Genetics - biology.

Genetics - biology. I INTRODUCTION Genetics, study of the function and behavior of genes. Genes are bits of biochemical instructions found inside the cells of every organism from bacteria to humans. Offspring receive a mixture of genetic information from both parents. This process contributes to the great variation of traits that we see in nature, such as the color of a flower's petals, the markings on a butterfly's wings, or such human behavioral traits as personality or musical talent. Geneticists seek to understand how the information encoded in genes is used and controlled by cells and how it is transmitted from one generation to the next. Geneticists also study how tiny variations in genes can disrupt an organism's development or cause disease. Increasingly, modern genetics involves genetic engineering, a technique used by scientists to manipulate genes. Genetic engineering has produced many advances in medicine and industry, but the potential for abuse of this technique has also presented society with many ethical and legal controversies. Genetic information is encoded and transmitted from generation to generation in deoxyribonucleic acid (DNA). DNA is a coiled molecule organized into structures called chromosomes within cells. Segments along the length of a DNA molecule form genes. Genes direct the synthesis of proteins, the molecular laborers that carry out all life-supporting activities in the cell. Although all humans share the same set of genes, individuals can inherit different forms of a given gene, making each person genetically unique. Since the earliest days of plant and animal domestication, around 10,000 years ago, humans have understood that characteristic traits of parents could be transmitted to their offspring. The first to speculate about how this process worked were Greek scholars around the 4th century BC, who promoted theories based on conjecture or superstition. Some of these theories remained in favor for several centuries. The scientific study of genetics did not begin until the late 19th century. In experiments with garden peas, Austrian monk Gregor Mendel described the patterns of inheritance, observing that traits were inherited as separate units. These units are now known as genes. Mendel's work formed the foundation for later scientific achievements that heralded the era of modern genetics. II THE IMPORTANCE OF GENETICS The modern science of genetics influences many aspects of daily life, from the food we eat to how we identify criminals or treat diseases. In agriculture, genetic advances enable scientists to alter a plant or animal to make it more useful. For instance, some food crops, such as oranges, potatoes, wheat, and rice, have been genetically altered to withstand insect pests, resulting in a higher crop yield. Tomatoes and apples have been modified so that they resist discoloration or bruising on their way to market, enhancing their appeal on supermarket shelves. The genetic makeup of cows has been modified to increase their milk production, and cattle raised for beef have been altered so that they grow faster. Genetic technologies have also helped convict criminals. DNA recovered from semen, blood, skin cells, or hair found at a crime scene can be analyzed in a laboratory and compared with the DNA of a suspect. An individual's DNA is as unique as a set of fingerprints, and a DNA match can be used in a courtroom as evidence connecting a person to a crime. Genetics has revolutionized the way industries produce certain substances, many of which formerly required costly and arduous manufacturing methods. In medicine, scientists can genetically alter bacteria so that they mass-produce specific proteins, such as insulin used by people with diabetes mellitus or human growth hormone used by children who suffer from growth disorders. In other medical applications, genetic technologies have been instrumental in the development of gene therapy. In this still-experimental form of treatment, scientists try to cure disease by replacing malfunctioning genes with healthy ones. Gene therapy has shown promise in treating some devastating conditions, including some forms of cancer and cystic fibrosis. Genetically engineered vaccines are being tested for possible use against the human immunodeficiency virus (HIV), the virus that causes acquired immunodeficiency syndrome (AIDS). The field of human genetics has been energized in recent years by the Human Genome Project, an international collaboration of scientists, governments, and drug companies from around the world. Scientists working on this project have developed detailed maps that identify the chromosomal locations of the estimated 20,000 to 25,000 human genes. The vast databases emerging from the project help scientists study previously unknown genes as well as many genes all at once to examine how gene activity can cause disease. Scientists expect that the project will lead to the development of new drugs targeted to specific genetic disorders. Despite the benefits derived from genetic advancements, some observers have voiced concerns that genetically engineered organisms could harm people or the environment. Others fear that new genetic technologies may enable scientists to modify genes that affect characteristics other than those responsible for disease. They warn that determining who has undesirable genetic characteristics may lead to discriminatory practices. Others are concerned about the common misperception that a person's genes determine all aspects of a person's life, including health and behavior. This misperception leads people to blame their genetic makeup for problems, leaving no room for the influence of free will, personal responsibility, or hope for change. These and other challenging issues place geneticists at the crossroads of science and social responsibility, where they work to promote understanding of genetic advances and prevent the abuse of them. III PRINCIPLES OF GENETICS The site where genes work is the cell. Some organisms, such as paramecia or amoebas, are made up of a single cell. Other organisms are made of many kinds of cells, each having a different function. For instance, a tree contains some cells that form the root system and other cells that form leaves. Each cell's function within an organism is determined by the genetic information encoded in DNA. In animals, plants, and other eukaryotes (organisms whose cells contain a nucleus), DNA resides within membrane-bound structures in the cell. These structures include the nucleus, the energy-producing mitochondria, and, in plants, the chloroplasts (structures where photosynthesis takes place). In prokaryotes, one-celled organisms and bacteria that lack internal membrane-bound structures, DNA floats freely within the cell body. A Cell Division and Reproduction Organisms could not grow or function properly if the genetic information encoded in DNA was not passed from cell to cell. DNA is packaged into structures called chromosomes within a cell. Every chromosome in a cell contains many genes, and each gene is located at a particular site, or locus, on the chromosome. Chromosomes vary in size and shape and usually occur in matched pairs called homologues. The number of homologous chromosomes in a cell depends upon the organism--for example, most cells in the human body contain 23 pairs of chromosomes, while most cells of the fruit fly Drosophila contain 4 pairs. Within all organisms, cells divide to produce new cells, each of which requires the genetic information found in DNA. Yet simply splitting the DNA of a dividing cell between two new cells would lead to disaster--the two new cells would have different instructions and each subsequent generation of cells would have less and less genetic information to work with. Imagine how chaotic it would be to rip an architectural blueprint in two, give each half to different contractors, and tell them to construct identical buildings. Just as each contractor would require a full copy of the blueprint to construct a complete building, each new cell needs a complete copy of an organism's genetic information to function properly. Organisms use two types of cell division to ensure that DNA is passed down from cell to cell during reproduction. Simple one-celled organisms and other organisms that reproduce asexually--that is, without the joining of cells from two different organisms--reproduce by a process called mitosis. During mitosis a cell doubles its DNA before dividing into two cells and distributing the DNA evenly to each resulting cell. Organisms that reproduce sexually use a different type of cell division. These organisms produce special cells called gametes, or egg and sperm. In the cell division known as meiosis, the chromosomes in a gamete cell are reduced by half. During sexual reproduction, an egg and sperm unite to form a zygote, in which the full number of chromosomes is restored. A1 Mitosis Mitosis occurs in five stages: prophase, prometaphase, metaphase, anaphase, and telophase. During prophase, the start of mitosis, the DNA of each chromosome replicates. Each chromosome then reorganizes into paired structures called sister chromatids, with each member of the pair containing a full copy of the DNA sequence. The sister chromatids condense, thickening until they appear joined at a single site, known as the centromere. Prometaphase is marked by the disintegration of the nuclear membrane. The sister chromatids line up in the middle of the cell halfway between the poles. In metaphase, exactly half of the chromatids face one pole, and half face the other pole. This equilibrium position is called the metaphase plate. In anaphase, the chromatid pairs split apart at the centromere, and each half of the pair then moves toward opposite poles of the cells. In telophase, the final stage of mitosis, a nuclear membrane forms around the chromosomes at each pole of the cell. Mitosis ends with the formation of two new cells, each with a matching full set of chromosomes as well as an identical complement of cellular structures. A2 Meiosis During meiosis, two cell divisions occur to produce four daughter cells from the original parent cell. Each resulting cell has half the chromosomal DNA of the parent cell. A half set of chromosomes in an organism is known as the haploid number. In the first cell division of meiosis the chromosomes of a gamete cell duplicate and join in pairs. The paired chromosomes align at the equator of the cell, and then separate and move to opposite poles in the cell. The cell then splits to form two daughter cells. As meiosis proceeds, the two daughter cells undergo another cell division to form four cells, each of which bears half of the number of chromosomes found in the other cells of the organism. Meiosis ensures that reproduction will produce a zygote that has received one set of chromosomes from the male parent and one set of chromosomes from the female parent to form a full set of chromosomes. The entire set of chromosomes in an organism is known as the diploid number. Once formed, the zygote continues to divide and grow through the process of mitosis. B Patterns of Inheritance In life forms that reproduce asexually, such as bacteria and amoebas, all offspring share the exact same genes and are identical to their parents. The genetic transmission that occurs in organisms that reproduce sexually is far more complex. An individual that forms by the union of two gametes inherits its chromosomes from two distinct parents. Consequently, sexual reproduction guarantees that offspring with new combinations of genes will continually arise. Certain patterns of inheritance were evident long before scientists discovered the molecular structure of DNA and chromosomes. Throughout history, people have recognized that certain traits, whether in humans, animals, or agricultural crops, could be passed from generation to generation. Yet for centuries, people were unable to reconcile many confusing observations about the mechanisms of inheritance. The first person to make sense of this complex subject was Austrian monk Gregor Mendel, who conducted a series of experiments on pea plants beginning in the 1850s. Mendel observed the results of crossbreeding plants with different characteristics, such as height, flower color, and seed shape. His conclusions from these experiments led him to develop explanations for how traits are transmitted from generation to generation. Mendel's theories form the foundation of modern genetics (see Mendel's Laws). B1 Mendel's Rules In his research, Mendel observed that characteristics were inherited as separate units, each of which was inherited independently of the others. Mendel suggested that each parent has pairs of these units but contributes only one of each pair to offspring. The units that Mendel described were later given the name genes. Mendel recognized that a gene can exist in different forms. Today these alternate forms are known as alleles. For example, pea seeds, the edible part of the plant we call peas, have a texture trait controlled by a single gene. This gene occurs in two alleles: one corresponding to round (smooth) peas, the other to wrinkled peas. Although an individual can carry only two alleles for a particular gene, each gene may have dozens of different alleles. Mendel's experiments focused on interbreeding different strains of pea plants and then observing the traits that appeared in subsequent generations. When he crossbred plants with round peas and those with wrinkled peas, he discovered that all of the resulting offspring had round peas. Today we know that peas are round and smooth when they contain the right amount of sugar. If peas are missing the gene that produces a protein called starch branching enzyme 1 (SBE1), the peas make too much sugar, causing the peas to swell and then wrinkle and shrivel as they dry. Mendel concluded that when an organism has two different alleles corresponding to the same genetic trait, one of the two may be dominant. The other allele is said to be recessive, meaning that its presence will be detectable only if an organism has inherited the recessive gene from both parents. For convenience, geneticists designate alleles by a single letter--the dominant allele is represented by a capital letter and the recessive allele by a small letter. In the pea texture example, a plant inherits one allele for pea texture from each parent. The dominant allele that produces SBE1, resulting in round, smooth peas, is designated as R, while the recessive allele that does not produce SBE1 and produces wrinkled peas is designated as r. To determine the set of alleles an organism has for a given trait just by visual observation can often be difficult. In the pea plant example, for instance, plants with smooth peas might be carrying two dominant alleles for that characteristic (RR) or one dominant and one recessive allele (Rr). Geneticists use the term genotype to refer to the combination of genes that code for a trait, while the term phenotype describes the physical manifestation of that trait. Therefore, the presence of two dominant alleles for pea texture (RR) would reflect the genotype while a smooth pea indicates the phenotype. Mendel did not limit his experiments to testing the rules of inheritance of single traits. He also studied plant traits involving multiple pairs of genes, breeding plants that have round, yellow seeds with plants that produce wrinkled, green seeds. Such experiments demonstrated that the patterns of inheritance he observed in his experiments with single traits also apply to cases involving more complex gene combinations. B2 Exceptions to Mendel's Rules Mendel published his studies in a science journal in 1865, at which time no other scientist commented on his work. Since that time, geneticists have learned that sometimes genes do not easily conform to so-called Mendelian patterns of inheritance. B2a Incomplete Dominance In cases of incomplete dominance, the inheritance of a dominant and a recessive allele results in a blending of traits to produce intermediate characteristics. For example, four-o'clock paint plants may have red, white, or pink flowers. Plants with red flowers have two copies of the dominant allele R for red flower color (RR). Plants with white flowers have two copies of the recessive allele r for white flower color (rr ). Pink flowers result in plants with one copy of each allele (Rr), with each allele contributing to a blending of colors. B2b Quantitative Inheritance Mendel focused his studies on traits determined by a single pair of genes, and the resulting phenotype was easy to distinguish. A tall plant can be markedly different from a short one, and a green pea can easily be distinguished from a yellow one. There are some traits, however, that are not easy to distinguish. Human skin color, for example, may be any of a wide variety of shades. Traits such as skin color differ from the ones Mendel studied because they are determined by more than one pair of genes. In this form of inheritance, known as quantitative inheritance, each pair of genes has only a slight effect on the trait, while the cumulative effect of all the genes determines the physical characteristics of the trait. At least four pairs of genes control human skin color. Multiple genes also control many traits important in agriculture, such as milk production in cows and ear length in corn. B2c Multiple Alleles Another exception to Mendelian genetics involves genes with multiple alleles. Certain traits are controlled by multiple alleles that have complex rules of dominance. In humans, for example, the gene for blood type has three alleles: IA, IB, and i. With three alternatives for each member of a gene pair, there are six possible combinations of these genes (IAIA, IBIB, ii, IAi, IBi, IAIB). Although there are six possible combinations, humans have only four major blood types: A, B, AB, and O. This results because both IA and IB dominate over i, but not over each other, so a person with a gene combination of IAIA or IAi has blood type A. The gene combinations IBIB and IBi both produce blood type B. IAIB results in a blood type AB, and ii results in blood type O. B3 Gene Linkage In his experiments, Mendel was careful to study traits in pea plants where one trait did not appear to influence another, such as the plant's height or the pea's texture. These two phenotypes (height and texture) occur randomly with respect to one another in a manner known as independent assortment. Today scientists understand that independent assortment occurs when the genes affecting the phenotypes are found on different chromosomes. An exception to independent assortment develops when genes appear near one another on the same chromosome. When genes occur on the same chromosome, they are inherited as a single unit. Genes inherited in this way are said to be linked. For example, in fruit flies the genes affecting eye color and wing length are inherited together because they appear on the same chromosome. But in many cases, genes on the same chromosome that are inherited together produce offspring with unexpected allele combinations. This results from a process called crossing over. Sometimes at the beginning of meiosis, a chromosome pair (made up of a chromosome from the mother and a chromosome from the father) may intertwine and exchange sections of chromosome. The pair then breaks apart to form two chromosomes with a new combination of genes that differs from the combination supplied by the parents. Through this process of recombining genes, organisms can produce offspring with new combinations of maternal and paternal traits that may contribute to or enhance survival. B4 Sex-Linked Traits Most chromosome pairs consist of identical, or homologous, partners. In many species, including humans, there is one pair of chromosomes in which the partners noticeably differ from each other. These are called the sex chromosomes because they determine the differences between males and females. Genes located on the sex chromosomes display different patterns of inheritance than genes located on other chromosomes. In human females, the sex chromosomes consist of two X chromosomes, while males have an X chromosome and a shorter Y chromosome with many fewer genes. In males the X chromosome contains many genes that have no corresponding gene on the Y chromosome. A male's X chromosome may contain a recessive allele associated with a genetic disorder, such as hemophilia or Duchenne muscular dystrophy. In this case, males do not have a normal second copy of the gene on the Y chromosome to mask the effects of the recessive gene, and disease typically results. Additional examples of sex-linked traits include red-green color blindness in humans and eye color in fruit flies. C The Genetic Code The structure of DNA encodes all the information every cell needs to function and thrive. In addition, DNA carries hereditary information in a form that can be copied and passed intact from generation to generation. A gene is a segment of DNA. The biochemical instructions found within most genes, known as the genetic code, specify the chemical structure of a particular protein. Proteins are composed of long chains of amino acids, and the specific sequence of these amino acids dictates the function of each protein. The DNA structure of a gene determines the arrangement of amino acids in a protein, ultimately determining the type and function of the protein manufactured. C1 DNA Structure DNA molecules form from chains of building blocks called nucleotides. Each nucleotide consists of a sugar molecule called deoxyribose that bonds to a phosphate molecule and to a nitrogen-containing compound, known as a base. DNA uses four bases in its structure: adenine (A), cytosine (C), guanine (G), and thymine (T). The order of the bases in a DNA molecule--the genetic code--determines the amino acid sequence of a protein. In the cells of most organisms, two long strands of DNA join in a single molecule that resembles a spiraling ladder, commonly called a double helix. Alternating phosphate and sugar molecules form each side of this ladder. Bases from one DNA strand join with bases from another strand to form the rungs of the ladder, holding the double helix together. The pairing of bases in the DNA double helix is highly specific--adenine always joins with thymine, and guanine always links to cytosine. These base combinations, known as complementary base pairing, play a fundamental role in DNA's function by aiding in the replication and storage of genetic information. Complementary base pairing also enables scientists to predict the sequence of bases on one strand of a DNA molecule if they know the order on the corresponding, or complementary, DNA strand. Scientists use complementary base pairing to help identify the genes on a particular chromosome and to develop methods used in genetic engineering. Genes line up in a row along the length of a DNA molecule. In humans a single gene can vary in length from 100 to over 1,000,000 bases. Genes make up less than 2 percent of the length of a DNA molecule. The rest of the DNA molecule is made up of long, highly repetitive nucleotide sequences. Once dismissed as "junk" DNA, scientists now believe these nucleotide sequences may play a role in the survival of cells. Identifying the function of these sequences is a thriving field of genetics research. C2 DNA Replication In order for inherited traits to be transmitted from parent to child, the genetic information encoded in DNA must be copied with great precision during cell division. The accuracy of DNA replication depends upon the complementary pairing of bases. During replication, the DNA double helix unwinds and bonds joining the base pairs break, separating the DNA molecule into two separate strands. Each strand of DNA directs the synthesis of another complementary strand. The unpaired bases of each DNA strand attach to bases floating within the cell. But the DNA strand's unpaired bases bond only with specific, complementary bases--for example, an adenine base will bond only with a thymine base and a cytosine bases will pair only with a guanine base. Once all of the bases of a DNA strand bond to complementary bases, the complementary bases then link to each other, forming a new DNA double-helix molecule. Thus the original DNA molecule replicates into two DNA molecules that are exact duplicates. D Protein Synthesis DNA replication ensures that the genetic instructions encoded in DNA can be used continuously through generations to produce the proteins that build and operate the cells of an organism. The process of tapping the genetic code to create proteins, known as protein synthesis, has two crucial steps: transcription and translation. D1 Transcription Transcription transfers the genetic code from a molecule of DNA to an intermediary molecule called ribonucleic acid (RNA). The basic nucleotide structure of RNA resembles that of DNA, but the two compounds have three critical differences. First, the structure of RNA incorporates the sugar ribose rather than deoxyribose, the sugar in DNA. Second, RNA uses the base uracil (U) instead of thymine (T). In RNA uracil binds with adenine just as thymine does in DNA. Third, RNA usually exists as a single strand, unlike the double-helix structure that normally characterizes DNA. Transcription involves the production of a special kind of RNA known as messenger RNA (mRNA). The process begins when the two strands of a DNA molecule separate, a task directed by the enzyme RNA polymerase. After the double helix splits apart, one of the strands serves as a template, or pattern, for the formation of a complementary mRNA molecule. Free-floating individual bases within the cell bind to the bases on the DNA template using complementary base pairing. The individual bases then link together to form a strand of mRNA. In eukaryotes (organisms whose cells have a nucleus), the mRNA strand undergoes an additional step before the next stage of protein synthesis can occur. The mRNA strand consists of coding regions called exons separated by regions called introns. The introns do not contribute to protein synthesis. Special enzymes in the nucleus remove the introns from the mRNA strand. The remaining exons then link together to form an mRNA strand that contains the entire code for making a protein. D2 Translation Once transcription is complete and the genetic code has been copied onto mRNA, the genetic code must be converted into the language of proteins. That is, the information coded in the four bases found in mRNA must be translated into the instructions encoded by the 20 amino acids used in the formation of proteins. This process, called translation, takes place in cellular organelles called ribosomes. In eukaryotes, mRNA travels out of the nucleus into the cell body to attach to a ribosome. In prokaryotes (organisms without a nucleus), the ribosome clasps mRNA and starts translation before these strands have finished transcription and separated from the DNA. In both eukaryotes and prokaryotes, the ribosome acts like a workbench and clamp that holds the mRNA strand and coordinates the activity of enzymes and other molecules essential to translation. Another form of RNA called transfer RNA (tRNA) is found in the cytoplasm of the cell. There are many different types of tRNA, and each type binds with one of the 20 amino acids used in protein formation. One end of a tRNA binds with a specific amino acid. The other end carries three bases, known as an anticodon. The tRNA with an amino acid attached travels to the ribosome where the mRNA is stationed. The anticodon of the tRNA undergoes complementary base pairing with a series of three bases on the mRNA, known as the codon. The mRNA codon codes for the type of amino acid carried by the tRNA. A second tRNA bonds with the next codon on the mRNA. The resident tRNA transfers its amino acid to the amino acid of the incoming tRNA and then leaves the ribosome. This process continues repeatedly, with new tRNA receiving the growing chain of amino acids, known as a polypeptide chain, from a resident tRNA. The ribosome moves the mRNA strand one codon at a time, making new codons available to bind with tRNAs. The process ends when the entire sequence of mRNA has been translated. The polypeptide chain falls away from the ribosome as a newly formed protein, ready to go to work in the cell. E Mutations Occasionally mistakes occur during DNA replication and protein synthesis. Any alteration in the structure of a gene results in a mutation. Mutations occur during DNA replication when the chemical structure of genes undergoes random modifications. Once a change has occurred, the altered genes continue to replicate in their changed form unless another mutation occurs. Sometimes mutations occur during transcription or translation, causing protein synthesis to go awry. Although mutations may occur in any living cell, they are most important when they occur in gametes because then the change affects the traits of following generations. Most mutations harm an organism. If a mutation occurs in a gene sequence that codes for a particular protein, the mutation may result in a change in the amino acid sequence directed by the gene. This change, in turn, may affect the function of the protein. The implications can be significant: The amino acid sequence distinguishing normal hemoglobin from the altered form of hemoglobin responsible for sickle-cell anemia differs by only a single amino acid. Some mutations may be neutral or silent and do not affect the function of a protein. Occasionally a mutation benefits an organism. Over the course of evolutionary time, however, mutations serve the crucial role of providing organisms with previously nonexistent proteins. In this way, mutations are a driving force behind genetic diversity and the rise of new or more competitive species better able to adapt to changes, such as climate variations, depletion of food sources, or the emergence of new types of disease (see Evolution). Mutations can produce a change in any region of a DNA molecule. In a point mutation, for example, a single nucleotide replaces another nucleotide. Although a point mutation produces a small change to the DNA sequence, it may cause a change in the amino acid sequence, and thus the function, of a protein. Far more serious are mutations that involve the addition or deletion of one or more bases from a DNA molecule. Adding or subtracting even a single base from a normal sequence during transcription can disrupt translation by shifting the "reading frame" of every subsequent codon. For example, an mRNA strand may include two codons in the following sequence: AUG UGA. The addition of a cytosine base at the beginning of this sequence shifts the "spelling" of these codons so that they read: CAU GUG. This may result in an incorrect amino acid sequence during translation, or the protein may be truncated. Known as frameshift mutation, this type of alteration could result in the production of a protein with no real function or one with a harmful effect. Sometimes mutations are caused by transposition, in which long stretches of DNA (containing one or more genes) move from one chromosome to another. These jumping genes, called transposons, can disrupt transcription and change the type of amino acids inserted into a protein. Transposons rearrange and interrupt genes in a way that generally improves the genetic variation of a species. While mutations can occur spontaneously, some can be caused by exposure to physical or chemical agents in the environment called mutagens. Common environmental mutagens include ultraviolet rays from the sun and various chemicals, such as asbestos, cigarette smoke, and nitrous acid. High-energy radiation, such as medical X rays, can cause DNA strands to break, leading to the deletion of potentially important genetic information. Radiation damage can also affect an entire chromosome, disrupting the function of many genes. In chromosomal translocation, a piece of one chromosome breaks off and merges with another chromosome. In some cases, large sections of chromosomes may break off and be lost. The cell has highly effective self-repair mechanisms that can correct the harmful changes made by mutations and prevent some mutations from being passed on. Some 50 specialized enzymes locate different types of faulty sequences in the DNA and clip out those flaws. Another repair mechanism scans DNA after replication and marks mismatched base pairs for repair. F Gene Regulation The processes that enable information to be copied from genes and then used to synthesize proteins must be regulated if an organism is to survive. Different cells within an organism share the same set of chromosomes. In each cell some genes are active while others are not. For example, in humans only red blood cells manufacture the protein hemoglobin and only pancreas cells make the digestive enzyme known as trypsin, even though both types of cells contain the genes to produce both hemoglobin and trypsin. Each cell produces different proteins according to its needs so that it does not waste energy by producing proteins that will not be used. A variety of mechanisms regulate gene activity in cells. One method involves turning on or off gene transcription, sometimes by blocking the action of RNA polymerase, an enzyme that initiates transcription. Gene regulation may also involve mechanisms that slow or speed the rate of transcription, using specialized regulatory proteins that bind to DNA. Depending on an organism's particular needs, one regulatory protein may spur transcription for a particular protein, and later, another regulatory protein may slow or halt transcription. F1 In Prokaryotes The bacterium Escherichia coli (commonly referred to as E. coli), found in the intestines of humans and other mammals, provides a good example of gene regulation. E. coli uses three enzymes to digest lactose, the primary sugar found in milk. The bacterium produces great quantities of lactose-digesting enzymes when lactose is present and saves energy by not synthesizing the enzymes when the sugar is not available. E. coli prefers consuming glucose to lactose, so the bacterium produces these enzymes in the presence of lactose only when no glucose is available. A region of DNA known as an operon controls this gene regulation process. In E. coli, the operon includes at least five genes: Three genes, called lac genes, code for the enzymes that digest lactose; one gene encodes for a regulatory protein, called a repressor, that can sense the presence or absence of lactose; and one gene, called an operator, activates transcription, the first step in the synthesis of the lactose-digesting enzymes. In the absence of lactose, the repressor protein binds with the operator gene to block transcription. This prevents the lac genes from being transcribed and halts production of the lactose-digesting enzymes. If lactose is present, the repressor protein binds to the sugar, leaving the operator gene free to trigger transcription of the lac genes. The transcription of the lac genes produces the mRNA that will direct the production of the three lactose-digesting enzymes. F2 In Eukaryotes Gene regulation in eukaryotes is more complex than in bacteria and other prokaryotes. Even the simplest eukaryotes have far more genes than prokaryotes, and these genes must be turned on or off as conditions dictate. Most multicellular organisms contain different types of cells that serve specialized functions. The cells of an animal's heart, blood, skin, liver, and muscles all contain the same genes. But in order to carry out their specific functions within the body, each cell must produce different proteins and respond to changing environmental stimuli, such as glucose levels in the blood or body temperature. Such specialization is possible only with sophisticated gene regulation. Eukaryotes use a variety of mechanisms to ensure that each cell uses the exact proteins it needs at any given moment. In one method, eukaryotic cells use DNA sequences called enhancers to stimulate the transcription of genes located far away from the point on the chromosome where transcription occurs. If a specific protein binds to an enhancer site on the DNA, it causes the DNA to fold so that the enhancer site is brought closer to the site where transcription occurs. This action can activate or speed up transcription in the genes surrounding the enhancer site, thereby affecting the type and quantity of proteins the cell will produce. Enhancers often exert their effects on large groups of related genes, such as the genes that produce the set of proteins that form a muscle cell. Gene regulation can also take place after transcription has occurred by interfering with the steps that modify mRNA before it leaves the nucleus to take part in translation. This process typically involves removing exons (segments that code for specific proteins) and introns. These sections of the mRNA can be modified in more than one way, enabling a cell to synthesize different proteins depending on its needs. G Genes in Development Gene regulation helps individual cells within an organism function in a specialized way. Other regulatory mechanisms coordinate the genes that determine how cells develop. All of the specialized cells in an organism, including those of the skin, muscle, bone, liver, and brain, derive from identical copies of a single fertilized egg cell. Each of these cells has the exact same DNA as the original cell, even though they have vastly different appearances and functions. Genes dictate how these cells specialize. Early in an organism's embryonic development the overall body plan forms. Individual cells commit to a particular layer and region of the embryo, often migrating from one location to another to do so. As the organism grows, cells become part of a particular body organ or tissue, such as skin or muscle. Ultimately, most cells become highly specialized--not only to develop into a neuron rather than a muscle cell, for example, but to become a sensory neuron instead of a motor neuron. This process of specialization is called differentiation. At each stage of the differentiation process, specific genes known as developmental control genes actively turn on and switch off the genes that differentiate cells. One class of developmental control genes, known as homeotic genes, directs the formation of particular body parts. Activating one set of homeotic genes instructs part of an embryo to develop into a leg, for example, while another set initiates the formation of the head. If a homeotic gene becomes altered or damaged, an organism's body development can be dramatically disrupted. A change in a single gene in some insects, for instance, can cause a leg to grow where an antenna belongs. Homeotic genes work by regulating the activity of other genes. Homeotic genes code for the production of a regulatory protein that can bind to DNA and thus affect the transcription of one or more genes. This enables homeotic genes to initiate or halt the development and specialization of characteristics in an organism. Nearly identical homeotic genes have been identified in varied organisms, such as insects, worms, mice, birds, and humans, where they serve similar embryonic development functions. Scientists theorize that homeotic genes first appeared in a single ancestor common to all these organisms. Sometime in evolutionary history, these organisms diverged from their common ancestor, but the homeotic genes continued to be passed down through generations virtually unchanged during the evolution of these new organisms. IV HOW SCIENTISTS WORK WITH GENES Scientists have developed a number of biochemical and genetic techniques by which DNA can be separated, rearranged, and transferred from one cell to another. Some of these laboratory methods help scientists study the properties of genes in nature--for example, by comparing DNA from different animals to find out whether those animals are closely related to each other or only distant relatives. Other DNA techniques provide tools for genetic engineering--the alteration of genes in an organism. These tools are used in industry to develop commercial products, such as hardier crops, microbes that can break down oil slicks or decompose garbage, and improved medicines. A Recombinant DNA The DNA molecules of all life forms, from oak trees to sea horses, have the same structure and the same four bases. Scientists have made use of these similarities in a technology called recombinant DNA. In this laboratory method, one or more genes of an organism are introduced into a second organism. The new genes, sometimes known as foreign DNA, become functional in the second organism and produce a desired protein. In this way, scientists can create changes in the genetic makeup of an organism that would be unlikely to occur through natural processes. Scientists use recombinant DNA when they want to obtain large amounts of a protein, such as insulin, produced by a gene. Insulin was once in short supply for diabetics, whose bodies lack adequate supplies. Insulin supplies were derived from cows in an expensive and time-consuming process. Today recombinant DNA techniques produce insulin cheaply and in abundance. The first step in creating insulin using recombinant DNA is to isolate the sequence of nucleotides in the DNA of a human cell that forms the insulin gene. Scientists use restriction enzymes, specialized proteins that act like molecular scissors, to cut the double-stranded DNA at the point where the insulin gene occurs. The isolated DNA can then be recombined, or spliced, with a vector, a fragment of DNA that is able to transport genes from one organism to another. A vector may be a plasmid, a small, circular segment of DNA found in bacteria. Bacteriophages, viruses that are parasites of bacteria, also act as vectors. Scientists insert the vector containing the insulin gene into a bacterium, such as E. coli. Within just a few hours, a single E. coli will reproduce hundreds of times to make millions of cells, all containing exact copies of the insulin-producing gene inserted by the scientists. This process of making many cells with identical DNA is known as cloning. B DNA Libraries A DNA library is a storehouse of genetic information maintained in bacteria instead of books. These bacteria are clones created by recombinant DNA, and the foreign DNA they hold is the library's store of information. DNA libraries are helpful to scientists who require a plentiful supply of particular DNA segments to do their work. These repositories of genetic information are stored in small tubes, which can easily be shipped to other researchers for study. Each library has a unifying theme. For example, a library may contain the entire chromosomal DNA, or genome, of a given organism, or it may consist of genes that are active within certain types of cells, such as heart cells. To create a library of the human genome, DNA from all the human chromosomes would be cut into many pieces. These pieces would be randomly inserted into vectors, such as plasmids, which would then be placed into a population of bacteria. Taken together, the entire population of bacteria would contain all the DNA of the human chromosomes. C Polymerase Chain Reaction Polymerase chain reaction (PCR) offers an alternative to vector-based cloning as a means of generating numerous copies of DNA from a small initial sample. Performed in a test tube, PCR mirrors the way in which DNA is replicated within a cell. To perform PCR, scientists isolate the piece of DNA to be amplified (multiplied) in a test tube and heat it to separate the two strands of the molecule. As cooling occurs, short pieces of DNA called primers are added to the test tube. The primers attach to each strand, marking the segment that will be cloned. Free-floating nucleotides and an enzyme called DNA polymerase are then added to the mixture. DNA polymerase uses the free-floating nucleotides to build a complementary copy of each amplified DNA segment, resulting in two new double-stranded DNA molecules. Each cycle of heating and cooling doubles the amount of the desired DNA fragment in the test tube. In a matter of hours, scientists can obtain millions of copies of a desired piece of DNA. PCR enables scientists to amplify traces of DNA found at a crime scene or in a fossil animal to produce sufficient quantities to study. D Gel Electrophoresis PCR and recombinant DNA techniques create large amounts of DNA segments. To study the structure of these segments, researchers use a process known as gel electrophoresis. This technique can be used to identify genes in humans that have previously been identified in other organisms, such as fruit flies. It can also be used to compare the DNA found from blood or hair samples at a crime scene with the DNA of a suspect in the crime. In gel electrophoresis, restriction enzymes break up the DNA under study into restriction fragments of varying lengths. Solutions containing these fragments are placed within a thick gel. An electric current is applied to the gel, causing one end of the gel to have a positive charge and the other to have a negative charge. All of the restriction fragments begin to move from the negative end of the gel toward the positive end. The smaller fragments move faster than the larger fragments. When the current shuts off, typically after several hours, the DNA fragments have spread out across the gel, with the smaller ones closer to the positive end. The dispersed fragments display a pattern resembling a bar code. Each bar in this pattern contains DNA fragments of a certain size. Scientists can identify specific restriction fragments by their location on the gel. A complementary sequence of DNA can be used as a probe to find a restriction fragment on the gel that has a particular nucleotide sequence. Scientists may use DNA found in blood at a crime scene as the probe to see if it pairs up with any of the DNA fragments in the gel electrophoresis. If pairing occurs, the DNA from the crime scene is from the same person who provided the DNA sample for the gel electrophoresis. E DNA Sequencing Once an interesting piece of DNA has been isolated or identified, scientists often need to determine if the sequence of nucleotides in the fragment is related to known genes and to determine what kind of protein it might make. Scientists use DNA sequencing to detect genetic mutations linked to diseases such as cystic fibrosis. Scientists have also used this method to alter the sequence of a gene and study the function of the resulting protein. In DNA sequencing, scientists create many copies of a single-stranded DNA fragment that will be used to synthesize a new DNA strand. An equal number of copies of the fragment are placed into four different test tubes to act as the template for the synthesis of a new strand. The enzyme DNA polymerase and free nucleotides are added to each test tube. Each test tube also receives one type of dideoxy nucleotide--a nucleotide that closely resembles either adenine, guanine, thymine, or cytosine. These nucleotides can attach to the end of the new complementary DNA strand, but they cannot bind to anything else, thus they terminate the synthesis of the new DNA strand. DNA polymerase uses the free nucleotides to build a complementary DNA strand. If the original DNA fragment contains guanine, DNA polymerase delivers a cytosine dideoxy nucleotide to pair with the guanine base on the original strand. The cytosine links with the growing chain of nucleotides on the complementary DNA strand, but it is unable to bind with any other nucleotide. The newly formed DNA fragment terminates with the cytosine dideoxy nucleotide at the end of the chain. The reactions in each of the four test tubes produce a series of DNA fragments in which the new strands terminate at a known base. Each test tube produces fragments that differ in length from the other test tubes. The newly formed fragments are sorted in an electrophoresis gel that can detect differences as small as one nucleotide in length. By analyzing these sorted fragments, scientists can determine the complementary base sequence for the original DNA fragment. This sequencing method has become a routine laboratory technique, automated with specialized machines and computers that can prepare DNA samples and read nucleotide sequences far faster and more accurately than people can. F Gene Chip The gene chip, also known as a DNA chip or DNA microarray, is a thumbnail-sized chip of glass or silicon that carries DNA instead of electronic circuits. Gene chips can identify the genes that are active within a cell and help identify mutated genes. In one application, scientists take a single strand of DNA that contains a defective gene and use ultraviolet light to attach the strand onto a glass or silicon chip. A second DNA strand isolated from a patient is attached to fluorescent markers and deposited onto the chip. If the patient's DNA strand bonds with the DNA already bonded to the chip, then the individual's DNA contains the defective gene. When the DNA on the chip pairs with the fluorescent DNA, it develops a fluorescent glow that can be viewed with a microscope and interpreted by a computer. A diagnostic gene chip may soon be manufactured to hold the DNA sequences of all the known disease-causing genes, making diagnosis for genetic disorders fast, reliable, and inexpensive. Gene chips also distinguish between active DNA--DNA that is being transcribed to produce mRNA--and inactive DNA. Researchers use these chips to learn how the transcription of a group of genes is affected when cells are exposed to a drug. V HUMAN GENETICS Our understanding of human genetics builds on a foundation of information obtained from studying other organisms. Until the 1980s, genetic researchers focused their work on the fundamental genetic processes in simpler organisms, such as bacteria, plants, and fruit flies. Today an expanded array of tools available for the direct study of human genetics attracts scientists from around the world to collaborate to identify and study every human gene. The genetic principles that Mendel first discovered in plants apply to humans as well. As in all other life forms, the DNA found in human cells encodes the proteins that are essential for reproduction, survival, and growth. The unique structure and behavior of DNA ensures that human traits are passed from generation to generation and accounts for why parents, children, and grandchildren often have similar facial features, hair color, height, and athletic or artistic abilities (see Heredity). Yet each of us inherits a unique genetic legacy from our parents and more distant ancestors. With the exception of identical twins, no two people have the exact same combination of alleles for the estimated 20,000 to 25,000 human genes. Some human traits are controlled largely by a single gene. But most inheritable characteristics are influenced by a number of genes that interact in a complex fashion. Also, personal experiences and environmental factors combine with genetic influences to shape certain traits, including vulnerability to disease and characteristics such as intelligence, emotions, talents, and personality. A Human Genome Human genes reside on 23 pairs of chromosomes found in the nucleus of every body cell except gamete cells. In each pair, one of the chromosomes is inherited from the mother and the other is passed down from the father. About 2 m (7 ft) of DNA is packaged into each chromosome. All of the genes carried on chromosomes form the human genome. A lesser amount of DNA can be found in mitochondria, cellular organelles responsible for creating the energy used in cell activities. All but one of these 23 pairs are composed of chromosomes nearly identical in shape. Each of these 22 chromosome pairs, known as autosomes, contains the same genes (although they likely carry different alleles). The autosome pairs vary considerably in length, and scientists number them according to their relative size: Pair number 1 is the longest pair and pair number 22 is the shortest. Rounding out the human genome is the 23rd pair of chromosomes, known as the sex chromosomes, which determine the sex of an individual. Females inherit two X chromosomes, a matched pair carrying the same genes. One X chromosome is inherited from the mother and one X chromosome is inherited from the father. Males inherit an X chromosome from their mother and a Y chromosome from their father. The Y chromosome is shorter than the X chromosome and bears far fewer genes. One gene on the Y chromosome causes an embryo to develop as a male rather than a female. Humans produce gamete cells for sexual reproduction. These gametes contain a haploid number of chromosomes--23 chromosomes instead of the full complement of 46. Female gamete cells mature into eggs, with each egg containing chromosomes 1 through 22 and an X chromosome. Males produce gametes that mature into sperm, and each sperm cell has a single set of chromosomes 1 through 22 and either an X or a Y chromosome. During fertilization, an egg that joins with a sperm containing a Y chromosome develops into a male, and an egg fertilized by a sperm containing an X chromosome develops into a female. B Human Genetic Disorders Thousands of inherited diseases caused by altered genes and chromosomal abnormalities affect humans (see Genetic Disorders). These disorders cause problems such as physical deformities, metabolic dysfunction, and developmental problems. Medical surveys indicate that roughly 1 percent of newborns in the United States have a single-gene defect. As many as 1 baby in 200 is born with a chromosomal abnormality serious enough to produce physical defects or mental retardation. It is misleading to say that a person "inherits the gene" for a disease, since humans are born with the same number and types of genes. We inherit allele forms of specific genes, and these alleles may be defective. Most of the known inherited genetic disorders are caused by the mutation of a single gene, resulting in alleles that produce disease. These defects often produce disturbances in the body's biochemical processes, such as inhibiting the action of an important enzyme or stimulating the overproduction of a harmful substance. Frequently the consequences of such problems can cause severe disability or be fatal. Many single-gene disorders follow Mendelian patterns of inheritance. A mother and father each pass an allele for a specific gene on to a child. If one of the alleles is defective and causes disease, the child will develop the disease according to a dominant-recessive pattern of inheritance. For example, cystic fibrosis (CF), a metabolic disorder that causes a progressive loss of lung function, is caused by a mutation in the recessive allele of a gene responsible for regulating salt content in the lungs. The recessive allele is unable to direct the production of a key protein, resulting in a salt imbalance that causes thick, suffocating mucus to build up in the lungs. If a baby inherits the defective allele from just one parent, no disease results. But the infant who inherits the defective allele from both parents will be born with the disease. In other cases, a single dominant allele causes genetic disease. Huntington's disease, a condition characterized by involuntary movements, dementia, and eventually death, is caused by the inheritance of a pair of alleles in which a defective allele dominates the normal allele for the gene. An affected parent has a 50 percent chance of passing the defective allele to a child. A child who inherits the dominant defective allele from just one parent will develop the disease. Other inherited genetic diseases are caused by defects in the genes found on the X chromosome. Hemophilia, the inability of the blood to clot and heal a wound, is caused by a defect in an allele located on the X chromosome that helps produce proteins involved in the clotting process. Women who inherit this defective allele usually have the normal allele on their second X chromosome, which produces enough of these clotting proteins for the body to remain healthy. Women who inherit this faulty allele have a 50 percent chance of passing the defective allele on to their children. Males who inherit this defective allele do not have a normal version of the allele on their Y chromosome and so cannot produce clotting proteins to heal wounds. Hemophiliacs are almost always males who have inherited an X chromosome with the faulty allele from their mother. Other genetic disorders arise due to the inheritance of an abnormal number of chromosomes or a defective chromosome structure. These chromosomal abnormalities have a devastating impact: Many fetuses with such defects, particularly those with missing chromosomes, will die prenatally, resulting in miscarriage (spontaneous abortion). In other cases, newborns with chromosomal abnormalities suffer from physical problems or varying degrees of mental retardation. Down syndrome occurs when an individual's cells carry an extra copy of chromosome 21. People born with this condition have characteristic facial features, short stature, severe developmental disabilities, and a shortened life expectancy. C Genetics and Cancer Cancer is a common name for many diseases that affect different body tissues, including the skin and the liver. All cancers involve alterations in genes that control cell division. These alterations cause cells to replicate abnormally and form tumors. Cancers generally arise from mutations that occur directly in the somatic cells, any cells of the body with the exception of the gametes (sperm and egg cells). Since the genetic mutations have not occurred in gametes, the mutations are not inherited by the next generation. While cancer is not a traditional inherited genetic disorder, scientists have determined that a genetic component plays a strong role in the development of the disease. Geneticists have identified many different genes with certain alleles that appear to increase an individual's susceptibility to cancer. A notable example involves two genes linked to breast cancer. Researchers estimate that more than half of the women with a family history of breast cancer who inherit mutated alleles of these two genes, known as BRCA1 and BRCA2, will develop breast cancer by the age of 70. In contrast, women who lack either of the mutated alleles have only a 13 percent chance of developing the disease. For many cancers, researchers believe that mutations in several different genes must accumulate before cancer develops. As a person ages, errors in DNA replication may occur during cell division, or cells may be damaged by exposure to certain environmental factors, including cigarette smoke, radiation, and chemical pollutants. As a result, an accumulation of mutations may develop in two types of genes: tumor suppressor genes and oncogenes. Tumor suppressor genes normally function to halt cell division, while oncogenes function to activate cell division. A mutation in either type of gene can stimulate nonstop cell division. These types of defects have been linked to some cases of leukemia as well as to cancers of the ovaries, lungs, colon, and other organs. D Genetics and Aging A growing area of study focuses on the link between aging and genetics. Scientists have determined that structures called telomeres, long, repetitive sequences of nucleotides at the end of chromosomes, affect the aging process. Each time a cell divides, telomeres become shorter. When the structures shorten to a certain length, the process of cell division terminates. The cells of these chromosomes continue to live, but they never divide again. Laboratory tests suggest that an enzyme produced in gamete cells of the human body, called telomerase, can maintain telomere length in human cells, enabling them to continue dividing, perhaps indefinitely. Scientists hoping to lasso the life-extending properties of telomerase have been confounded by research indicating that telomerase is also active in rapidly dividing cancer cells. Before telomerase can be used to slow or halt aging, scientists must learn how to manipulate the enzyme so that it does not promote cancer growth. E Genes and Behavior Scientists actively explore the links between genes and behavior to determine both the patterns and the limits of genetic influence. Such studies continue to be controversial because behavior or mental processes can be difficult to measure objectively. Furthermore, many behavioral traits, both normal and abnormal, are complex, influenced by many genes as well as by personal experiences. Studies of the possible genetic components of psychiatric disorders have yielded mixed results. Geneticists have identified at least two genes linked to schizophrenia, a condition characterized by hallucinations, delusion, paranoia, and other symptoms. Other studies that reported the discovery of genes that influence bipolar disorder (also known as manic-depressive illness) and alcoholism have been reversed or questioned. Though attempts to identify genes linked to these disorders have been flawed, scientists have little doubt that the conditions do have a genetic component. Scientists have established links between genes and certain antisocial or violent behaviors. For instance, researchers have identified a gene on the X chromosome that has been tied to extremely violent behavior in men. They identified the gene in members of several families with a multigenerational history of violent, criminal behavior. They identified gene codes for monoamine oxidase inhibitor (MAO), an enzyme that helps nerve cells in the brain communicate with each other. Males in an affected family who inherit a defective allele for MAO do not produce enough of the enzyme. As a result, low levels of MAO change the activity of certain brain nerve cells, possibly contributing to socially unacceptable behavior. While research suggests that men who have a defective allele for the MAO gene are more prone to aggressive behavior, experts cite numerous reasons for concern and doubt. Few scientists believe that a single gene could have a leading role in influencing complex behaviors. Others charge that these kinds of investigations promote an unreasonably simplistic view of genetic determinism, in which genes can be blamed for certain behaviors. Critics note that studies have identified many men who carried the defective allele for MAO production and never committed a violent act. Clearly, nongenetic influences--as varied as an individual's family life, work circumstances, attitudes, diet, and emotional state--affect complex behaviors. F Identifying Genetic Disorders Health-care professionals who specialize in genetic disorders use a variety of methods to identify inherited conditions. Analysis of a family medical history, known as pedigree analysis, is used to track the transmission of a condition through generations. Blood tests that identify specific DNA sequences can reveal carriers of a diseasecausing gene who have no symptoms of the disease (see Genetic Counseling). Geneticists collect a person's medical family history to trace the inheritance of a genetic trait among multiple generations. The information is placed in a pedigree, which resembles a traditional multigenerational family tree but includes information about individuals who were diagnosed with a particular disorder or who suffered from certain medical symptoms. A pedigree can help researchers recognize diseases that express themselves in dominant or recessive alleles. Dominant disorders affect every generation. Recessive disorders may cluster in a single generation, reflecting when two parents who both carry a recessive allele for a disease have one or more children who develop the disease. A pedigree can also identify diseases that show X-linked inheritance. Pedigree analysis can be useful when combined with certain genetic tests. A blood sample taken from a person who is at risk for a genetic disorder can be compared with a DNA sequence known to cause the disorder in question. Other genetic tests can reveal if a person has extra chromosomes, missing chromosomes, or chromosomes that have attached to one another in unusual ways. In some cases, these chromosomal abnormalities may produce genetic disorders in children or they may affect a person's ability to conceive a child. Genetic testing can also identify disorders in a fetus, enabling parents to learn early in a pregnancy if a fetus will likely be born with health problems or develop them later in life. Presymptomatic testing can identify DNA abnormalities in a person before health problems develop. In the case of certain inherited heart conditions, for example, these tests enable a person to make healthy lifestyle changes or take other preventative measures, such as medications, to lower the risk of illness or death. Medical genetic testing raises challenging issues because such tests typically provide statistical possibilities rather than a definite prediction of whether a person will develop a given genetic disease. A test result may indicate, for example, that a person has a 75 percent risk of developing colon cancer by the age of 65. Such results enable a physician to perform appropriate screening tests on the at-risk person in order to identify the disease at its earliest stages, when it is most treatable. At the same time, however, physicians must decide at what age the person's screening should begin and whether the benefits of early screening are worth the drawbacks of frequent screening. These drawbacks include expense, patient anxiety and discomfort, and exposure to radioactivity or other harmful substances used in testing. Different problems are posed by genetic screening tests that diagnose conditions for which no preventive measures exist, such as Alzheimer's disease, a progressive brain disorder that causes the loss of mental function. People may find it devastating to learn that they are at risk for a deadly disease that cannot be prevented by medical measures or lifestyle choices. G Gene Therapy A recent development in genetic technology known as gene therapy focuses on curing inherited disorders. In experiments using gene therapy, researchers have replaced defective genes with normal alleles, inactivated a mutated gene, or inserted a normal form of a gene into a chromosome. The earliest success in human gene therapy involved the treatment of infants who cannot produce adenosine deaminase (ADA), an enzyme important to normal function of the immune system. Scientists have successfully inserted the normal allele for the gene that codes for the enzyme into cells in ADA-deficient children. Preliminary evidence indicates that this gene therapy leads to better immune function in recipients. Researchers are also exploring gene therapy's potential to help treat people with many other conditions, including certain cancers, hemophilia, heart disease, and cystic fibrosis. Although the United States Food and Drug Administration (FDA) has approved more than 400 clinical trials in gene therapy, this method of treating disease remains far from an unqualified medical success. Treatments usually produce some improvement in the underlying condition, but not enough to consider the therapy suitable for large-scale use. The death of a patient involved in a gene therapy experiment in 1999 caused the National Institutes of Health (NIH), a federal agency that monitors gene therapy studies, to reevaluate the safety and effectiveness of gene therapy clinical trials. H Human Genome Project The Human Genome Project is the most ambitious project in the history of biology. The program's challenging goal was to identify and sequence all of the DNA in human chromosomes. The project was initiated in 1990 in the United States with government funding, and it rapidly grew into an international consortium of academic centers and drug companies in China, France, Germany, Japan, the United Kingdom, and the United States. The consortium initially hoped to reach its goal by the year 2005. In 1998 Celera Genomics, a privately funded biotechnology firm, announced that it would sequence the human genome by the year 2000 using different sequencing strategies than those used by the public consortium. This announcement triggered a heated race between Celera Genomics and the public consortium to complete the genome project. In June 2000 both teams declared victory when they jointly announced that they had separately completed a rough draft of the genome. The two teams published their findings simultaneously, although in two different journals, in February 2001. The draft provided a basic outline of 90 percent of the human genome. Scientists from the public consortium completed the final sequencing of the human genome in April 2003, two years earlier than planned. The completed human genome has provided scientists with a detailed blueprint of our complex genetic code. Large computer databases of genetic information enable scientists to look for patterns and relationships among the actions of different genes. Among the findings about the human genome was that the number of genes in the human genome is much lower than was predicted--only about 20,000 to 25,000 genes compared to the expected 100,000 genes. This number is a little more than twice the number of genes found in the fruit fly. Scientists are now turning their attention to studying how the relatively low number of genes in the human genome can produce the complex structures found in humans. Scientists have long known that a single gene produces a single protein and that this single protein subsequently may be processed into several different proteins. In a new science known as proteomics, scientists seek to identify and understand the function of all the proteins in the human body. They theorize that there may be many more proteins than there are genes--that is, more than 25,000. Among other advances, the database of proteins derived from proteomics is expected to help scientists better understand the regulation of gene expression in the body and how it leads to the complexity of cellular structures and functions. In addition, proteomics may lead to the development of breakthrough drugs for a variety of genetic disorders. VI GENES AND OUR WORLD Breakthroughs in decoding and manipulating the genetic information stored in DNA promise a world of benefits. These scientific advances already help to diagnose and treat disease, develop new medicines, bring criminals to justice, improve our food supply, and clean up the environment. At the same time, however, genetic technologies also present society with the potential for new and serious social or environmental problems. Many of the developments that worry critics of genetic technologies remain on the horizon, but the debate over their inevitable arrival is already in full swing. A Genes and the Environment Humans have tampered with the genetic composition of other organisms for thousands of years. Most of this manipulation has been decidedly low-tech: domestication of animals and selective breeding of desirable food crops. The development and use of genetic engineering techniques has accelerated the pace at which humans can alter nature, creating some products that have unquestionable benefits and others that raise serious concerns. Some scientists fear that genetic engineering techniques will damage genetic diversity. Domestication and selective breeding, which aim to produce many similar organisms with particular desirable traits, reduce the natural variation of genes within a species. Genetic engineering techniques take this effect a giant step further. Many crop species--including wheat, corn, tomatoes, and strawberries--have been manipulated to maximize yield, appearance, resistance to pests and chemicals, hardiness, and other commercially valuable traits. Once attractive varieties have been developed, agricultural techniques favor wide-scale planting of such genetically similar or identical stocks. The impact of this practice on biodiversity can be ominous because older plant varieties that carry diverse and useful alleles may be lost forever. The forfeited genetic material could leave a species vulnerable to annihilation from a single factor in the environment, such as an insect pest or an infectious virus. Fortunately, efforts to combat decreasing biodiversity are under way. Farmers, gardeners, government agencies, and other interested parties have collaborated to create seed banks to maintain genetic diversity. These banks catalogue, store, and distribute the seeds of rare or endangered plants, enabling gardeners and farmers to continue cultivating rare plant varieties so that the unique genetic makeup of these plants does not disappear. In the same vein, zoos and other institutions breed endangered species of animals that may no longer be able to survive in their native habitats. Other animal programs seek to preserve or enhance the genetic variation within certain endangered animal populations. For example, all cheetahs are almost identical genetically, most likely due to their near extinction about 12,000 years ago. Inbreeding among the few remaining individuals has resulted in a loss of genetic diversity in modern cheetahs that may have affected the cheetah's immune system, leaving the animal vulnerable to disease. Scientists hope to use genetic engineering techniques to introduce new genes into the cheetah population to increase the genetic diversity of the species. The broad use of genetic engineering techniques in agriculture has raised other concerns beyond issues of biodiversity. From a consumer point of view, for instance, new technologies may have compromised a food's taste or nutritional value in exchange for a plant or animal that can be grown faster or at less cost. In addition, some critics question the safety of genetically engineered foods. They fear that plants or animals that have received new genes will produce proteins that would not be present in nonmanipulated organisms. Such changes could have a serious effect: causing allergies or toxicity in humans who eat these foods, for example, or disrupting a plant's production of key nutrients. Though there has been much speculation about the potential health risks of genetically engineered foods, rigorous scientific investigation into the effects of these foods on humans is just beginning. The potential environmental impact of genetically engineered agriculture is equally controversial. Critics fear that transgenic organisms, which contain DNA from other species, could give rise to populations of genetically altered life forms that could cause disease, displace native species, or otherwise harm delicate ecosystems. Consider the example of a genetically engineered form of oilseed rape, the plant that yields canola oil. The altered form, which has been grown commercially in the United States since 1993, contains inserted genes that increase its resistance to herbicides (weed-killing chemicals). The altered plants can grow unabated even when a farmer sprays a field with enough herbicide to kill troublesome weeds. Yet a curious problem has emerged: The transgenic rape can interbreed with weedy relatives that grow nearby. Some scientists fear that this interbreeding could create weed varieties that also have a genetic resistance to known herbicides. The biological and economic impact of such a development could be enormous. B Genes and Society Advances in genetic technologies allow scientists to take an unprecedented glimpse into the genetic makeup of every person. The information derived from this testing can serve many valuable purposes: It can save lives, assist couples trying to decide whether or not to have children, and help law-enforcement officials solve a crime. Yet breakthroughs in genetic testing also raise some troubling social concerns about privacy and discrimination. For example, if an individual's genetic information becomes widely available, it could give health insurers cause to deny coverage to people with certain risk factors or encourage employers to reject certain high-risk job applicants. Furthermore, many genetically linked problems are more common among certain racial and ethnic groups--for example, the BRCA1 breast cancer allele is more common in Ashkenazi Jews, and the blood disorder sickle-cell anemia is more prevalent among blacks of African ancestry. Many minority groups fear that the expansion of genetic testing could create whole new avenues of discrimination. Of particular concern are genetic tests that shed light on traits such as personality, intelligence, and mental health or potential abilities. Genetic tests that indicate a person is unlikely to get along with other people could be used to limit a person's professional advancement. In other cases, tests that identify a genetic risk of heart failure could discourage a person from competing in sports. New technologies that allow the manipulation of genes have raised even more disturbing possibilities. Gene therapy advances, which allow scientists to replace defective genes with normal alleles, give people with typically fatal diseases new hope for healthy lives. To date, gene therapy has focused on manipulating the genetic material in body cells other than gametes, so the changes will not be passed on to future generations. However, the application of gene therapy techniques to gametes--the cells involved in reproduction--seems inevitable. Such manipulation might help prevent the transmission of disease from one generation to another, but it could also produce unforeseen problems with long-lasting consequences. For instance, many people worry that new genetic techniques could be used to alter or encourage traits now viewed as part of normal human variability, such as shortness or baldness. At various times in the past century, people have advocated efforts to improve the human condition by promoting the perpetuation of certain genes. This concept, known as eugenics, typically involves encouraging people with "positive" genes to reproduce and discouraging those with "inferior" genes from having offspring. Many people fear that new genetic technologies used to manipulate the human genome could give people previously unattainable methods to resort to extreme forms of eugenics. Advances in genetic technologies have turned some genes into valuable commercial commodities, spawning a host of controversial questions. Who owns a genetically altered organism or the genes it contains? Is it right to patent the use of a naturally occurring gene? Some people feel that genetic material should not be owned or used for profit. Costa Rica has enacted laws to prevent foreign companies from patenting and then profiting from genes of native Costa Rican plant and animal species. Balancing the need to limit patents on genes are concerns that the profit motive of companies must be protected to maintain incentives to make new discoveries for medical products. The citizens of Iceland, for example, are cooperating with a biotechnology company in a study of the genetic makeup of the Icelandic people. The information compiled will be used to learn about genetic diseases. VII HISTORY Humans have had some understanding of heredity since prehistoric times, observing how similar traits pass from parent to offspring and noting that differences arise with each generation. Most of the mechanisms of heredity, however, were shrouded in mystery until early in the 20th century. Since that time, the rate of discovery has reached a feverish pace, enabling the advancement of modern molecular biology and the current Human Genome Project. A Early Views of Heredity In ancient times, people understood some basic rules of heredity and used this knowledge to breed domestic animals and crops. By about 5000 BC, for example, people in different parts of the world had begun applying selective breeding techniques to grow new plant varieties, including types of wheat, maize, rice, and date palms, that had never existed in the wild. Ancient people understood that the rules of inheritance also applied to humans. The ancient Greeks were particularly interested in human heredity and evolution. Greek scientists and philosophers hotly debated whether a male or female parent contributed more to an offspring. In the 4th century BC, Aristotle speculated that acquired characteristics, such as a scar that was incurred during life, could be passed on to offspring. He also believed in a widely held theory known as pangenesis. This theory proposed that particles in the body, called gemmules, reside in the limbs and organs. The gemmules become imprinted with any changes acquired by the body, such as muscle development from exercise. The gemmules then move to the reproductive cells and transfer information about the body's alterations to these cells. The reproductive cells transmit the acquired traits to offspring through particles called pangenes. The theories about the inheritance of acquired characteristics and pangenesis persisted until the middle of the 19th century. French zoologist Jean-Baptiste Lamarck formalized the theory of acquired characteristics in his treatise Philosophie Zoologique (1809). Lamarck proposed that organisms evolve by responding to changes in their environment. When organisms undergo a change in order to adjust to their environment, that change acts as a trait that can be passed on to offspring. B Influences of Darwin and Mendel A surprising supporter of pangenesis was the British naturalist Charles Robert Darwin, who believed that the theory accounted for the process of heredity and the wide variety of traits seen among offspring. Despite his mistaken belief in pangenesis, Darwin nonetheless had an enormous impact on human understanding of heredity. During his years of extensive worldwide travel, Darwin collected many observations of how related species adapt to their local environments. Darwin and British naturalist Alfred Wallace independently formulated the theory of natural selection, which holds that members of a given species born with more favorable characteristics to deal with their environment would be most likely to survive to pass on these traits to the next generation. This important theory was popularized by Darwin's publication On the Origin of Species (1859). The book was an immediate sensation, but it raised many questions. Foremost among these was the mystery of how organisms could appear with modified or entirely new traits. At roughly the same time that Darwin published his natural selection theories, the answer to many questions about the mechanisms of heredity were being unraveled by Gregor Mendel, a reclusive Austrian monk. Mendel conducted a long series of experiments on pea plants during the 1850s and 1860s. Mendel crossbred plants that expressed differing traits, such as height and flower color. His conclusions from these experiments helped him formulate a comprehensive theory of how such traits pass from one generation to another. In his studies, Mendel recognized that characteristics were inherited as discrete units, and that each of these was inherited independently of the others. He speculated that each parent has pairs of these units but passes only one to an offspring. He also noted that certain forms of one trait were always dominant over others. Today the units that Mendel described are known as genes. C Emergence of the Science of Genetics Mendel published his findings in 1866, but they went largely unnoticed for more than three decades. In the year 1900, however, Dutch botanist Hugo Marie de Vries, German botanist Karl Correns, and Austrian botanist Erich Tschermak independently rediscovered the monk's works and verified his conclusions. Advances in cytology, the science of the structure and function of cells, enabled scientists to more deeply appreciate Mendel's work. In 1902 American biologist Walter S. Sutton and German cell biologist Theodor Boveri separately noted the parallels between Mendel's units and chromosomes. The demonstration of the chromosomal basis of inheritance gave rise to the modern science of genetics. The term genetics itself was coined in 1905 by British biologist William Bateson. The terms gene and genotype were contributed in 1909 by German scientist Wilhelm Johannsen. In 1905 American biologists Edmund B. Wilson and Nettie Stevens independently discovered and identified the sex chromosomes. Wilson discovered the X chromosome in a butterfly, and Stevens discovered the Y chromosome in a beetle. The discoveries of the X and Y chromosomes helped scientists begin to unravel new patterns of inheritance. Foremost among this research was the work of American biologist Thomas Hunt Morgan on fruit flies. In 1910 Morgan identified the first proof of a sexlinked trait, an eye-color characteristic that resides on the X chromosome of fruit flies. With this finding, Morgan became the first scientist to pin down the location of a gene to a specific chromosome. Morgan was also the first to explain the implications of linkage, unusual patterns of inheritance that occur when multiple genes found on the same chromosome are inherited together. A student of Morgan's, American biologist Alfred Sturtevant, found early evidence of the mechanisms of crossing over, the phenomenon in which chromosomes interchange genes. More definitive proof emerged in the 1930s with work by American geneticists Harriet Creighton and Barbara McClintock. The pair demonstrated gene recombination with experiments on seed color in corn. McClintock later gained notice for her work on transposable elements, large genetic segments that move within a chromosome or even between chromosomes. Her research into these elements, commonly known as jumping genes, earned McClintock the 1983 Nobel Prize in physiology or medicine. D Breakthroughs in DNA Studies While cytologists and geneticists were studying the properties and location of genes on chromosomes, other scientists focused their studies on the composition of genes. In 1928 British microbiologist Frederick Griffith ran a series of experiments on two strains of bacteria, one that kills mice and another that is harmless to them. When Griffith injected mice with killed cells of the virulent bacteria, all of the mice survived. But in a second trial, when Griffith injected a combined cocktail of dead virulent bacteria and live "harmless" bacteria, the mice all died. He concluded that something in the dead virulent cells "transformed" the hereditary material of normally harmless bacteria so that they became killers. Most scientists at the time theorized that the transforming factor was composed of a protein. The real identity of the transforming factor in this experiment was not identified until 1944, when American geneticists Oswald Avery, Colin MacLeod, and Maclyn McCarty revisited Griffith's research. After isolating different molecular components from dead bacterial cells, Avery and his colleagues determined that DNA was the agent that transformed the live harmless bacteria into killers. Despite a growing body of evidence about the function of DNA, many scientists were not ready to reject proteins as the hereditary material. The debate was largely quieted in 1952 by American geneticists Alfred Hershey and Martha Chase. Hershey and Chase showed that when a type of virus called a bacteriophage infects a bacterium, it is the virus's DNA--not protein--that enters the bacterium to cause infection. Their studies confirmed that DNA contained the virus's genetic information, which triggered viral replication within the bacteria. The experiments of Hershey and Chase convinced most scientists that DNA was the molecule of heredity, but many questions about the structure and mechanisms of DNA remained. In the early 1950s researchers began to apply techniques of X-ray diffraction to learn about the basic structure of DNA. X-ray diffraction can determine molecular structures by measuring patterns of scattered X rays after they pass through a crystalline substance. British physical chemist Rosalind Franklin and British biophysicist Maurice Wilkins used X-ray diffraction to obtain DNA images of unprecedented clarity. Yet the exact three-dimensional structure of DNA remained unclear. The groundbreaking work of American biochemist James Watson and British biophysicist Francis Crick solved that mystery. In 1953 the two proposed a model of DNA that is still accepted today: A double helix molecule formed by two chains, each composed of alternating sugar and phosphate groups, connected by nitrogenous bases. Watson and Crick (along with Wilkins) were awarded the 1962 Nobel Prize in physiology or medicine for their discoveries. Watson and Crick speculated that the structure of DNA provided some obvious clues about how the molecule could replicate itself. They proposed a replication model in which each strand of DNA serves as a template for making exact copies. This model of replication, called semi-conservative replication, was demonstrated in 1958 by American molecular biologists Matthew Meselson and Franklin Stahl. Their experiments demonstrated the mechanisms of replication by tracking DNA containing a heavy nitrogen isotope through a series of replications. With DNA's structure and replication mechanisms largely solved, scientists turned their attention to identifying the genetic code--learning how a gene's nucleotide sequence determines what type of protein is made. In the late 1950s, South African geneticist Sydney Brenner and other scientists confirmed that RNA acted as an intermediary between DNA and protein production. Researchers still were uncertain how the sequence of nucleotides in DNA corresponded to the production of specific amino acids. In 1961 Crick and Brenner determined that groups of three nucleotides, now known as codons, code for the 20 amino acids that form the foundation of proteins. The exact relationship between codons and amino acids was clarified after several important discoveries. American biochemists Marshall Nirenberg and J. Heinrich Matthaei synthesized repeated nucleotide sequences that led to the production of repeated single amino acids. They identified how certain codon combinations code for a specific amino acid. A process developed by American geneticist Har Gobind Khorana helped scientists create a "dictionary" of codons that defined specific amino acids, thus resolving the remaining ambiguities in the genetic code. Only 12 years after the structure of DNA was deduced, the genetic code was solved. E Learning to Manipulate DNA After scientists had unraveled the structure and replication mechanisms of DNA, many felt that the major discoveries of genetic research were resolved. They predicted that the only task left in genetics was to sort out the molecular details of how genes work. But in the process of studying gene function, researchers developed powerful new molecular techniques, enabling them to analyze and manipulate genes with a speed and precision never before possible. A number of discoveries made during the 1960s and 1970s shed light on how distinct fragments of DNA could be isolated. The work of Swiss molecular biologist Werner Arber focused on specialized enzymes that digest, or "restrict," the DNA of viruses infecting bacteria. These enzymes were subsequently dubbed restriction enzymes. In the following decade, scientists learned that restriction enzymes could also act like molecular scissors to cut DNA. In 1970 American molecular biologist Hamilton Smith and colleagues determined that restriction enzymes could cleave DNA molecules at precise and predictable locations. Hamilton concluded that the enzymes were able to recognize specific nucleotide sequences. Scientists quickly realized that restriction enzymes could be used in the laboratory to manipulate DNA. In 1973 American biochemist Herb Boyer used restriction enzymes to produce a DNA molecule with genetic material from two different sources. This splicing technique is now known as recombinant DNA. Boyer inserted foreign genes into plasmids and observed that the plasmids could replicate to make many copies of the inserted genes. In subsequent experiments, Boyer, American biochemist Stanley Cohen, and other researchers demonstrated that inserting a recombinant DNA molecule into a host bacteria cell would lead to extremely rapid replication and the production of many identical copies of the recombinant DNA. This process, known as cloning, gave scientists the power to make many copies of desired DNA for molecular study. The speed and efficiency of DNA cloning were vastly improved in the 1980s with the invention of polymerase chain reaction (PCR). Developed by American biochemist Kary Mullis, PCR enables scientists to produce large amounts of DNA sequences in a test tube. In a matter of hours, the process can produce millions of cloned DNA molecules. Yet all of the advances in isolating and replicating DNA would not be possible or be of much use if researchers could not determine the nucleotide sequence of genetic material. In the late 1970s and early 1980s, British biochemist Frederick Sanger and his associates developed DNA sequencing techniques. Sanger's methods, which used special compounds called dideoxy nucleotides, rapidly yielded the exact nucleotide sequence of a desired sample. With the use of automated equipment, the new techniques transformed genetic sequencing into a speedy, routine laboratory procedure. Many of the new techniques for isolating, sequencing, and replicating DNA have been put to practical use through the field of genetic engineering. The Human Genome Project and the new field of proteomics have both benefited from continuing technical advances and have accelerated the development of new genetic technologies. Modern genetics is poised to radically change the practice of medicine and the biotechnology industry. Contributed By: Dennis Liu Microsoft ® Encarta ® 2009. © 1993-2008 Microsoft Corporation. All rights reserved.