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AP BIOLOGY 2016-17February 2, 2017Today’s Agenda (Day 94)Housekeeping:Homework Check Ch 15 Notes Basic Genetics Practice Ch 15 VocabularyClass Activity Lab: Chi Square Modeling Lab: Hardy-Weinberg SimulationHOMEWORK:Read Ch 16 – Molecular Basis of InheritanceComplete Genetics Problems #2, Genetics Problems #3, Genetics Problems #4Continue Project: Human Genetics Diseases – see p. 6 of document (WORK WITH A PARTNER)Complete Ch 16 Vocabulary – definition and sentence onlyCh 16 VocabularyPhagesDouble helixAntiparallelDNA replicationSemiconservativeReplication forkDNA pol I/IIILeading strandMismatch repairLagging strandOkazaki fragmentsDNA ligaseHelicasePrimasePrimerNucleotide excision repairNucleasesTelomeresHistonesNucleosomesEuchromatinheterochromatinREMINDERS:Ch 16 Vocabulary – Feb. 3Genetics Practice Problems #2 – 4 Feb. 3Ch 16 Notes – Feb. 6Ch 16 Test Feb. 7Genetics Project – Feb. 10DATEASSIGNMENTS - AP BiologyJan. 27Ch 15 Vocabulary & Basic Genetics PracticeJan. 30 Ch 15 NotesJan. 31TEST - Ch 15 postponed till Feb. 1Feb. 3Genetics Practice ProblemsFeb. 7TEST - Ch 16Feb. 10Genetics ProjectFeb. 14TEST - Ch 17Feb. 21TEST - Ch 18Feb. 28TEST - Ch 19AP BIOLOGY 2016-17 ACTIVITYChi Square (X2) Modeling Using CandyThe Chi Square test is often used in science to determine if data you observe from an experiment is close enough to the predicted data. In genetics, for instance, you might expect to get a 75% to 25% ratio if you crossed two heterozygous tall plants (Tt x Tt). Calculating the?X2?values help you determine whether the results follow the prediction and if the variations from the exact ratio are due to random chance. It's the question of "how close is close enough?" If the numbers differ greatly from your expected results, then it's possible that other factors may be influencing your results.The Chi-square test is intended to test how likely it is that an observed distribution is due to chance. It is also called a?"goodness of fit"?statistic, because it measures how well the observed distribution of data fits with the distribution that is expected if the variables are independent.?Another way to describe the Chi-square test is that it tests the?null hypothesis?that the variables are independent, that there is no relationship between the two things being tested. Wherever the observed data doesn't fit the model, the likelihood that the variables are dependent becomes stronger, thus proving the null hypothesis incorrect!?Question: Do Companies Selling Candy Equally Distribute Candy Colors in Bags?Null Hypothesis: Candy is evenly distributed; each bag contains the same number of colors.Alternate Hypothesis: One (or more) colors is found in greater frequency.Materials: several bags of colored candy, such as M & M's, Skittles, Reese's Pieces, or Gummy Bears. You will need approximately 100-200 candies.Procedure:1) Look into the bag and determine how many colors are present and write them into Table 12) Without counting, estimate the number (percentage out of 100%) of each color and write them into Table 1 under "Percentage Expected"3) Sort the candy and write down the number of each color into Table 1 under "Number Observed"4) Complete the table by determining the total number of candies and "number expected" columnsColor of CandyPercentage EstimateNumber ObservedNumber Expected?(total # of candy x percentage estimate)??????????????????????Total # of candies =?As you look at the data above, consider the two comparable numbers. The number you would expect to count if your percentage estimate was correct, and then the number you actually counted (number observed). For example, if you initially thought that you'd see 25% yellow candies, and you counted 200 pieces, you would then expect to see 50 yellow candies. You may have only counted 40 yellows.The Chi Square (X2) EquationIn order to complete the calculation, you sum each of the traits (colors) that you measured. To help you with this, we will break the process into steps.?Classes (colors)Expected (e)Observed (o)1????2????3????4????5?????Sum (add the values from row 1-5); this is your?X2?value?Use the chi square chart below to determine if your?X2?supports or rejects your hypothesis.The degree of freedom is determined by subtracting 1 from the number of colors you analyzed. (For example, if you had 4 colors to count, the degrees of freedom is 3)Summary and Analysis1) What was your initial hypothesis??2) How do you show that your hypothesis is correct (or incorrect)??3) Explain what is meant by a "good fit"??4) Propose a way that a chi square analysis could be used in other experiments, such as genetics or drug trials.AP BIOLOGY 2016-17 ACTIVITY Hardy Weinberg SimulationCase Study - Random MatingIn this simulation, you will simulate 5 generations of offspring beginning with a parental population that are all heterozygous. To represent alleles, you will use colored beads. Red represents the dominant allele T and green represents the recessive allele t. Place a bead in each hand and have your lab partner choose at random (without seeing the beads in your hand). You then do the same for your partner. The beads chosen represent the genotype of the next generation. You will need to do this twice so that you always have 2 children created from a "mating". For the next generation, you will need to replace your beads with your offspring - in effect you play your offspring as the parents of the next generation.Now that you are playing the offspring from your first mating. Find someone in the class at RANDOM to mate with again. To produce the second generation. Again you do this twice, so that you and your mate can both play the offspring for the next generation.Initial Parental Populationp2?+ 2pq + q2?= 1.0?25 + .50 + .25 = 1.0Now playing the offspring of the second generation, repeat the mating process again at random with anyone in the class. You will perform a total of 6 matings. At this point the class will need to report what their final genotypes are. When everyone is done, the teacher will tally the results on the board.Frequencies: TT ________ Tt _________ tt _________Determine the number of T alleles present in the last generation:Number of offspring with genotype TT _______________ x 2 = ______________ of A allelesNumber of offspring with the genotype Tt _____________x 1 = ______________ of A allelesTotal = _____________of T allelesDetermine the number of t alleles present in the last generation:Number of offspring with genotype tt _______________ x 2 = ______________ of a allelesNumber of offspring with the genotype Tt _____________x 1 = ______________ of a allelesTotal = _____________of t allelesDetermine p and qp = total number of T alleles divided by total number of alleles in population:(Total number of alleles in population is the number of people in the class x 2)?p = _______________q = total number of t alleles divided by total number of alleles in population:(Total number of alleles in population is the number of people in the class x 2)?q = _______________How does the final generation compare to the initial population in reference to the Hardy-Weinberg equation?Case 2 - SelectionInitial Parental Populationp2?+ 2pq + q2?= 1.0?25 + .50 + .25 = 1.0In this case, you will modify the simulation to make it more realistic. In the natural environment, not all genotypes have the same rate of survival. In this simulation, you will assume that offspring who are homozygous recessive (tt) never survive. You will run this simulation similar to the last one, except that if your offspring is aa, it does not reproduce and contribute to the next generation. In order to keep the population size constant, parents must mate until they get two surviving offsring, either TT or TtFrequencies: TT ________ Tt _________ tt _________Determine the number of T alleles present in the last generation:Number of offspring with genotype TT _______________ x 2 = ______________ of A allelesNumber of offspring with the genotype Tt _____________x 1 = ______________ of A allelesTotal = _____________of T allelesDetermine the number of t alleles present in the last generation:Number of offspring with genotype tt_______________ x 2 = ______________ of a allelesNumber of offspring with the genotype Tt _____________x 1 = ______________ of a allelesTotal = _____________of t allelesDetermine p and qp = total number of T alleles divided by total number of alleles in population:(Total number of alleles in population is the number of people in the class x 2)?p = _______________q = total number of t alleles divided by total number of alleles in population:(Total number of alleles in population is the number of people in the class x 2)?q = _______________How do the new frequencies of p and q compare to the initial frequencies in case 1?In a large population would it be possible to completely eliminate a lethal recessive allele? Explain.AP BIOLOGY 2016-17 ACTIVITY Hardy Weinberg Problem Setp2?+ 2pq + q2?= 1 and p + q = 1?p = frequency of the dominant allele in the populationq = frequency of the recessive allele in the populationp2?= percentage of homozygous dominant individualsq2?= percentage of homozygous recessive individuals2pq = percentage of heterozygous individuals1. ?? View the Dragons below.? The winged trait is dominant.2. You have sampled a population in which you know that the percentage of the homozygous recessive genotype (aa) is 36%. Using that 36%, calculate the following:?A. The frequency of the "aa" genotype.?B. The frequency of the "a" allele.?C. The frequency of the "A" allele.?D. The frequencies of the genotypes "AA" and "Aa."?E. The frequencies of the two possible phenotypes if "A" is completely dominant over "a."3. There are 100 students in a class. Ninety-six did well in the course whereas four blew it totally and received a grade of F. Sorry. In the highly unlikely event that these traits are genetic rather than environmental, if these traits involve dominant and recessive alleles, and if the four (4%) represent the frequency of the homozygous recessive condition, please calculate the following:?A. The frequency of the recessive allele.?B. The frequency of the dominant allele.?C. The frequency of heterozygous individuals.4. Within a population of butterflies, the color brown (B) is dominant over the color white (b). And, 40% of all butterflies are white. Given this simple information, which is something that is very likely to be on an exam, calculate the following:?A. The percentage of butterflies in the population that are heterozygous.?B. The frequency of homozygous dominant individuals.5. After graduation, you and 19 of your closest friends (lets say 10 males and 10 females) charter a plane to go on a round-the-world tour. Unfortunately, you all crash land (safely) on a deserted island. No one finds you and you start a new population totally isolated from the rest of the world. Two of your friends carry (i.e. are heterozygous for) the recessive cystic fibrosis allele (c).Assuming that the frequency of this allele does not change as the population grows, what will be the incidence of cystic fibrosis on your island? ?______6. Cystic fibrosis is a recessive condition that affects about 1 in 2,500 babies in the Caucasian population of the United States. Please calculate the following.?The frequency of the recessive allele in the population. ?______The frequency of the dominant allele in the population. ?______The percentage of heterozygous individuals (carriers) in the population. ?____7. This is a classic data set on wing coloration in the scarlet tiger moth (Panaxia dominula). Coloration in this species had been previously shown to behave as a single-locus, two-allele system with incomplete dominance. Data for 1612 individuals are given below:White-spotted (AA) =1469 Intermediate (Aa) = 138 Little spotting (aa) =5Calculate the allele frequencies (p and q )8. The allele for a widow's peak (hairline) is dominant over the allele for a straight hairline. In a population of 500 individuals, 25% show the recessive phenotype. How many individuals would you expect to be homozygous dominant and heterozygous for the trait??9. The allele for a hitchhiker's thumb is recessive compared to straight thumbs, which are dominant? In a population of 1000 individuals, 510 show the dominant phenotype. How many individuals would you expect for each of the three possible genotypes for this trait.10. REAL WORLD APPLICATION PROBLEMChoose a human trait to study and survey a population at your school. (Aim for at least a sample size of 50 to get meaningful results). Use your sample to determine the allele frequencies in the human population.Traits (dominant listed first)Hitchhiker's Thumb vs. Straight Thumbs?Widow's peak vs straight hairlinePTC taster vs non-tasterShort Big toe vs long big toeFree earlobes vs attached earlobesTongue rolling vs non-rollingBent little fingers vs straight little fingersArm crossing (left over right) vs right over leftEar points vs no ear pointsAP BIOLOGY 2016-17PROJECTHuman Genetic Diseases ProjectModified from Kathryn WeatherheadUse your textbook, the websites below, and other principle resources you can find to complete this assignment. on “Show featured gene” (near the top, on right side) a partner, select 5 of the following genetic disorders from List 1 and 5 of the disorders from list 2. For each one, using your own words:Tell on what chromosome(s) the gene occurs with the gene markedGenetic basis (explanation) of diseaseList symptoms/ means of diagnosisTell which group (gender, ethnic, age) is at most riskDescribe a treatment or cure (if there is one)Tell if its dominant recessive, autosomal, or sex-linked (explain)Draw a map of the chromosome, showing the location of the specified gene List 1List 2Alzheimer’s Disease● RetinoblastomaBreast Cancer● Polycystic Kidney diseaseCystic Fibrosis● ObesityDuchenne Muscular Dystrophy● Juvenile onset diabetesFragile X syndrome (X linked Retardation)● Colon Cancer type 1 or 2Huntington’s Disease● Amyotrophic lateral sclerosis Marfan Syndrome (ALS) “Lou Gehrig’s Disease”Phenylketonuria (PKU)● AutismSevere combined immunodeficiency (ADA)● SCIDSDown’s Syndrome● Werner’s Syndrome● EpilepsyFormat: You will be required to complete a “one pager” for each disorder. Make a Title Sheet that includes your name and title of project. Put list 1 first then list 2 diseases.Sources: Minimum of 3 citations from credible sources REQUIRED for each disease (on the back of each page). Remember to cite the sources of photos and images, too! Human Genetics Diseases Data FormDisorder:Source:Chromosome #:Symptoms:Diagnosis:Genetic explanation:Group at risk:Treatment:Cure:Autosomal/ Sex-linked:Dominant/ Recessive:Chromosome (sketch) map showing locus:Human Genetic DiseaseGrading CriteriaNAME_________________________________________SCORE____________10 diseases chosen/named (10 points)__________________Chromosome number (10 points)__________________Symptoms/ Diagnosis/ Genetic Explanation (30 points)__________________Group(s) at risk (10 points)__________________Treatment/ Cure (20 points)__________________Dominant/ Recessive/ Autosomal/ Sex-linked (20 points)__________________With explanationChromosomes Map (10 points) __________________Neatness/ creativity/ Format (10 points)__________________Sources (min. of 3) (10 points)__________________Total points earned:__________________Grade out of 130 points __________________Comments: ................
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