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Week 3 Notes - Genetics

by: Emma Notetaker

Week 3 Notes - Genetics CELL 2050

Marketplace > Tulane University > CELL > CELL 2050 > Week 3 Notes Genetics
Emma Notetaker
GPA 3.975

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Week 3 of notes, covering both lecture and book notes.
Dr. Meadows
Class Notes
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This 10 page Class Notes was uploaded by Emma Notetaker on Tuesday September 13, 2016. The Class Notes belongs to CELL 2050 at Tulane University taught by Dr. Meadows in Fall 2016. Since its upload, it has received 6 views. For similar materials see Genetics in CELL at Tulane University.


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Date Created: 09/13/16
Monday, September 12, 2016 Week 3 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 • 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 1 Monday, September 12, 2016 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 r d • M m :drestricted • 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 • 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 2 Monday, September 12, 2016 • 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 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 3 Monday, September 12, 2016 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 b • 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 • females are only bearded if they are homozygous (B B ) 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 4 Monday, September 12, 2016 • 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 • 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 5 Monday, September 12, 2016 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 • 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 6 Monday, September 12, 2016 • 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 • • 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 7 Monday, September 12, 2016 •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 • 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% 8 Monday, September 12, 2016 Situation Progeny of testers Percentage 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 • • distance of additional gene helps resolve orientation • 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 recombination frequency of 50% is expected with independent assortment - this means • they may be on different chromosomes or very far apart • 3 point testcross: more efficient • determining gene order • identify nonrecombinant progeny (2 most numerous phenotypes) • identify double crossover progeny (2 lest numerous) • compare phenotypes of double crossover progeny with non recombinant - should be alike in 2 characteristics and differ in one • the characteristic that differs is encoded by the MIDDLE gene • determining location of crossovers 9 Monday, September 12, 2016 • calculating recombination frequencies • 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 • coefficient of coincidence: # observed double crossovers/#expected double crossovers • 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 10


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