Week I Notes: 1/11-1/15
Week I Notes: 1/11-1/15 CELL 2050
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Joseph Merritt Ramsey
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This 16 page Class Notes was uploaded by Joseph Merritt Ramsey on Tuesday January 19, 2016. The Class Notes belongs to CELL 2050 at Tulane University taught by Dr. Meenakshi Vijayaraghavan in Winter 2016. Since its upload, it has received 78 views. For similar materials see Genetics in Science at Tulane University.
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Date Created: 01/19/16
January 13, 2016 Chapter 2: Mendelian Genetics (Cont.) Overall Process o 1. Self-Fertilization His initial step involved insuring that his plants were indeed true breeding Self-fertilization for 9 Generations to achieve true breeding parents o 2. Hybridization Those parents were then crossed to produce the organisms in which he was truly interested The F1 Generations Observed that there were generally speaking two variables of the trait o 3. Self-Fertilization (of the Hybrids) He then self-fertilized the F1 Generation to get the F2 Removed the anther in this process Mendel’s Studies o Traits Studies 1. Flower Color – PURPLE, white 2. Flower Position – AXIAL, terminal 3. Seed Color – YELLOW, green 4. Seed Shape – ROUND, wrinkled 5. Pod Shape – INFLATED, condensed 6. Pod Color – GREEN, yellow 7. Height – TALL, short o Methodology Mendel’s method was not strictly scientific He simply performed experiments and analyzed his numbers He did not have a hypothesis His methodology is known as “Quantification” Involved a mathematical analysis of his findings to search for significance Used an empirical approach to deduce laws Law Number One: Law of Segregation o Diagram of Mendel’s Characteristic Cross Terms to Know: Parent Generation Cross Fertilization Single Factor Cross Monohybrid F1 (First Filial) Generation Self-Fertilization F2 (Second Filial) Generation o Summary and Observations Unit factors of inheritance will segregate during crossing These “unit factors” are now known as “Genes” The variants of these are called Alleles o Having the same alleles is known as Homozygous, different alleles is Heterozygous o This composition is now known as Genotype Mendel observed the Phenotype, the observable characteristics o Punnett Squares Mendel didn’t explicitly use Punnett Squares, but his predictions can be neatly displayed in Punnett Squares Punnett Squares have their limitations, though, due to practicality General Hybridization: o Possible Gametes = (#alleles) (#traits) 2 o Possible Offspring = (#gametes) Monohybrid Cross o Gametes = (2) = 2 o Offspring = (2) 2 Dihybrid Cross o Gametes = (2) = 4 o Offspring = (4) = 16 Trihybrid Cross 3 o Gametes = (2) = 8 o Offspring = (8) = 64 But for Monohybrid and Dihybrid Crosses they are useful Monohybrid – A a A AA Aa a Aa aa Dihybrid – AF Af aF af AF AAFF AAFf AaFF AaFf Af AAFf AAff AaFf Aaff aF AaFF AaFf aaFF aaFf af AaFf Aaff aaFf aaff o So how, using these techniques (considering Genotype, Phenotype, an Punnett Squares), can you determine genotypes from phenotypic observations? 1) Back Cross The given organism displaying the dominant trait is crossed back with another from the generation before (usually another dominant) This is practiced most in agricultural circles to produce mass amounts of a given trait Here the genotype is irrelevant and only the phenotype is desired 2) Test Cross This is the true test to determine the Genotype of an organism by only viewing its Phenotype The F Generation Monohybrid with a Dominant Phenotype (Often assumed to be Heterozygous) is crossed with the P Generation Recessive Depending on the Genotype of the Dominant Phenotype, we’ll see a certain number of recessive offspring from the cross Law Number Two: Law of Independent Assortment o Diagram of the Experiment - Standard Test to Display Independent Assortment Terms to Know Two Factor Cross Dihybrids Process Initial Hypothetical Actual o Genes segregate independently of one another during separation Independent Assortment deals with Genes and Multiple (Two Factor or More) Segregation deals with alleles, Assortment deals with Genes Genes Assort independently and the segregation process does not link their alleles In essence, Dominants alleles don’t have to stick together in different genes Refers to the Segregation of alleles, but with Multiple genes o Occurs in Anaphase I of Meiosis (four in a line, homologues split) They are independent of each other on different loci in the chromosomes The chromosomes are in lines of four, with homologues and duplicates (sisters) being present Modern Genetics o The question now is “What is the relation with molecular mechanisms?” How do external and even internal observations relate to genetic mechanisms? A lot of this methodology involves detecting defects and tracing them back to discover the genetic origin This method, though, only goes so far, considering not all defects can be easily phenotypically detected This has found, however, that small genetic mutations in defective alleles are a source of overall deficiencies o Dominant and Recessive Genes Overall Most genes have two variants Defects in the alleles cause the rise of diseases Relation to Diseases Recessive Genetic Disease – two of the allele must be present Dominant Genetic Disease – only one of the allele needs to be present o These types of genetic disease are almost always fatal prenatally o Known as “de novo” mutations o They randomly occur during gamete formation o Pedigrees Examples to Consider 1. Two Carrier Parents (25% Infected) – H h H HH Hh h Hh hh 2. Two Infected Parents (100% Infected) – h h h hh hh h hh hh Two Odd Pedigree Symbols 1. Fraternal (Dizygotic) vs. Identical (Monozygotic) Twins 2. Consanguineous (Cousins) Probability o Eugenics vs. Euthenics Eugenics – the aim of improving the genetic quality of humanity Counseling aimed towards preparing and informing women on genetic possibilities and dangers Important with aged mothers as well A maintenance of strong genes in the human population Euthenics This is the improvement of functioning and well being through the improvement of living conditions and external factors These factors increase the reproductive rate by increasing survival January 15, 2016 Chapter 2: Mendelian Genetics (Cont.) Probability o Eugenics vs. Euthenics o Some Broad Notes 1. Simple Probability Measuring times something occurs against the times it could have occurred ???????????????????? ???????????????????? ???????????????????? ???????????????????? ???????????????????????? ???????????????????????????? ???????????????????????????????????????? ???????????????????? ???????????????????????????????? ???????????????????????? = ???????????????????????????????? ????ℎ???????????????????????????????? 2. Accuracy Very dependent on sample size Error should be small o Error is between observed and expected o Ensures error is by chance, not an external affecter o Random Sampling Error is Minimized by Large Sample 3. Sum Rule You can add mutually exclusive probabilities Looked at as an “Either/Or” event o They are mutually exclusive Mutually Exclusive or Independent Mutually Exclusive Independent *Event = Brown and *Event with 2 People, Blue Eyes Eye Color *These types of events *The outcomes are can be summated unrelated to each other *These types of events are multiplied in some fashion 4. Product Rule Independent Set of Events in a Given Order o What is the probability of the First and Second being… The event is in a given order 5. Binomial Expansion Independent Event in No Order Say five events are happening, one can search for the possibility of the event simply occurring three times 6. Chi-Squared Test Tests “goodness of fit,” or how much variance is due to random sampling o Sum Rule Ex: Considering two traits, Tail Length and Ear Type Each event is Mutually exclusive – you cannot have a normal and abnormal tail/ear So, because each is Mutually Exclusive, you can summate their probabilities What is the probability of having a Normal Eared, Normal Tailed Organism? o Find the total possibilities (16) o Find the specific possibilities (9) o Product Rule You want a specific order of events with independent events Can consider two individuals now Ex: Cystic Fibrosis Chances of one child = ¼ Chances of not one child = ¾ Chances of children 1,3 out of 3: ¼ x ¾ x ¼ o Binomial Expansion Not a specific order, but still independent Ex: 2 1 ???? = ????! ???? ????????−???? ⇒???????????????????????????? ???????????????? = 3! ( ) ( ) ????! ???? − ???? ! 2! 3 − 2 ! 4 4 n Total number of 3 Kids occurrences x Desired Event 2 Kids Recessive p Probability of individual ¼ event q Probability of “not p” for ¾ individual event o Chi-Squared Displays variance of expected versus observed and determines how random the results are An assumption must be made to count as the hypothesis 1 Trait, Segregation (3:1, Two Phenotypes) 2 Traits, Assortment (9:3:3:1, Four Phenotypes) Ex: Assessing Chi-Squared for wing shape and body color 1. Propose Hypothesis (as above, to eventually determine expectations) 2. Analyze the Observed Values 3. Use expected values based on hypothesis 4. Use formula (smaller value is better) 5. Compare to Degrees of Freedom Null Hypothesis: occurs merely because of chance o Degrees of Freedom Always equals (n-1) Chapter 4: Extensions of Mendelian Genetics Limitations of Mendel’s Work o Only looks at purely dominant and recessive from a narrow point of view Dominant: present, wild type – the right cell, right protein, right time But what if the wild type (beneficial type) is recessive? Recessive: generally mutant variety, a loss of function So what if this occurs as the dominant fashion? Balding is an example o Mendel Looked at only 7 Pea Traits Pea Color, Pea Shape, Pod Color, Pod Shape, Flower Position, Height, Flower Color But his finding and explorations didn’t go beyond that o So Consider Genetic Disorders and Diseases They are generally recessive, but as considered above, they can be dangerous as dominant So how do these developments occur? Modern Genetics Begins to Ask Why? o Why would the Dominant Gene be Enough? 1. 50% of the protein being transcribed is enough to have the effect 2. Cellular recognition mechanisms to upregulate a particular gene o So how do other mutations manifest themselves other than the simple above potential mechanisms? 1. Gain of Function A mutation gives a gene a new function and ability o But this ability ends up being bad for the cell and is then upregulated because of the new ability o So a loss of function does not occur – the normal allele is still fine o It is merely being down regulated for the novelty allele Ex: p53 o P53 is a tumor suppressant o It generally functions in a dominant, wild type manner o But when a mutation giving a new ability occurs, it becomes upregulated This upregulation (so dominant form now) of the new ability is actually harmful because the new ability is to proliferate cancer cell metastasis 2. Dominant Negative Antagonistic Mechanisms occur o The mutation occurs that inhibits the ability of the other (proper) gene to function properly No loss of function occurs – the gene is still perfectly fine, it’s simply “drowned out” by the mutated allele o Ex: ras Gene Works with GDP to activate a kinase (conversion to GTP) The mutated allele ends up creating a protein that binds to ras and stops it from working It can no longer move Can no longer switch to GTP to activate 3. Haploinsufficiency Generally genes are transcribed and proteins created by a combination of each allele on the chromosomes o So both contribute to the functioning Ex: Consider a deletion January 11, 2016 Chapter 1: Overview of Genetics Human Genome Project o A General Overview of Facts National Institute of Health and the Department of Education implemented the Human Genome Project from 1990 to 2003 Haploid set has 3 Billion Base Pairs, so a Haploid Human Cell has 6 Billion Base Pairs The Molecule is 2 Meters Long Codes for about 20,000 – 25,000 Genes o New Technologies that Enhances the Project and Have Developed 1. DNA Fingerprinting – criminal investigations, parental information, genetic defects 2. Cloning – advanced organisms Dolly the Sheep Cop Cat 3. Genetic Engineering – various applications Gene injection for therapy Insulin production through animals GFP to mice (shows up on skin) o Technique used to identify, sterilize, and eradicate mosquitoes and stop pesticide use Genes and Traits o Gene Basic Definition – basic unit of biological information; a functional unit of heredity More Applicable Definition – segment of DNA that encodes for a functional peptide Structural Gene – segment that encodes for a protein As opposed to RNA encoding genes o Cell Overview Definition – basic unit of life (membrane enclosed) Macromolecules: Genes code for Macromolecule Production in Cells 1. Proteins 2. Lipids 3. Carbohydrates 4. Nucleic Acid o DNA’s Properties and Considerations Central Dogma: DNA RNA Proteins Proteins and Traits Proteins – work horses of the cell; tools of gene expression Traits – characteristics an organism expresses; often looking at the phenotypic expression Building Blocks Nucleotide monomers for a strand Two strands are held together by Hydrogen bonding Additional Pieces Histones attach in order to make Chromosomes The Chromosomes for the Genome Accessing DNA DNA can only be accessed during gene expression o The process during which information present in genes is used to change characteristics in an organism Transcription – a copy is made into mRNA to be later read and translated Translation – amino acid sequence is encoded in the cytosol o Traits Type of Traits: 1. Morphological Traits – a displayed phenotype o Physical appearance o Ex: color of a flower 2. Physiological Traits – the capacity of an organism to function, mechanisms reliant on genes o Process depends on genes and propagates life o Ex: Cellular Respiration 3. Behavioral Traits – a behavioral response contingent on a genetic pathway o Response to a given environment o Ex: mating calls How Does Molecular Composition Affect Traits? – The Butterfly Example Color in the wing is contingent on the translation of pigmentation Gene Classes with Traits: o Normal Gene – makes the right gene in the right amount in the right cell o Abnormal Gene – a mutation causes the balance to be thrown off The Butterfly that has properly functioning genes creates a large amount of pigmentation o It is seen as very dark because of high pigment concentration This observation can be expanded to the population level – how much of the gene is present? o This then becomes an ethological question o How does evolution and environment change gene translation? o Thought Process of a Geneticist – It Moves Backwards The butterfly example also of shows a sort of backwards movement of the thought process Look at the Organism, look at the Cellular factors, the go back to the Population It starts with observation of the organism and goes backwards to figure out what’s happening A “Symptom to Cause” methodology Interplay of Genes with Evolution o Evolution Definition – accumulation of changes over time Neutral and Beneficial mutations accumulate o Horse Example Displays Vertical Evolution, the only type when tracing small mutations actually matters The development of a small, goat-like animal to the strong horse we know today Specific differences are selected for that change the appearance o What Are Morphs? Morphs are members of the same species that look dramatically different, representative of evolutionary changes What makes a Species? o 1. Similar Genetic Makeup o 2. Capability to Interbreed But Morphs are dramatically different Panther Example Panthera onca is the Panther and the Jaguar And their differences are representative of their environments o Chromosome Changes: another method of genetic change and evolution that can only remain present through natural selection 1. Chromosome Aberration – any sort of change in the Chromosome Breaks Duplications Inversions Transmutation 2. Genomic Mutation – change in the Chromosome number Diploidy – a duplicate chromosome Polyploidy – a ubiquitous change in all the cells o The Most Important Part? Genetic Fields and Studies o Fields: 1. Molecular – change of genome leads to changes in the proteome 2. Cellular – the nature and composition of the cell’s proteins identify that cell 3. Organismal – the cellular composition is reflected in the observed traits 4. Population – what are the composition of those trait variants in the population? o Studies: 1. Transmission – process by inheriting traits Quantitative Mendelian analysis of gene expression 2. Molecular Biochemical composition of genes and their expression DNA/RNA composition Functional Aspects and the Central Dogma 3. Population Allele distributions in a population Ethological considerations of environmental effects Chapter 2: Mendelian Genetics Who Was Mendel? Why the Pea Plant? o Overall Reasons Easy to observe Short harvest time (30-40 Days) Small space required to grow Large flower is easy to manipulate and handle o Anther/Reproduction Manipulation o Isolate Traits
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