ࡱ>  Lbjbj .ڇڇD8 <#(#*#*#*#*#*#*#,$['tV#V#k#d(#(#:@","@b.{p rzl" ##0#v"R''""LV#V##' :   Mendelian Genetics Gregor Mendel described a model by which heritable characters are passed from one generation to the next. Much of what he described is still useful today in predicting the outcomes of various types of crosses between individuals. In lab today we will explore some of the tenets of Mendelian genetics, and use them to determine part of the genetic makeup of some ears of corn, and of humans. Before we explore Mendelian genetics, however, we need to have some understanding about probability. An easy way to illustrate some principles of probability is to use some familiar objects coins or dice. PROBABILITY coin-flipping and its relation to genes and alleles. Probability is a method of predicting the number of times a random event will occur in a specified number of trials. There are three principles of probability that are very important to know and understand: The outcome of one trial of a chance event has no influence on the outcome of subsequent trials. For example, flipping a coin and getting either a head or a tail has no effect on whether you will get a head or a tail on the next flip. The probability of two or more independent events occurring simultaneously is the product of their individual probabilities. For example, if you flip two coins at the same time, the odds of getting two heads = X = . (The odds of getting a head is , and the odds of getting a tail is also ). The probability of either one or the other of two mutually exclusive events occurring is the sum of their individual probabilities. For example, if you roll a standard die, the odds of rolling either a 1 (which has a 1/6 probability) or a 2 (also a 1/6 probability) on the die = 1/6 + 1/6 = 1/3. It is usually impossible to measure or control the many factors involved when a coin is tossed. The end result (heads or tails) is said to occur by chance, or to be a random event. When a single coin is tossed several times it is expected that about half the tosses will result in tails facing up, and about half the tosses will result in heads facing up. ACTIVITY ONE Toss a single coin 30 times. Record the occurrence of either heads or tails in the table below. What is the expected number of heads and tails? What is the difference or deviation (O E) between the observed number and the expected number? Be sure to record whether or not the difference is positive or negative. Observed Number (O)Expected Number (E)Difference (O E) (O E)2 / EHeads Tails TOTALS 3030 P = If the deviations are small you can attribute them to chance. But, if the deviations are large you will need to consider whether or not there is some cause other than chance. Are your coin-flip data close to the expected 50:50 ratio? How close? Close enough to accept your prediction? What if the ratio was 55:45? Or 60:40? Or 70:30? Rather than just guess, we can use statistics to determine if our data are a close enough fit to what we hypothesized, that is a 50:50 ratio. Lets take a look at a test that will help us determine if our data is close enough to what we predicted. The test we will use is called the Chi-square statistic. Note that you have not placed any values into the right hand column above. In order to calculate the Chi-square statistic simply sum all the values for (O E)2 / E taken from the table. Place this sum in the lower right cell of the table (P). This is the Chi-square value. This value is compared to 3.841 (a value determined by statisticians for this type of test). If the P value is less than 3.841 than you may conclude that your values are, in fact, close enough to the predicted 50:50 ratio and that only chance is needed to explain any deviation. If the P value is greater than 3.841 then you must suspect that something other than chance is involved. Maybe the coin you used is not fair. Note that this coin-tossing situation is exactly analogous to a situation where there are only two possible traits. For example: gender, the color of the seed coat in corn, attached vs. unattached earlobes in humans, and many others. Of greater significance for our understanding of genetics, coin-tossing is exactly analogous to determining the probability that a gamete (sperm or egg) contains one or the other allele from a parent. ACTIVITY TWO Now toss two coins together 40 times. Record the results in the table below. When calculating the expected number in each category keep in mind that when two or more coins are tossed together, each is independent and each has an equal chance of coming up either heads or tails. Use rules of prob Observed number (O)Expected Number (E)Deviation (O E) (O E)2 / EHeads on both coinsOne head and one tailTails on both coins TOTALS 40 40 P =  Perform a Chi-square analysis on these data to determine if you have been using fair coins. For this you will need to apply some of the rules of probability in order to make your predictions. Now, however, since there are three possible outcomes the number you calculate is compared to a Chi-square value of 5.99 for evaluating fairness. In 1866, Gregor Mendel published a paper that documented a breeding experiment using pea plants. Using several different traits (including seed coat color and texture) Mendel was the first to understand that the traits of an organism are determined by bits of genetic information, or genes. Even though we use the term gene today, remember that Mendels work pre-dated the discovery of genes and chromosomes. This is what we call particulate inheritance, which is very different from the dominant idea of Mendels time - fluid inheritance. The basis of particulate inheritance, which Mendel observed, is that bits of information (genes) are not blended away by breeding between different organisms, as was predicted by the then theory of fluid inheritance. Because Mendels work was unappreciated and undiscovered by the biological community until the beginning of the 20th century, another revolutionary theory Charles Darwins theory of natural selection also fell into disrepute because Darwins critics thought that all variation would be blended away by interbreeding. Without genetic variation, natural selection does not occur. Thus, the rediscovery of Mendels principles at the turn of the century would spark new interest in natural selection. Ironically, both these revolutionary thinkers died before their ideas gained wide support. One of Mendels important tools was the recognition that the genes were hidden away from view (as we now know, in the DNA of the nucleus). Therefore, he had to infer what the genes of an organism were from what the organism looked like. The traits that are observed are referred to as the phenotype of an organism. The actual genetic information is referred to as the genotype of the organism. A phenotype can be observed. Until recently, a genotype could not be observed and had to be inferred. Based on his principles, Mendel was able to make predictions about how many different phenotypes should result from crossing one type of parent to another. The theory of particulate inheritance provides for different predicted phenotypes than would the theory of fluid inheritance. It is important to note that the theory of particulate inheritance predicts that recessive traits are not lost or blended away, but are only hidden or masked. Mendels principles of inheritance follow from his idea of genes as particulate, and that each individual contains a pair of alleles (the variant forms of the genes) for any of a number of traits. These principles are: Law of Segregation: the alleles for each gene are not blended. Law of Dominance: the alleles of each gene are dominant or recessive to each other. The dominant allele is expressed in individuals with one or two dominant alleles. The recessive allele is expressed only in individuals with two recessive alleles. Law of Independent Assortment: - genes for different traits are unaffected by one another, therefore, the presence or absence of one trait in offspring is not affected by the presence or absence of another trait. A gene is most simply defined as a position or location on a chromosome that codes for a trait. Because humans, and most organisms that are familiar to you, spend most of their life cycle as diploid organisms (i.e., possessing two sets of identical chromosomes) each person has two copies of each gene that is, two alleles per gene. It is the alleles that determine how individuals differ from one another. For example, there is a gene for eye color, and alleles for blue eyes and brown eyes. ACTIVITY THREE Next, lets attempt to corroborate Mendels principles. You will generate predictions (i.e., expected frequencies) based on Mendels principles. These expectations will be the basis for your hypotheses. A technique for generating expected frequencies using Mendels laws. Genetic Notation. To make predictions, we make use of genetic notation. Letters are used to represent the genotype of an individual. A letter (or letters) is used to indicate a gene; uppercase letters denote the dominant allele; lowercase letters indicate the recessive allele. A + indicates a wild-type allele, which means the most commonly found allele in a natural population of the organism. The tables below show some examples of how genetic notation is used: Considering one gene as in a monohybrid cross GenotypePhenotypeRRSeed coat is round (peas)RrSeed coat is round (peas)rrSeed coat is wrinkled (peas)ap/apWingless fruit fly (apterous)+/apWinged fruit fly+/+Winged fruit fly (wild type) Considering two genes as in a dihybrid cross GenotypePhenotypeRRYYSeed coat is round and yellow (peas)RrYySeed coat is round and yellow (peas)rryySeed coat is wrinkled and green (peas)+/ap; +/seWinged fruit fly with red eyes+/+;se/seWinged fruit fly with brown eyesap/ap;se/seWingless fruit fly with brown eyes The Punnett Square for a monohybrid cross. Lets consider the simplest example of a cross. In a monohybrid cross a single trait is being examined, for example seed coat color. In peas, seed coat color is either green or yellow. Yellow is the dominant allele, while green is recessive. Lets begin with parents that are homozygous for this trait, that is, each parent possesses identical alleles for the gene. P (parental generation) Phenotypes yellow X green Genotypes (homozygous) YY X yy To construct the Punnett Square, simply place all the possible gametes from each parent along the margins of a square, and fill in the boxes within the Punnett Square with the genotypes that might result considering all possible outcomes: Y Y Yy Yy Yy Yy y y The boxes contain the genotypes. The boxes are also used to predict the number of each phenotype that will be produced. The offspring of the parental generation (above) are known as the first filial generation (or F1 generation). From the Punnett Square described above, then, all the offspring should be the same genotype, and thus the same phenotype: yellow seed coat. In this example we can see that each parent can only contribute one possible gamete, so we can simplify the Punnett Square down to a single box: Y Yy  y We see that all the offspring from this cross would have a yellow seed coat. Now, lets do another monohybrid cross, but this time cross the F1 generation with itself: P (parental generation) Phenotypes Yellow X Yellow Genotypes Yy X Yy Construct the Punnet Square:   What are the predicted phenotypic and genotypic ratios for this F1 monohybrid cross? Does the Punnett Square support this? Could you construct a Punnett Square for these crosses? Yy X yy yy X yy     The Punnett Square for a dihybrid cross. Let us consider one of Mendels crosses in which he investigated the seed coat color (green or yellow) and texture (round or wrinkled) of pea plants. Again, he began his crosses with parents that were homozygous, that is, possessing the same two alleles for each gene, for both traits. See below: P (parental) generation Phenotypes yellow and round X green and wrinkled Genotypes (homozygous) YYRR X yyrr Mendel, applying his principles, predicted that all the offspring from this cross would be heterozygous have different alleles for a gene and would be yellow and round (the dominant alleles). We can use the Punnett Square to do the same thing. First, we determine the possible allele combinations that could be found in gametes. ParentsYYRR X yyrrPossible allelesYR x yr Because each parent can only produce one kind of gamete in this case, the Punnett Square is still very simple: YR YyRr  yr The box contains the genotypes. The box also is used to predict the number of each phenotype that will be produced. From the Punnett Square described above, all the offspring should be the same genotype, and thus the same phenotype: yellow and round. Before proceeding further, convince yourself that this is true. Next, lets cross these F1 offspring. The F1 generation will produce several kinds of gametes: YR, Yr, yR, and yr. Now, place these possible gametes in the Punnett Square to predict the expected genotype and phenotype frequencies. Female gametes YR Yr yR yr    Male gametes YR Yr yR yr From this determine the expected frequencies for all possible allele combinations: Genotypic Phenotypic YYRR = Yellow and round Yellow and wrinkled Green and round Green and wrinkled Ratio: Total 16 Examine the details of this F1 cross to make sure you understand the genotypes and phenotypes and how the Punnett Square is used to predict the expected genotypic and phenotypic frequencies in the next generation for this dihybrid cross. Can you construct a Punnett Square for a trihybrid cross? Now we are ready to put this information to use. ACTIVITY FOUR You will use corn, Zea mays, as your genetic model to test Mendels principles. The ears will have both yellow and purple kernels, and the kernels will be either smooth or wrinkled. You may work with a partner for this activity. Obtain an ear of corn. For now, lets just look at the monohybrid crosses. Count 100 kernels from the ear of corn and record the number of yellow kernels and the number of purple kernels. Also, record the number of smooth kernels and the number of wrinkled kernels. You will need to know that in corn purple is dominant to yellow for kernel color, and that smooth is dominant to wrinkled for kernel texture. From your observed numbers for kernel color form an hypothesis for the genotypes of the parents that were crossed to produce your ear of corn. Test your hypothesis by constructing a table to perform a Chi-square analysis. Do the same thing for kernel texture. Now, since there are only two possible outcomes, use the Chi-square value of 3.84 again; just like for flipping a coin. Was your hypothesis correct? If time permits, try the same thing with a dihybrid cross. For this you will need to keep track of four different phenotypes: Purple smooth kernels Purple wrinkled kernels Yellow smooth kernels Yellow wrinkled kernels Now, since there are four possible outcomes, the Chi-square value you use to compare is different again. Now you must compare your calculated value to a Chi-square value of 7.82. Have you noticed yet that the Chi-square value is different each time there is a different number of possible outcomes? ACTIVITY FIVE An important and useful tool provided by Mendel is that ones genotype can often be inferred from knowing the phenotype of the individual and parents, grandparents, other children, etc. The alleles for autosomal characteristics are carried on the non-sex chromosomes (not the X or Y chromosomes). If individuals are homozygous dominant or heterozygous, their phenotype will show the dominant characteristic. If individuals are homozygous recessive their phenotype will show the recessive characteristic. Work with a partner to determine your phenotype for the traits listed in the table below. Record your phenotype and possible genotype. After the totals for the entire class are tallied, determine the phenotype ratios. Now for the weird part. Imagine that the entire class is the result of a breeding experiment gone terribly wrong, and that you are all brothers and sisters. Scary, huh? Can you determine the genotypes of your parents for each of these traits? 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