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  • 1. Introduction to Genetics This wonderful activity developed from: Students will: 1. Use genotype to produce phenotype on the organism “marshmallow bug” that has two pair of chromosomes, with a total of 10 genes 2. The marshmallow bug chromosomes will undergo meiosis, and the new genetic material will produce the next generation of offspring 3. The chromosomes will crossover. 4. The chromosomes will randomly assort. 5. Students will examine the frequency of the genotypes of the above genes through the use of a Punnett square. 6. Students will calculate the total number of genotypic combinations possible in this 10-gene system. 7. Students will calculate the total number of phenotypic combinations possible in this same 10-gene system. Benchmarks (these old standards have been superceded by the standards adopted in 2009. When completing your lab report, please apply those given you with your syllabus: Life Science CCG Organisms: Understand the characteristics, structure, and functions of organisms. SC.03.LS.01 Recognize characteristics that are similar and different between organisms. SC.05.LS.01 Group or classify organisms based on a variety of characteristics. SC.05.LS.01.01 Classify a variety of living things into groups using various characteristics. CCG Heredity: Understand the transmission of traits in living things. SC.03.LS.03 Describe how related plants and animals have similar characteristics. SC.05.LS.04 Describe the life cycle of an organism. SC.05.LS.04.01 Describe the life cycle of common organisms. SC.05.LS.04.02 Recognize that organisms are produced by living organisms of similar kind, and do not appear spontaneously from inanimate materials. SC.08.LS.03 Describe how the traits of an organism are passed from generation to generation. SC.08.LS.03.01 Distinguish between asexual and sexual reproduction. 1
  • 2. SC.08.LS.03.02 Identify traits inherited through genes and those resulting from interactions with the environment. SC.08.LS.03.03 Use simple laws of probability to predict patterns of heredity with the use of Punnett squares. CCG Diversity/Interdependence: Understand the relationships among living things and between living things and their environments. SC.08.LS.05 Describe and explain the theory of natural selection as a mechanism for evolution. SC.08.LS.05.01 Identify and explain how random variations in species can be preserved through natural selection. Mathematics Calculations and Estimations CCG: Numbers: Understand numbers, ways of representing numbers, relationships among numbers, and number systems. MA.03.CE.04 Order, model, compare, and identify commonly used fractions (halves, thirds, fourths, eighths, tenths) using concrete models and visual representations. MA.03.CE.05 Develop understanding of fractions as parts of unit wholes, as parts of a collection, as locations on number lines, and as divisions of whole numbers. MA.04.CE.01 Read, write, order, model, and compare whole numbers to one million, common fractions, and decimals to hundredths. MA.04.CE.03 Locate common fractions and decimals on a number line. MA.05.CE.01 Order, model, and compare common fractions, decimals and percentages. MA.05.CE.03 Model, recognize, and generate equivalent forms of commonly used fractions, decimals, and percents. MA.06.CE.01 Order, model, and compare positive rational numbers (fractions, decimals, and percentages). MA.06.CE.03 Understand rates and ratios as comparisons of two quantities by division. MA.06.CE.04 Differentiate between rates and ratios and express both as fractions. MA.06.CE.05 Solve problems by calculating rates and ratios. MA.06.CE.09 Model square numbers and recognize their characteristics. MA.07.CE.03 Use rates, ratios, and percents to solve problems. MA.08.CE.02 Apply proportions to solve problems. CCG: Computation and Estimation: Compute fluently and make reasonable estimates. MA.03.CE.15 Identify the operation (add, subtract, multiply, or divide) for solving a problem. 2
  • 3. MA.03.CE.16 Develop and use strategies (overestimate, underestimate, range of estimates) to make reasonable estimates. MA.03.CE.17 Recognize which place value will be the most helpful in estimating an answer. MA.04.CE.14 Identify the most efficient operation (add, subtract, multiply, or divide) for solving a problem. MA.04.CE.15 Select and use an appropriate estimation strategy (overestimate, underestimate, range of estimates) based on the problem situation when computing with whole numbers or money amounts. MA.05.CE.13 Select and use an appropriate estimation strategy (overestimate, underestimate, range of estimates) based on the problem situation when computing with decimals. MA.06.CE.15 Solve problems involving common percentages. MA.06.CE.16 Convert mentally among common decimals, fractions and percentages. MA.06.CE.18 Develop and use strategies to estimate the results of positive rational number computations and judge the reasonableness of results. MA.07.CE.13 Develop and use strategies to estimate the results of integer computations and judge the reasonableness of results. MA.08.CE.07 Develop and use strategies to estimate the results of rational number computations and judge the reasonableness of results. Statistics and Probability CCG: Probability: Understand and apply basic concepts of probability. MA.04.SP.02 Determine probability of a single event. MA.04.SP.03 Understand that the probability of an event can be represented by a number from 0 (impossible) to 1 (certain). MA.05.SP.02 Connect simple fractional probabilities to events (e.g., heads is 1 out of 2; rolling a 5 on a six-sided number cube is 1/6). MA.06.SP.02 Determine experimental probability of an event from a set of data. MA.06.SP.03 Express probability using fractions, ratios, decimals and percents. MA.06.SP.04 Understand that probability cannot determine an individual outcome, but can be used to predict the frequency of an outcome. MA.06.SP.05 Determine the number of possible combinations of two or more classes of objects (e.g., shirts, pants and shoes). 3
  • 4. MA.07.SP.02 Compute experimental probabilities from a set of data and theoretical probabilities for single and simple compound events, using various methods (e.g., organized lists, tree diagrams, area models). MA.07.SP.03 Determine probabilities of simple independent and dependent events. MA.07.SP.04 Compare experimental probability of an event with the theoretical probability and explain any difference. MA.07.SP.05 Determine all possible outcomes of a particular event or all possible arrangements of objects in a given set by applying various methods including tree diagrams and systematic lists. MA.08.SP.03 Understand and use appropriate terminology to describe complementary and mutually exclusive events and determine their probabilities. MA.08.SP.04 Apply theoretical probability to determine if an event or game is fair or unfair and pose and evaluate modifications to change the fairness. CCG: Collect and Display Data: Formulate questions that can be addressed with data and collect, organize, and display relevant data to answer them. MA.03.SP.02 Ask and answer simple questions that can be answered by collecting, organizing and displaying data. MA.03.SP.03 Represent and interpret data using tally charts, pictographs, and bar graphs, including identifying the mode and range. MA.04.SP.04 Conduct experiments and simulations to determine experimental probability of different outcomes. MA.04.SP.05 Represent and interpret data collected from probability experiments and simulations using tallies, charts, pictograms, and bar graphs, including determining probabilities of single events. MA.05.SP.03 Design investigations to address a question and recognize how data collection methods affect the nature of a set of data. MA.05.SP.04 Understand basic concepts of sampling (e.g., larger samples yield better results, the need for representative samples). MA.05.SP.05 Represent and interpret data using tables, circle graphs, bar graphs, and line graphs or plots (first quadrant). MA.05.SP.06 Compare different representations of the same data and evaluate how well each representation shows important aspects of the data (e.g., circle and bar graphs, histograms with different widths). MA.05.SP.07 Evaluate the appropriateness of representations of categorical and numeric data (e.g., categorical: types of 4
  • 5. lunch food; and numerical: heights of students in a class). MA.06.SP.06 Design experiments and simulations to determine experimental probability of different outcomes. MA.06.SP.07 Understand that experimental probability approaches theoretical probability as the number of trials increases. MA.06.SP.08 Recognize and understand the connections among concepts of independent outcomes, picking at random, and fairness. MA.06.SP.09 Represent and interpret the outcome of a probability experiment using a frequency distribution, including determining experimental probabilities. MA.07.SP.06 Formulate questions and design experiments or surveys to collect relevant data. MA.07.SP.07 Identify situations in which it makes sense to sample and identify methods for selecting a sample (e.g., convenience sampling, responses to survey, random sampling) that are representative of a population. MA.07.SP.08 Distinguish between random and biased samples and identify possible sources of bias in sampling. MA.07.SP.09 Represent and interpret data using frequency distribution tables, box-and whisker-plots, stem-and- leaf plots, and single- and multiple- line graphs. MA.07.SP.10 Determine the graphical representation of a set of data that best shows key characteristics of the data. MA.07.SP.11 Recognize distortions of graphic displays of sets of data and evaluate appropriateness of alternative displays. CCG: Data Analysis and Predictions: Develop and evaluate inferences and predictions that are based on data. MA.03.SP.04 Draw conclusions and make predictions and inferences from tally charts, pictographs, or bar graphs. MA.04.SP.06 Predict the degree of likelihood of a single event occurring using words such as certain, impossible, most often, least often, likely, and unlikely. MA.04.SP.07 Predict the likelihood of an outcome prior to an experiment and compare predicted probability with the actual results. MA.06.SP.10 Make predictions for succeeding trials of a probability experiment given the outcome of preceding repeated trials. MA.06.SP.11 Predict the outcome of a probability experiment by computing and using theoretical probability. MA.07.SP.12 Analyze data from frequency distribution tables, box- and whisker-plots, stem-and-leaf plots using measures of center and spread and draw conclusions. 5
  • 6. MA.08.SP.07 Estimate or predict the occurrence of future events using data. Mathematical Problem Solving CCG Conceptual Understanding: Select, apply, and translate among mathematical representations to solve problems. MA.02.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.03.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.04.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.05.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.06.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.07.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. MA.08.PS.01 Interpret the concepts of a problem-solving task and translate them into mathematics. CCG Processes and Strategies: Apply and adapt a variety of appropriate strategies to solve problems. MA.02.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.03.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.04.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.05.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.06.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.07.PS.02 Choose strategies that can work and then carry out the strategies chosen. MA.08.PS.02 Choose strategies that can work and then carry out the strategies chosen. CCG Verification: Monitor and reflect on the process of mathematical problem solving. MA.02.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.03.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.03.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. 6
  • 7. MA.04.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.05.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.06.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.07.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. MA.08.PS.03 Produce identifiable evidence of a second look at the concepts/strategies/calculations to defend a solution. CCG Communication: Communicate mathematical thinking coherently and clearly. Use the language of mathematics to express mathematical ideas precisely. MA.02.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.03.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.04.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.05.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.06.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.07.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. MA.08.PS.04 Use pictures, symbols, and/or vocabulary to convey the path to the identified solution. CCG: Accuracy: Accurately solve problems that arise in mathematics and other contexts. MA.02.PS.05 Accurately solve problems using mathematics. MA.03.PS.05 Accurately solve problems using mathematics. MA.04.PS.05 Accurately solve problems using mathematics. MA.05.PS.05 Accurately solve problems using mathematics. MA.06.PS.05 Accurately solve problems using mathematics. MA.07.PS.05 Accurately solve problems using mathematics. MA.08.PS.05 Accurately solve problems using mathematics. 7
  • 8. Materials (for 30 students working with a partner) Permanent Consumable • 15 Pennies • Pencils • 15 Red dice • Genotype to Phenotype handout • 15 Green dice • “Chromosomes” copies-2 colors • 15 Scissors to indicate “Father” and • 15 - 4x4 Punnett Squares boards “Mother” • 15 - 8x8 Punnett Squares boards • Large marshmallows • 15 - 16x16 Chess boards • Small color marshmallows • ~2000 Red poker chips • Chocolate chips • ~2000 Blue poker chips • Licorice whips – red and black • ~2000 Green poker chips • Twizzle pull-apart– pink and red o or any other kind of token in • Butterscotch chips 3 colors • Frosting (chocolate, lemon, and • Plastic knives vanilla) • Wax paper • Sandwich plastic bags Discussion: Although it seems a circuitous route to DNA fingerprints, following these steps allow students to visualize and comprehend exactly how DNA varies individually. They model crossover and independent assortment of genetic material. From this step, students next learn that this variation is carried by DNA base pairs. DNA code is the 4 molecules of adenine (A), Thymine (T), cytosine (C), and guanine (G), and we know that A pairs with T, C pairs with T. DNA sequences are the instructions for primarily proteins, and proteins make us. If the DNA (genotype) varies, that translates in how the organism looks or functions (phenotype). Both elementary and middle school students gain a deeper understanding of this whole process, either building a foundation, or expanding their present understanding. Your focus for this class is pretty clear, but you can also incorporate INDEPENDENT ASSORTMENT, a particularly difficult concept. For older students, emphasize replicated chromosome pairs crossover and exchange genetic material between the homologous pairs before the chromosomes randomly assort. For younger students, you can actually simulate meiosis with your paper chromosome pairs, separating mom and dad first into two “cells,” and then separate the replicated DNA into a total of 4 cells. Depending on the sophistication of your middle school students, you may also want to simulate meiosis by actually replicating your DNA, dividing the homologous pairs, and then dividing the replicated pairs. To emphasize independent assortment, use a coin to determine if a particular chromosome goes to the cell on the left or the cell on the right. One of the benchmarks is use of Punnett squares. This is a perfect time to meet that particular benchmark, and hence Activity 2. You can start with 1 gene – nose color or antenna number, and determine the number of offspring that will have the dominant and how many will have the recessive phenotype. Second, examine for two genes – for 8
  • 9. example the number and color of legs, which in our simulation are controlled by two different genes on two different chromosomes. Ask the middle school students how many squares would be needed to work out the phenotypic ratios for 3 genes (64 squares, or a grid that is 8 x 8 squares). Have the students try out different combinations (for example, one parent is homozygous for the recessive traits and the other parent is heterozygous) and determine the frequency of genotypes. For your advanced students, challenge them to determine the total number of possible outcomes and correctly find the phenotypic ratios for 4 genes. Finally, students LOVE building the marshmallow bugs (however, I do not let them eat their bugs until the end of class). Before you teach this lesson, you need to find out if any of your students are vegetarian or vegan. Trader Joes carries vegan marshmallows. This unit can be taught in a 90-minute class by streamlining the activities, and introducing genetics with the focus solely on variation in a population. It can also be extended to two 90-minute classes by following the extended activities and discussing the concepts more fully, especially sample size, probability, and meiosis. Overview of Activities: • Using “independent assortment,” students assigned alleles to two different pair of chromosomes, determine the genotype and build the phenotype of a marshmallow bug. The bug chromosomes undergo meiosis, forming 4 new “cells.” They keep one of these “cells” and receive another “cell.” The two cells fuse, and the students determine the genotype and build the phenotype of the offspring. About 1 hour. • Students, using a Punnett square, determine the frequency that an offspring will show recessive traits for a single trait, and then two traits. Run these examples using both parents as heterozygous for the alleles. Additional examples start with a parent recessive homozygous for an allele, or both parents homozygous, one dominant and the other recessive, to determine the frequency of the homozygous dominant, homozygous recessive and heterozygous states for a single allele, or two alleles. About 30 minutes. Set-up for class (of 30): Students work with a partner, but everyone participates with their own analysis • Set out for each pair of students:  15 pennies  15 red dice  15 blue dice  15 Scissors  15 “Cells”  15 Genotype to Phenotype handout  15 Pencils  blank “Chromosomes”  15 large sheets wax paper 9
  • 10.  30 sandwich plastic bags • Put in convenient location but away from students:  15 Punnett Squares boards  Poker chips (divided into 15 piles of ~125 - 150 for each color)  Large marshmallows  Small color marshmallows  Chocolate chips  Licorice whips – red and black  Twizzle pull-apart and cut into 1” pieces – pink and red  Butterscotch chips  frosting  plastic knives 10
  • 11. Marshmallow Bug Genetics Activity 1 Supplies: • Pennies • Wooden cubes • Scissors • “Cells” • Genotype to Phenotype handout • Pencils • “Chromosomes” • Large marshmallows • Small color marshmallows • Chocolate chips • Licorice whips – red and black • Twizzle pull-apart– pink and red • Butterscotch chips • Vanilla frosting • Chocolate frosting • Plastic knives • Wax paper • Sandwich plastic bags Discussion: Mendelian inheritance (or Mendelian genetics or Mendelism) is a set of primary tenets relating to the transmission of hereditary characteristics from parent organisms to their children; it underlies much of genetics. They were initially derived from the work of Gregor Mendel published in 1865 and 1866 which was "re-discovered" in 1900, and were initially very controversial. When they were integrated with the chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics. History The laws of inheritance were derived by Gregor Mendel, a 19th century Moravian monk conducting plant hybridity experiments. Between 1856 and 1863, he cultivated and tested some 28,000 pea plants. His experiments brought forth two generalizations which later became known as Mendel's Laws of Heredity or Mendelian inheritance. These are described in his essay "Experiments on Plant Hybridization" that was read to the Natural History Society of Brno on February 8 and March 8, 1865, and was published in 1866. Mendel's results were largely rejected. Though they were not completely unknown to biologists of the time, they were not seen as being crucial. Even Mendel himself did not see their ultimate applicability, and thought they only applied to certain categories of species. In 1900, however, the work was "re-discovered" by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak. The exact nature of the "re- discovery" has been somewhat debated: De Vries published first on the subject, and Correns pointed out Mendel's priority after having read De Vries's paper and realizing 11
  • 12. that he himself did not have priority, and De Vries may not have acknowledged truthfully how much of his knowledge of the laws came from his own work, or came only after reading Mendel's paper. Later scholars have accused Von Tschermak of not truly understanding the results at all. Regardless, the "re-discovery" made Mendelism an important but controversial theory. Its most vigorous promoter in Europe was William Bateson, who coined the term "genetics", "gene", and "allele" to describe many of its tenets. The model of heredity was highly contested by other biologists because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observable. Many biologists also dismissed the theory because they were not sure it would apply to all species, and there seemed to be very few true Mendelian characters in nature. However later work by biologists and statisticians such as R.A. Fisher showed that if multiple Mendelian factors were involved for individual traits, they could produce the diverse amount of results observed in nature. Thomas Hunt Morgan and his assistants would later integrate the theoretical model of Mendel with the chromosome theory of inheritance, in which the chromosomes of cells were thought to hold the actual hereditary particles, and create what is now known as classical genetics, which was extremely successful and cemented Mendel's place in history. Mendel's findings allowed other scientists to simplify the emergence of traits to mathematical probability. A large portion of Mendel's findings can be traced to his choice to start his experiments only with true breeding plants. He also only measured absolute characteristics such as color, shape, and position of the offspring. His data was expressed numerically and subjected to statistical analysis. This method of data reporting and the large sampling size he used gave credibility to his data. He also had the foresight to look through several successive generations of his pea plants and record their variations. Without his careful attention to procedure and detail, Mendel's work could not have had the impact it made on the world of genetics. The Law of Segregation, also known as Mendel's First Law, essentially has four parts. 1. Alternative versions of genes account for variations in inherited characteristics. This is the concept of alleles. Alleles are different versions of genes that impart the same characteristic. For example, each human has a gene that controls eye color, but there are variations among these genes in accordance with the specific color for which the gene "codes". 2. For each characteristic, an organism inherits two alleles, one from each parent. This means that when somatic cells are produced from two alleles, one allele comes from the mother and one from the father. These alleles may be the same (true-breeding organisms/homozygous e.g. ww and rr in Fig. 3), or different (hybrids/heterozygous, e.g. wr in Fig. 3). 3. If the two alleles differ, then one, the allele that encodes the dominant trait, is fully expressed in the organism's appearance; the other, the allele encoding the recessive trait, has no noticeable effect on the organism's appearance. In other words, only the dominant trait is seen in the phenotype of the organism. 12
  • 13. This allows recessive traits to be passed on to offspring even if they are not expressed. Not all traits have a dominant-recessive relationship, however. The "Japanese wonder flower" Mirabilis jalapa illustrates incomplete dominance (Figure 3). There is also codominance e.g. Human blood types where A and B are codominant and O is recessive. 4. The two alleles for each characteristic segregate during gamete production. This means that each gamete will contain only one allele for each gene. This allows the maternal and paternal alleles to be combined in the offspring, ensuring variation. N.B It is often misconstrued that the gene itself is dominant, recessive, codominant, or incompletely dominant. It is, however the trait, or gene product that the allele encodes that is dominant, etc. Figure 1: Dominant and recessive phenotypes. Figure 2: The color alleles of Mirabilis jalapa are not (1) Parental generation. (2) F1 generation. (3) F2 generation. dominant or recessive. Dominant (red) and recessive (white) phenotype look alike (1) Parental generation. (2) F1 generation. (3) F2 generation. in the F1 (first) generation and show a 3:1 ratio in the F2 The "red" and "white" allele together make a "pink" (second) generation phenotype, resulting in a 1:2:1 ratio of red:pink:white in the F2 generation. Law of Independent Assortment The Law of Independent Assortment, also known as "Inheritance Law" or Mendel's Second Law, states that the inheritance pattern of one trait will not affect the inheritance pattern of another. While his experiments with mixing one trait always resulted in a 3:1 ratio (Fig. 1) between dominant and recessive phenotypes, his experiments with mixing two traits (dihybrid cross) showed 9:3:3:1 ratios (Fig. 2). But the 9:3:3:1 table shows that each of the two genes are independently inherited with a 3:1 ratio. Mendel concluded that different traits are inherited independently of each other, so that there is no relation, for 13
  • 14. example, between a cat's color and tail length. This is actually only true for genes that are not linked to each other. The reason for these laws is found in the nature of the cell nucleus. It is made up of several chromosomes carrying the genetic traits. In a normal cell, each of these chromosomes has two parts, the chromatids. A reproductive cell, which is created in a process called meiosis, usually contains only one of those chromatids of each chromosome. By merging two of these cells (usually one male and one female), the full set is restored and the genes are mixed. The resulting cell becomes a new embryo. The fact that this new life has half the genes of each parent (23 from mother, 23 from father for total of 46) is one reason for the Mendelian laws. The second most important reason is the varying dominance of different genes, causing some traits to appear unevenly instead of averaging out (whereby dominant doesn't mean more likely to reproduce - recessive genes can become the most common, too). There are several advantages of this method (sexual reproduction) over reproduction without genetic exchange: 1. Instead of nearly identical copies of an organism, a broad range of offspring develops, allowing more different abilities and evolutionary strategies. 2. There are usually some errors in every cell nucleus. Copying the genes usually adds more of them. By distributing them randomly over different chromosomes and mixing the genes, such errors will be distributed unevenly over the different children. Some of them will therefore have only very few such problems. This helps reduce problems with copying errors somewhat. 3. Genes can spread faster from one part of a population to another. This is for instance useful if there's a temporary isolation of two groups. New genes developing in each of the populations don't get reduced to half when one side replaces the other, they mix and form a population with the advantages of both sides. 4. Sometimes, a mutation (e. g. Sickle Cell Anemia) can have positive side effects (in this case Malaria resistance). The mechanism behind the Mendelian laws can make it possible for some offspring to carry the advantages without the disadvantages until further mutations solve the problems. Mendelian trait A Mendelian trait is one that is controlled by a single locus and shows a simple Mendelian inheritance pattern. In such cases, a mutation in a single gene can cause a disease that is inherited according to Mendel's laws. Examples include sickle-cell anemia, Tay-Sachs disease, cystic fibrosis and xeroderma pigmentosa. A disease controlled by a single gene contrasts with a multi-factorial disease, like arthritis, which is affected by several loci (and the environment) as well as those diseases inherited in a non-Mendelian fashion. The Mendelian Inheritance in Man database is a catalog of, among other things, genes in which Mendelian mutants causes disease. In Genetics, dominance describes a specific relationship between the effects of different versions of a gene (alleles) on a trait or phenotype. Animals (including humans) and plants are ‘diploid’ (see ploidy), with two copies of each gene, one inherited from each 14
  • 15. parent. If the two copies are not identical (not the same allele), their combined effect may be different than the effect of having two identical copies of one or the other allele. But if the combined effect is the SAME as the effect of having two copies of one of the alleles, we say that allele’s effect is dominant over the other. For example, having two copies of one allele of the EYCL3 gene causes the eye’s iris to be brown and having two copies of another allele causes the iris to be blue. Because having one copy of each allele causes brown eyes, the brown allele is said to be dominant over the blue allele (and the blue allele is said to be recessive to the brown allele). We now know that in most cases a dominance relationship is seen when the recessive allele is defective. In these cases a single copy of the normal allele produces enough of the gene’s product to give the same effect as two normal copies, and so the normal allele is described as being dominant to the defective allele. This is the case for the eye color alleles described above, where a single functional copy of the ‘brown’ allele causes enough melanin to be made in the iris that the eyes appear brown even when paired with the non-melanin-producing ‘blue’ allele. Dominance was discovered by Mendel, who introduced the use of uppercase letters to denote ‘dominant alleles’ and lowercase to denote ‘recessive alleles’, as is still commonly used in introductory genetics courses (e.g. B b for alleles causing brown and blue eyes). Although this usage is convenient it is misleading, because dominance is not a property of an allele considered in isolation but of a relationship between the effects of two alleles. When geneticists loosely refer to a dominant allele or a recessive allele, they mean that the allele is dominant or recessive to the standard allele. Geneticists often use the term dominance in other contexts, distinguishing between simple or complete dominance as described above, and other relationships. Relationships described as incomplete or partial dominance are usually more accurately described as giving an intermediate or blended phenotype. The relationship described as codominance describes a relationship where the distinct phenotypes caused by each allele are both seen when both alleles are present. Genes are indicated in shorthand by a combination of one or a few letters - for example, in cat coat genetics the alleles Mc and mc (for "mackerel tabby") play a prominent role. Alleles producing dominant traits are denoted by initial capital letters; those that confer recessive traits are written with lowercase letters. The alleles present in a locus are usually separated by a slash; in the Mc - mc case, the dominant trait is the "mackerel- stripe" pattern, and the recessive one the "classic" or "oyster" tabby pattern, and thus a classical-pattern tabby cat would carry the alleles mc/mc, whereas a mackerel-stripe tabby would be either Mc/mc or Mc/Mc. Humans have 23 homologous chromosome pairs (22 pairs of autosomal chromosomes and two distinct sex chromosomes, X and Y). It is estimated that the human genome contains 20,000-25,000 genes. Each chromosomal pair has the same genes, although it is generally unlikely that homologous genes from each parent will be identical in sequence. The specific variations possible for a single gene are called alleles: for a single eye-color 15
  • 16. gene, there may be a blue eye allele, a brown eye allele, a green eye allele, etc. Consequently, a child may inherit a blue eye allele from their mother and a brown eye allele from their father. The dominance relationships between the alleles control which traits are and are not expressed. An example of an autosomal dominant human disorder is Huntington's disease, which is a neurological disorder resulting in impaired motor function. The mutant allele results in an abnormal protein, containing large repeats of the amino acid glutamine. This defective protein is toxic to neural tissue, resulting in the characteristic symptoms of the disease. Hence, one copy suffices to confer the disorder. Directions: 1) Students cut out the two pairs of chromosomes, one from each of the 2 colors of paper, for example yellow and green. Note that yellow Paternal Chromosome 1 is a homologous pair with green Maternal Chromosome 1. The yellow Paternal Chromosome 2 is a homologous pair with Maternal Chromosome 2. 2) Starting with one color (in this example, the green), ask students to flip their penny. If the penny lands as a “heads,” they will identify the character trait as a capital letter. If it lands as “tails,” they will identify the character trait as a small letter. They are only working with one chromosome at this point. If, for example, the student rolls a TTHTTHTHTH, he/she would letter the chromosome as “naBseLrCtG” in the appropriate row for the chromosomes 1 and 2. a) Extension: As a class, build a table with columns labeled “student,” “# heads,” and “# tails.,” Put each student’s name as the row. Ask the class what is the probability for flipping heads? What is the probability for flipping tails. Ask each student to record the total number of times that student flipped heads, and flipped tails. Add the individual heads flipped and tails flipped for a class total. . Which comes closer to the predicted probability of rolling a head 1 out of 2 times, the individual results or the class results? Why? Discuss the importance of a large enough sample size to reduce individual natural variation in any probability. 3) Using the Genotype to Phenotype handout, the student records the genes in the appropriate column for the green chromosomes and the yellow chromosomes. 4) Using the information on the left column of their Genotype to Phenotype handout, students record the phenotype in the appropriate column. 5) Using the phenotype, students gather the materials to build their marshmallow bug. DO NOT LET THEM EAT IT AT THIS TIME!!! The gender frosting is to hold all the different parts together. 6) Now we want to bugs to breed (tee hee hee hee). Students take 4 blank chromosomes 1 and 2, two yellow, two green (following the maternal and paternal lines of inheritance). 7) NOTE TO INSTRUCTOR: The next directions are to model meiosis. For elementary students, the steps are streamlined, beginning with the first indented direction. 8) Replicating DNA - Have the students copy the allele codes from their parent chromosome to the blank chromosomes, matching colors. Cut the chromosomes 16
  • 17. out (if this hasn’t already been done). You will now have 2 copies of paternal chromosome 1, 2 copies of maternal chromosome 1, 2 copies of paternal chromosome 2, and 2 copies of maternal chromosome 2. 9) Crossover – Each student has a red die and a blue die. Students roll the 2 dice, working with one homologous pair (for example, the paternal and maternal chromosome 1 pair). The dice have gene numbers on them. The number rolled are the genes exchanged during crossover. For example, if one die has 2 and the other die has 4&5, the student would cut out those genes on each of the pair of chromosomes, swap them and tape them back together. Repeat for Chromosome 2. You only need to have 1 pair of the replicated chromosomes crossover for this demonstration. 10) Prophase I – stack the 4 cells, stack the replicated chromosomes and place in the cell. 11) Metaphase I – line up the chromosomes so that paternal and maternal Chromsome 1 are next to each other, and paternal and maternal Chromsome 2 are next to each other. Flip a coin. If heads, place paternal chromsome 1 on the left and maternal chromosome 1 on the right. If tails, place the paternal Chromosome on the right. Repeat for Chromosome 2. 12) Anaphase I – Separate maternal and paternal chromesomes on top of the cells, separating two of the stacked cells from the other two. 13) Telophase I – Completely separate the two stacked cells. 14) Metaphase II – line the chromosomes up for both cells. Flip a coin. If heads, place crossover chromsome 1 on the left and non-crossover chromosome 1 on the right. If tails, place the non-crossover Chromosome on the right. Repeat for Chromosome 2. 15) Anaphase II –Separate the chromesomes on top of the cells, separating two of the stacked cells from the other two. 16) Telophase I – Completely separate the 4 stacked cells. i) For younger students, skip the crossover steps, but model the rest of meiosis. 17) Collect 3 of the 4 cells’ chromosomes from all the students. Randomly assign each person a different set of chromosomes. Be sure that the students does not get one of their own sets. 18) Repeat steps 3 – 5 to produce offspring. 19) Have the students try to find identical marshmallow bugs. Remind them that “almost the same” is NOT identical. 20) Our marshmallow bugs only have 2 pair of chromosomes with a total of 10 genes. Humans have 23 pair of chromosomes with a total of ~ 26,000 genes! Now that is a lot of room for variation! a) Discuss that we have been examing organisms that have a 50% frequency of allele N and 50% of allele n, and so on. In actuality, the frequency of alleles can vary from population to population. This would be in preparation for the Hardy-Weinberg Principle activity in Blood extension activity. 17
  • 18. 18
  • 19. Punnett Squares Activity 2 Supplies: • 6 - 4x4 Punnett Squares boards • 6 - 8x8 Punnett Squares boards • 6 - 16x16 Chess boards • ~800 Red poker chips • ~800 Blue poker chips • ~800 Green poker chips Discussion: The genetic combinations possible with simple dominance can be expressed by a diagram called a Punnett square. One parent's alleles are listed across the top and the other parent's alleles are listed down the left side. The interior squares represent possible offspring, in the ratio of their statistical probability. In the previous example of flower color, P represents the dominant purple-colored allele and p the recessive white-colored allele. If both parents are purple-colored and heterozygous (Pp), the Punnett square for their offspring would be: In the PP and Pp cases, the offspring is purple colored due to the dominant P. Only in P p the pp case is there expression of the recessive white-colored phenotype. P PP Pp Dominant allele p P p p p Dominant trait refers to a genetic feature that hides the recessive trait in the phenotype of an individual. A dominant trait causes the phenotype that is seen in a heterozygous (Aa) genotype. Many traits are determined by pairs of complementary genes, each inherited from a single parent. Often when these are paired and compared, one allele (the dominant) will be found to effectively shut out the instructions from the other, recessive allele. For example, if a person has one allele for blood type A and one for blood type O, that person will always have blood type A because it is the dominant allele. For a person to have blood type O, both their alleles must be O (recessive). When a person has two dominant alleles, they are referred to as homozygous dominant. If they have one dominant allele and one recessive allele, they are referred to as heterozygous. A dominant trait when written in a genotype is always written before the recessive gene in a heterozygous pair. A heterozygous genotype is written Aa, not aA. Types of dominances Simple dominance or complete dominance Consider the simple example of flower color in peas, first studied by Gregor Mendel. The dominant allele is purple and the recessive allele is white. In a given individual, the two corresponding alleles of the chromosome pair fall into one of three patterns: • both alleles purple (PP) • both alleles white (pp) • one allele purple and one allele white (Pp) If the two alleles are the same (homozygous), the trait they represent will be expressed. But if the individual carries one of each allele (heterozygous), only the dominant one will be expressed. The recessive allele will simply be suppressed. 19
  • 20. Incomplete dominance Discovered by Karl Correns, incomplete dominance (sometimes called partial dominance) is a heterozygous genotype that creates an intermediate phenotype. In this case, only one allele (usually the wild type) at the single locus is expressed, and the expression is doseage dependent. Two copies of the gene produce full expression, while one copy of the gene produces partial expression in an intermediate phenotype. A cross of two intermediate phenotypes (= monohybrid heterozygotes) will result in the reappearance of both parent phenotypes and the intermediate phenotype. There is a 1:2:1 phenotype ratio instead of the 3:1 phenotype ratio found when one allele is dominant and the other is recessive. This lets an organism's genotype be diagnosed from its phenotype without time-consuming breeding tests. The classic example of this is the color of carnations. R R' R is the allele for red pigment. R' is the allele for no pigment. R RR RR' Thus, RR offspring make a lot of red pigment and appear red. R'R' offspring make no red pigment and appear white. Both RR' and R'R offspring make some pigment R' RR' R'R' and therefore appear pink. Codominance In codominance, neither phenotype is completely dominant. Instead, the heterozygous individual expresses both phenotypes. A common example is the ABO blood group system. The gene for blood types has three alleles: A, B, and i. i causes O type and is recessive to both A and B. The A and B alleles are codominant with each other. When a person has both an A and a B allele, the person has type AB blood. When two persons with AB blood type have children, the children can be type A, type B, or type AB. There is a 1A:2AB:1B phenotype ratio instead of the 3:1 phenotype ratio found when one allele is dominant and the other is recessive. This is the same phenotype ratio found in matings of two organisms that are heterozygous for incomplete dominant alleles. A i Example Punnett square for a father with A and i, and a mother with B and i: B AB B A roan horse has codominant follicle genes, expressing individual red and white follicles. i A O Dominant negative Most loss-of-function mutations are recessive. However, some are dominant and are called "dominant negative" or antimorphic mutations. Typically, a dominant negative mutation occurs when the gene product adversely affects the normal, wild-type gene product within the same cell. This usually occurs if the product can still interact with the same elements as the wild-type product, but block some aspect of its function. Such proteins may be competitive inhibitors of the normal protein functions. Types: • A mutation in a transcription factor that removes the activation domain, but still contains the DNA binding domain. This product can then block the wild-type transcription factor from binding the DNA site leading to reduced levels of gene activation. 20
  • 21. • A protein that is functional as a dimer. A mutation that removes the functional domain, but retains the dimerization domain would cause a dominate negative phenotype, because some fraction of protein dimers would be missing one of the functional domains. Recessive allele The term "recessive allele" refers to an allele that causes a phenotype (visible or detectable characteristic) that is only seen in homozygous genotypes (organisms that have two copies of the same allele) and never in heterozygous genotypes. Every diploid organism, including humans, has two copies of every gene on autosomal chromosomes, one from the mother and one from the father. The dominant allele of a gene will always be expressed while the recessive allele of a gene will be expressed only if the organism has two recessive forms. Thus, if both parents are carriers of a recessive trait, there is a 25% chance with each child to show the recessive trait. The term "recessive allele" is part of the laws of Mendelian inheritance formulated by Gregor Mendel. Examples of recessive traits in Mendel's famous pea plant experiments include the color and shape of seed pods and plant height. Nomenclature of recessiveness Technically, the term "recessive gene" is imprecise because it is not the gene that is recessive but the phenotype (or trait). It should also be noted that the concepts of recessiveness and dominance were developed before a molecular understanding of DNA and before molecular biology, thus mapping many newer concepts to "dominant" or "recessive" phenotypes is problematic. Many traits previously thought to be recessive have mild forms or biochemical abnormalities that arise from the presence of the one copy of the allele. This suggests that the dominant phenotype is dependent upon having two dominant alleles and the presence of one dominant and one recessive allele creates some blending of both dominant and recessive traits. Gregor Mendel performed many experiments on pea plant (Pisum sativum) while researching traits, chosen because of the simple and low variety of characteristics, as well as the short period of germination. He experimented with color (green vs. yellow), size (short vs. tall), pea texture (smooth vs. wrinkled), and many others. By good fortune, the characteristics displayed by these plants clearly exhibited a dominant and recessive form. This is not true for many organisms. For example, when testing the color of the pea plants, he chose two yellow plants, since yellow was more common than green. He mated them, and examined the offspring. He continued to mate only those that appeared yellow, and eventually, the green ones would stop being produced. He also mated the green ones together and determined that only green ones were produced. Mendel determined that this was because green was a recessive trait which only appeared when yellow, the dominant trait, was not present. Also, he determined that the dominant trait would be displayed whether or not the recessive trait was there. Dominance/recessiveness refers to phenotype, not genotype. An example to prove the point is sickle cell anemia. The sickle cell genotype is caused by a single base pair change in the beta-globin gene: normal=GAG (glu), sickle=GTG (val). There are several phenotypes associated with the sickle genotype:- 1. anemia (a recessive trait) 2. blood cell sickling (co-dominant) 3. altered beta-globin electrophoretic mobility (co-dominant) 21
  • 22. 4. resistance to malaria (dominant) This example demonstrates that one can only refer to dominance/recessiveness with respect to individual phenotypes. Mechanisms of dominance Many genes code for enzymes. Consider the case where someone is homozygous for some trait. Both alleles code for the same enzyme, which causes a trait. Only a small amount of that enzyme may be necessary for a given phenotype. The individual therefore has a surplus of the necessary enzyme. Let's call this case "normal". Individuals without any functional copies cannot produce the enzyme at all, and their phenotype reflects that. Consider a heterozygous individual. Since only a small amount of the normal enzyme is needed, there is still enough enzyme to show the phenotype. This is why some alleles are dominant over others. In the case of incomplete dominance, the single dominant allele does not produce enough enzyme, so the heterozygotes show some different phenotype. For example, fruit color in eggplants is inherited in this manner. A purple color is caused by two functional copies of the enzyme, with a white color resulting from two non-functional copies. With only one functional copy, there is not enough purple pigment, and the color of the fruit is a lighter shade, called violet. Some non-normal alleles can be dominant. The mechanisms for this are varied, but one simple example is when the functional enzyme is composed of several subunits. In this case, if any of the subunits are nonfunctional, the entire enzyme is nonfunctional. In the case of a single subunit with a functional and nonfunctional allele (heterozygous individual), the concentration of functional enzymes is 50% of normal. If the enzyme has two identical subunits, the concentration of functional enzyme is 25% of normal. For four subunits, the concentration of functional enzyme is about 6% of normal. This may not be enough to produce the wild type phenotype. There are other mechanisms for dominant mutants. Other factors It is important to note that most genetic traits are not simply controlled by a single set of alleles. Often many alleles, each with their own dominance relationships, contribute in varying ways to complex traits. Some medical conditions may have multiple inheritance patterns, such as in centronuclear myopathy or myotubular myopathy, where the autosomal dominant form is on chromosome 19 but the sex-linked form is on the X chromosome. Punnett Squares The Punnett square is a diagram designed by Reginald Punnett and used by biologists to determine the probability of an offspring having a particular genotype. It is made by comparing all the possible combinations of alleles from the mother with those from the father. Typical monohybrid cross The Punnett square, founded by George Punnett, shows every possible combination when combining one maternal allele with one paternal allele. In this example, both organisms have the genotype Bb. They can produce gametes that contain either the B or b alleles. The probability of an individual offspring having the genotype BB is 25%, Bb is 50%, and bb is 25%. 22
  • 23. Maternal It is important to note that Punnett squares only give B b probabilities for genotypes, not phenotypes. The way in B BB Bb which the B and b alleles interact with each other to Paternal affect the appearance of the offspring depends on how b Bb bb the gene products (proteins) interact (see Mendelian inheritance). For classical dominant/recessive genes, like that which determines whether a rat has black hair (B) or white hair (b), the dominant allele will mask the recessive one. Thus in the example above 75% of the offspring will be black (BB or Bb) while only 25% will be white (bb). The ratio of the phenotypes is 3:1, typical for a monohybrid cross. Typical dihybrid cross More complicated crosses can be made by looking at two or more genes. The Punnett square only works, however, if the genes are independent of each other, which means that having a particular allele of gene X does not imply having a particular allele of gene Y. The following example illustrates a dihybrid cross between two heterozygous pea plants. R represents the dominant allele for shape (round), while r represents the recessive allele (wrinkled). Y represents the dominant allele for color (yellow), while y represents the recessive allele (green). Each plant has the genotype Rr Yy, and since the alleles for shape and color genes are independent, they can produce four types of gametes with all possible combinations: RY, Ry, rY and ry. RY Ry rY ry Since dominant traits mask recessive traits, there are RY RRYY RRYy RrYY RrYy nine combinations that have the phenotype round Ry RRYy RRyy RrYy Rryy yellow, three that are round green, three that are wrinkled yellow and one that is wrinkled green. The rY RrYY RrYy rrYY rrYy ratio 9:3:3:1 is typical for a dihybrid cross. ry RrYy Rryy rrYy rryy Situations where Punnett squares do not apply The phenotypic ratios of 3:1 and 9:3:3:1 are theoretical predictions based on the assumptions of segregation and independent assortment of alleles (see Mendelian inheritance). Deviations from the expected ratios can occur if any of the following conditions exists: • the alleles in question are physically linked on the same chromosome • one parent lacks a copy of the gene, e.g. human males have only one X chromosome, from their mother, so only the maternal alleles have an effect on the organism (see sex linkage) • the survival rate of different genotypes is not the same, e.g. one combination of alleles may be lethal so that the affected offspring dies in utero • alleles may show incomplete dominance or co-dominance (see dominance relationship) • there are genetic interactions (epistasis) between alleles of different genes • the trait is inherited on genetic material from only one parent, e.g. mitochondrial DNA is only inherited from the mother (see maternal effect) • the alleles are imprinted An example of a Trihybrid Cross is located at the end of this document. Directions: 23
  • 24. Please note: These are probabilities, and the actual results, as we all know, will vary. In addition, the text is written as if it is fact rather than probability. Be sure to clarify that individual results vary, like the coin flipping. • Give each pair of students 128 red poker chips, 128 blue poker chips, 128 yellow poker chips, one 4x4, 8x8 Punnett squares and a chess board. • One student will be the paternal alleles and the partner will be the maternal alleles. • Each gene is a single color. On one side of the poker chip is a large black dot. This represents the upper case letter (dominant) state. The other side of the chip does not have the dot. This side represents the lower case letter (recessive) state. • Begin with a brief introduction to Mendel and his peas. He started with homozygous parents. • Tell your students to use the 4x4 square. Instruct them to complete the Punnett square with one partner acting with only the dominant allele, and the other partner acting with only the recessive allele. For our example here, let’s use the nose color (, NN and nn ) of our Marshmallow bugs. • What is the phenotype for each of the offspring? (They will all be heterozygous and green noses). • Using the same 4x4 square, repeat this with the heterozygote parents. • What is the phenotype for each of the offspring? (They wil be 1 homozygote dominant, 1 homozygote recessive, and 2 heterozygotes, or 3 green and 1 yellow noses). • Using the same 4x4 square, repeat with one parent homozygote recessive and one heterozygote for this same gene. • What is the phenotype for each of the offspring? (They will be 2 heterozygote and 2 homozygote recessive, or two green and two yellow noses). • Introduce analyzing 2 genes, this time number of legs (L or l) and color of legs (R or r) using the 8x8 squares. • What is the phenotype for each of the offspring? (9, 3, 3, 1). • Repeat with one parent homozygous recessive and the other parent is heterozygote. How do the phenotype results change? • Using the genes number of marshmallow spots (co-dominant S or s) and number of eyes (incomplete dominance), what is the probability of the offspring phenotype? • Introduce analyzing 3 genes, this time with number of antenna (A or a), number of body segments (B or b) and color of antenna (T or t). Have the students predict if the results will be different because these genes are found on two different chromosomes. • What is the phenotype for each of the offspring (27, 9, 9, 9, 3, 3, 3, 1). • For advanced students, have them calculate the probability of the phenotypes for 4 genes. 24
  • 25. Trihybrid Cross ABD ABd AbD Abd aBD aBd abD abd ABD AABBDD AABBDd AABbDD AABbDd AaBBDD AaBBDd AaBbDD AaBbDd ABd AABBDd AABBdd AABbDd AABbdd AaBBDd AaBBdd AaBbDd AaBbdd AbD AABbDD AABbDd AAbbDD AAbbDd AaBbDD AaBbDd AabbDD AabbDd Abd AABbDd AABbdd AAbbDd AAbbdd AaBbDd AaBbdd AabbDd Aabbdd aBD AaBBDD AaBBDd AaBbDD AaBbDd aaBBDD aaBBDd aaBbDD AaBbDd aBd AaBBDd AaBBdd AaBbDd AaBbdd aaBBDd aaBBdd aaBbDd aaBbdd abD AaBbDD AaBbDd AabbDD AabbDd aaBbDD aaBbDd aabbDD aabbDd abd AaBbDd AaBbdd AabbDd Aabbdd aaBbDd aaBbdd aabbDd aabbdd Phenotypic Ratio 27 9 9 9 3 3 3 1 25