater dehydration conditions than those observed dur- ing the isolation of A- and B-DNA. Two other forms, D-DNA and E-DNA , occur in helices lacking guanine in their base composition. And most recently, it has been observed that if DNA is artificially stretched, still another conformation is assumed, called P-DNA (named for Linus Pauling). Finally, still another form of DNA, called Z-DNA , was discovered in 1979, when a small synthetic DNA oligonucleotide containing only G ‚ C base pairs was studied. Z-DNA takes on the rather remarkable con- figuration of a left-handed double helix. Speculation has occasionally run high over the possibility that regions of Z-DNA exist in the chromosomes of living organisms. The unique helical arrangement has the potential to pro- vide an important recognition site for interaction with DNA-binding molecules. However, the extent to which Z-DNA, or any of the forms mentioned above, occur in vivo is still not clear.
their initial 1953 article in Nature, the authors observed, “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” Two months later, Watson and Crick pursued this idea in a second article in Nature, suggesting a specific mechanism of replication of DNA—the semiconservative mode of replication (described in Chapter 11). The second article also alluded to two new concepts: (1) the storage of genetic information in the sequence of the bases and (2) the mutations or genetic changes that would result from an alteration of bases. These ideas have received vast amounts of experimental support since 1953 and are now universally accepted. Watson and Crick’s synthesis of ideas was highly significant with regard to subsequent studies of genet- ics and biology. The nature of the gene and its role in genetic mechanisms could now be viewed and studied in biochemical terms. Recognition of their work, along with that of Wilkins, led to all three receiving the Nobel Prize in Physiology and Medicine in 1962. Unfortunately, Rosalind Franklin had died in 1958 at the age of 37, making her con- tributions ineligible for consideration, since the award is not given posthumously. The Nobel Prize was to be one of many such awards bestowed for work in the field of molec- ular genetics.
eVolVing ConCept oF the gene Based on the model of DNA put forward by Watson and Crick in 1953, the gene was viewed for the first time in molecular terms as a sequence of nucleotides in a DNA helix that encodes genetic information.
10.8 Alternative Forms of DNA exist
Under different conditions of isolation, different con- formations of DNA are seen. At the time when Watson and Crick performed their analysis, two forms— A-DNA and B-DNA —were known. Watson and Crick’s analysis was based on Rosalind Franklin’s X-ray studies of the B form, which is seen under aqueous, low-salt condi- tions and is believed to be the biologically significant conformation. While DNA studies around 1950 relied on the use of X-ray diffraction, more recent investigations have been performed using single-crystal X-ray analysis. The earlier studies achieved resolution of about 5 Å, but single crystals diffract X rays at about 1-Å intervals, near atomic resolu- tion. As a result, every atom is “visible,” and much greater structural detail is available. With this modern technique, A-DNA, which is preva- lent under high-salt or dehydration conditions, has now been
B-DNA A-DNA Figure 10–15 An artist’s depiction illustrating the orientation of the base pairs of b-DNA and A-DNA. Note that in b-DNA the base pairs are perpendicular to the helix, while they are tilted and pulled away from the helix in A-DNA. in comparison to b-DNA, A-DNA also displays a slightly greater diameter and contains one more base pair per turn.
FOR REVIEW ONLY
250 10 DNA S tructure AND ANAlySiS
in addition to a molecule’s mass, the size and shape of the molecule also affect its rate of sedimentation (S). As you can see in Table 10.4, RNA molecules come in a wide range of sizes. Ribosomal RNA usually constitutes about 80 per- cent of all RNA in an E. coli cell. Ribosomal RNAs are important structural components of ribosomes , which function as nonspecific workbenches where proteins are synthesized during translation. The various forms of rRNA found in prokaryotes and eukaryotes differ dis- tinctly in size. Messenger RNA molecules carry genetic information from the DNA of the gene to the ribosome. The mRNA molecules vary considerably in size, reflecting the range in the sizes of the proteins encoded by the mRNA as well as the different sizes of the genes serving as the templates for transcription of mRNA. While Table 10.4 shows that about 5 percent of RNA is mRNA in E. coli, this percentage varies from cell to cell and even at different times in the life of the same cell. Transfer RNA, accounting for up to 15 percent of the RNA in a typical cell, is the smallest class (in terms of aver- age molecule size) of these RNA molecules and carries amino acids to the ribosome during translation. Because more than one tRNA molecule interacts simultaneously with the ribosome, the molecule’s smaller size facilitates these interactions. We will discuss more detailed functions of these three classes of RNA later in the text (see Chapters 13 and 14). While these RNAs represent the major forms of the mol- ecule involved in genetic expression, other unique RNAs exist that perform various roles, especially in eukaryotes. For example, telomerase RNA and RNA primers are involved in DNA replication at the ends of chromosomes
10–2 In sea urchin DNA, which is double stranded, 17. percent of the bases were shown to be cytosine (C). What percentages of the other three bases are expected to be present in this DNA? Hint: This problem asks you to extrapolate from one measurement involving a unique DNA molecule to three other values characterizing the molecule. The key to its solution is to understand the base-pairing rules in the Watson–Crick model of DNA.
10.9 the Structure of rNA is
chemically Similar to DNA, but Single
Stranded
The structure of RNA molecules resembles DNA, with several important exceptions. Although RNA also has nucleotides linked into polynucleotide chains, the sugar ribose replaces deoxyribose, and the nitrogenous base uracil replaces thymine. Another important difference is that most RNA is single stranded, although there are two important exceptions. First, RNA molecules sometimes fold back on themselves to form double-stranded regions of complementary base pairs. Second, some animal viruses that have RNA as their genetic material contain double- stranded helices. As established earlier (see Figure 10–1), three major classes of cellular RNA molecules function during the expression of genetic information: ribosomal RNA (rRNA), messenger RNA (mRNA) , and transfer RNA (tRNA). These molecules all originate as complementary copies of one of the two strands of DNA segments dur- ing the process of transcription. That is, their nucleotide sequence is complementary to the deoxyribonucleotide sequence of DNA that served as the template for their syn- thesis. Because uracil replaces thymine in RNA, uracil is complementary to adenine during transcription and dur- ing RNA base pairing. Table 10.4 characterizes these major forms of RNA as found in prokaryotic and eukaryotic cells. Different RNAs are distinguished according to their sedimenta- tion behavior in a centrifugal field and by their size (the number of nucleotides each contains). Sedimentation behavior depends on a molecule’s density, mass, and shape, and its measure is called the Svedberg coefficient (S). While higher S values almost always designate mol- ecules of greater molecular weight, the correlation is not direct; that is, a twofold increase in molecular weight does not lead to a twofold increase in S. This is because,
table 10.4 Principal Classes of RNA
Class
% of Total RNA*
Svedberg Coefficient
Eukaryotic (E) or Prokaryotic (P)
Number of Nucleotides Ribosomal 80 5 P and E 120 (rRNA) 5.8 E 160 16 P 1542 18 E 1874 23 P 2904 28 E 4718 Transfer (tRNA)
15 4 P and E 75–
Messenger (mRNA)
5 varies P and E 100–10,
*In E. coli.
FOR REVIEW ONLY
