MBG 2400; Summary Notes.docx

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University of Guelph
Molecular Biology and Genetics
MBG 2400
Elizabeth Lee

MBG 2400 Final Summary Notes Lecture 01 Pleiotrophy: one locus affects two or more traits. - Example: White cat (WW or Ww where W is dominant, W allele also causes deafness because of melanocytes. Epistasis: alleles at one locus affect the expression of alleles at a different locus. - Example: coat colour in labs where E expresses dark colour, e masks dark colour, B is black and b is chocolate (brown). Black lab (B-E-) x Yellow lab (likely BBee) have a litter of all black labs therefore black lab parent is BBEE. Linkage: two or more loci are on the same chromosome. Allele frequencies: p = P + 0.5H (dominant allele) q = Q + 0.5H (recessive allele) p + q = 1 Freqency of AA = p Freqency of Aa = H Frequency of aa = Q P + H + Q = 1 Lecture 02 Hardy-Weinburg (H-W) equilibrium: allele frequencies and genotypic frequencies remain constant and genotypic frequencies are determined by allele frequencies (in a large, random mating population in the absence of migration, mutation and selection). - Only use f(aa) to estimate q if f(Aa) is not available (q= f√(aa) ) Detection of carriers: Example: Black Angus bull (BB or Bb) test mated with bb Red Angus cow. For each mating, probability of red will be ½ and this is a low level of confidence if there is only one mating. Bun if we make the mating n times and do not see a bb (red) calf P(Bb bull) = (1/2) since each calf is independent, for large n P(Bb) gets tiny and there is a high level of confidence. After n test crosses, P(Bb bull has n B_ calves) = P(Bb carrier after n) = (1/2) which is equivalent to P(no detection of Bb after n) but with a binary (two outcome) process, P(do not detect Bb) = 1 – P(detect Bb) therefore P(detect Bb) = 1 – P(Bb carrier after n). If mated to either 8 cows, ½ are Bb and ½ are bb, P(detect Bb) = 1 – [3/4(1/2) + ½(1/2)]= 0.9767 or about 98%. Lecture 03 Sex chromosomes are a special case of equilibrium. Mammals: XX (female) and XY (male). Avian species: Zw or Z_ (female) and ZZ(male) with offspring of ZZ or wZ. - Frequency in males = previous frequency in females 2p fp m - p is the allelic frequency of both males and females where p= 3 Sex-limited inheritance: phenotypes can only be observed in one sex. Sex-influenced inheritance: heterozygotes express one phenotype in a certain sex and another in the other sex. Example: Frequency of the H allele for hen-feathering has a frequency of 0.8. What percent of the entire population do we expect to be cock-feather under Hardy-Weinburg equilibrium? p = 0.8, q = 0.2, Q = q = (0.2) = 0.04 Only males will exhibit cock-feathering so we can expect the phenotypic frequency to be 1/2Q = 0.02 Imprinted genes: one parent’s allele is imprinted while still in the gamete stage, destined to be inactive. Lecture 04 Migration: movement of alleles from one population to another. Population 1: Frequency A = p 1 Population 2: Frequency A = p 2 Frequency a = q 1 Frequency a = q 2 Population 2 immigrates (m) and Population 1 are native (1 – m) ' Population 1 after the migration: p1=p +1(p −p 2 1 Selection: process that determines which individuals become the parents of the next generation. p = po(1−s q1) o 1 1−2s p q −s q 2 where s =1-fitness(H) and s =1-f2tness(Q) 1 o o 2 o Lecture 05 Natural selection: the environment “decides”, adapt to the environment or die. - Pressures: Evolution (subtle pressure), “bottlenecks” (moderate pressure), extinction (massive pressure). Artificial selection: humans decide, goal oriented (appearance, use, productivity, satisfaction, whimsy). Lecture 06 Qualitative traits: ordered by one or a few loci, discrete phenotypes. - Eye colour, coat colour, seed texture. Quantitative traits (polygenic traits): controlled by multiple loci, continuous phenotypes. - Height, weight, racing speed, milk yield, temperament. - Range is measured as a variation, many loci contributing to the phenotype. - P = G + E or phenotype = genotype + environment Threshold traits: quantitative, polygenic, and categorized by a small number of discrete phenotypic classes. Variance: measure of how much variability there is within a population for a certain trait. Lecture 07 Genotype = additive (alleles contributing to phenotype) + dominance (loci expressing dominance) + interaction (epistatic interaction between loci) Partitioning genetic variance: gametes contain ½ of the genetic material P = A (additive effects passed on) + D (dominance effects are not passed on, just dominant alleles) + I (epistatic interaction effects are not passed on, just alleles that may interact) + E P = G + E Var(P) + Var(G) + Var(E) Var(G) = Var(A) + Var(D) + Var(I) Var(P) = Var(A) + Var(D) + Var(I) + Var(E) Heritability = Var(A)/Var(P) If a trait has a strong genetic influence from parents, heritability is high (heritability ranges from 0 to 1, rarely more than 0.50 or 50%). Lecture 08 Behaviour: reaction to stimuli, external or internal, that can alter an organism’s response to its environment. Behavioural patterns: result of the interaction of genetic and environmental factors. Study of behaviour in genetics: - Development, structure, and function of the nervous system is studied (it senses the environment, processes, initiates the response). - Behaviour-first: specific behaviour is identified, genetic crosses are used to produce strains that bred true for either a high or low level of this behavioural response. Once strains are established, further crosses identify and analyze the genetic components of this behaviour. o Quantitative trait loci (QTL) mapping is used to identify and map genes controlling emotional behaviour. - Gene-first: mutagenesis followed by screening is used to identify single-gene mutations associated with variant or abnormal behaviour. Geotaxis: movement toward or away from gravity. - Test flies in a maze where flies are repeatedly required to choose between moving up or down. - Flies were selected both for positive (going up) and negative (going down) geotaxis, establishing the existence of a genetic influence on this behavioural response. Selection is stronger for negative geotaxis than positive geotaxis. - Effects of chromosomes X, 2 and 3 on geotaxis have been identified. Microarrays: identify genes that influence complex polygenic behavioural traits (makes it possible to measure changes in hundred or thousands of genes in a single experiment). Lecture 09 Gene-first approach allows quantifiable impact of single genes on a complex behavioural response. - Lines are individuals, each is affected by a mutagen in a different spot on the chromosome, and they are marked. - Impulses are generated in the dendrite and travel to the axon, then transmits the impulse to adjacent neurons. - Impulse is propagated by transport of sodium and potassium ions across plasma membrane of neuron (sodium pumped in, potassium pumped out), this can be measured as electrical potential of membrane. - Electrophysiological studies showed defective sodium and potassium transport associated with conduction of nerve impulses in specific mutants. - Genes were mapped and isolated, and it was discovered Paralytic gene encodes a sodium channel protein while the Shaker gene encodes a potassium channel protein. - Use of olfactory-based shock avoidance-learning systems with flies. o With no mutation: do learn to avoid in the short term. o With mutation: lack of ability to learn. cAMP creates a learning response to a stimulus. Without cAMP, it would be the same as experiencing the stimulus for the first time every time. Need Rutabaga gene and turnip protein to produce cAMP (if mutated, no cAMP is produced). Dunce protein usually has no effect, but when mutated it causes the enzyme to be inactive and stops the production of cAMP. Short-term memory is mediated by changes in potassium channels. Long-term memory is associated with changes in gene expression with mushroom body neurons. Lecture 10 Genetic control of behaviour is difficult. Huntington’s Disease (HD) is an autosomal dominant disease and causes development, structure and/or function of the brain and nervous system. - Located on chromosome 4 in humans, chromosome 3 in c. lupis and chromosome 6 in b. taurus. - Have expanded cytosine-adenine-guanine repeats on exon 1, mutant allele will code for more than forty repeats (usually only 7-24 repeats). - Complex disease but simple inheritance. - Histone modification used to treat HD. Schizophrenia is a complex brain disorder. Not just one gene controls schizophrenia. Multifactorial and quantitative trait. Autism spectrum disorders (ASD) are also complex, multifactorial diseases with a genetic component. Phenotypically difficult to diagnose in animals. Copy number variations (CNVs) may be important to schizophrenia and ASD. Lecture 11 Population: a group of individuals with a common set of genes that lives in the same geographic area and actively or potentially interbreeds. Gene pool: all of the alleles present in that population. - Sum of all the alleles at each locus that is present in the population. Genetic variation: phenotype will change over time - Large amount of variation and heterozygosity in wild species. As we domesticate, we decrease variation. - Compare nucleotide sequences of genes carried by individuals in a population. Neutral theory: some genetic variation is expected simply as a result of mutation and drift. Natural theory: mutations leading to amino acids are usually detrimental or neutral, with only a very small fraction being favorable. - Large population and small amount of mutations, less genetic variation will be introduced (and vice versa). Wallace-Darwin concept of natural selection: - Individuals of a species exhibit variation in phenotype, many of these variations are heritable and are passed on. - Organisms tend to reproduce in exponential fashion and more offspring are produced than can survive, creating a struggle for survival and some phenotypes are more successful at surviving. As a consequence natural selection, population and species change. - Natural selection is the principle force that shifts allele frequencies within large populations and is one of the
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