BIOL 4003 Midterm 1 Study Guide
BIOL 4003 Midterm 1 Study Guide 4003
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This 22 page Study Guide was uploaded by Rachel Heuer on Tuesday February 16, 2016. The Study Guide belongs to 4003 at University of Minnesota taught by Robert Brooker in Spring 2016. Since its upload, it has received 146 views. For similar materials see Principles of Genetics in Biology at University of Minnesota.
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Chapter 2: Mendel’s Experimental Approach: - Experimental Cross: Breeding 2 plants w/ very different characteristics o Also known as hybridization experiment o Offspring are called hybrids - For Mendel, Peas were very advantageous à several varieties o Variable height, pea colors, and pod shapes - Gametes: haploid reproductive cells o Fuse together to form a zygote § Sperm = male gametes • In plants these are formed in anther (pollen) • Produced via spermatogenesis • Spermatogonial cell: Spermat cell and spermocyte o Spermocyte: 4 spermatids and 1 sperm cell • Acrosome: enzyme that allows sperm cell to penetrate the eggs § Eggs = female gametes • In plants these are formed in the ovules • Produced via Oogenesis o Forms oocytes that are halted into prophase of Meiosis I until sexual maturity o Each cycle produces one active oocyte o Produced via gametogenesis § Isogamous: Gametes that are morphologically similar (egg and egg) § Heterogamous: Gametes that are different morphological (egg and sperm) o Peas reproduce when pollen lands on the stigma, stimulating the growth of a pollen tube o Sperm cells enter the stigma and migrate toward an ovule - Self-fertilization: Egg and pollen from same plant (natural) - Cross-fertilization: Egg and pollen from different plants - The general characters of an organism are called characters (eye color) o Trait/variant: the specific property of character (green eyes) o True Breeding Line: Produces same trait after several generations of self fertilization - Mendel started with single factor crosses o Monohybrid: single character hybrids - One character is dominant over to another (recessive) - Particulate theory of inheritance: the genetic determinants that govern traits are inherited as discrete units that remain unchanged as they are passed from parent to offspring - Genes: unit of heredity that may influence the outcome of an organism’s traits (height) - Allele: Versions of a gene (tall or dwarf) - Homozygous: two identical copies of a gene - Heterozygous: carries different alleles - Genotype: genetic composition of an individual - Phenotype: an observable characteristic of an organism - Law of Segregation: Two copies of a gene separate during transmission o A gamete has only one copy of gene o At fertilization, two gametes combine randomly, potentially producing different allelic combinations - Punnet Square: Used to predict the outcome of genetic crosses - 1. Write down the genotypes of both parents - 2. Write down the possible gametes that each parent can make - 3. Create and empty Punnett square - 4. Fill in the possible genotypes of the offspring by combining the alleles of the gametes in the empty boxes - 5. Determine the relative proportions of genotypes and phenotypes of the offspring - two-factor crosses: inheritance of two different characters within the same group of individuals - Nonparental Outcome: Genetic combination not found in F1 generation or parents - Law of independent Assortment: Different genes assort randomly during the formation of haploid cells o RrYy individual yields RY, Ry, rY, and ry (unless linked) o A double cross of heterozygous individuals yields phenotypic ratio of 9:3:3:1 - Linked genes (close to one another on the same chromosome) do not assort independently - A single individual can produce a vast array of genetically different gametes - Genetic recombination: when an offspring receives a combination of alleles that differs from those in the parental generation - If attempting to analyze more than two genes the forked line method or multiplication method can be used - A dihybrid testcross (ttyy X TtYy) yields a phenotypic ratio of 1:1:1:1 - Defective genes: contain loss of function alleles à can be explained by finding the protein that is defective - Pedigree: Genetic family tree o Pedigree analysis: Used to determine inheritance patterns o Two heterozygote normal individuals will have ¼ of their offspring affected by a recessive disease o All offspring of two affected individuals will be affected o A dominant trait predicts that affected individuals will have inherited the gene from at least one affected parent - Probability: the chance that an outcome will occur in the future - Probability = # of times a particular outcome occurs / total # of possible outcomes - accuracy depends on the sample size - random sampling error: deviation between the observed and expected outcomes à large with small sample sizes - Product Rule: used in problems in which the outcomes are independent of each other - Independent = one outcome does not affect the probability of another - probability that two or more independent outcomes will occur is equal to the product of their individual probabilities - Binomial expansion: used in problems having an unordered combination of outcomes - When more than two outcomes are possible, we use a multinomial expansion equation to solve a problem - hypothesis testing: to determine if the data from genetic crosses are consistent with a particular pattern of inheritance - evaluate the goodness of fit between the observed data and the data that are predicted from a hypothesis (null hypothesis à assumes that there is no real difference between the observed and expected values) - can never PROVE that a hypothesis is correct, but can support hypothesis - Chi Square Test: used to analyze population data in which the members of the population fall into different categories - Chi square values are interpreted using a chi square table - a low chi square value indicates a high probability that the observed deviations could be due to random chance alone - degrees of freedom: measure of the number of categories that are independent of each other (usually n-1) Chapter 3: - Mitosis: Sorts chromosomes before splitting into two identical cells - Meiosis: Sorts chromosomes into two o Splits cells into four nonidentical cells with half the number of chromosomes as the parent cell § For sex in eukaryotes - Chromosomes contain the genetic material o Long segments of DNA o Organized by helper proteins o Protein + DNA complex is called Chromatin in eukaryotes - Prokaryotes have no nucleus (made up of bacteria and archaea) o DNA in the nucleoid o Plasma Membrane encloses cytoplasm o Rigid cell wall protects the cell from breakage - Eukaryotes o Have a nucleus with chromosomes o Membrane-bound Organelles with specific function o Mitochondria make ATP o Mitochondria and chloroplasts have DNA - Cytogenetics; o Microscopic examination of chromosomes o Chromosomes are examined when they are actively dividing because they are tightly coiled and produce distinctive shapes that become visible with a light microscope - Blood cells are somatic cells o Non-gametic - Karyotype: visualized representation of chromosomes, reveals how many chromosomes are found within an actively dividing somatic cell - Most eukaryotes are Diploid, each type of chromosome is a member of a pair - Homologous pair: Members of a diploid pair (single = homolog) - one chromosome is inherited from the mother and its homolog is inherited from the father - homologs have the same genes, but may carry different version of that gene à alleles - Allelic differences are determined by differences in DNA à greater than 99% of the DNA make-up of homologs are identical, however that 1% is due to different base sequences resulting in different alleles and phenotypes - Sex chromosomes are not homologs - The location of a gene on a chromosome is called the locus - Sexual reproduction occurs when two gametes fuse to form a new organism à fertilization - Gametogenesis: formation of gametes à which are haploid - Isogamous: gametes are morphologically similar - Heterogamous: gametes are morphologically different - **males gametes are small (sperm cells) and travel large distances to reach the female gamete (egg cell, or ovum) - spermatogenesis: the production of sperm; occurs within glands known as the testes; primary spermatocyte à secondary spermatocyte à spermatid à sperm cell (flagellum and acrosomal head) - oogenesis: production of egg cells; meiosis produces only one cell that is destined to become an egg - Plants alternate between haploid and diploid o Haploid generation: Gametophyte (spores) o Diploid generation: Sporophyte o Meiosis occurs in two different structures of the sporophyte: anthers (male) and the ovaries (female) o Gametophytes specialize to turn into gametes § Diploid (male) creates 4 microspores that turn into pollen (male gametophyte) § Pollen must land on a stigma and form a pollen tube § Embryo sac: Mature female gametocyte § For sex of plant • Pollen lands on stigma à pollen tube grows into ovule o Sperm endospore (endosperm): Specialize in food storage o Sperm and egg fusion create diploid zygote (plant embryo) § An endospore is then produced § Double fertilization occurs § Ovule turns into the seed • Ovary = fruit o Animals get gametes from meiosis o Plants get gametes from mitosis - Chromosome Theory of Inheritance o Chromosome has genes o Chromosomes are replicated and passed on o Diploid cells get one set from father and one from mother o During haploid formation, different types of chromosomes segregate independently o Each parent gives one set of chromosomes o Gametes are haploid - The random assignment of homologous pairs during meiosis I can lead to an independent assortment of genes - Sex chromosomes determine sex of offspring o XY: Heterogametic sex (male) o XX: homogametic sex o Any presence of Y chromosome makes a male (XXY = male) o 1 pair of X chromosomes and 22 pairs of autosomes à chromosomes that are not sex chromosomes o X-linked genes: genes that are physically located within the X chromosome o Testcross: individual with a dominant phenotype and unknown genotype is crossed to an individual with a recessive phenotype - Thomas Hunt Morgan determined that eye color is on the X chromosome Chapter 4: - Alleles most common in nature: Wild type o More than one wild type is genetic polymorphism o Mutant alleles are different than wild type § Rare § Recessive (typically) § WT is dominant § Often defective in their ability to express a functional protein o Heterozygote displays dominant phenotype because 50% of protein product is adequate to provide wild-type phenotype, or the heterozygote produces more than 50% of the functional protein because it is up-regulated o Dominant mutant is less common § Occurs via • Gain of function mutation • Dominant-negative mutation o Mutant genes antagonize normal proteins • Haploinsufficiency o Dominant mutant allele is a loss of function allele o Heterozygote exhibits an abnormal or disease phenotype - Incomplete Penetrance: expected phenotype does not always occur o Polydactyly à due to an autosomal dominant allele o Depends on expressivity § How much is expressed (how many extra digits?) § Occurs via environmental conditions and modifier genes • Many alleles are temp sensitive • Phenotypic effects are dependent on temperature • Arctic fox is white during the cold winter and brown during the warm summer • Phenylketonuria (PKU)- autosomal recessive disease o Caused by a defect in the gene that encodes the enzyme phenylalanine hydroxylase o Unable to metabolize the amino acid phenylalanine o When patients follow a restricted diet free of phenylalanine, they develop normally - Norm of Reaction: Refers to the effects of environmental variation on a phenotype o Phenotypic range seen in individuals with the same genotype - Incomplete, co, and overdominance o Heterozygous phenotype is different than homozygotes - Incomplete Dominance: o Heterozygous phenotype is intermediate (Red à Pink ß white) o 50% of the functional protein cannot accomplish the same level of pigment synthesis that 100% of the protein can - Overdominance (heterozygote advantage): o Heterozygous have superior traits § Both homozygous recessive and dominant traits have negative effects o Sickle cell anemia § Those who are heterozygous are also resistant to malaria § Altered form of hemoglobin (sickle cell shaped), reducing life span o Usually due to two alleles that produce proteins with slightly different amino acid sequences à heterozygote can produce homodimer that is more stable or able to function under a wider range of conditions o The proteins encoded by each allele of the heterozygote may exhibit differences in their functional activity, making the organism more resistant to environmental changes - Codominance: o 2+ genes can be dominant § Both alleles expressed in heterozygous o ABO blood group of antigens § ii = O blood group (recessive) (prevents the attachment of an additional sugar, making it shorter and smaller) § I = A blood group (dominant) b § a b B blood group (dominant) § I I = universal recipients § ii = universal donor - X – linked inheritance: o Genes located on X, but not Y, § Moms pass on § Males exhibit more often o Males transmit x-linked genes only to their daughters o Sons receive their x-linked genes from their mothers - Reciprocal Cross o Cross of affected male with unaffected female and a separate cross of unaffected male with affected female - Sex linked gene: Gene on one chromosome but not both o Hemizygous: Single copy of X-linked gene in male o Holandric: Single copy located on Y linked (SRY gene stimulating male development) § Very very rare! - Pseudoautosomal inheritance o Short segments of matching genes on sex chromosomes o Refers to the idea that the inheritance pattern of certain genes on sex chromosomes is the same as the inheritance pattern of a gene located on an autosome even though the gene is actually located on the sex chromosomes - Sex influenced: o Allele is dominant in one sex but recessive in the other o NOT ON SEX CHROMOSOME!!! o Phenomenon of heterozygotes o Scurs (horns) in cattle § Dominant in males and recessive in females § Heterozygous male has scurs § Heterozygous female does not have scurs - Sex limited inheritance o Trait occurs in only one of the two sexes § Controlled by sex hormones § Testes vs. Ovary o Responsible for sexual dimorphism à members of the opposite sex have different morphological features o May be autosomal or X-linked o Females only produce eggs, males only produce sperm - A lethal allele has the potential to cause death o Recessive o Causes loss of function of essential gene § About 1/3 of all genes are essential o Nonessential genes: not absolutely required for survival, although they are likely to be beneficial to the organism § Not all lethal mutations occur in essential genes, as over- expression of nonessential gene can cause death as well o Conditional lethal alleles § Only lethal in certain environment § Occurs often in temperature sensitive alleles § Caused by mutations that alter the structure of the encoded protein so it does not function correctly at the nonpermissive temperature or becomes unfolded and is rapidly degraded o Semilethal alleles: § Only kills some individuals - Age of Onset is the age when symptoms appear - Pleiotropy: Single gene affects multiple traits o Nearly all genes are pleiotropic o Occurs because: § The expression of a single gene can affect cell function in more than one way § A gene may be expressed in different cell types in a multicellular organism § A gene may be expressed at different stages of development o Cystic fibrosis: gene for cystic fibrosis encodes a protein called the cystic fibrosis transmembrane conductance regulator (CFTR) - Gene interaction: how several genes can affect one trait - Epistasis: alleles of one gene mask the phenotypic effects of the alleles of other genes o Wild-type phenotype is the reference phenotype o cc is epistatic to PP or Pp and pp is epistatic to CC or Cc à recessive epistasis o occurs because two (or more) different proteins participate in a common function - Complementation: 2 parents that have recessive phenotypes produce offspring with a WT phenotype (Figure 4-17) - Gene modifier effect: the alleles of one gene modify the phenotypic effect of the alleles of a different gene - Gene knockout: abolishing gene function by creating an organism that is homozygous for a loss-of-function allele o used to understand how a gene affects the structure and function of cells or the phenotypes of organisms - Gene redundancy: o The phenomenon that one gene can compensate for the loss of function of another gene o Because: § Certain genes have been duplicated during evolution • Paralogs: copies of genes that are not identical due to the accumulation of random changes during evolution § Proteins are involved in common cellular functions Chapter 5: - Nonmendelian inheritance patterns still follow some of these rules: o Expression of genes influence traits o Genes are passed unaltered from generation to generatoin o Obey the laws of segregation o Obey law of independent assortment - Maternal Effect: breaks Rule 1 o Heterozygous mom can produce homozygous recessive offspring with dominant phenotype § Genotype of mother directly affects phenotype of the offspring § Genotype of father does not affect offspring phenotype o Caused by oogenesis § As egg cell forms, nurse cells surround oocyte and provide nutrients and other material § Oocyte still gets only a D or d allele, but may receive the protein products from both alleles § Also gets gene product from nurse cell (whatever mom produces) throughout the early stages of development § Immediate expression during the development overrules the effect of sperm genotype (which takes affect to late) o Maternal genes encode preteins important in early steps of embryogenesis § Allows quick development of embryo after fertilization § Defective allele has dramatic effect on phenotype (changes morphologically) - Epigenetic Inheritance o Modification to chromosome or nuclear gene alters gene expression, but is not permanent over the course of many generations § Result of DNA and chromosomal modifications that occur during oogenesis, spermatogenesis or embryogenesis o Epigenetic changes alter the expression of particular genes in a way that may be fixed during an individual’s lifetime § Epigenetic changes can permanently affect the phenotype of the individual § Epigenetic modifications are not permanent over the course of many generations § Do not change the actual DNA sequence à just the expression/amount § Permanent for single individual, not for offspring o Does not change actual DNA o Dosage Compensation: results in similar levels of gene expression between the sexes § Refers to the phenomenon in which the level of expression of many genes on the sex chromosomes is similar in both sexes even though males and females have a different complement of sex chromosomes § Offsets differences in number of sex chromosomes § 1 altered sex chromosome creates similar level of gene expression even though they don’t have same pair (such as male XY and female XX) § Females can equalize effect of having one extra X by inactivating one § The difference in gene dosage—two copies in females versus one copy in males—is being compensated for at the level of gene expression § X-Chromosome Inactivation (Lyon Hypothesis): female mammals equalize the expression of X-linked genes by turning off one of their two X chromosomes • Condense inactive X-chromosome into a Barr body • Initially, both X chromosomes are active • However, patching patterns can occur because separate cells can randomly inactivate different X-chromosomes during early stages of development à creating a Barr body • Compaction causes most genes to be unable to be expressed • Replication keeps the XCI inactive • Multiple X can be inactive (3 X = 2 inactivated Barr bodies) • X-inactivation Center, Xic: used for recognition and inactivation of X chromosomes, found on X chromosome o If missing cell will not inactivate correct number § Lethal à having more than one X chromosome activated is deadly to an embryo • Xist (gene found within Xic): is needed to turn X chromosome into a barr body, found on X chromosome o Active on X chromosome even when that X is inactive o Produces RNA (not proteins) to coat inactive X chromosome and inactivate it • Tsix: prevents X inactivation o Present on active X chromosome within Xic to inhibit transcription of Xist o Expression of the Tsix gene inhibits the transcription of the Xist gene o On active X chromosome, the Tsix gene is expressed and the Xist gene is not, and vice versa X-Chromosome Inactivation Occurs in 3 stages: o Initiation: During embryonic development § Labels active and inactive X chromosome o Spreading: Inactivation occurs § Xist expression occurs • Xist RNA coats the inactivated X chromosome • Recruits proteins to help with compacting • Compaction involves DNA methylation and the modification of histone proteins • Spreads in both directions along X chromosome o Maintainance: § Barr body reproduced and kept compact during cell division • Some genes can escape the Barr body - Genomic Imprinting: o DNA segments are marked with memory § Mark is retained and recognized throughout whole life cycle § Occurs prior to fertilization § Because only 1 allele is marked, only one allele is expressed (monoallelic) • The marking process causes the offspring to distinguish between maternally and paternally inherited alleles • Results in the expression of one allele but not the other • One allele is transcribed into RNA but the other allele is transcriptionally silent o Imprinting occurs during gametogenesis and occurs in 3 stages § Establish imprint during gametogenesis § Maintain imprint during embryogenesis and in adult somatic cells § Erasure and Reestablishment of the imprint in germ cells • Whether mark is reestablished depends on sex of parent § In the germline, the imprint is erased and it will be reestablished according to the sex of the animal § Permanent in the somatic cells of an animal § Unmarked gene is always transcriptionally inactive § Can be just a single gene, or up to a whole chromosome § Can assist in process of XCI o Methylation helps with marking: attachment of a methyl groups onto cytosine bases à common way for eukaryotic genes to be regulated § Imprinted gene has imprinting control region (ICR) near start § ICR is either methylated in the sperm or the egg § ICR Contains proteins binding sites for transcription § Methylation inhibits transcription o Important for diseases - Extranuclear Inheritance or cytoplasmic inheritance o Occurs from mitochondria or chloroplasts because they contain their own DNA o DNA is found within organelle in nucleoid o DNA is found in singular circular chromosome in organelle § Size and # can vary greatly o Organelle can have more than one nucleoid region and more than one circular chromosome o Mitochondria and chloroplasts are not sorted during cell division o Mitochondrial DNA (mtDNA) encode ribosomal RNA and transfer RNA § mtDNA encodes 13 polypeptides that function in oxidative phosphorylation to use oxygen and synthesize ATP § most mitochondrial proteins are encoded by genes within the cell nucleus o Chloroplast genomes are larger than mitochondrial genomes § Carries between 110-120 different genes § cpDNA encodes rRNA, tRNA and proteins for photosynthesis § most proteins required by the chloroplast are encoded by genes found in the cell nucleus o inheritance of extranuclear genetic material is non-mendelian § mitochondria and chloroplasts are not sorted during meiosis and do not segregate into gametes in the same way as nuclear chromosomes o Maternal Inheritance: Chloroplasts are inherited only from the eggs (not enough room in sperm to house chloroplasts) § Leaves can produce all one color, opposite color, or mixture (variegated) à because of chloroplasts § Heteroplasmy: when leaf of plant contains both types of chloroplasts, it becomes variegated § Heterogamous species: two kinds of gametes are made (egg and sperm) • Female gametes are large and provide most of the cytoplasm and therefore mitochondria and chloroplasts to the zygote § Mitochondria inherited from the paternal parent is called paternal leakage § mtDNA causes many diseases • some mitochondrial mutations are transmitted from mother to offspring • mitochondrial mutations may occur in somatic cells and accumulate as a person ages § mitochondria are particularly susceptible to DNA damage • excess O 2reatly damages mitochondrial DNA because of the production of free radicals • mitochondria have limited repair abilities • symptoms of mitochondrial diseases vary widely - Endosymbiotic Theory o Cyanobacteria moved into eukaryote and then evolved into mitochondria/chloroplast o mtDNA and chDNA is more like bacDNA than euDNA o Allowed for cells with useful characteristics o Eukaryotes get ATP energy or photosynthesis o Bacteria get nutrient rich environment in eukaryotic cell § Lost most traits and genes to eukaryotic nucleus o Transfer of DNA from euNucleus to organelle rarely occurs Chapter 6: - Genetic map: a diagram that describes the order of genes along a chromosome - Eukaryotic Chromosome: Long and Linear - Synteny: 2 or more genes are on the same chromosome o Syntenic genes: physically linked to eachother because they are on the same chromosome - Genetic Linkage: Genes that are close together on the same chromosome are transmitted as a unit - Linkage Groups: Another name for chromosome because they contain a group of genes that are physically linked together o in species that have been characterized genetically, the number of linkage groups equals the number of chromosome types - According to Mendel, double heterozygous crosses should yield a 9:3:3:1 phenotypic ratio o Linkage causes this ratio not to happen - Even though linkage occurs, crossing over can create new recombinant chromosomes - **occurs during prophase of meiosis I à homologous chromosomes exchange pieces with each other o bivalent: made up of two pairs of sister chromatids - genetic recombination: event that leads to a new combination of alleles o à creates recombinant cells à which create recombinant offspring o nonrecombinant offspring: received the same combination of alleles found in the chromosomes of their parents - In original experiment leading to crossing over, they found that the F2 offspring had phenotypes of the parental generation and the 9:3:3:1 phenotypic ratio was not observed - With the fruit flies, Thomas Hunt Morgan found that the F2 generation yielded a large amount of offspring with the phenotypes of the parental generation because of x-linked genes o The few recombinant offspring were due to crossing over; this does not happen as often because the alleles for these traits are located very close together on the x chromosome, which decreases the chance of crossing over o He found that two of these genes were more likely to produce recombinant phenotypes than two other genes § He concluded that this was because the genes were farther apart on the chromosome and were more likely to experience crossing over - Thomas Hunt Morgan proposed that the likelihood of crossover depends on distance between the genes o Longer distance away means more likely - Chi-squared analysis is used to determine whether reproduction is due to independent assortment or linkage o In a two-factor cross, the standard hypothesis is that the two genes are not linked o **without the expected numbers of recombinant and nonrecombinant offspring, we cannot conduct a chi square test o Null hypothesis is independent assortment à hypothesis we are testing § Assumes there is no real difference between the observed and expected values o If the chi-square value is low, we cannot reject the null hypothesis and we infer that the genes assort independently o If the chi-square value is high, we can reject the null hypothesis and accept the alternative hypothesis, that the genes are linked o Rejected null hypothesis means nonmendelian assortment occurred § Not necessarily due to linkage o How to conduct a chi-square test: § Propose a hypothesis: law of independent assortment (not linked) § Based on the hypothesis, calculate the expected value of each of the four phenotypes (1/4) and multiply that by the total number of offspring § Apply the chi square formula, using the data for the observed values (O) and the expected values (E) 2 2 • X =(O-E) /E + … § Interpret the calculated chi square value - Genetic Mapping o Used to identify location, linear order, and distance of separation among genes that are linked to each other along the same chromosome § Genes all have unique loci (gene location on a chromosome) § Many uses • Allows geneticists to understand the overall complexity and genetic organization of a particular species • Portrays the underlying basis for the inherited traits an organism displays • Can help molecular geneticists to clone that gene and obtain greater information about its molecular features • Useful to determine evolutionary relationships among species • Used to diagnose and treat inherited human diseases • Used to help genetic counselors predict the likelihood of a couple producing a child with inherited diseases • Used in agriculture § **Determining the number of recombinant offspring due to crossing over provides a way to deduce the linear order of genes along a chromosome § Genetic linkage map shows the linear arrangement of genes on chromosomes • Hard to map large chromosomes o Mapping = % recombinant is proportional to distance between genes § If two genes are far apart, a crossover is more likely to be initiated in this region, recombining the alleles of two genes o Use a testcross to determine § Between a heterozygote and homozygote recessive § Used to determine if recombination has occurred during meiosis in the heterozygous parent § New combinations of alleles only from heterozygotes (not homozygous recessive b/c they are homozygous) § Figure 6.9 § Recombinant offspring are all due to crossing over § Amount of recombination can be used as an estimate of the physical distance between two genes on the same chromosome • Map distance: the number of recombinant offspring divided by the total number of offspring, multipled by 100 • MD = number of recombinant offspring / total number of offspring x 100 § Calledmap units (mu) or centiMorgans (cM) § 1 map unit is equivalent to 1% recombinant offspring in a test- cross § Maximum of only 50% recombination • Over 50% genes appear to follow independent assortment o To determine order and distance between 3 genes in three-factor cross § Cross 2 true breeding strains that differ with regard to three alleles (homozygous recessive and homozygous dominant to create heterozygote) • All dominant alleles are located on 1 chromosome and all recessive alleles are located on 1 chromosome § Conduct test cross with F1 female heterozygote and true bred homozygous recessive males § Collect data for the F2 generation • In crosses involving linked genes, the nonrecombinant phenotypes occur most frequently in the offspring • The remaining phenotypes are due to crossing over • Double crossover is always expected to be the least frequent o Double crossover indicates which gene is in the middle § Calculate map distance between pairs of genes § Construct map based of distances o Double crossover is very rare because of positive interference § Crossover in one spot decreases likelihood of crossover in a nearby region § Coefficient of coincidence, C = observed # of double crossovers/expected number of double crossovers § Interference, I = 1-C Chapter 8: - Genetic variation refers to the genetic differences that occur between individuals of the same or different species o Can be allelic but can also be due to the number of chromosomes or structure of these chromosomes - Larger genotype changes affect expression of many genes and influence multiple phenotypes o This is critical to the evolution of new species - To determine the normal chromosome composition of a species, a cytogeneticist (scientist who studies chromosomes microscopically) will examine chromosomes of many members of the given species - Phenotypically normal individuals should all have the same # and type of chromosomes o Chromosomes are best studied when undergoing cell division § More compact and visible § Within the same species, all chromosomes are very similar (except for sex chromosomes) - 3 common ways to classify chromosomes 1. Centromere location - Metacentric: centromere near center/middle - Submetacentric: Centromere is slightly off center - Acrocentric: centromere is significantly off center - Telocentric: centromere is At one end 2. Size 3. Banding patterns - Chromosomes have a long (q) and short arm (p) - Karyotype o A micrograph used to identify and arrange chromosomes o Arranged and numbered based off of size (besides sex chromosomes) o Arranged so that the short arms are on top and the long arms are on the bottom o Largest chromosomes have the smallest number o If two chromosomes are close in size and shape, banding patterns are used to distinguish them § More bands in prometaphase than in metaphase (because metaphase is more compact) § G banding à expose chromosomes to heat or proteolytic enzymes that partially digest chromosomal proteins à expose chromosomes to Giemsa dye and chromosome regions bind the dye and produce dark bands § Banding patterns can be used to detect differences in chromosomes, changes in chromosomes structure, or evolutionary relationships between species o Sex chromosomes are named with letters, not numbers Changes in the total amount of genetic material: - Deletion: Causes chromosome to lose significant portion of genetic material o Also called a Deficiency à missing portion of a chromosome - Duplication: sequence in a chromosome is repeated compared to normal chromosome Chromosomal rearrangements: - Inversion: Change in direction of genetic material - Translocation: One part of chromosome attaches to new chromosome or to a different part of the same chromosome o Simple: Single piece of chromosome is attached to another chromosome o Reciprocal: Exchange between two nonhomologous chromosomes § Two different types of chromosomes exchange pieces, thereby producing two abnormal chromosomes carrying translocations - Deletion o Tends to be detrimental o Occurs when chromosome breaks and a fragment is lost § Terminal Deletion: • Creates two pieces o One with a centromere o One without a centromere § Piece without centromere is degraded and lost o A piece lost at the end is called a Terminal deletion o Can also occur when recombination occurs at incorrect locations between homologous chromosomes (along with duplication) o Interstitial Deletion: break in two spots which creates three pieces § Middle piece is degraded and lost § Outside pieces rejoin o Phenotypic consequences of deletion depend on: § Size of deletion • Larger is more harmful § Whether or not genes are vital to development - Duplication o Less harmful than deletion o Results in extra genetic material o Caused by abnormal events during recombination § Such as misaligned crossover between homologs • Because DNA has repetitive sequences for DNA to misread as original for crossover (transposable elements) o Called Nonallelic homologous recombination • Still occurs at homologous sites, but neighboring alleles do not align correctly • Causes a deletion in one chromatid and a duplication in another o In most cases, duplication occurs as rare sporadic event during evolution o Consequences of duplication are correlated with size § Small deletions are likely to have larger effects than small duplications of the same size § Having 1 copy of gene is worse than having 3 copies § Majority of small chromosomal duplications have no phenotypic effect o Increases amount of DNA in chromosomes § Leads to formation of gene families • Consist of two or more genes in a particular species that are similar to each other • Members of gene family are derived from same ancestor • Two copies will accumulate mutations and diverge à stay similar but not identical • Homologous: two or more genes from single ancestor • Paralogs: Homologous genes within the same species, constitute a gene family • Gene families produces genes that are more specialized in their function - Copy number variation: o Refers to the type of structural variation DNA exhibits compared to members of the same species o A type of structural variation in which a segment of DNA, which is usually 1000 bp or more in length, commonly exhibits copy number differences among members of the same species o Occurs at the populational level o Can be either deletion or duplication o Most CNV is inherited/happened previously § Can be from nonallelic homologous recombination § Proliferation of transposable elements can also increase copy numbers of DNA § Errors in DNA replication o In many cases, CNV has no phenotypic consequences - Comparative genomic hybridization can be used to determine if there are deletions or duplications in a chromosome - Inversion: o Often do not cause phenotypic consequences o Classified by the location of centromere § Pericentric Inversion: inverted region of the chromosome contains centromere § Paracentric Inversion: centromere is found outside the inverted region o Genetic material amount stays the same o If inversion occurs within a vital gene, the function of the gene is disrupted and can produce a phenotypic effect o An inversion may reposition a gene on a chromosome in a way that alters its normal level of expression o Position effect: Change in phenotype that occurs when the position of a gene changes from one chromosomal site to a different location o Consequences are not seen unless gene is broken during inversion o Somewhat common o Inversion Heterozygote: § Carry one normal chromosome and one inverted chromosome § Normally phenotypically normal § May have high probability of producing haploid germ cells that are abnormal in their total genetic content • Due to crossing over within inverted region • During meiosis, homologous chromosomes must synapse o Inversion loop must form to permit the homologous genes on both chromosomes to align all genes properly o If a crossover occurs within the inversion loop, highly abnormal chromosomes are produced o A crossover is more likely to occur in this region if the inversion is large, so individuals carrying large inversions are more likely to produce abnormal gametes • If paracentric, gametes produced contain: o one acentric chromosome- chromosome without any centromere à is degraded o dicentric chromosome- chromosome with two centromeres à is degraded § contains a dicentric bridge: region of the chromosome connecting the two centromeres § dicentric bridge will break during anaphase, producing two chromosomes that contain deletions o one normal chromosome o one chromosome with an inversion • If pericentric inversion, produces two abnormal chromosomes: o Each chromosome has a segment that is deleted and a different segment that is duplicated • Larger inversion means better chance of producing abnormal gametes - Translocation o Occurs when piece of one chromosome attaches to another, nonhomologous chromosome o Telomeres of eukaryotic chromosomes prevent attachment to the end of chromosomes and prevent translocations o Telomeres: specialized repeated sequences of DNA that are found at the ends of normal chromosomes § If chromosomes break, the broken ends lack telomeres and are said to be highly reactive (sticky) § 2 reactive ends will bind together o if a single chromosome break occurs, DNA repair enzymes will usually recognize the two reactive ends and join them back together o If multiple chromosomes are broken, reactive ends may reconnect improperly and produce abnormal chromosomes § Causes reciprocal translocations to occur § Can also happen due to crossing over between non homologous chromosome o Balanced translocation: total amount of genetic material is not altered § Can usually occur without any phenotypic consequences o Offspring, however, can receive unbalanced translocation which leads to abnormalities and death à significant portions of genetic material are duplicated and/or deleted § Usually associated with phenotypic abnormalities or even lethality § Familial Down syndrome (Robertsonian translocation) • Occurs when breaks near centromeres of two nonhomologous acrocentric chromosomes • Only involve the acrocentric chromosomes (13, 14, 15, 21, 22) § Translocation cross: occurs when 4 sister chromatids all align • Figure 8.14 • Alternate segregation: chromosomes diagonal to eachother within the translocation cross sort into the same cell o Two gametes have normal chromosomes and two have reciprocal translocations • Adjacent segregation: adjacent chromosomes sort into the same cell o Each daughter cell receives one normal chromosome and one translocated chromosome o All gametes are genetically unbalanced because part of one chromosome is missing and part of another is duplicate o semisterile à decreased viability, which lowers the fertility of the parent - Variations in chromosome number can be categorized in two ways: variation in the number of particular chromosomes and variation in the number of particular chromosomes within a set - Euploidy: o Have a chromosome number that is an exact multiple of a chromosome set § Diploid (2 sets, 2n) vs tetraploid (4 sets, 4n) vs triploid (3 sets, 3n) § Polyploid: organisms with three or more sets of chromosomes o Normally not tolerated well o Can occur before or after segregation o Endopolyploidy: Specific tissue that can alternate number of chromosome sets dependent on amount of gene expression needed o Plants with euploidy are more advantageous with greater adaptability § With 3n or 5n are often sterile • Cant divide evenly for meiosis - Aneuploidy: alteration in the number of particular chromosomes, so the total number of chromosomes is not an exact multiple of a set o 1 extra or less chromosome § trisomy: having one extra chromosome (2n+1) § monosomy: having one less chromosome (2n-1) o Causes overload of gene expression o Usually produces abnormal phenotypes o Imbalance occurs between the level of gene expression on the chromosomes § Trisomy: 150% gene expression à too much § Monosomy: 50% of gene expression à not enough o If egg produces embryo with aneuploidy, 50% are aborted naturally o Most common aneuploidy are trisomy of 13, 18, 21 or abnormalities in the number of sex chromosomes § Occurs with small chromosomes with less genes o Alterations in other chromosomes are lethal o Variation in number of X is not lethal § X-inactivation o Older parents are more likely to produce children with abnormalities in chromosome number o Nondisjunction most commonly occurs during meiosis I in the oocyte § Chromosomes do not segregate properly (results in Down syndrome) o In Haplodiploid species, one sex is haploid while other is diploid o Endopolyploidy- the occurrence of polyploid tissues or cells in organisms that are otherwise diploid § Polytene chromosomes connected at the chromocenter in Drosophila o Plants commonly exhibit euploidy § Polyploid plants that have an odd number of chromosome sets are sterile because of unequal division of chromosomes during meiosis I
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