1. Exam II Lectures and Text Pages I. Cell Cycles – Mitosis (218 – 228) – Meiosis (238 – 249) II. Mendelian Genetics III. Chromosomal Genetics IV. Molecular Genetics – Replication – Transcription and Translation V. Microbial Models VI. DNA Technology

2. Chromosomal Genetics Genes are located on chromosomes Chromosomes can be visualized using various techniques Figure 15.1

3. Chromosomes: The Physical Basis of Mendelian Inheritance Several researchers proposed in the early 1900s that genes are located on chromosomes The behavior of chromosomes during meiosis was said to account for Mendel’s laws of segregation and independent assortment

4. CHROMOSOMAL GENETICS Discoveries in genetics and cytology – 1860s: Mendel - discrete inherited factors segregate and assort independently during gamete formation – 1875: Cytologists worked out mitosis – 1890s: Cytologists worked out meiosis – 1900: Several scientists independently rediscovered Mendel's principles

5. Discoveries in Genetics and Cytology 1902: Sutton, Boveri, and others noted parallels in the behavior of Mendel's factors (genes) and the behavior of chromosomes – both are paired in diploid cells – Both homologous chromosomes and allele pairs segregate during meiosis – fertilization restores the paired condition for both From these observations, biologists deduced the chromosomal basis of Mendel’s Laws

6. Chromosome Theory of Inheritance Figure 15.2 Yellow-round seeds (YYRR) Green-wrinkled seeds (yyrr) Meiosis Fertilization Gametes All F 1 plants produce yellow-round seeds (YyRr) P Generation F 1 Generation Meiosis Two equally probable arrangements of chromosomes at metaphase I LAW OF SEGREGATION LAW OF INDEPENDENT ASSORTMENT Anaphase I Metaphase II Fertilization among the F 1 plants 9: 3 : 1 1414 1414 1414 1414 YR yr yR Gametes Y R R Y y r r y R Y yr R y Y r R y Y r R Y r y rR Y y R Y r y R Y Y R R Y r y r y R y r Y r Y r Y r Y R y R y R y r Y F 2 Generation Starting with two true-breeding pea plants, we follow two genes through the F 1 and F 2 generations. The two genes specify seed color (allele Y for yellow and allele y for green) and seed shape (allele R for round and allele r for wrinkled). These two genes are on different chromosomes. (Peas have seven chromosome pairs, but only two pairs are illustrated here.) The R and r alleles segregate at anaphase I, yielding two types of daughter cells for this locus. 1 Each gamete gets one long chromosome with either the R or r allele. 2 Fertilization recombines the R and r alleles at random. 3 Alleles at both loci segregate in anaphase I, yielding four types of daughter cells depending on the chromosome arrangement at metaphase I. Compare the arrangement of the R and r alleles in the cells on the left and right 1 Each gamete gets a long and a short chromosome in one of four allele combinations. 2 Fertilization results in the 9:3:3:1 phenotypic ratio in the F 2 generation. 3 Genes are found on chromosomes. It is the chromosomes that segregate and independently assort during gamete formation.

7. Morgan’s Experiments Support Chromosome Theory Thomas Hunt Morgan (early 1900’s) – Provided convincing evidence that chromosomes are the location of Mendel’s heritable factors – He traced a gene to a specific chromosome

8. Morgan’s Choice of Experimental Organism He chose Drosophila melanogaster because they: a. Are easily cultured in the laboratory b. Are prolific breeders c. Have a short generation time d. Have only four pairs of chromosomes; – autosomes (II, III, and IV); and sex chromosomes (Females XX, males XY)

9. Wild Types vs. Mutants and Genetic Symbols Morgan first observed and noted wild type, or normal, phenotypes that were common in the fly populations Traits alternative to the wild type are called mutant phenotypes Morgan’s genetic symbols are now convention. A gene’s symbol is based on the first mutant discovered. – If the mutant is recessive: the first letter is lowercase. – If the mutant is dominant: the first letter is capitalized. – Wild-type trait: designated by a superscript +.

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Correlating Behavior of a Gene’s Alleles with Behavior of a Chromosome Pair Morgan discovered a single male fly with white eyes. He mated this mutant white-eyed male with a red-eyed (wild-type) female. Figure 15.3 – The F 1 generation all had red eyes (wild-type is dominant)

11. Figure 15.4 The F 2 generation showed a typical Mendelian 3:1 ratio of red eyes to white eyes. However, no females displayed the white-eye trait; they all had red eyes. Half the males had white eyes, and half had red eyes. Morgan then bred an F 1 red-eyed female to an F 1 red-eyed male to produce the F 2 generation. RESULTS P Generation F 1 Generation X F 2 Generation Morgan mated a wild-type (red-eyed) female with a mutant white-eyed male. The F 1 offspring all had red eyes. EXPERIMENT Eye Color is Linked to Sex – The F 2 generation showed the 3:1 red:white eye ratio, but only males (1/2) had white eyes Morgan deduced – That the white- eye mutant allele must be located on the X chromosome

12. White-Eye Allele is on the X CONCLUSION Since all F 1 offspring had red eyes, the mutant white-eye trait (w) must be recessive to the wild-type red-eye trait (w + ). Since the recessive trait—white eyes—was expressed only in males in the F 2 generation, Morgan hypothesized that the eye-color gene is located on the X chromosome and that there is no corresponding locus on the Y chromosome, as diagrammed here. P Generation F 1 Generation F 2 Generation Ova (eggs) Ova (eggs) Sperm X X X X Y W W+W+ W+W+ W W+W+ W+W+ W+W+ W+W+ W+W+ W+W+ W+W+ W+W+ W W+W+ W W W

13. Discovery of sex-linkage Females (XX) carry two copies of the gene, males (XY) have only one. – A mutant allele recessive, white-eyed female must have that allele on both X chromosomes, impossible for F 2 females in the experiment. – A white-eyed male has a single copy of the mutant allele - confers white eyes. Sex-linked genes: Genes on sex chromosomes. - commonly applied only to genes on the X.

14. White-Eyes: Specific Gene on a Specific Chromosome Morgan’s discovery that transmission of the X chromosome in fruit flies correlates with inheritance of the eye-color trait – Was the first solid evidence indicating that a specific gene is associated with a specific chromosome

15. Linked Genes Linked genes tend to be inherited together because they are located near each other on the same chromosome Each chromosome – Has hundreds or thousands of genes

16. How Linkage Affects Inheritance Morgan did other experiments with fruit flies – To see how linkage affects the inheritance of two different characters

17. Two Character (Dihybrid) Crosses Morgan crossed flies – That differed in traits of two different characters Double mutant (black body, vestigial wings) Double mutant (black body, vestigial wings) Wild type (gray body, normal wings) P Generation (homozygous) b + b + vg + vg + x b b vg vg F 1 dihybrid (wild type) (gray body, normal wings) b + b vg + vg b b vg vg TESTCROSS x b + vg + b vg b + vg b vg + b vg b + b vg + vgb b vg vg b + b vg vg b b vg + vg 965 Wild type (gray-normal) 944 Black- vestigial 206 Gray- vestigial 185 Black- normal Sperm Parental-type offspring Recombinant (nonparental-type) offspring RESULTS EXPERIMENT Morgan first mated true-breeding wild-type flies with black, vestigial-winged flies to produce heterozygous F 1 dihybrids, all of which are wild-type in appearance. He then mated wild-type F 1 dihybrid females with black, vestigial-winged males, producing 2,300 F 2 offspring, which he “scored” (classified according to phenotype). CONCLUSION If these two genes were on different chromosomes, the alleles from the F 1 dihybrid would sort into gametes independently, and we would expect to see equal numbers of the four types of offspring. If these two genes were on the same chromosome, we would expect each allele combination, B + vg + and b vg, to stay together as gametes formed. In this case, only offspring with parental phenotypes would be produced. Since most offspring had a parental phenotype, Morgan concluded that the genes for body color and wing size are located on the same chromosome. However, the production of a small number of offspring with recombinant phenotypes indicated that some mechanism occasionally breaks the linkage between genes on the same chromosome. Figure 15.5 Double mutant (black body, vestigial wings) Double mutant (black body, vestigial wings)

18. Autosomal Linkage Morgan determined that – Genes that are close together on the same chromosome are linked and do not assort independently – Unlinked genes are either on separate chromosomes or are far apart on the same chromosome and assort independently Parents in testcross b + vg + b vg b + vg + b vg Most offspring X or

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Recombination of Unlinked Genes: Independent Assortment of Chromosomes When Mendel followed the inheritance of two characters – He observed that some offspring have combinations of traits that do not match either parent in the P generation Gametes from green- wrinkled homozygous recessive parent (yyrr) Gametes from yellow-round heterozygous parent (YyRr) Parental- type offspring Recombinant offspring YyRryyrrYyrryyRr YR yr Yr yR yr

20. Recombinant (non-parental) Offspring Recombinant offspring – Are those that show new combinations of the parental traits When 50% of all offspring are recombinants – Geneticists say that there is a 50% frequency of recombination – This correlates to assortment between unlinked genes

21. Recombination of Linked Genes: Crossing Over Morgan discovered that genes can be linked – Sometimes the F 2 offspring in a dihybrid testcross do NOT occur in the 1:1:1:1 phenotypic ratio expected between unlinked genes – With complete linkage we expect to see only two phenotypes (the parental types) in the F 2 of a dihybrid testcross – If we see any recombinant phenotypes in a similar cross, then the linkage appears incomplete

22. Crossing Over Breaks Linkage Morgan proposed that – Some process must occasionally break the physical connection between genes on the same chromosome – Crossing over of homologous chromosomes was the mechanism

23. Figure 15.6 Testcross parents Gray body, normal wings (F 1 dihybrid) b+b+ vg + bvg Replication of chromosomes b+b+ vg b+b+ vg + b vg Meiosis I: Crossing over between b and vg loci produces new allele combinations. Meiosis II: Segregation of chromatids produces recombinant gametes with the new allele combinations.  Recombinant chromosome b + vg + b vg b + vg b vg + b vg Sperm b vg Replication of chromosomes vg b b b b vg Meiosis I and II: Even if crossing over occurs, no new allele combinations are produced. OvaGametes Testcross offspring Sperm b + vg + b vg b + vgb vg + 965 Wild type (gray-normal) b + vg + b vg b vg + b + vg + b vg + 944 Black- vestigial 206 Gray- vestigial 185 Black- normal Recombination frequency = 391 recombinants 2,300 total offspring  100 = 17% Parental-type offspring Recombinant offspring Ova b vg Black body, vestigial wings (double mutant) b Linked Genes – Exhibit recombination frequencies less than 50%

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Linkage Mapping: Using Recombination Data A genetic map – Is an ordered list of the genetic loci along a particular chromosome – Can be developed using recombination frequencies

25. Some Genes Are Linked More Tightly Than Others. Alfred H. Sturtevant, Morgan's student assumed: if crossing over occurs randomly, the probability of crossing over between two genes is directly proportional to the distance between them. – He used recombination frequencies to assign genes a linear position on a chromosome map – He defined one map unit (centimorgan) as 1% recombination frequency.

26. A Linkage Map Is the actual map of a chromosome based on recombination frequencies Sturtevant crossed flies using three characters (wing shape, body color and eye color) Recombination frequencies 9% 9.5% 17% bcn vg Chromosome The b–vg recombination frequency is slightly less than the sum of the b–cn and cn–vg frequencies because double crossovers are fairly likely to occur between b and vg in matings tracking these two genes. A second crossover would “cancel out” the first and thus reduce the observed b–vg recombination frequency. In this example, the observed recombination frequencies between three Drosophila gene pairs (b–cn 9%, cn–vg 9.5%, and b–vg 17%) best fit a linear order in which cn is positioned about halfway between the other two genes: RESULTS A linkage map shows the relative locations of genes along a chromosome. APPLICATION TECHNIQUE A linkage map is based on the assumption that the probability of a crossover between two genetic loci is proportional to the distance separating the loci. The recombination frequencies used to construct a linkage map for a particular chromosome are obtained from experimental crosses, such as the cross depicted in Figure 15.6. The distances between genes are expressed as map units (centimorgans), with one map unit equivalent to a 1% recombination frequency. Genes are arranged on the chromosome in the order that best fits the data. Figure 15.7

27. Incomplete Linkage The farther apart genes are on a chromosome – The more likely they are to be separated during crossing over – Linked genes, so far apart on a chromosome that the recombination frequency is 50%, are indistinguishable from unlinked genes that assort independently. – Linked genes that are far apart can be mapped using intermediate genes

28. Many Fruit Fly Genes Were mapped initially using recombination frequencies Figure 15.8 Mutant phenotypes Short aristae Black body Cinnabar eyes Vestigial wings Brown eyes Long aristae (appendages on head) Gray body Red eyes Normal wings Red eyes Wild-type phenotypes II Y I X IV III 0 48.557.567.0 104.5

29. Linkage Groups Correspond to Chromosomes Sturtevant and his coworkers mapped other Drosophila genes in linear arrays – Crossover data clusters known mutations into four major linkage groups. – Drosophila has four sets of chromosomes, so this clustering is evidence of genes on chromosomes.

30. Genetic Mapping Types of mapping – Maps based on crossover gives the relative position of linked genes. – Cytogenetic maps: locate genes with respect to chromosomal features, such as stained bands that can be viewed. – The ultimate genetic maps are constructed by sequencing DNA; in this case, distances between gene loci can be measured in nucleotides.