BIOS101 W8: Cells and Replication (PDF)

CELLS AND HOW THEY REPLICATE. PROKARYOTES AND EUKARYOTES 11/11/2024. Monday session Characteristic Prokaryotes Eukaryotes --------------------------- ------------------------------------------- -------------------------------------------------------...

CELLS AND HOW THEY REPLICATE. PROKARYOTES AND EUKARYOTES 11/11/2024. Monday session Characteristic Prokaryotes Eukaryotes --------------------------- ------------------------------------------- ----------------------------------------------------------------------------------------------------- Nucleus No nucleus, DNA is in the nucleoid region Nucleus with a nuclear membrane DNA structure Single chromosomes, generally circular Multiple linear chromosomes within the nucleus Membrane bound organelles NO YES Cell division Binary fission Mitosis and meiosis Size (typical range) 1-10µm 10-100µm Metabolic diversity High, excluding extremophiles Limited -- autotrophic (produce their own energy) or heterotrophic (get energy from somewhere else) Cell wall composition Common. Peptidoglycan in bacteria Variable. Cellulose in plants, chitin in animals and fungi Ribosome size Smaller (70S) Larger (80S in cytoplasm; 70S in mitochondria/chloroplasts) Plasmids YES, used in horizontal gene transfer NO, very very rare Example organisms Bacteria, archaea, cyanobacteria Plants, animals, fungi - Archaea may have some differences with prokaryotes Apply Knowledge - If a newly discovered cell lacks a true nucleus, its genetic material would be in the condensed area of the cytoplasm, called the nucleoid - The circular structure of DNA in prokaryotes allows for faster replication cycles - Binary fission allows prokaryotes to reproduce faster because fewer organelles need to be replicated - Eukaryotes have higher metabolic efficiency because of their specialized organelles, like mitochondria - Prokaryotes utilize diverse energy sources, so that they thrive in more extreme environments than eukaryotes - Lots of prokaryotes have the ability to use photosynthesis (cyanobacteria), or inorganic compounds they have much more opportunities to get energy, rather than eukaryotes - Eukaryotes rely on autotrophic systems (plant photosynthesis), or heterotrophic systems (they have to consume other organisms) - The presence of 70S ribosomes in mitochondria and chloroplasts supports the theory of endosymbiosis because these organelles likely evolved from symbiotic prokaryotes Case Study - Bacterial and Fungal infections require асооеиехш treatments -- a treatment for a fungus is not the same as a treatment for bacteria. Different replication (binary fission and meiosis/mitosis), difference in cell walls (way that we'd target them is very different), - Successful treatment relies on understanding the cellular biology of the pathogen and that of the host - If we are targeting eukaryotes, we need to think carefully about targeting something unique to this specific eukaryote that isn't going to target the cells of the host Cellular differences between bacteria and fungi A screenshot of a cell Description automatically generated - In fungi, we target cell membranes - In bacteria, we target cell wall synthesis -- penicillin Cell wall composition - Different ways of targeting them, which are based on their components in the cell membrane/wall - Bacteria use peptidoglycan - Fungi use chitin How Treatments work - In bacteria, there are a number of different targets, which we can use to try to treat. - The targets may depend on whether the infection is in a gram-positive or gram-negative bacteria - In yeast, there are limitations because they are eukaryotes. Some things we may target (protein and ribosome production) are all things that the host may have, and we can't target them to treat the infection - Most common fungal treatment is amphotericin B nystatin, which targets the ergosterol in the cell wall. - This isn't present in other eukaryotes Treating a patient with Dual Infections - Both fungal and bacterial - We need to choose appropriate antibiotics and antifungals that don't cause harm to the person/animal or drug resistance in the pathogen - Understand what the causative agents were, do some sampling, culture, look at what antibiotics and antifungals these are sensitive to, then do a dual therapy - If you were to prescribe the wrong drug - Pathogens could develop antibiotic resistance - You could affect the host's metabolic pathways - There are some drugs, which, despite their effects on humans, they are still prescribed because there isn't much else available - Some drugs may cause dysbiosis - knocking out the normal microflora of an organism by using antibiotics because some antibiotics can affect every bacteria in the body. If a drug is taken with no positive effect, there would be bad dysbiosis. Implications for Medical Practice - Distinguishing between cell types REALLY MATTERS in clinical settings - Know how to characterize an infection, know the likelihood of the organisms present, know how to culture them to confirm - Accurate diagnosis, understanding cellular biology of the organism, BOTH HOST AND PATHOGEN are really important because - They limit treatment failures - Drug resistance - Unnecessary dysbiosis in the host Other Examples - Parasitic infections (malaria) - Eukaryotic organism and shares some cellular structures with human cells - Difficult to develop drugs that selectively target the parasites - Some parasitic infections are intracellular -- it's hard to reach the pathogenic organism - Cancer treatment - Cancer cells are eukaryotic, but exhibit abnormal cell division and structural characteristics, but they are still host cells - Some drugs target specific structures in cancer cells, such as rapidly dividing DNA, mutated protein receptor, overexpressed enzymes - Understanding cancer cell structure and behavior allows for the development of targeted therapies that aim to reduce harm to normal cells - Autoimmune diseases - Immune system targets the bodies of own cells - Treatment focuses on modulating the immune response because we can't really focus on the cells -- they are our own! - Helps to prevent damage to healthy cells and tissues - Antibiotic selection in multi-drug-resistant bacterial infections - Bacteria can develop resistance - For example, resistance to penicillins by producing an enzyme to break down the drug - Requires the use of alternatives - Testing to determine what the bacteria is sensitive to Why some antibiotics target bacterial ribosomes? - Bacterial/prokaryotic ribosomes: 70S, made up of 30S and 50S subunits - Eukaryotic ribosomes: 80S, made up of 40S and 60S subunits - "S" stands for Svedberg units, which measure sedimentation rate and reflect ribosome size - When looking at the different units, then pass them through a centrifuge, - The units will sediment at different forces - The bigger the number, the higher the force needed for it to sediment - Antibiotics like *tetracycline* and *erythromycin* specifically bind to bacterial ribosomal subunits (30S or 50S), disrupting protein synthesis - These antibiotics prevent bacterial cells from making essential proteins, ultimately inhibiting growth or leading to cell death - Human cells have 80S ribosomes with different structural characteristics, so these antibiotics don't recognize or bind to them effectively - If you give tetracycline to humans, it won't affect them - Antibiotics target specific structures, which aren't present in eukaryotic organelles/parts - Structural specificity means antibiotics can selectively inhibit bacterial cells without harming eukaryotic cells Examples of common Ribosome-Targeting Antibiotics - Tetracycline -- Binds to the 30S subunit, blocking tRNA from attaching and halting protein synthesis - Erythromycin -- Binds to the 50S subunit, preventing the ribosome from moving along mRNA, stopping protein production - Streptomycin -- binds to the 30S subunit, causing misreading of mRNA and resulting in faulty/non-functioning proteins SUMMARIES - Selective targeting -- Antibiotics can selectively bind to bacterial ribosomes without affecting eukaryotic ribosomes - Structural differences -- the difference in ribosome size and subunit composition is crucial for this selective effect - Implication for Treatment -- This selectively allows antibiotics to combat bacterial infections, without generally harming human cells MITOSIS, MEIOSIS, MENDEL, DOMINANCE, RELATIONSHIPS BETWEEN ALLELES OF THE SAME GENE Session 2 THE TRANSMISSION OF CHROMOSOMES BY MITOSIS OR MEIOSIS MITOSIS - Produces chromosomally and genetically identical diploid cells from parental diploid cells - Cell splits, get 2 identical daughter cells - Typically in somatic cells -- non-sex cells Cell Cycle - To duplicate and to split, cells go through the cell cycle - The majority is in interphase -- normal cellular function phase before it gets ready to duplicate - When there are cells, which need to continuously divide (like in the stomach), they enter the cycle, they go through: - Maturation -- DNA is copied, prepares for division Mitotic phase -- different phases Cell divides - There is a need of constant replacement of those cells - Such cells don't enter the G0 phase, they directly start the dividing process, they continuously divide - Differentiated cells exit at G0 so that they can go their paths and specialize - Cells with DNA damage -- they are arrested at G1 -- cellular senescence. They can potentially become cancerogenic, impaired functions, malformed proteins they need to be stopped, arrested, enter cellular senescence - Hayflick limit -- came up with phase 1,2,3. Initial lag active division cellular senescence. Found that every time a cell divides, it lose a small section of the telomere. Every time there is duplication of DNA, the cell loses a small section of the lagging strand -- over time, it reduces its size. - Telomeric ends are made out of repeats of DNA - As the cells progress through cell division, the telomeres on the end of the chromosome get smaller and smaller -- hinder the function - Hayflick limit -- the theoretical limit to the number of times a cell may divide until the telomere becomes so short that division is inhibited, and the cell enters senescence. Number of times a cell can divide - Some organisms have modified their DNA to prolong their cell life, so that they don't lose the telomeres - Centrosomes -- composed of two centrioles, connected by interconnecting fibres and surrounded by the pericentriolar material (PCM), during mitosis they are actively duplicated. Pull chromosomes apart. - During mitosis, the centrosomes are equally divided, so that each daughter cell inherits one centrosome - Active duplication of the DNA, also active duplication of the centrosomes  A diagram of cell division Description automatically generated Mitosis - DNA replication (Interphase) Pairing of sister chromatids (Prophase) Chromosomes align on metaphase plate (Metaphase) Sister chromatids pulled apart, the mitotic spindle grabs onto the kinetochores = daughter chromosomes (Anaphase) 2 Identical daughter cells (Telophase) 1. Duplication of the centrosomes -- they go to the opposite poles 2. Pairing of sister chromatids 3. Chromosomes align on the metaphase plate (middle of the cell) 4. Microtubules on the mitotic spindles grab onto the kinetochores of the chromosomes -- they pull them apart 5. Cytokinesis results in 2 identical diploid cells - Telophase and cytokinesis result in the two daughter cells - In animal cells, we have the formation of actin filaments in a ring structure, which results in a cleavage furrow - The cleavage furrow acts from the outside in, and it comes in, pulled by the actin filaments, until it splits the two daughter cells - In plants, we get the alignment of Golgi and other vesicles along the equator of the cell - They fuse to form a central plate, which then forms the membrane and the cell wall Transmission of chromosomes by Meiosis MEIOSIS - Produces gametes with a haploid set of chromosomes from diploid parent cells - Produces genetic diversity between the gametes - Random Orientation of Bivalents (ROB) -- independent segregation I independent assortment - Recombination of non-sister chromatids - Meiosis forms gametes/germline cells!!! - N = 23 - Sperm and egg fertilize and form a diploid zygote of the individual -- combination of the two gametes, N=46 - Produces haploid gametes, based on the segregation of a diploid set of chromosomes - There are 2 stages -- Meiosis I and Meiosis II - Diploid set of homologous chromosomes DNA is replicated at S phase, creates sister chromatids and the homologous pair in meiosis MEIOSIS I -- Separation of homologous chromosomes, diploid to haploid Meiosis II -- Separation of sister chromatids, forming 4 haploid gametes - Meiosis produces haploids gametes based on the segregation of a diploid set of chromosomes - Chromosomes are duplicated at the start of MEIOSIS I ONLY! - Happens during S phase - M and P chromosomes duplicate and form homologous chromosomes, which are made from sister chromatids - Throughout Meiosis 1, the pairs remain together  A diagram of a cell structure Description automatically generated Creation of Genetic Diversity - Recombination at pachytene (1) -- once synapsed together in Prophase 1, the non-sister chromatids from each homologue can undergo recombination - There is a crossing over event/recombination event -- at the chiasma, site of recombination - Crossing over creates diversity -- swapping genetic material at a section of the chromosome to make unseen before chromosomes - Takes place only in non-sister chromatids -- P and M, not P and P - The newly created genetic differences enter the next generation - Forms a hybrid or a recombinant chromatid, consisting of a mixture of the parental chromatids and their alleles - Random orientation of bivalents, ROB (2) - In Metaphase I - Once the chromosomes are aligned on the metaphase plate, they are pulled apart by the microtubules of the centrosomes. Centrosomes grab onto the kinetochores of individual pairs. - Centrioles send microtubules, which grab onto the kinetochores - Synapsed chromosomes (bivalents) align RANDOMLY on the metaphase plate -- determines which cell gets which duplicate of the chromosome. One cell may have blue-blue-red, the other red-red-blue - The orientation of the bivalents will influence which of the new cells gets which complement of chromatids -- either the P or the M pair of sister chromatids - All these different orientations and combinations are the reason for the diversity in the vast possible cells, which can be produced - Random orientation produces a vast majority of genetic diversity - In metaphase I, there is random orientation of BIVALENTS, in metaphase II, there is just random orientation because there are NO BIVALENTS - ROB, combined with the recombination in Prophase I create a lot of genetic diversity  Diagram of a diagram of a dna sequence Description automatically generated with medium confidence  Mendel's principles of independent assortment and segregation - ROB is the basis of Mendel's principles - SYNAPSIS = CROSSING OVER - Synapsed chromosomes (bivalents) align RANDOMLY on the metaphase plate - Each daughter cell receives only one copy of the parent homologous chromosome, while the sister chromatids remain together - In Meiosis I, the microtubules grab onto the fused kinetochores of the pair of sister chromatids, while in Meiosis II, the microtubules grab onto the individual kinetochores of each chromatid pair - Each daughter cell then enters prophase II -- chromosomes condense, and nuclear envelope breaks down and spindle fibres form - There is NO crossing over of homologous chromosomes, since there is only 1 copy present - Sister chromatids are no longer identical -- there are more ways to align - Microtubules of centromeres in Meiosis I attach to the kinetochores of each PAIR of sister chromatids -- the pair goes to each cell, while in Meiosis II, the microtubules attach to each INDIVIDUAL sister chromatid - MENDEL'S MAIN PRINCIPLES: - Based on ROB - Independent segregation of two alleles of the same gene. Either get A or a, depending on the random orientation. - Independent assortment of two genes on separate chromosomes -- gametes get either AB, ab, Ab, Ba. Genetic diversity - Because of ROB, a gamete in the son has a ½ chance of receiving the grand maternal or grand paternal chromosomes - So, with 23 pairs of chromosomes, it can get 2 \^23 possible combinations of the grand parental chromosomes Summary of meiosis - Prophase I -- homologous chromosomes pair and recombination happens, or crossing over occurs between them. Thus, some chromosomes are recombinants and some of parental type - Anaphase I -- One of each pair of homologous chromosomes is pulled to each pole. Random Orientation of the Bivalents leads to shuffling of maternally and paternally derived chromosomes. - Meiosis II -- sister chromatids, some of which are no longer identical, are divided into four haploid cells A diagram of cell division Description automatically generated Errors Can Occur - Non-disjunction -- chromosomes may fail to segregate correctly. Can happen in homologous chromosomes in meiosis I and on sister chromatids in meiosis II - Non-disjunction results in Aneuploidy -- results in gametes with abnormal chromosome number - Aneuploidy is defined as when the diploid number of the cell is not an exact multiple of the haploid number - Occurs 5% of times in human meiosis and results in nonviable embryos - Non-disjunction is the most common, but not the only cause of aneuploidy Examples of autosomal aneuploids - Autosomes are the non-sex chromosomes - Monosomy -- loss of a chromosomes, very rare, not compatible with normal development, shortened lifespan in Monosomy 21, usually only 1 example in live births of human. 2N-1 - Trisomy -- gaining of the chromosome, more viable than monosomy. Klinefelter Syndrome, Down syndrome (Trisomy 21), 2N+1 - Most common in chromosome 21 because it's the smallest, often doesn't get grabbed by the microtubules, so it just goes to the other side of the cell Examples of human sex chromosomes aneuploids - Monosomy: - 45X-Ullrich Turner syndrome - Loss of either an X or a Y, leaving only 1 X - Always female, short stature, webbed neck - Trisomy - Two very common examples - 47 XXY -- Klinefelter's syndrome, male with some feminized features - 47 XYY -- Nearly normal male phenotypically  A diagram of different types of chromosomes Description automatically generated SUMMARY - Mitosis -- somatic cells, produces chromosomally and genetically identical diploid cells from parental diploid cells - Meiosis -- germline cells, produces gametes with haploid sets of chromosomes from diploid cells, produces genetic diversity between gametes - Genetic diversity is created from meiosis -- Random Orientation of Bivalents includes independent segregation and independent assortment, also recombination of non-sister chromatids/crossing over Gene Segregation in Meiosis - Is synonymous with Gregor Mendel - Today, Mendel's first law of inheritance, the principle of Independent Segregation provides the basis of our understanding of gene inheritance - In today's terms, PIS states that the two members of a gene pair (alleles) segregate from each other during meiosis - The principle is based on the behavior of the chromosomes during meiosis - Mendel knew nothing about chromosomes, they hadn't been discovered when he published his work in 1866 - He concluded that his observed patterns of inheritance were under the control of Factors - The Chromosomal theory of inheritance was published by Sutton and Boveri in 1902, nearly 40 years after Mendel's publication Mendel's Method of Analysis - Performed carefully controlled crosses using Garden Peas - Used monohybrid crosses -- cross between two plants that differ by a single antagonistic trait/character (either one, or the other, makes it much easier to calculate phenotypes) - Used discontinuous traits, which have a distinct phenotype -- seed color and shape, plant height - Used pure-breeding parental lines for each cross: when two such individuals are crossed, the progeny/offspring is always the same as the parents for the trait in question - He was able to identify the First Filial generation, F1 -- offspring resulting from the monohybrid cross, and the second Filial generation, F2 -- offspring resulting from the self-fertilization of the F1 generation, or crossing of two F1 generations Key Findings and Terminology - In monohybrid crosses, hybrid F1 seed is indistinguishable from ONE of the parents - Dominant trait -- the trait of the antagonistic pair seen in the F1 - Recessive trait -- the trait of the antagonistic pair, which is NOT seen in F1 -- masked by the dominant trait - Reciprocal crosses -- showed that the parent, which contributed to the dominant or recessive form did not matter - A dominant character is dominant -- doesn't matter whether is paternal or maternal - White x Purple = Purple x White - Pollen from purple flower, put on white flower is the same as pollen from white flower, put on purple flower  Mendel's Model - Mendel proposed a model, now called the First Law: The Principle of Segregation - For each trait, every plant carrier two copies of a unit of inheritance (YY, yy, Yy....) - During reproduction, these two units (alleles) separate, and each gamete contains only one of these units. One P and one M - During fertilization, gametes unite at random to produce zygotes A diagram of a gene sequence Description automatically generated - Y masks the effect of y - F1 plants from a monohybrid cross are all genetically identical heterozygotes - F2 plants, however, segregate for genotypes and phenotypes - Punnett square illustrates the possible combinations of alleles that can rise in F2 - The Punnett square also shows the link between ROB and PIS  A diagram of a yellow and green color Description automatically generated with medium confidence - Y\_ - doesn't matter what the other allele is, it will express the Y in the phenotype Testing the Phenotype of Different Genetic Strains - Test crossing -- cross the strain in question with a pure-breeding recessive strain - How can you distinguish YY pure-breeding yellow peas from Yy hybrid yellow peas? - Is it homozygous double dominant, or heterozygous dominant? - Cross with a pure-breeding recessive strain homozygous(yy) - First case -- the combination is Yy, yellow. 100% yellow - Second cross -- one Yy and one yy -- there is a green pea from the hybrid original. Yellow:Green -- 1:1 - We can uncover the hidden recessive - y, which has been masked by the Y in the heterozygous individual  MOLECULAR BASIS OF DOMINANCE - DNA sequences can acquire mutations form differences between alleles - Wild-type gene: original gene sequence, which gets changed/mutated - If the mutation causes a beneficial effect, it's probably going to be retained in the population and offspring - Fitter individuals tend to be retained, and their DNA is passed to the next generations - There are allelic forms of a wild-type gene (original gene) - Mendel was clever -- he chose to breed pairs of antagonistic phenotypic traits -- constant, but mutually exclusive traits (one OR the other) - He also studied phenotypic traits that are controlled by a single gene, whose alleles showed complete dominance or recessiveness to each other -- easy to obtain and record results - However, most phenotypic traits involve more complex patterns of inheritance - Incomplete dominance or Codominance - A trait can be controlled by a single gene, but its alleles don't show complete dominance or recessiveness to each other. - Pleiotropy -- one gene may control several phenotypic traits. Vestigial *Drosophila* wings can't fly properly and affect egg laying - Polygenic -- traits that are controlled by multiple genes, most human traits are like that. Complex disorders, such as alcoholism, schizophrenia -- contributed to by a polygenic trait Types of Dominance - Complete dominance -- the dominant character is clearly expressed, shows which trait is dominant to which, one parental phenotype is seen - Incomplete dominance -- the hybrid isn't any like the two parents, A1 and A2 are incompletely dominant to each other. A new phenotype appears, none of the genes are clearly expressed. Each genotype has its own phenotype. - The phenotypic ratio is the same as the genotypic ratio -- 1:2:1 A diagram of a variety of animals Description automatically generated with medium confidence  - Alleles still segregate, but the phenotypic ratio isn't the same - Codominance -- the hybrid is a mixture from both parents -- both traits are expressed Molecular explanation of Incomplete dominance and dominance - With flower color, the A gene encodes a pigment producing enzyme - The A allele encodes a functional enzyme - The a allele encodes a non-functional enzyme - AA -- 2 functional alleles, red color, plenty of pigment - Aa -- partially functional alleles, pink color, less pigment - aa -- no functional alleles, white color, no pigment - With pea seed color, the Y gene encodes a chlorophyll degradation enzyme. - The Y allele encodes a functional enzyme - The y encodes a non-functional enzyme - YY -- 2 functional alleles plenty of enzyme - Yy -- 1 functional allele enough enzyme - yy -- 0 functional alleles no enzyme Codominance - BOTH parental phenotypes are seen in the F1 hybrid - As in incomplete dominance, the phenotype of the F1 heterozygous is distinct from the homozygous, and the F2 segregation of phenotypes is also 1:2:1 - Human blood type exhibits codominance - Alternative alleles of the "I" gene (Ia and Ib) encode enzymes, which add slightly different sugars to the cell membranes of RBCs. - In IaIb, both parental sugars are seen - Many genes have more than two alleles - These may show different codominance/recessive relationships between each other - Three alleles of the "I" gene control blood type in humans - Ia produces surface sugar A - Ib produces surface sugar B - I produces NO surface sugar - Mendel's principle of segregation still holds true - As usual, each individual carries 2 copies of the I gene, but there are 3 possible alleles, instead of 2 - Because there are 3 possible alleles for blood type, there are six possible genotypes: A table with black text and white text Description automatically generated  - There is I and there is Ia -- A blood group is expressed. Ia is dominant to i A table with text and numbers Description automatically generated with medium confidence - There is Ia and Ib -- both are expressed Ia is codominant to Ib Dominance Series - When there are numerous alleles for a gene, we can use pair-wise crosses to determine the dominance relationships between them - See which allele is dominant for each pair to establish a dominance series - For example, there are 5 alleles of the gene that determines seed coat patterns in lentils  A chart of different types of phenotypes Description automatically generated  Pleiotropy - One gene controls multiple phenotypes - In such cases, unconnected phenotypes can be inherited - Coat color and the recessive-lethal allele in mice and sickle-cell anemia - In mice: A close-up of several mice Description automatically generated - If we were to do a cross, - We never get AyAy homozygotes - Heterozygote cross gives phenotypic ration of 2:1 - Does this violate Mendel's Principle of Segregation? - 2:1 is the signature of a recessive lethal allele. It's a modification of the 3:1 ratio, not a violation. The AyAy mice were never born, so the phenotypic segregation is 2:1, but they are later found in the uterus of the mother - Sickle cell anemia: - Hemoglobin is composed of two types of polypeptides -- alpha and beta globin - An abnormal allele of the beta globin gene (Bs) causes an abnormal polypeptide to form - Homozygous BsBs causes many abnormal phenotypes -- more fragile, break easily, less flexible cells, cause clotting, flow less easily in the bloodstream, clogging, poor circulation, tissues become deprived of oxygen, - "Sickling" of red blood cells at low oxygen is perhaps the best known - Thus, co-inheritance of different phenotypic trait from one mutant allele - Bs allele persists in humans because it offers some resistance to malaria -- heterozygous advantage SUMMARY OF PATTERNS OF INHERITANCE - Dominance - Chromosomal segregation in Meiosis Mendelian patterns of inheritance 3:1 phenotypic and 1:2:1 ratios in F2 - Modification of phenotypes can occur due to factors, such as: incomplete dominance (1:2:1), Codominance (1:2:1) and lethal alleles (2:1) - BUT Mendel's principle of IS, based on ROB, still applies!!! COMPLEMENTATION IN DIPLOIDS 15/11/2024 Session 3 Allelic Forms of a Gene - A gene on a chromosome. Through different mutations, we get different allelic forms between the population - Alleles that enhance the function of the gene it's kept if beneficial, if not, it doesn't survive - Mutations in a population, sequence the gene, identify different mutations, just looking at one mutation, you build a tree, look at the function of the allele, how it's evolved and how the different branches of the gene have been retained - Pattern of Inheritance of two phenotypes controlled by 2 different genes obeys Mendel's second law -- two genes on different chromosomes segregate/assort independently from one another in meiosis. INDEPENDENT ASSORTMENT Terminology  - True breeding -- If it was a plant, when you grew the plant, the progeny would be identical to the parent, it breeds true Review of Principle of Segregation - YY x yy - Peas -- double dominant, crossed with double recessive - In the F1, we get the heterozygous class -- Yy. Combine gametes from homozygous parents to form heterozygous offspring - If we cross the F1 together, we place the alleles in the punter square and we get the alleles coming from the F1. Look at the segregation pattern in the F2 population - Dominant x recessive - Rules from monohybrid crosses - Monohybrid crosses result in a 1:2:1 ratio of genotypes - Result in a 3:1 ratio of phenotypes - Dihybrid crosses -- 2 genes controlling 2 different genes - Mendel crossed yellow round YYRR peas with green wrinkled yyrr peas - Gametes will be 2 dominant and 2 recessive classes - YR x yr form a mixture of dominant-recessive in the F1 - These alleles WILL segregate independently in the dihybrid cross - The gametes will be YR, Yr, Yr, yr - Some offspring will have recombinant phenotypes often not seen in the parental generation (green and round peas, yellow and wrinkled) - Again, this is because of ROB, each bivalent can orientate randomly on the metaphase plate - Mendel was smart/lucky to have worked on genes that were on separate chromosomes - If the genes were on the same chromosome, the only way for segregation would be by crossing over - We generate genetic diversity by Random Orientation of the Bivalents -- ROB - PIS -- Principle of Independent Segregation - Two alleles of the same gene, we can get Aa or aA - PIA - Principle of Independent Assortment - Two genes on separate chromosomes, when they assort, gametes can either get AB or ab, OR Ab or aB A diagram of a cell division Description automatically generated  A diagram of a diagram of a game Description automatically generated with medium confidence  For today: Dihybrid Crosses - During gamete formation, different genes segregate independently from each other when on different chromosomes - Determining the possible genotypes and phenotypes - By drawing out a Punnett square, we see - Segregation ratio: 9:3:3:1 -- 9 double dom., 3 single dom., 3 single dom., 1 double recessive (phenotypic) - Double dom. -- yellow round - Single dom. -- yellow wrinkled and green round (1 dominant gene and 3 recessive) - Double recessive -- green wrinkled - Crosses that obey the 9:3:3:1 ratio are obeying Mendel's Principle of Independent assortment - Can use a Punnett square to determine all possible genotypes and their phenotypes Branched-line Diagrams - Use a branched-line diagram to generate the probabilities for all possible genotypes resulting from the selfing of a YyRr - An alternative to Punnett squares - For example, we will look at the probabilities for phenotypes in the F2 generation, resulting from a dihybrid cross between the yellow round and the green wrinkled peas A diagram of a number of different colored lines Description automatically generated with medium confidence - When we start with the gene for color, we know that if we look at ONE character, they segregate 12:4/ 3:1. So, we've got ¾ yellow and ¼ green because yellow is dominant to green - After we look at the first class/gene, we look at the second gene -- shape - The shape is divided into ¾ round and ¼ wrinkled because round is dominant to wrinkled. ¾ of the phenotypes of the first gene will be round, and ¼ will be wrinkled - We multiply across -- 4x4=16, 3x3=9, 3x1=3 - For the green phenotypes -- 4x4=16, 1x3=3, 1x1=1 - 9/16 yellow round, 3/16 yellow wrinkled, 3/16 green round, 1/16 green wrinkled - We can generate the probabilities for all possible genotypes resulting from the selfing of the YyRr plant (genotype ratio -- 1:2:1)  Dihybrid Cross Genotypic Ratio A screenshot of a computer Description automatically generated - Phenotypic Traits are Often Controlled by More and One Gene - Polygenic - Polygenic inheritance is a large and complex topic and has 2 main points: - Complementation and the identification of genes controlling the same phenotype in Diploids - Interactions between genes, controlling the same phenotype -- Epistasis The Identification of More than One Gene Involved in Controlling the Same Phenotypic Trait - Use mutational analysis to identify genes involved in controlling the same trait - To do that, we need to: - Generate and identify sets of mutants - What is the relationship between mutations involved in the same phenotype? - Unknown mutant = X phenotype - Different unknown mutant = X phenotype - So, are these mutations in the same gene, or a different gene? -- big question - Complementation analysis is a key approach for deciding this - We need to know whether the mutant is the same as the other - Used in microbiology -- many metabolic pathways, enzyme key takeaways -- decided from microbiology Diploid Complementation - 2 Genes may have different functions in the generation of the same phenotype - Different genes may be mutants, they could both result in a change in phenotype - Wild type -- original, non-mutant gene - Both of these organisms are mutants, they both have the same mutated phenotype, so we assume that the mutations are the same just by looking at them - However, we see that they are on different genes - In reality, there are 2 different genes, which take part in this mutation pathway, shown by the picture - If we cross them together, we get alleles from each parent, carrying the mutation. We get mutant gene 1 from parent 1 and wild-type gene 1 from parent 2. Also, mutant gene 2 from parent 2 and wild-type gene 2 from parent 1 - This time, we have a WILD-TYPE PHENOTYPE - The mutation is complemented by the wild-type allele - Presence of one wild-type allele from both genes complements the mutation to give a wild-type phenotype  - A dominant mutation, by definition, is one that appears in a heterozygote - A good example is in *drosophila* body color: - We get *drosophila* flies with black body color and red eyes - 2 genes determine black body color -- e (ebony) and b (black) - \+ denotes the wild-type allele - When we cross 2 mutants with one mutation on the e gene of one fly, and the other on the b gene of the other fly, - We get a mutant ebony fly, with complementation between both mutant genes to get a wild-type phenotype - If the mutation was on the same gene, the offspring will carry it, we'd get a black progeny and not the wildtype - 2 mutant genes result in a wild-type phenotype - Mutations in the same gene -- same complementation group - Mutations in different genes -- different complementation group - Allelic mutations are mutations of the same complementation group, same gene Complementation Table Analysis A diagram of a table Description automatically generated with medium confidence  A diagram of a gene sequence Description automatically generated  - Drosophila mutants -- A,B,C,D,E,F,G - This is the type of test we do with different mutant strains - When there is complementation, a "+", the wild type complements the mutant, it rescues the wild-type phenotype. - When there is no complementation, a "-", the mutant alleles are the same, therefore the mutant phenotype is expressed - A and G's pairing -- the wild-type genes complement the mutations - A and F's pairing -- the mutant phenotype is expressed because the mutation is in the same gene -- there is no complementation to save it - The number of different complementation groups = the number of genes affected - In this case, we've got 3 groups without complementation the mutation is carried on by 3 different genes - If you get a new mutation, a fly with brown eyes, just cross it to an individual from each of the complementation groups, to see which gene has the mutation, or on its own group (a new gene that's been mutated) Summary A diagram of a fly Description automatically generated - Different allelic forms of a gene can restore wild type WORKSHOP EXERCISES: WORKSHOP 1: MEIOSIS  A questionnaire with red and black text Description automatically generated - ROB is a very key function of creating genetic diversity - Genetic diversity enables for different phenotypes in progeny/offspring - ROB, crossover during meiosis... - Filial1 is derived from the crossing of the 2 parents, - Filial2 is derived from the crossing of the F1 generation - When there are base changes in the allelic forms of a gene, each of those can be considered polymorphism  WORKSHOP 2: Dominance and Complementation in Diploids A paper with text on it Description automatically generated  - Dosage effects -- you have more and 1 copy of a gene, more gene products produced A screenshot of a test Description automatically generated  - For an O group child, we need both heterozygous parents, so that the i0i0 double recessive genotype is present in the child - AB group doesn't provide the i0 gene for the child to be blood group 0 A group baby test Description automatically generated - Look at the obvious ones - AB blood group can't be achieved if a parent has a 0 group A x AB gives AB 25% of the times  - Father is a carrier of the I gene, but is group A his gene is IaI0 A screenshot of a question Description automatically generated  - HDHD die a lot sooner the father is older than 45, so he must have an HDhd genotype. - We do a test-cross (with recessive hdhd) and because HD is dominant, there is a 50% chance - ½ for the man AND ½ for the son A screenshot of a test Description automatically generated -  A screenshot of a test Description automatically generated  A diagram of a diagram with red circles and lines Description automatically generated