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Genetics Exam 1 Study Guide

by: Emma Notetaker

Genetics Exam 1 Study Guide CELL 2050

Marketplace > Tulane University > CELL > CELL 2050 > Genetics Exam 1 Study Guide
Emma Notetaker
GPA 3.975

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Comprehensive study guide including lecture notes, book notes and helpful hints I found while doing the online quizzes.
Dr. Meadows
Study Guide
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This 20 page Study Guide was uploaded by Emma Notetaker on Friday September 16, 2016. The Study Guide belongs to CELL 2050 at Tulane University taught by Dr. Meadows in Fall 2016. Since its upload, it has received 77 views. For similar materials see Genetics in CELL at Tulane University.


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Date Created: 09/16/16
Thursday, September 15, 2016 Exam I Chapter 2 • prokaryote: • cell wall • unicellular domains: eubacteria abd archaebacteria • • no nucleus • 1-10 micrometers • one circular DNA molecule, loosely associated • DNA without histones in eubacteria • some histones in archaebacteria no organelles • • eukaryote • unicellular and multicellular • membrane-bound organelles • nucleus • DNA associated with histones to form tight chromosomes scientists compared DNA sequences to determine differences between the 3 domains • • viruses • neither prokaryotic or eukaryotic • outer viral protein coat surrounds nucleic acid - contains DNA and RNA • prokaryotic cell reproduction - binary fission • simple division - separation of replicated circular chromosome origin of replication - signals replication • • high rate of replication • prokaryotes have one chromosome, and as it replicates the origins move to opposite sides • origins anchored to opposite sides of cells that start to split • new cells (2) have identical copies of original chromosomes • eukaryotic cell replication eukaryotic chromosomes: • • homologous pair (humans have 23 pairs of chromosomes, 46 total) • diploids carry 2 sets of chromosomes - 2 sets of genetic info • haploids carry one set • alleles: sites containing genes • chromosome structure centromere: attachment point for spindle microtubules • • kinetochores form - bind to microtubules and attach sister chromatids • if a chromosome lost its centromere, the chromosome would not be drawn into a newly formed nucleus • telomeres: tips of a linear chromosome, chromosomal stability • stable end prevents ends from touching each other • • 4 telomeres on pair of sister chromatids • origins of replication: where DNA synthesis begins • sometimes chromosome is ONE chromatid - one DNA molecule 1 Thursday, September 15, 2016 • sister chromatids stuck together at the centromere (still considered one chromosome as long as chromatids attached) 2 DNA molecules • • cell cycle: passage of genetic info from a parent cell to daughter cell • mainly takes place in somatic cells (non-reproductive cells) • interphase: extended period between cell division • DNA synthesis and replication • nuclear membrane is PRESENT in interphase chromosomes are relaxed • • G1: growth • proteins for cell division are made • G0: non dividing phase • G1/S checkpoint: regulated decision point • after this, now committed to division S: DNA synthesis/duplication • • G2: biochemical preparation for cell division • G2/M checkpoint: only passed is DNA completely replicated and undamaged • M phase: • mitosis: separation of sister chromatids • cytokinesis: cytoplasm separates phase check points are key transition points • • important in cancer - cancer disrupts check points • centrosomes give way to spindles • spindles made up of tubulin subunits • mitosis: • prophase • chromosomes condense - can start to see individual chromosomes • 4 chromosomes (2 pairs of homologous) • 8 DNA molecules (8 chromatids) • each chromosome has 2 chromatids • mitotic spindle forms between centrosomes • prometaphase • nuclear membrane disintegrating • chromosomes vert apparent • spindle microtubules attached to chromatids • metaphase • chromosomes line up on metaphase plate • attached at the centromere to the centrosome • anaphase • sister chromatids separate and move toward opposite poles • 8 chromosomes (sisters separated) • 8 DNA molecules (8 chromatids) • telophase • chromosomes at spindle poles • nuclear membrane re-forms • chromosomes relax - can’t see as well • each new cell has 4 chromosomes and 4 DNA molecules • genetic consequences of mitosis • 2 cells that care genetical equal to each other and mother cell 2 Thursday, September 15, 2016 • new cells have full complement of chromosomes • each new cell has 1/2 the cytoplasm and organelle content of the original parent sexual reproduction and genetic variation • • meiosis: production of haploid gametes • fertilization: fusion of haploid gametes • genetic variation: consequences of meiosis • meiosis: • interphase: DNA synthesis and chromosome replication meiosis I: reduction division • • start with 2n = 4 chromosomes • separation of homologous pairs • reduction of chromosome number by half • phases: • prophase I: middle prophase I: chromosomes continue to condense and spindle forms • • late prophase I: homologous chromosomes PAIR (unlike mitosis) • crossing over (aka chiasmata): segments of one sister go to another - generates variation in gametes (during late prophase I) • synapsis: close pairing of homologous chromosomes • tetrad: closely associated 4-sister chromatids of 2 homologous chromosomes metaphase I: random alignment of homologous pairs of chromosomes on • metaphase plate • in mitosis, no pairing • anaphase I: • spindles connect to kinetochores of centromeres • separation of homologous chromosome pairs to opposite poles • random distribution of chromosomes into 2 newly divided cells • generates variation • at end of anaphase, haploid system (because homologous chromosomes separated) • telophase I: • chromosomes arrive at spindle poles • cytoplasm divides • haploid cell • interkinesis • meiosis II: equational division - ends with 4 haploid cells • separation of sister chromatids • prophase II: chromosomes re-condense • spindles attach • metaphase II: individual chromosomes line up along plate • anaphase II: sister chromatids move to opposite poles • telophase II: chromosomes arrive at the spindle poles, cytoplasm divides • 4 single chromatids • consequences of meiosis: • 4 cells from original cell • chromosome number in each cell is reduced by 1/2 • new cells haploid • new cells are genetically different from each other and parents • crossing over 3 Thursday, September 15, 2016 random separation of homologous chromosomes • • genetic variation via crossing over • one chromosome possesses A and B alleles while other has a and b • DNA replication in the S phase produces identical sister chromatids • during crossing over in prophase I, segments of nonvoter chromatids are exchanged after meiosis I and II, each of the resulting cells carries unique combination of alleles • • genetic variation via random separation of homologous chromosomes • cells have 3 homologous pairs of chromosomes • maternal: lm, llm, lllm • paternal: lp, llp, lllp • 4 possible ways for these to be combined in interphase I Event Mitosis Meiosis I Meiosis II Cell Division yes yes yes Chromosome no yes no reproduction genetic variation no yes no crossing over no yes no random dist. of no yes no maternal and paternal chromosomes metaphase individual chromosomes homologous pairs line individual chromosomes line up up line up anaphase chromatids separate homologous chromatids separate chromosomes separate • separation of chromatids occurs in meiosis II, NOT meiosis I • separation of sister chromatids and homologous chromosomes • cohesin: protein holding chromatids together • key to bx of chromosomes in mitosis and meiosis • shugoshin: protects cohesin at centromere from being broken down mitosis: • • sister kinetochores orient towards different poles and cohesin keeps sisters together • breakdown of cohesion all chromatids to separate • meiosis: • cohesin along arms hold homologous pairs together at chiasmata cohesin along arm breaks form, allowing homologs to separate (need to keep sister • chromatids intact) • shugoshin keeps kinetochores together while allowing homologs to be pulled apart • at anaphase II, shugoshin is degraded by separase so sisters can come apart • meiosis in animals • spermatogenesis - male gamete production • spermatogonia in testes can undergo repeated mitosis to keep diploid • OR spermatogonium enters prophase I to become primary spermatocyte • each spermatocyte competes meiosis I to make 2 secondary spermatocytes these go through meiosis II to make 2 haploid spermatids (become sperm) • 4 Thursday, September 15, 2016 • oogenesis - female gamete production • oogonia enters prophase to become primary oocyte oocytes go through meiosis I to make large secondary oocyte and smaller polar body • • secondary oocyte complete meiosis II to make ovum and second polar body (polar bodies disintegrate) • meiosis in plants Heredity • Gregor Mendel: • proper experimental model • experimental approach and mathematically analyzed results • studied easily differentiated characteristics • pea plant - analyzed seed color, shape, seed coat color, pod shape and color, flower position and stem length • gene: inherited factor (region on DNA) that helps determine characteristic • allele: one of 2+ forms of a gene • locus: specific place on a chromosome occupied by an allele genotype: set of alleles in an organism • • heterozygote: organism with 2 different alleles at a locus • homozygote: organism with 2 of the same alleles at a locus • phenotype (trait): appearance/manifestation of a characteristic • characteristic/character: attribute/feature • monohybrid cross: cross between 2 parents that differ in a single characteristic one character is encoded by 2 genetic factors • • 2 alleles separate when gametes are formed • concept of dominant and recessive traits • 2 alleles separate with equal probability into the gametes • Mendel’s method: removed anthers of flowers to prevent self-fertilization and dusted stigma with pollen from a different plant P generation: homozygous round male with homozygous wrinkled female seeds • • they were crossed • F1 (filial) seeds were all round • let f1 self-fertilize • 3/4 of F2 were round, 1/4 were wrinkled (3:1 ratio) • reciprocal cross: homozygous round female with homozygous wrinkled male (same results as above experiment) • traits of parent cells DO NOT BLEND • principle of segregation (Mendel’s 1st law): each individual diploid organism possessed 2 alleles for any particular characteristic. These 2 alleles segregate when gametes are formed, and each gamete gets 1 allele • dominance: only the trait encoded by dominant allele is observed - recessive is not seen 2 genetic alleles separate when gametes are formed with equal probability • • gametes are haploid • Sutton: chromosomal theory of heredity - genes are located on chromosomes (meiosis) • genetic crosses in relation to meiosis: • 2 alleles of genotype Rr located on homologous chromosomes which replicate in S phase • in prophase I of meiosis, cross over MAY take place 5 Thursday, September 15, 2016 • in anaphase I, homologous chromosomes separate • two chromatids of each chromosome separate in anaphase II if no crossing over, identical • • if crossing over, different alleles segregate in anaphase II • Punnet square used to determine results of genetic cross • backcross: crossing F1 with parent generation • multiplication rule: probability of 2+ independent events taking place together is calculated by multiplying independent probabilities independent: outcome of one doesn’t affect outcome of the other • • keyword: AND • used to predict the GENETIC ratio of progeny • addition rule: probability of and one of two or more mutually exclusive events calculated my adding the events • keywords: either, or used to predict PHENOTYPIC ratio of progeny (phenotype results from different genotypic • backgrounds) • testcross of a tall plant (can be TT or Tt): cross with homozygous recessive • if genotype TT, all plants will be tall • if Tt, half will be tall and half will be short • inheritance of an allele from the male is independent of an allele contributed by the female dihybrid crosses: examine 2 traits at a time • • reveal the principle of independent assortment to meiosis • gametes on different chromosomes will sort independently • multiplication rule applies here • broken into 2 monohybrid crosses • independent assortment: alleles at different loci separate independently of one another • independent assortment occurs in anaphase I • relating meiosis to independent assortment: • cell contains 2 pairs of homologous chromosomes • in anaphase I, each pair separates independently, which leads to multiple combinations • genes located on different pairs of chromosomes assort independently, which produces different combinations of alleles in the gametes after separating in anaphase II • probability and dihybrid crosses • 2 round yellow seeds, both heterozygotes in both traits • broken down into 2 monohybrid crosses • look at expected proportions for each character • these proportions are then combined using the branch method (multiplication rule) • multiply each proportion from shape by each proportion of color - this is the total proportion • example: AaBbccDdEe x AaBbBcddEe, which proportion is aabbccddee? • Aa x Aa —> aa is 1/4 • Bb x Bb —> bb is 1/4 • cc x Cc —> cc is 1/2 • Dd x dd —> dd is 1/2 • Ee x Ee —> ee is 1/4 • —> 1/4*1/4*1/2*1/2*1/4 = 1/256 • dihybrid testcross: cross with homozygous recessive for BOTH traits • chi-square goodness of fit: indicates the probability that the difference between the observed and expected values is due to chance 6 Thursday, September 15, 2016 • X = ∑(observed - expected) 2 expected • cutoff value is .05 • P < .05: NOT due to chance • P > .05: chance is responsible • n: number of expected phenotypes • expected values obtained by multiplying expected proportions by the total chi square value is then calculated • Sex Determination and Sex-Linked Characteristics • sex determination: mechanism by which sex is establishes • sex: sexual phenotype • sexual reproduction: alternates between haploid and diploid states in most eukaryotes • meiosis produces haploid gamets • fertilization produces a diploid zygote • most organisms have 2 sexual phenotypes, male and female • gamete size different in each sex • sex determination mechanisms: • monoecious: both male and female reproductive structures are in the same organism (hermaphroditism) - plants dioecious: either male or female structures in one organisms (humans) • • chromosomal sex determination systems: sex chromosomes and autosomes • autosome: non-sex chromosome • O: ansence of sex chromosome • XX-XO system: • XX: female (homogametic) • XO: male (heterogametic • example: grasshoppers • during meiosis, 1 gamete receives an X and the other gets nothing • XX-XY system: • XX: female (homogametic) XY: male (heterogametic) • • mammals • 1:1 sex ratio produced in F1 generation • X and Y chromosome pair during meiosis even though they are NOT homologous • genes located on each are different • homologous only at pseudoautosomal regions (which are needed for XY chromosome pairing in meiosis in the male • this is the way they pair - similar at these regions even though a large size different • primary pseudoautosomal region on top • secondary pseudoautosomal region on the bottom • ZZ-ZW system: flipped from our’s (male is homo, female is hetero) ZZ: male (homogametic) • • ZW: female (heterogametic) • birds, snakes, butterflies, some amphibians, fish • haplodiploidy system: • haploid set: male 7 Thursday, September 15, 2016 • diploid set: female • bees, wasps, ants gametes of the heterogametic sex have different sex chromosomes, while gametes of • homogametic sex have the same sex chromosome • **sex is determined by individual genes EVEN in chromosomal systems** • genic sex-determining system: • no sex chromosomes, only sex-determining genes • plants, fungi, protozoans and fish environmental sex determination: • • environmental factor examples: • limpet position in the stack • larva that settles onto unoccupied substrate develops into a female • this female produces chemicals that attract other larvae • these new larvae settle on top of female and become males, which mate with original female • eventually, the males on top switch sex to become female • these females attract new larvae, which settle on top and are male • temperature change in turtles/alligators dictates which sex they are • sex determination in drosophilia melanogaster (XX-XY) • X:A ratio X = X chromosomes • • A = haploid sets of autosomes) • ignore Y • this ratio can help determine the sex of the fly • table 4.2 • ex: XXYYY sex chromosomes and two sets of autosomes —> 2:2 ratio (2X, 2A) —> female • sex determination in humans XX-XY: • SRY gene on y chromosome determines maleness • y-linked (ONLY on y) • this gene turns on enzyme to eliminate female part as well - females are “default” because they lack y gene • located on the short arm (top) • experiment: scientists put SRY gene on X chromosome in mice • this gave mouse a male phenotype (even though mouse was XX) • androgen insensitivity syndrome: caused by defective androgen receptor • female externally but internalized testes • genotype XY • testes produce testosterone BUT testosterone receptor (androgen) is defective • —> so, female characteristics form even with Y chromosome present • sex not just determined by SRY (other genes too) • abnormal sex chromosome numbers: • Turner syndrome: XO (1/3000 female births) • missing a chromosome • broad chests, sterile, neck folds • Klinefelter syndrome: XXY or XXXY or XXXXY or XXYY (1/1000 male births) • always multiple X with Y chromosomes - always male • Poly-X: many more X chromosomes (1/1000 female births) • the more X chromosomes, the worse the condition is 8 Thursday, September 15, 2016 • YY: not viable - die as embryos (lethal, need at least one X) • role of sex chromosomes: x chromosome has genetic info essential for both sexes (NEED at least one x to survive) • • y chromosome contains male-determining gene • one y even with many x’s will produce male • absence of y = female • genes affecting fertility are located on x and y chromosomes • female needs 2 x to be fertile usually additional x copies may upset normal development in both males and females • • **+ means wild type/normal • x-linked characteristics • x-linked white eye in drosophila • Thomas Hunt Morgan - came up with idea of sex inheritance • experiment: are white eyes in fruit flies inherited as autosomal recessive trait? crossed red eyed X+X+ female with white eyed male (XwY) • • got red-eyed males and females (suggested autosomal trait) • reciprocal cross: white-eyed female (XwXw) with red-eyed male (X+Y) • red-eyed female and white-eyed male (XwY) • males more likely to get white eyes because the mutation is on the X chromosome • x-linked color blindness in humans (red-green) sons receive recessive x linked disorders from mother only • • example: hemophilia is x-linked. A woman with hemophilia mates with a man with normal blood clotting. • probability of their child having hemophilia is 1/2 (female child will be normal, male child will have hemophilia) • dosage compensation: • amount of protein produced usually a function of the number of gene • because males only have one x, this is a problem for balancing protein production when compared to females (they would have less protein available) • balanced by dosage compensation: equalization of gene expression/protein amount produced by x-linked genes • fruit flies: males double expression of x • humans: females inactivate one x • Lyon hypothesis: female cells inactivate one x chromosome randomly • mosaic: some cells express genes from one x while others express genes from the other x • barr body: inactive x • regardless of how many x’s, only ONE will be active • if you have more X’s, more will be inactive Barr bodies so that only one remains functional • Xist: RNA molecule that aids in x-inactivation • if a man had issues with this, there would likely be no consequences because he only has one x • random X inactivation: leads to mosaicism of fur color in cats (tortoiseshell/calico) • random inactivation of gold cells and black cells (create random clusters of cells) • Y-Linked characteristics: • evolution of y chromosome (lost DNA over time) • used to be that we only had autosomal chromosomes • mutation of gene on one chromosome causes maleness 9 Thursday, September 15, 2016 • mutations at other genes affect male characteristics • suppression of crossing over keeps genes for male traits linked to the male- determining gene • over time, lack of crossing over between x and y leads to a degeneration of the y • only in males • all male offspring will have trait (y-linked markers on DNA used to trace ancestry) • important for sex determination in SRY • Z-linked characteristics: same as x-linked, but male and female inheritance is reversed • • females more likely to get the characteristics because they are Z-W • common misconceptions: • characteristics in which male and females differ is NOT sex linked • character found more frequently in one sex is NOT sex linked Extensions and Modifications of Basic Principles • genes at the same locus - 2 versions of the same gene • each version is an allele dominance: interaction between genes at the same allele • • influences the ways in which genes are expressed, NOT inheritance of the gene • complete dominance: phenotype of the heterozygote is the same as the phenotype of the homozygous dominant (normal dominance) • incomplete dominance: phenotype of the heterozygote falls between the phenotypes of the 2 homozygotes (intermediate) blending of phenotypes • • ex: eggplants - purple and white fruit will combine to form violet fruit • genotypic ratio: 1PP : 2Pp : 1 pp • phenotypic ratio: 1 purple : 2 violet : 1 white • codominance: heterozygote displays phenotypes of both homozygotes • ex: heterozygotes red/white flowers will display both red and white colors penetrance: percentage of individuals with a particular genotype that actually express the • expected phenotype • incomplete penetrance: genotype doesn’t express the predicted phenotype • ex: polydactyly - formation of extra digits • caused by dominant allele BUT not all people with this allele are polydactyl • expressivity: degree to which a character is expressed ex: polydactyly - variability (may be fully functional extra digit or extra skin tag) • • ex: assume that gene for long fingers is a recessive trait with 80% penetrance. • 2 people heterozygous for long fingers mate - what is the probability that their first child has long fingers • because recessive, 1/4 of offspring have ff genotype • answer: because 80% penetrance, multiply 1/4 by 80% to get 20% lethal allele: causes death at an early stage of development, so some genotypes may not • appear among progeny • indicated by 2:1 ratio • affects mendelian genotypic and phenotypic ratios in progeny • because gives rise to death, termed as recessive even though dominant allele 10 Thursday, September 15, 2016 • ex: yellow gene in rats (YY means death) - Y considered recessive lethal allele even though it is dominant • 2 Yy heterozygotes crossed • babies are 1/4 YY, 1/2 Yy, 1/4 yy BUT the YY die —> 2:1 ratio Yy and yy surviving • 2/3 are Yy yellow, 1/3 are yy non yellow • ex: cross between 2 green corn plants yields 2/3 progeny that are green and 1/3 white progeny • white genotype: gg • green genotype: Gg • GG: lethal allele causing death in homozygous (recessive lethal allele) multiple alleles: for a given locus, more than 2 alleles are present within a group of individuals • • there is a hierarchy of dominance; all different in terms of each other • ex: ABO blood: I > i, I > i, I = I B Phenotype Genotype Antigen Type Antibodies A I I or I i A anti-B B I I or I i B anti-A AB I IB A and B none O ii none anti-A and anti-B • A and B are codominant • red blood cells that don’t react with recipient antibody remain evenly dispersed, so blood is compatible with donors • blood cells that react with recipient clump together, so NOT compatible • type O can donate to any recipient (universal donor) - this is because they have no antigens • type AB can receive from anyone (because have no antibodies) - universal acceptor • ex: duck-feather patterns: M (restricted) p> M (mallard) > m (dusky) • M M: restricted M m : restricted • d • M m : mallard • m m : dusky • ex: what blood types possible with cross between type A man and type B woman • ALL possibilities • gene interactions: effects of genes at one locus depend on the presence of genes at another locus • gene interactions that produce novel phenotypes: • ex: red (Y+Y+C+C+) pepper crossed with cream (yycc) • f1 is heterozygous red, which is then self crossed • Y and C locus interact to produce a single phenotype • colors are red, peach, orange, cream • epistasis: one gene masks effects of another gene at a different locus • epistatic gene: masking gene • hypostatic gene: gene being masked recessive epistasis: • • 2 recessive alleles inhibit expression of an allele at a different locus • ex: expression of ABO antigens depends on alleles at H locus 11 Thursday, September 15, 2016 • dominant H allele encodes an enzyme that converts an intermediate into compound H • compound H adds terminal sugar (this can be A antigen or B antigen) • OR it may not add a terminal sugar, which can be compound O • genotypes at the ABO locus determine type of terminal sugar which determines blood type recessive mutation (hh) FAILS to convert intermediate to compound H • • known as Bombay phenotype • completely bypasses the possibility for A or B • this results in blood type O, with no terminal sugar • —> genotypes at the H locus AND the ABO locus determine blood type h is epistatic to ABO genes • • dominant epistasis: only a single copy of allele is required to inhibit expression of allele at a different locus • ex: yellow pigment in summer squash (allele W is epistatic to alleles Y and y) • compound A: white compound B: green • • compound C: yellow • green squash requires enzyme I (to convert from A to B) • yellow requires enzyme II (to convert from B to C) • dominant allele W inhibits conversion of A into B (shuts down enzyme I) plants with yy don’t have functional enzyme II • • allele W is epistatic to Y and y • if W, removes the possibility of enzyme I and II (because one after the other) - Y or y doesn’t have any effect if the dominant W is present • possibilities: W_Y_: white squash, no enzyme I • • W_yy: white squash, no enzyme I • wwY_: yellow, both enzyme I and II • wwyy: green squash, enzyme I ONLY • duplicate recessive epistasis: 2 recessive alleles at either of 2 loci are capable of suppressing a phenotype • • ex: albinism in snails • compound A and B are albino, only compound C is pigmented • dominant allele at A locus is required to produce enzyme I, which converts A into B • dominant allele at B required to make enzyme II, which converts B into C (pigment) pigmented snails must be able to produce BOTH enzymes, which needs A_B_ • • albinism arises from absence of enzyme I (aaB_), so compound B isn't produced • OR from absence of enzyme II (A_bb) so C is never produced • OR from absence of both enzymes aabb • a is epistatic to B and b is epistatic to A Ratio A_B_ A_bb aaB_ aab interaction example b 9:3:3:1 9 3 3 1 none seed shape and color in peas 12 Thursday, September 15, 2016 Ratio A_B_ A_bb aaB_ aab interaction example b 9:3:4 9 3 4 recessive epistasis coat color in labrador retrievers 12:3:1 12 3 1 dominant epistasis color in squash 9:7 9 7 duplicate recessive epistasis albinism in snails 9:6:1 9 6 1 duplicate interaction 15:1 15 1 duplicate dominant epistasis 13:3 13 3 - dominant and recessive epistasis • complementation: determines whether mutations are at the same locus or at different loci • ex: fruit fly eye color • a = white color (X linked recessive mutation) • b = apricot (X linked recessive mutation) • do a and b occur at the same locus? • complementation test: cross homozygous mutant with homozygous mutant for a different mutation (**look at slide 25**) • if mutations are allelic (at same locus): heterozygous offspring will have only mutant alleles (a and b) and will exhibit mutant phenotype • if at different loci, heterozygous offspring will have wild type and mutant alleles and exhibit wild type phenotype • complex genetics of coat color in dogs • agouti (A) • black (B) • extension (E) • spotting (S) Genetic Phenomenon Phenotype determined by sex-linked genes located on sex chromosome sex-influenced genes on autosomal chromosomes that are more readily expressed in one gene sex-limited autosomal genes whose expression limited to one sex genetic maternal effect nuclear genotype of maternal parent cytoplasmic inheritance cytoplasmic genes, which are usually inherited entirely from ONLY ONE parent genomic imprinting genes whose expression is affected by the sex of the transmitting parent • sex-influenced traits: determined by autosomal genes which are inherited normally (according to Mendel’s rule) BUT express differently in males and females 13 Thursday, September 15, 2016 • ex: bearding in goats - B is dominant in males but recessive in females males with be bearded if they have one OR 2 B b • b b • females are only bearded if they are homozygous (B B ) • sex-limited traits: encoded by autosomal genes that are only expressed in one sex (NO penetrance in the other) • ex: feathering in domestic chickens cock feathering only present in males (females will never have cock feathering even if • hh genotype) • HH: both males and females will have hen feathering • Hh: both will have hen feathering • hh: males will have cock feathering, females will have hen feathering ex: precocious puberty in humans • • autosomal dominant allele P - both males and females can transmit the gene, but only expressed in males • PP and Pp will cause precocious puberty in males, nothing will cause it in females • cytoplasmic inheritance: exception to Mendel’s rule not all genetic material is located on chromosomes —> some is in the cytoplasm • (mitochondria and chloroplasts) • mitochondria segregate randomly in cell division, which results in progeny that differ in their number of mitochondria with wild-type and mutated genes • present in males and females usually inherited from one parent (typically maternal) • • mitochondrial DNA almost always from the mother • reciprocal crosses give different results • exhibit extensive phenotypic variation even in single family • ex: stem and leaf color inheritance in 4-o’clock plant (white, green, variegated) took pollen from 3 types of plants and crossed with all types of seed plants • • maternally derived phenotype • in plants, phenotype of progeny determined by phenotypes of the branch from which the seed originated, not from the branch the pollen originated from • stem and leaf color exhibit cytoplasmic inheritance genetic maternal effect: genes inherited from both parents, but the offspring’s phenotype is • determined by genotype of the mother (NOT by its own genotype) • ex: snails • dextral (right handed coil) results from S+ which is dominant over s (left-handed coil) • S+S+ (male) cross with ss (female) —> all heterozygous S+S S+s would suggest dextral, BUT sinistral because the mother is sinistral • • S+s self fertilize • since mother of F2 progeny has genotype S+S, all progeny are dextral (even though 1/4 ss which would suggest sinistral) • even though phenotypically mother is sinistral, her genotype is dextral so all offspring are dextral • genomic imprinting: differential expression of genetic material depending on whether inherited from male or female parent (can make a difference whether inherited from mom or dad) • paternal allele is active, protein stimulates fetal growth • maternal allele is silent - absence of protein does not stimulate growth size of fetus determined by combined effects of both alleles • • anticipation: genetic trait becomes more strongly expressed OR expressed earlier as it is passed on generation to generation 14 Thursday, September 15, 2016 • occurs due to expansion of unstable region of DNA from generation to generation • larger expansion causes increased disease severity (disease worse with each generation) environmental effects • • temperature sensitive allele - product is functional only at certain temperatures • ex: coat color in rabbits • ex: vestigial wings in fruit flies • phenocopy: observed result of an environmentally induced, non genetic alteration of a phenotype to a form that resembles the expression of a known genetic mutation continuous characteristics: • • discontinuous characteristics: relatively few phenotypes (Mendel’s peas) • continuous: continuous distribution of phenotypes - occurs when genes interact at many loci (height in humans) • polygenic characteristics: encoded by genes at many loci • pleiotropy: one gene affects multiple characteristics Pedigree Analysis • study of human genetics is constrained by special features controlled mating not possible • • long generation time • small family size • pedigree: pictorial representation of a family history - outlines inheritance of one or more characteristics • each generation identified with roman numeral children listed left to right in birth order • • symbols: • male: square • female: circle • unknown: diamond • unaffected: blank affected: filled • • obligate carrier: dot in the middle • asymptomatic carrier (may later exhibit trait): line through • multiple persons: number in the middle • deceased: slash through • proband (first affected family member studies by geneticist ): p with arrow unknown family history: ? • • adoption: brackets with dashed line to adopted parents • consanguinity (mating between related people): double line • autosomal recessive traits • usually appear equally in males and females • tend to skip generations usually have children with wild-type (non family usually RR) • • affected offspring usually born to unaffected parents • more likely to appear among progeny of related parents (consanguinity) • ex: Tay-Sachs disease: physical and neurological conditions leading to blindness, deafness • usually leads to death at 2-3 years of age 15 Thursday, September 15, 2016 • lack enzyme that breaks down lipid in the brain - leads to accumulation of lipid • autosomal dominant traits usually appear equally in males and females • • all affected people have at least one affected parent • if homozygous for the trait, all offspring will have the trait • if heterozygous, about 1/2 will get trait • does not skip generations • unaffected people cannot transmit the trait (they do not have it at all) ex: familial hypercholesterolemia: blood cholesterol greatly evaluated due to defect in • cholesterol transport • leads to increased risk of coronary artery disease • heart attacks by 35 years of age • ex: Waardenburg syndrome • deafness, fair skin, white forelock and visual problems x-linked recessive traits • • appear more frequently in males • never passed from father to son (X in males is from MOM) • affected male can pass allele to daughter (unaffected) • she passes it to sons who ARE affected (usually half of carrier’s sons are affected) • all daughters of affected fathers are carriers usually skips a generation because it’s passed via a female carrier • • ex: hemophilia A: absence of protein for blood clotting - excessive bleeding • can be controlled by administering factor VIII • X-linked dominant traits: • don’t skip generations • usually more females affected • affected sons must have affected mother, affected daughters must have either affected mom or dad • affected males pass on the trait to all daughters (none of the sons because they receive Y from the dad) • affected females (if heterozygous) will pass trait onto half of sons and daughters • if affected females homozygous, will pass trait on to all children • ex: familial vitamin-D resistant rickets: defective transport of phosphate, especially in kidney cells • bone deformities, stiff spines and joints, bowed legs, mild growth issues • Y-linked traits: • appear only in males - females do not have a Y chromosome • all male offspring of affected males are affected • doesn’t skip generations Linkage, Recombination and Gene Mapping recombination: alleles sort into new combinations - increased genetic variation • • of gametes that are formed in meiosis • independent separation results in recombination • nonrecombinant alleles: original combinations (same as parents) • recombinant gametes: new combinations due to independent separation 16 Thursday, September 15, 2016 • ex: AABB x aabb —> AaBb (self-fertilize) —> AB ab (nonrecombinant) and Ab aB (recombinant) linked genes: • • notated by 2 genes marked on same chromosome • genes located closely on the same chromosome - belong to the same linkage group • travel together in meiosis, getting into the same gamete • not expected to assort independently • segregate together and crossing over produces recombination between them complete linkage leads to ONLY non recombinant gametes and non recombinant • progeny • ex: MD gamete and md gamete (won’t assort more) • independent assortment will produce 4 types of progeny with 1:1:1:1 ratio (half recombinant and half non recombinant) • this will be the highest numbers of progeny - looking the same as the parents if no crossover, each gamete receives a non recombinant chromosome with original • combination of alleles • in meiosis 2 genes that are normally linked will then assort independently and end up in different gametes • crossing over with linked genes leads to recombinant gametes and recombinant progeny no crossover: homologous chromosomes pair in prophase I, and without crossover • each gamete gets non recombinant chromosome • IF crossover takes place in prophase I • half of the resulting gametes will have unchanged chromosome (nonrecombinant) and half will have recombinant • generally, genes on the same chromosome go through some crossing over • linked genes that cross over are incompletely linked • ex: for single crossovers, the frequency of recombinant gametes is half the frequency of crossing over because each crossover takes place between only 2 of the 4 chromatids of a homologous pair • example of crossing over between linked genes: • normal leaves/tall crossed with mottled, dwarf • because no crossing over leads to recombinant and crossing over leads to half, non recombinant dominates in TOTAL numbers • **lowest 2 numbers of progeny are always the recombinant** • recombinant doesn’t always look different, non recombinant doesn’t always look the same • it’s based on the GAMETES • recombination frequency: • # of recombinant progeny * 100 • total number of progeny • coupling and repulsion configuration of linked genes • coupling (cis configuration): one chromosome contains both wild-type alleles, one chromosome contains both mutant alleles • P B • p b • repulsion (trans): wild-type allele and mutant are on the same chromosome • P b • p B 17 Thursday, September 15, 2016 • why is allelic configuration important? numbers differ depending on whether the alleles are coupled or in repulsion • • lowest 2 numbers of progeny always the recombinant EVEN IF THEY LOOK THE SAME as the parents • those in repulsion configuration will have non recombinant that look different Situation Progeny of testers Percentage independent assortment AaBb (nonrecombinant) 25% (1:1:1:1 ratio) aabb (nonrecombinant) 25% Aabb (recombinant) 25% aaBb (recombinant) 25% complete linkage (genes in AaBb (nonrecombinant) 50% (1:1 ratio) coupling - NO crossing over) aabb (nonrecombinant) 50% linkage with some crossing over AaBb (nonrecombinant) more than 50% (genes in coupling) aabb (nonrecombinant) Aabb (recombinant) less than 50% aaBb (recombinant) • ex: testcross produces progeny shown: • AaBb x aabb —> 10 AaBb, 40 Aabb, 40 aaBb, 10 aabb • find % recombination: 10+10 / 10+10+40+40 = 20/100 = 20% • • were the genes in AaBb parent in coupling or repulsion? • find which ones were nonrecombinant —> Aabb and aaBb • ignore the recessives from the testcross plant (bc can only contribute a and b) • A b must have been one chromosome a B must have been another • • predicting the outcome of crosses with linked genes • geneticists have determined that the recombination frequency between 2 genes (warty vs smooth, dull vs glossy) in cucumbers is 16%. How can we use this info to predict results of the cross? because the recombination frequency is 16%, the total population of recombinant gametes • is .16 • each recombinant gamete will have .08 frequency • then take 1-.16 = .84 • split that in half to get the 2 nonrecombinant gametes for one the other testcross fruit will have 100% nonrecombinant • • gene mapping with recombination frequencies • genetic map: chromosomal map calculated using recombination • map unit: 1% recombination (aka centiMorgan) • determined by recombinant frequency ex: • • gene pair recombination frequency • A and B 5 • B and C 10 • A and C 15 you know A to C is the largest, so the order is either ABC or CBA • • distance of additional gene helps resolve orientation (adding in D helps to show that the order is DABC (look at slides 30 and 31) 18 Thursday, September 15, 2016 • 2 strand double crossover between 2 linked genes produces only non recombinant gametes • single crossover will switch the alleles on homologous chromosomes • BUT second crossover will reverse the effects of the first • restores original parental combo • produces only nonrecominant genotypes EVEN THOUGH parts of the chromosomes have recombined • double crossovers between genes go undetected, so map distances between distant genes tend to underestimate genetic distances • constructing genetic map with 2 point test crosses • ex: Gene Loci in testcross Recombination frequency (%) a and b 50 a and c 50 a and d 50 b and c 20 b and d 10 c and d 28 • **recombination frequency of 50% is expected with independent assortment - this means a and b may be on different chromosomes or very far apart • linkage group 1 is a linkage group 2 is dbc • • 3 point testcross: more efficient • three types of crossovers with 2 linked loci • single crossover between A and B • single crossover between B and C double crossover • • steps: • identify nonrecombinant progeny (2 most numerous phenotypes) • identify double crossover progeny (2 least numerous) • determining gene order compare phenotypes of double crossover progeny with non recombinant - should • be alike in 2 characteristics and differ in one (GENOTYPICALLY, not phenotypically) • the characteristic that differs is encoded by the MIDDLE gene • determining location of crossovers the remaining progeny (after the non recombinants and the double crossovers have • been eliminated) are the recombinants • SINGLE crossovers • calculating recombination frequencies: use equation from before • double cross over already gave us the gene order interference: one crossover tends to inhibit additional crossovers in the same region, so • double crossovers are less frequent than expected • interference: 1-coefficient of coincidence 19 Thursday, September 15, 2016 • coefficient of coincidence: • # of observed double crossovers # of expected double crossovers • • ex: a 3 point testcross is carried out between 3 linked genes. The resulting nonrecominant progeny and s+r+c+ and src, and the double-crossover progeny are src+ and s+r+c. Which is the middle locus • answer: c locus • effects of multiple crossovers (between multiple chromatids): as the distance between genes increases, more multiple crossovers are likely and the • discrepancy between genetic distances (based on recombination rates) and physical distances increases. • physical mapping methods used to determine physical positions of genes on particular chromosomes • somatic cell hybridization: assigns gene to particular human chromosome deletion mapping • • physical mapping through molecular analysis • in situ hybridization • recombination rates exhibit extensive variation • levels of recombination vary widely • among species among chromosomes of single species • • between males and females • recombination hotspots 20


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