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BIOL 205 Chin-Sang Reading Notes.pdf

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Queen's University
BIOL 205

BIOL 205 – Chin-Sang Notes Chapter #1 – Genetic Approach To Biology - the physical system of genetic info passage needs 4 properties o ability to replicate (mech of rep for copying the info) o diversity of structure (info for developing lots of dif cells) o mutability (must be capable fo undergoing changes) o translation (machines that translate info into diverse structures) - Genes – basic elements of the system of inherited info - Genome – collection of all the genes in an organism - the key to genetic analysis is to examine the effects of mutations - genetic info never stops being read; cells have limited life so new ones prod often - structure and physiological property of organism based on proteins - proteins synthesized by DNA (deoxyribonucleic acid) o phosphate/deoxyribose backbone; nucleotide bases  adenine, thyamine, guanine, cytosine o bases that form base pairs are termed complementary - Diversity of Structure – tons of diff combos of bases; not every sequence carries diff info, but the variability is still huge - Ability to Replicate – make two identical copies of original double helix - Mutability – incorrect bases may be put in; all copies will differ from original - Translation – reading the DNA and making a specific form/function out of it - Transcription - creating a complementary mRNA sequence from DNA o Similar structure to DNA except Ribose and Uracil with adenine o mRNA copy is called a Transcript  increases number of genetic info copies (used more than once)  mRNA can leave the nucleus or immediate gene vicinity  stability and lifetime of mRNA regulates protein synthesis - Translation – production of amino acid chain from nucleotide sequence of mRNA - mRNA is read in groups of three bases – codons - tRNA attaches to the mRNA molecule using an anticodon and contains an AA - protein is a finished polypeptide chain folded in specific sequence o AA sequence constrains the folding, but does not totally determine it - Final protein folding depends on cellular conditions - most DNA encodes for regulatory functions of when/where it should be read o regulation occurs at attachment of RNA polymerase and its mvmt  negative control o a molecule can fall off the DNA which allows it to be transcribed  positive control - genetic polymorphism – variation among individuals in the same AA sequence o variation in DNA sequence at the same loci; genetic variance o accounts for diversity among individuals in a population - phenotype – observed variation in morphology or physiology o beginning point for forward genetics o starts with abnormal variant in character; normal = WT; variant = mutant - most phenotype characters are the process of numerous interacting pathways  tyrosinase  tyrosine  melanin Figure 1-8 pg 11 - vermillion mutation in Drosophila makes the eyes bright red - To separate multiple gene effects; crosses are used to create mutations in diff gene combinations o Some DNA changes are diff AA sequences (alter protein structure) o Some are altering rate of protein production - reverse genetics begins at known genetic mutation and looks for resulting organism changes o create knockout mutation at the gene (stops protein synthesis) o allows large numbers of specific mutations to be made o analyze how the knockout mutation affects the phenotype Genetic Mehtods 1) Isolation of mutations affecting biological process under study 2) Analysis of progeny from controlled crosses btwn mutants and WT a. Identifies genes and their alleles as well as inheritance patterns 3) Genetic analysis of cell’s biochemical pathways a. How are genes important to these reactions? b. How cellular chemistry interrupted in mutation; deduce gene role 4) Microscopic analysis a. Isotropic labeling of genes and chromosomes 5) Direct DNA analysis a. Via cloning and insertion into bacterial genome - Probing – method for detecting specific macromolecules in a mixture o Probe labeled by radioactive atom; binds only specific macromolec - Southern Blot – DNA cute by enzymes, electrophoresis seperates fragments by size, fragments move through gel inversely proportional to size o used to detect specific DNA fragments of the gene - Northern Blot – total mRNA extracted, fractionated, blotted o Probing for specific mRNA sequence - Western Blot – protein mixture seperated into distinct protein bands o Probing for a specific protein - Model Organisms – short generation time, smaller, mated with ease, lots of young - Viruses – great for studying DNA replication/mutation and DNA’s physical/chemical structure - Prokaryotes – Escherichia coli - Eukaryotes – yeasts (Saccharomyces cerevisiae), fungi (Neurospora) - Multicell – Arabidopsis (higher plant dvlpmt), Drosophila (great for mutations), C. elegans (few thousand cells), Mus musculus (vertebrate model) Genetic Determination Model - phenotypic differences btwn mutant and WT alleles are many times insensitive to environmental conditions (ie dark skin in Canada) o genes are phenotypic determinant; enviro provides raw materials Environmental Determination - monozygotic twins, separated at birth, raised in different environments o enviro determines the actual course of dvlpmnt (same genes) Genotype-Environment Interaction - a balancing act btwn the genes and environmental factors on an organism o what enviro and it encounters and when affect organism dvlpmnt o both genes and enviro play roles in determination of phenotype - genotype – complete set of genes inherited - phenotype – all aspects of morphology, physiology, behaviour o genotype is a fixed character, most phenotypes change continually Developmental Noise - Drosophila has a compound eye; mutations can alter number of eye facets - Number of eye facets also effected by temp which fly develops o If same enviro of development why do some flies develop diff sized eyes? o Random events in dvlpmnt lead to pheno variation; dvlpmnt noise - genes, environment and developmental noise interact to produce a phenotype  Figure 1-19 p26 Chapter #2 – Single Gene Inheritance - normal form of organism = WT; through crosses look for mutants - genetic modus operandi – mate mutated form to the wild type o Offspring are interbred; represent whether its single gene control - Genetic dissection - selecting for particular mutated trait in subsequent corsses - More complex than single gene does occur; enviro can also change phenol - Genome – organism’s complete, unique set of genetic info (DNA) - Information stored in DNA supercoils on Chromosomes o Single piece of coiled DNA, genes, regulatory elements - In diploid nucleus; two members of chromo pair: homologous chromosomes o Also called simply homologs - Homologs carry the same basic info (some mild variations); so every gene is present in a gene pair - Nucleosomes – octamer of histones that help supercoil the DNA o DNA and associated nucleosomes are chromatin (stuff of chromos) o Chromatin varies in thickness along chromo length o Dense chromatin often found at center; centromere of chromo  Heterochromatin = dense chromatin; euchromatin =less dense o Telomeres – tips of chromos; unique to replication mechanisms - Introns – non coding regions that interrupt gene coding sequences o Size, location of introns provides variation in species o Coding region is constant among most species; introns make variation o Get transcribed, but removed during mRNA production Single Gene Inheritance Patterns - Mendel interested in hereditary units; not dissecting organisms - Pure lines – all offspring produced by mating of that line were identical o Mendel selfed plants as well as crossed them - F1 generation also called first filial generation o Obtained a 3:1 ratio in F2 generation after diff colour cross o F1 crost with green seeds was 1:1 yellow to green - Mendel’s 1 Law – gene pair separate equally into eggs and sperm o single gene contains one member of the gene pair - Monohybrid – heterozygote for one gene o Monohybrid cross = Y/y x Y/y o Generally dominant phenol is written as Y/- Cell Cycles - Mitosis is the somatic cell division that takes place in all cells o Each chromosome have the same genetic content as parent - Meiosis involves two nuclear divisions: 2N1N; start with meiocytes o Replicate sister chromatids form a dyad; split by SC o Both dyads together called tetrad; entire thing is bivalent o Each cycle goes: G1SG2M Stage Characteristics Interphase - inclusion of the two gap phases as well as DNA synthesis in the S phase (no second Interphase in meiosis) Prophase - chromosomes condense and become distinct; also shorten Metaphase - homologs or sister chromatids line up at the equatorial plane of the cell Anaphase - homologs/sister chromatids are pulled apart to opposite end of the cell Telophase - nuclear membrane reforms, chromosomes uncoil - interkinesis is the interphase stage after telophase 1; no synthesis of new DNA  Fig 2-19 p 52  Chromosome replication at molec level - RFLP – DNA profilers that cut the DNA at specific enzyme sites Sites are distributed throughout the genes  Fig 2-20 p53  Explains RFLP better - Phenylketonuria (PKU) – Mendelian recessive disorder, can’t make phenylanine hydroxylase  Makes phenylalanine  tyrosinase  Instead phenylalanine  phenylpyruvic acid (bad for you) o Mutations at protein encoding regions of the gene: exons o Mutations of genes encode for defective PAH - Null alleles – completely lack the proper function to encode for their proteins - Leaky Mutations – reduce the level of enzyme/protein activity - Haplosufficient – one copy produces enough gene product to carry out norm func - Haploinsufficent – null/mutant allele will be dominant because in a heterozygote, WT allele cannot provide enough product for proper functioning Segregation Ratios - standard procedure in discovering a mutant is to cross it with a wild type - Dominant mutation first shows up in pop; will be in hetero state o Recall forward and reverse genetics - Forward: pheno of interestfind mutantscheck mutants for single gene inheritanceidentify gene actiondo genomic DNA analysis - Testcross – unknown heterozygosity with fully recessive parent o recessive parent is tester  tester alleles can be ignored because it can only give recessive o or if no tester; self the unknown species (3:1 progeny it was hetero) Sex-Linked Inheritance - Dioecious – plants showing animal sexual dimorphism - Sex-linkage – single gene inheritance pattern from the sex chromosomes o Pseudoautosomal regions 1+2 pair the sex chromos - X-Linked Inheritance – eye colour in Drosophila o All white eyed flies were male in red eyed cross o X chromo from hetero mother; dominant with father’s Y  Not just single inheritance o Sex chromos not necessarily totally related to sexual function Human Pedigree Analysis - propositus – diff phenotype person who comes to attention of geneticist o need lots of pedigrees to analyze inheritance patterns o few children so 3:1 and 1:1 ratios not always seen Autosomal Recessive - mutation inherited as a recessive allele; sufferers are phenotype p/p o appears in unaffected parents progeny o affected are male and female - simple Mendelian inheritance on autosome not sex chromo - relatively rare to have two heterozygotes (get recessive allele from 2 sepereate blood lines) o inbreeding increases the effect - cystic fibrosis Autosomal Dominant - defective allele is dominant, but rare in a pop o appears in every generation o affects sons and daughters with equal frequency o Huntington’s, polydactyl, piebald spotting, pseudoachrondoplasia Autosomal Polymorphisms - coexistence of two or more phenotypes; inherited as alleles of one autosomal gene o dimorphism – simplest; only 2 diff morphs o taste/smell the chemical in asparagus X-Linked Recessive - more males than females - none of affected males sons show phenol; daughters are carriers - normal female of unknown genotype is assumed homozygous o hemophilia, muscular dystrophy, testicular feminization syndrome  chromosomally males, develop as females X-Linked Dominant - affected males pass condition to all daughters, but none of sons - affected hetero females cross unaffected male pass condition to half their progeny o not common; vitamin D resistant Ricket’s - SRY gene (testis determining factor), has no real Y-linked disorders o Unless you call being male a disorder Fig 2-41 p76  Finger mitosis and meiosis Chapter #3 – Independent Assortment of Genes - Law of independent Assortment – alleles are on independent chromosomes and segregate independently at meiosis o Gametes have an equal chance of gaining either allele o Applies to genes on diff chromos  Genes on dif chromos separated by ;  Same chromo separated by /  Unknown position, separated by . - Dihybrid – double heterozygote such as A/a * B/b o dihybrid cross give a 9:3:3:1 ratio - 3:1 ratios hidden within the 9:3:3:1 ratios (p91)* o FIG 3-4 p93  dihybrid cross on diff chromos o Testcross produces 1:1:1:1 ratio - Product rule – probability of independent events occurring together - Sum Rule – probability of either of two mutually exclusive events o Sum of their individual probabilities - Product rule focus on A and B; sum rule is A or A’ o Page 97 How many progeny do we need to grow? - Chi square test – observed results are compared with those of a hypothesis to see if the null hypothesis should be rejected  (O-E) /E  add all the chi squares together Synthesizing Pure Lines - used to maintain stocks for research; interbreed and used as constant source - pure lines are made through repeated generation of selfing o star with heterozygote cross A/a A/a o ½ progeny will be A/a o after 8 generations (1/2)  1/256 or 0.4% heteros - Hybrid Vigor – general superiority of multiple heterozygotes o Parental lines must be grown separately and then intercrossed (costly) Chromosomal Basis of Independent Assortment - heteromorphic pair – partial homology; chromosome pair has non-identical members - in diploid organisms each possibility occurs four times  Fig 3-8 p104; Fig 3-9 p105 - Recombination – process of new allele combinations - Meiotic Recombination – meiotic process that generates a 1N product with combos of alleles different rom parental contributions o Compare meiosis inputs vs. outputs o Recombinant is any product that has new combos of alleles Detecting Recombinants Experimentally - done in haploid organisms; genos are observable as phenotypes (recombs have diff phenos) - in diploid; need the input/output gametes to detect recombination o input: pure breeding diploid parents o output: testcross diploid individual and observe its progeny  testcross allows us to concentrate on one meiosis - recombinant frequency – test for if two genes are on diff chromos o recomb frequency of 50% after testcross; genes assort independently Polygenic Inheritance - continuous variation – quantitative characters; height, mass, colour intensity o bell shape curve o environment rounds off the histogram bars creating smooth curve - polygenes/QTL’s – interacting genes underlying hereditary continuous variation o typically show independent assortment Non-Nuclear Inheritance - can be inheritance patterns not relating to the nucleus o chloroplasts and mitochondrial inheritance o rely on nuclear genes for its function, but have copies of their own chromo o each cell has many copies of its chromo o The DNA sometimes packaged into suborganeller structure
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