Popular in Genetics
Joseph Merritt Ramsey
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This 65 page Study Guide was uploaded by Joseph Merritt Ramsey on Tuesday February 9, 2016. The Study Guide belongs to CELL 2050 at Tulane University taught by Dr. Meenakshi Vijayaraghavan in Winter 2016. Since its upload, it has received 181 views. For similar materials see Genetics in Science at Tulane University.
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Date Created: 02/09/16
Extra Readings Study Guide – Test I “No Sex Required” o Albert-Ludwigs University in Freburg, Germany Ralf Reski and Nir Ohad o Summary: Scientist recently discovered a gene trigger in moss Physcomitrella that leads to offspring without fertilization The mechanism is assumed to be conserved in evolution o The gene BELL1 had been identified as a potential regulator for the ormation and development of Embryos in Physcomitrella They were able to induce embryo development by activating the gene o The protein belongs to the Homeobox Trascription Factors category These are known to control development o Applications? The question at hand now is if this gene (or ones like it) are integral to embryo development in all species Could also lead to producing genetically identical crops “Seeing X-Chromosomes in a New Light” o The origin of the phrase “X-Chromosome” came from Hermann Henking, who discovered the anomalous homologues o Contains over 1,000 genes o Susumu Ohno first found the Barr Body o Understanding X-Chromosome Inactivation may pave the way for better stem cell understanding o The Experiment Scientists made it so that one parental X would be green, while the other would be Red This is connected to the idea of Mosaicism, the idea that cells can vary greatly What they found was that this is true, but that entre organs or even halves of organs (like the brain) can be predominantly comprised of either red or green This means that tissues within a given organism could act differently depending on which X dominates o They still don’t know how the cell chooses which to inactivate, but we do know (roughly) what happens after Xist is highly involved Xist molecules swarm and coat the Chromosome o What are some theories as to why? 1. Males could simply upregulate their own X, but that could lead to females potentially overdosing themselves with X- Genes 2. An evolutionary advantage arises because females can “choose” not to express a defective X-Chromosome, if they have one 3. They also found that an inactived Xist protein leads to cancer (presumably because the cell overproduces now) This often occurs in stem cell research 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 polypeptide 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 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) o Possible Offspring = (#gametes) 2 Monohybrid Cross o Gametes = (2) = 2 o Offspring = (2) 2 Dihybrid Cross 2 o Gametes = (2) = 4 o Offspring = (4) = 16 Trihybrid Cross o Gametes = (2) = 8 2 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 wellbeing 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: ????! ???????????????????????????????? ???????????????????????? 3! 1 2 3 1 ???? = ???? ????????−???? ⇒ ???? = ( ) ( ) ????! ???? − ???? ! 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 Ex: ras Gene o Works with GDP to activate a kinase (conversion to GTP) o 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 20, 2016 Chapter 4: Extensions of Mendelian Genetics Limitations of Mendel’s Work Modern Genetics Begins to Ask Why? o So how do other mutations manifest themselves other than the simple above potential mechanisms? 1. Gain of Function 2. Dominant Negative 3. Haploinsufficiency Generally genes are transcribed and proteins created by a combination of each allele on the chromosomes Ex: Consider a deletion In essence, one is not enough (the Haplo is not enough to express) Thinks of it this way: o A gene will be expressed with 50 Units of protein X created o You have two alleles that are both wild type, one is just highly expressive (varies per person) o In the highly expressive, each allele codes for 50 units, so it is Haplo sufficient o But in the low expressive, each is only 30 – haploinsufficient Diagram Looking at Dominance o 1. Simple Dominance (3:1) Straightforward Mendelian Expectations with the 3:1 Raito o 2. Incomplete Dominance (1:2:1) One copy of the dominant allele is not enough to express the gene Ex: 4 O’clock Flower A mix occurs Punnett Square View (Diagram) Ex: A Molecular Look at the Pea Shape Take a look at protein composition and it becomes clear that the Homozygous Dominant varies from the Heterozygous Looking at the EET1 Gene Expression But must be done molecularly speaking Ex: PKU (Phenylketonuria) Molecular Perspective Same idea here PKU patients lack the functioning protein “Phenylalanine Hydroxilase” o This breaks down Phenylalanine o Without it, Phenylalanine releases damaging ketones So blood samples can be taken and checked for Phenylalanine composition, reflective of its proper breakdown o Healthy (Homozygous) – 1mg/dL o Carrier (Heterozygous) – 2-3mg/dL o Infected (Homozygous Recessive) – 6-8mg/dL o 3. Incomplete Penetrance (Varies by Generation) Normally, the genotype penetrates the phenotype in order to express the present gene The dominant trait is said to have the ability to “penetrate” the phenotype But when the dominant trait is present but somehow unexpressed, it is known as incomplete penetrance Important to note the different between Penetrance and Expressivity Penetrance – viewed in the population, the capacity to be expressed in Heterozygous individuals o Only consider Heterozygotes because the other two are easy to identify and explain already o So within a population, the gene has 66% penetrance Expressivity – deals with an individual, how is the gene expressed? In the example below, the consistent lack of expression of the dominant allele is penetrance while one person having 12 and another having 11 is expressivity Ex: Polydactism Being a heterozygote with the Dominant Polydactyl This allows for the trait to skip generations with relative ease Possible Explanations? 1. Environmental – environmental factors influence the gene expression o I. Light Snapdragon present different colors depending on what temperature it is in which they grow o II. Temperature Drosophilia facets are more present when growing in cold weather and less so in warm weather. o III. Diet PKU patients cannot have Phenylalanine in their diet, but strict regulations allow them to live perfectly fine. Can they be reversed? A question may be, however, if they don’t catch it early can it be reversed? PKU doesn’t present such a prospect, but the conditioned allele on Shibiar alleles can be Flies grown at given temperatures can have the effects reversed 2. Modifier Genes 3. Combination of the First Two o 4. Overdominance (1:2:1, But Heterozygotes are Selected for) Overdominance deals with Heterozygous individuals – only looking at the carriers and only looking at one gene These Carriers have an advantage Ex: Sickle Cell Hemoglobin overview o Made up of four subunits, Two Alpha, Two Beta o A small point mutation occurs on the Alpha GAG goes to GTG on the DNA Goes from Glycine (charged) AA to Valine (Neutral) AA o Pressure then results in cytoskeletal transformation due to the neutral Valine connection 1. Stiffness occurs because the cytoskeleton is inefficient, leads to clotting 2. They morphed form leads to inefficient Oxygen transport Cells of Sickle Cell Lifespan o Each cell normally lives 90-120, but sickle cell cells only survive 10-20 o So the body can’t keep up But Carriers have an advantage: o Hb and Hb are the alleles o Their cells are mostly fine and properly functioning, but a few of them present some sickle traits o When their cells are attacked by Malaria plasmodium, propagation cannot occur 1. They burst because of the shape 2. They have a particular antigen from the trait expression o But non-malarial environments don’t have high heterozygote populations Ex: Tay-Sachs A mutation occurs in a lipid storage and synthesis protein Allow them to fight TB Ex: PKU Females In certain areas, the likelihood to ingest the Ochratoxin A is much higher o Normally even a small ingestion is enough to cause a likely miscarriage but is not fatal to the mother But PKU females do not experience such miscarriages Why does Overdominance Occur? 1) Cellular Morphology o Antigen is present because of the slight expression (Sickle Cell example) 2) Dimerization of the Protein o Dimerization occurs to form the final protein (Quartneary structure) 2 units come together o With another type of allele, three possible dimerization possibilities arise With two of the same allele, only one permutation exists Results in the creation of different Monodimers and Heterodimers o New capacities are created 3) Protein Reactivity o Say one allele reacts at a given temp (low) and another at a different temp (high) With both present, the organism can respond to low and high temperatures o So a range of enzyme activity is created That range creates a survival advantage o 5. Heterosis This example begins to look at multiple genes Multiple genes are introduced – so the genetic benefits are not from an allelic mixture of a given gene, they are from a conglomeration of genetic effects from multiple genes Ex: Crops Genes are introduced to optimize crop life The phrase here is “Hybrid Vigor” Merely referring to the mix of alleles Considering Multiple Alleles o Overview Several mutations exist for a given gene, each showing a slightly different and altered phenotype Morphologies: 1. Monomorphic – one wild type exists 2. Polymorphic – multiple wild types exist 3. Multiple Alleles o Polymorphism (Only deals with One Gene) Hair and Eye Color may be a common consideration, but consider how those manifest themselves: They are a mix of genetic influences, influenced by Polyploidy genes A true example is blood type: They are all the same gene and are not phenotypically affected by other genes But there are three different forms of the gene And if not force chooses for a particular phenotype, it is Polymorphic But if the wild type is chosen, it is Monomorphic January 22, 2016 Chapter 4: Extensions of Mendelian Genetics Continued Limitations of Mendel’s Work Modern Genetics Begins to Ask Why? o So how do other mutations manifest themselves other than the simple above potential mechanisms? 1. Gain of Function 2. Dominant Negative 3. Haploinsufficiency Looking Dominance o 1. Simple Dominance (3:1) o 2. Incomplete Dominance (1:2:1) o 3. Incomplete Penetrance (Varies by Generation) o 4. Overdominance (1:2:1, But Heterozygotes are Selected for) o 5. Heterosis Considering Multiple Alleles o Overview o Polymorphism (Only deals with One Gene) Hair and Eye Color may… A true example is blood type o Monomorphism The mutation distribution is not equal Other alleles can exist, but one wild type predominates, so the phenotype is monomorphic The mouse coat color is a good example: o Agouti is dominant (A) o But the Black/Yellow Body is possible (a ) t o And Black is also possible (a) So in essence, polymorphic alleles can be monomorphically expressed Mouse Fur Example This deals with pigmentation o Tyrosinase is responsible for pigmentation Different Melanins can be acted upon EuMelanin is a Dark Brown/Black color PheoMelanin is a Yellow Color o The gene for properly functioning Tyrosinase is C So CC is complete Tyrosinase, which Gives a lot of Eumelanin Cc is a mix of Eumelanin and Pheomelanin, which gives a grayish Agouti color Then other recessive alleles exist o But there are Recesive alleles as well, mutations that occurred on the tyrosine gene cCh – Chinchilla c – Himalayan c – Albino o So Phenotypic expressions Can include: ch ch c c – Chinchilla c c – Incomplete Dominance c /c c – Paler Version of the other o As a side note, these have interesting Thermolable properties, specifically with the Himalayan variety Body temperature influences gene expression The cold causes and increased expression when the Himalayan allele is present (c )h This causes a darkening of the extremities o Examples of Multiple Alleles Mouse Fur Color (True Monomorphism) Mentioned above, the distribution is not equal Rabbit Fur Color (Like Monomorphism, but still all present) Detailed above Lintels (Like Monomorphism, but still all present) Some predominate more than others, but all alleles are still present Marbled 1 > Marbled II > Spotted, Dotted (They are equivalent) > Clear Dominant Form 1 Dominant Form II Strong Recessive Completely Recessive Blood Types (True Polymorphism) Different types of blood exist that are all equally as present Conditional Alleles o Definition: particular environmental conditions cause the gene expression These alleles were mentioned in regards to the PKU discussion in Incomplete Penetrance But unlike with penetrance (reversal is much more difficult and/or impossible), purely environmental factors can often be reversed o Examples Rabbits Himalayan gene in rabbits Tyrosine activation in the recessive Himalayan gene are influenced by temperature (upregulated in the cold) Siamese Cats Same Tyrosine effects in the cold Cattle Cold now down regulated Tyrosine action for Cattle color Drosophilia Shibire genes (regulating cytoskeletal development) occurs normally at 21 or lower Codominance o Definition Multiple alleles present themselves as wild type dominate equal in phenotypic expression o Blood Types is a great View The Blood Gene codes for Particular Antigens (used for self- recognition) i = isoglutanogen (mutant form lacks enzyme binding spot on the blood cell) A = UDP (Uridine DiPhosphate) N-Acetyl Galactosamine (NAG) binding site B = UDP Galactose (G) Binding Site Glycosyltransferase (Transfers sugars) moves the sugar to the blood cell binding site When exposed to the given blood types with sugar markers, antibodies are generated because the host cell has no binding site for the foreign sugar (eg., O blood cell has no sites for A or B sugars) Blood Genotype Options: A – I I or I i B – I I or I i A B AB – I I O – ii Rhesus factor is the Rh factors for plasmid antigens And M/N blood types are for blood protein antigens H-Factor (Bombay Blood Disorder) The HFactor generates the H-Antigen, which is the precursor to A and B antigens So a mutation in the H-Factor gene is detrimental to blood type because no A or B antigens exist So no matter what, the blood type is O (no antigens) o Cattle Color Spots become present when Red/Brown is crossed with White Sex Linked Genes o Linked – they are present on a Sex Chromosomes Y: Holandric Genes (only about 83 present) X: About 500 present This phrase is generally used considering inheritance o Hemizygous This term refers to the Y Chromosome One type of allele is present (the idea behind homozygous) but only one chromosome will carry that given allele (whether on X or Y) So the phrase is Hemizygous – there’s only one “slot” to fill o Ex: Duchenne Dystrophy Dystropin is a cytoskeletal protein that attached the cytoskeleton to the plasma membrane o So dysfunctional dystropin leads to inefficient muscle cell development o So the person has not development The disease affects men much more, demonstrated by the reciprocal cross (shows and X-Linked Inheritance) X D XD X d X d Xd X X d X X d X D X X d X X d Y X Y X Y Y X Y X Y Teeth Color The enamel and coloration gene is located on the X Chromosome Sex Related Traits o Important Differences Sex Influenced Refers to hormonal influences on gene expression This is usually with Autosomal genes When it is Allosomal, it’s generally known as Pseudoautosomal (because it displays autosomal tendencies on a sex gene, so it must be present on both) o MIC (Development) is present on both Sex Chromosomes Sex Limited Refers to genes only present on a given Sex Chromosome SRY is only present on the Y Chromosome to induce male development o Types: 1. Sex Influenced – Pattern Baldness Mutation on Chromosome 3 Looking at Heterozygotes (that’s where the influence is noted) Genotype Female Male Phenotype Phenotype BB Bald Bald Bb Normal Bald bb Normal Normal Why does this happen? o 5α Reductase is present in all people o It works on Testosterone to produce Dihydroxytestosterone This acts on the hair follicles o A case study looking at an adrenal gland tumor in a woman displayed an upregulation of Testosterone in her system, resulting in all parts increasing 2. Sex Limited – Breast Development Limited is an Either/Or sort of thing This only occurs in Females 3. Sexual Dimorphism – Hen/Rooster Color This is an offshoot of limited genes that specifically separates phenotypes into male or female Roosters are most colorful and elaborate Ovary hormones repress color expression Lethal Alleles (1:2) o Definition – very important alleles, critical to proper functioning and survival o Genotypic Expressions With a Homozygous Lethal allele, the organism dies, so the ratio becomes 1:2 o Examples Manx Cat They lack a tail, which has to do with a skeletal spine formation gene But if they have the Homozygous Dominant Genotype (because having it all produces defects it is dominant), it dies before birth o The two mutant alleles messes up spinal development too much Mice Coat Yellow or Non Yellow coat Scenarios: o Homozygous Recessive – normal o Heterozygous – pleiopatry causes negative growth effects o Homozygous Dominant – death January 25, 2016 Chapter 4: Extensions of Mendelian Genetics Continued Limitations of Mendel’s Work Modern Genetics Begins to Ask Why? o So how do other mutations manifest themselves other than the simple above potential mechanisms? 1. Gain of Function 2. Dominant Negative 3. Haploinsufficiency Looking Dominance o 1. Simple Dominance (3:1) o 2. Incomplete Dominance (1:2:1) o 3. Incomplete Penetrance (Varies by Generation) o 4. Overdominance (1:2:1, But Heterozygotes are Selected for) o 5. Heterosis Considering Multiple Alleles Conditional Alleles Codominance Sex Linked Genes Sex Related Traits Lethal Alleles (1:2) o Definition o Genotypic Expressions o Examples Manx Cat Mice Coat o Differentiating Between Codominant, Incomplete Penetrance, and SemiLethal Looking at Heterozygous Individuals Codominant? It’s tempting to say the allele is Codominant because an in between form is expressed But the allele cannot be “partially lethal,” and it occurs before birth So it’s considered a recessive wild-type allele behaving in a recessive manner, even though it’s a dominant allele Incomplete Penetrance? Incomplete penetrance deals with a gene that is actually expressed o Lethal alleles result in the 2:1 ratio because they occur before birth Huntington’s is a good example o Not semilethal, which are often sex specific and affect given ratios o And not lethal either, since they act after birth o Variants on Lethal (or more accurately, Genes that appear Lethal) 1. Semilethal Alleles Kill about half the population in a lethal, before birth manner (hence the applicability of the ‘lethal’ nomenclature) The dominant/recessive “lethal” allele is present in Homozygous manner (Genotypically Speaking), but only half the organisms die Ex) Drosophilia Eyes o The recessive eye color for drosophila is white o But if 100 males are predicted to have the recessive genotype for white eyes, only 50 will even be born Side note: presence only in males suggests hemizygous effects 2. Incomplete Penetrance Different than Lethal or Semi-Lethal, the gene just happens to result in death o So this isn’t even considered lethal because it occurs after birth Ex) Huntington’s Disease o Tripeptide Repeats The Tripeptide ‘CAD’ repeats, but depending on the number functionality can differ Below 26 – Normal 27-30 – Slight Changes (Intermediate) 31-35 – Moderate Changes (Incomplete) 36-39 – Notable Changes (Incomplete) Above 40 – Drastic Changes (Disease) Males vs. Females Female Oogenesis is a much more concentrated, fail prove process that results in minimal coding errors Spermogenesis has more errors, resulting in more repeats of the CAD sequence o Creates various Possible Combinations in Parents Normal + Normal = Small Chance of Disease Incomplete + Incomplete = Decent Chance for Late Onset Incomplete + High = Strong Chance for Early Onset o Looking at those trends, CAD repeats only determines and influence penetrance but not lethality o Anticipation is a notable side effect Each generation shows early and early onset of the disease (trinucleotide repeats) They are incompletely dominant, not purely so Effects on Phenotype o 1) Pleiopatry Definition – one gene influences many phenotypic traits 1) The gene can make a given protein a different stages of cell life 2) The gene protein can affect numerous cell types Example Population: Maori Tribe in New Zealand (Chromosome 7) Respiratory Issues and Sterile What is the common thread? Similar Microtubule Proteins o Sperm Flagella o Respiratory Cilia Additional Example: Mice Coats Tumor Susceptibility, Diabetes Development, and Coat Color are all affected by the same gene o 2) Gene Interactions Definition – two or more different genes influence a given trait Two Types Discrete Multiple Gene (Discrete meaning discontinuous) o There is an Either/Or effect present o No gradient occurs o Ex: Purple and White flowers only Quantitative Multiple Genes (Quantitative Meaning Continuous) o A range occurs, variation Results from polygenic nature (several contributing genes) o Most traits fall into this category o Ex: Height, Skin Color o 3) Gene Dosage Effect Definition – inheritance of single gene depends on particular allele of the gene So having more alleles present could contribute Example: Drosophilia Eye Color Females have a Dark Eoisin (Homozygous Recessive) Males have a light Eosin (Hemizygous) Important Interactions: o 1. Two Gene Interactions (9:3:3:1) How is it Different Than Mendel’s Studies? Presence of Parental Alleles o Mendel’s parent pea generations phenotypes always showed up in the filial generations o They could have various combinations, but nothing in and of itself was novelty Formation of New Dominant Alleles o Here, however, completely new phenotypes are produced Examples Ex) Hen Combs o Roosters have different types of Combs Rose Pea Walnut Single o Have various Genotypes (R) Rose is Dominant to (r) (P) Pea is Dominant to (p) R and P are Codominant to form the Walnut All recessive produces the Single Comb o Punnet Square (Rose (RRpp) and Pea (rrPP) are the Original Parents) Walnut (RrPp) Walnut (RrPp) Ex) Fur Color o The same thing occurs: AAbb = Tan aaBB = Gray A_B_ = Brown aabb = White o 2. Epistasis (9:7) Definition – one gene masks another The genes affect one another (recessive epistasis) Two White Flowers are Bred CCpp (White) X ccPP (White) It becomes clear that they are somehow epigenetically related (A large number of Purple Show Up – 9:7) How? There’s a molecular pathway needed to have the protein be expressed o 1) Precursor o 2) Intermediate o 3) Functioning Pigment Each has an intermediate enzyme that functions on the pathway o If one enzyme is messed up, the pigment cannot be created o 3. Complementation ECTURE Definition – two recessive alleles give rise to a dominant phenotype o 4. Modifier Genes Definition – genes on separate chromosomes influence each other o 5. Gene Redundancy Definition – one functional copy is enough to exhibit the gene o 6. Intergenic Suppressors Definition – the phenotypic effects of one gene are reversed due to a suppressor mutation another gene WILL BE COVERED NEXT L January 27, 2016 Chapter 4: Extensions of Mendelian Genetics Continued Limitations of Mendel’s Work Modern Genetics Begins to Ask Why? o So how do other mutations manifest themselves other than the simple above potential mechanisms? 1. Gain of Function 2. Dominant Negative 3. Haploinsufficiency Looking Dominance o 1. Simple Dominance (3:1) o 2. Incomplete Dominance (1:2:1) o 3. Incomplete Penetrance (Varies by Generation) o 4. Overdominance (1:2:1, But Heterozygotes are Selected for) o 5. Heterosis Considering Multiple Alleles Conditional Alleles Codominance Sex Linked Genes Sex Related Traits Lethal Alleles (1:2) o Differentiating Between Codominant, Incomplete Penetrance, and SemitLethal o Variants on Lethal (or more accurately, Genes that appear Lethal) 1. Semilethal Alleles 2. Incomplete Penetrance Effects on Phenotype o 1) Pleiopatry o 2) Gene Interactions o 3) Gene Dosage Effect Important Interactions: o 1. Two Gene Interactions (9:3:3:1) o 2. Epistasis Definition – one gene masks another I. Recessive Complementation Epistasis (9:7) – The recessive alleles together affect another gene (recessive epistasis) Two White Flowers are Bred CCpp (White) X ccPP (White) How? o There’s a molecular pathway needed to have the protein be expressed 1) Precursor (Colorless) 2) Intermediate (Colorless) 3) Functioning Pigment (Anthocyanin) o Each has an intermediate enzyme that
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