Comprehensive Genetics Study Notes (SI Handouts Combined) Flashcards

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Genetics

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The study of heredity and variation, focusing on how genetic information is encoded, replicated, and expressed, and how it evolves over time. It encompasses transmission, molecular, and population-level perspectives.

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Genome

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The complete set of genetic instructions for an organism, composed of DNA or RNA. It includes all genes and noncoding sequences that direct development and function.

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Model Organisms

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Organisms widely used in genetic research because they have advantageous traits such as short generation time and large progeny numbers that facilitate genetic analysis. Examples include E. coli, Drosophila, C. elegans, yeast, mouse, and Arabidopsis.

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Cell theory

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The principle that all life is composed of cells, that cells arise only from preexisting cells, and that the cell is the fundamental unit of structure and function in organisms. This concept underpins modern biology and heredity.

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Germplasm

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The theory that cells in reproductive organs carry a complete set of genetic information that is passed to offspring. It contrasts with ideas that somatic changes are inherited.

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Homologous chromosomes

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Matched chromosome pairs in diploid organisms, one inherited from each parent, similar in size, shape, gene arrangement, and centromere position. They carry the same genes but may have different alleles.

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Cohesin

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A protein complex that holds sister chromatids together after DNA replication to ensure accurate chromosome segregation during mitosis and meiosis. Proper cohesin function prevents premature chromatid separation and aneuploidy.

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Binary fission

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A simple asexual reproduction process used by prokaryotes in which the cell replicates its DNA and divides into two genetically identical daughter cells. It lacks the complex mitotic machinery of eukaryotes.

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Mitosis

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A eukaryotic cell division process that produces two genetically identical daughter cells from a single parent cell, maintaining the same chromosome number. It involves stages (prophase, metaphase, anaphase, telophase) that separate sister chromatids.

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Meiosis

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A specialized cell division that reduces chromosome number by half to form haploid gametes, producing genetic variation via crossing over and independent assortment. It consists of two successive divisions: meiosis I (reductional) and meiosis II (equational).

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Crossing over

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The reciprocal exchange of chromosome segments between homologous chromosomes during prophase I of meiosis, creating recombinant chromosomes that increase genetic diversity. It does not normally occur during mitosis.

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Spermatogenesis

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The process in males where spermatogonia undergo mitosis and meiosis to produce four haploid spermatids that mature into sperm. It yields many genetically diverse gametes because of meiosis and independent assortment.

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Oogenesis

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The process in females where oogonia undergo mitosis and meiosis to produce typically one large egg and polar bodies; meiosis is arrested at stages until fertilization. Polar bodies are small byproducts that preserve cytoplasm for the oocyte.

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Dominant trait

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An allele or phenotype expressed in both homozygotes (AA) and heterozygotes (Aa); a single copy of the dominant allele produces the dominant phenotype. Heterozygotes display the dominant phenotype over recessive alleles.

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Recessive trait

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An allele or phenotype that is expressed only in homozygotes (aa) and is masked in heterozygotes (Aa) by a dominant allele. Two copies of the recessive allele are required for the trait to appear.

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Phenotype

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The observable appearance or manifestation of a characteristic resulting from the interaction of genotype and environment. Phenotype includes morphology, behavior, and biochemical traits.

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Genotype

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The set of alleles possessed by an individual organism at one or more loci, which contributes to potential phenotypes. Environmental and genetic interactions determine whether genotype is expressed.

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Mendel's segregation

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Mendel's principle that each diploid organism has two alleles per locus and that these alleles segregate into separate gametes during meiosis so each gamete receives one allele. This segregation occurs during anaphase I of meiosis.

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Independent assortment

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Mendel’s second law stating that alleles of different genes located on different chromosomes assort independently into gametes, producing new combinations of traits. It applies only to genes on different chromosomes or far apart on the same chromosome.

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Addition rule

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A probability rule stating that the chance of any one of two or more mutually exclusive events occurring equals the sum of their individual probabilities. Use it when events cannot happen simultaneously.

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Multiplicative rule

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A probability rule stating that the probability of two or more independent events occurring together is the product of their individual probabilities. Use it to combine independent trait probabilities across events.

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Binomial probability

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A method to calculate the likelihood of obtaining a specified number of successes in a fixed number of independent trials with two possible outcomes per trial. It uses binomial coefficients and probabilities for each outcome.

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Testcross

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A cross between an individual of unknown genotype and a homozygous recessive individual to determine the unknown genotype based on offspring phenotypes. It reveals whether the unknown parent is homozygous or heterozygous for the trait.

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Chi-square test

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A goodness-of-fit test that compares observed and expected counts using the statistic $\chi^2 = \sum \frac{(O - E)^2}{E}$. It assesses whether deviations from expected Mendelian ratios are due to chance.

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Autosomal dominant

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An inheritance pattern where a single copy of a mutant allele on an autosome is sufficient to express the trait in offspring. Affected individuals usually have an affected parent and both sexes are equally likely to show the trait.

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X-linked recessive

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A pattern where mutant alleles on the X chromosome cause the phenotype predominantly in males (XY) since they have only one X; females (XX) must have two copies to express the trait. Carrier females can transmit the allele to sons.

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Codominance

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An allelic interaction in which the heterozygote simultaneously expresses phenotypes of both homozygotes, so both alleles contribute to the phenotype. An example is AB blood type where both A and B antigens appear.

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Incomplete dominance

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A dominance type where the heterozygote phenotype is intermediate between the two homozygotes, often giving a $1:2:1$ phenotypic ratio when heterozygotes are crossed. It differs from simple dominance because neither allele is completely dominant.

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Penetrance

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The percentage of individuals with a particular genotype who actually express the expected phenotype. For example, if 80 of 100 mutation carriers show the trait, penetrance is $80\%$.

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Dosage compensation

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Mechanisms that equalize expression of X-linked genes between sexes; in placental mammals this is achieved by random inactivation of one X chromosome in females. This balances gene product levels from X chromosomes in males and females.

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Lyon hypothesis

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Mary Lyon's proposal that one X chromosome in each female cell becomes randomly inactivated to form a Barr body, and that the choice of which X is inactivated varies among cells. This explains mosaic X-linked expression in females.

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Pseudo-Autosomal region

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Homologous, gene-dense regions at the tips of X and Y chromosomes that pair and recombine during male meiosis to ensure proper segregation. Genes here escape X-inactivation.

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Random X-inactivation

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An epigenetic process where one X chromosome is silenced in each female somatic cell early in development, and that inactive choice is stably inherited in daughter cells. It produces mosaic phenotypes like calico coat patterns.

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Sex-determination systems

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Different mechanisms (chromosomal, genic, or environmental) that determine sex, such as XX-XY, ZZ-ZW, XX-XO, genic sex determination, and temperature-dependent systems. All converge on gonad development, hormone action, and adult sexual phenotype.

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Linked genes

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Genes located on the same chromosome that tend to be inherited together because they are physically close; recombination between them is less frequent than between unlinked genes. Linkage reduces independent assortment.

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Recombination frequency

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A measure of genetic distance equal to the proportion of recombinant progeny; it is used to construct genetic maps and is often expressed in map units (centimorgans). It can be calculated as $\frac{\text{SCO} + \text{DCO}}{\text{Total}}$.

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Map unit (centimorgan)

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A genetic distance unit corresponding to a $1\%$ recombination frequency between two loci; map units estimate relative positions of genes on chromosomes. They do not always equal physical distances.

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Double crossover

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Two separate exchange events between the same two chromatids during meiosis that can restore parental allele combinations for outer genes and reveal the middle gene in three-point mapping. DCOs are rare and critical for ordering three linked genes.

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Coupling vs repulsion

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Configurations of alleles on homologous chromosomes: coupling (cis) has both wild-type alleles on one chromosome and both mutant alleles on the other, while repulsion (trans) has wild-type and mutant alleles on the same chromosome. The configuration changes which progeny phenotypes are nonrecombinant versus recombinant.

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Genetic vs physical map

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A genetic map shows relative gene positions based on recombination frequencies, while a physical map shows actual DNA distances between loci measured in base pairs. Genetic distances may not correlate perfectly with physical distances due to variation in recombination rates.

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Three-point testcross

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A cross used to determine gene order, map distances, and interference by analyzing parental, single-crossover, and double-crossover progeny for three linked genes. Comparing observed and expected DCOs yields coefficient of coincidence and interference.

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Coefficient of coincidence

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The ratio of observed double crossovers (DCO) to expected DCO, calculated as $\text{COC} = \frac{\text{Observed DCO}}{\text{Expected DCO}}$. It quantifies how often double crossovers occur relative to expectation from single-crossover rates.

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Interference

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A measure of how one crossover event affects the likelihood of another nearby crossover, calculated as $\text{Interference} = 1 - \text{COC}$. Positive interference (close to 1) means fewer DCOs than expected; negative values indicate more DCOs than expected.