THE LIVING WORLD

Unit Three. The Continuity of Life

 

11. DNA: The Genetic Material

 

11.5. Mutation

 

There are two general ways in which the genetic message is altered: mutation and recombination. A change in the content of the genetic message—the base sequence of one or more genes—is referred to as a mutation. As you learned in the previous section, DNA copies itself by forming complementary strands along single strands of DNA when they are separated. The template strand directs the formation of the new strand. However, this replication process is not foolproof. Sometimes errors are made and these are called mutations. Some mutations alter the identity of a particular nucleotide, while others remove or add nucleotides to a gene. A change in the position of a portion of the genetic message is referred to as recombination. Some recombination events move a gene to a different chromosome; others alter the location of only part of a gene. The cells of eukaryotes contain an enormous amount of DNA, and the mechanisms that protect and proofread the DNA are not perfect. If they were, no variation would be generated.

Mistakes Happen

In fact, cells do make mistakes during replication, as shown in figure 11.9. And mutations can also occur because of DNA alteration by chemicals, like those in cigarette smoke, or by radiation, like the ultraviolet light from the sun or tanning beds. However, mutations are rare. In humans, sequencing the genomes of an entire family has revealed that only about 60 out of the 3 billion nucleotides of the genome are altered by mutation each generation. If changes were common, the genetic instructions encoded in DNA would soon degrade into meaningless gibberish. Limited as it might seem, the steady trickle of change that does occur is the very stuff of evolution. Every difference in the genetic messages that specify different organisms arose as the result of genetic change.

 

 

Figure 11.9. Mutation.

Fruit flies normally have one pair of wings, extending from the thorax. This fly is a bithorax mutant. Because of a mutation in a gene regulating a critical stage of development, it possesses two thorax segments and thus two sets of wings.

Kinds of Mutation

The message that DNA carries in its genes is the “instructions” of how to make proteins. The sequence of nucleotides in a strand of DNA translates into the sequence of amino acids that makes up a protein. This process was introduced in section 10.5 on page 194 and will be described in more detail in chapter 12. If the core message in the DNA is altered through mutation, as shown by the substitution of T (in red) for G in figure 11.10, then the protein product can also be altered, sometimes to the point where it can no longer function properly. Because mutations can occur randomly in a cell’s DNA, most mutations are detrimental, just as making a random change in a computer program usually worsens performance. The consequences of a detrimental mutation may be minor or catastrophic, depending on the function of the altered gene.

 

 

Figure 11.10. Base substitution mutation.

(a) Some changes in a DNA sequence can result in a change in a single amino acid. (b) This results in a mutated protein that may not function the same as the normal protein.

 

Mutations in Germ-Line Tissues. The effect of a mutation depends critically on the identity of the cell in which the mutation occurs. During the embryonic development of all multicellular organisms, there comes a point when cells destined to form gametes (germ-line cells) are segregated from those that will form the other cells of the body (somatic cells). Only when a mutation occurs within a germ-line cell is it passed to subsequent generations as part of the hereditary endowment of the gametes derived from that cell. Mutations in germ-line

 

The Importance of Genetic Change

All evolution begins with alterations in the genetic message that create new alleles or alter the organization of genes on chromosome. Some changes in germ-line tissue produce alterations that enable an organism to leave more offspring, and those changes tend to be preserved as the genetic endowment of future generations. Other changes reduce the ability of an organism to leave offspring. Those changes tend to be lost, as the organisms that carry them contribute fewer members to future generations. Evolution can be viewed as the selection of particular combinations of alleles from a pool of alternatives. The rate of evolution is ultimately limited by the rate at which these alternatives are generated. Genetic change through mutation and recombination provides the raw material for evolution.

Genetic changes in somatic cells do not pass on to offspring, and so they have no direct evolutionary consequence. However, changes in the genes of somatic cells can have an important immediate impact if the gene affects development or is involved with regulation of cell proliferation.

 

Key Learning Outcome 11.5. Rare changes in genes, called mutations, can have significant effects on the individual when they occur in somatic tissue, but they are inherited only if they occur in germ-line tissue. Inherited changes provide the raw material for evolution.

 

Today’s Biology

DNA Fingerprinting

Only identical twins have exactly the same DNA sequence. All other people differ from one another at many sites. In 1985 British geneticist Alec Jeffreys took advantage of this to develop a new forensic (that is, crime scene investigation) tool, DNA fingerprinting. The procedure involves cleaving an individual's DNA into small bits, which are spread apart on a gel to yield a pattern of bands, a "DNA fingerprint” characteristic of that person. The photo on the right shows the DNA fingerprints a prosecuting attorney presented in a rape trial in 1987. They consisted of autoradiographs, parallel bars on X-ray film. Each bar represents the position of a DNA fragment produced by techniques that will be described in more detail in chapter 13. The dark lanes with many bars represent standardized controls. Two different ways of producing the DNA fragments are shown, each highlighting particular sequences. A sample had been taken from the victim within hours of her attack; from it semen was collected and the semen DNA analyzed for its patterns.

Compare the DNA fingerprint patterns of the semen to that of the suspect. You can see that the suspect's two patterns match that of the rapist, and these patterns are quite different from those of the victim. Clearly the semen collected from the rape victim and the blood sample from the suspect came from the same person. The suspect was Tommie Lee Andrews, and on November 6,

1987, the jury returned a verdict of guilty.

Since the Andrews verdict, DNA fingerprinting has been used as evidence in many court cases. DNA can be obtained at a crime scene from several different sources, such as small amounts of blood, hair, or semen. As the man who analyzed Andrews's DNA says: "It's like leaving your name, address, and social security number at the scene of the crime. It's that precise.”

While some ways of detecting DNA differences highlight profiles shared by many people, others are quite rare. Using several, identity can be clearly established or ruled out. The DNA profiles of O. J. Simpson and blood samples from the murder scene of his former wife from his highly publicized and controversial murder trial in 1995 are presented on the right.

DNA fingerprinting is certainly not restricted to prosecution. It can also be used to establish innocence. More than 120 convicted people have been freed in the last 14 years using DNA evidence presented by The Innocence Project lawyers, for example.

 

 

 

Of course, the procedures involved in creating the DNA fingerprints and in analyzing them must be carried out properly—sloppy procedures could lead to a wrongful conviction. After widely publicized instances of questionable lab procedures, national standards have been developed.

 

 

Tracing the DNA of Irish Kings

Every time a mutation occurs in germ-line DNA—the DNA producing egg or sperm—there is the possibility that it will be passed on to future generations. However, there are a lot of "ifs": if the DNA change is not corrected by the cell's error-detecting machinery; if that particular egg or sperm is used to make a child; if that child survives and has children. Still, despite all the "ifs," we humans have over the centuries accumulated lots of mutations in our DNA. "Our DNA is a history book," geneticists say.

With the molecular tools that modern genetics provides, scientists are beginning to read that book, to trace the course of our species's history by tracking the changes that have occurred in our DNA. The National Geographic Society, for example, has been conducting a Geno-graphic Project comparing over 100,000 DNA samples from people all over the world, from Arctic Inuit Eskimos and Kenya's Masai to Australian aborigines and North American Pueblo Indians. Their hope is to create a picture of ancestral migratory routes, the historical paths people have taken as they populated the globe.

To gain the clearest possible picture of the past, gene researchers focus on DNA of the Y chromosome and the mitochondria. The Y chromosome of males does not recombine with other chromosomes. This has the effect of keeping mutations together once they occur. Similarly, the mitochondrial DNA of females is passed down from mother to child without recombination (sperm contribute no mitochondria to the fertilized egg).

To compare large numbers of DNA samples, it is not practical to sequence the entire Y chromosome or mitochondrial DNA of each individual. Instead, investigators monitor several dozen highly variable DNA locations, short bits of the chromosome within which lots of mutations have occurred. Because DNA mutations are rare events and there has been no recombination to shuffle the changes, when the same particular combination of mutations (what gene researchers call a haplotype) occurs in two people, they almost certainly are related, having inherited their Y chromosome or mitochondrial DNA from a common ancestor. Looking at many individuals in this way, investigators can build up a picture of who is related to whom—a portrait of the past, inscribed on our genes.

 

 

To see how this works, consider a study carried out in 2006 by Daniel Bradley and colleagues at Trinity College in Dublin, Ireland. They set out to apply DNA studies to Irish history, which has always been a bit of a muddle. Writing did not become common in Ireland until 600 a.d., and little is known for sure of earlier events in Irish history. This has not, of course, prevented the Irish from preserving a rich story of those times.

Much as the British tell of a mythical King Arthur who few historians believe was a real person, so the Irish recount the tale of an Irish high king of the fifth century a.d. from whom an alarming number of Irishmen claim descent. Niall Noigiallach—Niall of the Nine Hostages—was so named because early in his reign he consolidated his power by taking hostages from the royal families of each of the five provinces that then constituted Ireland, as well as from Scotland, the Saxons, the Britons, and the Franks.

He founded a dynasty, the Ui Neill ("the descendants of Niall"), which ruled the northwest of Ireland from about 600 to 900 a.d. When the Irish took surnames around 1000 a.d., some chose names associated with the Ui Neill dynasties, names like Gallagher, Boyle, Doherty, O'Conner, Reilly, Flynn, Devlin, Donnelly, McLoughlin, Molloy, O'Rourke, and of course O'Neill (the prefix "O" is often added).

Did Niall of the Nine Hostages really exist? The DNA evidence gathered by Bradley argues yes. Some 20% of men in northwest Ireland have a distinctive genetic signature on their Y chromosomes, a haplotype carried down for over a thousand years. As you can see on the map to the left, this signature haplotype predominates in the northwest, the seat of Ui Neill power.

Indeed, wherever in the world you look (the Irish were particularly adept at migrating—over 400,000 residents of New York City claim Irish ancestry), this haplotype is much more common among Irishmen with the Ui Neill surnames than among Irishmen as a whole.

Niall is said to have had 14 sons, a large number even for those days, which might go a long way towards explaining that some 2 million men worldwide now carry his distinctive Y chromosome. Like Genghis Khan, ancestor of 16 million men in Asia, Niall of the Nine Hostages seems to have left quite a genetic footprint.

Percent of men carrying what is thought to be the distinctive genetic signature of King Niall of the Nine Hostages tissue are of enormous biological importance because they provide the raw material from which natural selection produces evolutionary change.

Mutations in Somatic Tissues. Change can occur only if there are new, different allele combinations available to replace the old. Mutation produces new alleles, and recombination puts the alleles together in different combinations. In animals, it is the occurrence of these two processes in germline tissue that is important to evolution because mutations in somatic cells (somatic mutations) are not passed from one generation to the next. However, a somatic mutation may have drastic effects on the individual organism in which it occurs, because it is passed on to all of the cells that are descended from the original mutant cell. Thus, if a mutant lung cell divides, all cells derived from it will carry the mutation. Somatic mutations of lung cells are, as we shall see, the principal cause of lung cancer in humans.

Altering the Sequence of DNA. One category of mutational changes affects the message itself, producing alterations in the sequence of DNA nucleotides (table 11.1). If alterations involve only one or a few base pairs in the coding sequence, they are called point mutations. Sometimes the identity of a base changes (base substitution), while other times one or a few bases are added (insertion) or lost (deletion). If an insertion or deletion throws the reading of the gene message out of register, a frame-shift mutation results. Figure 11.10 shows a base substitution mutation that results in the change of an amino acid, from proline to threonine. This could be a minor change or catastrophic. However, suppose that this had been the deletion of a nucleotide, that the cytosine base nucleotide had been skipped during replication. This would shift the register of the DNA message (imagine removing the w from this sentence, yielding “This oulds hiftt her egistero fth eDN Amessag”) and you can see the problem. Many point mutations result from damage to the DNA caused by mutagens, usually radiation or chemicals. The latter class of mutations is of particular importance because modern industrial societies often release many chemical mutagens into the environment.

 

TABLE 11.1. SOME CATEGORIES OF MUTATION

 

 

 

Changes in Gene Position. Another category of mutations affects the way the genetic message is organized. In both prokaryotes and eukaryotes, individual genes may move from one place in the genome to another by transposition (see also page 259). When a particular gene moves to a different location, its expression or the expression of neighboring genes may be altered. In addition, large segments of chromosomes in eukaryotes may change their relative locations or undergo duplication. Such chromosomal rearrangements often have drastic effects on the expression of the genetic message.

Biology and Staying Healthy

Protecting Your Genes

This text's discussion of changes in genes—mutations—has largely focused on heredity, how changes in the information encoded in DNA can affect offspring. It is important, however, to realize that inherited mutations occur only in germ-line tissue, in the cells that generate your eggs or sperm. Mutations in the other cells of your body, in so-called somatic tissues, are not inherited. This does not, however, mean that such mutations are not important. In fact, somatic mutations can have a disastrous impact upon your health because they can lead to cancer. Protecting the DNA of your body's cells from damaging mutation is perhaps the most important thing you can do to prolong your life. Here we will examine two potential threats.

 

 

Smoking and Lung Cancer

The association of particular chemicals in cigarette smoke with lung cancer, particularly chemicals that are potent mutagens (see chapters 8 and 24), led researchers early on to suspect that lung cancer might be caused, at least in part, by the action of chemicals on the cells lining the lung.

The hypothesis that chemicals in tobacco cause cancer was first advanced over 200 years ago in 1761 by Dr. John Hill, an English physician. Hill noted unusual tumors of the nose in heavy snuff users and suggested tobacco had produced these cancers. In 1775, a London surgeon, Sir Percivall Pott, made a similar observation, noting that men who had been chimney sweeps exhibited frequent cancer of the scrotum. He suggested that soot and tars might be responsible. These observations led to the hypothesis that lung cancer results from the action of tars and other chemicals in tobacco smoke.

It was over a century before this hypothesis was directly tested. In 1915, Japanese doctor Katsusaburo Yamagiwa applied extracts of tar to the skin of 137 rabbits every two or three days for three months. Then he waited to see what would happen. After a year, cancers appeared at the site of application in seven of the rabbits. Yamagiwa had induced cancer with the tar, the first direct demonstration of chemical carcinogenesis. In the decades that followed, this approach demonstrated that many chemicals can cause cancer.

But do these lab studies apply to people? Do tars in cigarette smoke in fact induce lung cancer in humans? In 1949, the American physician Ernst Winder and the British epidemiologist Richard Doll independently reported that lung cancer showed a strong link to the smoking of cigarettes, which introduces tars into the lungs. Winder interviewed 684 lung cancer patients and 600 normal controls, asking whether each had ever smoked. Cancer rates were 40 times higher in heavy smokers than in nonsmokers. From these studies, it seemed likely as long as 50 years ago that tars and other chemicals in cigarette smoke induce cancer in the lungs of persistent smokers. While this suggestion was resisted by the tobacco industry, the evidence that has accumulated since these pioneering studies makes a clear case, and there is no longer any real doubt. Chemicals in cigarette smoke cause cancer.

As you will learn in chapter 24 (page 525), tars and other chemicals in cigarette smoke cause lung cancer by mutating DNA, disabling genes that in normal lung cells restrain cell division. Lacking these restraints, the altered lung cells begin to divide ceaselessly, and lung cancer results. Just under 160,000 Americans died of lung cancer last year, and almost all of them were cigarette smokers.

If cigarette smoking is so dangerous, why do so many Americans smoke? Fully 23% of American men smoke, and 18% of women. Are they not aware of the danger? Of course they are. But they are not able to quit. Tobacco smoke, you see, also contains another chemical, nicotine, which is highly addictive. The nature of the addiction is discussed in detail in chapter 28 (page 592). Basically, what happens is that a smoker's brain makes physiological compensations to overcome the effects of nicotine, and once these adjustments are made the brain does not function normally without nicotine. The body's physiological response to nicotine is profound and unavoidable; there is no way to prevent addiction to nicotine with willpower.

Many people attempting to quit smoking use patches containing nicotine to help them, the idea being that providing nicotine removes the craving for cigarettes. This is true, it does—as long as you keep using the patch. Actually, using such patches simply substitutes one (admittedly less dangerous) nicotine source for another. If you are going to quit smoking, there is no way to avoid the necessity of eliminating the drug to which you are addicted, nicotine. There is no easy way out. The only way to quit is to quit.

Clearly, if you do not smoke, you should not start. Asked what three things were most important to improve Americans' health, a prominent physician replied: "Don't smoke. Don't smoke. Don't smoke.”

 

Tanning and Skin Cancer

Almost all cells in the human body undergo cell division, replacing themselves as they wear out. Some adult cells do this quite frequently, others rarely if ever. Skin cells divide quite frequently. Exposed to a lot of wear-and-tear, they divide about every 27 days to replace dead or damaged cells. The skin sloughs off dead cells from the surface and replaces these with new cells from beneath. The average person will lose about 105 pounds of skin by the time he or she turns 70.

While skin can be damaged in many ways, the damage that seems to have the most long-term affect is caused by the sun. The skin contains cells called melanocytes that produce a pigment called melanin when exposed to UV light. Melanin produces a yellow to brown color in the skin. The type of melanin and the amount produced is genetically determined. People with darker skin types have more melanocytes and produce a melanin that is dark brown in color. Protected by UV- absorbing melanin, they almost never burn. Fair-skinned people have fewer melanocytes and produce melanin that is more yellow in color. Unprotected by melanin, these people sunburn easily and rarely tan. When cells on the body's surface are badly damaged by the sun—what we call a sunburn, the cells slough off. Recall the peeling that you experienced if you have ever had a bad sunburn.

Up until the early 20th century, a tan was a condition that people went to great lengths to avoid. A tanned body was a sign of the working class, people who had to work in the sun. The wealthy elite avoided the sun with pale skin being in fashion. All of this changed in the 1920s, when tans became a status symbol, with the wealthy able to travel to warm, sunny destinations, even in the middle of winter. That tan, bronzed glow that people would sit in the sun for hours to achieve was thought to be both healthy and attractive.

During the 1970s, doctors started to see an uptick in the number of cases of melanoma, a deadly form of skin cancer. New cases were increasing about 6% each year. Researchers proposed that UV rays from the sun were the underlying cause of this epidemic of skin cancer and warned people to avoid the sun when possible and protect themselves with sunscreen.

Malignant melanoma is the most deadly of skin cancers, although treatable if caught early. Melanoma is cancer of melanocyte cells. Melanoma lesions usually appear as shades of tan, brown, and black and often begin in or near a mole, and so changes in a mole are a symptom of melanoma. Melanoma is most prevalent in fair-skinned people, but unlike the other forms of skin cancer, it can also affect people with darker complexions.

The public has been slow to respond to warnings about avoiding sun exposure, perhaps because the cosmetic benefits of tanning are immediate while the health hazards are much delayed. The desire to achieve that tanned, bronzed body is as strong as ever.

A good tan requires regular exposure to the sun to maintain it, so indoor tanning salons have become popular. Tanning booths emit concentrated UV rays from two sides, allowing a person to tan in less time and in all weather conditions (sun, rain, snow). The indoor tanning business has grown in the United States to a $2 billion-a-year industry with an estimated 28 million Americans tanning annually.

People thought that building up a tan through the use of tanning booths would protect a person's skin from burning and would reduce the time exposed to the UV radiation, both leading to a reduced risk of skin cancer. However, recent research does not support these assumptions. A 2003 study of 106,000 Scandinavian women showed that exposure to UV rays in a tanning booth as little as once a month can increase your risk of melanoma by 55%, especially when the exposure is during early adulthood. Those women who were in their 20s and used sun lamps to tan were at the highest risk, about 150% higher than those who didn't use a tanning bed. As with other studies, fair-skinned women were at the greatest risk. In fact, tanning booths, even for those people who tan more easily, heighten the risk for skin cancer because people use the tanning booths year-round, increasing their cumulative exposure.

It is difficult to avoid the conclusion that to protect your genes you should avoid tanning booths. Like smoking cigarettes, excessive tanning is gambling with your life.

 

 

Inquiry & Analysis

Are Mutations Random or Directed by the Environment?

Once biologists appreciated that Mendelian traits were in fact alternative versions of DNA sequences that resulted from mutations, a very important question arose and needed to be answered—are mutations random events that might happen anywhere on the DNA in a chromosome, or are they directed to some degree by the environment? Do the mutagens in cigarettes, for example, damage DNA at random locations, or do they preferentially seek out and alter specific sites such as those regulating the cell cycle?

This key question was addressed and answered in an elegant, deceptively simple experiment carried out in 1943 by two of the pioneers of molecular genetics, Salvadore Luria and Max Delbruck. They chose to examine a particular mutation that occurs in laboratory strains of the bacterium E. coli. These bacterial cells are susceptible to T1 viruses, tiny chemical parasites that infect, multiply within, and kill the bacteria. If 105 bacterial cells are exposed to 1010 T1 viruses, and the mixture spread on a culture dish, not one cell grows—every single E. coli cell is infected and killed. However, if you repeat the experiment using 109 bacterial cells, lots of cells survive!

When tested, these surviving cells prove to be mutants, resistant to T1 infection. The question is, did the T1 virus cause the mutations, or were they present all along, too rare to be present in a sample of only 105 cells but common enough to be present in 109 cells?

To answer this question, Luria and Delbruck devised a simple experiment they called a "fluctuation test,” illustrated here. Five cell generations are shown for each of four independent bacterial cultures, all tested for resistance in the fifth generation. If the T1 virus causes the mutations (top row), then each culture will have more or less the same number of resistant cells, with only a little fluctuation (that is, variation among the four). If, on the other hand, mutations are spontaneous and so equally likely to occur in any generation, then bacterial cultures in which the T1-resistance mutation occurs in earlier generations will possess far more resistant cells by the fifth generation than cultures in which the mutation occurs in later generations, resulting in wide fluctuation among the four cultures. The table presents the data they obtained for 20 individual cultures.

 

 

 

1. Applying Concepts. Is there a dependent variable in this experiment? Explain.

2. Interpreting Data. What is the mean number of T1-resistant colonies found in the 20 individual cultures?

3. Making inferences

a. Comparing the 20 individual cultures, do the cultures exhibit similar numbers of T1-resistant bacterial cells?

b. Which of the two alternative outcomes illustrated above, (a) or (b), is more similar to the outcome obtained by Luria and Delbruck in this experiment?

4. Drawing Conclusions Are these data consistent with the hypothesis that the mutation for T1 resistance among E. coli bacteria is caused by exposure to T1 virus? Explain.

 

 

Test Your Understanding

1. In his experiments, Frederick Griffith found that

a. hereditary information within a cell cannot be changed.

b. hereditary information can be added to cells from other cells.

c. mice infected with live R strains die.

d. mice infected with heat-killed S strains die.

2. The experiment performed by Alfred Hershey and Martha Chase showed that the molecule viruses use to specify new viruses is

a. a protein.

b. a carbohydrate.

c. ATP.

d. DNA.

3. Erwin Chargaff, Rosalind Franklin, Francis Crick, and James Watson all worked on pieces of information relating to the

a. structure of DNA.

b. function of DNA.

c. inheritance of DNA.

d. mutations of DNA.

4. The four DNA nucleotides are all different in terms of

a. their sizes.

b. the number of hydrogen bonds they can form with their base pair.

c. the type of nitrogen base.

d. the type of sugar.

5. Which of the following lists the purine nucleotide bases?

a. adenine and cytosine

b. guanine and thymine

c. cytosine and thymine

d. adenine and guanine

6. If one strand of a DNA molecule has the base sequence ATTGCAT, its complementary strand will have the sequence

a. ATTGCAT.

b. TAACGTA.

c. GCCATGC.

d. CGGTACG.

7. Regarding the duplication of DNA, we now know that each double helix

a. rejoins after replicating.

b. splits down the middle into two single strands, and each one then acts as a template to build its complement.

c. fragments into small chunks that duplicate and reassemble.

d. All of these are true for different types of DNA.

8. DNA polymerase can only add nucleotides to an existing chain, so ____ is required.

a. a primer

b. helicase

c. a lagging strand

d. a leading strand

9. Genetic messages can be altered in two ways:

a. through semiconservative replication or conservative replication.

b. through the chromosome or through the protein.

c. by mutation or by recombination.

d. by activation or by repression.

10. Mutations can occur in

a. germ-line tissues and are passed on to future generations.

b. somatic tissues and are passed on to future generations.

c. germ-line tissues but not in somatic tissues.

d. somatic tissues but not in germ-line tissues.