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BIOL10005: Genetics and the Evolution of Life Lecture 1: Genetics: Variation and the Genome Genetics is the study of the variation between and among living things, and how it is inherited. Variation may result from: • environmental factors • genetic factors • a combination of genetic and environmental factors DNA is the hereditary material Genes, the units of biological information, are composed of DNA Word Gene Genotype Phenotype Genome Definition The fundamental physical and functional unit of heredity, which carries information from one generation to the next; a segment of DNA The specific allele constitution of an organism, either of the entire organism or for a certain set of genes or a certain gene The morphological, biochemical and behavioural properties of an organisms resulting from a specific genotype and its interaction with the environment The genetic complement in a set of chromosomes Lecture 2: Structure and Replication of DNA Semi-conservative replication of DNA in prokaryotes and eukaryotes The replication fork, polarity of DNA Differences between replication origins in prokaryotes and eukaryotes Enzymes involved Lagging strand and leading strand replication Replication of telomeres Polymerase Chain Reaction (PCR) – a technique that mimics replication Word Semi-conservative replication Complementary base paring Purine Polynucleotide Phosphodiester bond 5’ (PO4) end 3’ (OH) end Leading/lagging strand Definition The method of DNA replication where the new molecule of DNA has one strand which comes from the parent molecule and one strand which is newly synthesised Nucleotides or nucleotide sequences that are able to base pair, for example G and C are complementary, as are A and T One of the two types of nitrogenous base compounds found in nucleotides. The purine bases in DNA are adenine and guanine A polymer consisting of nucleotide subunits The chemical bond that links the adjacent nucleotides in a polynucleotide The end of the polynucleotide that terminates with a phosphate attached to the 5’carbon of the sugar The end of the polynucleotide which terminates with a hydroxyl group attached to the 3’-carbon of the sugar The leading strand is that which is synthesised continuously, whereas the lagging strand is synthesised in a discontinuous fashion during DNA replication 1" Okazaki fragment One of the RNA-primed short segments of DNA synthesised during replication of the lagging strand of the double helix DNA helicase An enzyme that uses energy from ATP to unwind the DNA Topoisomerase An enzyme which can relax DNA by cutting and reforming the polynucleotide (gyrase) backbones Single-strand One of the proteins that attaches to single-stranded regions of DNA and prevents the binding protein reformation of the base pairs, particularly in the region of the replication fork Primase An enzyme which synthesises the RNA primer DNA Polymerase An enzyme which adds nucleotides to gaps when primers are removed I DNA Polymerase The main polymerase which adds nucleotides to the template in a complementary way III RNA primer Sequence of RNA to make a stretch of double-stranded DNA on which the DNA polymerase III can work Ligase An enzyme which joins sequences of DNA together Lecture 3: Genes, Alleles and Chromosomes The one gene – one polypeptide hypothesis The products of genes are polypeptides and RNA A polypeptide is a chain of amino acids linked by peptide bonds Genes are defined by mutations; the concept of alleles Genes are mostly located in chromosomes Chromosomes consist of DNA and protein: • Chromatin, nucleosomes – histones Behaviour of chromosomes – non disjunction Word Mutation Locus Haploid Diploid Aneuploidy Euploidy Autosome Sex Chromosome Chromatin Nucleosome Definition A change in the genetic material which can be passed from cell to cell or parent to offspring. A somatic mutation will occur in a somatic cell and hence will not be passed on to the next generation, compared to a germline mutation which can be passed to offspring The position of a gene on a chromosome One copy of each chromosome Two of each type of chromosome; the two similar chromosomes are described as homologous Addition or deletion of a single chromosome or sometimes extra single chromosomes Addition of deletion of a complete haploid set/s of chromosomes A chromosome not involved in determining the sex of the organism A chromosome involved in determining the sex of the organism DNA and protein (histones) Basic unit of chromatin where DNA is wrapped around histone proteins Lecture 4: Behaviour of Chromosomes and Alleles; Segregation of Alleles Meiosis includes 3 processes which are important to patterns of inheritance: • Segregation of alleles • Independent assortment of chromosomes 2" • Crossing over and recombination of alleles A single factor cross and the principle of segregation: • P, F1 and F2 generations, phenotype/genotype • Dominance/recessiveness • Homozygote/heterozygote • Punnett square • Complete dominance • Incomplete dominance, e.g. snapdragons • Codominance, e.g. haemoglobin and blood groups • Allelic notation • The F2 monohybrid ratio of 3:1 • The reciprocal cross • The test cross • The backcross Word Dominant phenotype Recessive phenotype Monohybrid cross Complete dominance Codominance Incomplete dominance Definition The phenotype expressed in the heterozygote The phenotype not expressed in the heterozygote A crossing involving one gene where on parent is homozygous recessive, the other homozygous dominant, the F1 is heterozygote and the F2 is in a ratio 1:2:1 or 3:1 The homozygous dominant and the heterozygote have the same phenotype The effect of each allele can be seen in the heterozygote, e.g. sickle cell anaemia The heterozygote is a blended phenotype, e.g. flower colour Lecture 5: Multiple Alleles and other Extensions to Mendel Multiple alleles, e.g. clover, tabbying in cats, ABO blood group Pleiotropy, e.g. sickle cell anaemia, albinism Phenocopy, e.g. amelia-meromelia/thalidomide, vitamin D deficiency/vitamin D resistant crickets Variable expression, e.g. polydactyly Penetrance, expressivity, e.g. eyeless in Drosophila, polydactyly Lethality, e.g. yellow locus in mice, achondroplasia in humans, Manx locus in cats (all of these are recessive lethals) Changes to the monohybrid ratio resulting from some of these effects Word Pleiotropy Phenocopy Lethal allele, lethal genotype, lethal mutation Recessive lethal Dominant lethal Definition A single mutation which simultaneously affects several apparently unrelated aspects of the phenotype A phenotype that results from an environmental factor that mimics a genetically caused phenotype mutation An allele, genotype or mutation which results in death (may be lethal at different stages of development) Results in death only in the homozygous state Results in death when heterozygous or homozygous 3" Lecture 6: Two Genes and Independent Assortment One of the processes of meiosis which affects the outcome of a genetic cross is independent assortment of chromosomes. This is relevant when there is more than one pair of chromosomes Independent assortment in the context of meiosis – homologous, non-homologous chromosomes, the consequences for segregation of alleles Gamete formation for two or more loci Punnett square: F2 genotypic ratio, F2 phenotypic ratio 9:3:3:1 The use of a test cross: one locus; two loci Lecture 7: Gene Interaction A reminder of the 9:3:3:1 phenotypic ratio and how it is generated Reminder of the action of a single gene in a biosynthetic pathway Genes do not operate in isolation – the phenotype results from the interaction of the gene products from more than one locus Gene interaction where the ratio in the F2 of a dihybrid cross is 9:3:3:1, e.g. the dense/dilute pigment locus in dogs and cats interacting with the black/brown pigment locus, comb shape in fowl Gene interaction, e.g. recessive epistasis 9:3:4 – an explanation of the interaction which results in the ratio: • Illustration of how a 9:3:4 phenotypic ratio can be explained using a biosynthetic pathway Gene interaction, e.g. dominant epistasis 12:3:1 – an explanation of the interaction which results in this ratio The genetic explanation for a 9:7, 13:3, 9:6:1 and 15:1 ratio Word Recessive epistasis Dominant epistasis Definition Interaction between two genes affecting the same phenotypic trait, where the homozygous recessive genotype at one locus masks the effect of the alleles at the other locus, e.g. coat colour in mice Interaction between two genes affecting the same phenotypic trait, where the allele for the dominant trait at one locus masks the effect of the alleles at the other locus, e.g. colour in plants (green/yellow/white) Lecture 8: Sex Determination Sex determining mechanisms: • Environmental • Genes, e.g. androgen insensitivity in humans (TDF locus), tra in Drosophila • Haplo/diploidy in hymenoptera (bees and wasps) • Balance of autosomes to sex chromosome, e.g. Drosophila • The presence of a sex determining chromosome, e.g. Y in humans • Aneuploidies of sex chromosomes, how do they arise Lecture 9: Inheritance Relation to Sex and X Inactivation The human X and Y chromosomes: • Pseudoautosomal region The pattern of inheritance of a trait on the X chromosome (brief comparison with Z or birds) 4"