1 1 BASIC MENDELIAN AND MOLECU LAR GENETICS 1.1 Genetic terms you should know and understand Gene Locus Allele Dominance Recessiveness Wild type Mutation Genotype Phenotype Homozygote Heterozygote Autosome Sex chromosome Hemizygous Pleiotropy Epistasis Haploid Diploid Nuclear DNA Mitochondrial DNA Chloroplast DNA Chromosome Homologous chromosome Sister chromatid Tetrad Mitosis Meoisis Independent assortment Recombination Crossing over Transcription Translation Mendelian genetics skills you should have mastered Basic Probability (Sum rule, product rule, conditional probability) Monohybird (1-locus) crosses Dihybrid (2-locus) crosses Sex Linkage 1.2 Features of the Genetic Code y ou should know A, G (purines), C, T (pyrimidines) Genetic Code (based on mRNA sequence) Degeneracy (wobble) Replacement mutation (nonsynonymous) Silent mutation (synonymous) Frameshift mutations2 1.3 Features of Genome St ructure you should know Coding regions code for polypeptides (proteins) or tRNAs, rRNAs Noncoding regions contain repetitive DNA sequences, e.g., microsatellite loci (Short Tandem Repeats), longer repeats (Alu is 300 bp long and copies occur 300.000 times in human genome = 5% of human DNA) Psedogenes are the result of duplications that have acquired a mutation producing a stop codon inside the coding region. Introns (transcribed but not translated portions of a gene) Exons (transcribed and translated portions of a gene)3 2 MENDEL'S POSTULATES Basis of Mendel's success: • chose research organism well-suited to his objectives • experiments carefully designed • collected large amounts of data • used mathematical analysis to show that results were consistent with hypotheses Peas will self-fertilize unless they are cross-pollinated by hand. Must clip off anthers to prevent selfing. They’re available in wide array of distinct true-breeding types (produce only progeny like themselves when they self). Grew them for two years to insure true-breeding. Provided cont rol for hybridization. Mendel obtained seeds for plants with distinct characteristics or phenotype s. Bred true for flower color, pod shape, seed shape, seed color, etc. True-breeding types used as parents in hy bridization experiments. 2.1 Mendel’s First Postulate: Genetic characters are controlled by unit factors that exist in pairs in individual organisms. Pollen from round-seeded plant used to pollinate wrinkled-seeded plant, & vice versa. <--Reciprocal Monohybrid Crosses--> Maternal parent Paternal parent Maternal parent Paternal parent P: wrinkled x round round x wrinkled F1: all round all round (selfed) (selfed) F2: 2737 round 923 wrinkled 2750 round 920 wrink F2 Ratio 2.99:1 3: 1 Prevailing notion of heredity at the time was that the traits of parents bl ended together to produce a hybrid with an intermediate phenotype. But blending of characteristics was not observed in Mendel's experiments—he saw partic ulate inheritance. Based on his experiments, Gregor Mendel concluded that certain "factors" (which we now call genes) are passed from parents to their offspring (Darwin’s first postulate). According to Mendel, each organism has a pair of these factors that control the development of a specific trait. When two organisms produce offspring, each parent gives the offspring one of the factors from each pair. In the offspring, the two genes - one from each parent - act together. 2.2 Mendel’s Sec ond Postulate: Dominance/Recessiveness: When two unlike for a single character are present in a single individual, one unit factor is d ominant to the other, which is said to be recessive. In the above monohybrid cross, a recessive factor is covered up by a dominant factor in the F1 of a cross, but it reappears in the F2 in a predictable proportion (1/4). The F1 plants all look like one of the parents (round), but retain the potential to produce wrinkle-seeded offspring.4 Thus, F1 plants are no longer true-breeding: they are hybri ds. Mendel invented terms dominant and rece ssive to describe this phenomenon. The trait that is masked in the F1 is recessive. The other is dominant. According to the principle of dominance, one gene in each pair may be "stronger" and prevent the other from being seen. The recessive gene can, however, reappear in the F2 generation. 2.3 Mendel’s Third Post ulat e: Equal Segre gation During the formation of gametes, the paired unit factors segregate randomly so that each gamete receives one or the other with equal likelihood. Demonstrate using a Punnet Square: Using modern notation (capital letters denote dominant allele, lower-case letters denote recessive allele, and the letter is often derived from the abnormal (mutant) form, rather than from the normal (wild-type) form: F1 Female Eggs 1/2 W 1/2 w Equal Segregation of genes into gametes. F1 Male 1/2 W 1/4 WW 1/4 Ww Random union of gametes. All these Sperm 1/2 w 1/4 Ww 1/4 ww combinations equally likely. 1 WW : 2 Ww : 1 ww 3 with dominant phenotype : 1 recessive 2.4 Putting it all toget her Parental phenotype round wrinkled Parental genotype WW x ww diploid--two copies of gene Gametes W w haploid--single copy of gene F1 Ww diploid--W dominant to w F1 gametes ___ W and ___ w F2 (from selfed F1) ___ WW: ___ Ww: ___ ww 2.5 Test Cross: Since the WW and Ww individuals all have the same phenotype, how would you determine if you actually had the above genotypic ratio? (That is, If an individual has the recessive phenotype (wrinkled), we know what it's genotype is (ww). But if it has the dominant phenotype (round), we don't know what the genotype is. Individuals with a dominant phenotype can be either homozygous (WW) or het erozygous (Ww) in genotype.5 To determine genotype, can cross an individual with the dominant phenotype to a plant with the recessive phenotype (and recessive genotype). WW x ww Ww x ww   Gentoype Ww 1/2 Ww 1/2 ww Phenotype all round 1/2 round 1/2 wrink. 2.6 The Dihybrid Cross and Mendel’s Fourth Postulat e: Independent Segregat ion During gamete formation, the segregation of one gene pair is independent of other gene pairs What if plants differ in 2 traits? Mendel used the dihybrid cross in which 2 traits are examined simultaneously: seed color (G,g) and seed shape (W,w) P: yellow, round green,