Genetics Exam 1 Study Guide
Genetics Exam 1 Study Guide 85033 - GEN 3000 - 002
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85033 - GEN 3000 - 002
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This 15 page Study Guide was uploaded by Toni Franken on Saturday January 23, 2016. The Study Guide belongs to 85033 - GEN 3000 - 002 at Clemson University taught by Kate Leanne Willingha Tsai in Summer 2015. Since its upload, it has received 355 views. For similar materials see Fundamental Genetics in Biomedical Sciences at Clemson University.
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GEN 3000 – Exam 1 2016 Study Guide Dr. Tsai, Clemson University Exam 1: Chapters 1 – 4 Modeled around Dr. Tsai’s recommended subjects to study – color coded/organized by chapter. Chapter 1: Introduction to Genetics 1. Heredity is the basis of genetics, regardless of what definition you look at. 2. Types of Genetics We will be looking at: Transmission Genetics: Mendel’s work (peas), generational genetics. Genetic information passed from one generation to the next. Molecular Genetics: The fine details within the big picture. The “why?” and “how?” – Involves DNA Replication>transcription>translation(RNA)>protein creation. This process is the central idea. Population Genetics: Genetics on a broader scale that spans multiple generations of a population. This is especially relevant in the work of Darwin and theories of evolution. 3. Model organisms and their importance: Model Organisms Used in Genetic Studies: It is important to see that there are a multitude of organisms than can and do get used for studies of human diseases and disorders without using actual human subjects. The following are some of the common ones, which we discussed in class. E.coli: used to study colon cancer and other cancers. S. Cerevisiae: used to study cancer and Werner Syndrome. D. melanogaster: used to study disorders of the nervous system, as well as cancer. C. elegans: used to study diabetes. D. rerio: used to study cardiovascular disease. M. musculus: used to study LeschNyhan disease, cystic fibrosis, fragileX syndrome, among others. Canis lupus familaris: Aka the dog used to study genetics in general. 4. The early theories of heredity and transmission Pangenesis: The early idea that specific particles (called gemmules) carried information from all over the body to reproductive organs to be passed to the embryo at conception. At this time, sperm and egg hadn’t been visualized, but the concept of gemmules was similar to gametes. The term gene, did, however, come from this early theory. This idea led to the idea of inheritance of acquired characteristics Inheritance of Acquired Characteristics: The idea that learned skills and trades could be passed onto offspring. Later found that they could not, only genotypic information can be passed on. Preformation: The idea that inside egg or sperm is a tiny version of an adult (this tiny person was called a homunculus). Fertilization allows it to grow and develop. Originally the homunculus was thought to be in the sperm, then maybe in the egg. Then, the idea of blending inheritance was born. Blending Inheritance: The idea that offspring are a blend of both parents, and contain traits from each. 5. Influential People in the History of Genetics and their Major Contributions: Robert Hooke: Invented and used the early microscope to discover the cell. This allowed for the visualization of gametes, which led to the concept of Preformationism (see above). Schleiden and Schwann: Developed the cell theory – the idea that cells are the basic unit of all living things, and they divide and arise from preexisting cells, even on the single cellular level. Helped to push the idea that there is no such thing as a sudden appearance of an organism. Darwin: Developed the theory of evolution through natural selection. (His published work was “On the Origin of Species”). Established that heredity is the fundamental of evolution, and created the idea that evolution and natural selection are based on the passing of genes. Gregor Mendel: Worked around same time as Darwin. Discovered basic principles of heredity using pea plants and the analysis of their patterns of transmission in the mid 1800’s. However, this work went largely ignored until the 1900s. Walter Flemming: Observed the division of chromosomes. Then it was discovered in 1885 that hereditary information is contained in the nucleus. August Weismann: The idea of inheritance of acquired characteristics was hard put to die out. So, Weismann experimented by cutting off the tails of mice for 22 generations. This showed that tail length did not change in subsequent generations. The germplasm theory was then developed, which suggested cells of the reproductive system carry complete sets of information. The idea that the sperm and egg carry preexisting information. Sutton: Credited with developing the Chromosomal Theory of Inheritance, or the idea that the genetic material in living organisms is contained in chromosomes. Chapter 2: Mitosis and Meiosis 1. Prokaryotes versus Eukaryotes and viruses: There are 3 major groups of life: eubacteria, archaea, eukaryotes. Eu = “true”; Pro = “pre”; Karyote = “nucleus” All organisms have different numbers of base pair genomes, but that number doesn’t necessarily denote complexity. Prokaryote: Has a cell wall and a plasma membrane, contains ribosomes and DNA. Tend to be small and less complex. Contain no membranebound nucleus or organelles. It includes the classifications of eubacterium and the archaebacterium. Archaebacterium contain characteristics of bacteria and eukaryotes. Eubacteria = true bacteria. Generally reproduce asexually through binary fission. o Reproduction: Contains a single, circular chromosome attached to the plasma membrane. The chromosome begins to replicate, and the plasma membrane grows, causing two chromosomes to separate, followed by separation of organism into two individual cells. Each cell is identical. Eukaryotes: Tend to be relatively large and complex with multiple linear DNA molecules. Contain membrane bound organelles, nucleus, and a cytoskeleton. Includes fungi and larger, multicellular organisms. Usually reproduce sexually. o Reproduction: Eukaryotes typically have 2 sets of chromosomes per cell as a result of sexual reproduction. One set from mother, one from father (called homologous pairs). Viruses are NOT cells. They contain a viral protein coat, and a core of genetic information. They can only reproduce inside of a host cell, and it has been discovered that most viruses are closely related, according to genetic sequence, (evolutionarily) to their host. 2. Ploidy: In sexual reproduction of eukaryotes: If there are 2 sets of genetic information, a cell is diploid (2n – most eukaryotic cells). Most cells are diploid in eukaryotic organisms. If a cell has only 1 set of genetic information, it is haploid (1n – reproductive cells.) Only reproductive cells are haploid. 3. Chromosomes and their Structure: Centromere: Can be located anywhere along the chromosome length. It is incredibly important, because without it, you can lose that chromosome. It is a landing spot for the kinetochore that will form and be instrumental in the movement of chromosomes. We also use the centromere to count chromosomes. If you have a distinct centromere, we have a distinct chromosome. Two sister chromatids, a duplicated chromosome and its partner, are attached at the centromere. Both chromatids together are considered one chromosome. o There are four major types of chromosomes classified by centromere location: Metacentric – divided equally by the centromere. Submetacentric – a short arm (p arm) and a q arm (long arm) towards the middle of the chromosome. Acrocentric – very very small p arm (all dog chromosomes, except sex, are acrocentric). Telocentric centromere at very end of the chromosome, no p arm. Telomere: End of a chromosome – acts as a cap that protects the chromosome (like a shoelace tip). You don’t want to lose your telomeres. They are essential on each end of your chromosome. 4. Cell Cycle: The cell cycle is split into two major parts: The Interphase and the M phase, or Mitosis. The majority of a cell’s life is spent in Interphase where it grows and functions as a normal, healthy cell. Interphase: ~ 15 hours 1. G1: Cell is metabolically active, functioning as a cell. No time limit. This is where the cell grows. ~ 5 hours 2. G0: Arrested, nondividing stage, short. Sometimes cyclical and repeats. 3. G1/S checkpoint: Beyond this point, the cell is committed to divide. It is going to take inventory and make sure it is healthy and large enough for division. 4. S: Genetic information is replicated. The diploid cell gets copied, but does not change its diploid status. ~ 7 hours 5. G2: Checking health, make sure it has finished replicating the DNA ~ 3 hours 6. G2/M checkpoint: Check health, then enter M phase. M Phase (Mitosis/Cell Division): ~ 1 hour 1. Prophase: ~ 36 minutes 2. Metaphase: ~ 3 minutes 3. Anaphase: ~ 3 minutes 4. Telophase ~ 18 minutes 5. Mitosis: Produces Diploid Cells. Mitosis occurs regularly in the body, such as in bone marrow and blood production, or inside the lining of the gut. New cells are created through mitosis. There are some exceptions, such as mature neurons, which don’t usually undergo a full cell cycle. DNA is ALREADY REPLICATED AT THIS POINT. Phases and important events 1 Prophase: The already replicated chromosomes condense, and the mitotic spindle forms from the centrosomes. These centrosomes are only present in animal cells, and will not be found in plants. During this phase, we’re looking at diploid cells – each chromosome consists of 2 sister chromatids. We’ll see the centrosomes start to move to opposite ends of the cell, and they organize the spindle fibers, which are also called microtubules or microtubular filaments. The nuclear membrane, also called the nuclear envelope, begins to break down. 2 Prometaphase: The nuclear envelope disappears completely, and microtubules contact the chromatids. They will attach at the centromere of each chromosome, and then will be able to move them. Once contact is established, they will either lengthen or shorten to move the chromosomes to the metaphase plate. 3 Metaphase: Trigger word – Middle. Spindle fibers arrange the chromosomes in a single plane called the metaphase plate. Unlike in Meiosis, which we’ll look at later, the chromosomes don’t care what the other chromosomes are doing. 4 Anaphase: Trigger word – Apart. Sister chromatids are separated, and they move toward the opposite poles creating separate chromosomes. This separation is called disjunction. If they do not separate, this is called nondisjunction. 5 Telophase: Trigger word – Twins. Chromosomes arrive at spindle poles, and the nuclear membrane reforms to form 2 nuclei. The chromosomes begin to disappear from view. If everything has gone properly, they will be exact copies. Cytokinesis: The division of the plasma membrane and organelles – considered to happen at the same time as telophase, and some consider it part of telophase, while others say it is a separate phase itself. Spindle fibers: o Spindle fibers are going to connect to the centromere to form the kinetochore. Spindle fibers are made up of tubulin subunits that can be added or removed according to which direction they need to move. There are molecular motors that help with this. They’ll lengthen by adding subunits, and shorten the tubules by removing subunits. This process is ESSENTIAL. If the spindle fibers cannot change length, the process will halt and kill the cell. o Some drugs specifically target spindle fibers to freeze them, or prevent the molecular motors from working, which forces the cell to shut down. This is used commonly in cancer treatments. If something happens and a single fiber breaks, the process of disjunction won’t work properly. You can end up with something like Turner syndrome (lacking a Y chromosome, or a second half to the X chromosome). Has consequences on the cell, and is usually fatal. 6. Meosis Unlike Mitosis, which produces diploid gametes, Meiosis produces haploid gametes. It has two round of Prophase, Metaphase, Anaphase, and Telophase instead of 1. The first round of meiosis is considered the reduction division, where the cells are reduced from diploid to haploid, and stay as such through the second round. The second round of meiosis is more like mitosis with sister chromatid separation. Phases and important events: 1 Prophase 1: Starts a lot like mitosis where the chromatin condenses, and the nuclear envelope begins to break down. Unlike in mitosis, homologous chromosomes from mom and dad line up together to create a synapsis (very close association). These two sets of chromosomes are also called a tetrad, or bivalent. There are 4 chromatids total in this junction, two sets of sister chromatids. CROSSING OVER TAKES PLACE IN PROPHASE 1! Crossing over is where, at a chiasma (direct contact of chromatids), genetic material is physically broken and swapped as the homologous, nonsister chromatids entangle. The chromatids will then have pieces from both parents, creating four unique chromatids Crossing over, as far as we’re concerned, is between nonsister chromatids. Nonsister chromatids are the same in overall genetic information, but their alleles may contain different characteristics. Even if sister chromatids swap information, we would be unable to tell genetically due to identical genes. Can take place many places along the length of chromosome 2 Metaphase I: The homologous pairs of male and female chromosomes are still attached. They line up together in the middle via microtubules along metaphase plate. Every time the homologous pairs of chromosomes line up to divide for a meiosis cycle, the chromosomes can line up in a different order, with different parent chromosomes on either side of the metaphase plate. This results in a multitude of genetic possibilities. The number can be calculated with 2^n, where n = number of homologous pairs. Humans have 23 sets of chromosomes, which results in over 8 million different combos. 3 Anaphase I: Homologous pairs of chromosomes are separated, causing a reduction in the number of chromosomes. THIS IS WHERE THE CELLS BECOME HAPLOID. 4 Telophase I: This phase is not the same across every organism and species. The chromosomes will be at opposite poles in separate cells, but not all form a complete nuclear envelope. Some will form partially, others completely. 5 Prophase II: Chromosomes recondense, and the nuclear envelope breaks down. 6 Metaphase II: Like metaphase of mitosis, chromosomes align in no particular order on the metaphase plate. 7 Anaphase II: Sister chromatids separate, each forming a separate chromosome. 8 Telophase II: Chromosomes arrive at spindle poles, nuclear envelope reforms, and cytoplasm divides. Should result in four genetically distinct cells. Genetic variability: Cells produced from meiosis are genetically distinct due to crossing over (creating sister chromatids that are not identical), as well as random distribution of chromosomes in Anaphase I due to random line up in Metaphase I. Unequal division: In meiosis, the result is usually 4 genetically distinct cells. Human females are an exception to this rule. o Both a male and female start with a diploid cell (arise from spermatogonium or oogonium). Sperm goes through process of meiosis without any deviation. However, on the female side, there is a difference. o On the nuclear level, meiosis occurs as expected. But, at the end of meiosis I (which occurs in the embryonic ovary and freezes), there is unequal cytokinesis. All the possible extra cytoplasm that can be deviated to once cell will be to create the secondary oocyte. The smaller half is called the first polar body, and will not become an actual gamete. o Upon ovulation, the secondary oocyte formed in Meiosis I will then undergo meiosis II, and once again has unequal cytokinesis, creating 1 viable 1n ovum, and a second polar body. The cycle will stop here unless fertilization occurs. Chapter 3: Mendelian Genetics Mendel 1. Definitions Gene: A genetic factor that is responsible for determining characteristics – Johannsen established the term “gene” from the original term of pangenesis. Allele: One of the possible forms of a gene. In Mendel’s experiments, the same gene with a different allele was what produced the two different colors of pods, or wrinkled versus round, as well as the other varied characteristics. Locus/Loci: A location on a chromosome where an allele is located. Genotype: The set of alleles than an individual possesses. Can be heterozygous or homozygous. This is the ONLY thing that is inherited. Phenotype is not (see below). Heterozygote: An Individual with two different alleles at a locus. Homozygote: An individual with two of the same allele at a locus. Phenotype or Trait: The appearance or manifestation of a character – this is equal to the genotype combined with the environmental factors that contribute. Character or characteristic: An attribute or feature. Blue or green eye color, etc. Homologous chromosomes can have alleles that occupy the same locus, but may have different characteristic exhibition. This is true across species. 2. Mendel experiments Crosses: o Started with a monohybrid cross, or two pure parents that had one characteristic opposite of each other, such as two tall plants with green pods and seed coats, but one plant had a smooth seed coat, the other wrinkled seed coats. He did this to look at one characteristic at a time. (Ex: RR x rr) o Later did dihybrid crosses, or two parents that exhibited two characteristics purely. The genotype for one parent would be RRYY, dominant homozygous dominant for two characteristics, and the other parent would be rryy, homozygous recessive for two characteristics. o Reciprocal cross: The concept that, when experimenting, crosses in both directions are done. An example would be where first the female plant would have the wrinkled seeds, then the second time the male plant would have the wrinkled seeds. By doing this, Mendel showed that inheritance was independent of the sex of the parent. o Backcross: Experimental action where an offspring is fertilized back to a parent individual. Can be done with either parent. o Test cross: Cross of a dominant expressing individual of unknown genotypic makeup (R_) to a heterozygous recessive individual (rr) to see what offspring are produced. This allows us to determine the second allele in the individual with a dominant trait. A test cross MUST be done with a homozygous recessive individual. If there is a 50/50 split of offspring with dominant and recessive traits, a test cross shows there is a recessive allele with the dominant in the test plant (Rr). If there are only dominant traits in the offspring, the test plant is homozygous dominant (RR). Dominance: Mendel hypothesized that Dominant and Recessive traits existed, and that those that disappeared were recessive and required 2 of them to show in the phenotype. That’s why one trait present in the P (parent) generation disappears in the first filial generation (F1), and returns in F2. Principle of Segregation: Mendel determined that the alleles had equal genetic opportunity in hybrid, or heterozygous, individuals. He suggested that the genes are separated into the gametes where each parent only contains 1, and they have equal opportunity to be passed on. Principle of Independent Assortment: The idea that, during gamete formation, the different alleles (different forms of the gene in question) do not impact each other. 3. Punnett Square: Developed by R.C. Punnett in 1917 Allows us to quickly determine the possible genotypic and phenotypic ratios based on parental allele contribution. For a cross of Rr x Rr, a simple Punnett Square would look as follows: Both parents heterozygous R (round) r (wrinkled) (phenotypically round seeds) R (round) RR (homozygous dominant/round) rR (heterozygous/round) r (wrinkled) Rr (heterozygous/round) rr (homozygous recessive/wrinkled) 4. Phenotypic and Genotypic Ratios: Monohybrid crosses: Two heterozygous parents (Rr x Rr): 1:2:1 Genotypic ratio, (1RR, 2Rr, 1rr), but a phenotypic ratio of 3:1 (3 dominant, 1 recessive). Heterozygous parent crossed to a homozygous parent (Rr x rr): 1:1 Genotypic ratio (2Rr, 2rr), with a phenotypic ratio of 1:1 (2 dominant, 2 recessive). Two homozygous parents crossed (RRxrr;RRxRR,rrxrr): Uniform progeny result, phenotypically and genotypically. In other words, all offspring will be dominant in (RRxrr or RRxRR) or all recessive in (rrxrr). If the genotype in such a cross cannot be determined, it is shown with an underscore as the second allele (R_). Dihybrid crosses (phenotypic only): The genotype for one parent would be RRYY, dominant homozygous dominant for two characteristics, and the other parent would be rryy, homozygous recessive for two characteristics. o The F1 generation, once again, shows that all are heterozygous for all traits (All RrYy). o The F2 generation, when crossed with various possibilities, produced a 9:3:3:1 phenotypic ratio. (9 with 2 dominant traits; 3 with the first dominant, and second recessive trait; 3 with the first recessive, and the second dominant trait; and 1 with only recessive traits). 5. Branch Diagram: Another method to determine heredity in a dihybrid cross is the use of a branch diagram, also called a fork diagram. You need to know within each gene what ratio you’re expecting in order to use it accurately. Expected ratios of tMultiplication of each second loci only expected ratio in the Expected ratios of the 9/16branch first loci only 3/4 Y_ R_Y_ Parent Cross 3/4 R_ 3/16 1/4 yy RrYy x R_yy RrYy 3/4 Y_ 3/16 rrY_ 1/4 rr 1/16 1/4 yy rryy 6. Probability: Multiplication Rule: o The multiplication/product rule is used any time you are asking AND, where you have independent events, and you want to figure out the probability of these events happening one after the other. The events MUST BE INDEPENDENT OF EACH OTHER. You then multiply the probability of each individual event to the other. AND = MULTIPLICATION o Example 1: In a coin toss, there is a ½ chance of getting heads the first time, and ½ chance of getting heads the second time. If you want to know how probably it is to get heads the first AND second time, you multiply ½ x ½ to get ¼, or 25% chance of getting heads both times. o Example 2: The multiplication rule can be applied to hybrid, dihybrid, or even greater crosses. The easiest way to work with probability in larger crosses is by looking 1 loci at a time (In other words, when looking at RrYy x RrYy, only look at the R’s first, then the Y’s). How likely is it the offspring will have the genotype rryy? First, we look at the R loci. In parent 1, there is a ½ chance to get the r, which is the same as parent two. Since we’re looking for r AND r, we must multiply the two probabilities together. ½ x ½ = ¼ chance of getting an rr. If we look at the Y loci, there is a ½ chance to get the y out of both parents, allowing us to do the same process of ½ x ½ = ¼ chance of getting y AND y. However, we need to get rr AND yy. Since we need both of these combinations, we must multiply the probability of each loci occurring (which we just found) as follows: ¼ x ¼ = 1/16 chance to get the genotype of rryy. Addition Rule: o When two mutually exclusive events are connect by an “either” or an “or,” we must use the addition rule. In other words, if two evens can happen separately, and do not rely on each other, we must add the probability of each individual event happening together. o If we are wondering what the probability of getting heads OR tails of a coin flip, we would take ½ + ½ = 1, or 100%. o If we look at a die, and we want to see what the probability of rolling EITHER a two OR a three is, we look at each one. We know, with 6 sides, the probability of rolling a two is a 1/6, as is the probability of rolling a three a 1/6. Since we’re using the addition rule, we must add them together to get 1/6 + 1/6 = 2/6. NOTE: 2/6 can then be simplified to 1/3. ALL FRACTIONS SHOULD BE SIMPLIFIED. 7. ChiSquare: To rule out errors as a cause of variation from probability when conducting experiments, we use the chi square test. It won’t tell you where you went wrong, only the likelihood that the difference between what was expected (probability) to what actually happened was due to chance. What the Chisquare test DOES: Uses found values to determine the probability that a number different than what was expected is due to chance. What it DOESN’T do: Tell you where the problem is. Tell you if the cross has been done correctly. Tell you if your results are correct 2 (¿observed−¿expected) The formula for the Chisquare test is x =∑ ¿expected Degrees of Freedom: We will then cross reference what is found using the chisquare test with the degrees of freedom (n1) on the chart of critical values for the chisquared test. We must take the number of possible outcomes, and subtract that number by 1. For instance, in a single allele cross (TtxTt), there is a phenotypic ratio of 3:1 dominant to recessive. Therefore, there are only two possible outcomes. Our degrees of freedom will be 21 = 1. This is on the left side of the chart we reference. Once we have our value and our degrees of freedom, we go to the left, and look at the row for degrees of freedom to see where the value from our chisquare calculation falls according to the numbers (P) along the top of the chart. If our P value falls above .05, or 5%, there is a greater than 5% probability that variation from expected outcomes is due to chance. If our P value falls below .05, there is less than a 5% chance that variation from expected outcomes is due to chance, and we must go back and see where our experiment went wrong. In an experiment, we start with something called the null hypothesis0(H ). This hypothesis cannot be proved as correct, but can either be rejected by showing data to be faulty (variable due to something other than chance), or fail to be rejected. o If the P≥.05, we fail to reject the null hypothesis, because the experiment variation was probably due to chance. o If the P≤.05, we reject the null hypothesis, because something went wrong, and our values vary from the expected outcome due to something other than chance. Example: A cross of pea plants that are known to be RrYy x RrYy for the traits of tall (R), short (r), yellow pods (Y) and green pods (y) should yield a ratio of 9/16 tall with yellow pods, 3/16 tall with green pods, 3/16 short with yellow pods, and 1/16 short with green pods – so, if we get 36 offspring, in numbers we should have 18, 6, 6, and 2, respectively. Instead, we get 15, 9, 7, and 1, respectively. Is this due to chance? o Degrees of freedom: n1 = 4 possible outcomes (combos of tall/short and yellow/green) – 1. We have 3 degree of freedom. o X value: Must be done for each possibility: Of tall with yellow pods = (15 – 18) /18 = .5 2 Of tall with green pods = (9 – 6) /6 = 1.5 Of short with yellow pods = (7 – 6) /6 = .167 Of short with green pods = (1 – 2) /2 = .5 Total: 2.667 2 o Cross reference the degrees of freedom (3) with the X value (2.667) to find a P value. In this case it is between .5 and .2, which means P≥.05. We can safely assume that this variation is due to chance, and fail to reject the null hypothesis. 8. Pedigree Analysis: Identification: Male Female Unknown/Unspecified P P P P Sex Unaffected individuals Affected individuals Obligate carrier: not affected, carries trait Asymptomatic carrier: Has trait, but is unaffected for now. Multiple individuals 3 3 represented (3) 3 Deceased Individual Proband: The first affected family member coming to attention of genetics Family history of individual is unknown ? ? ? Family: In this case, a father, mother, and four children (in order of I birth from left to right). Note: the roman numerals on the left represent generation numbers. II Adoption: If an offspring is adopted, it is shown in brackets. A dotted line goes from its adoptive parents, and a I solid line from its biological parents in a separate family line. II Twins: From Right to left: Identical, nonidentical, and unkown if identical or nonidentical. ? Consanguinity: Mating between related individuals. Represented by a double line connection. I II Determining genotypes: o Genetic diseases within the human population are often more rare, particularly autosomal recessive disorders. They are, instead, more commonly seen in animaIIIedigrees. o Recessive traits or diseases: Recall that, when looking at a recessive gene, there must be two recessive alleles present in order to see the phenotype, making it less commonly seen. A recessive disease often skips generations in a pedigree chart. If there is an affected offspring, both parents HAVE to be carriers, or also affected by the disease. Recessive diseases tend to be rare, even within a family. If there is a huge skip of generational appearance, and then suddenly a very common appearance of a disease, there is probably some level of consanguinity (mating of related individuals). More commonly associated with animal pedigrees o Dominant trait or disease: Genetic diseases can also be caused by dominant alleles, meaning that only one copy of the allele is needed to get an affected offspring. Every generation is going to have an affected individual. If two affected individuals produce an unaffected offspring, that offspring must have recessive alleles only, and will NOT be able to pass on the trait unless someone new brings it into the genetic line. Generally speaking, affected individuals are going to heterozygous instead of homozygous for the allele. Probabilities: Play a huge role in pedigree analysis, and the possibility of two individuals resulting in an affected child. o Example: A male individual with a family history of a recessive disease, but who is not affected himself, is to have an offspring with a female individual. They want to know what the likelihood of their offspring having the disease will be. o The disease is autosomal recessive, meaning two recessive alleles must be present in order to be expressed. Since the male is unaffected, he either has Dd, dD, or DD, and no possible chance of being a dd (therefore we can eliminate this from possibility). Therefore, dad has a 2/3 chance of carrying the affected gene. o Mom’s history is very important in this case. She is unaffected, so if there is no history of the disease in her lineage, we can assume that she has a DD genotype, and the offspring will have no chance of being affected due to the impossibility of a dd phenotype. However, if mom does have a genetic history, we must go back through her lineage to determine the likelihood of her having the disease. So, let’s say her parents are unaffected, but she does have a sibling that is affected. This means both of her parents carry the d gene, meaning she has a 2/3 chance (just like dad) of being a carrier. Then, should they produce an offspring, and they were both carriers, that offspring would have a ¼ chance of getting two d alleles. All three of these probabilities have to happen, meaning we must take 2/3 x 2/3 x ¼ = 4/36 = 1/9 chance of the child being affect. Chapter 4: Modification of Mendelian Ratios: 1. Alleles: Allele: Different forms of the same gene (Eye color: allele for brown or an allele for blue). If the allele loses its ability to work properly, it has a lossoffunction mutation. Lossoffunction mutation: A partial loss of function (black pigmentation: loses some capability to create the black color, so a grey color results. Loses color partially) Null allele: Allele is not working at all. (black pigmentation no longer causes black coloration.) Gainoffunction mutation: The allele is working so much the offspring ends up gaining more work for the protein, or doing it at the wrong time. (black pigmentation is showing up in the wrong spot, or is just a very dark color) Change of function/neutral mutation: alleles can change function as well. This is a neutral mutation that doesn’t affect what happens normally, but it does something else. Gene Interaction: Some genes interact together to create different possibilities. This can cause a great deal of phenotypic variation. Xlinkage/Ylinkage: Sexchromosome linkage Pleiotropic Gene: A gene that can affect several aspects of the overall phenotype 2. Symbols: So far when differentiating alleles, we’ve been using capital and lowercase letters. However, this nomenclature isn’t always applicable. o Wildtype allele: Allele that is considered the most common in a population. Example: Red eyes in the fruit fly are normal. Anything that alters that is mutant. We no longer indicate if it is dominant or recessive, we consider it + or , where + is the wild type, and the – is for the mutant. o You can also distinguish between different alleles with superscripts – allele 1 and 2 for example. R or R – two forms of the allele. 3. Incomplete dominance: When Mendel set up his experiments, the offspring of two parents looked like one parent or the other. However, it doesn’t always work that way, because sometimes the parent traits combine to create a completely difference characteristic. If we had homozygous of each parent of a certain colored eggplant (PP(dark purple) x pp (white)), All of the offspring (Pp (violet – lighter purple)) have characteristics of both parents, creating an intermediate color. Then, in the second generation (Pp x Pp = 1PP:2Pp:1pp), you get three different genotypes, and three different phenotypes. 4. Codominance: Codominance is different than incomplete dominance. Instead of a blend, you clearly see the M effecN of both alleles aM oMce. AN eNample of this is a blood antigen group. There are two different aMleNes: L and L . Homozygous (L L or L L ) are only going to produce one antigen, while a heterozygous (L L ) allele combo produces BOTH M and N antigens. An exception to strictly codominance: Sickle Cell Anemia. This disease can be classified differently depending on how you look at it. Individuals that are heterozygous will have some of both cell shapes (wild type round, mutant sickle). You can distinguish between both alleles and they don’t block the production of one another. When taking the blood sample, you could consider this a codominance due to the visible effect of both alleles. But, if you look at the individual patient (not just their blood), they must be homozygous recessive to actually be considered to have sickle cell anemia. Heterozygous generally have no phenotypic effect on the health of the individual. This could result in the disease being considered recessive. 5. Multiple alleles: Genes can have more than just two alleles. Within any giving individual, there will be two alleles (one from each parent), but within the population in total, there can be numerous alleles. Most commonly recognized example of this is the ABO blood group, which has three alleles. First is the A A B allele (I ) for the A antigen. The second is the B allele (I ) for the B antigen. Then, there is the O allele (i) that simply makes no antigen. The O allele, i, is recessive to both I and I , while I and I are Codominant. This results in various combination possibilities: O blood type has to be ii since it is A B recessive, and AB blood type has to be I I to express both antigens. However, when only one antigen is expressed, the genotype may be I i, I I , I i, or I I . O (ii) is the universal donor to blood types since it is A B lacking antigens. AB (I I ) is the universal recipient, because it is used to both antigens, but can also receive the O type that lacks antigens. Some genes have a great many allele possibilities. In the Drosophila, the fruit fly, there are at least 100 allele combinations for the eye color. They are all designated with w , where n is any of the many allele designations. 6. Lethal alleles: Alleles that will cause death in certain expression Recessive lethal: Cuenot began to do crosses in mice to try to replicate Mendel’s work. He set up his experiment the same way that Mendel did, and found that there was a 3:1 ratio (just like pea plants in Mendel’s experiments) between gray (dominant) and white (recessive) mice when crossed. Then when he tried a different phenotype (Yellow crossed with gray), he was getting no truebreeding yellow mice, and was getting a 2:1 ratio of yellow to gray instead of 3:1 because ¼ of the mice were dying at birth. o It turns out that this yellow allele in mice is a pleiotropic gene: a gene that can impact several aspects of the overall phenotype. When looking at the phenotype, the Yellow gene appears dominant. However, if two copies of the Y were present, the mice were not born alive. Therefore, the homozygous dominant gene (YY) is lethal. o Note: even though lethality is related to a dominant gene, the lethality itself is recessive, because it is “hidden” in heterozygous mice (Yy). 2/3 of live progeny are Yy yellow, 1/3 of progeny are yy, nonyellow. o Another example of lethality is the manx phenotype in cats (lack of a tail). The M allele is the lethal allele in the cat, and it stops the spine from developing properly. The M allele is the normal L L one. If only one copy of the M gene is in the animal (M M), it is nonlethal, and only the tail is missing. However, if two copies of the M are present (M M ), it is embryonically lethal, making it recessively lethal for the dominant allele. Dominant Lethal: There are also examples of dominant lethal alleles, which can only happen and survive in a population if lethality is late onset (after an organism is able to reproduce). o An example is Huntington’s disease. It only takes one copy of the dominant allele to cause lethality in humans – H H, H H , or HH are all lethal 7. Epistasis: Where the occurrence of one gene will completely hide what’s going on at another gene. Recessive Epistasis: A common example of this is in Labrador retriever coloration: Black, chocolate, or yellow. The first gene (B or b) is the actual pigmentation of Black (B) or brown (b), where B is dominant to b. The second gene is responsible for attaching pigmentation to hair color, but is only functional at dominant E, and nonfunctional at recessive E. o Black genotypes: (BBEE, BbEE, BBEe, or BbEe); Chocolate genotypes: (bbEE or bbEe); and Yellow genotypes: (BBee, Bbee, bbee). o As long as there is an E present (which is dominant to e), the pigment will be attached to the hair. If it is homozygous for e, then the allele is nonfunctional, and adds no pigment. This e is our epistatic gene, which will mask the effect of B or b, the hypostatic, or hidden, gene. o How does this affect our ratios? We cross two homozygous pure animals (BBEE x bbee). Our F1 generation will produce an entire generation of black puppies due to presence of B and E in all. Then, in the F2 generation, we have 9:3:4 ratio of black(B_E_):brown(bbE_):yellow(_ _ ee). As a side note, you can distinguish between a BBee/Bbee and bbee – the BBee/Bbee will be a yellow lab with a black nose, and the bbee will be a yellow lab with a brown nose, giving us the expected 9:3:3:1 ratio. o Bombay Phenotype: Recessive epistasis example in humans. Identified in what used to be Bombay, and has to do with the ABO blood typing. Occurs when ABO blood appears to be O type, but reacts to antigens if given O blood due to the presence of two recessive h alleles. HH/Hh will attach A and B antigens to red blood cells, but hh will fail to do so. First example was a woman whose blood had the B allele, but the B antigens could not attach to her red blood cells since she was hh, making her appear to be an O blood type. Dominant Epistasis: A certain type of squash can be one of three colors: White, Green, or Yellow. This requires a process where compound A in a white squash is converted by Enzyme I to compound B to create a green squash. Then, compound B is converted by Enzyme II to create compound C, resulting in a yellow squash. If this pathway gets interrupted, the color expectation changes. o The ww genotype allows the first step to occur properly, converting to compound B. If there is a W present, it inhibits it to change, resulting in a white squash. If compound B is allowed to continue, but the enzyme II has yy, it inhibits enzyme II from changing compound B to compound C, keeping the squash green. If there is at least 1 Y allele, the enzyme is allowed to continue. o If the squash is W_Y_ or W_yy, the squash is white (since the W stops the process right at the beginning). The W gene is epistatic to the y gene (Yy is the hypostatic gene). If the squash is wwY_, the squash is yellow. If the squash is wwyy, the squash will be green. 12:3:1 ratio of white:green:yellow. 8. Complementation: Determining if mutations are in the same or different loci. Example: Harebell plants – usually produce blue flowers, the wild type gene (wt). Mutant plants produce white flowers, of which the white gene (A, B, or C) is recessive to (wt). o For every of these plants, we will set up Mendelian crosses: Two pure white mutants crossed (AA(wt)(wt)) x ((wt)(wt)BB) = wtABwt, which produces blue flowers because we have a wt allele for each gene. A and B complement each other when bred. o If the mutations were in the same gene (AAwtwt x BBwtwt), when the cross is carried out, we’ll end up with ABwtwt. Since we have two mutant copies on the first gene, we do not see complementation. We have a homozygous mutant, even though they are two different mutations. We CANNOT get a wild type from this cross. 9. Penetrance and Expressivity: Incomplete Penetrance: Genotype does not always produce the expected phenotype. Example: an individual that is heterozygous for polydactyly (having extra fingers or toes) has the GENOTYPE to be polydactyl, but may not be phenotypically polydactyl. We can calculate the number of people that typically shows the phenotype to get the level of penetrance. Penetrance: Percentage of individuals having a particular genotype that express the expected phenotype – if 45 out of 50 people exhibit trait: Penetrance = 45/50 = .9 (90%). Variable Penetrance will result in some individuals showing the trait completely, and others not showing it at all. Expressivity: Degree to which a character is expressed. (small, nonfunctional digit versus a fully functional additional digit). Variable Expressivity will show all individuals showing a trait, but to varying degrees. Variable Expressivity and Penetrance: Some individuals will express a trait to varying degrees, but others will not be affected at all. 10. Temperature Effect: Some alleles’ phenotype is determined by temperature. Himalayan rabbits: They contain a temperature sensitive allele that makes a black pigment, the proteins of which are sensitive to heat. If the rabbit grows up in a warm environment (above 30° C), the pigment will not show up, giving a completely white animal. If they grow up in a cooler environment (20° C or less), they will have black extremities. At 25° C, some pigment may show up, making it gray. Norm of Reaction: Range of phenotypes produced by a genotype in different environments. If you were to apply an ice pack to the body of the rabbit, the hair could grow back into a dark pigmented spot. 11. Sex chromosomes: Sexlinked characteristics Involves genes located directly on the sex chromosome: o Humans and Fruit Flies: XX = female, XY = male. In the next generation, you would expect a 50/50 split of male and female offspring. The female gives an X to every child. The male gives half of his offspring an X, and half of his offspring a Y. o Thomas Hunt Morgan: Worked mostly with fruit flies, through which he first explained sex linked inheritance because he discovered that a single male in his fruit fly colony had white eyes, so he set up crosses. He assumes that W (red) is dominant over w (white). WW (female) x ww(male) would give all Ww redeyed offspring. Then, in the next generation (Ww x Ww), get 3:1 ratio red to white eyes. However, he found that all of the whiteeyed flies were males. There were NO females with white eyes. So, Morgan did a reciprocal cross of a Whiteeyed female with a redeyed male, which produced ¼ redeyed males, ¼ redeyed females, ¼ whiteeyed males, and ¼ redeyed females. He concluded that this trait is not independent of sex. The males only received 1 copy of the X, so they must’ve gotten it from mom. o Hemizygosity: Have one copy of a gene in a diploid cell. Males cannot be homozygous or heterozygous for the gene located on the X chromosome. Xlinked recessive: o RedGreen color blindness is one of the most common sexlinked traits in humans. It is called Xlinked color blindness. If a normalcolor vision female X X has children with a colorblind c male X Y, the female can ONLY pass on the wild type allele. The male will pass on the color blind allele to all daughters, and the Y to all of his sons. All children will have normal vision due to normal alleles of mom. In the reciprocal cross, a colorblind female X X with a normalcolor + vision male X Y, their daughters will all be normal colored vision due to one color blind allele from mom, and one normal from dad. All sons, however, will be color blind due to the X only from the colorblind male. Males, therefore, are more commonly affected than females due to them having only 1 X chromosome. Affected males CANNOT pass the trait to their sons since they contribute the Y chromosome. o Another example of an Xlinked recessive disease is hemophilia A, a disease of the royal family. It is believed that Queen Victoria was the first carrier. Xlinked Dominant Traits: o Do not skip generations, and affected males pass to all daughters, and no sons. Heterozygote females pass the trait to half of their sons, and half of their daughters. Looking at an affected father can be most telling when looking at sexlinked traits. An example of this is hypophosphatemia (Familial vitamin Dresistant rickets) Ylinked traits: Will ONLY appear in males in every generation, because only males carry a Y. Sex influenced/limited Genes on autosomal (nonsex) chromosomes that are more readily expressed in one sex: Sex influenced: o Example: If a beardless male goat (B B ) is crossed with a bearded female (B B ) to get (B B ), b b the male offspring will be bearded, and the female will not. In other words, the B gene is recessive in females, and dominant in males. Males will express a beard in homozygous and heterozygous for B genes. Only homozygous B females will have a beard. o Human Example – Male Pattern Baldness: Pattern baldness is autosomal, and can be inherited from either parent, but it is influenced by the sex of the individual. If men just get one bald allele, they will show the balding phenotype, whereas females require two. Castration limits baldness, so testosterone seems to have an effect, even though it isn’t a likely practice. Sex limited: These traits look like sexinfluenced characteristics, but will completely limited to one sex or the other. ZERO penetrance in one sex. Cock feathering is autosomal recessive – HH males are hen feathered, as are HH females. Hh males and females are both hen feathered. Males with hh will be cock feathered, while hh fem
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