1. Topic 4 Genetics

2. 4.1 Chromosomes, genes, alleles, mutations Eukaryotic chromosomes are structures made up of DNA and proteins. Animation of chromosome structure Second Animation

3. Some definitions Gene: a heritable factor that controls a specific characteristic. Coded by a portion of DNA. Allele: Alternate form of a gene. Codes for the same characteristic and is at the same location (locus) on the chromosome but the DNA sequence is slightly different. Genome: The entire set of genetic information of an organism Gene Mutation: A change in the base sequence of a gene. This can be a small as one base change in an entire gene.

4. Sickle Cell Anemia An example of just one change in a base that causes a significant change in the organism and a life threatening disease. The triplet code on the mRNA GAG is changed to GTG. This means that the amino acid Valine is translated instead of Glutamic acid These 2 amino acids are very different chemically and so affect the final protein, in this case hemoglobin. The Hbs hemoglobin does not carry oxygen as well as normal, Hba hemoglobin

5. Sickle Cell Anemia This causes the red blood cell to have a sickled shape. These RBCs do not pass through the small capillaries well and get stuck, occluding blood flow This causes problems in many body systems and causes severe pain Animation 1 Animation 2

7. 4.2 Meiosis Meiosis is a reduction of the number of chromosomes by half and division of the nucleus. A diploid nucleus (one with a pair of each chromosome) is divided into a haploid nucleus (one that has only one of each chromosomes. So for humans meiosis reduces a gamete to 23 chromosomes from the original 46.

8. Homologous chromosomes In a diploid cell (all cells but gametes) the pairs of chromosomes are called homologous because they have the same genes on each chromosome. Although the gene is the same the genetic information may be different. Each gene has two possible types (alleles). Homologous chromosomes have the same size and shape and have the same genes at the same place.

10. Process of meiosis Meiosis happens in 2 steps: meiosis I and II In the first step the chromosome number is halved In the second step the chromosomes are replicated, this is just like mitosis The process is sometimes called reduction-division. The parent cell is 2n and the result is 4 daughter cells with n # of chromosomes. How is this different than mitosis?

11. Meiosis I overview

12. Prophase and Metphase I

13. In Prophase homologous chromosomes are paired together, called tetrads Crossing over is the exchange of DNA between non sister chromatids Points where crossing over occurs is called chiasmata In metaphase the homologous pairs line up at the equator The way a pair of chromosomes is oriented is by chance, this is called Independent Assortment. There is a 50/50 chance which allele will end up in which cell. (remember one allele is maternal, one is paternal)

14. Anaphase, Telophase, Cytokinesis Homologous chromosomes are pulled apart Sister chromatids are still attached

15. Anaphase I, Telophase I, Cytokinesis In telophase each ½ of the cell has a haploid set of replicated chromosomes, each chromosome I made up of 2 sister chromatids. One or both chromatids have regions of nonsister DNA Cytokinesis happens during telophase There is no additional replication between MI and MII

16. Prophase II, Metaphase II

17. Spindle fibers reform in prophase Single chromosome line up at the equator The sister chromatids are NOT identical The assortment of non identical sister chromatids further adds to genetic variation

19. At the end of meiosis there are 4 daughter cells Each cell is genetically different from the others and from the parent cell

21. Meiosis II

23. Animation/quiz Animation 2/ questions

24. Compare mitosis and meiosis

26. Non-disjunction Non-disjunction means that in either meiosis I or II, the chromosomes do not split apart. What would happen in MI if the homologous pairs did not split? What would happen if they didn’t split in MII? In both cases this leads to disease or more often the fertilized egg does not even develop. Some cells will be missing that chromosome and some will have an extra copy. Cells without the chromosome do not develop at all.

31. Trisomy 21 If it has an extra copy of a chromosome it will also not usually develop. In the case of chromosome #21 the fetus does develop but has significant problems. Other trisomies: 13, XY

32. Karyotyping A karyotype is a display of condensed chromosomes arranged in pairs. Cells are grown in a culture and then stopped when they are in metaphase. They are then stained and photographed Chromosomes are paired based on size and shape A karyotype can be used to screen for abnormal number of chromosomes or for defective chromosomes Sex can also be determined

33. Human karyotype

35. 4.3 Theoretical Genetics Genotype: the alleles of an organism Phenotype: the characteristic of an organism Homozygous: 2 identical alleles Heterozygous: 2 different alleles Dominant allele: an allele that has the same effect on the phenotype whether it is present in homozygous or heterozygous state Recessive allele: an allele that only has an effect when it is in homozygous state Codominant allele: both alleles are expressed

36. Apply Definitions Using our Rebop creatures, give an example of each of the definitions: Genotype: Phenotype: Homozygous: Heterozygous: Dominant allele: Recessive allele: Codominant allele

37. Genotype: Tt Phenotype: curly Homozygous: TT or tt Heterozygous: Tt Dominant allele: T- curly Recessive allele: t- straight Codominant: QQ= red, Qq= orange, qq= yellow

38. Punnet Square A way to determine genotypes and phenotypes of genetic crosses. We will follow some genetic crosses Pure breeding individuals are homozygous P generation is parent

46. Practice with Punnet squares Cross a true breeding pea plant with yellow seeds with a true breeding plant with green seeds. Yellow is dominant. Cross one of the offspring from above with a green seeded plant. You can deduce some rules:  Cross homozygous dominant with recessive and get  Cross 2 heterozygous and get  Cross a heterozygous with a recessive and get

47. Test Cross What is you have an individual with a dominant phenotype, how do you know if it is homozygous or heterozygous? Cross it with a recessive phenotype. Determine the genotypic and phenotypic ratios for the 2 possibilities

49. Practice problems

50. Locus: position of gene on chromosome Test cross: a way to test if a dominant phenotype is heterozygous or homozygous dominant. Cross the individual with a recessive phenotype  if any offspring have recessive phenotype then the individual was heterozygous

51. Some genes have more than 2 alleles This is called multiple alleles Any one individual can only have 2 alleles, but there can be more that 2 in the population An example is blood type in humans: There are 3 alleles: A, B and O A and B are codominant and O is recessive to both A and B So blood type in humans is an example of codominance AD multiple alleles

53. What possible genotypes could a person have if they had type B blood? Type O blood? Type B: BB or Bi, O only ii A baby girl is born with blood type O. Her brother is blood type AB and her mother is blood type A. What is the father’s blood type? What are the genotypes of everyone. Baby girl: ii, brother: I A I B, father: I B i, mother:I a i.

54. Inheritance in Corn We will look at phenotypes of corn seeds and analyze the results to determine the genotypes and inheritance patterns. Because we will not be counting enough seeds to approach exact theoretical numbers we need a way of knowing if our actual results are close enough to the theory. We will use a test called the chi-square test.

55. Chi square test Test compares observed and expected outcomes. In biology we need to be 95% sure that any differences we see are due to chance and not some alternate mechanism. We will look at some of Mendel”s actual results: Flower position in F1 generation. Axial:651, terminal: 207. What do you think the dominant trait is, explain the inheritance pattern, what is the theoretical ratio you would expect? What is the real ratio?

56. Axial is dominant, the pattern is based on 2 heterozygous parents, produces a theoretical ratio of 3:1 and an actual ratio of 3.14 to 1. Are the differences due to chance or some other inheritance pattern? Use chi square to find out. First determine the expected numbers: total # is 858, so we would expect 214.5 terminal and 643.5 axial.

57. x 2 = sum of (0-E)2/E (207-214.5)2/214.5=.262 (651-643.5)2/643.5=.087 Sum of these=.347 Go to table of p values, look for.05 across the top then go down to the row with correct degrees of freedom (n- 1). If the value is less than your x 2 then the results you see are not significantly different.

58. Sex Chromosomes Sex chromosomes determine sex of the individual. In humans: XX-  female, XY-  male So all humans have an X and the X chromosome has important genetic information Since these are not homologous chromosomes, this means that traits carried on the X chromosome do not follow the same rules. Genes on the sex chromosome (X in humans) are sex linked

59. Dihybrid cross Color in mice is codominant: a CRCW genotype produces a spotted cat. Long ears is completely dominant over short ears. What is the genotypic and phenotypic ratio of a cross between 2 heterozygous cats? 6:3:3:2:1:1

60. Inheritance in sex linkage Because the sex chromosomes are not homologous, inheritance patterns are different. An example of the human genetic disorder that is sex- linked is color blindness The condition is recessive- which means you need to have 2 recessive alleles or if you are male only one because you do not have the corresponding allele. So X b X b or X b Y would be color blind

61. Problem A woman with normal sight marries a normal sighted male and has a son who is color blind. What are the genotypes of the family? What chance does this family have of having another son who is colorblind, chance of having a daughter who is colorblind? Chance that next child will be colorblind? Mother: XbXB, father XBY, son XbY 50% chance next son will have it 0% chance daughter will get it (must get a b from mom and dad 25%chance next child will have it

62. Hemophilia Follows the same pattern: recessive, X linked. A girl is born with hemopilia, her mother is normal, what are the genotypes and phenotypes of her parents? Girl: XhXh, Mother: XhXH, Father XhY

63. Females can be heterozygous or homozygous with respect to sex-linked genes Carrier: In human genetics, with reference to a recessive condition, an individual who is heterozygous Female carriers are heterozygous and normal, if condition is recessive.

64. More Problems Arizona genetics problems sex-linked A female calico cat mated with a black cat. All the female cats were black and all the male cats were calico. Explain. Female cat: XcXc, male: XBY, all female offspring: XcXB, all male XcY

65. Human Genetics Because human inheritance is normally based on looking back at the families history, we have a different way of analyzing inheritance patterns called a pedigree. A pedigree is a family tree that describes the traits and of parents and children across generations.