Biologists in the 1940s had difficulty in accepting DNA as the genetic material because of the apparent simplicity of its chemistry. DNA was known to be a long polymer composed of only four types of subunits, which resemble one another chemically. Early in the 1950s, DNA was first examined by x-ray diffraction analysis, a technique for determining the three-dimensional atomic structure of a molecule (discussed in Chapter 8). The early x-ray diffraction results indicated that DNA was composed of two strands of the polymer wound into a helix. The observation that DNA was double-stranded was of crucial significance and provided one of the major clues that led to the Watson-Crick structure of DNA. Only when this model was proposed did DNA's potential for replication and information encoding become apparent. In this section we examine the structure of the DNA molecule and explain in general terms how it is able to store hereditary information.
A DNA Molecule Consists of Two Complementary Chains of Nucleotides
A DNAmolecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. Hydrogen bonds between the base portions of the nucleotides hold the two chains together (Figure 4-3). As we saw in Chapter 2 (Panel 2-6, pp. 120-121), nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen-containing base. In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “backbone” of alternating sugar-phosphate-sugar-phosphate (see Figure 4-3). Because only the base differs in each of the four types of subunits, each polynucleotide chain in DNA is analogous to a necklace (the backbone) strung with four types of beads (the four bases A, C, G, and T). These same symbols (A, C, G, and T) are also commonly used to denote the four different nucleotides—that is, the bases with their attached sugar and phosphate groups.
DNA and its building blocks. DNA is made of four types of nucleotides, which are linked covalently into a polynucleotide chain (a DNA strand) with a sugar-phosphate backbone from which the bases (A, C, G, and T) extend. A DNA molecule is composed of two (more...)
The way in which the nucleotide subunits are lined together gives a DNA strand a chemical polarity. If we think of each sugar as a block with a protruding knob (the 5′ phosphate) on one side and a hole (the 3′ hydroxyl) on the other (see Figure 4-3), each completed chain, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation. Moreover, the two ends of the chain will be easily distinguishable, as one has a hole (the 3′ hydroxyl) and the other a knob (the 5′ phosphate) at its terminus. This polarity in a DNA chain is indicated by referring to one end as the 3′ end and the other as the 5′ end.
The three-dimensional structure of DNA—the double helix—arises from the chemical and structural features of its two polynucleotide chains. Because these two chains are held together by hydrogen bonding between the bases on the different strands, all the bases are on the inside of the double helix, and the sugar-phosphate backbones are on the outside (see Figure 4-3). In each case, a bulkier two-ring base (a purine; see Panel 2-6, pp. 120–121) is paired with a single-ring base (a pyrimidine); A always pairs with T, and G with C (Figure 4-4). This complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement in the interior of the double helix. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones an equal distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a double helix, with one complete turn every ten base pairs (Figure 4-5).
Complementary base pairs in the DNA double helix. The shapes and chemical structure of the bases allow hydrogen bonds to form efficiently only between A and T and between G and C, where atoms that are able to form hydrogen bonds (see Panel 2-3, pp. 114–115) (more...)
The DNA double helix. (A) A space-filling model of 1.5 turns of the DNA double helix. Each turn of DNA is made up of 10.4 nucleotide pairs and the center-to-center distance between adjacent nucleotide pairs is 3.4 nm. The coiling of the two strands around (more...)
The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel—that is, only if the polarity of one strand is oriented opposite to that of the other strand (see Figures 4-3 and 4-4). A consequence of these base-pairing requirements is that each strand of a DNAmolecule contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand.
The Structure of DNA Provides a Mechanism for Heredity
Genes carry biological information that must be copied accurately for transmission to the next generation each time a cell divides to form two daughter cells. Two central biological questions arise from these requirements: how can the information for specifying an organism be carried in chemical form, and how is it accurately copied? The discovery of the structure of the DNAdouble helix was a landmark in twentieth-century biology because it immediately suggested answers to both questions, thereby resolving at the molecular level the problem of heredity. We discuss briefly the answers to these questions in this section, and we shall examine them in more detail in subsequent chapters.
DNA encodes information through the order, or sequence, of the nucleotides along each strand. Each base—A, C, T, or G—can be considered as a letter in a four-letter alphabet that spells out biological messages in the chemical structure of the DNA. As we saw in Chapter 1, organisms differ from one another because their respective DNA molecules have different nucleotide sequences and, consequently, carry different biological messages. But how is the nucleotide alphabet used to make messages, and what do they spell out?
As discussed above, it was known well before the structure of DNA was determined that genes contain the instructions for producing proteins. The DNA messages must therefore somehow encode proteins (Figure 4-6). This relationship immediately makes the problem easier to understand, because of the chemical character of proteins. As discussed in Chapter 3, the properties of a protein, which are responsible for its biological function, are determined by its three-dimensional structure, and its structure is determined in turn by the linear sequence of the amino acids of which it is composed. The linear sequence of nucleotides in a gene must therefore somehow spell out the linear sequence of amino acids in a protein. The exact correspondence between the four-letter nucleotide alphabet of DNA and the twenty-letter amino acid alphabet of proteins—the genetic code—is not obvious from the DNA structure, and it took over a decade after the discovery of the double helix before it was worked out. In Chapter 6 we describe this code in detail in the course of elaborating the process, known as gene expression, through which a cell translates the nucleotide sequence of a gene into the amino acid sequence of a protein.
The relationship between genetic information carried in DNA and proteins.
The complete set of information in an organism's DNA is called its genome, and it carries the information for all the proteins the organism will ever synthesize. (The term genome is also used to describe the DNA that carries this information.) The amount of information contained in genomes is staggering: for example, a typical human cell contains 2 meters of DNA. Written out in the four-letter nucleotide alphabet, the nucleotide sequence of a very small human gene occupies a quarter of a page of text (Figure 4-7), while the complete sequence of nucleotides in the human genome would fill more than a thousand books the size of this one. In addition to other critical information, it carries the instructions for about 30,000 distinct proteins.
The nucleotide sequence of the human β-globin gene. This gene carries the information for the amino acid sequence of one of the two types of subunits of the hemoglobin molecule, which carries oxygen in the blood. A different gene, the α-globin (more...)
At each cell division, the cell must copy its genome to pass it to both daughter cells. The discovery of the structure of DNA also revealed the principle that makes this copying possible: because each strand of DNA contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand, each strand can act as a template, or mold, for the synthesis of a new complementary strand. In other words, if we designate the two DNA strands as S and S′, strand S can serve as a template for making a new strand S′, while strand S′ can serve as a template for making a new strand S (Figure 4-8). Thus, the genetic information in DNA can be accurately copied by the beautifully simple process in which strand S separates from strand S′, and each separated strand then serves as a template for the production of a new complementary partner strand that is identical to its former partner.
DNA as a template for its own duplication. As the nucleotide A successfully pairs only with T, and G with C, each strand of DNA can specify the sequence of nucleotides in its complementary strand. In this way, double-helical DNA can be copied precisely. (more...)
The ability of each strand of a DNAmolecule to act as a template for producing a complementary strand enables a cell to copy, or replicate, its genes before passing them on to its descendants. In the next chapter we describe the elegant machinery the cell uses to perform this enormous task.
In Eucaryotes, DNA Is Enclosed in a Cell Nucleus
Nearly all the DNA in a eucaryotic cell is sequestered in a nucleus, which occupies about 10% of the total cell volume. This compartment is delimited by a nuclear envelope formed by two concentric lipid bilayer membranes that are punctured at intervals by large nuclear pores, which transport molecules between the nucleus and the cytosol. The nuclear envelope is directly connected to the extensive membranes of the endoplasmic reticulum. It is mechanically supported by two networks of intermediate filaments: one, called the nuclear lamina, forms a thin sheetlike meshwork inside the nucleus, just beneath the inner nuclear membrane; the other surrounds the outer nuclear membrane and is less regularly organized (Figure 4-9).
A cross-sectional view of a typical cell nucleus. The nuclear envelope consists of two membranes, the outer one being continuous with the endoplasmic reticulum membrane (see also Figure 12-9). The space inside the endoplasmic reticulum (the ER lumen) (more...)
The nuclear envelope allows the many proteins that act on DNA to be concentrated where they are needed in the cell, and, as we see in subsequent chapters, it also keeps nuclear and cytosolic enzymes separate, a feature that is crucial for the proper functioning of eucaryotic cells. Compartmentalization, of which the nucleus is an example, is an important principle of biology; it serves to establish an environment in which biochemical reactions are facilitated by the high concentration of both substrates and the enzymes that act on them.
Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA is a double helix formed from two complementary strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs. Duplication of the genetic information occurs by the use of one DNA strand as a template for formation of a complementary strand. The genetic information stored in an organism's DNA contains the instructions for all the proteins the organism will ever synthesize. In eucaryotes, DNA is contained in the cell nucleus.
Human Genome Project Essay
Trevor DaleCopyright 1999
The human genome consists of 50,000 to 100,000 genes located on 23 pairs of chromosomes. One chromosome in each pair is inherited from the mother, and the other from the father. Each chromosome contains a long molecule of DNA, the molecule of which genes are made. The order of the four bases on the DNA strand determines the information content of a particular gene or piece of DNA. Mapping is the process of determining the position and spacing of genes, or other genetic landmarks, on the chromosomes relative to one another.
The possibility of initiating such a major and significant research program was extensively discussed in the scientific community during 1986 and 1987. In the spring of 1987, a report on the human genome initiative was prepared by the Health and Environmental Research Advisory Committee (HERAC) of the Department of Energy (DOE). In early 1988, further discussion culminated in the publication of two additional, widely circulated, influential reports. The U.S. Congress Office of Technology Assessment (OTA) report presented a comprehensive and detailed analysis of the scientific developments that had led to the promise of "mapping and sequencing" the human genome and presented an outline for a multi-phase research plan for accomplishing the goal of sequencing human DNA over the course of the following two decades. In fiscal year 1988, the Congress of the United States launched the human genome project by appropriating funds to both the DOE and the National Institutes of Health (NIH) specifically for support of research efforts to determine the structure of complex genomes. The NIH was delegated $17.2 million and the DOE received $10.7 million in 1988 by the human genome research institute.
It is generally agreed that the overall goal of the Human Genome Initiative is to acquire fundamental information needed to further our basic scientific understanding of human genetics and of the role of various genes in health and disease. As refined through the discussions over the last half of the 1980's and defined in the NRC report, the Human Genome Initiative has several interrelated goals:
- Construction of a high-resolution genetic map of the human genome;
- Production of a variety of physical maps of all human chromosomes and DNA of selected model organisms, with emphasis on maps that make the DNA accessible to investigators for further analysis;
- Determination of the complete sequence of human DNA and of the DNA of selected model organisms;
- Development of capabilities for collecting, storing, distributing, and analyzing the data produced;
- Creation of appropriate technologies necessary to achieve these objectives.
Because of the size of the human genome, the NRC committee and others recommended a multi-phase program. A general plan to eventually produce a human genome map over a five year period was approved by the NRC. The initial pilot phase would consist of the following:
- Expansion of the human genetic map to a resolution of one centimorgan;
- Construction of complete physical maps of the DNA of certain model organisms and beginning the construction of physical maps of human chromosomes;
- Development of new technology to increase the efficiency and accuracy, and lower the cost, of physical mapping and of DNA sequencing.
It was decided upon that the task of sequencing the complete human DNA would be taken up at a later date or phase. And this would only be completed if it could be done at a reasonable cost. The overall program was expected to take at least fifteen years to complete. This general plan is still appropriate, but some of the details changed as improvements in the technology occurred.
The international consortium currently includes three U.S. laboratories funded by the NHGRI of the NIH, the joint Genome Institute of the U.S. DOE, and the Sanger Centre supported in the United Kingdom by the Wellcome Trust. In the initial or pilot phase, eight scientific teams supported by NHGRI, DOE and international collaborators completed the sequence of over 480 million bases, of which 260 million (or close to 10 percent of the human genome) are in high-quality finished form. The pilot project also drove down the cost of sequencing to an average of 20 - 30 cents per base today. In 1986, it was estimated that one skilled person could sequence 100,000 base pairs per year at an average cost of $1/base pair. The consortium's goal is to produce a working draft covering at least 90 percent of the human genome sequence within one year or by the spring of 2000, and to have it completely finished by the year 2003. Besides sequencing human DNA, Genome Project researchers are developing new sequencing technologies and conducting studies of human genetic variation, genomic function, and genomic analysis of model organisms. Scientists can use these tools to help them "read" the information coded in the DNA sequence, which will help them understand human illnesses and, ultimately, to find dramatically new treatments and cures. In addition to these goals, the HGP will continue to vigorously support research on ethical, legal, and social implications of genome analysis.
While the mouse genome is not simpler than that of man, it is particularly useful for comparisons because of the many biological similarities between the mouse and man. The genetic map of the mouse, based on morphological markers, has already led to many insights into human genetics. There is every reason to believe that a physical map of the mouse genome will be equally useful so this was one of the early goals of the consortium. The HGP is also carrying out studies on E. coli to help develop the technology and interpret human gene function.
So the major goal of these groups and organizations is to complete a genetic map of the human genome as soon as possible. There are other goals such as the mouse but the most exciting and anticipated one is that of the human genome. There is some competition out in the industry that is why the federal government added substantial amounts of money to this fund. The consortium now projects to have the complete genome mapped by 2003. This information when complete should be available to the general public. With this information scientists and doctors can better treat diseases before they even occur or even after they have appeared in some instances. This information will allow those that are genetically predisposed to certain diseases to eliminate at least the genetic contribution to the diseases. In some cases the genetic contribution is significant to that person having a disease and in others it is not significant.
Here is a list of conditions and diseases associated with genes: Alzheimer's disease, Lou Gehrig's disease, Arthritis, Asthma, Cancers, Cystic fibrosis, Diabetes, Down syndrome, Hemophilia, High blood pressure, Hypercholesterolemia, Multiple sclerosis, Muscular dystrophy, Neurofibromatosis, Schizophrenia, Sickle-cell anemia, Spina bifida, Tay-Sachs disease, and many more. The length of this list gives people an idea of the potential impact of a map of the human genome. Each one of these diseases affects thousands of people and together probably many millions of people. With some of these diseases or conditions such as cancer and high blood pressure, are not solely controlled by genes. For example, a person that receives gene therapy could still get cancer from smoking. So people will still have to exercise and eat right to control blood pressure and reduce other problems.
The fist actual use of gene therapy began in September 1990, with the treatment of a child suffering from a rare genetic immunodeficiency disease caused by the lack of the enzyme adenosine deaminase (ADA). ADA-deficient people have persistent infections and high risk of early cancer, and many die in their first months of life. This young boy was treated with gene therapy and the disease was treated, but the ADA gene-corrected cells have to be re-infused every one or two months. This allowed the young man to lead a somewhat normal life. The minor difficulty of repeat infusions is a small price to pay for a normal life. People with diabetes often have to adjust insulin daily. This is an example of gene therapy, but this could not be done until the scientists knew exactly which gene was causing the problem. When the genomic map is complete, scientists will be able to better cure or aid in the cure of many diseases. As I am writing this I hear on the radio that at John's Hopkins Hospital they have successfully used gene therapy to cure colon cancer. Sometimes difficult to diagnose, hereditary nonpolyposis colorectal cancer (HNPCC) is believed to account for one in six of all colon cancer cases. Individuals who have a hereditary risk for cancer are born with one altered gene. This means that this individual already is one step into the cancer process.
Though scientists had known for years that an altered gene was to blame for this hereditary colon cancer, finding it was tricky for they had few clues as to where, on any of the 23 pairs of chromosomes, the gene might reside. Finally, using tools emerging from the Human Genome project, an international team tracked the gene to a region of chromosomes 2. Ten months later scientists found a second gene on chromosome 3 also involved in HNPCC. Together, these genes account for most cases of this inherited cancer.
A big advantage of using genetic engineering to produce drugs is that it's possible to mass-produce chemicals that might otherwise be difficult and costly to extract, or simply unavailable by conventional means. Another important advantage is that drugs produced in this way are pure and, if made using human genes, fully compatible with use in people. For example, before engineered bacteria were cloned to manufacture human insulin, the main source of this hormone (used to treat diabetes) was the pancreas of cattle of pigs. Although similar to human insulin, animal insulin is not identical and some allergic reactions occured. The human protein produced by bacteria with recombinant DNA, however, has no such effect. As another example, vaccines against disease are traditionally prepared from killed pathogens (disease-causing microbes). They are effective in the vast majority of people, but a small percentage of the population have allergic reactions to vaccines. Genetically engineered vaccines are safer because they contain no living organisms - only the proteins that stimulate the body to develop immunity.
Now that I have wrote about the many benefits of genome mapping and gene therapy, I will mention some of the disadvantages. Should information about an individual's genetic makeup become available to others without that person's knowledge and permission? How can we assure that genetic information does not lead to stigmatization or to discrimination in areas such as insurance or employment? These are just some questions that people raise when talking about the human genome. The significance of questions like these is expressed in the amount of money the consortium is spending on this topic. They are spending 3 to 5 percent of the total annual budget, which is approximately 200 million. This could amount to as much as 10 million dollars annually. I think the long term questions regarding the release of a human genome map are unanswerable. I feel there are so many possible questions or problems that will appear that we can't even imagine until the map is released. How might this affect insurance rates for different people. Will insurance premiums be based on your genetic map? I don't believe that this will ever happen, but I wouldn't say that it would never happen. These are some of the questions being talked about right now.
A complete map of the human genome is kind of scary to me, especially when the government is involved with its production. There are a lot of things that the government does that they don't tell the general public. I don't mean to sound like an anti-government person, but yet I am. I believe that they give me reason to be skeptical of their actions. I also worry in general about what this will do with the general public. For example, some people that can't be cured may feel left out because not all diseases or conditions can be cured. People have also raised questions in the areas of courts, schools, military, and many others. For example, could people be accepted in any situation based on their genetic map? And who controls or owns a persons genetic map, and where will it be stored or kept? Will anyone in the general public be able to access the information on your genetic map? I have read a specific paper where scientists ask whether the sequence of the entire human genome is needed. In other words do we need to know some of the junk DNA of the human genome. Instead I think that only the required or needed information from the human genome should be studied. However, this is my somewhat uneducated opinion. I would not want the responsibility of deciding some of these controversial questions regarding this project. The initial human genome map is not being done on one specific person, but rather on pieces from many people. I hope we stay at this point and don't come up with individual maps for each person. We will have the ability to treat most of our diseases or conditions through genetic therapy. I wonder what will happen when it comes to parents that want to have that perfect child. Some parents may be more interested in the genes of the child rather than the child itself. I am sure that there will be parents that are interested in knowing their unborn childs genes and to have the ability to repair any defects and there will be those parents that don't want to know. These are some concerns I have with the project, but there are numerous possible benefits to this project as well. I have talked to many other people about this project in recent weeks and this is a very interesting and scary subject for many.
In conclusion, the human genome has been a long process worked on by many research scientists at many different locations. The annual cost of the project is about 200 million dollars. This is primarily tax dollars, and there are a couple of private firms working on this project and other similar projects as well. As I have mentioned earlier, I have some doubts about this process. However I did learn more about the human genome and where it is going by preparing this paper. I do have to admit that there can and will be many major benefits from the human genome project. With this data, gene therapy is a possibility, and just to have the information of human DNA will probably be the basis of many future experiments. We will also have a genome map of the house mouse, fruit fly, and other organisms similar to that of the human. This will help scientists make decisions on future research involving the human genome.
This research has to be very exciting to work on. What these scientists are about to unveil will probably be the biggest discovery or project in the first half of the 21st century. I say that reluctantly because the way technology is progressing I think there will be much greater discoveries than that of the human genome in the next century. Even this project has had to updated to the advances made in technology. I would bet that if you had asked the founders of this project if they thought this project might be completed earlier and by two years they probably would have said no. This is a very big discovery and a big boost hopefully for mankind and now I wonder what will be next. I hope this doesn't cause to much trouble with the general public, because right now I know a large percent of the population has no idea how far along this is, and if they did know they probably can't understand it. Maybe the government or some university should be writing more about this. As I mentioned earlier in this paper I heard something about gene therapy at Johns Hopkins University, but I think that is a rare news event. I know it is rare because they are working on it right now, but they maybe should be letting more information out through the news to give people time to adjust or at least think about it. Maybe some organization could offer courses to help the general public understand just what is going on, because when you say that the human genome is nearly fully mapped that means absolutely nothing to a majority of the people. A class such as this class would be great, but it may go a little too far for certain segments of the population. Overall, I say again I just hope that this information is used for disease or conditions curing or aiding in cures only, and that it doesn't cause to many problems amongst the American people.
ReferencesGrace, E. S. 1998. Better health through gene therapy. Futurist. Jan-Feb, p. 39-42.
Kenen, R. H., 1999. Plain talk about the Human Genome Project. Social Science & Medicine 49:989-992.
Pennisi, E. 1999. Academic Sequencers Challenge Celera in a Sprint to the Finish. Science. 19 March, p. 1822-1823.
U.S. Dept. of Energy, From Maps to Medicine: Hereditary Colon Cancer. "Hereditary Colon Cancer", Obtained from WWW 10/20/99: http://www.nhgri.nih.gov/Policy_and_public_affairs/Communications/Publications/Maps_to_medicine/colon.html.
U.S. Dept. of Energy. Human Genome Project Information. "HGP Announce Accelerated Completion Date of Working Draft", Obtained from WWW 10/19/99:5/28/99: http://www.ornl.gov/hgmis/project/update.html.
U.S. Dept. of Energy. Human Genome Project Information. "Ethical, Legal, and Social Issues (ELSI) of the Human Genome Project", Obtained from WWW 10/19/99:9/7/99: http://www.ornl.gov/TechResources/Human_Genome/resource/elsi.html.
U.S. Dept. of Energy. Understanding our Genetic Inheritance the U.S. Human Genome Project. "The first Five Years: Fiscal Years 1991-1995", Obtained from WWW 10/19/99:1/13/99: http://www.ornl.gov/hgmis/project/5yrplan/intro.html.
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