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Final Exam Study Guide

by: Joseph Merritt Ramsey

Final Exam Study Guide CELL 2050

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Joseph Merritt Ramsey

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All Notes from the Semester Compiled into Chapter Divisions as Well as Additional Study Sheets of Specific Topics
Dr. Meenakshi Vijayaraghavan
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This 192 page Study Guide was uploaded by Joseph Merritt Ramsey on Monday April 25, 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 59 views. For similar materials see Genetics in Science at Tulane University.


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Date Created: 04/25/16
Overview of Genetics Chapter 1: Overview of Genetics Scientific Advancements Human Genome Project  A General Overview of Facts o National Institute of Health and the Department of Education implemented the Human Genome Project from 1990 to 2003 o Haploid set has 3 Billion Base Pairs, so a Haploid Human Cell has 6 Billion Base Pairs o The Molecule is 2 Meters Long o Codes for about 20,000 – 25,000 Genes New Technologies From the Project  1. DNA Fingerprinting – criminal investigations, parental information, genetic defects  2. Cloning – advanced organisms o Dolly the Sheep o Copy Cat  3. Genetic Engineering – various applications o Gene injection for therapy o Insulin production through animals o GFP to mice (shows up on skin)  Technique used to identify, sterilize, and eradicate mosquitoes and stop pesticide use Genes and Traits Important Overview  Gene o Basic Definition – basic unit of biological information; a functional unit of heredity o More Applicable Definition – segment of DNA that encodes for a functional polypeptide o Structural Gene – segment that encodes for a protein  As opposed to RNA encoding genes  Cell Overview o Definition – basic unit of life (membrane enclosed) o Macromolecules: Genes code for Macromolecule Production in Cells  1. Proteins  2. Lipids Overview of Genetics  3. Carbohydrates  4. Nucleic Acid DNA’s Properties and Considerations  Central Dogma: DNA  RNA  Proteins  Proteins and Traits o Proteins – work horses of the cell; tools of gene expression o Traits – characteristics an organism expresses; often looking at the phenotypic expression  Building Blocks o Nucleotide monomers for a strand o Two strands are held together by Hydrogen bonding  Additional Pieces o Histones attach in order to make Chromosomes o The Chromosomes for the Genome  Accessing DNA o DNA can only be accessed during gene expression  The process during which information present in genes is used to change characteristics in an organism o Transcription – a copy is made into mRNA to be later read and translated o Translation – amino acid sequence is encoded in the cytosol Traits  Type of Traits: o 1. Morphological Traits – a displayed phenotype  Physical appearance  Ex: color of a flower o 2. Physiological Traits – the capacity of an organism to function, mechanisms reliant on genes  Process depends on genes and propagates life  Ex: Cellular Respiration o 3. Behavioral Traits – a behavioral response contingent on a genetic pathway  Response to a given environment  Ex: mating calls  How Does Molecular Composition Affect Traits? – The Butterfly Example o Color in the wing is contingent on the translation of pigmentation o Gene Classes with Traits:  Normal Gene – makes the right gene in the right amount in the right cell  Abnormal Gene – a mutation causes the balance to be thrown off o The Butterfly that has properly functioning genes creates a large amount of pigmentation  It is seen as very dark because of high pigment concentration Overview of Genetics o This observation can be expanded to the population level – how much of the gene is present?  This then becomes an ethological question  How does evolution and environment change gene translation? Thought Process of a Geneticist – It Moves Backwards  The butterfly example also shows a sort of backwards movement of the thought process o 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 An Evolutionary Perspective  Evolution Definition – accumulation of changes over time o Neutral and Beneficial mutations accumulate  Horse Example o Displays Vertical Evolution, the only type when tracing small mutations actually matters o The development of a small, goat-like animal to the strong horse we know today o Specific differences are selected for that change the appearance  What Are Morphs? o Morphs are members of the same species that look dramatically different, representative of evolutionary changes  What makes a Species?  1. Similar Genetic Makeup  2. Capability to Interbreed  But Morphs are dramatically different o Panther Example  Panthera onca is the Panther and the Jaguar  And their differences are representative of their environments  Chromosome Changes: another method of genetic change and evolution that can only remain present through natural selection o 1. Chromosome Aberration – any sort of change in the Chromosome  Breaks  Duplications  Inversions  Transmutation o 2. Genomic Mutation – change in the Chromosome number  Diploidy – a duplicate chromosome  Polyploidy – a ubiquitous change in all the cells Overview of Genetics  The Most Important Part? Genetic Fields and Studies 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? Studies:  1. Transmission – process by inheriting traits o Quantitative Mendelian analysis of gene expression  2. Molecular o Biochemical composition of genes and their expression o DNA/RNA composition o Functional Aspects and the Central Dogma  3. Population o Allele distributions in a population o Ethological considerations of environmental effects Mendelian Genetics Chapter 2: Mendelian Genetics Who Was Mendel? Why the Pea Plant?  Overall Reasons o Easy to observe o Short harvest time (30-40 Days) o Small space required to grow o Large flower is easy to manipulate and handle  Anther/Reproduction Manipulation  Isolate Traits Overall Process of His Experiments  1. Self-Fertilization o His initial step involved insuring that his plants were indeed true breeding o Self-fertilization for 9 Generations to achieve true breeding parents  2. Hybridization o Those parents were then crossed to produce the organisms in which he was truly interested o The F1 Generations o Observed that there were generally speaking two variables of the trait  3. Self-Fertilization (of the Hybrids) o He then self-fertilized the F1 Generation to get the F2 o Removed the anther in this process Mendel’s Studies  Traits Studied o 1. Flower Color – PURPLE, white o 2. Flower Position – AXIAL, terminal o 3. Seed Color – YELLOW, green o 4. Seed Shape – ROUND, wrinkled o 5. Pod Shape – INFLATED, condensed o 6. Pod Color – GREEN, yellow o 7. Height – TALL, short  Methodology o Mendel’s method was not strictly scientific  He simply performed experiments and analyzed his numbers  He did not have a hypothesis o His methodology is known as “Quantification” Mendelian Genetics  Involved a mathematical analysis of his findings to search for significance  Used an empirical approach to deduce laws Mendel’s Laws I. Law Number One: Law of Segregation  Diagram of Mendel’s Characteristic Cross o Terms to Know:  Parent Generation  Cross Fertilization  Single Factor Cross  Monohybrid  F1 (First Filial) Generation  Self-Fertilization  F2 (Second Filial) Generation  Summary and Observations o Unit factors of inheritance will segregate during crossing Mendelian Genetics  These “unit factors” are now known as “Genes”  The variants of these are called Alleles  Having the same alleles is known as Homozygous, different alleles is Heterozygous  This composition is now known as Genotype  Mendel observed the Phenotype, the observable characteristics  Punnett Squares o Mendel didn’t explicitly use Punnett Squares, but his predictions can be neatly displayed in Punnett Squares o Punnett Squares have their limitations, though, due to practicality  General Hybridization:  Possible Gametes = (#alleles)#traits)  Possible Offspring = (#gametes)2  Monohybrid Cross 1  Gametes = (2) = 2  Offspring = (2)  Dihybrid Cross  Gametes = (2) = 4 2  Offspring = (4) = 16  Trihybrid Cross  Gametes = (2) = 8  Offspring = (8) = 64 o But for Monohybrid and Dihybrid Crosses they are useful  Monohybrid – A a A AA Aa a Aa aa o Dihybrid – AF Af aF af AF AAFF AAFf AaFF AaFf Mendelian Genetics Af AAFf AAff AaFf Aaff aF AaFF AaFf aaFF aaFf af AaFf Aaff aaFf aaff  So how, using these techniques (considering Genotype, Phenotype, an Punnett Squares), can you determine genotypes from phenotypic observations? o 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 o 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 II. Law Number Two: Law of Independent Assortment  Diagram of the Experiment - Standard Test to Display Independent Assortment o Terms to Know  Two Factor Cross  Dihybrids o Process  Initial  Hypothetical  Actual Mendelian Genetics  Genes assort independently of one another during separation o 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, Dominant alleles don’t have to stick together in different genes o Refers to the Segregation of alleles, but with Multiple genes Mendelian Genetics  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 “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 o This method, though, only goes so far, considering not all defects can be easily phenotypically detected o This has found, however, that small genetic mutations in defective alleles are a source of overall deficiencies Dominant and Recessive Genes  Overall o Most genes have two variants o Defects in the alleles cause the rise of diseases  Relation to Diseases o Recessive Genetic Disease – two of the allele must be present o Dominant Genetic Disease – only one of the allele needs to be present  These types of genetic disease are almost always fatal prenatally  Known as “de novo” mutations  They randomly occur during gamete formation Mendelian Genetics Pedigrees  Examples to Consider 1. Two Carrier Parents (25% Infected) 2. Two Infected Parents (100% Infected)  Two Odd Pedigree Symbols o 1. Fraternal (Dizygotic) vs. Identical (Monozygotic) Twins o 2. Consanguineous (Cousins) Probability Eugenics vs. Euthenics  Eugenics – the aim of improving the genetic quality of humanity o Counseling aimed towards preparing and informing women on genetic possibilities and dangers o Important with aged mothers as well o A maintenance of strong genes in the human population Mendelian Genetics  Euthenics o This is the improvement of functioning and wellbeing through the improvement of living conditions and external factors o These factors increase the reproductive rate by increasing survival Some Broad Notes  1. Simple Probability o Measuring times something occurs against the times it could have occurred ???????????????????? ???????????????????? ???????????????????? ???????????????????? ????????????????????????= ???????????????????????????? ???????????????????????????????????????? ???????????????????? ???????????????????????????????? ???????????????????????? ???????????????????????????????? ????ℎ????????????????????????????????  2. Accuracy o Very dependent on sample size o Error should be small  Error is between observed and expected  Ensures error is by chance, not an external affecter  Random Sampling Error is Minimized by Large Sample  3. Sum Rule o You can add mutually exclusive probabilities o Looked at as an “Either/Or” event  They are mutually exclusive o 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 o Independent Set of Events in a Given Order  What is the probability of the First and Second being… o The event is in a given order  5. Binomial Expansion o Independent Event in No Order o Say five events are happening, one can search for the possibility of the event simply occurring three times  6. Chi-Squared Test o Tests “goodness of fit,” or how much variance is due to random sampling Mendelian Genetics Probability Rules I. Sum Rule  Ex: Considering two traits, Tail Length and Ear Type o Each event is a Mutually exclusive – you cannot have a normal and abnormal tail/ear o So, because each is Mutually Exclusive, you can summate their probabilities o What is the probability of having a Normal Eared, Normal Tailed Organism?  Find the total possibilities (16)  Find the specific possibilities (9) II. Product Rule  You want a specific order of events with independent events  Can consider two individuals now  Ex: Cystic Fibrosis o Chances of one child = ¼ o Chances of not one child = ¾ o Chances of children 1,3 out of 3: ¼ x ¾ x ¼ III. Binomial Expansion  Not a specific order, but still independent  Ex: 2 1 ????! ???? ????−???? ???????????????????????????????? ???????????????????????? 3! 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 IV. 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 o 1 Trait, Segregation (3:1, Two Phenotypes) Mendelian Genetics o 2 Traits, Assortment (9:3:3:1, Four Phenotypes)  Ex: Assessing Chi-Squared for wing shape and body color o 1. Propose Hypothesis (as above, to eventually determine expectations) o 2. Analyze the Observed Values o 3. Use expected values based on hypothesis o 4. Use formula (smaller value is better) o 5. Compare to Degrees of Freedom  Null Hypothesis: occurs merely because of chance  Degrees of Freedom  Always equals (n-1) Cell Division Chapter 3: Cell Division Viewing the Cell Genetic Material  Eukaryotes o Double stranded, Linear DNA o Well defined organelles are present o Chromosomes are made of the Chromatin complex (60% protein (histones), 40% DNA  Prokaryotes o Double Stranded, Circular DNA o Naked DNA (no protein)  Somatic Cells vs. Germ Cells o Somatic Cells are Diploid (have two sets of chromosomes)  These sets are comprised of pairs, called Homologous Pairs  These pairs are identical in many ways o Germ Cells are Haploid (have one set of chromosomes) Cytogenetics  Definition – examination of the chromosomal compaction and composition of an organism  Process for Examination o 1. Addition of Division Inducing Agent (condenses and duplicates Chromosomes) o 2. Allowance of Replication o 3. Centrifuge to Stop Replication and Collect Sample (forms sample pellet) o 4. Addition of Hypotonic Solution (swells up cells) o 5. Drop Cells on a Slide and Fix Them (no more changes can occur) o 6. Stain Cells With Geimsa (stains different components differently) o 7. Addition of Trypsin (breaks down histones, reveals DNA bands) o 8. Photo Imaging (computer or camera) o 9. Karyotype Arrangement  Karyotype Arrangement – the entire chromosome complement of an organism arranged from tallest to shortest o Homologue Identification  1. Size  While size can help identify Homologues, it is no suggestive of overall genomic complexity of an organism  2. Centromere Position  1. Meta-Centric – in the middle Cell Division  2. Sub-Met-Centric – closer to the middle  3. Acro-Centric – closer to one end; ‘p’ is short, ‘q’ is long  4. Telo-Centric – only one arm  3. Banding Patterns  Banding is induced by the addition of the Trypsin  This can identify and differentiate based on Loci, not based on Alleles  Why are Karyotypes important? o 1. They Allow for Evolutionary Comparisons  Chimps have 48 Chromosomes, with Chromosome 2A and 2B each adding up to the total of Human Chromosome 2  Banding with Chimps is also seen to have high similarities to that of humans  So the Chromosomes are Similar, but not identical o 2. They Can Identify Abnormalities in an Organism Eukaryotic Chromosomes Overview  Homologues form the Diploid number  Cell Division o Why do Cells Divide?  1. Asexual Reproduction  Bacteria reproduce through Binary Fission  DNA is replicated, the Septum if formed, and the cell splits into two new identical cells o FTSZ: Filamentous Temperature Sensitive Mutant Z responds to trigger Cell Division o Forms a ring and vibrates and recruits eight other proteins to form on the ring around the membrane o The new nine protein complex forms the Septum  2. Multicellularity  In complex organisms, multicellularity is achieved through Mitosis o When do Cells Divide?  Density determines and initiates cellular  They accumulate nutrients and proteins (increasing density) Mitosis Overview  Mitosis is a highly complex process occurring in all Eukaryotic cell types o Its goal is Replication and Distribution o The cells maintain genetic consistency through generations o Equal distribution must occur  As a random side note, ferns have a Chromosome number over 1000 o Displays how sheer volume does not directly translate into complexity  All Cells go Through Stages (Common to all dividing cells, whether actively dividing or not) o 1. Interphase (G1, S, G2) o 2. Prophase o 3. Prometaphase o 4. Metaphase o 5. Anaphase o 6. Telophase o 7. Cytokinesis  Cells also differ in the time for these stages, depending on their purpose and function o Bone Marrow: constant replication o Elementary Canal Cells: twice a day replication o Liver: once a year o Neural Cells: terminally differentiated Mitotic Stages 1. Interphase  G1 Phase (Gap) – Key Words: Density o Restriction point is reached, it must progress o So progressed into the S Phase  S Phase (Synthesis) – Key Words: Replication, Centromere o Chromosomes are duplicated (DNA, Histones) o Sister Chromatids form around the Centromere  Part of Chromosome (DNA locus) that forms binding site Cell Division o Monad is a single Chromosome, Dyad is the Sister Chromatids  G2 Phase (Gap 2)– Key Words: Kinetochore, Organelles o Organelles now begin to divide o Kinetochore now deposits itself on the Centromere (will eventually connect with Centrosome)  It then moves into the Mitotic stage (M)  Now the cell has enough contents for two separate cells, so it needs to split (92 Chromosomes and Numerous Organelles)  Mitosis is the splitting process  Cytokinesis is triggered during Anaphase, which starts cytoplasmic division 2. Prophase  Quick Overview Condensation of Chromosome; Plasma membrane Breaks Down; Physical Assembly of Spindle Apparatus  All Euchromatic regions (less compacted) now become Heterochromatic  Nuclear membrane breaks down into fragments  The Nucleolus (area that creates rRNA) disappears  Spindle Apparatus forms o Physical Assembly from Centrosome and Centriole, the microtubule forming complex) o They are assembled, but that’s it: only assembly  1. Polar Microtubules – deviating the poles  2. Astin Microtubules – branching to the outside, holding it in position on the Membrane  3. Kinetochore Microtubules – go on to connect with Kinetochore proteins on the Centromere Cell Division 3. Prometaphase  Quick Overview Kinetochore Microtubule Connects to Centromere; Complete Nuclear Membrane Breakdown  The spindle apparatus exists to separate sister chromatin  Kinetochore begins polymerizing (growing) from the Centrosome to ‘randomly’ attach to the Centromere o Any that fails to attach depolymerizes o In this manner, the Spindle Apparatus becomes functional o It binds so that each sister chromatid is bound to each pole (giving functionality)  The Nuclear Membrane also completely disappears now 4. Metaphase  Quick Overview Arrangement on the Metaplate  Sister Chromatids are arranged on the Metaplate of the cell and are connected to each pole o The equatorial plane  This arrangement is random (paternal and maternal can line up on either side) and in a single file row Cell Division 5. Anaphase  Quick Overview Polymerization of Polar Microtubules and Depolymerization of Kinetochore  The Chromosome number must be maintained, so the sisters attached at each pole are now separated o I. Kinetochore Microtubules Shorten (depolymerizes)  This pulls the chromatids o II. Polar Microtubules Lengthen (polymerizes)  This pushes the cell poles  The pulling/tugging o This separates the Sisters  If not, nondisjunction occurs o Each pair of Sister Chromatids becomes single Chromosomes  Cytokinesis is initiated by these steps (when the chromosomes are on either end) 6. Telophase  Quick Overview “Reverse Prophase”  Everything in prophase is reversed now: o I. Chromosomes – begin to decondense o II. Nuclear Membrane – begins to reform o III. Nucleolus – begins to become evident again o IV. Microtubules Disappear – spindle apparatus breaks down  At this point, the cell is binucleate (two nuclei) 7. Cytokinesis  Plant Cells o Occur on the Cell Plate o Cell plate is formed from Golgi Vesicles carrying plate proteins  The vesicles merge and extend to the side  Once they reach the side Plasma Membrane, maturation of the Cell Wall occurs o Contains very large polysaccharides Cell Division  Animal Cells o Occurs through Actin movement (done through Myosin)  Actin is already present at the Cell Membrane o Cleavage furrow forms from actin overlapping  Ring diameter shrinks Mitosis + Cytokinesis gives you a Genetically Consistent Cell, Mitosis on its own merely gives a Binucleate Cell Sexual Reproduction  Cellular Overview o Gametes  Types Cell Division  I. Isogamy – identical gametes  II. Heterogamy – male and female are different and specialized  Reduction Division Occurs – division that reduces to haploid  Occurs before fertilization  They are not daughter cells – genetically inconsistent o Meiosis precedes by Syngamy (germ cell fusion, fertilization)  This:  1. Keeps Consistent Chromosome Number  2. Brings About Variation to Increase Survival A. Spermatogenesis  Testes have Spermatagonial Cells, which are self-renewing cells o This is a Diploid Cell (Spermatagonia) o These cells divide (through Mitosis) to produce two new cells, one that remains a Spermatagonial Cell and one that becomes the Primary Spermatocyte  The Primary Spermatocyte goes through Meiosis to produce Gametes o After Meiosis I the Primary Spermatocyte has been split into two Secondary Spermatocytes o The final phase (Meiosis II) results in four Spermatids o The spermatids go on to differentiate into the Sperm Cells  The main goal of Spermatogensis is to produce haploid nuclei  What does Sperm Differentiation add? o I. Motility  The develop a flagella, helps motility o II. Enzyme Capsule  This is known as the Acrosome (enzyme capsule that breaks down egg membrane) B. Oogenesis  Very important because the cell must initiate and sustain embryonic development  Accumulation (this is a much more complex process) for Embryo o I. Cytoplasm and Enzymes o II. mRNA o III. Proteins o IV. Organelles  Creation Process o Special diploid cells in the Ovary are called Oogonia  Mitosis is the first step again  But this isn’t Self-Renewing (constant division) o Oogonia develop into Primary Oocytes and an additional Oogonia Cell Division  This one will go through Meiosis I, but in an Asymmetrical manner  Spindle Apparatus forms to one side, and organelles follow, forming Secondary Oocyte and a Polar Body (which divides again) o By month seven, however, the addition Oogonia degenerate and leave the Primary Oocytes o Through a long activation process, the Primary Oocytes go on to become Three Polar Bodies and A Functional Egg  Activation Process o I. Early Development  Through Mitotic Proliferation of early ovary cells, about 7 Million Oogonia form  As development continues, this number declines to roughly 1 Million Functional Oogonia (undergo Meiosis) o II. Selection Process (7 Months)  At Seven Months, a selection process occurs to the 1,000,000 that results in 400-500 Primary Oocytes o III. Diplotene Arrest (Primary Signal, 7 Months, Before Birth)  At the same time as selection occurs, Primary Oocytes begin to undergo Meiosis  They are halted at Diplotene, however, in Prophase I  It’s important to note that Prophase has begun, so the spindle apparatus has formed  That’s why age creates problems o IV. Second Signal (12 Years, Puberty)  Hormonal shifts result in Meiosis progressing through to Metaphase II  Occurs in monthly cyclic process  So the first division has occurred, giving rise to a Polar Body o V. Final Signal (Sperm Cell)  Sperm cells arrive and attack the membrane of the Egg in order to fuse  This signal induces completion of Meiosis and creation of egg cell and ultimately embryo C. Plant Gametogenesis (Double Fertilization)  Methodology of Alternation o Gametophytes are the Haploid Phase, Sporophyte the Haploid Phase o Large visible structures are generally Gametophytes  Creation Spores Eggs Anther, Stamen (producer) = Male Stigma, Ovary (Producer) = Female Cell Division Diploid Parts Diploid Parts I. Microsporocyte (Meiosis)  I. Megasporocyte  Megaspores (4) Microspores II. Three Megaspores Degenerate II. Microspores  Pollen Grain This division occurs without III.Three Rounds of Mitotic Division Cytokinesis and Unequal Cytokinesis ultimately result in Seven Cells III. Pollen Grain is made of Tube Cell (Embryo Sac) (one is Binucleate) (Pollen Tube) and Generative Cell (Active Sperm Cells) Egg, Central Cell (Binucleate), Synergids (2), Antipodals (3)  Fertilization o I. Stigma (Female Part)  Nectar and lipids present on tip  Lipids and nectar initiate germination, maturation of pollen grain o II. Pollen Grain (Male) (Pollen Tube and Sperm Cell Nuclei)  Tube Cell – develops into the pollen tube  Generative Cell – splits into two germ cells (mitosis) to become active sperm (sperm nuclei) o III. Newly Created Sperm Cells Fertilize (Endosperm and Embryo, this is the Double Fertilization)  Central Cell (Female) – this Binucleate cells now becomes a large trinucleate, known as the Endosperm  Egg Cell (Female) – fertilization of the Egg results in the growing Embryo o IV. Fleshy fruit forms from the rest of the Ovary and Ovule  Plant vs. Animal o Plants Start with Meiosis, Animals End with Meiosis Sex Determination  Different species have different cellular sex mechanisms o Homogametic – XX, same sex chromosome o Heterogametic – XY, different sex chromosomes  Determination o 1) Human o 2) Insect  Number of X Chromosomes to Autosomal Sets  Ratio 1.0 = Females  Ratio 0.5 = Males Cell Division o 3) Bird  ZZ = Males  ZY = Females o 4) Alligators  33 = 100% Male  < 33 = 100% Female  > 33 = 95% Female o 5) Bonilla Worm  Hits the ocean floor? Becomes Female  Hits the Female? Become sperm producing machine o 6) Parthenogenesis  Bees, Wasps, all males are Haploid Organisms  Female are all diploid  Morgan’s Work on Chromosomes o Morgan wanted to experiment with Phenotypes, specifically hoping to induce some sort of mutation in his breeding flies  Inducing through Radiation o White eye mutation occurred and he found 44:1 ratio, with females being more red o Test Cross  Heterozygous Female with White Eyed normally gives 1:1, but white eyes males die before birth Extensions of Mendelian Genetics Chapter 4: Extensions of Mendelian Genetics A Broad Overview of The Extensions Limitations of Mendel’s Work  Only looks at purely dominant and recessive from a narrow point of view o Dominant: present, wild type – the right cell, right protein, right time  But what if the wild type (beneficial type) is recessive? o Recessive: generally mutant variety, a loss of function  So what if this occurs as the dominant fashion?  Balding is an example  Mendel Looked at only 7 Pea Traits o Pea Color, Pea Shape, Pod Color, Pod Shape, Flower Position, Height, Flower Color o But his finding and explorations didn’t go beyond that  So Consider Genetic Disorders and Diseases o They are generally recessive, but as considered above, they can be dangerous as dominant o So how do these developments occur? Modern Genetics Begins to Ask Why?  Why would the Dominant Gene be Enough? o 1. 50% of the protein being transcribed is enough to have the effect o 2. Cellular recognition mechanisms to upregulate a particular gene  So how do other mutations manifest themselves other than the simple above potential mechanisms? o 1. Gain of Function  A mutation gives a gene a new function and ability  But this ability ends up being bad for the cell and is then upregulated because of the new ability  So a loss of function does not occur – the normal allele is still fine  It is merely being down regulated for the novelty allele  Ex: p53  P53 is a tumor suppressant  It generally functions in a dominant, wild type manner  But when a mutation giving a new ability occurs, it becomes upregulated o This upregulation (so dominant form now) of the new ability is actually harmful because the new ability is to proliferate cancer cell metastasis Extensions of Mendelian Genetics o 2. Dominant Negative  Antagonistic Mechanisms occur  The mutation occurs that inhibits the ability of the other (proper) gene to function properly o No loss of function occurs – the gene is still perfectly fine, it’s simply “drowned out” by the mutated allele  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 o It can no longer move o Can no longer switch to GTP to activate o 3. Haploinsufficiency  Generally genes are transcribed and proteins created by a combination of each allele on the chromosomes  So both contribute to the functioning  Ex: Consider a deletion  In essence, one is not enough (the Haplo is not enough to express)  Thinks of it this way:  A gene will be expressed with 50 Units of protein X created  You have two alleles that are both wild type, one is just highly expressive (varies per person) Extensions of Mendelian Genetics  In the highly expressive, each allele codes for 50 units, so it is Haplo sufficient  But in the low expressive, each is only 30 – haploinsufficient Types of Dominance Patterns 1. Simple Dominance (3:1)  Straightforward Mendelian Expectations with the 3:1 Raito 2. Incomplete Dominance (1:2:1) One copy of the dominant allele is not enough to express the gene  Ex 1: 4 O’clock Flower o A mix occurs o Punnett Square View (Diagram)  Ex 2: A Molecular Look at the Pea Shape o Take a look at protein composition and it becomes clear that the Homozygous Dominant varies from the Heterozygous Looking at the EET1 Gene Expression o But must be done molecularly speaking  Ex 3: PKU (Phenylketonuria) Molecular Perspective o Same idea here o PKU patients lack the functioning protein “Phenylalanine Hydroxilase”  This breaks down Phenylalanine  Without it, Phenylalanine releases damaging ketones o So blood samples can be taken and checked for Phenylalanine composition, reflective of its proper breakdown  Healthy (Homozygous) – 1mg/dL  Carrier (Heterozygous) – 2-3mg/dL  Infected (Homozygous Recessive) – 6-8mg/dL 3. Incomplete Penetrance (Varies by Generation)  Normally, the genotype penetrates the phenotype in order to express the present gene o The dominant trait is said to have the ability to “penetrate” the phenotype o 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 o Penetrance – viewed in the population, the capacity to be expressed in Heterozygous individuals Extensions of Mendelian Genetics  Only consider Heterozygotes because the other two are easy to identify and explain already  So within a population, the gene has 66% penetrance o Expressivity – deals with an individual, how is the gene expressed? o 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 o Being a heterozygote with the Dominant Polydactyl o This allows for the trait to skip generations with relative ease  Possible Explanations? o 1. Environmental – environmental factors influence the gene expression  I. Light  Snapdragon present different colors depending on what temperature it is in which they grow  II. Temperature  Drosophilia facets are more present when growing in cold weather and less so in warm weather.  III. Diet  PKU patients cannot have Phenylalanine in their diet, but strict regulations allow them to live perfectly fine.  Can they be reversed? o A question may be, however, if they don’t catch it early can it be reversed? o PKU doesn’t present such a prospect, but the conditioned allele on Shibiar alleles can be o Flies grown at given temperatures can have the effects reversed o 2. Modifier Genes o 3. Combination of the First Two 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 o These Carriers have an advantage  Why does Overdominance Occur? o 1) Cellular Morphology  Antigen is present because of the slight expression (Sickle Cell example) o 2) Dimerization of the Protein  Dimerization occurs to form the final protein (Quartneary structure)  2 units come together  With another type of allele, three possible dimerization possibilities arise Extensions of Mendelian Genetics  With two of the same allele, only one permutation exists  Results in the creation of different Monodimers and Heterodimers  New capacities are created o 3) Protein Reactivity  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  So a range of enzyme activity is created  That range creates a survival advantage  Ex: Sickle Cell o Hemoglobin overview  Made up of four subunits, Two Alpha, Two Beta  A small point mutation occurs on the Alpha  GAG goes to GTG on the DNA  Goes from Glycine (charged) AA to Valine (Neutral) AA  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 o Cells of Sickle Cell Lifespan  Each cell normally lives 90-120, but sickle cell cells only survive 10-20  So the body can’t keep up o But Carriers have an advantage: A S  Hb and Hb are the alleles  Their cells are mostly fine and properly functioning, but a few of them present some sickle traits  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  But non-malarial environments don’t have high heterozygote populations  Ex: Tay-Sachs o A mutation occurs in a lipid storage and synthesis protein o Allow them to fight TB  Ex: PKU Females o In certain areas, the likelihood to ingest the Ochratoxin A is much higher Extensions of Mendelian Genetics  Normally even a small ingestion is enough to cause a likely miscarriage but is not fatal to the mother o But PKU females do not experience such miscarriages 5. Heterosis  This example begins to look at multiple genes o 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 o Genes are introduced to optimize crop life  The phrase here is “Hybrid Vigor” o Merely referring to the mix of alleles Considering Multiple Alleles Overview  Overview o Several mutations exist for a given gene, each showing a slightly different and altered phenotype o Morphologies:  1. Monomorphic – one wild type exists  2. Polymorphic – multiple wild types exist  3. Multiple Alleles  Examples of Multiple Alleles o A. Mouse Fur Color (True Monomorphism)  Mentioned above, the distribution is not equal o B. Rabbit Fur Color (Like Monomorphism, but still all present)  Detailed above o C. 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 o D. Blood Types (True Polymorphism)  Different types of blood exist that are all equally as present Extensions of Mendelian Genetics A. Polymorphism – (Only deals with One Gene )  Hair and Eye Color may be a common consideration, but consider how those manifest themselves: o They are a mix of genetic influences, influenced by Polyploidy genes  A true example is blood type: o They are all the same gene and are not phenotypically affected by other genes o But there are three different forms of the gene o And if not force chooses for a particular phenotype, it is Polymorphic o But if the wild type is chosen, it is Monomorphic B. Monomorphism  The mutation distribution is not equal o Other alleles can exist, but one wild type predominates, so the phenotype is monomorphic o The mouse coat color is a good example:  Agouti is dominant (A) t  But the Black/Yellow Body is possible (a )  And Black is also possible (a) o So in essence, polymorphic alleles can be monomorphically expressed  Mouse Fur Example – (This deals with pigmentation protein) 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:  c c ch – 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 Extensions of Mendelian Genetics  Body temperature influences gene expression  The cold causes and increased expression when the h Himalayan allele is present (c )  This causes a darkening of the extremities C. Conditional Alleles  Definition: particular environmental conditions cause the gene expression o These alleles were mentioned in regards to the PKU discussion in Incomplete Penetrance o But unlike with penetrance (reversal is much more difficult and/or impossible), purely environmental factors can often be reversed  Examples o Rabbits  Himalayan gene in rabbits  Tyrosine activation in the recessive Himalayan gene are influenced by temperature (upregulated in the cold) o Siamese Cats  Same Tyrosine effects in the cold o Cattle  Cold now down regulated Tyrosine action for Cattle color o Drosophilia  Shibire genes (regulating cytoskeletal development) occurs normally at 21 or lower D. Codominance  Definition o Multiple alleles present themselves as wild type dominate equal in phenotypic expression  Blood Types is a great View o 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 o Glycosyltransferase (Transfers sugars) moves the sugar to the blood cell binding site o 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) o Blood Genotype Options:  A – I I or I i  B – I I or I i A B  AB – I I Extensions of Mendelian Genetics  O – ii o Rhesus factor is the Rh factors for plasmid antigens o And M/N blood types are for blood protein antigens o H-Factor (Bombay Blood Disorder)  The H-Factor 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)  Cattle Color o Spots become present when Red/Brown is crossed with White E. Sex Linked Genes  Linked – they are present on a Sex Chromosomes o Y: Holandric Genes (only about 83 present) o X: About 500 present o This phrase is generally used considering inheritance  Hemizygous o This term refers to the Y Chromosome o One type of allele is present (the idea behind homozygous) but only one chromosome will carry that given allele (whether on X or Y) o So the phrase is Hemizygous – there’s only one “slot” to fill  Examples: o Duchenne Dystrophy  Dystropin is a cytoskeletal protein that attached the cytoskeleton to the plasma membrane  So dysfunctional dystropin leads to inefficient muscle cell development  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 Xd Xd Xd X X d X X d X D X Xd X X d Y X Y X Y Y X Y X Y Extensions of Mendelian Genetics o Teeth Color  The enamel and coloration gene is located on the X Chromosome F. Sex Related Traits  Important Differences o 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)  MIC (Development) is present on both Sex Chromosomes o Sex Limited  Refers to genes only present on a given Sex Chromosome  SRY is only present on the Y Chromosome to induce male development  Types: o 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?  5α Reductase is present in all people  It works on Testosterone to produce Dihydroxytestosterone o This acts on the hair follicles  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 o 2. Sex Limited – Breast Development  Limited is an Either/Or sort of thing  This only occurs in Females Extensions of Mendelian Genetics o 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 G. Lethal Alleles (1:2)  Definition – very important alleles, critical to proper functioning and survival  Genotypic Expressions o With a Homozygous Lethal allele, the organism dies, so the ratio becomes 1:2  Examples o 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  The two mutant alleles messes up spinal development too much o Mice Coat  Yellow or Non Yellow coat  Scenarios:  Homozygous Recessive – normal  Heterozygous – pleiopatry causes negative growth effects  Homozygous Dominant – death  Differentiating Between Codominant, Incomplete Penetrance, and SemiLethal o Looking at Heterozygous Individuals o 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 o Incomplete Penetrance?  Incomplete penetrance deals with a gene that is actually expressed  Lethal alleles result in the 2:1 ratio because they occur before birth  Huntington’s is a good example  Not semilethal, which are often sex specific and affect given ratios Extensions of Mendelian Genetics  And not lethal either, since they act after birth H. Variants on Lethal (or more accurately, Genes that appear Lethal)  1. Semilethal Alleles o Kill about half the population in a lethal, before birth manner (hence the applicability of the ‘lethal’ nomenclature) o The dominant/recessive “lethal” allele is present in Homozygous manner (Genotypically Speaki


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