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Bil 250 test 2 study guide

by: Annmarie Jaghab

Bil 250 test 2 study guide BIL 250

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Everything on exam 2 including independent reading notes
Dr. Alvarez
Study Guide
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This 20 page Study Guide was uploaded by Annmarie Jaghab on Wednesday February 17, 2016. The Study Guide belongs to BIL 250 at University of Miami taught by Dr. Alvarez in Winter 2016. Since its upload, it has received 85 views. For similar materials see Genetics in Biology at University of Miami.


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Date Created: 02/17/16
BIL 250 Exam 2 Study guide Chapter 7 -wide range of reproductive modes. –Some are totally asexual. Ex. bacteria –Some alternate between short periods of sexual reproduction and prolonged periods of asexual reproduction. Ex. Some algae and fungi –Sexual reproduction is only natural mechanism for producing new species. Meiosis ensures genetic constancy but also gives genotypic/phenotypic variability through segregation, recombination and independent assortment during the production of gametes. -In animals (including humans) differentiation of sexes is evident via phenotypic dimorphism of males and females -Dissimilar chromosomes (ex. XY in mammals) characterize one sex or the other in a wide range of species: Heteromorphic chromosomes –Example: Sex chromosomes X and Y –Genes rather than sex chromosomes determine the sex of the individual. -In multicellular organisms, it is important to distinguish between 1) primary sexual differentiation: involves only the gonads where gametes are produced. 2) secondary sexual differentiation: involves the overall appearance of the organism. (Includes clear differentiation in such organs as mammary glands and external genitalia) -Plants and animals that contain only male or female reproductive organs are unisexual (dioecious/ gonochoric). -Plants and animals that contain both male and female reproductive organs in the same organism are bisexual (monoecious/ hermaphroditic) and can produce both male and female gametes. -Chlamydomonas (green alga): Gametes that are not morphologically distinguishable are called isogametes. Most of his life cycle reproduces asexually (vegetative), but under Nitrogen scarcity it form isogametes of opposite matting types that fuse by fertilization. The zygote undergoes meiosis to make haploid cells of different matting type again. Asexually they produce daughter cells by mitotic division. Under unfavorable nutrient conditions, they undergo sexual reproduction and daughter cells function as gametes and the two gametes fuse together - + - during mating- Two mating types of mt and mt …mt cells can mate only with mt cells, and vice versa. Four haploids are produced called zoospores. There are chemical differences between these mating types -In maize (Zea mays), the diploid sporophyte stage predominates. It is a monoecious plant (both male and female structures are present on the adult plant). This indicates that sex determination must occur differently in different tissues of the same plant. The stamens (male organ) produce mature male microgametophyte (pollen grain), with 2 haploid sperm nuclei. The pistil (female organ) produces four haploid megaspores. Upon fertilization, one of the two sperm nuclei unites with the haploid oocyte, and the other sperm unites with the two endosperm nuclei (double fertilization occurs to form a triploid endosperm) -C.Elegans: Transparent, un-segmented nematode, popular animal model for Developmental Genetics, the specific lineage can be traced back to the embryo, was the first multicellular organism to have its whole genome sequenced. Two sexual phenotypes: 1) Males, which have only testes 2) Hermaphrodites, which have both testes and ovaries. They undergo self-fertilization and produce primarily hermaphrodite offspring, with less than 1 percent male offspring. As adults males can mate with hermaphrodites, producing about half male and half hermaphrodite offspring. The ratio of X chromosomes and autosomes determines the male or hermaphrodite in C. elegans. Sex determination in C. elegans results from the presence of only one X chromosome in the males (XO) and two in the hermaphrodites (XX) - Protenor (butterfly): XX/XO mode of sex determination. Depends on random distribution of X chromosome into half of male gametes. Two X chromosomes in zygote results in female offspring. One X chromosome results in male offspring -Lygaeus (Milkweed bug): XX/XY mode of sex determination. Female gametes have one X chromosome. Male gametes have either an X or Y chromosome -In both Lygaeus and Protenor modes of sex determination: female are homogametic (always XX) and males are heterogametic. -Females are the heterogametic sex in some moths, butterflies, most fish, reptiles, amphibians, and one species of plants that use the ZZ/ZW system. Females are the heterogametic (ZW) sex. Males are the homogametic (ZZ) sex. -The Y chromosome determines maleness in humans -Aneuploidy is a condition in which an organism has either more or fewer chromosomes than normally exist in its species’ full set. Caused by non-disjunction during meiosis. It is responsible for a large proportion of the miscarriages that occur in human pregnancies. -Females 45XO: Turner syndrome: Female external genitalia and internal ducts but ovaries are rudimentary. Short stature, skin flaps on back of neck, flat underdeveloped breasts, broad shield-like chest. Generally have normal intelligence, may have learning disabilities -Males 47XXY: Klinefelter syndrome: Tall stature, with long arms and legs, underdeveloped testes and prostate gland, no facial hair. Phenotypically male, infertile, slight breast enlargement, and hips often rounded. Normal intelligence but may be slow learners. Usually 47,XXY, but also 48,XXXY, 49,XXXXY; more severe manifestations with the greater number of X chromosomes. -XXX syndrome (triplo-X): The abnormal presence of three X chromosomes along with a normal set of autosomes (47,XXX) results in female differentiation, women are perfectly normal and unaware of condition in most cases, but in other cases, women have underdeveloped secondary sex characteristics, sterility, and mental retardation. Extra X-chromosome can disrupt normal female development. -XYY: The only consistently shared characteristic found so far in the 47,XYY karyotype is that such males are over 6 feet tall with subnormal intelligence. May have higher criminal behavior which can conclude that the presence of Y chromosome determines maleness in humans -In humans during early embryonic development, the embryo is hermaphroditic, the gonadal phenotype is sexually indifferent (first 5- weeks of pregnancy). As development continues, gonadal ridges can form either ovaries or testes (bipotential gonads). Triggered by presence or absence of Y chromosome. Ovaries in XX. Testes in XY -The Y chromosome has at least 75 genes, and the X chromosome has 900–1400 genes. The pseudoautosomal regions (PARs) present on both ends of the Y chromosome share homology with regions on the X chromosome and synapse and recombine with it during meiosis. The presence of such a pairing region is critical to segregation of the X and Y chromosomes during male gametogenesis. -The nonrecombining region of the Y chromosome is called the male- specific region of the Y (MSY). Some portions of MSY share homology with the X chromosome, others do not. It has euchromatic (functional genes) and heterochromatic regions (nonfunctioning genes). -The SRY (sex-determining region) is located adjacent to the PAR of the short arm of the Y chromosome. -At 6–8 weeks of development, the SRY genes become active in XY embryos. -The testis-determining factor (TDF) is a protein encoded by a gene in the SRY region that triggers testes formation. It is present in all mammals -Deviations from normal sex determination are seen with: 1) Males with two X chromosomes and no Y (SRY region attached to X chromosome) 2) Females with one X chromosome and one Y chromosome (The Y is missing the SRY gene) -SRY resulting in males is shown with experimental evidence: Transgenic mice research shows that XX normal mice eggs injected with DNA containing SRY transform the mice into males. -TDF is believed to be the transcription factor that behaves as a master switch controlling the genes involved in sexual differentiation -At 6–8 weeks of development SRY gene becomes active in XY embryos. Encodes protein that triggers testes formation. Transcription factor, a DNA-binding protein that interact with regulatory sequences of other genes to regulate gene expression. -Secondary sex determination: Hormonal regulation XY individuals with androgen insensitivity syndrome (AIS) will develop female secondary characters. They have the SRY gene, their testes (in the abdomen) make testosterone, but lack the receptor for testosterone, so they can not respond to that hormone. They develop as sterile female: lacking uterus and oviducts. AIS is an example of intersex condition which female and male traits are present in the same individual. X-linked recessive condition -XXXXY: can happen when the four X chromosomes come from mom: 26XXXX + 23Y OR Mom and dad both contribute X chromosomes 24XX + 25XXY. No association with parental age -The presence of a fetal testis that secretes both testosterone (T) and anti-Mullerian hormone (AMH) results in the induction of the Wolffian duct into the future vas deferens, epididymis, and seminal vesicles and the regression of the Müllerian duct, respectively. In females, the fetal ovary does not secrete either of these substances, so the Wolffian duct regresses, whereas the Müllerian duct gives rise to the fallopian tubes (oviducts), uterus and the upper portion of the vagina. Androgens (including testosterone) have a key role in the development of the male genital tract but are not the only signaling pathways involved. For a sperm and oocyte to meet in vivo, millions of spermatozoa leave the seminiferous tubules of the testis to mature in the epididymis before traveling through the vas deferens and urethra to enter the female, where they transverse the vagina, cervix and uterus before typically encountering a single oocyte in one of the fallopian tubes. Surgical contraception involves closing this pathway by removing segments of the two vas deferens (that is, vasectomy) in a man or both fallopian tubes (that is, tubal ligation) in a woman. -The Ratio of Males to Females in Humans Is Not 1. The actual proportion of male to female offspring is referred to as the sex ratio. The primary sex ratio reflects the proportion of males to females conceived in a population. The secondary sex ratio reflects the proportion of each sex that is born. Many more males are conceived but also have higher fetal mortality; nevertheless, more males are born than females. Sex ratio varies with ethnicity. We are assuming that: Males produce equal numbers of X- and Y-bearing sperm, each type of sperm has equal viability and motility in female reproductive tract, and egg surface is equally receptive to both types of sperm. Could the smaller Y chromosome make Y-bearing sperm lighter and therefore faster? -Dosage compensation: Balances dose of X chromosome gene expression in males and females. Prevents excessive expression of X- linked genes in humans and other mammals -The inactive X chromosomes are highly condensed, can be observed in stained interphase cells, and are referred to as Barr bodies. Arise from the random inactivation of either the originally maternal or paternal X chromosome. Occur early in embryonic development, and all cellular descendants have the same inactivated chromosome. Inactivation is due to an Epigenetic mechanism called DNA silencing -Regardless of how many X chromosomes a somatic cell possesses, all but one of them are inactivated (N-1 rule: N is the number of X chromosomes) 1) No Barr bodies in Turner’s (XO) 2) One Barr body in Klinefelter’s (XXY) 3) Two Barr bodies in 47,XXX -Although the apparent inactivation explains dosage compensation, it complicates certain perceptions in this matter. Why is Turner syndrome 45,XO not entirely normal? Why are females with triple or tetra X not normal? Why does an extra X in Klinefelter syndrome (47,XXY) result in the characteristic phenotype? Could be that inactivation does not take place in early stages of the development of gonadal tissue and not all X chromosomes in the Barr body are fully inactivated. -Lyon Hypothesis: inactivation of X chromosome is random. It occurs in somatic cells at an early stage of embryonic development and is then passed on to progeny cells by mitosis. Heterozygote female mice show mottling coat color for coat color genes on X chromosome. Random distribution of orange and black patches in female calico cat is due to X chromosome inactivation. Males only have a single X and so either the orange or the black hair color gene, not both (white is due to a different chromosome) -Anhidrotic ectodermal dysplasia is a disease that results in the absence of sweat glands. It is inherited as an X-linked recessive condition. Let X = normal sweat glands and X' = absence of sweat glands. Normal males are XY. Affected males are X'Y and do not have sweat glands. Normal females are XX, heterozygous females are XX' and have patches of skin with sweat glands and patches of skin without sweat glands due to random X inactivation. Females that are X'X' do not have sweat glands. Heterozygous females are “natural mosaics” for X-linked genes -Xic: X inactivation center: Active only on inactive X. Has X-inactive specific transcript (XIST) gene critical for X inactivation. Xist is active in the “inactive” chromosome and its product is an RNA molecule that coats the X chromosome and inactivates it. Two other noncoding genes in Xic locus. Tsix and Xite play important roles in X chromosome inactivation -sex in Drosophila: The Y chromosome does not determine sex. Y does not determine sex but is needed for fertility. Sex is determined by the ratio of X chromosomes to the haploid sets of autosomes (A). Normal female has 2X and 2A = 1:1. Normal male has XY and 2A= 0.5. X- inactivation not observed in Drosophila. Male X-linked genes transcribed at twice rate of females -A bilateral gynandromorph of Drosophila formed following the loss of one X chromosome in one of the two cells during the first mitotic division. Ex. Left is XO (male): X-linked alleles white-eye and miniature- wings. Right is wild-type XX (female) -Temperature-dependent sex determination (TSD): The environment, specifically temperature, has a profound influence on sex determination. Although many reptile species do use ZZ/ZW or XX/XY, in others TSD is the norm. For all crocodiles, most turtles, and some lizards, sex determination is achieved according to the incubation temperature of eggs during a critical period of embryonic development. Case I: Low temperatures yield 100 percent females, and high temperatures yield 100 percent males. Case II: The exact opposite occurs. Case III: Low and high temperatures yield 100 percent females, and intermediate temperatures yield various proportions of males. Seen in various species of crocodiles, turtles, and lizards This temperature difference is believed to involve steroids (mainly estrogens) and the enzymes involved in their synthesis. One enzyme in particular, aromatase, converts androgens (male hormones such as testosterone) to estrogens (female hormones such as estradiol). The enzyme activity seems to be temperature-sensitive Chapter 8 -Modifications at level of chromosome: phenotypic variations result from changes of individual genes -Chromosome mutations and aberrations: Total number of chromosomes vary (Deletions, Duplications, Rearrangements) -Most members of diploid species normally contain precisely two haploid sets of chromosomes. Many known cases (chromosomal mutations or aberrations) vary from this pattern, which include: a change in the total number of chromosomes, the deletion or duplication of genes or segments of a chromosome, or rearrangements of the genetic material within or among chromosomes. These changes can result in some form of phenotypic variation and may even be lethal. -aneuploidy: when an organism gains or loses one or few more chromosomes (2n+/- x) -euploidy: complete haploid sets of chromosomes are present. (multiples of n) -Polyploidy: when more than two sets of chromosomes are present. (3n,4n,5n…) -Chromosomal variation can arise from nondisjunction, in which chromosomes or chromatids fail to disjoin and move to opposite poles during meiosis I or II, leading to a variety of conditions in humans and other organisms. Nondisjunction disrupts normal distribution of chromosomes into gametes. Fertilization of abnormal gametes with normal gametes results in zygotes with three members (trisomy) or only one member (monosomy of this chromosome). -Monosomy: the loss of one chromosome (2n – 1), may have severe phenotypic effects. Monosomy for the X chromosome is viable in humans. Monosomy for any of the autosomes is usually not tolerated in humans and other animals but better tolerated in the plant kingdom. Death may occur due to lethal genes being unmasked –Haploinsuficiency: a single recessive gene may be insufficient to provide life-sustaining function for the organism. -Trisomy: (2n + 1 chromosomes) is usually more viable than the loss of a chromosome. Trisomies for autosomes have severe effects and are usually lethal during development. -Trisomic plants are viable, but their phenotype may be altered. Ex. Jimson weed (Datura stramonium) and Rice (Oryza sativa). -Down syndrome: (trisomy 21) The only human trisomy with long survival (more than 1 yr). Designated as 47, 21+. Has 12 to 14 characteristics, and affected individuals express 6 to 8 on average (Prominent epicanthic fold in each eye, Flat face, round head, short stature with protruding tongue, Short, broad hands with characteristic palm and fingerprint pattern, Mental retardation, average life span 50 years.) Children are prone to respiratory disease and heart malformations. Show a higher incidence of leukemia (20 times higher). Death in older individuals often due to Alzheimer’s disease, which usually occurs earlier than in normal population. Survival is up to 50 years. A critical region of chromosome 21 contains the genes that are dosage sensitive in this trisomy and are responsible for many of the phenotypes – Down syndrome critical region (DSCR): Having extra dose of that region seems to protect against some forms of cancer (avoid vascularization) -Down syndrome most frequently occurs due to nondisjunction of chromosome 21. (75% occur during Meiosis I). Fertilization with a normal gamete creates the trisomic condition. (95% the aberrant gamete comes from the mother). Incidence of Down syndrome increase as maternal age increases. Although, half of all the Down Syndrome births occur to women younger than 35 years old, because there are many more births among younger women -Prenatal diagnosis: Genetic counseling is recommended for women who become pregnant late in their reproductive years, and diagnostic testing may also be recommended. Diagnostic testing uses fetal cells obtained form amniotic fluid or placental chorion. Types include: 1) Amniocentesis (from amniotic fluid) 2) Chorionic villus sampling (CVS) 3) Percutaneous umbilical blood sampling (PUBS)—examines blood from the umbilical cord Noninvasive prenatal genetic diagnosis (NIPGD) is a new approach to deriving fetal cells from maternal circulation. Fetal cells are cultured, and the karyotype can be determined by cytogenetic analysis. -Mouse Model For Down Syndrome: Ts (trisomy) mouse models have been created and studied. Human chromosome 21 and mouse chromosome 16 contain Syntenic regions (chromosomal regions in different species that contain much of the same content and arrangement of orthologs (genes with similar sequences that are present in different species.) Mice with an extra chromosome 16 have some of the human down syndrome characteristics, but not all meaning that they are missing some of the critical orthologs on Hsa21. Mouse chromosomes 10 and 17 also have orthologs for genes on Hsa21. By combining regions of mouse chromosomes 10,16, and 17 they were able to develop a mouse model of down syndrome that is trisomic for all syntenic regions of Hsa 21. These mice show energy deficits, brain abnormalities, and hydrocephalus (accumulation of fluid in brain which is not on Hsa21 so this condition is likely caused by expressing multiple copies of several orthologs) -Familial down syndrome: Down syndrome is caused by nondisjunction of chromosome 21, thus the disorder is not expected to be inherited. Nevertheless, Down syndrome occasionally runs in families. Translocation of bottom part of chromosome 21 onto another chromosome, Ex. Chromosome 14 -Other trisomies survive to term in addition to Down syndrome, but manifest severe malformations and early lethality (Patau syndrome 47, 13+ and Edward syndrome 47, 18+) -Karyotype analysis of spontaneously aborted fetuses has revealed: 30% of all aborted fetuses contain an abnormal chromosome complement. Autosomal monosomies (n-1 gametes) are found less often than trisomies (n+1 gametes). Highest incidence of all chromosomal aberrations: monosomy 45, XO (Turner) -polyploidy: The state of having more than two sets of chromosomes. Many plants are polyploid, but the condition is inevitably fatal for human beings. -The naming of polyploids is based on the number of sets of chromosomes found: A triploid has 3n chromosomes. A tetraploid has 4n chromosomes. A pentaploid has 5n chromosomes and so forth. Polyploidy is relatively infrequent in many animal species but is well known in lizards, amphibians, and fish and is much more common in plant species. Polyploidy in plants can be beneficial since they grow more vigorously and/or develop larger fruits -autopolyploidy: addition of one or more sets of chromosomes identical to the haploid complement of the same species. (have additional sets of chromosomes; thus triploids are AAA, tetraploids are AAAA, and so on) Ex. 3n: bananas, potatoes or 4n: alfalfa, coffee, peanuts. Autotriploids can arise if a diploid gamete (due to nondisjunction of all chromosomes) is fertilized by a haploid gamete. Less commonly, it can be due to 2 sperm fusing with one egg. Because they have an even number, autotetraploids (4n) are theoretically more likely to be found in nature than autotriploids. Tetraploids are more likely to produce balanced gametes. Since two homologues of each specific chromosome are present, meiosis occurs normally and gametes are viable. Tetraploids arise when chromosomes have replicated and the parent cell fails to divide and instead enters interphase: the chromosome number will have duplicated. Experimentally done by applying heat or cold shock to diploid cells undergoing meiosis or by applying colchicine to somatic cells undergoing mitosis (colchicine disrupts microtubule polymerization and acts as a spindle poison. This causes anaphase failure so no spindle forms and no progression into cytokinesis just a jump from metaphase to interphase) -allopolyploidy: combination of chromosome sets from different species as a consequence of interspecific matings. Ex. American cotton comes from crossing Old world specie with wild American specie. Ex. Triticale is a hybrid between wheat and rye. Allotetraploids are polyploids that contain equivalent of four haploid genomes derived from separate species. Amphidiploid are allotetraploid where both original species are known. Amphidiploid plants often found in nature. Ex. Amphidiploid form of Gossypium (cotton plant) -endopolyploidy: Condition in which only certain cells are polyploid in otherwise a diploid organism. Ex. Human liver cells up to 16n. Mosquito larvae up to 16n. Some tissues in flowering plants. Water strider is 2n=22. Can have cells with 1024 to 2048 chromosomes. Endopolyploid seems to be related to the need of a greater rate of gene expression Ex. rRNA -There are two primary ways in which the structure of chromosomes can be altered. 1) The total amount of genetic information in the chromosome can change: Deletions or Duplications 2) The genetic material remains the same, but is rearranged: Inversions or Translocations (reciprocal and nonreciprocal) -Fragile sites are more susceptible to chromosome breakage when cells are cultured in the absence of certain chemicals such as folic acid. Could be regions along the chromosome where chromatin is not tightly coiled. There is a strong association between fragile sites and mental retardation and some types of Cancer (ex. Lung). -Fragile X Syndrome (Martin–Bell syndrome): dominant trait, most common form of inherited mental retardation. Fragile site gene FMR-1 has a trinucleotide repeat sequence CGG in the untranslated area of the gene. Normal individual: 6–54 repeats; unaffected "carriers": 55– 230 repeats; Fragile-X syndrome: more than 230 repeats, which causes the gene to become methylated and results in gene inactivation. The number of CGG repeats continues to increase in future generations (genetic anticipation), becoming more severe in successive generations provided it comes from the mother. A consequence of the higher number of repeats is the loss of expression of FMR-1. Normally this FMR-1 gene is expressed in the brain, which explains the neurological defects associated with the syndrome Chapter 9 -Observations revealed inheritance patterns fail to reflect Mendelian principles. Indicate apparent extranuclear influence on phenotype. Discovery of DNA in mitochondria and chloroplasts; extranuclear inheritance is now recognized as important aspect of genetics -Extranuclear inheritance: Transmission of genetic information to offspring through cytoplasm, not nucleus. Usually from one parent. Varieties in extranuclear inheritance include: 1) Organelle heredity: One variety of extranuclear inheritance. DNA contained in mitochondria or chloroplasts determines certain phenotypic characteristics of offspring. 2) Infectious heredity: Variation of extranuclear inheritance. Results from symbiotic or parasitic association with microorganism. Inherited phenotype affected by microbe in host’s cytoplasm. Ex. Some virus infection 3) Maternal effect: Variation of extranuclear inheritance. Nuclear gene products are stored in egg, then transmitted through ooplasm to offspring. Gene products in ovule distributed to embryo cells influence phenotype -Chloroplast mutation ex. Of organelle heredity: Mirabilis jalapa (four o’clock plant) has white, green, and variegated leaves. Genetic defect eliminated green chlorophyll (light- absorbing pigment within chloroplasts) -Another chloroplast mutation is seen in Chlamydomonas (unicellular green alga). Excellent model system for studying organelle heredity (plastid inheritance). Single large chloroplast with 75 copies of circular double-stranded DNA molecule. Streptomycin resistance in Chlamydomonas. Differences in reciprocal crosses with susceptible strains. Trait passed through only one of the parents. str is transmitted by matting type mt + -mitochondrial mutations: Mitochondrial studies in Neurospora (bread mold) and yeast reveal mitochondria also contain diverse genetic system. Mutations are transmitted through the cytoplasm. Slow growing mutant strain, poky. Associated with impaired mitochondrial function, mutation due to absence of several cytochrome proteins needed for electron transport -Mitochondrial mutation in Saccharomyces cerevisiae (yeast): Mutations named petite due to small size of colonies. Deficiency in cellular respiration. Some mutations were in the nuclear DNA and others in mtDNA. Mitochondria performs abnormal electron transport -Choroplasts and mitochondria have unique features: DNA in mitochondria and chloroplasts is unlike DNA seen in nucleus of eukaryotic cells that house these organelles. Similar to DNA in prokaryotes, circular and free of associated proteins. Organelle ribosomes also differ from the ones in the cytosol. Organelle-specific transcription-translation system -Endosymbiotic theory: Mitochondria and chloroplasts (organelles) arose independently 2 billion years ago from free-living bacteria. Organelles possessed attributes of aerobic respiration and photosynthesis, respectively. Bacteria were engulfed by larger eukaryotic cells beneficial symbiotic relationship developedbacteria lost ability to function autonomouslyEukaryotic cells gained oxidative respiration and photosynthesis -cpDNA: Chloroplast DNA. Genes encode products involved in photosynthesis and translation -Human mtDNA: Smaller than DNA in chloroplasts -Majority of proteins for mitochondrial function are encoded by nuclear genes: DNA and RNA polymerase, initiation and elongation factors, ribosomal Proteins, and Aminoacyl tRNA synthetases -mitochondrial inheritance: replication in mitochondria is dependent on genes encoded by nuclear DNA. Human mtDNA encodes: 2 rRNA, 22 tRNA, 13 polypeptides. Mitochondrial DNA is smaller than the DNA in chloroplasts. Introns are absent. Gene repetitions are rare. In vertebrates there are 5-10 copies of mtDNA per organelle. In mammals inheritance is mostly maternal -mtDNA in humans: contains 16,569 base pairs. Coding for 13 proteins required for aerobic cellular respiration. Disruption of mitochondrial genes via mutation has severe impacts on organism. Susceptible to mutations since there is no structural protection from histones, DNA repair mechanism limited, high concentrations of ROS (reactive oxygen species) generated by cell respiration, ROS is toxic and damages organelle contents (proteins, lipids, mtDNA). Mitochondria is prone to oxidative stress and posses a potent anti-oxidative defense -Heteroplasmy: Variation in genetic content of organelles. Zygote receives large number of organelles through egg. Mutation in one or few will be diluted out by many mitochondria that lack mutation and function normally. Adult cells have variable mixture of normal and abnormal organelles -MtDNA heteroplasmy and the threshold effect: mtDNA mutations that have occurred within approximately three human generations are usually heteroplasmic, and the same cell can contain varying proportions of mutated and wild type mtDNA. If a mutation is pathogenic the cell can usually tolerate a high percentage level of this variant before the biochemical threshold is exceeded and a defect in the respiratory chain is detected. Typically, this threshold level is greater than 80 percent suggesting that most mtDNA mutations are haploinsufficient or recessive -Criteria for human disorder to be attributed to mtDNA: Inheritance must exhibit maternal inheritance pattern. Disorder must reflect deficiency in bioenergetic function of organelle. Must have mutation in one or more mitochondrial gene. -Three disorders arising from mtDNA 1) MERRF (myoclonic epilepsy and ragged-red fiber disease): Pattern of inheritance consistent with maternal transmission, Lack of muscular coordination, “Ragged-red” skeletal muscle fibers, Epileptic seizures and other neurological symptoms, Mutation in one of the 22 tRNA- encoding genes (tRNA : the tRNA that delivers the amino acid lysine during translation), Heteroplasmy accounts for severity of the symptoms 2) LHON (Leber’s hereditary optic neuropathy) 3) KSS (Kearns–Sayre syndrome) - mtDNA-based disease can be detected by genetic testing, new therapies can prevent transmission of mtDNA mutations to offspring like Mitochondrial swapping in oocytes or Mitochondrial Replacement Technique (MRT). Method is you remove nuclear material from donor egg with mitochondrial defect and you take egg from a normal female with the nucleus removed and you fertilize the mormal egg into a reconstructed oocyte with donor nuclear material and then the developing bastocyst is implanted into a surrogate mother who then gives birth to a baby monkey. The baby monkey ends up with genetic material from three parents. It is controversial: safety, three-parent embryo. Approved last year in UK. FDA has not yet approve it in USA -Maternal effect (maternal influence): offspring’s phenotype is under control of nuclear gene products present in egg. Nuclear genes of female gamete transcribed; genetic products accumulate in egg’s cytoplasm. Products distributed among newly formed cells, influencing patterns/traits established early in development. For maternal effect genes, the genotype of the female parent and not that of the embryo determines the phenotype of the offspring. Ephestia demonstrates this maternal effect in which a cytoplasmically stored nuclear gene products (mRNA) influences the larval phenotype and temporarily overrides the genotype of the progeny (WT has brown eyes and pigmented skin from dominant allele “A” and mutant “a” does not make pigment: red eye and fair skin) -Shell coiling in the snail Lymnaea peregra is an example of maternal effect on a permanent rather than transitory phenotype. The genotype of the parent producing the egg determines the coiling pattern of the progeny snail regardless of the phenotype of the other parent (DD and Dd-dextral; dd-sinistral). The direction of snail coiling is determined by differences in the cleavage planes during early embryonic development. The origin of dextral and sinistral coiling can be traced to the orientation of the mitotic spindle at the two- to four-cell stage of embryonic development Chapter 5 -Crossing over: Physical breaking and rejoining of the DNA between homologue chromatids during prophase I of meiosis -Genes assort independently if they are on different chromosomes but show linkage if they are on the same chromosome. -With independent assortment of two pairs of chromosomes, each containing one heterozygous gene pair, no linkage is exhibited. Four genetically different gametes, each containing a different combination of alleles, are formed in equal proportions. -mendel’s dihybrid cross had no linkage so all gametes formed in equal proportions (1:1:1:1) -In genes linked on the same chromosome, no crossing over occurs and only two genetically different gametes are produced. Complete linkage produces parental or non-crossover gametes in equal proportions. -in complete linkage, there is no crossing over since the genes are very close and only the parental gametes are formed since there is no recombination -If complete linkage exists between two genes because of their close proximity and organisms heterozygous at both loci are mated, a unique F2phenotypic ratio results, the linkage ratio -Crossover between two linked genes involves two nonsister chromatids and generates two new allele combinations called recombinant or crossover gametes -When the loci of the two linked genes are far apart, the number of recombinants approaches and doesn’t exceed 50 percent. -Two parental types and two recombinant gametes result when recombination approaches 50 percent. Transmission of two unlinked genes is indistinguishable from two unlinked genes -Certain genes segregate as if they were linked and are part of the same chromosome, thus being inherited as a single unit (linked). During Meiosis I Prophase I, synapsed chromosomes reciprocally exchange segments which reshuffles (recombines) alleles between homologs. The frequency of crossing over is proportional to the distance between them. -Linkage ratio: Complete linkage between two genes due to close proximity. Unique F2phenotypic ratio results 1:2:1 (instead of 9:3:3:1) -Linkage group: Genes on the same chromosome are part of a linkage group. Number of linkage groups should correspond to haploid number of chromosomes -The percentage of offspring resulting from recombinant gametes depends on the distance between the two genes on the chromosome. -Morgan and his undergrad student Sturtevant were studying X-linkage in Drosophila. Studies with Drosophila show that synapsed chromosomes in meiosis wrap around each other to create chiasmata (X-shaped intersections, which are points of genetic exchange). Morgan suggested that such exchanges lead to recombinant gametes. -Sturtevant compiled data from crosses, saw recombination frequencies between linked genes are additive, and frequency of exchange is estimate of relative distance between two genes -Linked genes exist in a linear order along the chromosome, and the variable amount of exchange occurs between any two genes during gamete formation. Two genes located relatively close to each other along a chromosome are less likely to have a chiasma form between them, and it is less likely that crossing over will occur. -The frequency of crossing over (between linked alleles) is proportional to the distance between them. –The crossover frequency in % is defined as a linkage“map unit” = 1 cM= 1 centiMorgan -One map unit (mu) = 1 percent recombination between two genes on a chromosome. -Research has firmly established the chromosomal theory that chromosomes contain genes in linear order and are the equivalent of Mendel’s unit factors. -The farther apart two loci are along a chromosome, the more likely a random crossover will occur. -A single crossover (SCO) between two nonsister chromatids alters the linkage between two genes only if the crossover occurs between those two genes -When two linked genes are more than 50 map units apart, a crossover theoretically can be expected to occur between them in 100 percent of the tetrads. In that case the genes behave like “independent assortment” -Single crossovers can be used to determine the distance between two linked genes, but multiple crossovers between chromatids of a tetrad facilitate the production of more extensive chromosome maps. -Double exchanges of genetic material result from double crossovers (DCOs) and can be used to determine the order of three genes on the chromosome -The mathematical probability of two independent events occurring simultaneously is equal to the product of the individual probabilities (product law). -The expected frequency of double-crossover gametes is much lower than that of either single-crossover gamete class. Ex. SCO frequency is 15% (probability: 0.15), the DCO frequency in the same region should be 2.25% (probability: 0.15 x 0.15=0.0225). -map constructs: Large number of mutants in organisms such as: Drosophila, Maize, Mice. Allows for construction of extensive chromosome mapping. Linkage Mapping: linear order of genes in the chromosome (different than physical map) -Sister chromatid exchanges (SCEs) occur during mitosis but do not produce new allelic combinations. Sister chromatids involved in mitotic exchanges are sometimes called chromosomes because of their patchlike appearance when stained and viewed under a microscope -The significance of SCEs is still uncertain, but it has been observed that agents that induce chromosome damage increase the frequency of SCEs. Viruses, X rays, UV light, chemical mutagens. -Bloom syndrome, a recessively inherited disease, has elevated SCEs (10x), characterized by short stature, a skin rash that develops after exposure to the sun, cancer predisposition and genome instability, mutation in BLM gene in chromosome 15, BLM gene: Encodes enzyme DNA helicase, DNA helicase’s role is DNA replication, Researchers suggest that the increased SCE may be a response to DNA damage during the replication process. -Mendel didn’t encounter linking. The genes are so far apart that linkage is not detected. Thus it is not astonishing that Mendel did not run into the complications of linkage and did not avoid it by choosing one gene from each chromosome. If he had, he might not have recognized basic patterns of inheritance and might not have interpreted them correctly -Chromosomes are the unit of transmission in meiosis, not genes. -Linked genes can not undergo independent assortment -frequency of crossing over on a single chromosome is proportional to distance between them -Crossing over results in recombination, -Chromosome maps: Indicate relative location of genes on chromosome Chapter 6 -Bacteria may be classified by their shape: some are spherical cells (called cocci), some are rod shaped (referred to as bacilli), and others are spiral-shaped (known as spirilli). Bacteria usually reproduce asexually by binary fission, and in a few hours a single cell can form a culture containing thousands of cells. As a bacterial cell divides, the number of cells doubles every generation, producing a colony of cells, each of which is a clone of the original cell. Colonies of different species of bacteria look different, and experts can often identify a bacterium from its colony characteristics. The familiar human intestinal bacterium Escherichia coli forms beige or gray colonies that have smooth margins and a shiny covering of mucus. Species of Proteus, which are often responsible for spoiling food because they can grow at refrigerator temperatures, form colonies with a surface that looks like a contour map. Genetic material: Chromosome and sometimes plasmid. The genetic material need to be duplicated before cell division. When a bacteria cell divides, it creates two new daughter cells, each carrying the genetic information that was present in the chromosome of the mother cell. Thus, binary fission transmits genetic information from one bacterial generation to the next. -Gram-positive bacteria are colored purple by the stain because they have a thick layer of a protein called peptidoglycan on the outside of the cell wall. In Gram-negative bacteria the layer of peptidoglycan lies beneath a membrane and is not stained by the dye. Penicillin is effective in treating infections by Gram-positive bacteria because it interferes with the formation of peptidoglycan cross-links. Penicillin does not affect Gram-negative bacteria because it does not readily pass through the outer membrane that covers the peptidoglycan layer. The extensive interlocking bonds of the long peptidoglycan molecules provide strength to the cell envelope. Many bacteria also have a capsule that lies outside of the cell wall. This capsule may restrict the movement of water out of the cell and allow bacteria to live in dry places, such as on the surface of your skin. In other cases, the capsule may be important in allowing the bacteria to bind to solid surfaces such as rocks or to attach to human cells. -human microbiota is very important. Present in: skin, eyes, genitalia, gut, mouth, respiratory tract. It helps the body to digest certain foods that the stomach and small intestine have not been able to digest. It helps with the production of some vitamins (B and K). It helps us combat aggressions from other microorganisms, such as Clostridium difficile, maintaining the wholeness of the intestinal mucosa. It plays an important role in the immune system, performing a barrier effect. Recently, the unbalance in the microbiota composition has being linked to: chronic digestive disorders (Crohn’s disease, irritable bowel disease), autoimmune diseases, autism, depression, anxiety, etc. can treat with Probiotic therapy or fecal transplants -Benefits of using microorganisms in research: Bacteria and bacteriophages essential in genetic study. Bacteria and virus research is valuable: Exhibit extremely short reproductive cycles, haploid, can be isolated and studied in pure culture -Bacteria grow exponentially and have three growth phases 1) Lag phase: slow growth 2) Log phase: exponential growth 3) Stationary phase: cease dividing -Bacteria are grown in liquid culture medium or semisolid agar (petri dish). Minimal medium (Nutritional components simple, organic carbon source and inorganic ions) or Complete Medium (Amino acids are added as supplements to minimal medium) -selection after spontaneous mutations: Growth of organism under certain conditions (media). Only desired mutant grows well. Wild type does not. Able to isolate mutants - prototroph: can synthesize all essential organic compounds and therefore can be grown on minimal medium. Contains only an organic carbon source (glucose or lactose) and a variety of ions (Na , K , Mg , 2+ 2+ 4+ Ca , and NH ). -auxotroph: Through mutation (spontaneous or induced), an auxotroph has lost the ability to synthesize one or more essential compounds; it must be provided with them in the medium if it is to grow. Typically result from “loss-of-function” type mutations “Multiple aux-trop-s” - - means multiple mutations in different genes, e.g. met , thr , leu , bio Ex. A bacterium that losses the ability to synthetized the amino acid tryptophan is designated as trp . For that bacterium to grow it will need tryptophan to be supplemented in the media (complete medium). -one bacterial colony comes from one cell -Vertical gene transfer: the transmission of genes from the parental generation (same specie) to offspring via sexual or asexual reproduction. -Horizontal gene transfer: the transfer of genes between organisms (could be different species) in a manner other than traditional reproduction. Ex. Acquisition of chloroplasts and mitochondria by eukaryotes. Ex. Conjugation, transformation, and transduction in bacteria -Genetic recombination in bacteria refers to the replacement of one or more genes present in the chromosome of one cell with those of different cell -Conjugation: the process by which one bacterium transfers some or all of its DNA to another bacterium, even when the two bacteria are different species. Plasmid transfer has given the second bacterium genetic information it did not have before. These genes could allow the bacterium to make an enzyme that allows it to metabolize a new chemical or to defend itself against a new antibiotic. -Transformation: the process by which bacterial cells scavenge DNA from their environment, after other bacterial cells have burst open, releasing their cellular contents. The circular chromosomes break into short lengths of DNA that can be taken up by living bacterial cells and inserted into their own chromosomes, potentially adding genes they did not originally have. -Transduction: occurs when a kind of virus called a bacteriophage infects a bacterial cell. The virus reproduces inside the bacterial cell, and sometimes, inadvertently, the new viruses are filled with pieces of bacterial DNA along with the viral DNA. When those viruses infect new bacterial cells, the bacterial DNA can be inserted into the bacterial chromosome, passing new genes to that bacterium. -Bacterial conjugation with the F plasmid: Different strains of bacteria are involved in a unidirectional transfer of genetic material. Cells + serving as donors of parts of their chromosomes are designated F cells (F for fertility). Recipient bacteria receive the donor DNA and recombine it with part of their own chromosome and are designated as – F cells. Cell contact is essential for chromosome transfer to occur. Physical contact is the first step in conjugation established by the F pilus (or sex pilus; pl. pili). F+ cells contain a fertility factor (F factor) that confers the ability to donate part of their chromosome during conjugation. F factor is mobile and consists of a circular, double- stranded DNA molecule containing 19 genes. One strand of the double helix moves into the recipient cell via the sex pilus, and the other one remains. Both re-form their double helix and become F . + -E. coli may or may not contain the F factor. -Plasmids: composed of a double-stranded closed circle of DNA, exist in multiple copies in the cytoplasm, may contain one or more genes, are distributed to daughter cells, replicate independently of the bacterial chromosome, plasmids can exist autonomously in the cell or can integrate into the chromosome to form episomes. -Plasmids are classified according to the genetic information they transfer: 1) F factor plasmids confer fertility and contain genes for sex pilus formation on which genetic recombination depends. 2) R plasmids consist of two components: the resistance transfer factor (RTF) and one or more r-determinants. RTF encodes genetic information essential to transferring the plasmid between bacteria. R- determinants confer resistance to antibiotics. 3) Col plasmids encode colicins that can kill neighboring bacteria. -Allele configuration in double heterozygous can be: 1) Cis - Two dominant or two recessive alleles are on each chromosome 2) Trans - One dominant and one recessive allele are on each chromosome -Hfr (high-frequency recombination) are a special class of F cells. Hfr is a mutant F strain isolated that undergo recombination at a higher rate  +  than WT. Hfr strain donates genetic information to F cell. F x F recipient becomes F but with Hfrx F recipient remains F . Hfr cells have F-plasmid integrated into the chromosome. Integration into the Chromosome is unique for each F-plasmid strain. When F-plasmid material is replicated and sent across pili, chromosomal material is included.  -Interrupted mating technique: Culture mix of Hfr and F strains incubated, put in blender, force of blender interrupted conjugation at different times, transfer of chromosomes terminated, demonstrated that specific genes in Hfr strain are transferred/recombined sooner than others -An ordered linear transfer of genes is correlated with the length of time conjugation proceeded. The gene order and distance between genes could be predicted. Basis for first genetic map in bacteria. -Gene transfer by Hfr strains led to the understanding that the E. coli – chromosome is circular. During conjugation between an Hfr and an F cell, the position of the F factor determines the initial point of transfer. Conjugation rarely allows the entire chromosome to pass across the conjugation tube. This procedure has established the location of approximately 1000 genes. -The F factor can insert into the bacterial chromosome and also be excised from it. In some cases, an F factor is excised from the chromosome of an Hfr strain and reverts to the F state. In the process, the F factor (referred to as F') often brings several adjoining genes with it. Transfer of an F' to an F cell results in a partially diploid cell called a merozygote. -In transformation, small pieces of extracellular DNA are taken up by a living bacterial cell and are integrated stably into the chromosome. The recombinant region contains one host strand (present originally) and one donor strand. These strands are from different sources, so this helical region is referred to as a heteroduplex. The two strands of DNA are not perfectly complementary in this region. The mismatch activates a repair mechanism and after one round of cell division, one of the chromosomes now integrates the foreign DNA. Genes that are close enough to each other to be cotransformed are linked. -transformation in bacteria is useful for: 1.Human growth hormone (HGH) 2.Insulin 3.Erythropoietin 4.Edible vaccine against cholera (get it from contaminated food and then bacteria colonize and produce enterotoxins that invade small intestine and causes diharrea then death even. Genetically engineering plants that act as vaccines so that when an animal eats the plant the gene product acts as an antigen and the body produces antibodies against it) 5.Genetic-modified organisms (GMO) -Bacteriophages (or phages) are viruses that can infect a host bacterium by injecting their DNA. During reproduction, phages can be involved in genetic recombination called transduction. -The head of a virus is made of proteins and encloses the DNA. Viral DNA encodes around 150 proteins. The head of a virus is connected to a tail, with binding sites recognizing the E. coli cell wall. -The life cycle of phage T4 is initiated when the virus binds by adsorption to the bacterial host cell. The tail contracts, the central core penetrates the cell wall, and the DNA moves into the host cytoplasm. The bacterial DNA, RNA, and protein synthesis in the host cell is inhibited. Host DNA degradation is initiated. -Phage DNA replication occurs, then components of the head, tail, and tail fibers are synthesized. When approximately 200 new viruses have been constructed, the bacterial cell is ruptured by the enzyme lysozyme (a phage gene product) and mature phages are released from the host cell (Lytic phase) each phage can start a new cycle if it lands on a healthy intact bacterial cell -Lysogeny occurs when: the phage DNA integrates into the bacterial chromosome. It is replicated along with the chromosome. It is passed to daughter cells. The viral DNA that integrates into the bacterial chromosome is called a prophage. -transduction occurs if bacterial DNA instead of phage is packaged into phage particles and transferred to host. Transfer of bacterial genes. Used in linkage and chromosomal mapping -Cotransduction: Two genes are close enough to be transduced simultaneously. Two independent transduction events may occur if genes are not close enough


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