Warm Up: For these Guinea pigs, tan hair is dominant over black.

1. Warm Up: For these Guinea pigs, tan hair is dominant over black. • 1. What are the genotypes for each individual? • 2. Who is homozygous and who is heterozygous? • ----------------------------- Dad Mom tt Tt tt • What are the alleles? • What are the genotypes/phenotypes? • Where did the ALL alleles come from? • Predict the likelihood that this genotype/ phenotype would result. Baby

2. Key Ideas • How can a Punnett square be used in genetics? • How can mathematical probability be used in genetics?

3. Objectives: Using Mendelian Genetics • Describe how a Punnett square is used in genetics. • List ways to express mathematical probability in genetics.

4. Vocabulary • Punnett square • Probability • Pedigree • Genetic disorder

5. What You Should Recall. We’re looking as this… • You know that Mendel gave us two important laws. • Independent assortment: Speaks to the fact that genes separate independent of one another • Segregation: Speaks to the fact that alleles of the same gene have equal probability of segregating into gametes. • Once the gametes are formed, “Mendelian genetics” also gives us an outline on how to figure out what the likelihood of an offspring has to show particular traits, based upon dominant & recessive alleles. • Today you will learn how to figure out the probability of certain traits being inherited and shown, using Punnett Squares.

6. Using Punnett Squares • How can you predict the chances an offspring will have a certain genotype, therefore phenotype? • A Punnett square is a model that predicts the probability of likely outcomes of a genetic cross. • Remember that a cross is “to mate or breed two individuals.” • A Punnett square shows all of the genotypes that could result from a given hybrid cross. • The important thing to remember is that this shows what could happen…not necessarily what always happens. • The simplest Punnett square consists of a square divided into four boxes. • This is a monohybrid cross… • The combination of letters in each box represents one possible genotype in the offspring.

7. Meiosis EVERY CHILD BORN WOULD HAVE THE SAME CHANCES TO INHERIT ANY OF THE COMBINATIONS OF ALLELES! This isn’t necessarily one child… this represents the probability one child will have a certain genotype… & genotype determines phenotype Fertilization Meiosis Probable zygotes that can be produced by one fertilization

8. Using Punnett Squares Constructing a Simple Punnett square for Monohybrid Crosses • Draw a 2 x 2 chart. • Conclude what the genotype of the parents are based upon the description given. • Write the GENOTYPE of the parents on the top and sides of the chart. There is one letter per column & row. This represents the allele being donated by a gamete during fertilization. • Fill in the columns and rows corresponding with the heading allele. These are the possible allele combinations for the offspring

9. Ratios and Punnett Squares • A Punnett square basically predicts: .. • all the possible combinations for alleles for each trait examined. • This can be use to predict the likelihood of traits of an offspring… the probability of things happening. • It also reveals the ratio of one type of offspring compared to the other types offspring. • The ratio can help compare genotypes to other genotypes or phenotypes to other phenotypes. • It ultimately shows how the possible offspring compare to the other offspring.

10. Ratio Review • What is a ratio? • A ratio is an expression, of at least two numbers, that is used to compare values. • It is written separated by a colon. • Ex. If there are (normally) 5 fingers for every hand would be written as 5:1 ratio of fingers to hands. • It would be said as “a ratio of 5 fingers to one hand” • A ratio shows how many events happen compared to the events of others.

11. Ratios of Fingers to Hands • There is a ratio of five fingers to every one hand. • Written: 5:1 3 2 4 1 5 1

12. Using Punnett Squares • Punnett squares give us possible genotypes to determine phenotypes. • In a monohybrid homozygous dominant cross, all of the offspring will be homozygous. • The ratio of the genotypes will be 1 YY, meaning all the offspring will be the same genotype for the alleles. • This is called the genotypic ratio. • The phenotypic ratio describes the comparison of all the traits displayed. • The phenotypic ratio here is all the dominant form… all dominant.

13. Using Punnett Squares • In a monohybrid cross between a homozygous dominant and a homozygous recessive all the offspring will be heterozygous (ex. Yy). • What are the genotypic & phenotypic ratios here? • The genotypic ratio would again be all Yy. • Because there is no other alternative, there is no other thing to compare to. • Since there’s only 1 genotype, there can be only 1 phenotype. • As such, the phenotypes would be all the dominant form.

14. Using Punnett Squares • In a monohybrid heterozygous cross the genotypic ratio will be 1 YY : 2 Yy : 1 yy. • This is what Mendel observed in his F2 generations!

15. Using Punnett Squares • Phenotypes • Remember, genotype determines phenotype, but the ratio is not always the same between the two. • You need to think about the trait that will be shown depending upon the allele combination. • In a monohybrid cross between homozygotes all the offspring will be the same, therefore all the offspring will express the same trait. • However, in a monohybrid heterozygote cross, where the genotypic ratio is 1 : 2 : 1, • the phenotypic ratio will be 3 : 1.

16. Punnett Squares

17. Dihybrid Crosses Mendel noticed that alleles for one gene do not affect the inheritance of the alleles for another gene. = independent assortment • This makes predicting the probability of inheriting a combination of two non-linked genes more challenging but entirely possible. • What does non-linked mean?

18. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy • Take a minute and figure out the possible gametes.

19. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy • Take a minute and figure out the possible gametes. PY

20. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy • Take a minute and figure out the possible gametes. pY PY

21. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy • Take a minute and figure out the possible gametes. Py pY PY

22. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy • Take a minute and figure out the possible gametes. py Py pY PY

23. Dihybrid Crosses. • In order to accomplish this you must consider all possible gametes for an individual, then perform the cross. • Let’s try crossing two heterozygotes for pea color and flower color. • PpYy x PpYy… Conduct the cross PY pY Py py PY pY Py py

24. Trihybrid Crosses • We have over 30,000 genes. • Not all of them are “Mendelian” but many are. • How would you predict the chances an individual inherited: • Brown eyes • Blonde hair • A widows peak • Attached ear lobes • Hitchhikers thumbs • A taco tongue • & freckles? • The more variables you consider the higher the degree of difficulty is inheritant. • We’ll stop at three different, non-linked genes but considering these will help you appreciate just how unique you are!

25. Trihybrid Crosses • Consider crossing heterozygotes for flower color, pea color, & pea shape. • PpYyRr x PpYyRr • What should you do? • First consider all the gametes that could form from each parent (independent assortment & segregation assumed). • PYR – PYr – PyR – Pyr – pYR – pYr – pyR – pyr • Then set up your 8 x 8 grid and distribute the gametes.

28. Punnett Square Practice/Homework Complete the worksheet.

29. Wednesday February 6, 2013Copy onto your ‘Quizzie’ paper the following question. Answer it and save it to turn in. If you don’t know an answer, get a book and find it or review with a friend. Blanks will count against you and wrong answers don’t help you. • Quizzie • Q1: If a mom that’s homozygous recessive for hair color (she’s blonde) and a dad is heterozygous for hair color (he has black hair), what will be the possible genotypes of any children they have? Show this with a Punnett Square. • Q2: What chance do the children have to get blonde hair? • Q3: What are the ratios for the genotypes and phenotypes? • ----------------------------- • Agenda: • Check Punnett Squares • Discussion: Test Crosses. • QL: Test Crosses

30. Punnett Squares: Answers

31. Thursday February 7, 2013Copy onto your ‘Quizzie’ paper the following question. Answer it and save it to turn in. If you don’t know an answer, get a book and find it or review with a friend. Blanks will count against you and wrong answers don’t help you. • Quizzie #3:Imagine you are a farmer and wanted to start selling green sweet peas (what Mendel produced and studied). You buy a pea plant that is sold to you as a true-breeding green pea plant for nice round peas. You are skeptical because the guy who sold it to you seemed shady. You are intending to plant several acres with this plant’s seeds and have a lucrative business. • Q1: What specific technique could you perform to find out exactly what the genotype of your plant is? • Q2: What phenotype would you want all the offspring from this technique to be? • Q3: If the offspring of a test cross all have the dominant trait, is the genotype of the individual being tested heterozygous or homozygous? -------------------- • Agenda: • Discussion: Probabilities • Penny Genetics Lab • Hand in Testcross MiniLab

32. Using Probability • A Punnett square shows the possible outcomes of a cross, but it also is used to calculate the probability of each outcome. • Probability is the likelihood that a specific event will occur out of the total number of events. • Probability can be calculated and expressed in many ways. • Probability can be expressed in words, as a decimal, as a percentage, or as a fraction.

33. Using Probability, continued • Probability formulas can be used to predict the probabilities that specific alleles will be passed on to offspring. • Probabilities are usually expressed as decimals or as percentages although fractions are okay. • 2/4 = ½ = 0.5 = 50% • ¼ = 0.25 = 25% • ¾ = 0.75 = 75% • The possible results of a heterozygous cross (which is trying to predict the genotypes of offspring from the mating of two heterozygotes) are similar to those of flipping two coins at once.

34. Using Probability • Punnet Squares are nice tools to use but the real question remains… • How can you be sure that the Punnet squares accurately show how genetics really works? • The solution will hopefully be revealed in the next exercise… • Penny Genetics

35. Penny Genetics LabTesting the validity of Punnett Squares. • In groups of two you will perform an investigation into whether Punnett Squares can be used to predict randomness of nature. • For the next 5 minutes… Completely read the lab. I’ll answer questions then. • A Punnett Square makes a prediction but does it match the randomness in nature? Perform a Punnett Square and then flip coins to see if they match. • Part I: First: Figure out the PHENOTYPES based upon the description. Second: Predict if the PUNNETT SQUARE will match the COIN FLIPS Third: Complete the PUNNETT SQUARE (this is the prediction) Fourth: Flip the COINS 100x. Fifth: COMPARE the two. • You may write on the lab, but don’t lose it or you’ll have to hand write it or print it off the website. • Your objective is to get through all of Part I & Part II if everything goes good so work diligently! Complete everything today to save yourself homework. • This Lab is worth 125 points. Due Friday.

36. Monday February 11, 2013Copy onto your ‘Quizzie’ paper the following question. Answer it and save it to turn in. If you don’t know an answer, get a book and find it or review with a friend. Blanks will count against you and wrong answers don’t help you. • Quizzie #4: In pea plants, tallness (T) is dominant to shortness (t). Crosses between plants with these traits can be analyzed using a Punnett square similar to the one shown below. • Q1: Complete this Punnett Square. • Q2: Box 2 and box ____________________ in the Punnett square represent plants that would be heterozygous for the trait for tallness. • Q3: The phenotype of the plant that would be represented in box 4 of the Punnett square would be ____________________. -------------------------------------------------------------------------------------------------------------------------------- • Agenda: • Discussion: Pedigrees • In-class/ HW Activity Pedigree Analysis • Penny Genetics DUE. Turn these in to the inbox.

37. Applications of Mendelian Genetics • If a child expresses, shows, a recessive trait (for instance red hair) but the parents express the dominant trait what are the genotypes of the parents & how can you figure this out?

38. The point of using a Punnett Square • Punnett squares are useful when predicting the ratios of offspring. • For example, is you want to know the probability of how many siblings in your family can have the phenotype of black hair your can calculate that if you know the genotypes of your parents. • But what if you don’t know their genotypes? • The 1st option is using a test cross.

39. Test Cross Mini Lab • If you aren’t sure what the genotype of a parent showing a dominant trait is you perform a test cross. • In a test cross, you always cross the unknown with a homozygous recessive individual. • The difference is in the “?” allele. • What does it mean if half of the offspring show the recessive trait?

40. Test Cross • The test-cross mating can have two possible phenotype outcomes. • All dominant offspring • What would the “?” have to be?

41. Test Cross • The test-cross mating can have two possible phenotype outcomes. • Half recessive offspring. • What would the “?” have to be?

42. Mendel’s Second Experiments • Genes that are linked, or are located close together on the same chromosome, will rarely separate independently. • The one flaw in Mendelian genetics is that the law of independent assortment would suggest that each gene has nothing to do with other genes. • Genes are said to be linked when they are close together on chromosomes. • Examples include sex-linked genes…all X and Y genes stay together • Scientists now know that many genes are linked to each other as parts of chromosomes. • The only genes that follow Mendel’s law of independent assortment are those that are far apart or on different chromosomes.

43. Genes Linked Within Chromosomes • Many traits do not follow Mendel’s laws because he studied the simplest kinds of heredity where characters are determined by independent genes. • During meiosis, genes that are close together on the same chromosome are less likely to be separated than genes that are far apart. • We discussed this in section 2 when we challenged independent assortment. • Genes that are close together, as well as the traits they determine, are said to be linked. • Linked genes tend to be inherited together.

44. Linked v Non-linked

45. What is Sex-Linked? How does it happen? STANDARD GENDER DISTRIBUTION PROBABILITY = 50% MALE - 50% FEMALE STANDARD GENDER DISTRIBUTION PROBABILITY = 50/50 BUT ADD INTO THE MIX COLOR-BLINDNESS, WHICH IS ONLY FOUND ON THE ‘X’ CHROMOSOME

46. A Sex-Linked TraitRed-Green Color Blindness Can you see the numbers? Trace from x to x… there’s a line there. X X

47. Sex-Linked Gene Inheritance Notice the distribution of the alleles. In this case you must take two things into account. Sex & the allele.

48. Test Crosses & Linkage Exercises • Complete the worksheet for homework.

49. Show the cross of a man who is a carrier of hemophilia with a woman who is a carrier along with the genotypic ratio for the possible offspring.

50. The Royal Disease • European Royalty in the 19th & 20th centuries came with a price. • Although many were spared the horrible tragedy of bleeding to death, some were not so lucky due to the pervasive recessive X-linked trait hemophilia.