Genetics EXAM 2 Study Guide PDF

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GENETICS EXAM 2 STUDY GUIDE CHAPTER 27: QUANTITATIVE GENETICS > Quantitative Genetics = the study of traits that can be described numerically > Complex Traits = usually controlled by more than one gene and are significantly influenced by environmental factors (i.e. height and metabolism) > Quantitative Trait = any trait that varies measurably in a given species. Examples: > Anatomical Traits = height, weight, # of bristles in Drosophila, ear length in corn, degree of pigmentation in flowers and skin > Physiological Traits = metabolic traits, speed of running and flight, ability to withstand harsh temperatures, and milk production in mammals > Behavioral Traits = mating calls, courtship rituals, ability to learn a maze, ability to grow/move toward light > Diseases = predisposition toward heart disease, hypertension, cancer, diabetes, arthritis > Continuous Traits = quantitative traits that do not fall into discrete categories (i.e. height/weight) > Meristic Traits = can be expressed in whole numbers > Discontinuous Traits = traits that fall into two or more discrete categories (i.e. eye color) > Quantitative traits show a continuum of phenotypic variation within a group of individuals and are polygenic (i.e. range); do not naturally fall into a small number of discrete categories > Also described as a frequency distribution > To construct frequency distribution trait is divided into a number of discrete phenotypic categories; often falls in a normal distribution (“bell-shaped curve”) > Polygenic Inheritance = refers to the transmission of traits that are governed by 2 or more genes > i.e. Gene 1, Gene 2, Gene 3  Phenotype > Quantitative Locus Trait (QLT) = location on a chromosome that affects the outcome of a quantitative trait > QTLs are chromosomal regions identified by gene mapping > Joseph Kolreuter’s Experiment > Crossed tobacco plants: >P Tall X Dwarf > F1 (self cross) Intermediate > F2 (self cross) Broad Distribution in Heights > Resulted in a continuous range from dwarf to tall > Kolreuter did not understand the significance of his results > Herman Nilsson-Ehle Experiment > First demonstration that continuous variation is related to polygenic inheritance occurred in 1909 > Studied the inheritance of red pigment in the hull of wheat Triticum aestivum >P True Breeding Red X True Breeding White > F1 Intermediate Red > F2 Great Variation in Redness, Plus White

> Multiple-Gene (or Multiple-Factor) Hypothesis = implies that many genes or factors contribute to the phenotype in a quantitative way. Embodies following points: > At least 2 genes account for the hereditary influence of the phenotype in an additive way > Each gene locus may be occupied by either an additive or non-additive allele > The effect of additive alleles at each locus is equivalent > No allelic pairs exhibit dominance of on allele over another > No gene interactions occur among the alleles at different loci in a polygenic series > No genetic linkage is exhibited between the genes in a polygenic series > Example: Hull Color in Wheat >P AABB X aabb red white > F1

AaBb medium pink

> # of Additive Alleles > 4 = red > 3 = dark pink > 2 = medium pink > 1= light pink > 0 = white

Genotype AABB AABb AAbb AaBB AaBb AAabb aaBB aaBb aabb

Phenotype Red Dark pink Medium pink Dark pink Medium pink Light pink Medium pink Light pink White

Proportion (1/4) ( 1/4) = 1/16 (1/4) (2/4) =2/16 (1/4) (1/4) = 1/16 (2/4) (1/4) = 2/16 (2/4) (2/4) = 4/16 (2/4) (1/4) = 2/16 (1/4) (1/4) = 1/16 (1/4) (2/4) = 2/16 (1/4) (1/4) = 1/16

> Polygenic Inheritance and Environmental Factors > Studying quantitative traits is difficult b/c these traits are controlled by multiple genes and substantially influenced by the environment > Low Environmental Effect (One Gene - “Discrete Categories”)

> High Environmental Effect (One Gene - “Overlap”)

> Low Environmental Effect (Three Genes – “Hardly Overlap”)

> High Environmental Effect (Three Genes – “Significant Overlap”)

> Calculations: (where n = # of gene pairs involved) > Ratio of F2 individuals expressing either extreme phenotype = ¼ n > Number of distinct F2 phenotypic classes = 2n + 1 > QTLs are now mapped by linkage to molecular markers > Molecular markers (i.e. RFLPs & microsatellites) are now being used as reference points along chromosomes > These genetic markers have been used to construct detailed genomic maps > Maps make it easier to determine # of genes that affect a quantitative trait > Detailed genomic maps have been obtained from model organisms and organisms of agricultural importance > Researchers map eukaryotic genes by identifying molecular markers that are close to such genes > Eric Lander and David Botstein extended this to identify QTLs that govern a quantitative trait > Basis of QTL mapping is the association between genetically derived phenotypes (i.e. quantitative traits) and molecular markers > General strategy shown below:

> Fig. depicts 2 different strains of a diploid species w/ 4 chromosomes per set > The strains must be different in 2 ways: > W/ regard to a quantitative trait of interest (i.e. large vs. small fruit) > W/ regard to many molecular markers (i.e. 1A vs. 1B) > Markers should correspond to same chromosomal location and distinguishable at molecular level

CHAPTER 3: CHROMOSOMAL TRANSMISSION DURING CELL DIVISION AND SEXUAL REPRODUCTION > Gene = nucleotide sequence that codes for RNA > RNAs can be divided into 4 main types: > mRNA (messenger RNA) > tRNA (transfer RNA) > rRNA (ribosomal RNA) > sRNA(small RNA – plays role in gene regulation “gene on/off”) > Locus = precise position of a gene on the chromosome > Allele (“Allelomorph”) = alternative forma of a gene > Haploid (“Monoploid”) = a cell or organism with one complete set of chromosomes > Diploid = a cell or organism with 2 complete sets of chromosomes > Sex Chromosomes (X or Y) = chromosomes that play a role in sex determination > Autosomes = all chromosomes other than sex chromosomes > Karyotype = representation of the chromosome complement of a cell or organism, usually ordered by size

> Procedure for Creating Karyotype

> Blood is source > Treat w/ culturcine (plant derivate that stops cells in mitosis) > Centrifuge, etc. > Homologous Chromosomes = chromosomes that have the same genetic structure and loci > Chromosomes are characterized by 3 criteria: > Size (p = short arm/ q = long arm) > Position of centromere > Banding patterns > Special staining procedures reveal specific, reproducible and unique patterns that distinguish chromosomes from each other (middle)(off center)

(close to end)

(at end w/ small p arm)

> Basic number of chromosomes varies among species and is usually unrelated to size or biological complexity of an organism > Cellular Division > Serves 2 main purposes: > Is the means by which some unicellular organisms produce new individuals (asexual reproduction) > Means to accomplish multicellularity in many organisms > Cell division in most prokaryotes occurs through process of binary fission

> Somatic Cells = may be haploid or diploid; reproduce by process termed mitosis > Germ Cells = are diploid; go through mitosis then meiosis to yield haploid gametes

> Cell cycles consists of interphase and mitosis

> Interphase

> Cell that is not actively dividing is said to be in interphase > G1 = synthesis of proteins and RNA; cell prepares for DNA replication > S = synthesis of DNA > G2 = synthesis of proteins and RNA; cell prepares for mitosis > Total time for interphase varies with the organism, cell type and environmental conditions > Most variation is seen in length of G1 > Late in G1, cell will follow one of 2 paths: > It withdraws from the cycle and enters the G0 stage where cells > Either postponed making a decision to divide > OR made the decision to never divide again > OR it becomes committed to initiate DNA synthesis and complete the cycle; said to reach a restriction point > Then the cell advances to the S phase, where chromosomes are replicated > Kinetechore protein = where spindle fibers attach > Note: At the end of S phase a cell has 2x as many chromatids as there are chromosomes in the G1 phase > i.e. human has 46 chromosomes in G1 and 46 pairs of sister chromatids in S > Therefore, term chromosome is relevant > In G1 and M, refers to equiv. of 1 chromatid > In G2 and early M, refers to pair of sister chromatids

> Mitosis > Usually, shortest stage of life cycle > An asexual process used for ordinary growth, repair and replacement > Occurs in somatic cells and in early germline development > In mitosis, a diploid cell divides once to produce 2 diploid daughter cells > Divided into 5 stages: > Prophase > Prometaphase > Metaphase > Anaphase > Telophase > Karyokinesis = division of the nucleus > Cytokinesis = division of the cytoplasm > Prophase > Chromatin progressively shortens and thickens to form daughter chromosomes > Nuclear envelope breaks down; nucleolus (or nucleoli) disappears > Centrosomes (replicated in interphase) migrate to opposite cell poles > Spindle apparatus is formed (composed of microtubules) > Microtubules formed by rapid polymerization of tubulin proteins. 3 types: > Aster Microtubules = important for positioning of spindle apparatus > Polar Microtubules = help to push the poles away from each other > Kinetochore Microtubules = attach to the kinetochore, which is bound to the centromere of each individual chromosome

> Prometaphase > Spindle fibers interact with the sister chromatids > Kinetochore microtubules grow from the two poles > If they make contact with a kinetochore, the sister chromatid is “captured” > If not, the microtubule depolymerizes and retracts to the centrosome > The 2 kinetochores on a pair of sister chromatids are attached to kinetochore microtubules on opposite poles

> Metaphase > Chromosomes reach their maximum contraction > Pairs of sister chromatids align themselves along a plane called the metaphase plate

> Anaphase > Centromeric region divides longitudinally and paired sister chromatids separate > Each chromatid, now an individul chromosme, is linked to only one pole (“daughter chromatids”) > As anaphase proceeds: > Anaphase A > Kinetochores MTs shorten > Chromosomes move to opposite poles > Anaphase B > Polar MTs lengthen > Poles themselves more further away from each other > Note: movement of sister chromatids to opposite poles aided by motor proteins (use ATP)

> Telophase > Daughter chromosomes reach their respective poles > They uncoil and become diffuse chromatin again > Nuclear membrane reforms to form two separate nuclei > Spindle fibers disappear Interphase

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

> Cytokinesis > In animal cells, a cleavage furrow develops > In plant cells, a cell plate develops (presence of cell wall) > In general cytokinesis follows karyokinesis > However, in many instances it may be deffered or totally lacking = coenocytic cells > Common in fungi and muscle cells > Mitosis is significant because it maintains a constant number of chromosomes > Sexual Reproduction > During sexual reproduction, gametes are made that contain half the amount of genetic material > Some simple eukaryotic species are isogamous = produce gametes that are morphologically similar > Most eukaryotic species are heterogamous – produce gametes that are morphologically different > Sperm Cell = relatively small and mobile > Egg Cell = large and immobile; stores a large amount of nutrients in animal species > Meiosis > Only occurs in germline cells; ensures genetic continuity and variability > Begins after cell has progressed through interphase > Involves 2 successive divisions: > Meiosis I = reductional division, in which the chromosome number is halved > Meiosis II = equational division, in which the chromosome number remains the same

> Prophase I > Most complex and longest stage of meiosis > Subdivided into 5 stages: > Leptonema > Zygonema > Pachynema > Diplonema > Diakinesis

> Tetrads are organized along the metaphase plate > Pairs of sister chromatids are aligned in a double row, rather than a single row (as in mitosis) > The arrangement is rand with regards to the homologues > Furthermore > A pair of sister chromatids is linked to one of the poles > The homologous pair is linked to opposite poles > Meiosis II > Division similar to mitosis > Keep whatever chromosome number you have

> Significance of Meiosis > It allows the conservation of the chromosome number in sexually reproducing species

> It generates genetic variability through the various ways in which maternal and paternal chromosomes are combined into gametes > i.e. humans can produce 223=8388608 different gametes > human couple can produce (8388608)( 8388608) = 70368744177664 offspring > It enhances the potential genetic variation in gametes through the phenomenon of crossing over between maternal and paternal chromatid pairs > IMPORTANT

> Gametogenesis = production of gametes > Premordial Germ Cells = in early embryonic development a group of cells become committed to form germ line cells > PGCs proliferate through mitosis, and later undergo meiosis to produce mature sperm or eggs > Spermatogenesis > Takes place in the seminiferous tubules of the testes > In the fetus, the PGCs divide by mitosis and differentiate into spermatogonia (diploid cells) > Spermatogonia remain quiescent until puberty (diploid cells) > At puberty, spermatogonia differentiate into primary spermatocytes (diploid cells) > The primary spermatocytes undergo meiosis I to produce secondary spermatocytes (haploid cells)

> The secondary spermatocytes undergo meiosis II to produce spermatids (haploid cells) > Note: > Unlike oogenesis, the meiotic divisions in the psermatogenesis are symmetric > Throughout these meiotic divisions, the “daughter cells” do not completely separate; rather they remain attached by narrow cytoplasmic bridges > Last stage of germ cell development is spermiogenesis > No cell division > Spermatids undergo a dramatic change to form the spermatozoa > Sperm prod. aided by sertoli and leydig cell > Leydig = prod. testosterone > Sertoli = nourish cells/ prod. chemicals that help sperm mature

> In spermatogenesis, the two meiotic divisions are continuous > Human spermatogonia develop into mature sperm in roughly 9 weeks > Spermatogenesis results in the prod. of enormous numbers of sperm > Avg. adult male produces 100-400 million sperm/day > Oogenesis > Take place in the ovaries > Begins in the embryo and continues until menopause > Two meiotic divisions of oogenesis are not continuous > In fetus, the PGCs divide by mitosis and differentiate into oogonia > Oogonia differentiat into primary oocytes > Primary oocytes undergo meiosis I (arrested in prophase I until puberty) > At puberty, the primary oocytes complete meiosis I to produce secondary oocyte and first polar body > Cytokinesis in oogensis is asymmetric (20 oocytes gets most of the cytoplasm of parent) > First polar body usually degenerates but may divide to produce 2 second polar bodies > Secondary oocyte enters meiosis II but arrests in metaphase II > It is released into the fallopian tubes > If secondary oocyte is not fertilized, meiosis II is not completed and oocyte degenerates > If secondary oocyte is fertilized meiosis II is completed > Another asymmetric division yields the second polar body > The fertilized 20 oocyte become the zygote

> The zygote is diploid, containing a paternal and maternal set of chromosomes > Prior to ovulation, oocyte form in follicles

> Oogonia begin to develop into primary oocytes by the 3rd month of gestation > Primary oocytes are arrested in prophase I by the 7th month of gestation > The 5 month old fetus possesses about 7 million germ cells (1 million at birth, 40000 at puberty – only need approx. 444 oocytes) > Chromosome Theory of Inheritance (confirmed by Thomas Hunt) > Describes how transmission of chromosomes account for the Mendelian patterns of inheritance > Proposed independently by Theodore Boveri and Walter Sutton > Based on 5 key principles: > Chromosomes contain the genetic material > Chromosomes are replicated and passed along from parent to offspring > The nuclei of most eukaryotic cells contain chromosomes that are found in homologous pairs (segregates into one of 2 daughter nuclei during meiosis) > During formation of gametes, different types of non-homologous chromosomes segregate independently > Each parent contributes one set of chromosomes to its offspring; sets are functionally equivalent and each carries a full complement of genes > This theory allows us to see relationship between Mendel’s laws and chromosome transmission > Law of Segregation explained by homologous pairing and segregation of chromosomes during meiosis (fig. 3.15) > Law of Independent Assortment explained by relative behavior of different nonhomologous chromosomes during meiosis (fig. 3.16)

> Chromosomes and Sex Determination 1. XY system found in placental mammals > Females homogametic (XX); males heterogametic (XY) 2. ZW system found in birds, butterflies, moths, and some fish > Females heterogametic (ZW); males homogametic (ZZ) 3. XO system found in many species of insects > Females have 2 X chromosomes (XX); males have one X chromosome (XO) 4. X chromosome-autosome balance system found in Drosophila > Main factor in sex determination is ration between # of X chromosomes and # of sets of autosomes > Y is essential for male fertility NOT male development > Drosophila have 4 pairs of chromosomes (1 sex pair, 3 autosomes) > X:A = 1.00  Female > X:A = 0.50  male > 0.50 < X:A < 1.00  Intersex (features of male and female) > X:A > 1.00  metafemale (shorter generation time) > X:A < 0.50  metamale (shorter generation time) 5. Haplo-diploid system in bees > Males are known as drones; haploid; produced from unfertilized eggs > Females include workers and queen; diploid; produced from fertilized eggs > Reciprocal Crosses = between different strains in which the sexes are reversed > Reveal whether a trait is carried on a sex chromosome or an autosome > X-linked traits do not behave identically in reciprocal cross > Sex-linked Genes = found on one of the two types of sex chromosomes but not on both > X-linked Genes = found on X-chromosome. dominance and recessiveness only matter in female; male is hemizyouse (“half”-zygous) > Holandric Genes = found on the Y chromosome > Pseudoautosomal Regions = short regions of homology at one end of the X and Y chromosomes > Promote the necessary pairing of the two chromosomes in meisosis I of spermatogenesis > i.e. Mic2 (involved in antibody production) > Dosage Compensation > In mammals, females have 2 X chromosomes and males have 1 > Barr Body (or Sex Chromatin) allows for dosage compensation > In 1961, Mary Lyon proposed a hypothesis: > In female mammalian somatic cells one of the two X chromosomes is condensed and inactive > Inactivation occurs very early in embryonic life > Inactivation occurs independently and randomly in each cell > Once decision is made, the inactivated X remains inactivated through all subsequent mitotic events within that cell line > In normal female, both Xs are active > # Barr Bodies = # of chromosomes – 1 > Result of X inactive in females can sometimes be observed in phenotypes (i.e. calico cat) > Other Dosage Compensation Mechanisms > Caenorhabditis elegans > Dosage compensation occurs in the homogametic hermphrodite (XX) > Genes on the X chromosome are down regulated 50% > Drosophilia melanogaster

> Dosage compensation occurs in the heterogametic male > Genes on X chromosome are up regulated 2 fold

CHAPTER 6: GENETIC LINKAGE AND MAPPING IN EUKARYOTES > Genes in the same chromosome = linked > Linkage Group = group of genes located on the same chromosome; in general corresponds to the haploid # of chromosomes > Types of relative proportions of gametes produced by an ...