Lecture powerpoints under resources Pop quizzes are possible Quizzes during discussion sessions are not for a grade but are a valuable resource

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1 Day 1 General information Lecture powerpoints under resources Pop quizzes are possible Quizzes during discussion sessions are not for a grade but are a valuable resource Traits and behaviors that are transmitted through generations, and understanding the biological transmission of these traits and behaviors We see a lot of diversity in nature Controlled by genetics Gregor Mendel: late 1800s for 10 years; published in 1860s Looked into pea plants; 9 traits CONTRIBUTIONS Quantitative approach to research Concepts of units of heredity Concept of dominant and recessive traits Had no idea about the mechanism of the transmission of traits DNA: made of deoxyribose sugar, nucleotide, phosphate AT and CG are complementary base pairs Central Dogma : DNA, transcription, mrna, translation with ribosome, proteins (gene product) Genes do not necessarily code for proteins: can make trna, etc. Genes may change in a cell through mutation or genetic recombination Genes are NOT turned on all the time

2 Hormonal, developmental, environmental regulation, etc. Ex. Change from gamma-globin (produced in fetal liver) to beta-globin gene expression (produced in bone marrow) in fetus right before birth o Change occurs because gamma-globin will become toxic, and if there is too much oxygen in the blood, it won t release to the cells Sickle-cell: hemoglobin aggregates in the red-blood cells, which results in crescent-shaped red blood cells (controlled by a single gene) Model organisms in genetics: why use them? Monkeys, flies, rats, bacteria Each species is used for different purposes Much faster reproduction May be similar to humans, but not always Green fluorescent protein (GFP) fused to any gene a scientist wants, and that shows when the gene is expressed In 1900, chromosome movements during cell division discovered Shown that chromosomes drive genetics DNA is packaged by wrapping around histones to form nucleosomes, which fold to make chromatin, which condense to become chromosomes Solves space problem, but presents difficulty in having to express the DNA (the tightly packed DNA is hard to read) DNA + protein in a chromosome = chromatin Tightly packed chromatin = heterochromatin Loosely packed chromatin = euchromatin (looks like beads on a string) Day 2: Mitosis and Meiosis Mitosis: somatic cells that divide in sexually reproducing organisms Sexual reproduction produces much more genetic variation than asexual reproduction Germ cells undergo meiosis (important for sexual reproduction) Meiotic recombination Centromeres are the part of DNA that connect sister chromatids (don t have genes, but ARE made of DNA) Attached together by the protein cohesin

3 Telomere is DNA that has genes that don t code for anything and are at the top of the chromatids; stable ends of the chromosome When sister chromatids are alone, they are called chromosomes, not chromatids Chromosome 1 from mom and chromosome 1 from dad are homologous Are alike in size and structure and carry information for the same traits May have different alleles at different, and so are not identical Spindle microtubules form at the kinetochore Chromatin: DNA and protein in a chromosome The Cell Cycle and Mitosis Interphase: an extended period between cell divisions, DNA synthesis, and chromosome replication phase; normal function, growth Phase check points: key transition points that determine whether or not the cell will continue on to the next stage of mitosis G1 (initial growth; checkpoint at end), S (DNA synthesis), G2 (after this phase, there is a checkpoint) phases At the G0 stage, there is no replication or preparation for it Occurs in most cells, means that cells are not dividing M phase (mitotic phase) Prophase (chromosomes condense with 2 chromatids each, spindle forms) Prometaphase (nuclear membrane disintegrates, spindle microtubules attach to chromosomes) Metaphase (chromosomes line up in the middle of the cell at the metaphase plate) Anaphase (sister chromatids separate and move towards opposite poles) Telophase (chromosomes arrive at spindle poles, nuclear membrane reforms, chromosome start to unravel) Cytokinesis is NOT part of mitosis: must produce new cell membrane Cyclin-dependent kinase (CDKs): family of protein kinases that play a well-established role in the regulation of the eukaryotic cell division cycle and have also been implicated in the control of gene transcription and other processes P54 RNA helicase: transcription factor, protein that binds to a specific DNA sequence to control the transcription of DNA to mrna If the cell aborts the replication process after the S phase, it will have double the amount of DNA, making it polyploidy

4 Can be controlled with drugs In nature, many species are polyploidy, especially plants All species were polyploids at one time, but some evolved later to be diploid Mitosis produces 2 cells that are genetically identical to each other and their parent cell Newly formed cells have a full complement of chromosomes, about half (but not necessarily identical) cytoplasm and organelle content of parent cell In our body, the majority of cells don t divide, and thus do not undergo mitosis Meiosis: the basis of sexual reproduction and genetic variation; the production of haploid gametes Fertilization: the fusion of haploid gametes Before meiosis is interphase: DNA is synthesizes and chromosomes are replicated Two parts: in meiosis 1, homologous chromosomes are separated AKA reduction division because the chromosome number is reduced in half In meiosis 2, sister chromatids are separated AKA equational division; chromosome number is unchanged Methods for increasing genetic variation Crossing over happens in prophase 1, and the intersection of the sister chromatids is called the chiasmata o Occurs at random places along the chromosomes, making new combinations of maternal and paternal DNA Random distribution of chromosomes in meiosis: when homologous chromosomes line up at the metaphase plate in metaphase 1, and when sister chromosomes line up in metaphase 2 Meiosis 1 is very similar to mitosis except that it involves separating the homologous chromosomes Meiosis 2 is mitosis with sister chromatids (very similar method and processes) Cohesion: a protein that holds chromatids together; is the key to chromosome behavior Broken down in anaphase by separase, which allows sister chromatids to separate Holds homologs together at chiasmata along chromosome arms in meiosis Shugoshin: only in meiosis NOT mitosis Shugoshin protects the cohesion at the centromere during anaphase 1, which keeps the sister chromatids together while the homologous chromosomes are being separated

5 Broken down during anaphase 2, which allows the cohesion to degrade, which allows the sister chromatids to separate Independent assortment: different way that chromosomes line up at the metaphase plate Colchicine: hormone that inhibits microtubule polymerization during spindle formation (prophase), preventing chromosome movement When removed in late prophase, the cell re-enters interphase Results in a tetraploid cell Consequences of meiosis Four haploid cells (1/2 original chromosomes), each genetically different from both one another and from the parent cell Kinetochore: the protein structure on chromatids where the spindle fibers attach during cell division to pull the sister chromatids apart Form in eukaryotes, assemble on the centromere and link the chromosome to microtubule polymers from the mitotic spindle during mitosis AND meiosis Sister chromatids start out with identical genetic material in both mitosis and meiosis How would each of the following events affect the outcome of mitosis or meiosis? 1. Mitotic cohesin fails to form early in mitosis a. Because cohesin is the protein that attaches sister chromatids together at the centromere until anaphase, failure to form in mitosis would lead to the ability of the chromosomes to separate prior to anaphase, which could result in the improper segregation of the chromosomes. 2. Shugoshin is absent during meiosis a. Shugoshin is the protein that protects cohesin from being degraded in the anaphase stage of meiosis 1 and allows the sister chromatids of each chromosome to stay together until anaphase 2. If it is absent, the sister chromatids will separate at anaphase 1 along with the homologous chromosomes, which will lead to gametes with an incorrect number of chromosomes. 3. Shugoshin does not break down after anaphase 1 of meiosis a. If shugoshin does not break down after anaphase 1 of meiosis, cohesin will not be degraded in anaphase 2. This will make the sister chromatids unable to separate and result in improper segregation of chromosomes in the produced gametes. 4. Separase is defective a. Separase is the enzyme that breaks down cohesin, which allows sister chromatids and homologous chromosomes to separate in both mitosis and meiosis. If it does not work, the chromosomes and chromatids will not separate, and the result will be gametes with an improper number of chromosomes.

6 SAMPLE QUESTIONS FOR TESTS Design a genetic screen to identify mutants affected only in meiosis but not in mitosis. Genetic screen: test for a phenotype Find a way to identify the presence of shugoshin What model system would you use to perform this screen? Would need species that reproduces with meiosis, so not bacteria What difficulty might you face in identifying these mutants? How would you get around these problems? Day 3: Mendelian Genetics Sources of genetic variation Random fertilization Nature of 23 chromosomes: produces 2 23 different combinations We predict offspring genotypes and phenotypes with Punnett squares! Reduction division Gamete has ½ the alleles of the diploid genotype Mendel: father of genetics: important postulates 1. Genetic factors occur in pairs 2. When 2 different factors are present in an individual, one unit is dominant to the other, which is RECESSIVE (principle of dominance) 3. During gamete formation, the 2 units present in an individual separate randomly, so each gamete receives only 1 (segregation) a. Anaphase 2 separates sister chromatids so that each gamete ends up with only 1 copy of each chromosome 4. Independent assortment. Genetic factors for different traits sort independently into the gametes. a. Happens mostly in meiosis 1 during metaphase b. Metaphase 2 produces some variation because of the results of crossing over Meiosis 1 is when the homologous chromosomes are separated: the main place for segregation Even though we can say with confidence that someone is homozygous, the results could be due to chance and therefore we cannot be 100% SURE (think of example of father with 8 children who all have his dominant trait and the mother has the recessive. While it is most probable that he is homozygous dominant for this trait, you cannot be 100% SURE). Probability

7 Recombinant frequency: Unit: centimorgan (cm) 1 cm = 1% recombination; is a distance that they are apart Exception: if the genes are close to the centromere. If this is the case, the recombination frequency is extremely low regardless of where the genes are located Summary Gene interactions between two/more genes result in novel phenotypes Recessive epistasis shows homozygous recessive at one locus affect the pathway Duplicate recessive epistasis (homozygous recessive at either gene locus), because both gene products are needed for the pathway Dominant epistasis where one genotype produces the same dominant phenotype, regardless of genotype at the other locus Complementation test shows whether the two genes mutated are at the same locus or different locus Linked genes indicate 2 or more genes segregate with one another - basis for making linkage group Day 6 In some species, gender is determined by environmental or social cues rather than genotype (species like turtles and wrasses) In this case, they don t have obvious sex chromosomes Chromosomal sex determination: gender is determined by the complement of chromosomes and can be predicted usually at the time of fertilization A subset of genes are located on sex chromosomes that differ in number between genders Mammals and flies use X-Y system X-0 system in grasshoppers and nematodes (XX are female, X are make) Z-W system in birds, snakes, butterflies (ZW are female, ZZ are male) Haplo-diploid system in bees, wasps, ants (diploid are female, haploid are male) Plants are grouped into monoecious and dieocious Monoecious: one organism has both male and female reproductive parts Dieocious: one organism has only male OR female reproductive parts Haplodiploidy: sex determination system in which males (being haploid) produce their gametes by mitosis rather than meiosis

8 When you make a Punnett square with the sex chromosomes, you must add the allele to the X or Y chromosome Ex. X C or X a for an X chromosome that has the colorblindness trait X + or X A for a regular X chromosome We only have the cone cells for 3 colors, red, blue, and green in our eyes Most colorblind people have a mutation in the red and green chromosomes Alleles for 2 blood-clotting factor (usually blood factor 8) proteins are on the X chromosome, so hemophilia is a sex-linked condition If a female is a carrier but her husband is unaffected, ½ of their daughters will be carriers and ¼ of their children overall will be affected by a recessive sex-linked trait. Pedigrees sometimes reveal whether a trait is dominant or recessive or autosomal or sex-linked Transgene: foreign DNA that is successfully integrated into the genome of a host organism Secondary sexual differentiation: the development of sexually dimorphic characteristics, typically as a result of hormones Sexual dimorphism: differences between the secondary sexual characteristics in a species Size Coloration Organs of sexual display (the antlers of moose and deer) Androgen insensitivity syndrome (AIS): genetic condition in which a person with an XY genotype is unable to synthesize or respond to testosterone X chromosome inactivation: occurs randomly in female mammals at a time when the embryo is composed of cells Females develop as a genetic mosaic in which some tissues express the maternal X chromosome while some express the paternal X chromosome Occurs when RNAi (inhibitory) interacts with specific X loci, forming a Barr body with the inactive chromosome Is evolutionary in its basis because it ensures the X chromosome is the only one activated and passed to the next generation Summary The mechanism by which sex is established is sex determination Sex determination can be chromosomal, genetic, or environmentally regulated Sex-linked characteristics are determined by genes on the sex chromosomes The male-determining gene SRY is on the Y chromosome

9 Dosage compensation is achieved by random X-chromosome inactivation Day 7 Parental genotypes will always have the most progeny The reduction of chromosomes from diploid to haploid occurs in meiosis 1 Non-recombinant progeny will outnumber recombinant progeny, so whether alleles are in coupling or repulsion configurations determines the number of offspring that have different combinations of trait Coupling configuration: when one parent has two dominant alleles on the same chromosome, and the other chromosome has recessive alleles at both loci in question o When crossed in a test cross, the progeny are 4 times more likely to have both dominant or both recessive phenotypes than one dominant and one recessive Repulsion configuration: when the dominant alleles are located on different chromosomes in an organism o When crossed in a test cross, the progeny are four times more likely to have one dominant and one recessive trait than both recessive or both dominant χ 2 test helps determine whether or not the genes are linked (observed expected) 2 /expected Df = (number of rows 1) x (number of columns 1) Recombination frequencies can be used to help determine the proportion of predicted progeny Frequency of each of the recombined gametes can be determined by dividing the recombination frequency by 2 Even if crossing over does occur, if DOUBLE crossover occurs between the two loci being studied, the resulting chromosomes will still be non-recombinant The results of a three-point test cross can be used to map linked genes Steps to determine order of 3 gene loci, using recombinant frequencies 1. Identify the non-recombinant progeny 2. Identify the double-crossover progeny 3. Compare phenotype of double-crossover progeny with phenotype of parents (they should differ in one trait, which is the trait encoded by the middle gene) Type of Maps Genetic map o Visible markers o Molecular markers o RFLP (restriction fragment length polymorphism) o SSLP (simple sequence length polymorphism) o CAPS (cleaved amplified polymorphic sequence)

10 Loss-of-function allele is when the heterozygote makes enough protein to still work (recessive to wildtype) Haploinsufficiency: when having only one wild-type allele is NOT sufficient to produce the wildtype phenotype (the wild-type allele is recessive because the threshold for wild phenotype is high for the amount of protein) o Ex. Muscular dystrophy, loss of function of the protein dystrophin (dystrophin connects the actin cytoskeleton to the extracellular matrix of muscle fiber Null allele when the allele produces no functional gene product Gain-of-function allele: produces increased activity of the gene product Mutations in promoters can increase the level of gene expression or express the genes in tissues where it is not normally expressed These mutations are rare because there are so many ways to produce harmful mutations Dominant negative: alleles that are dominant to the wild-type allele because they encode a mutant gene product that interferes with the functioning of the wild-type gene product The heterozygote s wild-type proteins are insufficient to produce the wild-type phenotype Pleiotropy one gene locus affects many different aspects of the phenotypes of different tissues Ex. Sickle-cell disease and Marfan syndrome in humans Huntington s Disease (CAG repeats) and Fragile-X (CGG repeats) are triple-repeat disorders (ELABORATE) o Repeats may increase due to the formation of hairpins Genetic anticipation genetic disease that increases in severity in successive generations, because of increase in number of repeats of segments on a chromosome Sex-influenced traits sex influences the expression of the genotype (of the heterozygote) Ex. Male pattern baldness; the expression of the allele depends on the level of testosterone in the hair follicles Sex-limited traits autosomal genotypes, but expressed ONLY in one sex Ex. Cock-feathered tail appears in only make chickens. Female chickens never display cockfeathering, regardless of genotype Maternal effect pattern of inheritance in which gene products are transmitted from the mother to the offspring via the egg For a maternal effect gene, it is the genotype of the mother which determines the phenotype of her offspring