Written Assignment 2

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Can a gene be cruel? Consider this candidate: in humans, there is a gene for an enzyme called FMO3 (flavin-containing mono-oxygenase-3), which breaks down a chemical in our bodies that smells like rotting fish. Some unfortunate individuals inherit a defective FMO3 gene and can’t break down the noxious chemical. Instead, their urine, sweat, and breath excrete it, causing them to smell like rotting fish. Worst of all, because the odor comes from within their bodies, they cannot wash it away. Called “fish odor syndrome,” this disorder often causes those afflicted by it to suffer ridicule, social isolation, and depression. Currently, there is no cure for the rare disorder, although there are a few ways of reducing the odor such as reducing consumption of eggs, fish, and some meats that contain certain chemicals, including sulfur. For individuals born with this malady, beyond their own suffering there looms a scary question: “Will I pass this condition on to my children?” They might also wonder how they came to have the disorder, particularly if neither of their parents suffered from it (Figure 9-1). To address this concern, let’s recall from Chapter 8 that sexually reproducing organisms carry two copies of every chromosome in every cell (except their sex cells). Humans, for example, have 23 pairs of chromosomes (46 individual chromosomes). At each location—referred to as a locus—on the two chromosomes of a pair is the same gene: one copy from the mother and one from the father. As we noted in Chapter 6, each of the two copies of the gene is called an allele.

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The gene for FMO3 is on chromosome 1. There is a normal version—or allele—of the gene for FMO3, which most people carry, and there is a rare, defective version that is responsible for fish odor syndrome. As long as a person has at least one normal version of the FMO3 gene, he or she will produce enough of the enzyme to break down the fishy chemical. But if a person inherits two copies of the defective version of the fish odor gene, one from each parent, that person will inherit the disorder (Figure 9-2). Although individuals with fish odor syndrome will pass on one set of the bad instructions in every sperm or egg cell that they make, their children won’t necessarily inherit the disease. As long as the other parent supplies a normal version of the FMO3 gene, the child will not have fish odor syndrome. The unaffected children, though, will carry a silent copy of the fish odor allele. If they have children, the fish odor trait will be expressed only if it comes together with a defective FMO3 allele from another person. In this way, some alleles can exist in a population without always revealing themselves. Inheritance follows some simple rules that allow us to make sense of patterns of family resemblance, such as facial features or hair texture, and even to predict the likelihood that an offspring will inherit a particular trait (Figure 9-3). We’ll also examine why the behavior of some traits is easy to predict while many other traits have less straightforward patterns of inheritance.

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Like mother, like daughter. No one will ever seek a genetic test to prove that Zoe Kravitz is the daughter of Lisa Bonet (Figure 9-4).. We see all around us that offspring generally resemble their parents more than they resemble other random individuals in the population—a consequence of the passing of characteristics from parents to offspring through their genes. This is heredity.

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Observing heredity is easy. Elucidating how it works is not. For thousands of years before the mechanisms of heredity were discovered and understood, plant and animal breeders understood that there is a connection from parents to offspring across generations. In ancient Greece, for example, the poet Homer extolled the tremendous benefits to society that came from the skillful breeding of horses. Once breeders recognized the existence of heredity, they began selecting individual plants or animals with the desired traits to breed with each other, in the hope that the offspring would also have those desirable traits. Since then, it has been possible to create a rich world of sweeter corn, loyal dogs, docile livestock, beautiful flowers, and more. Practical successes were many, but people didn’t understand exactly how the outcomes were achieved. Patterns of similarity among related individuals are impossible to make sense of without an understanding of how heredity works. This understanding is the province of the field of genetics.

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Mechanisms of heredity become a bit easier to grasp when we focus on visible traits with well- established inheritance patterns. Coat color and fur length in cats fits this bill well. Virtually every short-haired cat, for instance, has at least one short-haired parent. And virtually every completely white-haired cat has at least one white-haired parent. In humans, many genetic diseases have similarly simple patterns of Inheritance. The neurodegenerative disorder known as Huntington’s disease, for example, follows such a pattern: individuals who develop the disease have a parent who developed the disease. Traits that are determined by the instructions a person carries on one gene are called single-gene traits (Figure 9-6). It is important to note here that most human characteristics are influenced by multiple genes as well as by the environment. However, because the mechanism by which single-gene traits pass from parent to child is the easiest pattern of inheritance to decipher, we first explore this process. Then we’ll expand our model of heritability to account for the passing on of more complex traits.

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What do parents “give” their offspring that confers similarity? In other words, how is it that a physical entity is inherited and how is it passed from parent to offspring? In the mid-1800s, Gregor Mendel, a monk living in what is now the Czech Republic, was the first to make headway in answering this question. Mendel conducted studies that not only shed light on the question but practically answered it completely. When Mendel turned to questions about heredity, there were no obvious answers. A popular idea from the late 1600s suggested that an entire pre-made human—albeit a tiny one—was contained in every sperm cell. Though imaginative, this idea failed to explain why children resemble both their mothers and their fathers, not just their fathers. A “blended blood” idea suggested that traits are blended in the blood of parents and imparted to offspring. But how, then, could brown-eyed parents give birth to blue-eyed children? Three features of Mendel’s research were critical to its success. 1) First, he chose a good organism to study: the garden pea. His goals were to understand inheritance in all organisms, not just plants. But cats and dogs or even mice would have been too hard to take care of in the large numbers he required—thousands and thousands of individuals. Humans, too, would have made a terrible study organism. We take too long to breed (and won’t produce offspring on command). Pea plants, on the other hand, are relatively easy to fertilize manually by “pollen dusting.” A single cross—the process in which male pollen (carrying sperm) is used to fertilize eggs— produces numerous offspring. In addition, pea plants reproduce quickly, so Mendel could conduct experiments that included multiple generations. 2) A second feature of Mendel’s research was that he chose to focus on easily categorized traits like shape and color. For instance, shape: all peas of the variety that Mendel studied are either round or wrinkled, with nothing in between. In addition, all peas are either yellow or green, never anything intermediate. In all, Mendel looked at seven different traits, but for each trait, only two variants ever appeared, so he and his research assistants could easily observe and unambiguously identify them. 3) A third critical feature of Mendel’s approach was that he began his studies by first repeatedly breeding together similar plants, until he had numerous distinct populations, each of which was unvarying for a particular trait. He described these plants as true-breeding for that trait because they always produced offspring with the same variant of the trait as the parents. True-breeding round-pea plants always produced round peas when they were crossed together. True-breeding purple-flowered pea plants always produced purple-flowered offspring, while true-breeding white-flowered pea plants always produced white-flowered offspring. It was a lot of prep work to establish these populations. But once he had them, he was in a position to set up all of the different crosses that enabled him to piece together the genetics puzzle. Mendel began a straightforward process of experimentation with his groups of true-breeding plants. He crossed plants with different traits and observed large numbers of their offspring. For example, he crossed plants with green peas and plants with yellow peas and counted the number of offspring plants that produced green peas and the number that produced yellow peas. (This cross, written as “green × yellow cross,” always resulted in plants that produced only yellow peas.) Mendel devised a hypothesis that would explain his observations and generate predictions about the outcomes of further crosses. Then he conducted those crosses to see whether the predictions generated by his hypothesis were borne out.

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Mendel was motivated by one odd and recurring result. Sometimes traits that weren’t present in either parent pea plant would show up in their offspring—just as brown-eyed parents can have blue-eyed children. When plants with purple flowers (those not in his true-breeding group) were fertilized by pollen from other plants with purple flowers, they produced mostly purple-flowered offspring, but sometimes they produced plants with white flowers. How was it possible to produce white flowers from a purple × purple cross? Where did the whiteness come from? Here’s where Mendel’s meticulous and methodical experiments paid off. First, he started with some true-breeding white-flowered plants. Then he got some true- breeding purple-flowered plants. He wondered: which color wins out when a white-flowered plant is crossed with a purple-flowered plant? The answer was definitive: purple wins (Figure 9-8). All of the offspring from these crosses were purple, every time. For this reason, Mendel called the purple-flower trait dominant, and he considered the white-flower trait to be the recessive trait. In general, a dominant trait masks the effect of a recessive trait when an individual carries both the dominant and the recessive versions of the instructions for the trait. Things got a bit more interesting when Mendel took the purple-flowered plants that came from the cross between true-breeding purple- and white-flowered plants and bred these purple offspring with each other. He found that these mixed-parentage plants were no longer true- breeding. Occasionally, they would produce white-flowered offspring. Apparently, the directions for building white flowers—last seen in one of their grandparents— were still lurking inside their purple-flowered parent plants. The existence of traits that could disappear for a generation and then show up again was perplexing.

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Mendel devised a simple hypothesis to explain this pat- tern of inheritance. It incorporated three ideas that helped him (and now help us) make predictions about crosses. 1. Rather than passing on the trait itself, each parent puts into every sperm or egg it makes a single set of instructions for building the trait. Today, we call that instruction set a gene. 2. Offspring receive two copies of the instructions for any trait. Often, both sets of instructions are identical, and the offspring produce the trait according to those instructions. Other times, though, each parent contributes a slightly different set of instructions—that is, a different allele—for that trait. So, for example, pea plants have two alleles for flower color: a purple-flower allele and a white-flower allele. Parents pass on the same gene (flower-color gene) but may contribute different alleles (purple or white). 3. The trait observed in an individual depends on the two copies of the gene it inherits from its parents. When an individual inherits the same two alleles for this gene, the individual’s genotype for that gene is said to be homozygous and the individual shows the trait specified by the instructions embodied in those alleles. When an individual inherits a different allele from each parent, the individual’s genotype for that gene is said to be heterozygous. Dominant and recessive alleles are defined by their action when they are in the heterozygous state. A dominant allele and is said to “mask” the effect of the other allele, which is called the recessive allele. Note that this is the sole defining feature of “dominant” and “recessive.” Describing an allele as dominant does not mean that it is more advantageous or more common than a recessive allele.

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When an individual reproduces, it contributes just one of its two copies of a gene to its offspring. The other parent contributes the other allele. So, when sperm and eggs are made, each sex cell gets only one copy of a gene—as opposed to the two copies present in every other cell in the body. For a male who is heterozygous for a particular gene, for example, it means that half of the sperm he produces will have one of the alleles and half will have the other. The idea that, of the two copies of each gene everyone carries, only one of the two alleles gets put into each gamete is so important that it is called Mendel’s law of segregation.

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Things are not always as they appear. Take skin coloration for example. Humans and many other mammals have a gene that contains the information for producing melanin, one of the chemicals responsible for giving our skin its coloring (Figure 9-10). This gene is one of many that influence skin color. Unfortunately, there is also a defective, non-functioning version of the melanin gene that is passed along through some families. An individual who inherits two copies of the defective version of the gene cannot produce pigment and has a condition known as albinism, a disorder characterized by little or no pigment in the eyes, hair, and skin. It is impossible to tell whether a normally pigmented individual carries one of the defective alleles just by looking—one would need to do a genetic analysis to discover this information. The outward appearance of an individual, such as skin pigment, is called its phenotype. A phenotype includes features visible to the naked eye, such as flashy coloration, height, or the presence of antlers. A phenotype also includes less easily visible characteristics such as the chemicals an individual produces to clot blood or digest lactose. An individual’s phenotype even includes the behaviors it exhibits. Underlying the phenotype is the genotype. This is an organism’s genetic composition. We usually speak of an individual’s genotype in reference to a particular trait. For example, an individual’s genotype might be described as “homozygous for the recessive allele for albinism.” Another individual’s genotype for the melanin gene might be described as “heterozygous.” Occasionally, the word genotype is also used as a way of referring to all of the genes that the individual carries.

When an organism exhibits a recessive trait, such as albinism, we know with certainty what its genotype is for the melanin gene. When it shows the dominant trait, on the other hand, it’s not possible to discern the genotype from the individual’s appearance. We can trace the possible outcomes of a cross between two individuals using a handy tool called the Punnett square. To see how this works, let’s investigate the cross of an albino giraffe with a normally pigmented giraffe. First, we assign symbols to represent the different variants of a gene. Generally, we use an uppercase letter for the dominant allele and lowercase letter for the recessive allele. In the case of pigmentation/albinism, we use the letter “m” for production of the pigment melanin: M for the dominant allele and m for the recessive allele. We represent the genotype of the albino giraffe as mm, because that individual must carry two copies of the recessive allele. The pigmented giraffe must have the genotype MM or Mm. If we don’t know which of the two possible genotypes the pigmented individual has, we can write M_ , where _ is a placeholder for the unknown second allele. In Figure 9-11 we illustrate the cross between a true-breeding pigmented individual, MM, and an albino, mm. Along the top of the Punnett square we list, individually, the two alleles that one of the parents produces, and along the left side of the square we list the two alleles that the other parent produces. We split up an individual’s two alleles in this way because only one of the alleles is contained in each sperm or egg cell that it produces. The two gametes that come together at fertilization produce the genotype of the offspring. In the four cells of the Punnett square, we enter the genotypes of all the possible offspring resulting from our cross. Each cell contains one allele given at the head of the column and one allele at the left of the row. In Cross 1 illustrated in Figure 9-11, every possible offspring would be heterozygous and would be normally pigmented, because all offspring receive a dominant allele from the pigmented parent and a recessive allele from the albino parent. In the second half of Figure 9-11 (Cross 2), we trace the cross between two heterozygous individuals. Note that each parent produces two kinds of gametes, one with the dominant allele and one with the recessive allele. This cross has three possible outcomes: one-quarter of the time the offspring will be homozygous dominant (MM), one-quarter of the time the offspring will be homozygous recessive (mm), and the remaining half of the time the offspring will be heterozygous (Mm). Phenotypically, three-quarters of the offspring will be normally pigmented (MM or Mm) and one-quarter will be albino (mm).

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