Presentation on theme: "Welcome to Part 2 of Bio 219 Lecturer – David Ray"— Presentation transcript:
1 Welcome to Part 2 of Bio 219 Lecturer – David Ray Contact info:Office hours – 1:00-2:00 pm MWThOffice location – LSB 5102Office phone – ext 31454–Lectures and other resources are available online atGo to ‘Courses’ link
2 Chapter 10: The Nature of the Gene and the Genome
3 Inheritance Observation: Offspring resemble their parents Question: How does this come about?Innumerable potential explanations can be proposed:Homunculi?Components of sperm and egg mix like paint?Are gametes and chromosomes involved?
4 The Gene A review of Gregor Mendel’s work Goal: to determine the pattern by which inheritable characteristics were transmitted to the offspringFour major conclusions
5 Mendelian Inheritance Named for Gregor MendelStudied discrete (+/-, white/black) traits in pea plants
6 Mendelian Inheritance A classic experimentWhat did it tell Mendel?What conclusions can be drawn?Pod color was inherited as a discrete trait, inheritance was not ‘blended’ for this traitOrganism characteristics may be carried as discrete ‘factors’ (now known as ‘genes’)
7 Mendelian Inheritance By continuing the experiment, more can be observedThe trait that was ‘lost’ in the first generation (F1) was regained by the second (F2), but in smaller numbersyellow + yellow = yellow and greenThe ‘factors’ come in different versions (alleles)‘Factors’ can mask one another – dominant/recessive – but they are not destroyedFurther support for the discrete gene hypothesis
8 Mendelian Inheritance By continuing the experiment, more can be observedThere was a definite mathematical pattern to the occurrence of the traits (3:1) in F2Comparison with mathematics suggests that each offspring inherits one allele from each parent (2 total)The phenotype (appearance) of the plants was determined by the genotype (actual combination of alleles)
9 Mendelian ‘Model’ of Inheritance The true-breeders had two copies of one type of allele (homozygous)Each parent passes on one of the alleles to the offspring randomlyThe first generation will all be heterozygous (have two different alleles)One of the alleles is able to block the other (is dominant vs. being recessive)The F1’s pass on both of their alleles randomlySimple math provides the expected ratios of phenotypes and genotypes
10 The Gene A review of Gregor Mendel’s work Goal: to determine the pattern by which inheritable characteristics were transmitted to the offspringFour major conclusions1. Characteristics were governed by distinct units of inheritance (genes)Each organism has 2 copies of gene that controls development for each trait, one from each parentThe two genes may be identical to one another or nonidentical (may have alternate forms or alleles)One of the two alleles can be dominant over the other and mask recessive alleles when they are together in same organism2. Gametes (reproductive cells) from each plant have only 1 copy of the gene for each trait; plants arise from union of male & female gametes3. Law of Segregation - an organism's alleles separate from one another during gamete formation and are carried in that organism’s gametes.
11 Mendelian Inheritance Mendel’s results held true for other plants (corn, beans)They can also be generalized to any sexually reproducing organism including humans
12 Mendelian Inheritance Simple Mendelian inheritanceAttached earlobesPTC (phenylthiocarbamide) tasting‘uncombable hair’Complex (multigenic) inheritanceEye colorHeightStudying inheritance in humans is difficult for ethical reasons but more easily done in other organisms10_05_gel.electrophor.jpg
13 Mendelian Inheritance Humans don’t typically have families large enough to see mendelian ratiosInheritance can be tracked through the use of pedigreesAre the traits in white and black dominant or recessive?
14 Mendelian Inheritance BBIf the trait indicated in black is dominant we would expect the cross between 2 and 3 to produce either ~50% black trait and ~50% white trait offspring or 100% black trait offspringThat ain’t the casebbBbBbBbBbBbBbBbbbBbbbbbbbBbBb
15 Mendelian Inheritance If the trait indicated in black is recessive we would expect the cross between 2 and 3 to produce all white trait offspringAlthough it is possible for individual 3 to have a Bb genotype, it is unlikelyWhat is the genotype of #2’s sister?bbBBBbBbBbBbBbBb
16 Mendelian Inheritance Using the information from the previous slides we can deduce most individual’s genotypesBbBBbbB?BbbbBbBbBbBbBbBb
17 Mendelian Inheritance The examples above are referred to as monohybrid crosses since they deal with only one trait at a timeMendel also followed dihybrid crosses in which two traits are followed at onceWould the traits segregate as a single unit or independently?
20 Mendelian Inheritance A dihybrid cross produced all possible phenotypes and genotypesThus, all of the alleles behaved independently of one anotherMendel’s Law of Independent Assortment – Each pair of alleles segregates independently from other pairs during gamete formation
21 The Gene A review of Gregor Mendel’s work Goal: to determine the pattern by which inheritable characteristics were transmitted to the offspringFour major conclusions1. Characteristics were governed by distinct units of inheritance (genes)Each organism has 2 copies of gene that controls development for each trait, one from each parentThe two genes may be identical to one another or nonidentical (may have alternate forms or alleles)One of the two alleles can be dominant over the other and mask recessive alleles when they are together in same organism2. Gametes (reproductive cells) from each plant have only 1 copy of the gene for each trait; plants arise from union of male & female gametes3. Law of Segregation - an organism's alleles separate from one another during gamete formation and are carried in that organism’s gametes.4. Law of Independent Assortment - segregation of allelic pair for one trait has no effect on segregation of alleles for another trait. (i.e. a particular gamete can get paternal gene for one trait & maternal gene for another)
22 Clicker QuestionLike most elves, everyone in Galadriel’s family has pointed ears (P), which is the dominant trait for ear shape in Lothlorien. Her family brags that they are a “purebred” line. She married an elf with round ears (p), which is a recessive trait. Of their 50 children (elves live a long time), three have round ears.What are the genotypes of Galadriel and her husband?♀ = Galadriel; ♂ = husbandA. ♀ PP; ♂PPB. ♀ pp; ♂ ppC. ♀ PP; ♂ PpD. ♀ Pp; ♂ pp
23 ChromosomesMendel made no effort to describe what carried the genes, how they were transmitted, or where they resided in an organism1880s – Chromosomes are discovered because :1. Improvements in microscopy led to…2. observing newly discernible cell structures..3. and the realization that all the genetic information needed to build & maintain a complex plant or animal had to fit within the boundaries of a single cellWalther Flemming observed:1. During cell division, nuclear material became organized into visible threads called chromosomes (colored bodies)2. Chromosomes appeared as doubled structures, split to single structures & doubled at next divisionWere chromosomes important for inheritance?
24 Chromosomes Are chromosomes important for inheritance? Hypothesis: If chromosomes are important for reproduction and inheritance, altering the number of chromosomes delivered to offspring should screw up the process.Theodore Boveri (German biologist) - studied sea urchin eggs fertilized by two sperm (polyspermy) instead of the normal one single sperm1. Disruptive cell divisions & early death of embryo2. Second sperm donates extra chromosome set, causing abnormal cell divisions3. Daughter cells receive variable numbers of chromosomesConclusion - normal development (reproduction/inheritance) depends upon a particular combination of chromosomes & that each chromosome possesses different qualities
25 Chromosomes Are chromosomes important for inheritance? Do chromosomes carry the genes?Whatever the genetic material is, it must behave in a manner consistent with Mendelian principlesHypothesis: If chromosomes carry the genes necessary for inheritance, they should mimic the theoretical behavior of genesTwo copies per organism, Discrete units, Segregate independently into gametes
26 Chromosomes Are chromosomes important for inheritance? Hypothesis: If chromosomes carry the genes necessary for inheritance, they should mimic the theoretical behavior of genesTwo copies per organism, Discrete units, Segregate independently into gametesExperimental observations:Egg & sperm nuclei had two chromosomes each before fusion; Somatic cells had 4 chromosomesWalter Sutton (1903) – Studied grasshopper sperm formation and observed:23 chromosomes (11 homologous chromosome pairs & extra accessory (sex chromosome))2 different kinds of cell division in spermatogoniamitosis (spermatogonia make more spermatogonia)meiosis (spermatogonia make cells that differentiate into sperm)
27 Chromosomes Are chromosomes important for inheritance? Haploid vs. DiploidHaploid – having a single complement of chromosomes in a cellDiploid – having a double set of chromosomes in a cellHumans gametes? Human somatic cells?23 chromosomes, 46 chromosomes
28 Chromosomes Are chromosomes important for inheritance? Hypothesis: There must be some mechanism to divide up the chromosomes in the formation of gametesExperimental observations:Meiotic division (only observed in the formation of gametes) includes a reduction division during which chromosome number was reduced by halfTwo different kinds of cell division in spermatogoniamitosis (spermatogonia make more spermatogonia)meiosis (spermatogonia make cells that differentiate into sperm)If no reduction division, union of two gametes would double chromosome number in cells of progenyDouble chromosome number with every succeeding generation
30 ChromosomesIn meiosis, members of each pair associate with one another then separate during the first divisionThis explained Mendel's proposals that :hereditary factors exist in pairs that remain together through organism's life until they separate with the production of gametesgametes only contain 1 allele of each genethe number of gametes containing 1 allele was equal to the number containing the other allele2 gametes that united at fertilization would produce an individual with 2 alleles for each trait (reconstitution of allelic pairs)Law of segregationA aAA aaAA aaA A a aAa
31 Chromosomes What about Mendel’s Law of Independent Assortment? Having traits all lined up on a chromosome suggests that they would assort together, not independently….as a linkage groupExperiments in Drosophila showed that most genes on a chromosome did assort independently… how?Is there some mechanism to allow neighboring genes to assort independenty?Humanchromosome 2
32 Chromosomes What about Mendel’s Law of Independent Assortment? Hypothesis: If neighboring genes on a chromosome can assort independently, there must be some observable mechanism to separate themHumanchromosome 2
33 Chromosomes What about Mendel’s Law of Independent Assortment? Hypothesis: If neighboring genes on a chromosome can assort independently, there must be some observable mechanism to separate themExperimental observations:1909 – homologous chromosomes wrap around each other during meiosisDuring this process there is breakage & exchange of pieces of chromosomesCrossing-over and recombination
36 Chromosomes Typically, several cross-over events will occur between well-separated genes on the same chromosome. Therefore,genes E and F or D and F are no more likely to be co-inheritedthan genes on different chromosomes.Genes that are very close together (A and B), on the other hand,are less likely to have cross-over events occur between them.Thus, they will often be co-inherited (linked) and do notstrictly follow the Law of Independent Assortment.
37 ChromosomesHypothesis: If the frequency of independent assortment is related to physical distance on the chromosome, we can predict how close two genes are by measuring frequency of recombination.Since the likelihood of alleles being inherited together is influenced by their proximity…Genetic maps were possible by determining the frequency of recombination between traits
38 Clicker QuestionThree genes (1, 2, and 3) are present on a chromosome. The recombination frequencies between them are:1-2 = 11%1-3 = 2%2-3 = 13%Which diagram best approximates the relative locations of the genes on the chromosome?A.123B.213C.123D.123
39 Chemical Nature of the Gene What is the genetic material?Observations:Chromosomes are likely the carriersChromosomes consist primarily of three componentsProtein, RNA and DNAAre any of these the genetic material?
40 Chemical Nature of the Gene Which one (DNA, RNA or protein) is the actual genetic material?Let’s narrow it down by hypothesis and experimentationEarly experiments had shown that pneumonia causing bacteria that are normally nonvirulent (R; rough) can be ‘transformed’ into the virulent (S; smooth) type by some ‘transforming factor’ – the likely genetic materialRoughSmooth
41 Chemical Nature of the Gene What was the ‘transforming’ or ‘genetic material’?Hershey and Chase (1952) – ‘blender experiment’Observations:Phage viruses consist of only two chemical components – DNA and proteinWhen a virus infects a cell, the cell makes many new virus particlesThus, genes must enter the cell and direct it to make new virus particlesWhich one enters the cell and actually becomes a part of the new viruses?
42 Chemical Nature of the Gene What was the ‘transforming’ or ‘genetic material’?Avery et al set up a multi-level hypothesisExtracted and separated DNA, RNA, and protein from smooth (S; virulent) bacteriaThree hypotheses:If protein is the genetic material, combining S-derived protein with R bacteria will transform the R bacterial into the S strainIf DNA is the genetic material, combining S-derived DNA with R bacteria will transform the R bacterial into the S strainIf RNA is the genetic material, combining S-derived RNA with R bacteria will transform the R bacterial into the S strainExperimental observation:Only DNA was able to transform the strains
43 Chemical Nature of the Gene Label the phosphates in DNA radioactively (32P) – no phosphate in the proteinLabel the sulfur in the protein (35S) – no sulfur in the DNAHypothesis: If the DNA enters the cell, we should find 32P in the infected cells but not 35S (and vice versa)Observation: 32P in the infected cellsAnimation online
44 Chemical Nature of the Gene Review of nucleic acid structure:PhosphateSugarRibose or deoxyriboseNitrogenous basePurinesAdenine and GuaninePyrimidinesCytosine andThymine/Uracil
45 Chemical Nature of the Gene Review of nucleic acid structure:Observation: Chargaff’s rules[A] = [T], [G] = [C][A] + [T] ≠ [G] + [C]Suggested base pairing to Watson and Crick, who later went on to describe the overall structure of DNA in vivo
46 Chemical Nature of the Gene Review of nucleic acid structure:Sugar-phosphate backboneNitrogenous base rungsDirectional – 5’ to 3’
47 Genome StructureGenome – the complete genetic complement of an organism; the unique content of genetic informationEarly experiments to determine the structure of the genome took advantage of the ability of DNA to be denaturedDenaturation – separation of the double helix by the addition of heat or chemicalsHow to monitor this separation?DNA absorbs light at ~260nmss DNA absorbs more light, dsDNA less light
48 Clicker QuestionWhich of the following 12 bp double helices will denature most quickly?A.5’-AATCTAGGTAC-3’3’-TTAGATCCATG-5’B.5’-GGTCTAGGTAC-3’3’-CCAGATCCATG-5’C.5’-AATTTAGATAT-3’3’-TTAAATCTATA-5’D.They are all DNA, they will alldenature at the same rate.
49 Genome StructureDNA renaturation (reannealing) – the reassociation of single strands into a stable double helixSeems unlikely give the size of some genomes but it does happen.What does renaturation analysis allow?Investigations into the complexity of the genomeNucleic acid hybridization – mixing DNA from different organismsMost modern biotechnology – PCR, northern blots, southern blots, DNA sequencing, DNA cloning, mutagenesis, genetic engineering
50 Genome StructureGenome complexity - the variety & number of DNA sequence copies in the genomeRenaturation kinetics – what determines renaturation rate?Ionic strength of the solutionTemperatureDNA concentrationIncubation lengthSize of the molecules
51 Genome Structure Complexity in bacterial and viral genomes MS-2 virus – 4000 bp genomeT4 virus – 180,000 bp genomeE. coli – 4,500,000 bp genomeA Cot curve uses theConcentration and timenecessary for a genometo renature to characterizea genomeSimple genomes havesimple Cot curvesWhy do the smaller genomesrenature more quickly?
52 Genome Structure Complexity in eukaryotic genomes Eukaryotic Cot curves are more complex because the genomes consist of different fractions
53 Genome Structure Complexity in eukaryotic genomes Highly repetitive DNA – Satellite DNAs - ~1-10% of eukaryotic genomesIdentical or nearly identical, tandemly arrayed sequencesMinisatellites – 10 – 100 bp repeats5’- ATCAAATCTGGATCAAATCTGGATCAAATCTGG-3’Microsatellites – 1 – 10 bp repeats5’-ATCATCATCATCATCATCATC-3’
54 Genome Structure Complexity in eukaryotic genomes Highly repetitive DNA – the importance of satellite DNACentromeric DNA – the sections of chromosomes essential for proper cell division are mostly microsatellite DNADNA fingerprinting utilizes polymorphic micro- and minisatellite DNA – CODIS loci
55 Genome Structure Complexity in eukaryotic genomes Repeat expansion and human pathogenicityCAG expansion in the huntingtin gene is associated with severity of Huntington’s diseaseCAG expansion produces long runs of glutamates in proteinsPolyglutamate chains tend to aggregate.Inverse relationship between CAG repeat size and severity of disease.Normal range = (CAG)6 – (CAG)39Disease range = (CAG)35 – (CAG)121
56 Genome Structure Complexity in eukaryotic genomes Moderately repetitive DNA – 10-80% of eukaryotic genomesCoding repeats – Ribosomal RNA genesrRNA is necessary in large amountsGenes are arrayed tandemlyNoncoding repeats – Interspersed aka mobile aka transposable elements~1/2 of your genomeMore on these later
57 Genome StabilityEukaryotic genomes are very dynamic over long and short periods of timeWhole genome duplication aka polyploidizationoffspring are produced that have twice the number of chromosomes in each cell as their diploid parentsMay occur in either of two ways:Two related species mate to form a hybrid organism that contains the combined chromosomes from both parents (occurs most often in plants)Single-celled embryo undergoes chromosome duplication but duplicates are not separated into separate cells, but are retained in single cell that develops into viable embryo (most often in animals)
58 Genome Stability Whole genome duplication aka polyploidization Polyploidization provides HUGE evolutionary potential"extra" genetic information can:- be lost by deletion- be rendered inactive by deleterious mutations- evolve into new genes that possess new functions
59 Genome StabilityGene duplication - duplication of a small portion of a single chromosomeMuch more common than whole genome duplicationThought to occur most often via unequal crossoverMisalignment of chromosomes during meiosisGenetic exchange causes one chromosome to acquire an extra DNA segment (duplication) & the other to lose a DNA segment (deletion)
60 Genome Stability Gene duplication – the globin cluster in primates Hemoglobin consists of 4 globin polypeptides(2 pairs: 1 pair always in ά-family, 1 in β-family)combinations differ with developmental stage (embryonic, fetal, adult)
61 Transposable Elements and the Genome Transposable elements are sequences that are interspersed throughout all eukaryotic genomes examined.They play a role in the structure, function, and evolution of the genome
62 Transposable Elements and the Genome Imagine a sequence that can copy itself and then insert that copy somewhere else in the genomeWhat would expect to find when you line some of them up?
66 Transposable Elements and the Human Genome Types of transposable elementsClass IRetrotransposonsLINEs, SINEs, SVA, LTR, ERVDefined as having an RNA intermediateClass IIDNA transposonsMariner, hAT, piggyBacDefined as having a DNA intermediate
69 Generating Genetic Variation: Normal SINE mobilizationReverse transcription and insertionPol III transcription1. Usually a single ‘master’ copy2. Pol III transcription to an RNA intermediate3. Target primed reverse transcription (TPRT) – enzymatic machinery provided by LINEs
72 Genome Analysis How many human genes? 80,000 Antequera F & Bird A, “Number of CpG islands and genes in human and mouse”, PNAS 90, (1993).120,000 Liang F et al., “Gene Index analysis of the human genomeestimates approximately 120,000 genes”, Nat. Gen., 25, (2000)35,000 Ewing B & Green P, “Analysis of expressed sequence tagsindicates 35,000 human genes”, Nat. Gen. 25, (2000)28,000-34,000 Roest Crollius, H. et al., “Estimate of human gene numberProvided by genome-wide analysis using Tetraodon nigroviridis DNASequence”, Nat. Gen. 25, (2000).41,000-45,000 Das M et al., “Assessment of the Total Number of HumanTranscription Units”, Genomics 77, (2001)
73 Genome AnalysisSequencing a eukaryotic genome has become relatively easyFiguring out what it all means is the hard partHuman genome - ~25-30,000 genes (latest estimate)Nematode worm - ~25,000 genesMustard plant - ~25,000 genesPuffer fish - ~25,000 genesWhat explains the differences in complexity and function among different genomes?Comparative genomics suggests:Alternative splicing (more later)Differential regulation (more later)
74 Genome AnalysisWhat explains the differences in complexity and function among different genomes?The protein-coding portion of the human genome represents a remarkably small percentage of total DNA (~ %)The great majority of the genome consists of DNA that resides between the genes & thus represents intergenic DNAEach of the 25-30,000 or more protein-coding genes consists largely of noncoding portions (intronic DNA)How do we figure out what is a gene and what isn’t?
75 Genome Analysis How do we determine what is important in a genome? Comparative genomicsConserved vs. nonconservedWhat are the “important” parts of a genome?Is most of the intergenic/intronic DNA subject to natural selection?Are the intergenic/intronic portions conserved or nonconservedProtein coding and genetic control sequences tend to be ____.……
76 Genome Analysis Comparative genomics The chimpanzee genome sequence was completed in 2005Much of what makes us human is likely to be determined through finding differences between our genome and that of the chimp
77 Genome Analysis Comparative genomics FOXP2 a regulatory gene common to many vertebrates2 amino acid differences are human specific (found only in humans, not chimps or any other studied organism)
78 Genome Analysis Comparative genomics FOXP2 a regulatory gene common to many vertebratesPersons with mutations in FOXP2 gene suffer from a severe speech & language disorderThey are unable to perform the fine muscular movements of lips & tongue that are required to engage in vocal communicationChanges in FOXP2 that distinguish it from the chimp version were fixed in human genome in the past 120, ,000 years; around the time modern humans may have emerged