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PCB3063: Chapter 3

by: Brittany Woody

PCB3063: Chapter 3 PCB3603

Brittany Woody
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These are notes from the first powerpoint and lecture. They are supplemented with information from the textbook. Concepts of Genetics 11th Edition
Dr. W. Brad Barbazuk
Class Notes




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This 8 page Class Notes was uploaded by Brittany Woody on Tuesday September 13, 2016. The Class Notes belongs to PCB3603 at University of Florida taught by Dr. W. Brad Barbazuk in Fall 2016. Since its upload, it has received 144 views. For similar materials see Genetics in Genetics at University of Florida.


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Date Created: 09/13/16
Chapter 3 What is Genetics? - Maintenance and transfer of information - Each child is a hybrid of two parents plus mutations - .1% (1/1000) genetic differences between each person - Genetics allows for sexual, artificial, or other types of selection - Transmission genetics: how genes are transmitted from parents to offspring - Galapagos Islands: 19 volcanic islands distributed over about 140 miles; environment varies from island to island; Darwin recognized that wildlife was related to but distinct from that on the mainland; each island has its own distinctive species of animals and plants - Darwin’s Finches: • at least 15 species, but clearly related based on physical structures • the beaks of the finches are different and appropriate for habitat on it’s island; all birds evolved from one parent species on mainland South America - What are underlying causes of the morphological differences in beaks between islands in Darwin’s finches? What is different in genes between finch species? • Sequence variation among individuals in a population - What biological processes can produce beaks of such different shapes, and make sure that this shape will be based on to the next generation? • Variation exists within (or near) genes that affect beak morphology. Amplification of one morphology over another within a population could be the result selection of one morphology due to improved fitness - In 2015, finch’s genomes were sequenced; associated genetic differences with beak morphology (phenotype) - Align genomes of each finch with a bird whose genome is sequenced; look for differences between each finch and the benchmark bird, and between each finch (base differences: A vs. C vs. T vs. G) 1 - Associated presences of a base or series of bases (allele) with particular phenotypes - ALX1: this gene is expressed in craniofacial region; mutations cause facial defects in mammals; slight differences result in beak differences in finches but not drastic differences or defects Mitosis & Meiosis - 2 copies of every chromosome in every cell; any more or less will result in malfunction - Charyotype: map (picture) of each chromosome set; shows each pair of chromosomes; a set of chromosomes are nearly identical - Long string of DNA is condensed into compact chromosomes during duplication - Each chromosome has centromere where you see “pinch”; mostly made up of repetitive sequences; position of centromere helps identify chromosome number - “big arm” of chromosome is Q and “small arm” is P - Sister chromatids are pair of identical chromosomes that are created in the beginning of duplication - Each copy of a chromosome is a homologue of the other copy; not exactly the same - Cell cycle: Interphase (G1, S, G2, G0) and Mitosis (Prophase, Metaphase, Anaphase, Telophase) - Genes are duplicated during S phase and sisters are connected, condensed during mitosis - Mitosis: (somatic cells, not gametes-sex cells) one 2n cell divides into two 2n cells • Interphase: two copies of every chromosome; chromosomes are extended and uncoiled, forming chromatin • Prophase: chromosomes coil and condense, breakdown of nuclear membrane, centrioles divide and move to opposite poles, microtubules from centrioles attach to centromere - Prometaphase: chromosomes are clearly double structures; centrioles reach the opposite poles; spindle fibers form • Metaphase: centromeres align at midline (metaphase plate) • Anaphase: centromeres split and daughter chromosomes migrate to opposite poles 2 • Telophase: daughter chromosomes arrive at the poles; cytokinesis (division of cytoplasm) - Meiosis: (replication of gametes: sperm and eggs) one 2n cell divides into four 1n cells • Reduces genetic material by half, each gamete is haploid; each gamete carries one member of each homologous chromosome pair; meiosis results in unique combinations of maternally and paternally derived chromosomes within the haploid complement of the gamete; “crossing- over” results in exchange of genetic material between each member of a homologous chromosome pair, mix of mom’s and dad’s chromosomes • One 2n cell results in four 1n cell in meiosis - 1n: one copy of each chromosome, 2n: two copies of each chromosome - Mitosis: one replication; Meiosis: two replications - Mitosis results in two identical sets of DNA; during meiosis, each pair of chromosomes synapse (process is called synapsis, chromosomes connect) to form a tetrad (two copies of mom’s chromosome, two copies of dad’s chromosome), and crossing over takes place; results in recombinant DNA - Meiosis I and II both have prophase, metaphase, anaphase, telophase - Prophase I has five substages • leptonema: chromomere formation and homology search begins • zygonema: initial alignment of homologs (rough pairing), homologous chromosomes have been replicated, formation of the synaptonemal complex • pachynema: chromosomes condense further • diplonema: each pair of sister chromatids begin to separate; chiasmata are apparent • diakinesis: two controllers of each tetrad attach to the spindle fibers - Primary spermatocyte undergoes meiosis I to produce two secondary spermatocytes, which undergo meiosis II to produces a total of four haploid spermatids - During oogenesis (egg duplication), the four daughter cells do receive equal cytoplasm; polar bodies do not undergo further division; primary oocyte splits cytoplasm three times but is unequal, so most cytoplasm is in 1 cell 3 - Eukaryotic DNA os wrapped around nucleosomes (which are made up of proteins called histones); the DNA+ protein complex is called chromatin - Overall charge of DNA is negative; histones are positively charged; histone and DNA associate electrostaticlly Mendelian Genetics - Did research on pea plants; many varieties (heritable features, character variants; flower color) - Features of a good organism for experimental genetics: controlled mating, fast generation time (for many data points), fecundity - Character choice: either/or (not somewhere in the middle, called true breeding plants), avoid traits that varied on a continuum, true breeding varieties - Parental generation is “P generation”; their offspring is F1, first filial generation; offspring of F1 is F2, second filial generation - Mendel observed the same pattern of inheritance on six other pea plant characters, each represented by two traits; gave same outcome as flowers; one feature is dominant, one is recessive - F1 only shows dominant trait; F2 shows ratio 3 dominant: 1 recessive - Reciprocal cross: done with both pollination of one phenotype by the other, and vice versa (not always using dominant trait holder as male in pollination, for example); results will not be sex-dependent - What Mendel called a “heritable factor”, we call a gene - Mendel proposed three postulates: (Independent Assortment) • Unit factors exist in pairs; diploid, one from mom and one from dad • In the pair of unit factors for a single characteristic in an individual, one unit is dominant and one is recessive • The paired unit factors segregate independently during gamete formation - Mendel’s segregation model accounts of the 3:1 ratio he observed in the F2 generation 4 - Parent generation allele is WW for purple, ww for white; F1 is Ww; F2 is 25% WW, 25% ww, 50% Ww • WW and Ww appear with dominant trait (purple flowers), 75% • ww appear with recessive trait (white flowers), 25% • 75% : 25% = 3:1 ratio - Two of the same alleles (WW or ww) is homozygous; Two different alleles (Ww) is heterozygous - Phenotype: physical characteristic; Genotype: genetic code • Phenotype: 3 purple: 1 white • Genotype: 1 WW: 2 Ww: 1ww - Test cross: to figure out the genotype of a purple flower (WW or Ww), cross it with a white flower (homozygous recessive ww); if the purple flower is WW, all offspring will have dominant trait and will be purple; if the purple flower is Ww, half of offspring will be white (ww) and half will be purple (Ww) - Selfing: self-fertilization of individuals from the first generation - Dihybrid cross: uses two traits (seed color and seed shape); if you cross one round yellow pea (dominant, dominant) with a wrinkled green pea (recessive, recessive), the result of pea colors would be 3 yellow: 1 green; the resulting pea shapes would be 3 round: 1 wrinkled; this proves that the traits are independent, they are on different chromosomes, different loci (singular is locus) - Phenotypic ratio with both traits is 9 yellow round: 3 yellow wrinkled : 3 green round: 1 green wrinkled • 9 both dominant traits: 3 one dominant trait and one recessive trait; 3 one recessive trait and one dominant trait: 1 both recessive traits - The law of independent assortment states that each pair of alleys segregate independently of each other pair of alleles during gamete formation - Strictly speaking, this law applies only to genes on different, non-homologous chromosomes - Genes located near each other on the same chromosome tend to be inherited together (linkage) 5 - Independent assortment leads to extensive genetic variability - Humans have 46 chromosomes in 23 homologue pairs. The number of gametes produced (combinations of independently assorting chromosomes) is calculated as 2^23, or 8.4 million - Random fertilization adds to genetic variation because any sperm can fuse with any ovum (unfertilized egg)- results in a zygote with any of about 70 trillion diploid combinations - The laws of probability govern Mendelian genetics; when tossing a coin, the outcome of one toss has no impact on the outcome of the next toss; in the same way, the alleles of one gene segregate into gametes independently of another gene’s alleles - Probability of 0: no chance of something happening; probability of 1.0: an event is certain to happen - Chance a coin lands on heads: 50%; chance two coins each land on heads: 25% - Product law: probability of two independent events happening is the product of each individual probability; chance a coin lands on heads: 50% (.5) ; chance two coins each land on heads: 25% (.5 x .5= .25) - Sum law: probability of either of two things happening; chance that rolling dice will yield a 1 OR a 6: 1/6 + 1/6= 2/6= 1/3 - Probability of genotypes in monohybrid cross: .25 WW, .25 ww, .5 Ww - All probabilities of an event sum to 1 - Probability of genotypes in dihybrid cross: multiply probability of first genotype by second genotype (mom by dad; top of Punnett square by side of Punnett square) - GGWw: one parent must be GW, the other must be Gw - Trihybrid crosses involve three independent traits; Mendel’s laws can be applied to any number of traits; trihybrid cross Punnett square will have 64 cells - Parent generation: AABBCC x aabbcc; F1 generation will all be AaBbCc - F2 generation: parents are AaBbCc x AaBbCc • AA probability= .25; Bb probability= .5; CC probability= .25 - AABbCC probability= .25 x .25 x .5= 1/32 - 1/4 x 1/4 x 1/2 = 1/32 6 - What is the probability that an unaffected sibling of a brother or sister expressing a recessive disorder is a carrier (heterozygote)? (assume parents are heterozygote) • Probability that unaffected sibling is heterozygote= 1/2 • Probability that sibling is unaffected= 3/4 • (1/2) / (3/4) = 2/3 - Binomial theorem: used to determine the probability of a particular combination, rather than going through all possibilities - Chi-square test compares actual outcomes to “expected” outcomes; determines if results are close enough to expected result to be correct or if there is a “statistically significant” difference is actual outcome compared to expectations - As sample size increases, the average deviation form expected fraction or ratio decreases; larger sample size reduces the impact of chance deviation on the final outcome - The null hypothesis is the assumption that the data will fit a given ratio, such as 3:1; assumes that there is no real difference between the measured values and the predicated values • If rejected, the deviation from the expected is NOT due to chance alone and you must reexamine your assumption (expected data) If it is failed to be rejected, then observed deviations can be contributed to chance • - When drawing a pedigree, the proband is the individual of interest; signified with a P; pedigree shows a family tree with respect to a given trait; pedigree analysis reveals patterns of inheritance - “p-value” of .05 is a commonly-accepted cut-off point - p>0.05 means that the probability is greater than 5% that the observed deviation is due to chance alone’ therefore the null hypothesis - p<0.05 means that the probability is less than 5% that observed deviation is due to chance alone; therefore null hypothesis is rejected; reassess assumptions, propose a new hypothesis - Identical twins are called monozygotic; fraternal are dizygotic - Related parents are called consanguineous; connected by a double line on a pedigree 7 - Transposable elements: have the ability to move from place to place in the genome of certain organisms - Tay-Sachs disease (TSD): recessive disorder involving unalterable destruction of the central nervous system; results from loss of activity of a single enzyme hexosaminidase A (Hex-A) 8


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